from __future__ import absolute_import, division, print_function from iotbx import pdb from cctbx.array_family import flex from libtbx.test_utils import Exception_expected, approx_equal, show_diff from libtbx.str_utils import show_string import hashlib from libtbx.utils import Sorry, format_cpu_times import libtbx.load_env from libtbx import Auto from six.moves import cStringIO as StringIO import math from six.moves import range from six.moves import zip try: from six.moves import cPickle as pickle except ImportError: import pickle import random import sys, os def exercise_atom(): a = pdb.hierarchy.atom() assert a.name == "" a.name = "abcd" assert a.name == "abcd" try: a.name = "xyzhkl" except (ValueError, RuntimeError) as e: assert str(e) == "string is too long for target variable " \ "(maximum length is 4 characters, 6 given)." else: raise Exception_expected assert a.segid == "" a.segid = "stuv" assert a.segid == "stuv" assert a.element == "" a.element = "ca" assert a.element == "ca" assert a.charge == "" a.charge = "2+" assert a.charge == "2+" assert a.serial == "" a.serial = "A0000" assert a.serial == "A0000" assert a.serial_as_int() == 100000 assert a.xyz == (0,0,0) a.xyz = (1,-2,3) assert a.xyz == (1,-2,3) assert a.sigxyz == (0,0,0) a.sigxyz = (-2,3,1) assert a.sigxyz == (-2,3,1) assert a.occ == 0 a.occ = 0.5 assert a.occ == 0.5 assert a.sigocc == 0 a.sigocc = 0.7 assert a.sigocc == 0.7 assert a.b == 0 a.b = 5 assert a.b == 5 assert a.sigb == 0 a.sigb = 7 assert a.sigb == 7 assert a.uij == (-1,-1,-1,-1,-1,-1) assert not a.uij_is_defined() a.uij = (1,-2,3,4,-5,6) assert a.uij == (1,-2,3,4,-5,6) assert a.uij_is_defined() a.uij_erase() assert not a.uij_is_defined() assert not a.siguij_is_defined() if (pdb.hierarchy.atom.has_siguij()): assert a.siguij == (-1,-1,-1,-1,-1,-1) a.siguij = (-2,3,4,-5,6,1) assert a.siguij == (-2,3,4,-5,6,1) assert a.siguij_is_defined() a.siguij_erase() assert not a.siguij_is_defined() assert a.fp == 0 a.fp = 0.1 assert a.fp == 0.1 assert a.fdp == 0 a.fdp = 0.2 assert a.fdp == 0.2 assert not a.hetero a.hetero = True assert a.hetero assert a.i_seq == 0 try: a.i_seq = 1 except AttributeError: pass else: raise Exception_expected assert a.tmp == 0 a.tmp = 3 assert a.tmp == 3 assert a.chain() is None # a = (pdb.hierarchy.atom() .set_name(new_name="NaMe") .set_segid(new_segid="sEgI") .set_element(new_element="El") .set_charge(new_charge="cH") .set_serial(new_serial="B1234") .set_xyz(new_xyz=(1.3,2.1,3.2)) .set_sigxyz(new_sigxyz=(.1,.2,.3)) .set_occ(new_occ=0.4) .set_sigocc(new_sigocc=0.1) .set_b(new_b=4.8) .set_sigb(new_sigb=0.7) .set_uij(new_uij=(1.3,2.1,3.2,4.3,2.7,9.3)) .set_fp(new_fp=0.3) .set_fdp(new_fdp=0.4) .set_hetero(new_hetero=True)) if (pdb.hierarchy.atom.has_siguij()): assert a.set_siguij(new_siguij=(.1,.2,.3,.6,.1,.9)) is a assert a.name == "NaMe" assert a.segid == "sEgI" assert a.element == "El" assert a.charge == "cH" assert a.serial == "B1234" assert approx_equal(a.xyz, (1.3,2.1,3.2)) assert approx_equal(a.sigxyz, (.1,.2,.3)) assert approx_equal(a.occ, 0.4) assert approx_equal(a.sigocc, 0.1) assert approx_equal(a.b, 4.8) assert approx_equal(a.sigb, 0.7) assert approx_equal(a.uij, (1.3,2.1,3.2,4.3,2.7,9.3)) if (pdb.hierarchy.atom.has_siguij()): assert approx_equal(a.siguij, (.1,.2,.3,.6,.1,.9)) assert a.hetero assert approx_equal(a.fp, 0.3) assert approx_equal(a.fdp, 0.4) assert a.tmp == 0 try: a.set_name(new_name="12345") except (ValueError, RuntimeError) as e: assert str(e) == "string is too long for target variable " \ "(maximum length is 4 characters, 5 given)." else: raise Exception_expected # a.tmp = 7 ac = a.detached_copy() assert ac.tmp == 0 assert ac.name == "1234" assert ac.segid == "sEgI" assert ac.element == "El" assert ac.charge == "cH" assert ac.serial == "B1234" assert approx_equal(ac.xyz, (1.3,2.1,3.2)) assert approx_equal(ac.sigxyz, (.1,.2,.3)) assert approx_equal(ac.occ, 0.4) assert approx_equal(ac.sigocc, 0.1) assert approx_equal(ac.b, 4.8) assert approx_equal(ac.sigb, 0.7) assert approx_equal(ac.uij, (1.3,2.1,3.2,4.3,2.7,9.3)) if (pdb.hierarchy.atom.has_siguij()): assert approx_equal(ac.siguij, (.1,.2,.3,.6,.1,.9)) assert ac.hetero assert approx_equal(a.fp, 0.3) assert approx_equal(a.fdp, 0.4) # for e in ["H", "H ", " H", "D", "D ", " D"]: a.element = e assert a.element_is_hydrogen() for e in ["", "h", "h ", " h", "d", "d ", " d"]: a.element = e assert not a.element_is_hydrogen() # Spot-check some elements to see if they are positive ions and ions for e in ["LI", "RH", "SI", "SN", "V", "GE", "CU", "ZN", "Cu", "Zn"]: a.element = e assert a.element_is_positive_ion(), e + " was not seen as a positive ion" assert a.element_is_ion(), e + " was not seen as an ion" for e in ["HE", "C", "XE", "RN", "KR", "F", "CL", "BR", "I"]: a.element = e assert not a.element_is_positive_ion(), e + " was not seen as a positive ion" # Spot-check some elements to see if they are negative ions and ions for e in ["F", "CL", "BR", "I"]: a.element = e assert a.element_is_negative_ion(), e + " was not seen as a negative ion" assert a.element_is_ion(), e + " was not seen as an ion" for e in ["HE", "C", "XE", "RN", "KR", "B", "LI", "RH", "SI", "SN", "V", "GE", "Sn", "Ge"]: a.element = e assert not a.element_is_negative_ion(), e + " was seen as a negative ion" # Spot-check some elements to ensure they are not ions of either polarity for e in ["HE", "C", "XE", "RN", "KR"]: a.element = e assert not a.element_is_ion(), e + " was seen as an ion" # a.name = "1234" a.element = "El" assert a.determine_chemical_element_simple() is None a.name = "NA " a.element = " N" assert a.determine_chemical_element_simple() == " N" a.element = "CU" assert a.determine_chemical_element_simple() == "CU" for e in ["", " ", " "]: a.element = e a.name = "NA " assert a.determine_chemical_element_simple() == "NA" a.name = " D" assert a.determine_chemical_element_simple() == " D" for d in "0123456789": a.name = d+"H" assert a.determine_chemical_element_simple() == " H" a.set_name(new_name=None) a.set_segid(new_segid=None) a.set_element(new_element=None) a.set_charge(new_charge=None) a.set_serial(new_serial=None) assert a.name == "" assert a.segid == "" assert a.element == "" assert a.charge == "" assert a.serial == "" # assert not a.set_chemical_element_simple_if_necessary() assert a.element == "" a.name = " N " assert a.set_chemical_element_simple_if_necessary() assert a.element == " N" a.name = " X " a.element = "" assert not a.set_chemical_element_simple_if_necessary() assert a.element == "" a.element = "Na" assert a.set_chemical_element_simple_if_necessary() assert a.element == "NA" a.element = "Na" assert not a.set_chemical_element_simple_if_necessary(tidy_existing=False) assert a.element == "Na" a.element = "N" assert a.set_chemical_element_simple_if_necessary() assert a.element == " N" a.element = "N" assert not a.set_chemical_element_simple_if_necessary(tidy_existing=False) assert a.element == "N" a.element = " N" assert not a.set_chemical_element_simple_if_necessary() assert a.element == " N" a.name = "" a.element = "" # assert a.charge == "" assert a.charge_tidy() == " " assert a.charge_tidy(strip=True) == "" def check(inp, out, value): a.charge = inp assert a.charge_tidy() == out assert a.charge_as_int() == value check("", " ", 0) check(" ", " ", 0) check(" ", " ", 0) check("0", " ", 0) check(" 0", " ", 0) check("0 ", " ", 0) check("00", " ", 0) check(" +", "1+", 1) check("+ ", "1+", 1) check("++", "2+", 2) check(" -", "1-", -1) check("- ", "1-", -1) check("--", "2-", -2) check("0+", "0+", 0) check("+0", "0+", 0) check("0-", "0-", 0) check("-0", "0-", 0) check("+-", None, 0) check("-+", None, 0) check("3+", "3+", 3) check("+4", "4+", 4) check("5-", "5-", -5) check("-6", "6-", -6) check("7 ", None, 0) check(" 8", None, 0) check("12", None, 0) check("1a", None, 0) check("a1", None, 0) check("a ", None, 0) check(" a", None, 0) a.charge = "" # assert a.distance(other=a) == 0 b = a.detached_copy() b.xyz = (3,5,2) assert approx_equal(a.distance(other=b), 3.56931365951) assert approx_equal(b.distance(other=a), 3.56931365951) assert approx_equal(a.distance(other_xyz=(3,5,2)), 3.56931365951) assert approx_equal(a.distance(other_xyz=(2,3,5)), 2.13072757527) assert a.angle(atom_1=a, atom_3=a) is None assert a.angle(atom_1=a, atom_3=a, deg=True) is None assert a.angle(atom_1_xyz=a.xyz, atom_3_xyz=a.xyz) is None assert a.angle(atom_1_xyz=a.xyz, atom_3_xyz=a.xyz, deg=True) is None assert approx_equal(a.angle(atom_1=b, atom_3=b), 0) assert approx_equal(a.angle(atom_1=b, atom_3=b, deg=True), 0) c = a.detached_copy() c.xyz = (5,3,1) assert approx_equal(a.angle(atom_1=b, atom_3=c, deg=True), 42.6776898341) assert approx_equal(math.degrees(a.angle(atom_1=c, atom_3=b, deg=False)), 42.6776898341) # ag = pdb.hierarchy.atom_group() ac = pdb.hierarchy.atom(parent=ag, other=a) assert ac.memory_id() != a.memory_id() assert ac.parent().memory_id() == ag.memory_id() assert ac.name == a.name assert ac.segid == a.segid assert ac.element == a.element assert ac.charge == a.charge assert ac.serial == a.serial assert ac.xyz == a.xyz assert ac.sigxyz == a.sigxyz assert ac.occ == a.occ assert ac.sigocc == a.sigocc assert ac.b == a.b assert ac.sigb == a.sigb assert ac.uij == a.uij if (pdb.hierarchy.atom.has_siguij()): assert ac.siguij == a.siguij assert ac.hetero == a.hetero assert ac.fp == a.fp assert ac.fdp == a.fdp assert ac.tmp == 0 # assert a.pdb_label_columns() == " " # a = pdb.hierarchy.atom() assert a.set_serial(new_serial="ABCDE") is a assert a.serial == "ABCDE" a.serial = "CDEFG" assert a.serial == "CDEFG" assert a.set_serial(new_serial=200000) is a assert a.serial == "A255S" assert a.serial_as_int() == 200000 a.serial = 100000 assert a.serial == "A0000" try: a.set_serial(new_serial="ABCDEF") except (ValueError, RuntimeError) as e: assert str(e) == "string is too long for target variable " \ "(maximum length is 5 characters, 6 given)." else: raise Exception_expected try: a.set_serial(new_serial=-10000) except ValueError as e: assert str(e) == "value is less than -9999" else: raise Exception_expected try: a.set_serial(new_serial=87440032) except ValueError as e: assert str(e) == "value is greater than 87440031" else: raise Exception_expected try: a.set_serial(new_serial=sys) except TypeError as e: assert str(e) == "value must be a Python str or int." else: raise Exception_expected try: a.serial = sys except TypeError as e: assert str(e) == "value must be a Python str or int." else: raise Exception_expected # atoms = pdb.hierarchy.af_shared_atom() atoms.reset_serial() atoms.reset_i_seq() atoms.reset_tmp() atoms.append(pdb.hierarchy.atom()) assert [atom.serial for atom in atoms] == [""] assert [atom.i_seq for atom in atoms] == [0] assert [atom.tmp for atom in atoms] == [0] atoms.reset_serial(first_value=2) atoms.reset_i_seq() sentinel = atoms.reset_tmp(first_value=2) assert [atom.serial for atom in atoms] == [" 2"] assert [atom.i_seq for atom in atoms] == [0] assert [atom.tmp for atom in atoms] == [2] atoms.append(pdb.hierarchy.atom()) atoms.append(pdb.hierarchy.atom()) assert [atom.serial for atom in atoms] == [" 2", "", ""] assert [atom.i_seq for atom in atoms] == [0,0,0] assert [atom.tmp for atom in atoms] == [2,0,0] del sentinel assert [atom.tmp for atom in atoms] == [0,0,0] atoms.reset_serial() atoms.reset_i_seq() sentinel = atoms.reset_tmp() assert [atom.serial for atom in atoms] == [" 1", " 2", " 3"] assert [atom.i_seq for atom in atoms] == [0,1,2] assert [atom.tmp for atom in atoms] == [0,1,2] del sentinel assert [atom.tmp for atom in atoms] == [0,0,0] sentinel = atoms.reset_tmp(first_value=0, increment=0) assert [atom.tmp for atom in atoms] == [0] * 3 del sentinel sentinel = atoms.reset_tmp(first_value=5, increment=-3) assert [atom.tmp for atom in atoms] == [5,2,-1] del sentinel # sentinel = atoms.reset_tmp_for_occupancy_groups_simple() assert [atom.tmp for atom in atoms] == [0,1,2] del sentinel atoms[0].element = "D" atoms[2].element = "H" sentinel = atoms.reset_tmp_for_occupancy_groups_simple() assert [atom.tmp for atom in atoms] == [-1,1,-1] del sentinel assert [atom.tmp for atom in atoms] == [0,0,0] # sentinel = atoms.reset_tmp() try: atoms.reset_tmp() except RuntimeError as e: assert str(e) == \ "Another associated atom_tmp_sentinel instance still exists." else: raise Exception_expected # for atom,n in zip(atoms, ["", "NA ", " X "]): atom.name = n for atom,e in zip(atoms, ["", "", "N"]): atom.element = e assert atoms.set_chemical_element_simple_if_necessary() == 2 assert [atom.element for atom in atoms] == ["", "NA", " N"] for atom,e in zip(atoms, ["", "", "N"]): atom.element = e assert atoms.set_chemical_element_simple_if_necessary( tidy_existing=False) == 1 assert [atom.element for atom in atoms] == ["", "NA", "N"] # assert sorted(atoms.build_dict().keys()) == ["", " X ", "NA "] assert sorted(atoms.build_dict(strip_names=True).keys()) == ["", "NA", "X"] atoms[0].name = "x " assert sorted(atoms.build_dict(upper_names=True).keys()) \ == [" X ", "NA ", "X "] d = atoms.build_dict( strip_names=True, upper_names=True, throw_runtime_error_if_duplicate_keys=False) assert sorted([atom.name for atom in d.values()]) == ["NA ", "x "] try: atoms.build_dict(strip_names=True, upper_names=True) except RuntimeError as e: assert not show_diff(str(e), '''\ Duplicate keys in build_dict(strip_names=true, upper_names=true,\ convert_stars_to_primes=false): pdb="x " pdb=" X "''') else: raise Exception_expected atoms[0].name = "x* " d = atoms.build_dict( strip_names=True, upper_names=True, convert_stars_to_primes=True) assert sorted(d.keys()) == ["NA", "X", "X'"] # a = pdb.hierarchy.atom() def check(scattering_type, e, c): a.set_element_and_charge_from_scattering_type_if_necessary( scattering_type=scattering_type) assert not show_diff(a.element, e) assert not show_diff(a.charge, c) a.element = "" a.charge = "" check("", " ", " ") a.element = "Na" a.charge = "" check("", "Na", "") a.charge = " " check("", "Na", " ") a.element = "" a.charge = "" check("Na+", "NA", "1+") a.element = "Na" a.charge = "+" check("NA1+", "Na", "+") a.element = "Na" a.charge = "2+" check("NA1+", "NA", "1+") def exercise_atom_group(): ag = pdb.hierarchy.atom_group() assert ag.altloc == "" assert ag.resname == "" ag = pdb.hierarchy.atom_group(altloc=None, resname=None) assert ag.altloc == "" assert ag.resname == "" ag = pdb.hierarchy.atom_group(altloc="a", resname="xyz") assert ag.altloc == "a" assert ag.resname == "xyz" ag.altloc = None ag.resname = None assert ag.altloc == "" assert ag.resname == "" assert ag.confid() == " " # ag.altloc = "l" ag.resname = "res" assert ag.confid() == "lres" ag.append_atom(atom=pdb.hierarchy.atom().set_name(new_name="n")) rg = pdb.hierarchy.residue_group() for i,agc in enumerate([ pdb.hierarchy.atom_group(parent=rg, other=ag), ag.detached_copy()]): assert agc.memory_id() != ag.memory_id() assert ag.parent() is None if (i == 0): assert agc.parent().memory_id() == rg.memory_id() else: assert agc.parent() is None assert agc.altloc == "l" assert agc.resname == "res" assert agc.atoms_size() == 1 assert agc.atoms()[0].memory_id() != ag.atoms()[0].memory_id() assert agc.atoms()[0].name == "n" ag.append_atom(atom=pdb.hierarchy.atom().set_name(new_name="o")) assert ag.atoms_size() == 2+i assert agc.atoms_size() == 1 # ag = pdb.hierarchy.atom_group() assert ag.parent() is None rg1 = pdb.hierarchy.residue_group() rg2 = pdb.hierarchy.residue_group() assert rg1.memory_id() != rg2.memory_id() ag = pdb.hierarchy.atom_group(parent=rg1) assert ag.parent(optional=False).memory_id() == rg1.memory_id() del rg1 assert ag.parent() is None try: ag.parent(optional=False) except RuntimeError as e: assert not show_diff(str(e), "atom_group has no parent residue_group") else: raise Exception_expected # rg1 = pdb.hierarchy.residue_group() ag = pdb.hierarchy.atom_group(altloc="a", resname="xyz") rg1.append_atom_group(atom_group=ag) assert ag.altloc == "a" assert ag.resname == "xyz" assert ag.parent().memory_id() == rg1.memory_id() del rg1 assert ag.parent() is None # ag.pre_allocate_atoms(number_of_additional_atoms=2) assert ag.atoms_size() == 0 assert ag.atoms().size() == 0 ag.append_atom(atom=pdb.hierarchy.atom().set_name(new_name="ca")) assert ag.atoms_size() == 1 assert ag.atoms().size() == 1 ag.append_atom(atom=pdb.hierarchy.atom().set_name(new_name="n")) assert ag.atoms_size() == 2 assert ag.atoms().size() == 2 assert (ag.get_atom("ca").name == "ca") assert [atom.name for atom in ag.atoms()] == ["ca", "n"] for i in range(3): ag.append_atom(pdb.hierarchy.atom()) assert ag.atoms_size() == 5 assert ag.atoms().size() == 5 for atom in ag.atoms(): assert atom.parent(optional=False).memory_id() == ag.memory_id() assert [a.name for a in ag.atoms()] == ["ca", "n", "", "", ""] # ag.insert_atom(i=0, atom=pdb.hierarchy.atom().set_name(new_name="0")) assert [a.name for a in ag.atoms()] == ["0", "ca", "n", "", "", ""] ag.insert_atom(i=-1, atom=pdb.hierarchy.atom().set_name(new_name="x")) assert [a.name for a in ag.atoms()] == ["0", "ca", "n", "", "", "x", ""] a = ag.atoms()[-1] assert a.parent().memory_id() == ag.memory_id() ag.remove_atom(i=-1) assert a.parent() is None assert [a.name for a in ag.atoms()] == ["0", "ca", "n", "", "", "x"] ag.remove_atom(i=1) assert [a.name for a in ag.atoms()] == ["0", "n", "", "", "x"] a = ag.atoms()[-2] assert a.parent().memory_id() == ag.memory_id() assert ag.find_atom_index(atom=a, must_be_present=True) == 3 ag.remove_atom(i=-2) assert a.parent() is None assert [a.name for a in ag.atoms()] == ["0", "n", "", "x"] a = pdb.hierarchy.atom().set_name(new_name="y") assert ag.find_atom_index(atom=a) == -1 try: ag.find_atom_index(atom=a, must_be_present=True) except RuntimeError as e: assert str(e) == "atom not in atom_group." else: raise Exception_expected ag.insert_atom(i=4, atom=a) assert ag.find_atom_index(atom=a) == 4 assert [a.name for a in ag.atoms()] == ["0", "n", "", "x", "y"] for a in ag.atoms() : a.occ = 1.0 assert ag.occupancy() == 1.0 ag.atoms()[0].occ = 0.5 assert ag.occupancy() == 0.9 try : ag.occupancy(raise_error_if_non_uniform=True) except ValueError : pass else: raise Exception_expected # try: pdb.hierarchy.atom_group(altloc="ab") except (ValueError, RuntimeError) as e: assert str(e) == "string is too long for target variable " \ "(maximum length is 1 character, 2 given)." else: raise Exception_expected # ag1 = pdb.hierarchy.atom_group() atom = pdb.hierarchy.atom() assert atom.parent() is None ag1.append_atom(atom=atom) assert atom.parent().memory_id() == ag1.memory_id() ag2 = pdb.hierarchy.atom_group() ag2.append_atom_with_other_parent(atom=atom) assert atom.parent().memory_id() == ag1.memory_id() del ag1 assert atom.parent() is None try: atom.parent(optional=False) except RuntimeError as e: assert not show_diff(str(e), "atom has no parent atom_group") else: raise Exception_expected def exercise_residue_group(): rg = pdb.hierarchy.residue_group() assert rg.resseq == "" assert rg.icode == "" assert rg.link_to_previous rg.resseq = 10000 assert rg.resseq == "A000" assert rg.resseq_as_int() == 10000 rg = pdb.hierarchy.residue_group( resseq=" 1", icode="i", link_to_previous=False) assert rg.resseq == " 1" rg.resseq = " 2" assert rg.resseq == " 2" assert rg.icode == "i" rg.icode = "j" assert rg.icode == "j" assert not rg.link_to_previous rg.link_to_previous = True assert rg.link_to_previous rg.link_to_previous = False # ag = pdb.hierarchy.atom_group(altloc="a") assert ag.parent() is None rg.append_atom_group(atom_group=ag) assert ag.parent().memory_id() == rg.memory_id() c = pdb.hierarchy.chain() for i,rgc in enumerate([ pdb.hierarchy.residue_group(parent=c, other=rg), rg.detached_copy()]): assert rgc.memory_id() != rg.memory_id() assert rg.parent() is None if (i == 0): assert rgc.parent().memory_id() == c.memory_id() else: assert rgc.parent() is None assert rgc.resseq == " 2" assert rgc.icode == "j" assert not rgc.link_to_previous assert rgc.atom_groups_size() == 1 assert rgc.atom_groups()[0].memory_id() != rg.atom_groups()[0].memory_id() assert rgc.atom_groups()[0].altloc == "a" rg.append_atom_group(atom_group=pdb.hierarchy.atom_group(altloc="%d"%i)) assert rg.atom_groups_size() == 2+i assert rgc.atom_groups_size() == 1 assert [ag.altloc for ag in rg.atom_groups()] == ["a", "0", "1"][:i+2] # c1 = pdb.hierarchy.chain(id="a") c2 = pdb.hierarchy.chain(id="b") assert c1.memory_id() != c2.memory_id() rg = pdb.hierarchy.residue_group() assert rg.parent() is None rg = pdb.hierarchy.residue_group(parent=c1) assert rg.parent(optional=False).memory_id() == c1.memory_id() del c1 assert rg.parent() is None try: rg.parent(optional=False) except RuntimeError as e: assert not show_diff(str(e), "residue_group has no parent chain") else: raise Exception_expected # c1 = pdb.hierarchy.chain(id="p") rg13l = pdb.hierarchy.residue_group(resseq="13", icode="l") c1.append_residue_group(rg13l) assert rg13l.resseq == "13" assert rg13l.icode == "l" # c1 = pdb.hierarchy.chain(id="a") c1.pre_allocate_residue_groups(number_of_additional_residue_groups=2) assert c1.residue_groups_size() == 0 assert len(c1.residue_groups()) == 0 for i in range(2): c1.append_residue_group(residue_group=pdb.hierarchy.residue_group()) assert c1.residue_groups_size() == 2 assert len(c1.residue_groups()) == 2 for residue_group in c1.residue_groups(): assert residue_group.parent().memory_id() == c1.memory_id() assert c1.atoms_size() == 0 assert c1.atoms().size() == 0 # for altloc in ["w", "v", "u"]: rg.insert_atom_group( i=0, atom_group=pdb.hierarchy.atom_group(altloc=altloc)) assert [ag.altloc for ag in rg.atom_groups()] == ["u", "v", "w"] rg.remove_atom_group(i=-1) assert [ag.altloc for ag in rg.atom_groups()] == ["u", "v"] ag = rg.atom_groups()[1] assert ag.parent().memory_id() == rg.memory_id() assert rg.find_atom_group_index(atom_group=ag) == 1 rg.remove_atom_group(atom_group=ag) assert ag.parent() is None assert rg.find_atom_group_index(atom_group=ag) == -1 try: rg.find_atom_group_index(atom_group=ag, must_be_present=True) except RuntimeError as e: assert str(e) == "atom_group not in residue_group." else: raise Exception_expected # ag1 = pdb.hierarchy.atom_group() ag2 = pdb.hierarchy.atom_group() a = pdb.hierarchy.atom() ag1.append_atom(atom=a) try: ag2.append_atom(atom=a) except RuntimeError as e: assert str(e) == "atom has another parent atom_group already." else: raise Exception_expected # rg = pdb.hierarchy.residue_group() assert rg.resid() == " " rg = pdb.hierarchy.residue_group(resseq="1", icode="i") assert rg.resid() == " 1i" rg = pdb.hierarchy.residue_group(resseq=" 1 ", icode="j") assert rg.resid() == " 1 j" rg = pdb.hierarchy.residue_group(resseq="ABCD", icode="") assert rg.resid() == "ABCD " rg = pdb.hierarchy.residue_group(resseq="ABCD", icode="E") assert rg.resid() == "ABCDE" # rg = pdb.hierarchy.residue_group() ag = pdb.hierarchy.atom_group(altloc=" ") rg.append_atom_group(atom_group=ag) assert not rg.have_conformers() ag = pdb.hierarchy.atom_group(altloc="") rg.append_atom_group(atom_group=ag) assert not rg.have_conformers() ag = pdb.hierarchy.atom_group(altloc="a") rg.append_atom_group(atom_group=ag) assert rg.have_conformers() # rg = pdb.hierarchy.residue_group() assert rg.move_blank_altloc_atom_groups_to_front() == 0 ag = pdb.hierarchy.atom_group(altloc="a") rg.append_atom_group(atom_group=ag) assert rg.move_blank_altloc_atom_groups_to_front() == 0 ag = pdb.hierarchy.atom_group(altloc=" ") rg.append_atom_group(atom_group=ag) assert rg.move_blank_altloc_atom_groups_to_front() == 1 # rg = pdb.hierarchy.residue_group() rg.resseq = "x" try: rg.resseq_as_int() except (ValueError, RuntimeError) as e: assert not show_diff(str(e), 'invalid residue sequence number: "x"') else: raise Exception_expected # rg = pdb.hierarchy.residue_group() assert len(rg.unique_resnames()) == 0 def rga(altloc, resname): rg.append_atom_group(atom_group=pdb.hierarchy.atom_group( altloc=altloc, resname=resname)) rga("", "RN1") assert list(rg.unique_resnames()) == ["RN1"] rga("", "RN") assert list(rg.unique_resnames()) == ["RN", "RN1"] rga("A", "RN1") assert list(rg.unique_resnames()) == ["RN", "RN1"] rga("A", "RN2") assert list(rg.unique_resnames()) == ["RN", "RN1", "RN2"] rg = pdb.hierarchy.residue_group(resseq=" 30", icode="I") rgc = pdb.hierarchy.chain(id="A") rgc.append_residue_group(rg) assert (rg.id_str() == " A 30I") def exercise_chain(): c = pdb.hierarchy.chain() assert c.id == "" c = pdb.hierarchy.chain(id="a") assert c.id == "a" c.id = "x" assert c.id == "x" # m1 = pdb.hierarchy.model(id="1") m2 = pdb.hierarchy.model(id="2") assert m1.memory_id() != m2.memory_id() c = pdb.hierarchy.chain() assert c.parent() is None c = pdb.hierarchy.chain(parent=m1) assert c.parent(optional=False).memory_id() == m1.memory_id() del m1 assert c.parent() is None try: c.parent(optional=False) except RuntimeError as e: assert not show_diff(str(e), "chain has no parent model") else: raise Exception_expected # c = pdb.hierarchy.chain() # c = pdb.hierarchy.chain() c.pre_allocate_residue_groups(number_of_additional_residue_groups=2) assert c.residue_groups_size() == 0 assert len(c.residue_groups()) == 0 for i in range(2): c.append_residue_group(residue_group=pdb.hierarchy.residue_group()) assert c.residue_groups_size() == 2 assert len(c.residue_groups()) == 2 for residue_group in c.residue_groups(): assert residue_group.parent().memory_id() == c.memory_id() assert c.atoms_size() == 0 assert c.atoms().size() == 0 # c.residue_groups()[0].resseq = "ugh" c.id = "ci" m = pdb.hierarchy.model() for i,cc in enumerate([ pdb.hierarchy.chain(parent=m, other=c), c.detached_copy()]): assert cc.memory_id() != c.memory_id() assert c.parent() is None if (i == 0): assert cc.parent().memory_id() == m.memory_id() else: assert cc.parent() is None assert cc.id == "ci" assert cc.residue_groups_size() == 2 assert cc.residue_groups()[0].memory_id() \ != c.residue_groups()[0].memory_id() assert cc.residue_groups()[0].resseq == "ugh" c.append_residue_group( residue_group=pdb.hierarchy.residue_group(resseq="%03d"%i)) assert c.residue_groups_size() == 3+i assert cc.residue_groups_size() == 2 assert [rg.resseq for rg in c.residue_groups()] \ == ["ugh", "", "000", "001"][:i+3] # c.insert_residue_group( i=3, residue_group=pdb.hierarchy.residue_group(resseq="b012")) assert [rg.resseq for rg in c.residue_groups()] \ == ["ugh", "", "000", "b012", "001"] c.remove_residue_group(i=1) assert [rg.resseq for rg in c.residue_groups()] \ == ["ugh", "000", "b012", "001"] rg = c.residue_groups()[1] assert rg.parent().memory_id() == c.memory_id() assert c.find_residue_group_index(residue_group=rg) == 1 c.remove_residue_group(residue_group=rg) assert rg.parent() is None assert c.find_residue_group_index(residue_group=rg) == -1 try: c.find_residue_group_index(residue_group=rg, must_be_present=True) except RuntimeError as e: assert str(e) == "residue_group not in chain." else: raise Exception_expected # rg1 = pdb.hierarchy.residue_group() rg2 = pdb.hierarchy.residue_group() ag = pdb.hierarchy.atom_group() rg1.append_atom_group(atom_group=ag) try: rg2.append_atom_group(atom_group=ag) except RuntimeError as e: assert str(e) == "atom_group has another parent residue_group already." else: raise Exception_expected # r = pdb.hierarchy.root() m = pdb.hierarchy.model() r.append_model(m) c = pdb.hierarchy.chain(id="c") m.append_chain(c) assert r.as_pdb_string() == "", r.as_pdb_string() rg = pdb.hierarchy.residue_group(resseq="s", icode="j") c.append_residue_group(residue_group=rg) ag = pdb.hierarchy.atom_group(altloc="a", resname="ALA") rg.append_atom_group(atom_group=ag) ag.append_atom(pdb.hierarchy.atom().set_name("n")) assert ag.only_atom().pdb_label_columns() == "n aALA c sj" assert not show_diff(r.as_pdb_string(), """\ ATOM n aALA c sj 0.000 0.000 0.000 0.00 0.00 TER """) rg = pdb.hierarchy.residue_group(resseq="t", icode="k") c.append_residue_group(residue_group=rg) ag = pdb.hierarchy.atom_group(altloc="b", resname="q") rg.append_atom_group(atom_group=ag) ag.append_atom(pdb.hierarchy.atom().set_name("m")) assert ag.only_atom().chain() == c rg = pdb.hierarchy.residue_group( resseq="u", icode="l", link_to_previous=False) c.append_residue_group(residue_group=rg) ag = pdb.hierarchy.atom_group(altloc="d", resname="p") rg.append_atom_group(atom_group=ag) ag.append_atom(pdb.hierarchy.atom().set_name("o")) assert not show_diff(r.as_pdb_string(), """\ ATOM n aALA c sj 0.000 0.000 0.000 0.00 0.00 ATOM m b q c tk 0.000 0.000 0.000 0.00 0.00 BREAK ATOM o d p c ul 0.000 0.000 0.000 0.00 0.00 """) # atoms = c.atoms() assert atoms.size() == 3 atoms[0].set_sigxyz((1,2,3)).set_sigocc(4).set_sigb(5) atoms[1].set_uij((6,7,8,3,5,4)) siguij_2_line = "" if (pdb.hierarchy.atom.has_siguij()): atoms[2].set_siguij((.6,.7,.8,.3,.5,.4)) siguij_2_line = """\ SIGUIJ o d p c ul 6000 7000 8000 3000 5000 4000 """ assert not show_diff(r.as_pdb_string(), """\ ATOM n aALA c sj 0.000 0.000 0.000 0.00 0.00 SIGATM n aALA c sj 1.000 2.000 3.000 4.00 5.00 ATOM m b q c tk 0.000 0.000 0.000 0.00 0.00 ANISOU m b q c tk 60000 70000 80000 30000 50000 40000 BREAK ATOM o d p c ul 0.000 0.000 0.000 0.00 0.00 %s""" % siguij_2_line) assert r.as_pdb_string(output_break_records=False) == """\ ATOM n aALA c sj 0.000 0.000 0.000 0.00 0.00 SIGATM n aALA c sj 1.000 2.000 3.000 4.00 5.00 ATOM m b q c tk 0.000 0.000 0.000 0.00 0.00 ANISOU m b q c tk 60000 70000 80000 30000 50000 40000 ATOM o d p c ul 0.000 0.000 0.000 0.00 0.00 """ atoms[0].set_uij((6,3,8,2,9,1)) siguij_0_line = "" if (pdb.hierarchy.atom.has_siguij()): atoms[0].set_siguij((.6,.3,.8,.2,.9,.1)) siguij_0_line = """\ SIGUIJ n a r c sj 6000 3000 8000 2000 9000 1000 Cg """ atoms[0].set_charge("Cg") assert not show_diff(r.as_pdb_string(), """\ ATOM n aALA c sj 0.000 0.000 0.000 0.00 0.00 Cg SIGATM n aALA c sj 1.000 2.000 3.000 4.00 5.00 Cg ANISOU n aALA c sj 60000 30000 80000 20000 90000 10000 Cg %sATOM m b q c tk 0.000 0.000 0.000 0.00 0.00 ANISOU m b q c tk 60000 70000 80000 30000 50000 40000 BREAK ATOM o d p c ul 0.000 0.000 0.000 0.00 0.00 %s""" % (siguij_0_line, siguij_2_line)) sio = StringIO() assert r.as_pdb_string(cstringio=sio, interleaved_conf=1) is sio assert r.as_pdb_string(cstringio=sio, interleaved_conf=2) is sio assert r.as_pdb_string(cstringio=sio, atom_hetatm=False) is sio assert r.as_pdb_string(cstringio=sio, sigatm=False) is sio assert r.as_pdb_string(cstringio=sio, anisou=False) is sio assert isinstance( r.as_pdb_string(cstringio=sio, siguij=False, return_cstringio=False), str) expected = """\ ATOM n aALA c sj 0.000 0.000 0.000 0.00 0.00 Cg SIGATM n aALA c sj 1.000 2.000 3.000 4.00 5.00 Cg ANISOU n aALA c sj 60000 30000 80000 20000 90000 10000 Cg SIGUIJ n a r c sj 6000 3000 8000 2000 9000 1000 Cg ATOM m b q c tk 0.000 0.000 0.000 0.00 0.00 ANISOU m b q c tk 60000 70000 80000 30000 50000 40000 BREAK ATOM o d p c ul 0.000 0.000 0.000 0.00 0.00 SIGUIJ o d p c ul 6000 7000 8000 3000 5000 4000 ATOM n aALA c sj 0.000 0.000 0.000 0.00 0.00 Cg SIGATM n aALA c sj 1.000 2.000 3.000 4.00 5.00 Cg ANISOU n aALA c sj 60000 30000 80000 20000 90000 10000 Cg SIGUIJ n aALA c sj 6000 3000 8000 2000 9000 1000 Cg ATOM m b q c tk 0.000 0.000 0.000 0.00 0.00 ANISOU m b q c tk 60000 70000 80000 30000 50000 40000 BREAK ATOM o d p c ul 0.000 0.000 0.000 0.00 0.00 SIGUIJ o d p c ul 6000 7000 8000 3000 5000 4000 SIGATM n aALA c sj 1.000 2.000 3.000 4.00 5.00 Cg ANISOU n aALA c sj 60000 30000 80000 20000 90000 10000 Cg SIGUIJ n aALA c sj 6000 3000 8000 2000 9000 1000 Cg ANISOU m b q c tk 60000 70000 80000 30000 50000 40000 BREAK SIGUIJ o d p c ul 6000 7000 8000 3000 5000 4000 ATOM n aALA c sj 0.000 0.000 0.000 0.00 0.00 Cg ANISOU n aALA c sj 60000 30000 80000 20000 90000 10000 Cg SIGUIJ n aALA c sj 6000 3000 8000 2000 9000 1000 Cg ATOM m b q c tk 0.000 0.000 0.000 0.00 0.00 ANISOU m b q c tk 60000 70000 80000 30000 50000 40000 BREAK ATOM o d p c ul 0.000 0.000 0.000 0.00 0.00 SIGUIJ o d p c ul 6000 7000 8000 3000 5000 4000 ATOM n aALA c sj 0.000 0.000 0.000 0.00 0.00 Cg SIGATM n aALA c sj 1.000 2.000 3.000 4.00 5.00 Cg SIGUIJ n aALA c sj 6000 3000 8000 2000 9000 1000 Cg ATOM m b q c tk 0.000 0.000 0.000 0.00 0.00 BREAK ATOM o d p c ul 0.000 0.000 0.000 0.00 0.00 SIGUIJ o d p c ul 6000 7000 8000 3000 5000 4000 ATOM n aALA c sj 0.000 0.000 0.000 0.00 0.00 Cg SIGATM n aALA c sj 1.000 2.000 3.000 4.00 5.00 Cg ANISOU n aALA c sj 60000 30000 80000 20000 90000 10000 Cg ATOM m b q c tk 0.000 0.000 0.000 0.00 0.00 ANISOU m b q c tk 60000 70000 80000 30000 50000 40000 BREAK ATOM o d p c ul 0.000 0.000 0.000 0.00 0.00 """ if (pdb.hierarchy.atom.has_siguij()): assert not show_diff(sio.getvalue(), expected) else: def filter_expected(): result = [] for line in expected.splitlines(): if (line.startswith("SIGUIJ")): continue result.append(line) return "\n".join(result)+"\n" assert not show_diff(sio.getvalue(), filter_expected()) assert not show_diff(r.as_pdb_string( atom_hetatm=False, sigatm=False, anisou=False, siguij=False), """\ BREAK """) # a = pdb.hierarchy.atom() assert a.pdb_label_columns() == " " a.set_name("n123") assert a.pdb_label_columns() == "n123 " ag = pdb.hierarchy.atom_group(altloc="a", resname="res") ag.append_atom(a) assert a.pdb_label_columns() == "n123ares " rg = pdb.hierarchy.residue_group(resseq="a000", icode="i") rg.append_atom_group(ag) assert a.pdb_label_columns() == "n123ares a000i" c = pdb.hierarchy.chain(id="ke") c.append_residue_group(rg) assert a.pdb_label_columns() == "n123areskea000i" # assert a.pdb_element_charge_columns() == " " a.set_element("e") assert a.pdb_element_charge_columns() == " e " a.set_charge("+") assert a.pdb_element_charge_columns() == " e+ " a.set_element("el") a.set_charge("2+") assert a.pdb_element_charge_columns() == "el2+" def exercise_model(): m = pdb.hierarchy.model() assert m.id == "" m = pdb.hierarchy.model(id="42") assert m.id == "42" m.id = "-23" assert m.id == "-23" # m = pdb.hierarchy.model(id="17") assert m.parent() is None m.pre_allocate_chains(number_of_additional_chains=2) assert m.chains_size() == 0 assert len(m.chains()) == 0 ch_a = pdb.hierarchy.chain(id="a") m.append_chain(chain=ch_a) assert ch_a.id == "a" assert ch_a.parent().memory_id() == m.memory_id() assert m.chains_size() == 1 assert len(m.chains()) == 1 ch_b = pdb.hierarchy.chain(id="b") assert ch_b.id == "b" assert ch_b.parent() is None m.append_chain(chain=ch_b) assert m.chains_size() == 2 chains = m.chains() assert len(chains) == 2 assert chains[0].memory_id() == ch_a.memory_id() assert chains[1].memory_id() == ch_b.memory_id() for i in range(3): m.append_chain(pdb.hierarchy.chain()) assert m.chains_size() == 5 assert len(m.chains()) == 5 for chain in m.chains(): assert chain.parent().memory_id() == m.memory_id() assert m.atoms_size() == 0 assert m.atoms().size() == 0 # r = pdb.hierarchy.root() for i,mc in enumerate([ pdb.hierarchy.model(parent=r, other=m), m.detached_copy()]): assert mc.memory_id() != m.memory_id() assert m.parent() is None if (i == 0): assert mc.parent().memory_id() == r.memory_id() else: assert mc.parent() is None assert mc.id == "17" assert mc.chains_size() == 5 assert mc.chains()[0].memory_id() != m.chains()[0].memory_id() assert mc.chains()[0].id == "a" m.append_chain(chain=pdb.hierarchy.chain(id="%d"%i)) assert m.chains_size() == 6+i assert mc.chains_size() == 5 assert [c.id for c in m.chains()] \ == ["a", "b", "", "", "", "0", "1"][:i+6] # m.insert_chain(i=-3, chain=pdb.hierarchy.chain(id="3")) assert [c.id for c in m.chains()] \ == ["a", "b", "", "", "3", "", "0", "1"] m.remove_chain(i=-2) assert [c.id for c in m.chains()] \ == ["a", "b", "", "", "3", "", "1"] c = m.chains()[0] assert c.parent().memory_id() == m.memory_id() assert m.find_chain_index(chain=c) == 0 m.remove_chain(chain=c) assert c.parent() is None assert m.find_chain_index(chain=c) == -1 try: m.find_chain_index(chain=c, must_be_present=True) except RuntimeError as e: assert str(e) == "chain not in model." else: raise Exception_expected # m1 = pdb.hierarchy.model() m2 = pdb.hierarchy.model() c = pdb.hierarchy.chain() m1.append_chain(chain=c) try: m2.append_chain(chain=c) except RuntimeError as e: assert str(e) == "chain has another parent model already." else: raise Exception_expected def exercise_root(): r = pdb.hierarchy.root() m = pdb.hierarchy.model() assert m.parent() is None m = pdb.hierarchy.model(parent=r) assert m.parent().memory_id() == r.memory_id() assert m.id == "" m = pdb.hierarchy.model(parent=r, id="2") assert m.parent(optional=False).memory_id() == r.memory_id() assert m.id == "2" del r assert m.parent() is None try: m.parent(optional=False) except RuntimeError as e: assert not show_diff(str(e), "model has no parent root") else: raise Exception_expected # r = pdb.hierarchy.root() assert r.info.size() == 0 r.info.append("abc") assert r.info.size() == 1 r.info = flex.std_string(["a", "b"]) assert r.info.size() == 2 r.pre_allocate_models(number_of_additional_models=2) assert r.models_size() == 0 assert len(r.models()) == 0 m_a = pdb.hierarchy.model(id="3") r.append_model(model=m_a) assert m_a.id == "3" assert m_a.parent().memory_id() == r.memory_id() assert r.models_size() == 1 assert len(r.models()) == 1 m_b = pdb.hierarchy.model(id="5") assert m_b.parent() is None r.append_model(model=m_b) assert r.models_size() == 2 models = r.models() assert len(models) == 2 assert models[0].memory_id() == m_a.memory_id() assert models[1].memory_id() == m_b.memory_id() for i in range(3): r.append_model(model=pdb.hierarchy.model()) assert r.models_size() == 5 assert len(r.models()) == 5 for model in r.models(): assert model.parent().memory_id() == r.memory_id() assert r.atoms_size() == 0 assert r.atoms().size() == 0 # rc = r.deep_copy() assert rc.memory_id() != r.memory_id() assert list(rc.info) == ["a", "b"] assert rc.info.id() != r.info.id() assert rc.models_size() == 5 assert rc.models()[0].memory_id() != r.models()[0].memory_id() assert rc.models()[0].id == "3" r.append_model(model=pdb.hierarchy.model(id="7")) assert r.models_size() == 6 assert rc.models_size() == 5 assert [m.id for m in r.models()] == ["3", "5", "", "", "", "7"] assert [m.id for m in rc.models()] == ["3", "5", "", "", ""] rc.append_model(model=pdb.hierarchy.model(id="8")) assert r.models_size() == 6 assert rc.models_size() == 6 assert [m.id for m in rc.models()] == ["3", "5", "", "", "", "8"] # r = rc.deep_copy() r.insert_model(i=4, model=pdb.hierarchy.model(id="M")) assert [m.id for m in r.models()] \ == ["3", "5", "", "", "M", "", "8"] r.remove_model(i=1) assert [m.id for m in r.models()] \ == ["3", "", "", "M", "", "8"] m = r.models()[-1] assert m.parent().memory_id() == r.memory_id() assert r.find_model_index(model=m) == 5 r.remove_model(model=m) assert m.parent() is None assert r.find_model_index(model=m) == -1 try: r.find_model_index(model=m, must_be_present=True) except RuntimeError as e: assert str(e) == "model not in root." else: raise Exception_expected # r1 = pdb.hierarchy.root() r2 = pdb.hierarchy.root() m = pdb.hierarchy.model() r1.append_model(model=m) try: r2.append_model(model=m) except RuntimeError as e: assert str(e) == "model has another parent root already." else: raise Exception_expected def exercise_atom_id_str(): a = pdb.hierarchy.atom() a.set_name(new_name="NaMe") a.set_serial(new_serial="B1234") assert a.id_str() == 'pdb="NaMe "' assert a.id_str(pdbres=True) == 'pdbres=" "' ag = pdb.hierarchy.atom_group(altloc="A", resname="GLY") ag.append_atom(a) assert a.id_str() == 'pdb="NaMeAGLY "' assert a.id_str(True) == 'pdbres="GLY "' rg = pdb.hierarchy.residue_group(resseq="1234", icode="J") rg.append_atom_group(ag) assert a.id_str() == 'pdb="NaMeAGLY 1234J"' assert a.id_str(pdbres=True) == 'pdbres="GLY 1234J"' ch = pdb.hierarchy.chain(id="Ch") ch.append_residue_group(rg) assert a.id_str() == 'pdb="NaMeAGLYCh1234J"' assert a.id_str(pdbres=True) == 'pdbres="GLYCh1234J"' md = pdb.hierarchy.model() md.append_chain(ch) assert a.id_str() == 'pdb="NaMeAGLYCh1234J"' assert a.id_str(pdbres=True) == 'pdbres="GLYCh1234J"' md.id = "" assert a.id_str() == 'pdb="NaMeAGLYCh1234J"' assert a.id_str(pdbres=True) == 'pdbres="GLYCh1234J"' md.id = "1" assert a.id_str() == 'model=" 1" pdb="NaMeAGLYCh1234J"' assert a.id_str(pdbres=True) == 'model=" 1" pdbres="GLYCh1234J"' md.id = "12345678" assert a.id_str() == 'model="12345678" pdb="NaMeAGLYCh1234J"' assert a.id_str(pdbres=True) == 'model="12345678" pdbres="GLYCh1234J"' #try: md.id = "123456789" #except (ValueError, RuntimeError), e: #assert str(e) == "string is too long for target variable " \ #"(maximum length is 8 characters, 9 given)." #else: raise Exception_expected md.id = "12345678" a.segid = "1234" assert a.id_str(suppress_segid=False) \ == 'model="12345678" pdb="NaMeAGLYCh1234J" segid="1234"' assert a.id_str(suppress_segid=True) \ == 'model="12345678" pdb="NaMeAGLYCh1234J"' assert a.id_str(pdbres=True) \ == 'model="12345678" pdbres="GLYCh1234J" segid="1234"' assert a.id_str(pdbres=True, suppress_segid=True) \ == 'model="12345678" pdbres="GLYCh1234J"' md.id = "" assert a.id_str() == 'pdb="NaMeAGLYCh1234J" segid="1234"' assert a.id_str(pdbres=True) \ == 'pdbres="GLYCh1234J" segid="1234"' assert a.id_str(pdbres=True, suppress_segid=True) \ == 'pdbres="GLYCh1234J"' rt = pdb.hierarchy.root() rt.append_model(md) assert a.id_str() == 'pdb="NaMeAGLYCh1234J" segid="1234"' assert a.id_str(pdbres=True) == 'pdbres="GLYCh1234J" segid="1234"' md.id = " " assert a.id_str() == 'model=" " pdb="NaMeAGLYCh1234J" segid="1234"' assert a.id_str(pdbres=True) \ == 'model=" " pdbres="GLYCh1234J" segid="1234"' # cf = ch.only_conformer() rd = cf.only_residue() assert rd.id_str() == 'model=" " pdbres="GLYCh1234J" segid="1234"' assert rd.id_str(suppress_segid=1) == 'model=" " pdbres="GLYCh1234J"' md.id = "12345678" assert rd.id_str() == 'model="12345678" pdbres="GLYCh1234J" segid="1234"' assert rd.id_str(suppress_segid=1) == 'model="12345678" pdbres="GLYCh1234J"' del cf assert rd.id_str(suppress_segid=-1) == 'pdbres="GLY 1234J" segid="1234"' assert rd.id_str(suppress_segid=1) == 'pdbres="GLY 1234J"' # a2 = pdb.hierarchy.atom().set_segid(new_segid="abcd") ag.append_atom(atom=a2) cf = ch.only_conformer() rd = cf.only_residue() assert rd.id_str(suppress_segid=1) == 'model="12345678" pdbres="GLYCh1234J"' assert rd.id_str(suppress_segid=-1) == 'model="12345678" pdbres="GLYCh1234J"' try: rd.id_str() except ValueError as e: assert not show_diff(str(e), '''\ residue.id_str(suppress_segid=false): segid is not unique: model="12345678" pdbres="GLYCh1234J" segid="1234"''') else: raise Exception_expected def exercise_format_atom_record(): a = (pdb.hierarchy.atom() .set_name(new_name="NaMe") .set_serial(new_serial="B1234") .set_xyz(new_xyz=(1.3,2.1,3.2)) .set_sigxyz(new_sigxyz=(.1,.2,.3)) .set_occ(new_occ=0.4) .set_sigocc(new_sigocc=0.1) .set_b(new_b=4.8) .set_sigb(new_sigb=0.7) .set_uij(new_uij=(1.3,2.1,3.2,4.3,2.7,9.3))) if (pdb.hierarchy.atom.has_siguij()): assert a.set_siguij(new_siguij=(.1,.2,.3,.6,.1,.9)) is a for hetero,record_name in [(False, "ATOM "), (True, "HETATM")]: a.set_hetero(new_hetero=hetero) for segid in ["", " ", "s", "sEgI"]: a.set_segid(new_segid=segid) for element in ["", " ", "e", "El"]: a.set_element(new_element=element) for charge in ["", " ", "c", "cH"]: a.set_charge(new_charge=charge) segielch = "%-4s%2s%-2s" % (segid, element, charge) s = a.format_atom_record() assert not show_diff(s, ("""%s\ B1234 NaMe 1.300 2.100 3.200 0.40 4.80 \ %s""" % (record_name, segielch)).rstrip()) sc = a.format_atom_record(replace_floats_with=None) assert not show_diff(sc, s) sc = a.format_atom_record(replace_floats_with="") assert not show_diff(sc, "%-27.27s%-8.8s" % (s[:27], s[72:])) sc = a.format_atom_record(replace_floats_with=" ") assert not show_diff(sc, "%-27.27s %-8.8s" % (s[:27], s[72:])) assert not show_diff(a.format_sigatm_record(), ("""SIGATM\ B1234 NaMe 0.100 0.200 0.300 0.10 0.70 \ %s""" % segielch).rstrip()) assert not show_diff(a.format_anisou_record(), ("""ANISOU\ B1234 NaMe 13000 21000 32000 43000 27000 93000 \ %s""" % segielch).rstrip()) if (pdb.hierarchy.atom.has_siguij()): assert not show_diff(a.format_siguij_record(), ("""SIGUIJ\ B1234 NaMe 1000 2000 3000 6000 1000 9000 \ %s""" % segielch).rstrip()) else: assert not show_diff(a.format_siguij_record(), ("""SIGUIJ\ B1234 NaMe -10000 -10000 -10000 -10000 -10000 -10000 \ %s""" % segielch).rstrip()) ag = pdb.hierarchy.atom_group(altloc="x", resname="uvw") ag.append_atom(atom=a) s = a.format_atom_record() assert not show_diff(s, ("""%s\ B1234 NaMexuvw 1.300 2.100 3.200 0.40 4.80 \ %s""" % (record_name, segielch)).rstrip()) sc = a.format_atom_record(replace_floats_with=".*.") assert not show_diff(sc, "%-27.27s.*.%-8.8s" % (s[:27], s[72:])) assert not show_diff(a.format_sigatm_record(), ("""SIGATM\ B1234 NaMexuvw 0.100 0.200 0.300 0.10 0.70 \ %s""" % segielch).rstrip()) assert not show_diff(a.format_anisou_record(), ("""ANISOU\ B1234 NaMexuvw 13000 21000 32000 43000 27000 93000 \ %s""" % segielch).rstrip()) if (pdb.hierarchy.atom.has_siguij()): assert not show_diff(a.format_siguij_record(), ("""SIGUIJ\ B1234 NaMexuvw 1000 2000 3000 6000 1000 9000 \ %s""" % segielch).rstrip()) else: assert not show_diff(a.format_siguij_record(), ("""SIGUIJ\ B1234 NaMexuvw -10000 -10000 -10000 -10000 -10000 -10000 \ %s""" % segielch).rstrip()) rg = pdb.hierarchy.residue_group(resseq="pqrs", icode="t") rg.append_atom_group(atom_group=ag) s = a.format_atom_record() assert not show_diff(s, ("""%s\ B1234 NaMexuvw pqrst 1.300 2.100 3.200 0.40 4.80 \ %s""" % (record_name, segielch)).rstrip()) sc = a.format_atom_record(replace_floats_with=".*.") assert not show_diff(sc, "%-27.27s.*.%-8.8s" % (s[:27], s[72:])) assert not show_diff(a.format_sigatm_record(), ("""SIGATM\ B1234 NaMexuvw pqrst 0.100 0.200 0.300 0.10 0.70 \ %s""" % segielch).rstrip()) assert not show_diff(a.format_anisou_record(), ("""ANISOU\ B1234 NaMexuvw pqrst 13000 21000 32000 43000 27000 93000 \ %s""" % segielch).rstrip()) if (pdb.hierarchy.atom.has_siguij()): assert not show_diff(a.format_siguij_record(), ("""SIGUIJ\ B1234 NaMexuvw pqrst 1000 2000 3000 6000 1000 9000 \ %s""" % segielch).rstrip()) else: assert not show_diff(a.format_siguij_record(), ("""SIGUIJ\ B1234 NaMexuvw pqrst -10000 -10000 -10000 -10000 -10000 -10000 \ %s""" % segielch).rstrip()) for chain_id in ["", "g", "hi"]: ch = pdb.hierarchy.chain(id=chain_id) ch.append_residue_group(residue_group=rg) s = a.format_atom_record() assert not show_diff(s, ("""%s\ B1234 NaMexuvw%2spqrst 1.300 2.100 3.200 0.40 4.80 \ %s""" % (record_name, chain_id, segielch)).rstrip()) sc = a.format_atom_record(replace_floats_with=".*.") assert not show_diff(sc, "%-27.27s.*.%-8.8s" % (s[:27], s[72:])) assert not show_diff(a.format_sigatm_record(), ("""SIGATM\ B1234 NaMexuvw%2spqrst 0.100 0.200 0.300 0.10 0.70 \ %s""" % (chain_id, segielch)).rstrip()) assert not show_diff(a.format_anisou_record(), ("""ANISOU\ B1234 NaMexuvw%2spqrst 13000 21000 32000 43000 27000 93000 \ %s""" % (chain_id, segielch)).rstrip()) if (pdb.hierarchy.atom.has_siguij()): assert not show_diff(a.format_siguij_record(), ("""SIGUIJ\ B1234 NaMexuvw%2spqrst 1000 2000 3000 6000 1000 9000 \ %s""" % (chain_id, segielch)).rstrip()) else: assert not show_diff(a.format_siguij_record(), ("""SIGUIJ\ B1234 NaMexuvw%2spqrst -10000 -10000 -10000 -10000 -10000 -10000 \ %s""" % (chain_id, segielch)).rstrip()) # assert not show_diff( a.quote(), '"'+a.format_atom_record(replace_floats_with=".*.")+'"') assert not show_diff( a.quote(full=True), '"'+a.format_atom_record()+'"') # del ag, rg, ch # rs = [ a.format_atom_record(), a.format_sigatm_record(), a.format_anisou_record()] if (a.has_siguij()): rs.append(a.format_siguij_record()) assert not show_diff( a.format_atom_record_group(), "\n".join(rs)) assert not show_diff( a.format_atom_record_group(atom_hetatm=False), "\n".join(rs[1:])) assert not show_diff( a.format_atom_record_group(sigatm=False), "\n".join(rs[:1]+rs[2:])) assert not show_diff( a.format_atom_record_group(anisou=False), "\n".join(rs[:2]+rs[3:])) if (a.has_siguij()): assert not show_diff( a.format_atom_record_group(siguij=False), "\n".join(rs[:-1])) else: assert not show_diff( a.format_atom_record_group(siguij=False), "\n".join(rs)) # atom = pdb.hierarchy.atom() atom.name = "NaMe" atom.xyz = (1.e6,-1.e5,1.e5) atom.occ = 9999. atom.b = 99999. assert not show_diff(atom.format_atom_record(), """\ ATOM NaMe 1000000.-100000.100000.09999.099999.""") atom.xyz = (0,1.e7,0) try: atom.format_atom_record() except RuntimeError as e: assert not show_diff(str(e), """\ atom Y coordinate value does not fit into F8.3 format: "ATOM NaMe " value: 10000000.000""") else: raise Exception_expected atom.xyz = (0,0,0) atom.occ = 100000 try: atom.format_atom_record() except RuntimeError as e: assert not show_diff(str(e), """\ atom occupancy factor does not fit into F6.2 format: "ATOM NaMe " occupancy factor: 100000.00""") else: raise Exception_expected atom.occ = 0 atom.b = 200000 try: atom.format_atom_record() except RuntimeError as e: assert not show_diff(str(e), """\ atom B-factor does not fit into F6.2 format: "ATOM NaMe " B-factor: 200000.00""") else: raise Exception_expected # atom.sigxyz = (1.e6,-1.e5,1.e5) atom.sigocc = 99999. atom.sigb = 9999. assert not show_diff(atom.format_sigatm_record(), """\ SIGATM NaMe 1000000.-100000.100000.099999.9999.0""") atom.sigxyz = (0,0,2.e7) try: atom.format_sigatm_record() except RuntimeError as e: assert not show_diff(str(e), """\ atom sigma Z coordinate value does not fit into F8.3 format: "SIGATM NaMe " value: 20000000.000""") else: raise Exception_expected atom.sigxyz = (0,0,0) atom.sigocc = 200000 try: atom.format_sigatm_record() except RuntimeError as e: assert not show_diff(str(e), """\ atom sigma occupancy factor does not fit into F6.2 format: "SIGATM NaMe " sigma occupancy factor: 200000.00""") else: raise Exception_expected atom.sigocc = 0 atom.sigb = 300000 try: atom.format_sigatm_record() except RuntimeError as e: assert not show_diff(str(e), """\ atom sigma B-factor does not fit into F6.2 format: "SIGATM NaMe " sigma B-factor: 300000.00""") else: raise Exception_expected # atom.uij = (0,1000,0,0,0,0) try: atom.format_anisou_record() except RuntimeError as e: assert not show_diff(str(e), """\ atom U22 value * 10000 does not fit into F7.0 format: "ANISOU NaMe " value * 10000: 10000000""") else: raise Exception_expected # atom.siguij = (0,0,0,0,3333,0) if (pdb.hierarchy.atom.has_siguij()): try: atom.format_siguij_record() except RuntimeError as e: assert not show_diff(str(e), """\ atom sigma U13 value * 10000 does not fit into F7.0 format: "SIGUIJ NaMe " value * 10000: 33330000""") else: raise Exception_expected else: assert not show_diff(atom.format_siguij_record(), """\ SIGUIJ NaMe -10000 -10000 -10000 -10000 -10000 -10000""") def exercise_construct_hierarchy(): def check(pdb_string, expected_root_as_str=None, expected_overall_counts_as_str=None, level_id=None, prefix=""): pdb_inp = pdb.input(source_info=None, lines=flex.split_lines(pdb_string)) root = pdb_inp.construct_hierarchy(sort_atoms=False) if (expected_root_as_str is not None): s = root.as_str(prefix=prefix, level_id=level_id) if (len(expected_root_as_str) == 0): sys.stdout.write(s) else: assert not show_diff(s, expected_root_as_str) if (expected_overall_counts_as_str is not None): s = root.overall_counts().as_str( prefix=prefix, residue_groups_max_show=3, duplicate_atom_labels_max_show=3) if (len(expected_overall_counts_as_str) == 0): sys.stdout.write(s) else: assert not show_diff(s, expected_overall_counts_as_str) return root # check("""\ MODEL 1 ATOM 1 N MET A 1 6.215 22.789 24.067 1.00 0.00 N ATOM 2 CA MET A 1 6.963 22.789 22.822 1.00 0.00 C HETATM 3 C MET A 2 7.478 21.387 22.491 1.00 0.00 C ATOM 4 O MET A 2 8.406 20.895 23.132 1.00 0.00 O ENDMDL MODEL 3 HETATM 9 2H3 MPR B 5 16.388 0.289 6.613 1.00 0.08 SIGATM 9 2H3 MPR B 5 0.155 0.175 0.155 0.00 0.05 ANISOU 9 2H3 MPR B 5 848 848 848 0 0 0 SIGUIJ 9 2H3 MPR B 5 510 510 510 0 0 0 TER ATOM 10 N CYSCH 6 14.270 2.464 3.364 1.00 0.07 SIGATM 10 N CYSCH 6 0.012 0.012 0.011 0.00 0.00 ANISOU 10 N CYSCH 6 788 626 677 -344 621 -232 SIGUIJ 10 N CYSCH 6 3 13 4 11 6 13 TER ENDMDL END """, """\ model id=" 1" #chains=1 chain id="A" #residue_groups=2 resid=" 1 " #atom_groups=1 altloc="" resname="MET" #atoms=2 " N " " CA " resid=" 2 " #atom_groups=1 altloc="" resname="MET" #atoms=2 " C " " O " model id=" 3" #chains=2 chain id="B" #residue_groups=1 resid=" 5 " #atom_groups=1 altloc="" resname="MPR" #atoms=1 "2H3 " chain id="CH" #residue_groups=1 resid=" 6 " #atom_groups=1 altloc="" resname="CYS" #atoms=1 " N " """, """\ total number of: models: 2 chains: 3 alt. conf.: 0 residues: 4 atoms: 6 anisou: 2 number of atom element+charge types: 4 histogram of atom element+charge frequency: " " 2 " C " 2 " N " 1 " O " 1 residue name classes: "common_amino_acid" 3 "other" 1 number of chain ids: 3 histogram of chain id frequency: "A" 1 "B" 1 "CH" 1 number of alt. conf. ids: 0 number of residue names: 3 histogram of residue name frequency: "MET" 2 "CYS" 1 "MPR" 1 other """) # check("""\ ATOM N1 AR01 ATOM N2 BR01 ATOM N1 CR02 ATOM N2 R02 """, """\ model id="" #chains=1 chain id=" " #residue_groups=2 resid=" " #atom_groups=2 altloc="A" resname="R01" #atoms=1 " N1 " altloc="B" resname="R01" #atoms=1 " N2 " resid=" " #atom_groups=2 ### Info: same as previous resid ### altloc="" resname="R02" #atoms=1 " N2 " altloc="C" resname="R02" #atoms=1 " N1 " """) # check("""\ ATOM N1 BR01 ATOM N1 R01 ATOM N2 R01 ATOM N3 BR01 ATOM N3 R01 ATOM N1 R02 ATOM N1 BR02 ATOM N2 R02 ATOM N3 BR02 ATOM N3 R02 ATOM N1 R03 ATOM N1 BR03 ATOM N2 R03 ATOM N3 BR03 ATOM N3 R03 """, """\ model id="" #chains=1 chain id=" " #residue_groups=3 resid=" " #atom_groups=3 altloc="" resname="R01" #atoms=1 " N2 " altloc=" " resname="R01" #atoms=2 " N1 " " N3 " altloc="B" resname="R01" #atoms=2 " N1 " " N3 " resid=" " #atom_groups=3 ### Info: same as previous resid ### altloc="" resname="R02" #atoms=1 " N2 " altloc=" " resname="R02" #atoms=2 " N1 " " N3 " altloc="B" resname="R02" #atoms=2 " N1 " " N3 " resid=" " #atom_groups=3 ### Info: same as previous resid ### altloc="" resname="R03" #atoms=1 " N2 " altloc=" " resname="R03" #atoms=2 " N1 " " N3 " altloc="B" resname="R03" #atoms=2 " N1 " " N3 " """) # root = check("""\ ATOM N1 BR01 ATOM N1 R01 ATOM N2 R01 ATOM N3 BR01 ATOM N3 R01 ATOM N1 AR02 ATOM N1 BR02 ATOM N2 R02 ATOM N3 BR02 ATOM N3 AR02 ATOM N1 R03 ATOM N1 BR03 ATOM N2 R03 ATOM N3 BR03 ATOM N3 R03 """, """\ model id="" #chains=1 chain id=" " #residue_groups=3 resid=" " #atom_groups=3 altloc="" resname="R01" #atoms=1 " N2 " altloc=" " resname="R01" #atoms=2 " N1 " " N3 " altloc="B" resname="R01" #atoms=2 " N1 " " N3 " resid=" " #atom_groups=3 ### Info: same as previous resid ### altloc="" resname="R02" #atoms=1 " N2 " altloc="A" resname="R02" #atoms=2 " N1 " " N3 " altloc="B" resname="R02" #atoms=2 " N1 " " N3 " resid=" " #atom_groups=3 ### Info: same as previous resid ### altloc="" resname="R03" #atoms=1 " N2 " altloc=" " resname="R03" #atoms=2 " N1 " " N3 " altloc="B" resname="R03" #atoms=2 " N1 " " N3 " """, """\ total number of: models: 1 chains: 1 alt. conf.: 3 residues: 3 atoms: 15 anisou: 0 number of atom element+charge types: 1 histogram of atom element+charge frequency: " " 15 residue name classes: "other" 3 number of chain ids: 1 histogram of chain id frequency: " " 1 number of alt. conf. ids: 3 histogram of alt. conf. id frequency: " " 1 "A" 1 "B" 1 residue alt. conf. situations: pure main conf.: 0 pure alt. conf.: 0 proper alt. conf.: 1 ### ERROR: improper alt. conf. ### improper alt. conf.: 2 chains with mix of proper and improper alt. conf.: 1 residue with proper altloc "ATOM N2 R02 .*. " "ATOM N1 AR02 .*. " "ATOM N3 AR02 .*. " "ATOM N1 BR02 .*. " "ATOM N3 BR02 .*. " residue with improper altloc "ATOM N2 R01 .*. " "ATOM N1 R01 .*. " "ATOM N3 R01 .*. " "ATOM N1 BR01 .*. " "ATOM N3 BR01 .*. " number of residue names: 3 histogram of residue name frequency: "R01" 1 other "R02" 1 other "R03" 1 other ### WARNING: consecutive residue_groups with same resid ### number of consecutive residue groups with same resid: 2 residue group: "ATOM N2 R01 .*. " ... 3 atoms not shown "ATOM N3 BR01 .*. " next residue group: "ATOM N2 R02 .*. " ... 3 atoms not shown "ATOM N3 BR02 .*. " next residue group: "ATOM N2 R03 .*. " ... 3 atoms not shown "ATOM N3 BR03 .*. " """, prefix=" ") oc = root.overall_counts() assert oc.warnings() == [ '### WARNING: consecutive residue_groups with same resid ###'] assert oc.errors() == ['### ERROR: improper alt. conf. ###'] assert oc.errors_and_warnings() == [ '### ERROR: improper alt. conf. ###', '### WARNING: consecutive residue_groups with same resid ###'] # check("""\ ATOM N1 BR01 ATOM N1 AR01 ATOM N2 CR01 ATOM N3 BR01 ATOM N3 AR01 ATOM N1 R02 ATOM N1 BR02 ATOM N2 R02 ATOM N3 BR02 ATOM N3 R02 ATOM N1 CR03 ATOM N1 BR03 ATOM N2 BR03 ATOM N2 CR03 ATOM N3 R03 """, """\ model id="" #chains=1 chain id=" " #residue_groups=3 resid=" " #atom_groups=3 altloc="B" resname="R01" #atoms=2 " N1 " " N3 " altloc="A" resname="R01" #atoms=2 " N1 " " N3 " altloc="C" resname="R01" #atoms=1 " N2 " resid=" " #atom_groups=3 ### Info: same as previous resid ### altloc="" resname="R02" #atoms=1 " N2 " altloc=" " resname="R02" #atoms=2 " N1 " " N3 " altloc="B" resname="R02" #atoms=2 " N1 " " N3 " resid=" " #atom_groups=3 ### Info: same as previous resid ### altloc="" resname="R03" #atoms=1 " N3 " altloc="C" resname="R03" #atoms=2 " N1 " " N2 " altloc="B" resname="R03" #atoms=2 " N1 " " N2 " """, """\ total number of: models: 1 chains: 1 alt. conf.: 4 residues: 3 atoms: 15 anisou: 0 number of atom element+charge types: 1 histogram of atom element+charge frequency: " " 15 residue name classes: "other" 3 number of chain ids: 1 histogram of chain id frequency: " " 1 number of alt. conf. ids: 4 histogram of alt. conf. id frequency: " " 1 "A" 1 "B" 1 "C" 1 residue alt. conf. situations: pure main conf.: 0 pure alt. conf.: 1 proper alt. conf.: 1 ### ERROR: improper alt. conf. ### improper alt. conf.: 1 chains with mix of proper and improper alt. conf.: 1 residue with proper altloc "ATOM N3 R03 .*. " "ATOM N1 CR03 .*. " "ATOM N2 CR03 .*. " "ATOM N1 BR03 .*. " "ATOM N2 BR03 .*. " residue with improper altloc "ATOM N2 R02 .*. " "ATOM N1 R02 .*. " "ATOM N3 R02 .*. " "ATOM N1 BR02 .*. " "ATOM N3 BR02 .*. " number of residue names: 3 histogram of residue name frequency: "R01" 1 other "R02" 1 other "R03" 1 other ### WARNING: consecutive residue_groups with same resid ### number of consecutive residue groups with same resid: 2 residue group: "ATOM N1 BR01 .*. " ... 3 atoms not shown "ATOM N2 CR01 .*. " next residue group: "ATOM N2 R02 .*. " ... 3 atoms not shown "ATOM N3 BR02 .*. " next residue group: "ATOM N3 R03 .*. " ... 3 atoms not shown "ATOM N2 BR03 .*. " """) # check("""\ REMARK ANTIBIOTIC 26-JUL-06 2IZQ ATOM 220 N ATRP A 11 20.498 12.832 34.558 0.50 6.03 N ATOM 221 CA ATRP A 11 21.094 12.032 35.602 0.50 5.24 C ATOM 222 C ATRP A 11 22.601 12.088 35.532 0.50 6.49 C ATOM 223 O ATRP A 11 23.174 12.012 34.439 0.50 7.24 O ATOM 234 H ATRP A 11 20.540 12.567 33.741 0.50 7.24 H ATOM 235 HA ATRP A 11 20.771 12.306 36.485 0.50 6.28 H ATOM 244 N CPHE A 11 20.226 13.044 34.556 0.15 6.35 N ATOM 245 CA CPHE A 11 20.950 12.135 35.430 0.15 5.92 C ATOM 246 C CPHE A 11 22.448 12.425 35.436 0.15 6.32 C ATOM 247 O CPHE A 11 22.961 12.790 34.373 0.15 6.08 O ATOM 255 N BTYR A 11 20.553 12.751 34.549 0.35 5.21 N ATOM 256 CA BTYR A 11 21.106 11.838 35.524 0.35 5.51 C ATOM 257 C BTYR A 11 22.625 11.920 35.572 0.35 5.42 C ATOM 258 O BTYR A 11 23.299 11.781 34.538 0.35 5.30 O ATOM 262 HB2CPHE A 11 21.221 10.536 34.146 0.15 7.21 H ATOM 263 CD2BTYR A 11 18.463 10.012 36.681 0.35 9.08 C ATOM 264 HB3CPHE A 11 21.198 10.093 35.647 0.15 7.21 H ATOM 265 CE1BTYR A 11 17.195 9.960 34.223 0.35 10.76 C ATOM 266 HD1CPHE A 11 19.394 9.937 32.837 0.15 10.53 H ATOM 267 CE2BTYR A 11 17.100 9.826 36.693 0.35 11.29 C ATOM 268 HD2CPHE A 11 18.873 10.410 36.828 0.15 9.24 H ATOM 269 CZ BTYR A 11 16.546 9.812 35.432 0.35 11.90 C ATOM 270 HE1CPHE A 11 17.206 9.172 32.650 0.15 12.52 H ATOM 271 OH BTYR A 11 15.178 9.650 35.313 0.35 19.29 O ATOM 272 HE2CPHE A 11 16.661 9.708 36.588 0.15 11.13 H ATOM 273 HZ CPHE A 11 15.908 9.110 34.509 0.15 13.18 H ATOM 274 H BTYR A 11 20.634 12.539 33.720 0.35 6.25 H ATOM 275 HA BTYR A 11 20.773 12.116 36.402 0.35 6.61 H ATOM 276 HB2BTYR A 11 20.949 10.064 34.437 0.35 6.78 H """, """\ model id="" #chains=1 chain id="A" #residue_groups=1 resid=" 11 " #atom_groups=3 ### Info: with mixed residue names ### altloc="A" resname="TRP" #atoms=6 altloc="C" resname="PHE" #atoms=11 altloc="B" resname="TYR" #atoms=12 """, """\ total number of: models: 1 chains: 1 alt. conf.: 3 residues: 1 (1 with mixed residue names) atoms: 29 anisou: 0 number of atom element+charge types: 4 histogram of atom element+charge frequency: " H " 12 " C " 10 " O " 4 " N " 3 residue name classes: "common_amino_acid" 3 number of chain ids: 1 histogram of chain id frequency: "A" 1 number of alt. conf. ids: 3 histogram of alt. conf. id frequency: "A" 1 "B" 1 "C" 1 residue alt. conf. situations: pure main conf.: 0 pure alt. conf.: 1 proper alt. conf.: 0 improper alt. conf.: 0 chains with mix of proper and improper alt. conf.: 0 number of residue names: 3 histogram of residue name frequency: "PHE" 1 "TRP" 1 "TYR" 1 """, level_id="atom_group") # root = pdb.input( source_info=None, lines=flex.split_lines("""\ BREAK """)).construct_hierarchy() assert root.models_size() == 0 root = pdb.input( source_info=None, lines=flex.split_lines("""\ BREAK ATOM 1 CB LYS 109 BREAK TER """)).construct_hierarchy() assert not root.only_residue_group().link_to_previous root = pdb.input( source_info=None, lines=flex.split_lines("""\ BREAK ATOM 1 CB LYS 109 ATOM 2 CG LYS 109 BREAK TER """)).construct_hierarchy() assert not root.only_residue_group().link_to_previous pdb_str = """\ ATOM 1 CB LYS 109 ATOM 2 CG LYS 109 ATOM 3 CA LYS 110 ATOM 4 CB LYS 110 BREAK ATOM 5 CA LYS 111 ATOM 6 CB LYS 111 ATOM 7 CA LYS 112 ATOM 8 CB LYS 112 """ lines = flex.split_lines(pdb_str) for i_proc in [0,1]: root = pdb.input(source_info=None, lines=lines).construct_hierarchy() residue_groups = root.only_chain().residue_groups() assert len(residue_groups) == 4 assert not residue_groups[0].link_to_previous assert residue_groups[1].link_to_previous assert not residue_groups[2].link_to_previous assert residue_groups[3].link_to_previous if (i_proc == 0): lines = lines.select(flex.size_t([0,2,4,5,7])) try: pdb.input( source_info=None, lines=flex.split_lines("""\ REMARK ATOM 1 CB LYS 109 BREAK ATOM 2 CG LYS 109 """)).construct_hierarchy() except RuntimeError as e: assert not show_diff(str(e), "Misplaced BREAK record (input line 3).") else: raise Exception_expected try: pdb.input( source_info="file abc", lines=flex.split_lines("""\ REMARK ATOM 1 CA LYS 109 ATOM 2 CB LYS 109 BREAK ATOM 3 CA LYS 110 BREAK ATOM 4 CB LYS 110 """)).construct_hierarchy() except RuntimeError as e: assert not show_diff(str(e), "Misplaced BREAK record (file abc, line 6).") else: raise Exception_expected # check(pdb_str, """\ :=model id="" #chains=1 := chain id=" " #residue_groups=4 := resid=" 109 " #atom_groups=1 := altloc="" resname="LYS" #atoms=2 := " CB " := " CG " := resid=" 110 " #atom_groups=1 := altloc="" resname="LYS" #atoms=2 := " CA " := " CB " := ### chain break ### := resid=" 111 " #atom_groups=1 := altloc="" resname="LYS" #atoms=2 := " CA " := " CB " := resid=" 112 " #atom_groups=1 := altloc="" resname="LYS" #atoms=2 := " CA " := " CB " """, """\ :=total number of: := models: 1 := chains: 1 (1 explicit chain break) := alt. conf.: 0 := residues: 4 := atoms: 8 := anisou: 0 :=number of atom element+charge types: 1 :=histogram of atom element+charge frequency: := " " 8 :=residue name classes: := "common_amino_acid" 4 :=number of chain ids: 1 :=histogram of chain id frequency: := " " 1 :=number of alt. conf. ids: 0 :=number of residue names: 1 :=histogram of residue name frequency: := "LYS" 4 """, prefix=":=") # check(pdb_str, """\ model id="" #chains=1 chain id=" " #residue_groups=4 resid=" 109 " #atom_groups=1 altloc="" resname="LYS" #atoms=2 resid=" 110 " #atom_groups=1 altloc="" resname="LYS" #atoms=2 ### chain break ### resid=" 111 " #atom_groups=1 altloc="" resname="LYS" #atoms=2 resid=" 112 " #atom_groups=1 altloc="" resname="LYS" #atoms=2 """, level_id="atom_group") # check(pdb_str, """\ model id="" #chains=1 chain id=" " #residue_groups=4 resid=" 109 " #atom_groups=1 resid=" 110 " #atom_groups=1 ### chain break ### resid=" 111 " #atom_groups=1 resid=" 112 " #atom_groups=1 """, level_id="residue_group") # check(pdb_str, """\ model id="" #chains=1 chain id=" " #residue_groups=4 """, level_id="chain") # check(pdb_str, """\ model id="" #chains=1 """, level_id="model") # check("""\ MODEL 1 ENDMDL MODEL 1 ENDMDL MODEL 1 ENDMDL """, """\ model id=" 1" #chains=0 ### ERROR: duplicate model id ### ### WARNING: empty model ### model id=" 1" #chains=0 ### ERROR: duplicate model id ### ### WARNING: empty model ### model id=" 1" #chains=0 ### ERROR: duplicate model id ### ### WARNING: empty model ### """, """\ total number of: ### ERROR: duplicate model ids ### ### WARNING: empty model ### models: 3 (3 with duplicate model ids; 3 empty) chains: 0 alt. conf.: 0 residues: 0 atoms: 0 anisou: 0 number of atom element+charge types: 0 residue name classes: None number of chain ids: 0 number of alt. conf. ids: 0 number of residue names: 0 """) # check("""\ MODEL 1 ATOM A ATOM B ATOM A ENDMDL MODEL 1 ATOM A 1 BREAK ATOM A 2 ATOM B ATOM A ENDMDL MODEL 2 ATOM A BREAK ATOM A I ATOM B ENDMDL """, """\ model id=" 1" #chains=3 ### ERROR: duplicate model id ### chain id="A" #residue_groups=1 ### WARNING: duplicate chain id ### resid=" " #atom_groups=1 altloc="" resname=" " #atoms=1 " " chain id="B" #residue_groups=1 resid=" " #atom_groups=1 altloc="" resname=" " #atoms=1 " " chain id="A" #residue_groups=1 ### WARNING: duplicate chain id ### resid=" " #atom_groups=1 altloc="" resname=" " #atoms=1 " " model id=" 1" #chains=3 ### ERROR: duplicate model id ### chain id="A" #residue_groups=2 ### WARNING: duplicate chain id ### resid=" 1 " #atom_groups=1 altloc="" resname=" " #atoms=1 " " ### chain break ### resid=" 2 " #atom_groups=1 altloc="" resname=" " #atoms=1 " " chain id="B" #residue_groups=1 resid=" " #atom_groups=1 altloc="" resname=" " #atoms=1 " " chain id="A" #residue_groups=1 ### WARNING: duplicate chain id ### resid=" " #atom_groups=1 altloc="" resname=" " #atoms=1 " " model id=" 2" #chains=2 chain id="A" #residue_groups=2 resid=" " #atom_groups=1 altloc="" resname=" " #atoms=1 " " ### chain break ### resid=" I" #atom_groups=1 altloc="" resname=" " #atoms=1 " " chain id="B" #residue_groups=1 resid=" " #atom_groups=1 altloc="" resname=" " #atoms=1 " " """, """\ total number of: ### ERROR: duplicate model ids ### models: 3 (2 with duplicate model ids) ### WARNING: duplicate chain ids ### chains: 8 (4 with duplicate chain ids; 2 explicit chain breaks) alt. conf.: 0 residues: 10 ### ERROR: duplicate atom labels ### atoms: 10 (2 with duplicate labels) anisou: 0 number of atom element+charge types: 1 histogram of atom element+charge frequency: " " 10 residue name classes: "other" 10 number of chain ids: 2 histogram of chain id frequency: "A" 5 "B" 3 number of alt. conf. ids: 0 number of residue names: 1 histogram of residue name frequency: " " 10 other number of groups of duplicate atom labels: 1 total number of affected atoms: 2 group "ATOM .*. A .*. " "ATOM .*. A .*. " """) # check("""\ ATOM 54 CA GLY A 9 ATOM 55 CA GLY A 9 ATOM 56 CA BGLY A 9 """, """\ model id="" #chains=1 chain id="A" #residue_groups=1 resid=" 9 " #atom_groups=2 altloc=" " resname="GLY" #atoms=2 " CA " " CA " altloc="B" resname="GLY" #atoms=1 " CA " """, """\ total number of: models: 1 chains: 1 alt. conf.: 2 residues: 1 ### ERROR: duplicate atom labels ### atoms: 3 (2 with duplicate labels) anisou: 0 number of atom element+charge types: 1 histogram of atom element+charge frequency: " " 3 residue name classes: "common_amino_acid" 1 number of chain ids: 1 histogram of chain id frequency: "A" 1 number of alt. conf. ids: 2 histogram of alt. conf. id frequency: " " 1 "B" 1 residue alt. conf. situations: pure main conf.: 0 pure alt. conf.: 0 proper alt. conf.: 0 ### ERROR: improper alt. conf. ### improper alt. conf.: 1 chains with mix of proper and improper alt. conf.: 0 residue with improper altloc "ATOM 54 CA GLY A 9 .*. " "ATOM 55 CA GLY A 9 .*. " "ATOM 56 CA BGLY A 9 .*. " number of residue names: 1 histogram of residue name frequency: "GLY" 1 number of groups of duplicate atom labels: 1 total number of affected atoms: 2 group "ATOM .*. CA GLY A 9 .*. " "ATOM .*. CA GLY A 9 .*. " """) # pdb_inp = pdb.input(source_info=None, lines=flex.split_lines("""\ ATOM 68 HD1 LEU B 441 ATOM 69 HD1 LEU B 441 ATOM 70 HD1 LEU B 441 ATOM 71 HD2 LEU B 441 ATOM 72 HD2 LEU B 441 ATOM 73 HD2 LEU B 441 """)) oc = pdb_inp.construct_hierarchy(sort_atoms=False).overall_counts() assert oc.errors() == ['### ERROR: duplicate atom labels ###'] assert len(oc.warnings()) == 0 oc.raise_improper_alt_conf_if_necessary() oc.raise_chains_with_mix_of_proper_and_improper_alt_conf_if_necessary() try: oc.raise_duplicate_atom_labels_if_necessary(max_show=1) except Sorry as e: assert not show_diff(str(e), '''\ number of groups of duplicate atom labels: 2 total number of affected atoms: 6 group "ATOM .*. HD1 LEU B 441 .*. " "ATOM .*. HD1 LEU B 441 .*. " "ATOM .*. HD1 LEU B 441 .*. " ... 1 remaining group not shown''') else: raise Exception_expected sio = StringIO() oc.show_duplicate_atom_labels(out=sio) assert not show_diff(sio.getvalue(), """\ number of groups of duplicate atom labels: 2 total number of affected atoms: 6 group "ATOM .*. HD1 LEU B 441 .*. " "ATOM .*. HD1 LEU B 441 .*. " "ATOM .*. HD1 LEU B 441 .*. " group "ATOM .*. HD2 LEU B 441 .*. " "ATOM .*. HD2 LEU B 441 .*. " "ATOM .*. HD2 LEU B 441 .*. " """) # check("""\ ATOM 68 HD1 LEU B 441 ATOM 69 HD2 LEU B 441 ATOM 70 HD3 LEU B 441 ATOM 71 HD4 LEU B 441 ATOM 72 HD1 LEU B 441 ATOM 73 HD2 LEU B 441 ATOM 74 HD3 LEU B 441 ATOM 75 HD4 LEU B 441 """, None, """\ total number of: models: 1 chains: 1 alt. conf.: 0 residues: 1 ### ERROR: duplicate atom labels ### atoms: 8 (8 with duplicate labels) anisou: 0 number of atom element+charge types: 1 histogram of atom element+charge frequency: " " 8 residue name classes: "common_amino_acid" 1 number of chain ids: 1 histogram of chain id frequency: "B" 1 number of alt. conf. ids: 0 number of residue names: 1 histogram of residue name frequency: "LEU" 1 number of groups of duplicate atom labels: 4 total number of affected atoms: 8 group "ATOM .*. HD1 LEU B 441 .*. " "ATOM .*. HD1 LEU B 441 .*. " group "ATOM .*. HD2 LEU B 441 .*. " "ATOM .*. HD2 LEU B 441 .*. " group "ATOM .*. HD3 LEU B 441 .*. " "ATOM .*. HD3 LEU B 441 .*. " ... 1 remaining group not shown """) # for segid in ["", "SEGI"]: oc = pdb.input(source_info=None, lines=flex.split_lines("""\ ATOM 68 HD1 LEU 441 %s ATOM 72 HD1 LEU 441 """ % segid)).construct_hierarchy(sort_atoms=False).overall_counts() if (segid != ""): oc.raise_duplicate_atom_labels_if_necessary() else: try: oc.raise_duplicate_atom_labels_if_necessary() except Sorry as e: assert not show_diff(str(e), '''\ number of groups of duplicate atom labels: 1 total number of affected atoms: 2 group "ATOM .*. HD1 LEU 441 .*. " "ATOM .*. HD1 LEU 441 .*. "''') else: raise Exception_expected # check("""\ HEADER HYDROLASE 19-JUL-05 2BWX ATOM 2038 N CYS A 249 68.746 44.381 71.143 0.70 21.04 N ATOM 2039 CA CYS A 249 68.957 43.022 71.606 0.70 21.28 C ATOM 2040 C CYS A 249 70.359 42.507 71.362 0.70 19.80 C ATOM 2041 O CYS A 249 71.055 42.917 70.439 0.70 19.80 O ATOM 2042 CB ACYS A 249 67.945 42.064 70.987 0.40 24.99 C ATOM 2044 SG ACYS A 249 66.261 42.472 71.389 0.40 27.94 S ATOM 2043 CB BCYS A 249 67.928 42.101 70.948 0.30 23.34 C ATOM 2045 SG BCYS A 249 67.977 40.404 71.507 0.30 26.46 S HETATM 2046 N CCSO A 249 68.746 44.381 71.143 0.30 21.04 N HETATM 2047 CA CCSO A 249 68.957 43.022 71.606 0.30 21.28 C HETATM 2048 CB CCSO A 249 67.945 42.064 70.987 0.30 24.99 C HETATM 2049 SG CCSO A 249 66.261 42.472 71.389 0.30 27.94 S HETATM 2050 C CCSO A 249 70.359 42.507 71.362 0.30 19.80 C HETATM 2051 O CCSO A 249 71.055 42.917 70.439 0.30 19.80 O HETATM 2052 OD CCSO A 249 66.275 42.201 72.870 0.30 23.67 O """, """\ model id="" #chains=1 chain id="A" #residue_groups=2 resid=" 249 " #atom_groups=3 altloc="" resname="CYS" #atoms=4 altloc="A" resname="CYS" #atoms=2 altloc="B" resname="CYS" #atoms=2 resid=" 249 " #atom_groups=1 ### Info: same as previous resid ### altloc="C" resname="CSO" #atoms=7 """, """\ total number of: models: 1 chains: 1 alt. conf.: 3 residues: 2 atoms: 15 anisou: 0 number of atom element+charge types: 4 histogram of atom element+charge frequency: " C " 7 " O " 3 " S " 3 " N " 2 residue name classes: "common_amino_acid" 1 "modified_amino_acid" 1 number of chain ids: 1 histogram of chain id frequency: "A" 1 number of alt. conf. ids: 3 histogram of alt. conf. id frequency: "A" 1 "B" 1 "C" 1 residue alt. conf. situations: pure main conf.: 0 pure alt. conf.: 1 proper alt. conf.: 1 improper alt. conf.: 0 chains with mix of proper and improper alt. conf.: 0 number of residue names: 2 histogram of residue name frequency: "CSO" 1 modified amino acid "CYS" 1 ### WARNING: consecutive residue_groups with same resid ### number of consecutive residue groups with same resid: 1 residue group: "ATOM 2038 N CYS A 249 .*. N " ... 6 atoms not shown "ATOM 2045 SG BCYS A 249 .*. S " next residue group: "HETATM 2046 N CCSO A 249 .*. N " ... 5 atoms not shown "HETATM 2052 OD CCSO A 249 .*. O " """, level_id="atom_group") # check("""\ HEADER OXIDOREDUCTASE 17-SEP-97 1OHJ HETATM 1552 C3 COP 188 11.436 28.065 13.009 1.00 8.51 C HETATM 1553 C1 COP 188 13.269 26.907 13.759 1.00 8.86 C HETATM 1582 O24 COP 188 13.931 34.344 22.009 1.00 20.08 O HETATM 1583 O25 COP 188 13.443 32.717 20.451 1.00 20.18 O HETATM 1608 O HOH 188 20.354 30.097 11.632 1.00 21.33 O HETATM 1569 C28ACOP 188 14.231 36.006 18.087 0.50 25.20 C HETATM 1571 C29ACOP 188 13.126 36.948 17.945 0.50 26.88 C HETATM 1604 O40ACOP 188 15.720 40.117 14.909 0.50 31.54 O HETATM 1606 O41ACOP 188 15.816 42.243 14.385 0.50 31.73 O HETATM 1570 C28BCOP 188 14.190 36.055 18.102 0.50 24.97 C HETATM 1572 C29BCOP 188 13.133 37.048 18.009 0.50 26.45 C HETATM 1605 O40BCOP 188 10.794 41.093 18.747 0.50 30.51 O HETATM 1607 O41BCOP 188 12.838 40.007 19.337 0.50 30.37 O """, """\ model id="" #chains=1 chain id=" " #residue_groups=3 resid=" 188 " #atom_groups=1 altloc="" resname="COP" #atoms=4 resid=" 188 " #atom_groups=1 ### Info: same as previous resid ### altloc="" resname="HOH" #atoms=1 resid=" 188 " #atom_groups=2 ### Info: same as previous resid ### altloc="A" resname="COP" #atoms=4 altloc="B" resname="COP" #atoms=4 """, """\ total number of: models: 1 chains: 1 alt. conf.: 2 residues: 3 atoms: 13 anisou: 0 number of atom element+charge types: 2 histogram of atom element+charge frequency: " O " 7 " C " 6 residue name classes: "other" 2 "common_water" 1 number of chain ids: 1 histogram of chain id frequency: " " 1 number of alt. conf. ids: 2 histogram of alt. conf. id frequency: "A" 1 "B" 1 residue alt. conf. situations: pure main conf.: 2 pure alt. conf.: 1 proper alt. conf.: 0 improper alt. conf.: 0 chains with mix of proper and improper alt. conf.: 0 number of residue names: 2 histogram of residue name frequency: "COP" 2 other "HOH" 1 common water ### WARNING: consecutive residue_groups with same resid ### number of consecutive residue groups with same resid: 2 residue group: "HETATM 1552 C3 COP 188 .*. C " ... 2 atoms not shown "HETATM 1583 O25 COP 188 .*. O " next residue group: "HETATM 1608 O HOH 188 .*. O " next residue group: "HETATM 1569 C28ACOP 188 .*. C " ... 6 atoms not shown "HETATM 1607 O41BCOP 188 .*. O " """, level_id="atom_group") # check("""\ ATOM 1 N R01 1I ATOM 2 N R02 1I ATOM 3 N R03 1I ATOM 4 N R04 1I ATOM 5 N R05 1I """, None, """\ total number of: models: 1 chains: 1 alt. conf.: 0 residues: 5 atoms: 5 anisou: 0 number of atom element+charge types: 1 histogram of atom element+charge frequency: " " 5 residue name classes: "other" 5 number of chain ids: 1 histogram of chain id frequency: " " 1 number of alt. conf. ids: 0 number of residue names: 5 histogram of residue name frequency: "R01" 1 other "R02" 1 other "R03" 1 other "R04" 1 other "R05" 1 other ### WARNING: consecutive residue_groups with same resid ### number of consecutive residue groups with same resid: 4 residue group: "ATOM 1 N R01 1I.*. " next residue group: "ATOM 2 N R02 1I.*. " next residue group: "ATOM 3 N R03 1I.*. " next residue group: "ATOM 4 N R04 1I.*. " ------------------------------------------ ... 1 remaining instance not shown """) # root = pdb.hierarchy.root() assert not show_diff(root.as_str(), """\ ### WARNING: empty hierarchy ### """) assert not show_diff(root.overall_counts().as_str(), """\ total number of: models: 0 chains: 0 alt. conf.: 0 residues: 0 atoms: 0 anisou: 0 number of atom element+charge types: 0 residue name classes: None number of chain ids: 0 number of alt. conf. ids: 0 number of residue names: 0 """) model = pdb.hierarchy.model() root.append_model(model=model) assert not show_diff(root.as_str(), """\ model id="" #chains=0 ### WARNING: empty model ### """) assert not show_diff(root.overall_counts().as_str(), """\ total number of: ### WARNING: empty model ### models: 1 (1 empty) chains: 0 alt. conf.: 0 residues: 0 atoms: 0 anisou: 0 number of atom element+charge types: 0 residue name classes: None number of chain ids: 0 number of alt. conf. ids: 0 number of residue names: 0 """) chain = pdb.hierarchy.chain() model.append_chain(chain=chain) assert not show_diff(root.as_str(), """\ model id="" #chains=1 chain id="" #residue_groups=0 ### WARNING: empty chain ### """) assert not show_diff(root.overall_counts().as_str(), """\ total number of: models: 1 ### WARNING: empty chain ### chains: 1 (1 empty) alt. conf.: 0 residues: 0 atoms: 0 anisou: 0 number of atom element+charge types: 0 residue name classes: None number of chain ids: 1 histogram of chain id frequency: "" 1 number of alt. conf. ids: 0 number of residue names: 0 """) residue_group = pdb.hierarchy.residue_group() chain.append_residue_group(residue_group=residue_group) assert not show_diff(root.as_str(), """\ model id="" #chains=1 chain id="" #residue_groups=1 resid=" " #atom_groups=0 ### WARNING: empty residue_group ### """) assert not show_diff(root.overall_counts().as_str(), """\ total number of: models: 1 chains: 1 alt. conf.: 0 residues: 1 atoms: 0 anisou: 0 ### WARNING: empty residue_group ### empty residue_groups: 1 number of atom element+charge types: 0 residue name classes: None number of chain ids: 1 histogram of chain id frequency: "" 1 number of alt. conf. ids: 0 number of residue names: 0 """) atom_group = pdb.hierarchy.atom_group() residue_group.append_atom_group(atom_group=atom_group) assert not show_diff(root.as_str(), """\ model id="" #chains=1 chain id="" #residue_groups=1 resid=" " #atom_groups=1 altloc="" resname="" #atoms=0 ### WARNING: empty atom_group ### """) oc = root.overall_counts() assert not show_diff(oc.as_str(), """\ total number of: models: 1 chains: 1 alt. conf.: 0 residues: 1 atoms: 0 anisou: 0 ### WARNING: empty atom_group ### empty atom_groups: 1 number of atom element+charge types: 0 residue name classes: "other" 1 number of chain ids: 1 histogram of chain id frequency: "" 1 number of alt. conf. ids: 0 number of residue names: 1 histogram of residue name frequency: "" 1 other """) assert len(oc.errors()) == 0 assert oc.warnings() == ['### WARNING: empty atom_group ###'] # pdb_inp = pdb.input(source_info=None, lines=flex.split_lines("""\ ATOM N1 BR01 1 ATOM N1 R01 1 ATOM N1 AR02 2 ATOM N1 BR02 2 ATOM N2 R02 2 """)) oc = pdb_inp.construct_hierarchy(sort_atoms=False).overall_counts() assert len(oc.warnings()) == 0 oc.raise_duplicate_atom_labels_if_necessary() try: oc.raise_improper_alt_conf_if_necessary() except Sorry as e: assert not show_diff(str(e), '''\ residue with proper altloc "ATOM N2 R02 2 .*. " "ATOM N1 AR02 2 .*. " "ATOM N1 BR02 2 .*. " residue with improper altloc "ATOM N1 R01 1 .*. " "ATOM N1 BR01 1 .*. "''') else: raise Exception_expected try: oc.raise_chains_with_mix_of_proper_and_improper_alt_conf_if_necessary() except Sorry as e: assert not show_diff(str(e), '''\ chains with mix of proper and improper alt. conf.: 1 residue with proper altloc "ATOM N2 R02 2 .*. " "ATOM N1 AR02 2 .*. " "ATOM N1 BR02 2 .*. " residue with improper altloc "ATOM N1 R01 1 .*. " "ATOM N1 BR01 1 .*. "''') else: raise Exception_expected # # pdb_inp = pdb.input(source_info=None, lines=flex.split_lines("""\ ATOM CA ASN 1 ATOM C ASN 1 ATOM O HOH 2 ATOM H1 HOH 2 ATOM H2 HOH 2 ATOM CA GLU 3 ATOM C GLU 3 ATOM O H2O 4 ATOM O OH2 5 ATOM O DOD 6 ATOM P U 7 ATOM O D2O 8 ATOM O OD2 9 ATOM CA ALA 10 ATOM C ALA 10 ATOM O TIP 11 ATOM O TIP 12 """)) oc = pdb_inp.construct_hierarchy(sort_atoms=False).overall_counts() assert oc.resname_classes == { 'common_water': 5, 'other': 3, 'common_rna_dna': 1, 'common_amino_acid': 3} # pdb_inp = pdb.input(source_info=None, lines=flex.split_lines("""\ ATOM N AASN 1 ATOM CA AASN 1 ATOM N AGLY 1 ATOM CA AGLY 1 ATOM CA AASN 2 ATOM CA AGLY 2 """)) oc = pdb_inp.construct_hierarchy(sort_atoms=False).overall_counts() assert not show_diff(oc.as_str(), """\ total number of: models: 1 chains: 1 alt. conf.: 1 residues: 2 (2 with mixed residue names) atoms: 6 anisou: 0 number of atom element+charge types: 1 histogram of atom element+charge frequency: " " 6 residue name classes: "common_amino_acid" 4 number of chain ids: 1 histogram of chain id frequency: " " 1 number of alt. conf. ids: 1 histogram of alt. conf. id frequency: "A" 1 residue alt. conf. situations: pure main conf.: 0 pure alt. conf.: 2 proper alt. conf.: 0 improper alt. conf.: 0 chains with mix of proper and improper alt. conf.: 0 number of residue names: 2 histogram of residue name frequency: "ASN" 2 "GLY" 2 ### ERROR: residue group with multiple resnames using same altloc ### residue groups with multiple resnames using same altloc: 2 residue group: "ATOM N AASN 1 .*. " ... 2 atoms not shown "ATOM CA AGLY 1 .*. " residue group: "ATOM CA AASN 2 .*. " "ATOM CA AGLY 2 .*. " """) # pdb_inp = pdb.input(source_info=None, lines=flex.split_lines("""\ ATOM N AASN 1 ATOM N AGLY 1 ATOM CA AGLY 1 ATOM CA AASN 2 ATOM CA AGLY 2 """)) oc = pdb_inp.construct_hierarchy(sort_atoms=False).overall_counts() try: oc \ .raise_residue_groups_with_multiple_resnames_using_same_altloc_if_necessary( max_show=1) except Sorry as e: assert not show_diff(str(e), """\ residue groups with multiple resnames using same altloc: 2 residue group: "ATOM N AASN 1 .*. " "ATOM N AGLY 1 .*. " "ATOM CA AGLY 1 .*. " ... 1 remaining instance not shown""") else: raise Exception_expected def exercise_set_i_seq(): pdb_str = """\ HEADER HYDROLASE 19-JUL-05 2BWX ATOM 2038 N CYS A 249 68.746 44.381 71.143 0.70 21.04 N ATOM 2039 CA CYS A 249 68.957 43.022 71.606 0.70 21.28 C ATOM 2040 C CYS A 249 70.359 42.507 71.362 0.70 19.80 C ATOM 2041 O CYS A 249 71.055 42.917 70.439 0.70 19.80 O ATOM 2042 CB ACYS A 249 67.945 42.064 70.987 0.40 24.99 C ATOM 2043 CB BCYS A 249 67.928 42.101 70.948 0.30 23.34 C ATOM 2044 SG ACYS A 249 66.261 42.472 71.389 0.40 27.94 S ATOM 2045 SG BCYS A 249 67.977 40.404 71.507 0.30 26.46 S HETATM 2046 N CCSO A 249 68.746 44.381 71.143 0.30 21.04 N HETATM 2047 CA CCSO A 249 68.957 43.022 71.606 0.30 21.28 C HETATM 2048 CB CCSO A 249 67.945 42.064 70.987 0.30 24.99 C HETATM 2049 SG CCSO A 249 66.261 42.472 71.389 0.30 27.94 S HETATM 2050 C CCSO A 249 70.359 42.507 71.362 0.30 19.80 C HETATM 2051 O CCSO A 249 71.055 42.917 70.439 0.30 19.80 O HETATM 2052 OD CCSO A 249 66.275 42.201 72.870 0.30 23.67 O TER HETATM 1 O AHOH B 1 0.000 0.000 0.000 1.0 20.0 O HETATM 2 O BHOH B 1 0.500 0.000 0.000 1.0 20.0 O HETATM 3 O HOH B 2 4.000 0.000 0.000 1.0 20.0 O """ pdb_in = pdb.input(source_info=None, lines=flex.split_lines(pdb_str)) assert pdb_in.atoms().extract_i_seq().all_eq(0) hierarchy = pdb_in.construct_hierarchy(set_atom_i_seq=False) # check deep_copy h = pdb.input(source_info=None, lines=flex.split_lines(pdb_str)).construct_hierarchy(set_atom_i_seq=True) h2 = h.deep_copy() assert not h2.atoms().extract_i_seq().all_eq(0) # pdb_atoms_1 = hierarchy.atoms() assert pdb_atoms_1.extract_i_seq().all_eq(0) pdb_atoms_1.reset_i_seq() pdb_in = pdb.input(source_info=None, lines=flex.split_lines(pdb_str)) hierarchy = pdb_in.construct_hierarchy(set_atom_i_seq=True) pdb_atoms_2 = hierarchy.atoms() i_seqs_2 = pdb_atoms_2.extract_i_seq() assert not i_seqs_2.all_eq(0) assert i_seqs_2.all_eq(pdb_atoms_1.extract_i_seq()) pdb_in = pdb.input(source_info=None, lines=flex.split_lines(pdb_str)) hierarchy = pdb_in.construct_hierarchy() hierarchy.reset_atom_i_seqs() pdb_atoms_3 = hierarchy.atoms() i_seqs_3 = pdb_atoms_3.extract_i_seq() assert not i_seqs_3.all_eq(0) assert i_seqs_3.all_eq(pdb_atoms_1.extract_i_seq()) def exercise_convenience_generators(): pdb_inp = pdb.input(source_info=None, lines=flex.split_lines("""\ MODEL 1 ATOM 1 N AR11 A 1 ATOM 2 O AR11 A 1 ATOM 3 N BR21 A 1 ATOM 4 O BR21 A 1 ATOM 5 N AR12 A 2 ATOM 6 O AR12 A 2 ATOM 7 N BR22 A 2 ATOM 8 O BR22 A 2 TER ATOM 9 N AR11 B 1 ATOM 10 O AR11 B 1 ATOM 11 N BR21 B 1 ATOM 12 O BR21 B 1 ATOM 13 N AR12 B 2 ATOM 14 O AR12 B 2 ATOM 15 N BR22 B 2 ATOM 16 O BR22 B 2 TER ENDMDL MODEL 2 ATOM 1 N AR11 A 1 ATOM 2 O AR11 A 1 ATOM 3 N BR21 A 1 ATOM 4 O BR21 A 1 ATOM 5 N AR12 A 2 ATOM 6 O AR12 A 2 ATOM 7 N BR22 A 2 ATOM 8 O BR22 A 2 TER ATOM 9 N AR11 B 1 ATOM 10 O AR11 B 1 ATOM 11 N BR21 B 1 ATOM 12 O BR21 B 1 ATOM 13 N AR12 B 2 ATOM 14 O AR12 B 2 ATOM 15 N BR22 B 2 ATOM 16 O BR22 B 2 TER ENDMDL """)) obj = pdb_inp.construct_hierarchy(residue_group_post_processing=False) assert [model.id for model in obj.models()] == [" 1", " 2"] assert [chain.id for chain in obj.chains()] == ["A", "B"] * 2 assert [rg.resid() for rg in obj.residue_groups()] == [" 1 ", " 2 "] * 4 assert [ag.confid() for ag in obj.atom_groups()] \ == ["AR11", "BR21", "AR12", "BR22"] * 4 assert obj.atoms_size() == 32 assert obj.atoms().size() == 32 assert [atom.name for atom in obj.atoms()] == [" N ", " O "] * 16 obj = obj.models()[0] assert [chain.id for chain in obj.chains()] == ["A", "B"] assert [rg.resid() for rg in obj.residue_groups()] == [" 1 ", " 2 "] * 2 assert [ag.confid() for ag in obj.atom_groups()] \ == ["AR11", "BR21", "AR12", "BR22"] * 2 assert obj.atoms_size() == 16 assert obj.atoms().size() == 16 assert [atom.name for atom in obj.atoms()] == [" N ", " O "] * 8 obj = obj.chains()[0] assert [rg.resid() for rg in obj.residue_groups()] == [" 1 ", " 2 "] assert [ag.confid() for ag in obj.atom_groups()] \ == ["AR11", "BR21", "AR12", "BR22"] assert obj.atoms_size() == 8 assert obj.atoms().size() == 8 assert [atom.name for atom in obj.atoms()] == [" N ", " O "] * 4 obj = obj.residue_groups()[0] assert [ag.confid() for ag in obj.atom_groups()] \ == ["AR11", "BR21"] assert obj.atoms_size() == 4 assert obj.atoms().size() == 4 assert [atom.name for atom in obj.atoms()] == [" N ", " O "] * 2 obj = obj.atom_groups()[0] assert obj.atoms_size() == 2 assert obj.atoms().size() == 2 assert [atom.name for atom in obj.atoms()] == [" N ", " O "] def exercise_only(): pdb_inp = pdb.input(source_info=None, lines=flex.split_lines("""\ MODEL 1 ATOM 2 N ARES C 3I ENDMDL """)) hierarchy = pdb_inp.construct_hierarchy(residue_group_post_processing=False) obj = hierarchy assert obj.only_model().id == " 1" assert obj.only_chain().id == "C" assert obj.only_residue_group().resid() == " 3I" assert obj.only_atom_group().altloc == "A" assert obj.only_atom().name == " N " obj = obj.only_model() assert obj.only_chain().id == "C" assert obj.only_residue_group().resid() == " 3I" assert obj.only_atom_group().resname == "RES" assert obj.only_atom().name == " N " obj = obj.only_chain() assert obj.only_residue_group().resid() == " 3I" assert obj.only_atom_group().altloc == "A" assert obj.only_atom().name == " N " obj = obj.only_residue_group() assert obj.only_atom_group().resname == "RES" assert obj.only_atom().name == " N " obj = obj.only_atom_group() assert obj.only_atom().name == " N " # obj = hierarchy assert obj.only_conformer().altloc == "A" assert obj.only_residue().resname == "RES" obj = obj.only_model() assert obj.only_conformer().altloc == "A" assert obj.only_residue().resname == "RES" obj = obj.only_chain() assert obj.only_conformer().altloc == "A" assert obj.only_residue().resname == "RES" obj = obj.only_conformer() assert obj.only_residue().resname == "RES" assert obj.only_atom().name == " N " obj = obj.only_residue() assert obj.only_atom().name == " N " # pdb_inp = pdb.input(source_info=None, lines=flex.split_lines("""\ ATOM 1 R01 A ATOM 2 R01 A ATOM 3 R02 A ATOM 4 R02 A ATOM 5 R01 B """)) hierarchy = pdb_inp.construct_hierarchy(residue_group_post_processing=False) sio = StringIO() for chain in hierarchy.chains(): for residue in chain.residues(): for atom in residue.atoms(): print(atom.quote(), file=sio) assert not show_diff(sio.getvalue(), """\ "ATOM 1 R01 A .*. " "ATOM 2 R01 A .*. " "ATOM 3 R02 A .*. " "ATOM 4 R02 A .*. " "ATOM 5 R01 B .*. " """) exercise_merge_pdb_inp = pdb.input( source_info=None, lines=flex.split_lines("""\ ATOM 1716 N ALEU 190 28.628 4.549 20.230 0.70 3.78 N ATOM 1717 CA ALEU 190 27.606 5.007 19.274 0.70 3.71 C ATOM 1718 CB ALEU 190 26.715 3.852 18.800 0.70 4.15 C ATOM 1719 CG ALEU 190 25.758 4.277 17.672 0.70 4.34 C ATOM 1829 N BLEU 190 28.428 4.746 20.343 0.30 5.13 N ATOM 1830 CA BLEU 190 27.378 5.229 19.418 0.30 4.89 C ATOM 1831 CB BLEU 190 26.539 4.062 18.892 0.30 4.88 C ATOM 1832 CG BLEU 190 25.427 4.359 17.878 0.30 5.95 C ATOM 1724 N ATHR 191 27.350 7.274 20.124 0.70 3.35 N ATOM 1725 CA ATHR 191 26.814 8.243 21.048 0.70 3.27 C ATOM 1726 CB ATHR 191 27.925 9.229 21.468 0.70 3.73 C ATOM 1727 OG1ATHR 191 28.519 9.718 20.259 0.70 5.22 O ATOM 1728 CG2ATHR 191 28.924 8.567 22.345 0.70 4.21 C ATOM 1729 C ATHR 191 25.587 8.983 20.559 0.70 3.53 C ATOM 1730 O ATHR 191 24.872 9.566 21.383 0.70 3.93 O ATOM 1833 CD1BLEU 190 26.014 4.711 16.521 0.30 6.21 C ATOM 1835 C BLEU 190 26.506 6.219 20.135 0.30 4.99 C ATOM 1836 O BLEU 190 25.418 5.939 20.669 0.30 5.91 O ATOM 1721 CD2ALEU 190 24.674 3.225 17.536 0.70 5.31 C ATOM 1722 C ALEU 190 26.781 6.055 20.023 0.70 3.36 C ATOM 1723 O ALEU 190 25.693 5.796 20.563 0.70 3.68 O ATOM 8722 C DLEU 190 26.781 6.055 20.023 0.70 3.36 C ATOM 8723 O DLEU 190 25.693 5.796 20.563 0.70 3.68 O ATOM 9722 C CLEU 190 26.781 6.055 20.023 0.70 3.36 C ATOM 9723 O CLEU 190 25.693 5.796 20.563 0.70 3.68 O """)) def exercise_merge_atom_groups(): lines = [] root = exercise_merge_pdb_inp.construct_hierarchy( residue_group_post_processing=False, sort_atoms=False) chain = root.models()[0].chains()[0] residue_groups = chain.residue_groups() assert len(residue_groups) == 3 for i_ag in [0,1]: primary_atom_group = residue_groups[0].atom_groups()[i_ag] assert (primary_atom_group.altloc, primary_atom_group.resname) \ == ("AB"[i_ag], "LEU") secondary_atom_group = residue_groups[2].atom_groups()[1-i_ag] try: residue_groups[0].merge_atom_groups( primary=secondary_atom_group, secondary=primary_atom_group) except RuntimeError as e: assert not show_diff(str(e), """\ "primary" atom_group has a different or no parent\ (this residue_group must be the parent).""") else: raise Exception_expected try: residue_groups[0].merge_atom_groups( primary=primary_atom_group, secondary=primary_atom_group) except RuntimeError as e: assert not show_diff(str(e), """\ "primary" and "secondary" atom_groups are identical.""") else: raise Exception_expected try: residue_groups[0].merge_atom_groups( primary=primary_atom_group, secondary=residue_groups[2].atom_groups()[i_ag]) except RuntimeError as e: assert str(e).find("secondary.data->altloc == primary.data->altloc") > 0 else: raise Exception_expected assert primary_atom_group.atoms_size() == 4 assert secondary_atom_group.atoms_size() == 3 residue_groups[0].merge_atom_groups( primary=primary_atom_group, secondary=secondary_atom_group) assert primary_atom_group.atoms_size() == 7 assert secondary_atom_group.atoms_size() == 0 sio = StringIO() for atom in primary_atom_group.atoms(): print(atom.format_atom_record(), file=sio) assert not show_diff(sio.getvalue(), ["""\ ATOM 1716 N ALEU 190 28.628 4.549 20.230 0.70 3.78 N ATOM 1717 CA ALEU 190 27.606 5.007 19.274 0.70 3.71 C ATOM 1718 CB ALEU 190 26.715 3.852 18.800 0.70 4.15 C ATOM 1719 CG ALEU 190 25.758 4.277 17.672 0.70 4.34 C ATOM 1721 CD2ALEU 190 24.674 3.225 17.536 0.70 5.31 C ATOM 1722 C ALEU 190 26.781 6.055 20.023 0.70 3.36 C ATOM 1723 O ALEU 190 25.693 5.796 20.563 0.70 3.68 O """, """\ ATOM 1829 N BLEU 190 28.428 4.746 20.343 0.30 5.13 N ATOM 1830 CA BLEU 190 27.378 5.229 19.418 0.30 4.89 C ATOM 1831 CB BLEU 190 26.539 4.062 18.892 0.30 4.88 C ATOM 1832 CG BLEU 190 25.427 4.359 17.878 0.30 5.95 C ATOM 1833 CD1BLEU 190 26.014 4.711 16.521 0.30 6.21 C ATOM 1835 C BLEU 190 26.506 6.219 20.135 0.30 4.99 C ATOM 1836 O BLEU 190 25.418 5.939 20.669 0.30 5.91 O """][i_ag]) def exercise_merge_residue_groups(): root = exercise_merge_pdb_inp.construct_hierarchy( residue_group_post_processing=False, sort_atoms=False) chain = root.models()[0].chains()[0] residue_groups = chain.residue_groups() assert len(residue_groups) == 3 try: chain.merge_residue_groups( primary=residue_groups[0], secondary=residue_groups[1]) except RuntimeError as e: assert str(e).find("secondary.data->resseq == primary.data->resseq") > 0 else: raise Exception_expected assert residue_groups[0].atom_groups_size() == 2 assert residue_groups[2].atom_groups_size() == 4 assert residue_groups[2].parent().memory_id() == chain.memory_id() assert chain.residue_groups_size() == 3 chain.merge_residue_groups( primary=residue_groups[0], secondary=residue_groups[2]) assert residue_groups[0].atom_groups_size() == 4 assert residue_groups[2].atom_groups_size() == 0 assert residue_groups[2].parent() is None assert chain.residue_groups_size() == 2 sio = StringIO() for atom_group in residue_groups[0].atom_groups(): for atom in atom_group.atoms(): print(atom.format_atom_record(), file=sio) assert not show_diff(sio.getvalue(), """\ ATOM 1716 N ALEU 190 28.628 4.549 20.230 0.70 3.78 N ATOM 1717 CA ALEU 190 27.606 5.007 19.274 0.70 3.71 C ATOM 1718 CB ALEU 190 26.715 3.852 18.800 0.70 4.15 C ATOM 1719 CG ALEU 190 25.758 4.277 17.672 0.70 4.34 C ATOM 1721 CD2ALEU 190 24.674 3.225 17.536 0.70 5.31 C ATOM 1722 C ALEU 190 26.781 6.055 20.023 0.70 3.36 C ATOM 1723 O ALEU 190 25.693 5.796 20.563 0.70 3.68 O ATOM 1829 N BLEU 190 28.428 4.746 20.343 0.30 5.13 N ATOM 1830 CA BLEU 190 27.378 5.229 19.418 0.30 4.89 C ATOM 1831 CB BLEU 190 26.539 4.062 18.892 0.30 4.88 C ATOM 1832 CG BLEU 190 25.427 4.359 17.878 0.30 5.95 C ATOM 1833 CD1BLEU 190 26.014 4.711 16.521 0.30 6.21 C ATOM 1835 C BLEU 190 26.506 6.219 20.135 0.30 4.99 C ATOM 1836 O BLEU 190 25.418 5.939 20.669 0.30 5.91 O ATOM 8722 C DLEU 190 26.781 6.055 20.023 0.70 3.36 C ATOM 8723 O DLEU 190 25.693 5.796 20.563 0.70 3.68 O ATOM 9722 C CLEU 190 26.781 6.055 20.023 0.70 3.36 C ATOM 9723 O CLEU 190 25.693 5.796 20.563 0.70 3.68 O """) for i_rg,j_rg,s in [(2,2,"primary"),(0,2,"secondary")]: try: chain.merge_residue_groups( primary=residue_groups[i_rg], secondary=residue_groups[j_rg]) except RuntimeError as e: assert not show_diff(str(e), """\ "%s" residue_group has a different or no parent\ (this chain must be the parent).""" % s) else: raise Exception_expected def exercise_chain_merge_residue_groups(n_trials=30): pdb_inp = pdb.input(source_info=None, lines=flex.split_lines("""\ HEADER HYDROLASE 22-NOV-07 2VHL HETATM 6362 O HOH B2048 47.616 10.724 150.212 1.00 46.48 O HETATM 6363 O AHOH B2049 46.408 16.672 146.066 0.50 12.81 O HETATM 6364 O HOH B2050 29.343 12.806 185.898 1.00 35.57 O HETATM 6365 O BHOH B2049 43.786 12.615 147.734 0.50 28.43 O HETATM 6366 O HOH B2052 35.068 19.167 155.349 1.00 15.97 O """)) for rgpp in [False, True]: chain = pdb_inp.construct_hierarchy( residue_group_post_processing=rgpp).only_chain() if (not rgpp): assert chain.residue_groups_size() == 5 indices = chain.merge_disconnected_residue_groups_with_pure_altloc() assert list(indices) == [1] assert chain.residue_groups_size() == 4 indices = chain.merge_disconnected_residue_groups_with_pure_altloc() assert indices.size() == 0 del chain lines = flex.split_lines("""\ HETATM 6363 O AHOH B2049 HETATM 6364 O ZHOH B2050 HETATM 6365 O BHOH B2049 HETATM 6366 O YHOH B2052 HETATM 9365 O CHOH B2049 HETATM 9367 O XHOH B2052 """) pdb_inp = pdb.input(source_info=None, lines=lines) chain = pdb_inp.construct_hierarchy( residue_group_post_processing=False).only_chain() assert chain.residue_groups_size() == 6 indices = chain.merge_disconnected_residue_groups_with_pure_altloc() assert list(indices) == [0, 2] assert chain.residue_groups_size() == 3 indices = chain.merge_disconnected_residue_groups_with_pure_altloc() assert indices.size() == 0 for i_trial in range(n_trials): pdb_inp = pdb.input( source_info=None, lines=lines.select(flex.random_permutation(size=lines.size()))) chain = pdb_inp.construct_hierarchy( residue_group_post_processing=False).only_chain() indices = chain.merge_disconnected_residue_groups_with_pure_altloc() assert indices.size() <= 2 indices = chain.merge_disconnected_residue_groups_with_pure_altloc() assert indices.size() == 0 del chain chain = pdb_inp.construct_hierarchy().only_chain() indices = chain.merge_disconnected_residue_groups_with_pure_altloc() assert indices.size() == 0 # pdb_inp = pdb.input(source_info=None, lines=flex.split_lines("""\ HEADER SERINE PROTEASE 10-NOV-95 1RTF HETATM 2397 P PO4 1 -7.520 25.376 38.369 1.00 39.37 P HETATM 2398 O1 PO4 1 -6.610 24.262 38.967 1.00 40.00 O HETATM 2399 O2 PO4 1 -6.901 25.919 37.049 1.00 41.07 O HETATM 2400 O3 PO4 1 -8.894 24.741 38.097 1.00 45.09 O HETATM 2401 O4 PO4 1 -7.722 26.556 39.350 1.00 42.48 O HETATM 2402 C1 BEN 1 -6.921 31.206 33.893 1.00 23.35 C HETATM 2403 C2 BEN 1 -8.189 30.836 34.344 1.00 23.15 C HETATM 2404 C3 BEN 1 -8.335 29.863 35.342 1.00 20.74 C HETATM 2405 C4 BEN 1 -7.206 29.254 35.893 1.00 19.45 C HETATM 2406 C5 BEN 1 -5.932 29.618 35.445 1.00 20.83 C HETATM 2407 C6 BEN 1 -5.794 30.589 34.450 1.00 20.99 C HETATM 2408 C BEN 1 -6.767 32.249 32.859 1.00 24.30 C HETATM 2409 N1 BEN 1 -5.570 32.641 32.497 1.00 24.56 N HETATM 2410 N2 BEN 1 -7.824 32.785 32.299 1.00 24.58 N HETATM 2415 O HOH 1 4.020 20.521 19.336 1.00 38.74 O HETATM 2418 O WAT 2 14.154 16.852 21.753 1.00 49.41 O """)) chain = pdb_inp.construct_hierarchy( residue_group_post_processing=False).only_chain() assert chain.residue_groups_size() == 4 assert [residue_group.resid() for residue_group in chain.residue_groups()] \ == [" 1 ", " 1 ", " 1 ", " 2 "] for residue_group in chain.residue_groups(): assert residue_group.atom_groups_size() == 1 assert residue_group.atom_groups()[0].parent().memory_id() \ == residue_group.memory_id() assert [residue_group.atom_groups()[0].resname for residue_group in chain.residue_groups()] \ == ["PO4", "BEN", "HOH", "WAT"] pdb_inp = pdb.input(source_info=None, lines=flex.split_lines("""\ HETATM 2418 O WAT 2 HETATM 2397 P PO4 1 HETATM 2398 O1 PO4 1 HETATM 2402 C1 BEN 1 HETATM 2403 C2 BEN 1 HETATM 2404 C3 BEN 1 HETATM 2415 O HOH 1 HETATM 9418 O WAT 2 HETATM 9397 P PO4 1 HETATM 9398 O1 PO4 1 HETATM 9402 C1 BEN 1 HETATM 9403 C2 BEN 1 HETATM 9404 C3 BEN 1 HETATM 9415 O HOH 1 """)) chain = pdb_inp.construct_hierarchy( residue_group_post_processing=False).only_chain() assert chain.residue_groups_size() == 8 for residue_group in chain.residue_groups(): assert residue_group.atom_groups_size() == 1 assert residue_group.atom_groups()[0].parent().memory_id() \ == residue_group.memory_id() # pdb_inp = pdb.input(source_info=None, lines=flex.split_lines("""\ HETATM 6362 O CHOH B 1 HETATM 6363 O AHOH B 1 HETATM 6364 O HOH B 2 HETATM 6365 O HOH B 1 """)) chain = pdb_inp.construct_hierarchy( residue_group_post_processing=False).only_chain() assert chain.residue_groups_size() == 3 assert chain.residue_groups()[2].only_atom_group().altloc == " " for rg in chain.residue_groups(): rg.edit_blank_altloc() assert chain.residue_groups()[2].only_atom_group().altloc == "" indices = chain.merge_disconnected_residue_groups_with_pure_altloc() assert indices.size() == 0 assert chain.residue_groups_size() == 3 def exercise_edit_blank_altloc(n_trials=30): pdb_inp = pdb.input(source_info=None, lines=flex.split_lines("""\ ATOM N1 ATOM N2 """)) for rgpp in [False, True]: residue_group = pdb_inp.construct_hierarchy( residue_group_post_processing=rgpp).only_residue_group() for i_proc in [0,1]: assert residue_group.edit_blank_altloc() == (1,0) del residue_group # pdb_inp = pdb.input(source_info=None, lines=flex.split_lines("""\ ATOM N1 A ATOM N2 B """)) for rgpp in [False, True]: residue_group = pdb_inp.construct_hierarchy( residue_group_post_processing=rgpp).only_residue_group() rgc = residue_group.detached_copy() assert rgc.move_blank_altloc_atom_groups_to_front() == 0 for i_proc in [0,1]: assert residue_group.edit_blank_altloc() == (0,0) del residue_group # pdb_inp = pdb.input(source_info=None, lines=flex.split_lines("""\ ATOM N1 ATOM N2 B """)) for rgpp in [False, True]: residue_group = pdb_inp.construct_hierarchy( residue_group_post_processing=rgpp).only_residue_group() if (not rgpp): atom_groups = residue_group.atom_groups() assert len(atom_groups) == 2 assert atom_groups[0].altloc == " " assert atom_groups[1].altloc == "B" for i_proc in [0,1]: if (not rgpp or i_proc != 0): assert residue_group.edit_blank_altloc() == (1,0) atom_groups = residue_group.atom_groups() assert len(atom_groups) == 2 assert atom_groups[0].altloc == "" assert atom_groups[1].altloc == "B" del atom_groups del residue_group # pdb_inp = pdb.input(source_info=None, lines=flex.split_lines("""\ ATOM N1 ATOM N1 B """)) residue_group = pdb_inp.construct_hierarchy( residue_group_post_processing=False).only_residue_group() atom_groups = residue_group.atom_groups() assert len(atom_groups) == 2 assert atom_groups[0].altloc == " " assert atom_groups[1].altloc == "B" rgc = residue_group.detached_copy() assert rgc.move_blank_altloc_atom_groups_to_front() == 1 for i_proc in [0,1]: assert residue_group.edit_blank_altloc() == (0,1) atom_groups = residue_group.atom_groups() assert len(atom_groups) == 2 assert atom_groups[0].altloc == " " assert atom_groups[1].altloc == "B" # pdb_inp = pdb.input(source_info=None, lines=flex.split_lines("""\ ATOM N1 B ATOM N1 """)) for edit_chain in [False, True]: chain = pdb_inp.construct_hierarchy( residue_group_post_processing=False).only_chain() residue_group = chain.only_residue_group() atom_groups = residue_group.atom_groups() assert len(atom_groups) == 2 assert atom_groups[0].altloc == "B" assert atom_groups[1].altloc == " " rgc = residue_group.detached_copy() assert rgc.move_blank_altloc_atom_groups_to_front() == 1 for i_proc in [0,1]: if (not edit_chain): assert residue_group.edit_blank_altloc() == (0,1) else: for rg in chain.residue_groups(): rg.edit_blank_altloc() atom_groups = residue_group.atom_groups() assert len(atom_groups) == 2 assert atom_groups[0].altloc == " " assert atom_groups[1].altloc == "B" del atom_groups del residue_group del chain # lines = flex.split_lines("""\ ATOM N1 B ATOM N1 ATOM N2 ATOM N3 B ATOM N3 """) for i_trial in range(n_trials): pdb_inp = pdb.input(source_info=None, lines=lines) residue_group = pdb_inp.construct_hierarchy( residue_group_post_processing=False).only_residue_group() atom_groups = residue_group.atom_groups() assert len(atom_groups) == 2 if (i_trial == 0): assert atom_groups[0].altloc == "B" assert atom_groups[1].altloc == " " else: assert sorted([atom_group.altloc for atom_group in atom_groups]) \ == [" ", "B"] for i_proc in [0,1]: assert residue_group.edit_blank_altloc() == (1,1) atom_groups = residue_group.atom_groups() assert len(atom_groups) == 3 assert atom_groups[0].altloc == "" assert atom_groups[1].altloc == " " assert atom_groups[2].altloc == "B" lines = lines.select(flex.random_permutation(size=lines.size())) def exercise_find_pure_altloc_ranges(): c = pdb.hierarchy.chain() assert c.find_pure_altloc_ranges().size() == 0 # pdb_inp = pdb.input(source_info=None, lines=flex.split_lines("""\ ATOM A 1 """)) c = pdb_inp.construct_hierarchy().only_chain() assert c.find_pure_altloc_ranges().size() == 0 # pdb_inp = pdb.input(source_info=None, lines=flex.split_lines("""\ ATOM A 1 ATOM B 1 """)) c = pdb_inp.construct_hierarchy().only_chain() assert c.find_pure_altloc_ranges().size() == 0 # pdb_inp = pdb.input(source_info=None, lines=flex.split_lines("""\ ATOM A 1 ATOM B 2 """)) c = pdb_inp.construct_hierarchy().only_chain() assert list(c.find_pure_altloc_ranges()) == [(0,2)] # pdb_inp = pdb.input(source_info=None, lines=flex.split_lines("""\ ATOM A 1 BREAK ATOM B 2 """)) c = pdb_inp.construct_hierarchy().only_chain() assert c.find_pure_altloc_ranges().size() == 0 # pdb_inp = pdb.input(source_info=None, lines=flex.split_lines("""\ ATOM A 1 ATOM B 1 ATOM 2 """)) c = pdb_inp.construct_hierarchy().only_chain() assert c.find_pure_altloc_ranges().size() == 0 # pdb_inp = pdb.input(source_info=None, lines=flex.split_lines("""\ ATOM A 1 ATOM B 2 ATOM C 3 ATOM 4 ATOM E 5 ATOM F 6 ATOM G 6 ATOM H 6 ATOM 7 ATOM 8 ATOM I 9 ATOM J 10 BREAK ATOM L 11 ATOM M 12 ATOM N1 N 13 ATOM N2 13 ATOM O 14 ATOM 14 ATOM P 15 ATOM 15 """)) c = pdb_inp.construct_hierarchy().only_chain() assert list(c.find_pure_altloc_ranges()) \ == [(0,3),(4,6),(8,10),(10,12),(13,15)] # pdb_inp = pdb.input(source_info=None, lines=flex.split_lines("""\ HEADER CELL CYCLE 13-SEP-05 2B05 HETATM10989 O HOH 29 -66.337 -28.299 -26.997 1.00 40.05 O HETATM10990 O AHOH 32 -57.432 -22.290 -45.876 0.50 2.46 O HETATM10991 O BHOH 32 -59.435 -22.422 -45.055 0.50 17.09 O HETATM10992 O HOH 36 -56.803 -18.433 -29.790 1.00 43.00 O HETATM10993 O HOH 37 -51.860 -26.755 -35.092 1.00 35.90 O HETATM10994 O AHOH 39 -68.867 -23.643 -49.077 0.50 12.37 O HETATM10995 O BHOH 39 -69.097 -21.979 -50.740 0.50 21.64 O HETATM10996 O HOH 40 -65.221 -13.774 -33.183 1.00 36.14 O """)) c = pdb_inp.construct_hierarchy().only_chain() assert c.find_pure_altloc_ranges().size() == 0 # caa = "common_amino_acid" pdb_inp = pdb.input(source_info=None, lines=flex.split_lines("""\ ATOM AALA 1 ATOM BGLY 1 ATOM ATYR 2 ATOM BTHR 2 ATOM AHOH 3 ATOM BHOH 3 """)) c = pdb_inp.construct_hierarchy().only_chain() assert list(c.find_pure_altloc_ranges()) == [(0,3)] assert list(c.find_pure_altloc_ranges(common_residue_name_class_only=caa)) \ == [(0,2)] # pdb_inp = pdb.input(source_info=None, lines=flex.split_lines("""\ ATOM AHOH 3 ATOM BHOH 3 ATOM AALA 1 ATOM BGLY 1 ATOM ATYR 2 ATOM BTHR 2 """)) c = pdb_inp.construct_hierarchy().only_chain() assert list(c.find_pure_altloc_ranges()) == [(0,3)] assert list(c.find_pure_altloc_ranges(common_residue_name_class_only=caa)) \ == [(1,3)] # pdb_inp = pdb.input(source_info=None, lines=flex.split_lines("""\ ATOM AALA 1 ATOM BGLY 1 ATOM AHOH 3 ATOM BHOH 3 ATOM ATYR 2 ATOM BTHR 2 """)) c = pdb_inp.construct_hierarchy().only_chain() assert list(c.find_pure_altloc_ranges()) == [(0,3)] assert c.find_pure_altloc_ranges(common_residue_name_class_only=caa).size() \ == 0 # pdb_inp = pdb.input(source_info=None, lines=flex.split_lines("""\ ATOM AALA 1 ATOM BGLY 1 ATOM AHOH 3 ATOM BHOH 3 ATOM ATYR 2 ATOM BTHR 2 ATOM ASER 4 ATOM BSER 4 """)) c = pdb_inp.construct_hierarchy().only_chain() assert list(c.find_pure_altloc_ranges()) == [(0,4)] assert list(c.find_pure_altloc_ranges(common_residue_name_class_only=caa)) \ == [(2,4)] # pdb_inp = pdb.input(source_info=None, lines=flex.split_lines("""\ ATOM ASER 4 ATOM BSER 4 ATOM AALA 1 ATOM BGLY 1 ATOM AHOH 3 ATOM BHOH 3 ATOM ATYR 2 ATOM BTHR 2 """)) c = pdb_inp.construct_hierarchy().only_chain() assert list(c.find_pure_altloc_ranges()) == [(0,4)] assert list(c.find_pure_altloc_ranges(common_residue_name_class_only=caa)) \ == [(0,2)] # pdb_inp = pdb.input(source_info=None, lines=flex.split_lines("""\ ATOM MET 1 ATOM ALEU 2 ATOM ASER 3 ATOM BSER 3 ATOM AALA 4 ATOM BGLY 4 ATOM AHOH 5 ATOM BHOH 5 ATOM AHOH 6 ATOM ATYR 7 ATOM BTHR 7 ATOM AGLY 8 ATOM BGLY 8 """)) c = pdb_inp.construct_hierarchy().only_chain() assert list(c.find_pure_altloc_ranges()) == [(1,8)] assert list(c.find_pure_altloc_ranges(common_residue_name_class_only=caa)) \ == [(1,4), (6,8)] pdb_1nym_60 = """\ HEADER HYDROLASE 12-FEB-03 1NYM ATOM 60 CA LYS A 32 10.574 8.177 11.768 1.00 11.49 C ATOM 63 CB ALYS A 32 9.197 8.686 12.246 0.29 14.71 C ATOM 64 CB BLYS A 32 9.193 8.732 12.170 0.71 12.23 C ATOM 74 CA VAL A 33 11.708 5.617 14.332 1.00 11.42 C ATOM 77 CB VAL A 33 11.101 4.227 14.591 1.00 11.47 C ATOM 82 CA ALYS A 34 14.979 4.895 12.608 0.60 15.67 C ATOM 83 CA BLYS A 34 14.977 5.207 12.331 0.40 16.38 C ATOM 88 CB ALYS A 34 15.128 3.896 11.472 0.60 12.11 C ATOM 89 CB BLYS A 34 15.132 4.867 10.839 0.40 13.86 C ATOM 100 CA AASP A 35 15.328 8.688 12.044 0.60 16.75 C ATOM 101 CA BASP A 35 15.474 8.937 12.096 0.40 17.43 C ATOM 106 CB AASP A 35 14.367 9.683 11.373 0.60 16.80 C ATOM 107 CB BASP A 35 14.491 9.903 11.431 0.40 18.66 C ATOM 115 CA ALA A 36 14.978 9.140 15.828 1.00 12.65 C ATOM 118 CB ALA A 36 13.768 8.688 16.639 1.00 13.00 C ATOM 121 CA AGLU A 37 17.683 6.514 16.549 0.59 12.26 C ATOM 122 CA BGLU A 37 17.999 6.949 16.048 0.41 12.47 C ATOM 127 CB AGLU A 37 17.694 5.030 16.164 0.59 11.08 C ATOM 128 CB BGLU A 37 18.148 5.560 15.440 0.41 12.53 C ATOM 139 CA AASP A 38 19.923 8.463 14.202 0.59 17.31 C ATOM 140 CA BASP A 38 19.789 9.284 13.597 0.41 19.32 C ATOM 145 CB AASP A 38 19.615 8.739 12.727 0.59 24.06 C ATOM 146 CB BASP A 38 19.279 9.626 12.201 0.41 26.28 C ATOM 155 CA AGLN A 39 19.069 11.941 15.596 0.62 19.31 C ATOM 156 CA BGLN A 39 18.919 12.283 15.753 0.38 20.06 C ATOM 161 CB AGLN A 39 17.681 12.586 15.630 0.62 21.92 C ATOM 162 CB BGLN A 39 17.560 12.987 15.681 0.38 21.79 C ATOM 172 CA LEU A 40 19.526 10.711 19.160 1.00 13.99 C ATOM 175 CB LEU A 40 18.478 9.858 19.880 1.00 13.56 C """ pdb_2izq_220 = """\ HEADER ANTIBIOTIC 26-JUL-06 2IZQ ATOM 220 N ATRP A 11 20.498 12.832 34.558 0.50 6.03 N ATOM 221 CA ATRP A 11 21.094 12.032 35.602 0.50 5.24 C ATOM 222 C ATRP A 11 22.601 12.088 35.532 0.50 6.49 C ATOM 223 O ATRP A 11 23.174 12.012 34.439 0.50 7.24 O ATOM 224 CB ATRP A 11 20.690 10.588 35.288 0.50 6.15 C ATOM 225 CG ATRP A 11 19.252 10.269 35.140 0.50 5.91 C ATOM 226 CD1ATRP A 11 18.524 10.178 33.986 0.50 7.01 C ATOM 227 CD2ATRP A 11 18.371 9.973 36.236 0.50 5.97 C ATOM 228 NE1ATRP A 11 17.252 9.820 34.321 0.50 9.83 N ATOM 229 CE2ATRP A 11 17.132 9.708 35.665 0.50 7.37 C ATOM 230 CE3ATRP A 11 18.543 9.924 37.615 0.50 6.38 C ATOM 231 CZ2ATRP A 11 16.033 9.388 36.460 0.50 8.25 C ATOM 232 CZ3ATRP A 11 17.448 9.586 38.402 0.50 8.04 C ATOM 233 CH2ATRP A 11 16.240 9.320 37.784 0.50 8.66 C ATOM 234 H ATRP A 11 20.540 12.567 33.741 0.50 7.24 H ATOM 235 HA ATRP A 11 20.771 12.306 36.485 0.50 6.28 H ATOM 236 HB2ATRP A 11 21.135 10.330 34.466 0.50 7.38 H ATOM 237 HB3ATRP A 11 21.045 10.023 35.993 0.50 7.38 H ATOM 244 N CPHE A 11 20.226 13.044 34.556 0.15 6.35 N ATOM 245 CA CPHE A 11 20.950 12.135 35.430 0.15 5.92 C ATOM 246 C CPHE A 11 22.448 12.425 35.436 0.15 6.32 C ATOM 247 O CPHE A 11 22.961 12.790 34.373 0.15 6.08 O ATOM 248 CB CPHE A 11 20.768 10.667 34.994 0.15 6.01 C ATOM 249 CG CPHE A 11 19.330 10.235 34.845 0.15 7.05 C ATOM 250 CD1CPHE A 11 18.847 9.877 33.587 0.15 8.78 C ATOM 251 CD2CPHE A 11 18.533 10.174 35.995 0.15 7.70 C ATOM 252 CE1CPHE A 11 17.551 9.436 33.473 0.15 10.43 C ATOM 253 CE2CPHE A 11 17.230 9.752 35.854 0.15 9.27 C ATOM 254 CZ CPHE A 11 16.789 9.396 34.594 0.15 10.98 C ATOM 255 N BTYR A 11 20.553 12.751 34.549 0.35 5.21 N ATOM 256 CA BTYR A 11 21.106 11.838 35.524 0.35 5.51 C ATOM 257 C BTYR A 11 22.625 11.920 35.572 0.35 5.42 C ATOM 258 O BTYR A 11 23.299 11.781 34.538 0.35 5.30 O ATOM 259 CB BTYR A 11 20.694 10.354 35.327 0.35 5.65 C ATOM 260 CG BTYR A 11 19.188 10.175 35.507 0.35 7.68 C ATOM 261 CD1BTYR A 11 18.548 10.134 34.268 0.35 9.45 C ATOM 262 HB2CPHE A 11 21.221 10.536 34.146 0.15 7.21 H ATOM 263 CD2BTYR A 11 18.463 10.012 36.681 0.35 9.08 C ATOM 264 HB3CPHE A 11 21.198 10.093 35.647 0.15 7.21 H ATOM 265 CE1BTYR A 11 17.195 9.960 34.223 0.35 10.76 C ATOM 266 HD1CPHE A 11 19.394 9.937 32.837 0.15 10.53 H ATOM 267 CE2BTYR A 11 17.100 9.826 36.693 0.35 11.29 C ATOM 268 HD2CPHE A 11 18.873 10.410 36.828 0.15 9.24 H ATOM 269 CZ BTYR A 11 16.546 9.812 35.432 0.35 11.90 C ATOM 270 HE1CPHE A 11 17.206 9.172 32.650 0.15 12.52 H ATOM 271 OH BTYR A 11 15.178 9.650 35.313 0.35 19.29 O ATOM 272 HE2CPHE A 11 16.661 9.708 36.588 0.15 11.13 H ATOM 273 HZ CPHE A 11 15.908 9.110 34.509 0.15 13.18 H ATOM 274 H BTYR A 11 20.634 12.539 33.720 0.35 6.25 H ATOM 275 HA BTYR A 11 20.773 12.116 36.402 0.35 6.61 H HETATM 283 N DLE A 12 23.179 12.148 36.720 1.00 7.16 N HETATM 284 CA DLE A 12 24.625 12.084 36.893 1.00 8.29 C HETATM 285 CB ADLE A 12 25.039 10.717 37.621 0.65 9.02 C HETATM 286 CB BDLE A 12 25.209 10.741 37.032 0.35 12.70 C HETATM 287 CG ADLE A 12 24.658 9.548 36.780 0.65 12.06 C HETATM 288 CG BDLE A 12 25.429 9.378 36.572 0.35 15.20 C HETATM 289 CD1ADLE A 12 25.656 9.433 35.596 0.65 16.84 C HETATM 290 CD1BDLE A 12 26.192 8.543 37.585 0.35 16.77 C HETATM 291 CD2ADLE A 12 24.682 8.288 37.613 0.65 15.34 C HETATM 292 CD2BDLE A 12 24.065 8.724 36.277 0.35 16.96 C HETATM 293 C DLE A 12 25.029 13.153 37.899 1.00 8.11 C HETATM 294 O DLE A 12 24.343 13.330 38.907 1.00 11.62 O HETATM 295 H ADLE A 12 22.682 12.228 37.418 0.50 8.60 H HETATM 296 HA ADLE A 12 25.095 12.196 36.041 0.50 9.94 H HETATM 297 HB1ADLE A 12 25.997 10.708 37.775 0.65 10.83 H HETATM 298 HB1BDLE A 12 26.135 11.000 37.162 0.35 15.23 H HETATM 299 HB2ADLE A 12 24.595 10.659 38.481 0.65 10.83 H HETATM 300 HB2BDLE A 12 24.897 10.541 37.929 0.35 15.23 H HETATM 301 HG ADLE A 12 23.753 9.685 36.429 0.65 14.47 H HETATM 302 HG BDLE A 12 25.946 9.409 35.740 0.35 18.24 H """ def exercise_occupancy_groups_simple(): def atom_serials(atoms, list_of_occ_groups): result = [] for groups in list_of_occ_groups: group_names = [] for group in groups: group_names.append([int(atoms[i].serial) for i in group]) result.append(group_names) return result # def grouped_serials( pdb_inp, common_residue_name_class_only="common_amino_acid", always_group_adjacent=True): hierarchy = pdb_inp.construct_hierarchy(sort_atoms=False) atoms = hierarchy.atoms() sentinel = atoms.reset_tmp_for_occupancy_groups_simple() chain = hierarchy.only_chain() return atom_serials(atoms, chain.occupancy_groups_simple( common_residue_name_class_only=common_residue_name_class_only, always_group_adjacent=always_group_adjacent)) # for altloc_o2_a in ["A", " "]: pdb_inp = pdb.input(source_info=None, lines=flex.split_lines("""\ ATOM 0 S SO4 ATOM 1 O1 SO4 ATOM 2 O2 %sSO4 ATOM 3 O2 BSO4 ATOM 4 O3 SO4 ATOM 5 O4 SO4 """ % altloc_o2_a)) assert grouped_serials(pdb_inp) == [[[2], [3]]] # pdb_inp = pdb.input(source_info=None, lines=flex.split_lines("""\ ATOM 6 S ASO4 1 1.302 1.419 1.560 0.70 10.00 S ATOM 7 O1 ASO4 1 1.497 1.295 0.118 0.70 10.00 O ATOM 8 O2 ASO4 1 1.098 0.095 2.140 0.70 10.00 O ATOM 9 O3 ASO4 1 2.481 2.037 2.159 0.70 10.00 O ATOM 10 O4 ASO4 1 0.131 2.251 1.823 0.70 10.00 O ATOM 11 S BSO4 1 3.302 3.419 3.560 0.30 10.00 S ATOM 12 O1 BSO4 1 3.497 3.295 2.118 0.30 10.00 O ATOM 13 O2 BSO4 1 3.098 2.095 4.140 0.30 10.00 O ATOM 14 O3 BSO4 1 4.481 4.037 4.159 0.30 10.00 O ATOM 15 O4 BSO4 1 2.131 4.251 3.823 0.30 10.00 O """)) assert grouped_serials(pdb_inp) == [[[6,7,8,9,10], [11,12,13,14,15]]] # pdb_inp = pdb.input(source_info=None, lines=flex.split_lines("""\ ATOM 16 O AHOH 2 5.131 5.251 5.823 0.60 10.00 O ATOM 17 O BHOH 2 6.131 6.251 6.823 0.40 10.00 O """)) assert grouped_serials(pdb_inp) == [[[16], [17]]] # pdb_inp = pdb.input(source_info=None, lines=flex.split_lines("""\ ATOM 18 O HOH 3 1.132 5.963 7.065 1.00 15.00 O ATOM 19 H1 HOH 3 1.160 5.211 6.437 1.00 15.00 H ATOM 20 H2 HOH 3 1.122 5.579 7.967 1.00 15.00 H """)) assert grouped_serials(pdb_inp) == [] # pdb_inp = pdb.input(source_info=None, lines=flex.split_lines("""\ ATOM 21 O HOH 4 6.131 7.251 5.000 0.50 15.00 O """)) assert grouped_serials(pdb_inp) == [[[21]]] # pdb_inp = pdb.input(source_info=None, lines=flex.split_lines("""\ ATOM 22 O HOH 5 0.131 7.251 5.000 0.00 15.00 O """)) assert grouped_serials(pdb_inp) == [] # pdb_inp = pdb.input(source_info=None, lines=flex.split_lines("""\ ATOM 23 S SO4 6 6.302 6.419 1.560 0.50 10.00 S ATOM 24 O1 ASO4 6 6.497 6.295 0.118 0.60 10.00 O ATOM 25 O2 ASO4 6 6.098 5.095 2.140 0.60 10.00 O ATOM 26 O3 ASO4 6 7.481 7.037 2.159 0.60 10.00 O ATOM 27 O4 ASO4 6 5.131 7.251 1.823 0.60 10.00 O ATOM 28 O1 BSO4 6 8.497 8.295 2.118 0.40 10.00 O ATOM 29 O2 BSO4 6 8.098 7.095 4.140 0.40 10.00 O ATOM 30 O3 BSO4 6 9.481 9.037 4.159 0.40 10.00 O ATOM 31 O4 BSO4 6 7.131 9.251 3.823 0.40 10.00 O """)) assert grouped_serials(pdb_inp) == [[[23]], [[24,25,26,27], [28,29,30,31]]] # pdb_inp = pdb.input(source_info=None, lines=flex.split_lines("""\ ATOM 1 O AHOH 1 O ATOM 2 O BHOH 1 O ATOM 3 H1 AHOH 1 H ATOM 4 H1 BHOH 1 H ATOM 5 H2 AHOH 1 H ATOM 6 H2 BHOH 1 H """)) assert grouped_serials(pdb_inp) == [[[1],[2]]] # pdb_inp = pdb.input(source_info=None, lines=flex.split_lines("""\ ATOM 1 O HOH 1 0.60 O ATOM 2 H1 HOH 1 0.60 H ATOM 3 H2 HOH 1 0.60 H """)) assert grouped_serials(pdb_inp) == [[[1]]] # pdb_inp = pdb.input(source_info=None, lines=flex.split_lines(pdb_1nym_60)) assert grouped_serials(pdb_inp) == [ [[63],[64]], [[82,88,100,106],[83,89,101,107]], [[121,127,139,145,155,161],[122,128,140,146,156,162]]] # pdb_inp = pdb.input(source_info=None, lines=flex.split_lines("""\ ATOM 82 CA AMOD A 34 14.979 4.895 12.608 0.60 15.67 C ATOM 83 CA BMOD A 34 14.977 5.207 12.331 0.40 16.38 C ATOM 88 CB AMOD A 34 15.128 3.896 11.472 0.60 12.11 C ATOM 89 CB BMOD A 34 15.132 4.867 10.839 0.40 13.86 C ATOM 100 CA AASP A 35 15.328 8.688 12.044 0.60 16.75 C ATOM 101 CA BASP A 35 15.474 8.937 12.096 0.40 17.43 C ATOM 106 CB AASP A 35 14.367 9.683 11.373 0.60 16.80 C ATOM 107 CB BASP A 35 14.491 9.903 11.431 0.40 18.66 C """)) assert grouped_serials(pdb_inp) == [ [[82,88],[83,89]], [[100,106],[101,107]]] # pdb_inp = pdb.input(source_info=None, lines=flex.split_lines(pdb_2izq_220)) assert grouped_serials(pdb_inp) == [ [[220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233], [244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254], [255, 256, 257, 258, 259, 260, 261, 263, 265, 267, 269, 271]], [[285, 287, 289, 291], [286, 288, 290, 292]]] # pdb_inp = pdb.input(source_info=None, lines=flex.split_lines("""\ ATOM 221 CA ATRP A 11 21.094 12.032 35.602 0.50 5.24 C ATOM 224 CB ATRP A 11 20.690 10.588 35.288 0.50 6.15 C ATOM 245 CA CPHE A 11 20.950 12.135 35.430 0.15 5.92 C ATOM 248 CB CPHE A 11 20.768 10.667 34.994 0.15 6.01 C ATOM 256 CA BTYR A 11 21.106 11.838 35.524 0.35 5.51 C ATOM 259 CB BTYR A 11 20.694 10.354 35.327 0.35 5.65 C HETATM 285 CB ADLE A 12 25.039 10.717 37.621 0.65 9.02 C HETATM 286 CB BDLE A 12 25.209 10.741 37.032 0.35 12.70 C HETATM 287 CG ADLE A 12 24.658 9.548 36.780 0.65 12.06 C HETATM 288 CG BDLE A 12 25.429 9.378 36.572 0.35 15.20 C """)) assert grouped_serials(pdb_inp) == [ [[221, 224], [245, 248], [256, 259]], [[285, 287], [286, 288]]] assert grouped_serials(pdb_inp, common_residue_name_class_only=None) == [ [[221, 224, 285, 287], [245, 248], [256, 259, 286, 288]]] # pdb_inp = pdb.input(source_info=None, lines=flex.split_lines("""\ ATOM 0 N SER A 41 4.113 5.460 7.786 1.00 5.58 N ATOM 6 N ALYS A 42 6.572 6.690 8.417 0.30 4.64 N ATOM 15 N BLYS A 42 6.744 6.602 8.454 0.20 5.86 N ATOM 24 N CLYS A 42 6.661 6.659 8.442 0.10 5.63 N ATOM 33 N DLYS A 42 6.664 6.660 8.439 0.40 4.72 N ATOM 42 N AGLU A 43 6.158 9.341 9.210 0.60 4.32 N ATOM 51 N BGLU A 43 6.272 9.302 9.294 0.40 5.00 N """)) assert grouped_serials(pdb_inp, common_residue_name_class_only=None) == \ [[[6, 42], [15, 51], [24], [33]]] assert grouped_serials(pdb_inp, common_residue_name_class_only=None, always_group_adjacent=False) == [[[6], [15], [24], [33]], [[42], [51]]] # pdb_inp = pdb.input(source_info=None, lines=flex.split_lines("""\ ATOM 1 O AHOH A 1 O ATOM 2 O BHOH A 1 O ATOM 3 O AHOH B 1 O ATOM 4 O BHOH B 1 O """)) hierarchy = pdb_inp.construct_hierarchy(sort_atoms=False) list_of_groups = hierarchy.occupancy_groups_simple( common_residue_name_class_only="common_amino_acid") assert list_of_groups == [[[0], [1]], [[2], [3]]] def conformers_as_str(conformers): s = StringIO() for cf in conformers: print("conformer:", show_string(cf.altloc), file=s) for rd in cf.residues(): assert rd.resseq_as_int() == pdb.hy36decode(width=4, s=rd.resseq) print(" residue:", \ show_string(rd.resname), \ show_string(rd.resseq), \ show_string(rd.icode), \ int(rd.link_to_previous), \ int(rd.is_pure_main_conf), file=s) for atom in rd.atoms(): print(" atom:", show_string(atom.name), file=s) return s.getvalue() def exercise_conformers(): assert len(pdb.hierarchy.chain().conformers()) == 0 assert len(pdb.hierarchy.residue_group().conformers()) == 0 # def check(pdb_string, expected): pdb_inp = pdb.input(source_info=None, lines=flex.split_lines(pdb_string)) chain = pdb_inp.construct_hierarchy(sort_atoms=False).only_chain() conformers = chain.conformers() s = conformers_as_str(conformers) if (len(expected) == 0): sys.stdout.write(s) else: assert not show_diff(s, expected) # for rg in chain.residue_groups(): for cf in rg.conformers(): assert cf.parent(optional=False).memory_id() == chain.memory_id() assert cf.residues_size() == 1 rgc = rg.detached_copy() for cf in rgc.conformers(): assert cf.parent() is None assert cf.residues_size() == 1 try: cf.parent(optional=False) except RuntimeError as e: assert not show_diff(str(e), "conformer has no parent chain") else: raise Exception_expected # if (chain.residue_groups_size() == 1): conformers = rg.conformers() s = conformers_as_str(conformers) if (len(expected) != 0): assert not show_diff(s, expected) # check("""\ ATOM N RES 1I """, """\ conformer: "" residue: "RES" " 1" "I" 0 1 atom: " N " """) # check("""\ ATOM N ARES 1I """, """\ conformer: "A" residue: "RES" " 1" "I" 0 0 atom: " N " """) # check("""\ ATOM N1 RES 1I ATOM N2 ARES 1I """, """\ conformer: "A" residue: "RES" " 1" "I" 0 0 atom: " N1 " atom: " N2 " """) # for altloc_o2_a in ["A", " "]: check("""\ ATOM S SO4 1I ATOM O1 %sSO4 1I ATOM O1 BSO4 1I """ % altloc_o2_a, """\ conformer: "%s" residue: "SO4" " 1" "I" 0 0 atom: " S " atom: " O1 " conformer: "B" residue: "SO4" " 1" "I" 0 0 atom: " S " atom: " O1 " """ % altloc_o2_a) # check("""\ ATOM S ASO4 1 ATOM O1 ASO4 1 ATOM O2 ASO4 1 ATOM S BSO4 1 ATOM O1 BSO4 1 ATOM O2 BSO4 1 """, """\ conformer: "A" residue: "SO4" " 1" " " 0 0 atom: " S " atom: " O1 " atom: " O2 " conformer: "B" residue: "SO4" " 1" " " 0 0 atom: " S " atom: " O1 " atom: " O2 " """) # check("""\ ATOM S ASO4 1 ATOM O1 ASO4 1 ATOM O2 ASO4 1 ATOM S BSO4 1 ATOM O1 BSO4 1 ATOM O2 BSO4 1 ATOM O HOH 2 """, """\ conformer: "A" residue: "SO4" " 1" " " 0 0 atom: " S " atom: " O1 " atom: " O2 " residue: "HOH" " 2" " " 1 1 atom: " O " conformer: "B" residue: "SO4" " 1" " " 0 0 atom: " S " atom: " O1 " atom: " O2 " residue: "HOH" " 2" " " 1 1 atom: " O " """) # check("""\ ATOM S SO4 6 ATOM O1 ASO4 6 ATOM O2 ASO4 6 ATOM O3 BSO4 6 ATOM O4 BSO4 6 """, """\ conformer: "A" residue: "SO4" " 6" " " 0 0 atom: " S " atom: " O1 " atom: " O2 " conformer: "B" residue: "SO4" " 6" " " 0 0 atom: " S " atom: " O3 " atom: " O4 " """) # check("""\ ATOM N1 R01 1I ATOM N2 R01 1I ATOM N1 R02 1I ATOM N2 R02 1I """, """\ conformer: "" residue: "R01" " 1" "I" 0 1 atom: " N1 " atom: " N2 " residue: "R02" " 1" "I" 1 1 atom: " N1 " atom: " N2 " """) # check("""\ ATOM N1 AR01 1I ATOM N2 R01 1I ATOM N1 R02 1I ATOM N2 R02 1I """, """\ conformer: "A" residue: "R01" " 1" "I" 0 0 atom: " N2 " atom: " N1 " residue: "R02" " 1" "I" 1 1 atom: " N1 " atom: " N2 " """) # check("""\ ATOM N1 AR01 1I ATOM N2 R01 1I ATOM N1 AR02 1I ATOM N2 R02 1I """, """\ conformer: "A" residue: "R01" " 1" "I" 0 0 atom: " N2 " atom: " N1 " residue: "R02" " 1" "I" 1 0 atom: " N2 " atom: " N1 " """) # check("""\ ATOM N1 AR01 1I ATOM N2 R01 1I ATOM N1 BR02 1I ATOM N2 R02 1I """, """\ conformer: "A" residue: "R01" " 1" "I" 0 0 atom: " N2 " atom: " N1 " residue: "R02" " 1" "I" 1 1 atom: " N2 " conformer: "B" residue: "R01" " 1" "I" 0 1 atom: " N2 " residue: "R02" " 1" "I" 1 0 atom: " N2 " atom: " N1 " """) # check("""\ ATOM N1 AR01 1I ATOM N2 BR01 1I ATOM N1 R02 1I ATOM N2 R02 1I """, """\ conformer: "A" residue: "R01" " 1" "I" 0 0 atom: " N1 " residue: "R02" " 1" "I" 1 1 atom: " N1 " atom: " N2 " conformer: "B" residue: "R01" " 1" "I" 0 0 atom: " N2 " residue: "R02" " 1" "I" 1 1 atom: " N1 " atom: " N2 " """) # check("""\ ATOM N1 AR01 1I ATOM N2 BR01 1I ATOM N1 CR02 1I ATOM N2 R02 1I """, """\ conformer: "A" residue: "R01" " 1" "I" 0 0 atom: " N1 " residue: "R02" " 1" "I" 1 1 atom: " N2 " conformer: "B" residue: "R01" " 1" "I" 0 0 atom: " N2 " residue: "R02" " 1" "I" 1 1 atom: " N2 " conformer: "C" residue: "R02" " 1" "I" 1 0 atom: " N2 " atom: " N1 " """) # check("""\ ATOM N1 AR01 1I ATOM N2 BR01 1I ATOM N1 CR02 1I ATOM N2 DR02 1I """, """\ conformer: "A" residue: "R01" " 1" "I" 0 0 atom: " N1 " conformer: "B" residue: "R01" " 1" "I" 0 0 atom: " N2 " conformer: "C" residue: "R02" " 1" "I" 0 0 atom: " N1 " conformer: "D" residue: "R02" " 1" "I" 0 0 atom: " N2 " """) # check(pdb_1nym_60, """\ conformer: "A" residue: "LYS" " 32" " " 0 0 atom: " CA " atom: " CB " residue: "VAL" " 33" " " 1 1 atom: " CA " atom: " CB " residue: "LYS" " 34" " " 1 0 atom: " CA " atom: " CB " residue: "ASP" " 35" " " 1 0 atom: " CA " atom: " CB " residue: "ALA" " 36" " " 1 1 atom: " CA " atom: " CB " residue: "GLU" " 37" " " 1 0 atom: " CA " atom: " CB " residue: "ASP" " 38" " " 1 0 atom: " CA " atom: " CB " residue: "GLN" " 39" " " 1 0 atom: " CA " atom: " CB " residue: "LEU" " 40" " " 1 1 atom: " CA " atom: " CB " conformer: "B" residue: "LYS" " 32" " " 0 0 atom: " CA " atom: " CB " residue: "VAL" " 33" " " 1 1 atom: " CA " atom: " CB " residue: "LYS" " 34" " " 1 0 atom: " CA " atom: " CB " residue: "ASP" " 35" " " 1 0 atom: " CA " atom: " CB " residue: "ALA" " 36" " " 1 1 atom: " CA " atom: " CB " residue: "GLU" " 37" " " 1 0 atom: " CA " atom: " CB " residue: "ASP" " 38" " " 1 0 atom: " CA " atom: " CB " residue: "GLN" " 39" " " 1 0 atom: " CA " atom: " CB " residue: "LEU" " 40" " " 1 1 atom: " CA " atom: " CB " """) # check(pdb_2izq_220, """\ conformer: "A" residue: "TRP" " 11" " " 0 0 atom: " N " atom: " CA " atom: " C " atom: " O " atom: " CB " atom: " CG " atom: " CD1" atom: " CD2" atom: " NE1" atom: " CE2" atom: " CE3" atom: " CZ2" atom: " CZ3" atom: " CH2" atom: " H " atom: " HA " atom: " HB2" atom: " HB3" residue: "DLE" " 12" " " 1 0 atom: " N " atom: " CA " atom: " C " atom: " O " atom: " CB " atom: " CG " atom: " CD1" atom: " CD2" atom: " H " atom: " HA " atom: " HB1" atom: " HB2" atom: " HG " conformer: "C" residue: "PHE" " 11" " " 0 0 atom: " N " atom: " CA " atom: " C " atom: " O " atom: " CB " atom: " CG " atom: " CD1" atom: " CD2" atom: " CE1" atom: " CE2" atom: " CZ " atom: " HB2" atom: " HB3" atom: " HD1" atom: " HD2" atom: " HE1" atom: " HE2" atom: " HZ " residue: "DLE" " 12" " " 1 1 atom: " N " atom: " CA " atom: " C " atom: " O " conformer: "B" residue: "TYR" " 11" " " 0 0 atom: " N " atom: " CA " atom: " C " atom: " O " atom: " CB " atom: " CG " atom: " CD1" atom: " CD2" atom: " CE1" atom: " CE2" atom: " CZ " atom: " OH " atom: " H " atom: " HA " residue: "DLE" " 12" " " 1 0 atom: " N " atom: " CA " atom: " C " atom: " O " atom: " CB " atom: " CG " atom: " CD1" atom: " CD2" atom: " HB1" atom: " HB2" atom: " HG " """) # check("""\ HEADER HORMONE 01-MAY-98 1ZEH HETATM 878 C1 ACRS 5 12.880 14.021 1.197 0.50 33.23 C HETATM 879 C1 BCRS 5 12.880 14.007 1.210 0.50 34.27 C HETATM 880 C2 ACRS 5 12.755 14.853 0.093 0.50 33.88 C HETATM 881 C2 BCRS 5 13.935 13.115 1.278 0.50 34.25 C HETATM 882 C3 ACRS 5 13.668 14.754 -0.945 0.50 33.82 C HETATM 883 C3 BCRS 5 14.848 13.014 0.238 0.50 34.30 C HETATM 884 C4 ACRS 5 14.707 13.834 -0.888 0.50 33.46 C HETATM 885 C4 BCRS 5 14.695 13.821 -0.884 0.50 34.40 C HETATM 886 C5 ACRS 5 14.835 13.001 0.219 0.50 33.30 C HETATM 887 C5 BCRS 5 13.635 14.719 -0.957 0.50 34.78 C HETATM 888 C6 ACRS 5 13.916 13.105 1.252 0.50 33.26 C HETATM 889 C6 BCRS 5 12.731 14.813 0.090 0.50 34.86 C HETATM 890 C7 ACRS 5 13.552 15.660 -2.169 0.50 33.90 C HETATM 891 C7 BCRS 5 16.001 12.014 0.353 0.50 34.77 C HETATM 892 O1 ACRS 5 11.973 14.116 2.233 0.50 34.24 O HETATM 893 O1 BCRS 5 11.973 14.107 2.248 0.50 35.28 O HETATM 894 O HOH 5 -0.924 19.122 -8.629 1.00 11.73 O HETATM 895 O HOH 6 -19.752 11.918 3.524 1.00 13.44 O """, """\ conformer: "A" residue: "CRS" " 5" " " 0 0 atom: " C1 " atom: " C2 " atom: " C3 " atom: " C4 " atom: " C5 " atom: " C6 " atom: " C7 " atom: " O1 " residue: "HOH" " 5" " " 1 1 atom: " O " residue: "HOH" " 6" " " 1 1 atom: " O " conformer: "B" residue: "CRS" " 5" " " 0 0 atom: " C1 " atom: " C2 " atom: " C3 " atom: " C4 " atom: " C5 " atom: " C6 " atom: " C7 " atom: " O1 " residue: "HOH" " 5" " " 1 1 atom: " O " residue: "HOH" " 6" " " 1 1 atom: " O " """) check("""\ HEADER HYDROLASE 22-NOV-07 2VHL HETATM 6362 O HOH B2048 47.616 10.724 150.212 1.00 46.48 O HETATM 6363 O AHOH B2049 46.408 16.672 146.066 0.50 12.81 O HETATM 6364 O HOH B2050 29.343 12.806 185.898 1.00 35.57 O HETATM 6365 O BHOH B2049 43.786 12.615 147.734 0.50 28.43 O HETATM 6366 O HOH B2052 35.068 19.167 155.349 1.00 15.97 O """, """\ conformer: "A" residue: "HOH" "2048" " " 0 1 atom: " O " residue: "HOH" "2049" " " 1 0 atom: " O " residue: "HOH" "2050" " " 1 1 atom: " O " residue: "HOH" "2052" " " 1 1 atom: " O " conformer: "B" residue: "HOH" "2048" " " 0 1 atom: " O " residue: "HOH" "2049" " " 1 0 atom: " O " residue: "HOH" "2050" " " 1 1 atom: " O " residue: "HOH" "2052" " " 1 1 atom: " O " """) def exercise_residue(): pdb_inp = pdb.input(source_info=None, lines=flex.split_lines("""\ ATOM 1 N MET A 1 ATOM 2 CA MET A 1 """)) h = pdb_inp.construct_hierarchy() residue = h.only_residue() assert residue.resid() == " 1 " assert residue.find_atom_by(name=None) is None assert residue.find_atom_by(name=" N ").name == " N " assert residue.find_atom_by(name="N ") is None assert residue.find_atom_by(name=" CA ").name == " CA " try: residue.parent(optional=False) except RuntimeError as e: assert not show_diff(str(e), "residue has no parent conformer") else: raise Exception_expected def exercise_is_identical_hierarchy(): pdb_inp = pdb.input(source_info=None, lines=flex.split_lines("""\ MODEL 0 ATOM 1 N MET A 1 ATOM 2 CA MET A 1 ATOM 3 N GLY A 2 ATOM 4 CA GLY A 2 ENDMDL MODEL 1 ATOM 1 N MET A 1 ATOM 2 CA MET A 1 ATOM 3 N GLY A 2 ATOM 4 CA GLY A 2 ENDMDL MODEL 2 ATOM 1 N MET A 1 HETATM 2 CA MET A 1 ATOM 3 N GLY A 2 ATOM 4 CA GLY A 2 ENDMDL MODEL 3 ATOM 1 N MET A 1 ATOM 12 CA MET A 1 ATOM 3 N GLY A 2 ATOM 4 CA GLY A 2 ENDMDL MODEL 4 ATOM 1 N MET A 1 ATOM 2 CA MET A 1 ATOM 3 NX GLY A 2 ATOM 4 CA GLY A 2 ENDMDL MODEL 5 ATOM 1 N MET A 1 E ATOM 2 CA MET A 1 ATOM 3 N GLY A 2 ATOM 4 CA GLY A 2 ENDMDL MODEL 6 ATOM 1 N MET A 1 ATOM 2 CA MET A 1 ATOM 3 N GLY A 2 X ATOM 4 CA GLY A 2 ENDMDL """)) models = pdb_inp.construct_hierarchy(sort_atoms=False).models() assert models[0].is_identical_hierarchy(models[1]) assert models[1].is_identical_hierarchy(models[0]) assert models[0].only_chain().is_identical_hierarchy( other=models[1].only_chain()) assert models[0].only_chain().residue_groups()[0].is_identical_hierarchy( other=models[1].only_chain().residue_groups()[0]) for other in models[2:]: assert not models[0].is_identical_hierarchy(other=other) assert not other.is_identical_hierarchy(other=models[0]) assert not models[0].only_chain().is_identical_hierarchy( other=other.only_chain()) assert not models[0].only_chain().residue_groups()[0] \ .is_identical_hierarchy(other=models[2].only_chain().residue_groups()[0]) def exercise_is_similar_hierarchy(): s0 = """\ MODEL 0 ATOM 1 %s MET A 1 ATOM 2 CA AMET A 1 ATOM 3 N GLY A 2 ATOM 4 CA AGLY A 2 ENDMDL MODEL 1 ATOM 1 N MET A 1 ATOM 2 CA AMET A 1 ATOM 3 N %3s A 2 ATOM 4 CA A%3s A 2 ENDMDL """ i1 = pdb.input(source_info=None, lines=flex.split_lines( s0 % ("N ", "GLY", "GLY"))) h1 = i1.construct_hierarchy() assert h1.is_similar_hierarchy(other=h1) assert h1.is_similar_hierarchy(other=h1.deep_copy()) assert h1.models()[0].is_similar_hierarchy( other=h1.models()[1]) assert h1.models()[0].only_chain().is_similar_hierarchy( other=h1.models()[1].only_chain()) assert h1.models()[0].only_chain().residue_groups()[0].is_similar_hierarchy( other=h1.models()[1].only_chain().residue_groups()[0]) for an,rn in [("C ", "GLY"), ("N ", "ALA")]: i2 = pdb.input(source_info=None, lines=flex.split_lines( s0 % (an, rn, rn))) h2 = i2.construct_hierarchy() assert not h1.is_similar_hierarchy(other=h2) assert not h2.is_similar_hierarchy(other=h1) assert not h1.models()[0].is_similar_hierarchy( other=h2.models()[0]) == (rn == "GLY") assert h1.models()[0].only_chain().is_similar_hierarchy( other=h2.models()[0].only_chain()) == (an == "N ") assert h1.models()[0].only_chain().residue_groups()[0] \ .is_similar_hierarchy( other=h2.models()[0].only_chain().residue_groups()[0]) == (an == "N ") def exercise_atoms(): pdb_inp = pdb.input(source_info=None, lines=flex.split_lines("""\ ATOM 1 N GLN A 3 35.299 11.075 19.070 1.00 36.89 N ATOM 2 CA GLN A 3 34.482 9.927 18.794 0.63 37.88 C SIGATM 2 CA GLN A 3 1.200 2.300 3.400 0.04 0.05 C ANISOU 2 CA GLN A 3 7794 3221 3376 -1227 1064 2601 C ATOM 3 Q GLN A 3 35.130 8.880 17.864 0.84 37.52 C ANISOU 3 Q GLN A 3 7875 3041 3340 -981 727 2663 C SIGUIJ 3 Q GLN A 3 75 41 40 -1 7 63 C ATOM 4 O GLN A 3 34.548 7.819 17.724 1.00 38.54 STUV ATOM 5 1CB AGLN A 3 32.979 10.223 18.469 1.00 37.80 X HETATM 6 CA AION B 1 32.360 11.092 17.308 0.92 35.96 CA2+ HETATM 7 CA ION B 2 30.822 10.665 17.190 1.00 36.87 """)) atoms = pdb_inp.atoms() assert list(atoms.extract_serial()) == [ " 1", " 2", " 3", " 4", " 5", " 6", " 7"] assert list(atoms.extract_name()) == [ " N ", " CA ", " Q ", " O ", "1CB ", "CA ", "CA "] assert (list(atoms.extract_segid()) == [ ' ', ' ', ' ', 'STUV', ' ', ' ', ' ']) xyz = atoms.extract_xyz() assert approx_equal(xyz, [ (35.299,11.075,19.070), (34.482,9.927,18.794), (35.130,8.880,17.864), (34.548,7.819,17.724), (32.979,10.223,18.469), (32.360,11.092,17.308), (30.822,10.665,17.190)]) sigxyz = atoms.extract_sigxyz() assert approx_equal(sigxyz, [ (0,0,0), (1.2,2.3,3.4), (0,0,0), (0,0,0), (0,0,0), (0,0,0), (0,0,0)]) occ = atoms.extract_occ() assert approx_equal(occ, [1.00,0.63,0.84,1.00,1.00,0.92,1.00]) sigocc = atoms.extract_sigocc() assert approx_equal(sigocc, [0,0.04,0,0,0,0,0]) b = atoms.extract_b() assert approx_equal(b, [36.89,37.88,37.52,38.54,37.80,35.96,36.87]) sigb = atoms.extract_sigb() assert approx_equal(sigb, [0,0.05,0,0,0,0,0]) uij = atoms.extract_uij() assert approx_equal(uij, [ (-1,-1,-1,-1,-1,-1), (0.7794, 0.3221, 0.3376, -0.1227, 0.1064, 0.2601), (0.7875, 0.3041, 0.3340, -0.0981, 0.0727, 0.2663), (-1,-1,-1,-1,-1,-1), (-1,-1,-1,-1,-1,-1), (-1,-1,-1,-1,-1,-1), (-1,-1,-1,-1,-1,-1)]) expected_siguij = [ (-1,-1,-1,-1,-1,-1), (-1,-1,-1,-1,-1,-1), (0.0075, 0.0041, 0.0040, -0.0001, 0.0007, 0.0063), (-1,-1,-1,-1,-1,-1), (-1,-1,-1,-1,-1,-1), (-1,-1,-1,-1,-1,-1), (-1,-1,-1,-1,-1,-1)] if (pdb.hierarchy.atom.has_siguij()): siguij = atoms.extract_siguij() assert approx_equal(siguij, expected_siguij) assert atoms.extract_fp().all_eq(0) assert atoms.extract_fdp().all_eq(0) assert list(atoms.extract_hetero()) == [5,6] assert list(atoms.extract_element()) == [" N"," C"," C"," ","X ","CA"," "] assert atoms.extract_element(strip=False).all_eq(atoms.extract_element()) assert list(atoms.extract_element(strip=True)) ==["N","C","C","","X","CA",""] atoms.reset_i_seq() assert list(atoms.extract_i_seq()) == list(range(7)) assert list( pdb.hierarchy.af_shared_atom([atoms[3], atoms[6]]).extract_i_seq()) == \ [3, 6] assert list(atoms.extract_tmp_as_size_t()) == [0]*7 for i,atom in enumerate(atoms): atom.tmp = i+3 assert list(atoms.extract_tmp_as_size_t()) == [3,4,5,6,7,8,9] atoms[3].tmp = -1 try: atoms.extract_tmp_as_size_t() except RuntimeError as e: assert not show_diff(str(e), "atom.tmp less than zero: cannot convert to unsigned value.") else: raise Exception_expected # assert atoms.set_xyz(new_xyz=xyz+(1,2,3)) is atoms assert approx_equal(atoms.extract_xyz(), [ (36.299,13.075,22.070), (35.482,11.927,21.794), (36.130,10.880,20.864), (35.548,9.819,20.724), (33.979,12.223,21.469), (33.360,13.092,20.308), (31.822,12.665,20.190)]) assert atoms.set_sigxyz(new_sigxyz=sigxyz+(1,2,3)) is atoms assert approx_equal(atoms.extract_sigxyz(), [ (1,2,3), (2.2,4.3,6.4), (1,2,3), (1,2,3), (1,2,3), (1,2,3), (1,2,3)]) assert atoms.set_occ(new_occ=occ+1.23) is atoms assert approx_equal(atoms.extract_occ(), [2.23,1.86,2.07,2.23,2.23,2.15,2.23]) assert atoms.set_sigocc(new_sigocc=sigocc+3) is atoms assert approx_equal(atoms.extract_sigocc(), [3,3.04,3,3,3,3,3]) assert atoms.set_b(new_b=b+10) is atoms assert approx_equal(atoms.extract_b(), [46.89,47.88,47.52,48.54,47.80,45.96,46.87]) assert atoms.set_sigb(new_sigb=sigb+5) is atoms assert approx_equal(atoms.extract_sigb(), [5,5.05,5,5,5,5,5]) assert atoms.set_uij(new_uij=flex.sym_mat3_double(expected_siguij)) is atoms assert approx_equal(atoms.extract_uij(), expected_siguij) if (pdb.hierarchy.atom.has_siguij()): assert atoms.set_siguij(new_siguij=uij) is atoms assert approx_equal(atoms.extract_siguij(), [ (-1,-1,-1,-1,-1,-1), (0.7794, 0.3221, 0.3376, -0.1227, 0.1064, 0.2601), (0.7875, 0.3041, 0.3340, -0.0981, 0.0727, 0.2663), (-1,-1,-1,-1,-1,-1), (-1,-1,-1,-1,-1,-1), (-1,-1,-1,-1,-1,-1), (-1,-1,-1,-1,-1,-1)]) new_fp = flex.double([0, 0.1, 0.2, 0, 0, 0, 0]) new_fdp = flex.double([0, 0.2, 0.3, 0.1, 0, 0, 0]) assert atoms.set_fp(new_fp=new_fp) is atoms assert atoms.set_fdp(new_fdp=new_fdp) is atoms assert approx_equal(atoms.extract_fp(), new_fp) assert approx_equal(atoms.extract_fdp(), new_fdp) # h = pdb_inp.construct_hierarchy(set_atom_i_seq=False, sort_atoms=False) for i in range(2): s = h.as_pdb_string() d = hashlib.md5(s.encode()).hexdigest() if (pdb.hierarchy.atom.has_siguij()): assert d == "c4089359af431bb2962d6a8e457dd86f", d else: assert d == "2c78c9a2e7113216a442c1866979ff26", d h.write_pdb_file(file_name="tmp_tst_hierarchy.pdb") with open("tmp_tst_hierarchy.pdb") as f: lines = f.read() assert not show_diff(lines, s) h = pdb.input( source_info=None, lines=flex.split_lines(s)).construct_hierarchy( set_atom_i_seq=False, sort_atoms=False) # atoms = h.atoms().select(indices=flex.size_t([2,5,3,0])) assert [a.name for a in atoms] == [" Q ", "CA ", " O ", " N "] atoms = atoms.select(indices=flex.size_t([3,0,1,2]), reverse=True) assert [a.name for a in atoms] == ["CA ", " O ", " N ", " Q "] atoms = atoms.select(indices=flex.size_t([3,0,1,2]), reverse=False) assert [a.name for a in atoms] == [" Q ", "CA ", " O ", " N "] atoms = atoms.select(flex.bool([False,True,False,False])) assert [a.name for a in atoms] == ["CA "] # assert [int(a.serial) for a in h.atoms_with_i_seq_mismatch()] \ == [2, 3, 4, 5, 6, 7] h.atoms().reset_i_seq() assert h.atoms_with_i_seq_mismatch().size() == 0 assert pdb.hierarchy.root().atoms_with_i_seq_mismatch().size() == 0 def check_wpf(hierarchy, kwargs={}, trailing=None, expected=None): if ("atoms_reset_serial_first_value" in kwargs): pdb_str = hierarchy.deep_copy().as_pdb_string(**kwargs) else: pdb_str = hierarchy.as_pdb_string(**kwargs) if (trailing is not None): pdb_str = pdb_str.replace(trailing, "") if (expected is None): sys.stdout.write(pdb_str) else: assert not show_diff(pdb_str, expected) hierarchy.write_pdb_file(file_name="tmp_tst_hierarchy.pdb", **kwargs) with open("tmp_tst_hierarchy.pdb") as f: pdb_file = f.read() if (trailing is not None): pdb_file = pdb_file.replace(trailing, "") assert not show_diff(pdb_file, pdb_str) # pdb_inp = pdb.input(file_name="tmp_tst_hierarchy.pdb") assert pdb_inp.atoms().size() == hierarchy.atoms_size() kwargs = dict(kwargs) for discard in ["atoms_reset_serial_first_value", "interleaved_conf"]: if (discard in kwargs): del kwargs[discard] pdb_inp.write_pdb_file(file_name="tmp2.pdb", **kwargs) pdb_str2 = pdb_inp.as_pdb_string(**kwargs) with open("tmp2.pdb") as f: lines = f.read() assert not show_diff(lines, pdb_str2) pdb_inp2 = pdb.input(file_name="tmp2.pdb") assert pdb_inp2.atoms().size() == pdb_inp.atoms().size() assert pdb_inp.extract_cryst1_z_columns() \ == pdb_inp2.extract_cryst1_z_columns() if ("cryst1_z" in kwargs): assert pdb_inp.extract_cryst1_z_columns() == ("%4s" % kwargs["cryst1_z"]) # return pdb_str def exercise_atoms_interleaved_conf(): pdb_inp = pdb.input(source_info=None, lines=flex.split_lines("""\ ATOM 1 N ATRP A 1I ATOM 4 N CPHE A 1I ATOM 2 C ATRP A 1I ATOM 8 CA BTYR A 1I ATOM 3 O ATRP A 1I ATOM 5 CA CPHE A 1I ATOM 6 C CPHE A 1I ATOM 9 C BTYR A 1I ATOM 7 O CPHE A 1I ATOM 10 O BTYR A 1I """)) hierarchy = pdb_inp.construct_hierarchy(sort_atoms=False) for obj in [hierarchy.only_residue_group(), hierarchy.only_chain(), hierarchy.only_model(), hierarchy]: for interleaved_conf in [-1,0,1]: rs = [atom.format_atom_record(replace_floats_with="") for atom in obj.atoms(interleaved_conf=interleaved_conf)] assert not show_diff("\n".join([r[:-8] for r in rs]), """\ ATOM 1 N ATRP A 1I ATOM 2 C ATRP A 1I ATOM 3 O ATRP A 1I ATOM 4 N CPHE A 1I ATOM 5 CA CPHE A 1I ATOM 6 C CPHE A 1I ATOM 7 O CPHE A 1I ATOM 8 CA BTYR A 1I ATOM 9 C BTYR A 1I ATOM 10 O BTYR A 1I""") for obj in [hierarchy.only_residue_group(), hierarchy.only_chain(), hierarchy.only_model(), hierarchy]: rs = [atom.format_atom_record(replace_floats_with="") for atom in obj.atoms(interleaved_conf=2)] assert not show_diff("\n".join([r[:-8] for r in rs]), """\ ATOM 1 N ATRP A 1I ATOM 4 N CPHE A 1I ATOM 2 C ATRP A 1I ATOM 6 C CPHE A 1I ATOM 9 C BTYR A 1I ATOM 3 O ATRP A 1I ATOM 7 O CPHE A 1I ATOM 10 O BTYR A 1I ATOM 5 CA CPHE A 1I ATOM 8 CA BTYR A 1I""") trailing = " A 1I 0.000 0.000 0.000 0.00 0.00" check_wpf(hierarchy, {"interleaved_conf":1}, trailing, """\ ATOM 1 N ATRP ATOM 2 C ATRP ATOM 3 O ATRP ATOM 4 N CPHE ATOM 5 CA CPHE ATOM 6 C CPHE ATOM 7 O CPHE ATOM 8 CA BTYR ATOM 9 C BTYR ATOM 10 O BTYR TER """) check_wpf(hierarchy, {"interleaved_conf":2}, trailing, """\ ATOM 1 N ATRP ATOM 4 N CPHE ATOM 2 C ATRP ATOM 6 C CPHE ATOM 9 C BTYR ATOM 3 O ATRP ATOM 7 O CPHE ATOM 10 O BTYR ATOM 5 CA CPHE ATOM 8 CA BTYR TER """) # pdb_inp = pdb.input(source_info=None, lines=flex.split_lines("""\ ATOM 1 N ATRP A 1I ATOM 4 N CPHE A 1I ATOM 2 C ATRP A 1I ATOM 8 CA BTRP A 1I ATOM 3 O ATRP A 1I ATOM 5 CA CPHE A 1I ATOM 6 C CPHE A 1I ATOM 9 C BTRP A 1I ATOM 7 O CPHE A 1I ATOM 10 O BTRP A 1I """)) hierarchy = pdb_inp.construct_hierarchy(sort_atoms=False) rs = [atom.format_atom_record(replace_floats_with="") for atom in hierarchy.only_residue_group().atoms(interleaved_conf=1)] assert not show_diff("\n".join([r[:-8] for r in rs]), """\ ATOM 1 N ATRP A 1I ATOM 2 C ATRP A 1I ATOM 9 C BTRP A 1I ATOM 3 O ATRP A 1I ATOM 10 O BTRP A 1I ATOM 8 CA BTRP A 1I ATOM 4 N CPHE A 1I ATOM 5 CA CPHE A 1I ATOM 6 C CPHE A 1I ATOM 7 O CPHE A 1I""") rs = [atom.format_atom_record(replace_floats_with="") for atom in hierarchy.only_residue_group().atoms(interleaved_conf=2)] assert not show_diff("\n".join([r[:-8] for r in rs]), """\ ATOM 1 N ATRP A 1I ATOM 4 N CPHE A 1I ATOM 2 C ATRP A 1I ATOM 6 C CPHE A 1I ATOM 9 C BTRP A 1I ATOM 3 O ATRP A 1I ATOM 7 O CPHE A 1I ATOM 10 O BTRP A 1I ATOM 5 CA CPHE A 1I ATOM 8 CA BTRP A 1I""") check_wpf(hierarchy, {"interleaved_conf":1}, trailing, """\ ATOM 1 N ATRP ATOM 2 C ATRP ATOM 9 C BTRP ATOM 3 O ATRP ATOM 10 O BTRP ATOM 8 CA BTRP ATOM 4 N CPHE ATOM 5 CA CPHE ATOM 6 C CPHE ATOM 7 O CPHE TER """) for interleaved_conf in [2,3,4]: check_wpf(hierarchy, {"interleaved_conf":interleaved_conf}, trailing, """\ ATOM 1 N ATRP ATOM 4 N CPHE ATOM 2 C ATRP ATOM 6 C CPHE ATOM 9 C BTRP ATOM 3 O ATRP ATOM 7 O CPHE ATOM 10 O BTRP ATOM 5 CA CPHE ATOM 8 CA BTRP TER """) check_wpf(hierarchy, {"interleaved_conf":2, "atoms_reset_serial_first_value": 13}, trailing, """\ ATOM 13 N ATRP ATOM 14 N CPHE ATOM 15 C ATRP ATOM 16 C CPHE ATOM 17 C BTRP ATOM 18 O ATRP ATOM 19 O CPHE ATOM 20 O BTRP ATOM 21 CA CPHE ATOM 22 CA BTRP TER """) assert list(hierarchy.atoms().extract_serial()) == [ " 13", " 15", " 18", " 14", " 21", " 16", " 19", " 22", " 17", " 20"] # hierarchy = pdb.input(source_info=None, lines=flex.split_lines("""\ MODEL 1 ATOM 1 N MET A 1 ATOM 2 CA MET A 1 ATOM 3 N GLY A 2 ATOM 4 CA GLY A 2 ENDMDL MODEL 2 ATOM 1 N MET A 1 ATOM 2 CA MET A 1 ATOM 3 N GLY A 2 ATOM 4 CA GLY A 2 ENDMDL """)).construct_hierarchy() hierarchy.atoms_reset_serial(interleaved_conf=0, first_value=10) assert list(hierarchy.atoms().extract_serial()) \ == [" 10", " 11", " 12", " 13"] * 2 hierarchy.atoms_reset_serial() assert list(hierarchy.atoms().extract_serial()) \ == [" 1", " 2", " 3", " 4"] * 2 def exercise_as_pdb_string(pdb_file_names, comprehensive): pdb_string = """\ HETATM 145 C21 DA7 3014 18.627 3.558 25.202 0.50 29.50 C ATOM 146 C8 ADA7 3015 9.021 -13.845 22.131 0.50 26.57 C """ pdb_inp = pdb.input(source_info=None, lines=flex.split_lines(pdb_string)) hierarchy = pdb_inp.construct_hierarchy(sort_atoms=False) check_wpf(hierarchy, expected=pdb_string) rem = "REMARK EXERCISE" # XXX Yes, pdb_inp and hierarchy are not consistent in terms of TER # records. It looks like a minor issue nowadays. hierarchy is compliant # with current PDB policy on TER. If pdb_inp is absolutely needed to # comply too, welcome to figure out how to modify # iotbx/pdb/construct_hierarchy.cpp: input_atoms_with_labels_generator::run with open("tmp_tst_hierarchy.pdb", "w") as f: print(rem, file=f) pdb_inp.write_pdb_file( file_name="tmp_tst_hierarchy.pdb", open_append=True, append_end=True) with open("tmp_tst_hierarchy.pdb") as f: lines = f.read() assert not show_diff(lines, rem+"\n"+pdb_string+"TER\nEND\n") with open("tmp_tst_hierarchy.pdb", "w") as f: print(rem, file=f) hierarchy.write_pdb_file( file_name="tmp_tst_hierarchy.pdb", open_append=True, append_end=True) with open("tmp_tst_hierarchy.pdb") as f: lines = f.read() assert not show_diff(lines, rem+"\n"+pdb_string+"END\n") check_wpf( hierarchy, kwargs={"crystal_symmetry": (2,3,4,80,90,100), "cryst1_z": 5}, expected="""\ CRYST1 2.000 3.000 4.000 80.00 90.00 100.00 P 1 5 SCALE1 0.500000 0.088163 -0.015793 0.00000 SCALE2 0.000000 0.338476 -0.060632 0.00000 SCALE3 0.000000 0.000000 0.253979 0.00000 """ + pdb_string) check_wpf( hierarchy, kwargs={"cryst1_z": 7, "write_scale_records": False}, expected="""\ CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 7 """ + pdb_string) # XXX see comment on L 4898 with open("tmp_tst_hierarchy.pdb", "w") as f: print(rem, file=f) pdb_inp.write_pdb_file( file_name="tmp_tst_hierarchy.pdb", cryst1_z="", write_scale_records=False, open_append=True) with open("tmp_tst_hierarchy.pdb") as f: lines = f.read() assert not show_diff(lines, rem + """ CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 """ + pdb_string+"TER\n") with open("tmp_tst_hierarchy.pdb", "w") as f: print(rem, file=f) hierarchy.write_pdb_file( file_name="tmp_tst_hierarchy.pdb", cryst1_z="", write_scale_records=False, open_append=True) with open("tmp_tst_hierarchy.pdb") as f: lines = f.read() assert not show_diff(lines, rem + """ CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 """ + pdb_string) # # only pdb entry (as of 2008 Mar 26) for which # s1 = h1.as_pdb_string(interleaved_conf=1) # s2 = h2.as_pdb_string(interleaved_conf=1) # leads to s1 != s2 i1 = pdb.input(source_info=None, lines=flex.split_lines("""\ HEADER TRANSPORT PROTEIN 21-AUG-07 2V93 ATOM 1549 O ACYS A 211 24.080 12.057 26.978 0.95 0.00 O ATOM 1550 SG ACYS A 211 24.960 15.526 27.230 0.16 0.00 S ATOM 1551 SG BCYS A 211 24.418 16.196 28.728 0.16 0.00 S ATOM 1552 N CCYS A 211 12.649 13.688 18.306 0.05 0.00 N ATOM 1553 CA CCYS A 211 12.104 13.010 17.135 0.05 0.00 C ATOM 1554 C CCYS A 211 13.148 12.135 16.481 0.05 0.00 C ATOM 1555 O CCYS A 211 12.770 11.031 16.051 0.05 0.00 O ATOM 1556 CB CCYS A 211 11.540 14.072 16.172 0.05 0.00 C ATOM 1557 SG CCYS A 211 24.361 15.163 26.341 0.16 0.00 S """)) h1 = i1.construct_hierarchy(sort_atoms=False) s1 = h1.as_pdb_string(interleaved_conf=1) assert not show_diff(s1, """\ ATOM 1549 O ACYS A 211 24.080 12.057 26.978 0.95 0.00 O ATOM 1555 O CCYS A 211 12.770 11.031 16.051 0.05 0.00 O ATOM 1550 SG ACYS A 211 24.960 15.526 27.230 0.16 0.00 S ATOM 1551 SG BCYS A 211 24.418 16.196 28.728 0.16 0.00 S ATOM 1557 SG CCYS A 211 24.361 15.163 26.341 0.16 0.00 S ATOM 1552 N CCYS A 211 12.649 13.688 18.306 0.05 0.00 N ATOM 1553 CA CCYS A 211 12.104 13.010 17.135 0.05 0.00 C ATOM 1554 C CCYS A 211 13.148 12.135 16.481 0.05 0.00 C ATOM 1556 CB CCYS A 211 11.540 14.072 16.172 0.05 0.00 C TER """) i2 = pdb.input(source_info=None, lines=flex.split_lines(s1)) h2 = i2.construct_hierarchy(sort_atoms=False) s2 = h2.as_pdb_string(interleaved_conf=1) assert not show_diff(s2, """\ ATOM 1549 O ACYS A 211 24.080 12.057 26.978 0.95 0.00 O ATOM 1555 O CCYS A 211 12.770 11.031 16.051 0.05 0.00 O ATOM 1550 SG ACYS A 211 24.960 15.526 27.230 0.16 0.00 S ATOM 1557 SG CCYS A 211 24.361 15.163 26.341 0.16 0.00 S ATOM 1551 SG BCYS A 211 24.418 16.196 28.728 0.16 0.00 S ATOM 1552 N CCYS A 211 12.649 13.688 18.306 0.05 0.00 N ATOM 1553 CA CCYS A 211 12.104 13.010 17.135 0.05 0.00 C ATOM 1554 C CCYS A 211 13.148 12.135 16.481 0.05 0.00 C ATOM 1556 CB CCYS A 211 11.540 14.072 16.172 0.05 0.00 C TER """) assert h1.is_similar_hierarchy(other=h2) assert h2.is_similar_hierarchy(other=h1) # with open("tmp_tst_hierarchy.pdb", "w") as f: f.write("""\ CRYST1 2.000 3.000 4.000 90.00 80.00 90.00 P 2 5 ATOM 0 S SO4 0 3.302 8.419 8.560 1.00 10.00 S ATOM 1 O1 SO4 0 3.497 8.295 7.118 1.00 10.00 O ATOM 2 O2 ASO4 0 3.098 7.095 9.140 0.80 10.00 O ATOM 3 O2 BSO4 0 3.498 7.495 9.440 0.20 10.00 O ATOM 4 O3 SO4 0 4.481 9.037 9.159 1.00 10.00 O ATOM 5 O4 SO4 0 2.131 9.251 8.823 1.00 10.00 O """) pdb.rewrite_normalized( input_file_name="tmp_tst_hierarchy.pdb", output_file_name="tmp_norm.pdb") with open("tmp_norm.pdb") as f: lines = f.read() assert not show_diff(lines, """\ CRYST1 2.000 3.000 4.000 90.00 80.00 90.00 P 1 2 1 SCALE1 0.500000 0.000000 -0.088163 0.00000 SCALE2 0.000000 0.333333 0.000000 0.00000 SCALE3 0.000000 0.000000 0.253857 0.00000 ATOM 1 O1 SO4 0 3.497 8.295 7.118 1.00 10.00 O ATOM 2 O3 SO4 0 4.481 9.037 9.159 1.00 10.00 O ATOM 3 O4 SO4 0 2.131 9.251 8.823 1.00 10.00 O ATOM 4 S SO4 0 3.302 8.419 8.560 1.00 10.00 S ATOM 5 O2 ASO4 0 3.098 7.095 9.140 0.80 10.00 O ATOM 6 O2 BSO4 0 3.498 7.495 9.440 0.20 10.00 O END """) pdb.rewrite_normalized( input_file_name="tmp_tst_hierarchy.pdb", output_file_name="tmp_norm.pdb", keep_original_crystallographic_section=True, keep_original_atom_serial=True) with open("tmp_norm.pdb") as f: lines = f.read() assert not show_diff(lines, """\ CRYST1 2.000 3.000 4.000 90.00 80.00 90.00 P 2 5 ATOM 1 O1 SO4 0 3.497 8.295 7.118 1.00 10.00 O ATOM 2 O3 SO4 0 4.481 9.037 9.159 1.00 10.00 O ATOM 3 O4 SO4 0 2.131 9.251 8.823 1.00 10.00 O ATOM 4 S SO4 0 3.302 8.419 8.560 1.00 10.00 S ATOM 5 O2 ASO4 0 3.098 7.095 9.140 0.80 10.00 O ATOM 6 O2 BSO4 0 3.498 7.495 9.440 0.20 10.00 O END """) # if (pdb_file_names is None): print("Skipping exercise_as_pdb_string(): input files not available") return prev_file_name = None for file_name in pdb_file_names: if (not comprehensive and random.random() > 0.05): continue pdb_inp_1 = pdb.input(file_name=file_name) hierarchy_1 = pdb_inp_1.construct_hierarchy() pdb_str_1 = hierarchy_1.as_pdb_string(append_end=False) pdb_inp_2 = pdb.input( source_info=None, lines=flex.split_lines(pdb_str_1)) hierarchy_2 = pdb_inp_2.construct_hierarchy() check_wpf( hierarchy=hierarchy_2, kwargs={"append_end": True}, expected=pdb_str_1+"END\n") assert hierarchy_1.is_similar_hierarchy(other=hierarchy_2) assert hierarchy_2.is_similar_hierarchy(other=hierarchy_1) if (prev_file_name is not None): if ( hierarchy_1.is_similar_hierarchy(other=prev_hierarchy) or prev_hierarchy.is_similar_hierarchy(other=hierarchy_1)): # some files are known to be similar p = os.path.basename(prev_file_name) c = os.path.basename( file_name) if ( p[:3] != c[:3] and (len(p) < 15 or len(c) < 15 or p[-12:] != c[-12:])): print("WARNING: similar hierarchies:") print(" ", show_string(prev_file_name)) print(" ", show_string(file_name)) prev_file_name = file_name prev_pdb_str = pdb_str_1 prev_hierarchy = hierarchy_1 # awls = [] for obj in [pdb_inp_2, hierarchy_2]: sio = StringIO() for awl in obj.atoms_with_labels(): print(awl.format_atom_record_group(), \ int(awl.is_first_in_chain), \ int(awl.is_first_after_break), \ awl.model_id, file=sio) awls.append(sio.getvalue()) assert not show_diff(*awls), file_name def exercise_atom_with_labels(): awl = pdb.hierarchy.atom_with_labels() assert not show_diff(awl.format_atom_record(), """\ ATOM 0.000 0.000 0.000 0.00 0.00""") assert not show_diff(awl.format_atom_record(replace_floats_with="#"), """\ ATOM # """) assert not show_diff(awl.format_atom_record_group(), """\ ATOM 0.000 0.000 0.000 0.00 0.00""") assert awl.serial == "" assert awl.name == "" assert awl.model_id == "" assert awl.chain_id == "" assert awl.resseq == "" assert awl.icode == "" assert awl.altloc == "" assert awl.resname == "" assert not awl.is_first_in_chain assert not awl.is_first_after_break awlc = awl.detached_copy() awl.serial = "12345" assert awlc.serial == "" awl.name = "NaMe" awl.model_id = "MoDl" assert awl.model_id == "MoDl" assert awlc.model_id == "" awl.chain_id = "Ch" awl.resseq = "ABCD" assert awl.resseq_as_int() == 24701 awl.icode = "I" assert awl.resid() == "ABCDI" awl.altloc = "l" awl.resname = "rNm" awl.is_first_in_chain = True assert awl.is_first_in_chain awl.is_first_after_break = True assert awl.is_first_after_break assert not show_diff(awl.format_atom_record_group(), """\ ATOM 12345 NaMelrNmChABCDI 0.000 0.000 0.000 0.00 0.00""") assert not show_diff(awl.format_atom_record(), """\ ATOM 12345 NaMelrNmChABCDI 0.000 0.000 0.000 0.00 0.00""") assert not show_diff(awl.quote(), '''\ "ATOM 12345 NaMelrNmChABCDI.*. "''') assert not show_diff(awl.quote(full=True), '''\ "ATOM 12345 NaMelrNmChABCDI 0.000 0.000 0.000 0.00 0.00"''') awl.sigxyz = (0.1,0.2,0.3) awl.uij = (1,2,3,0.1,0.2,0.3) awl.siguij = (3,1,2,0.3,0.1,0.2) assert not show_diff(awl.format_sigatm_record(), """\ SIGATM12345 NaMelrNmChABCDI 0.100 0.200 0.300 0.00 0.00""") assert not show_diff(awl.format_anisou_record(), """\ ANISOU12345 NaMelrNmChABCDI 10000 20000 30000 1000 2000 3000""") if (pdb.hierarchy.atom.has_siguij()): assert not show_diff(awl.format_siguij_record(), """\ SIGUIJ12345 NaMelrNmChABCDI 30000 10000 20000 3000 1000 2000""") assert not show_diff(awl.format_atom_record_group(), """\ ATOM 12345 NaMelrNmChABCDI 0.000 0.000 0.000 0.00 0.00 SIGATM12345 NaMelrNmChABCDI 0.100 0.200 0.300 0.00 0.00 ANISOU12345 NaMelrNmChABCDI 10000 20000 30000 1000 2000 3000 SIGUIJ12345 NaMelrNmChABCDI 30000 10000 20000 3000 1000 2000""") else: assert not show_diff(awl.format_siguij_record(), """\ SIGUIJ12345 NaMelrNmChABCDI -10000 -10000 -10000 -10000 -10000 -10000""") assert not show_diff(awl.format_atom_record_group(), """\ ATOM 12345 NaMelrNmChABCDI 0.000 0.000 0.000 0.00 0.00 SIGATM12345 NaMelrNmChABCDI 0.100 0.200 0.300 0.00 0.00 ANISOU12345 NaMelrNmChABCDI 10000 20000 30000 1000 2000 3000""") assert not show_diff( awl.format_atom_record_group(sigatm=False, anisou=False, siguij=False), """\ ATOM 12345 NaMelrNmChABCDI 0.000 0.000 0.000 0.00 0.00""") # assert not show_diff(awl.id_str(), 'model="MoDl" pdb="NaMelrNmChABCDI"') assert not show_diff(awl.id_str(pdbres=True), 'model="MoDl" pdbres="rNmChABCDI"') awl.segid = "sEgI" assert not show_diff(awl.id_str(), 'model="MoDl" pdb="NaMelrNmChABCDI" segid="sEgI"') assert not show_diff(awl.id_str(suppress_segid=True), 'model="MoDl" pdb="NaMelrNmChABCDI"') assert not show_diff(awl.id_str(pdbres=True), 'model="MoDl" pdbres="rNmChABCDI" segid="sEgI"') awl.model_id = "" assert not show_diff(awl.id_str(suppress_segid=False), 'pdb="NaMelrNmChABCDI" segid="sEgI"') assert not show_diff(awl.id_str(pdbres=True), 'pdbres="rNmChABCDI" segid="sEgI"') assert not show_diff(awl.id_str(pdbres=True, suppress_segid=True), 'pdbres="rNmChABCDI"') awl.segid = " " assert not show_diff(awl.id_str(), 'pdb="NaMelrNmChABCDI"') assert not show_diff(awl.id_str(pdbres=True), 'pdbres="rNmChABCDI"') # a = pdb.hierarchy.atom() a.serial = " 1A" try: a.serial_as_int() except (RuntimeError, ValueError) as e: assert not show_diff(str(e), 'invalid atom serial number: " 1A"') else: raise Exception_expected # awl.serial = " 1A" try: awl.serial_as_int() except (RuntimeError, ValueError) as e: assert not show_diff(str(e), """\ invalid atom serial number: ATOM 1A NaMelrNmChABCDI 0.000 0.000 0.000 0.00 0.00 ^^^^^""") else: raise Exception_expected # awl.resseq = " 18A" try: awl.resseq_as_int() except (RuntimeError, ValueError) as e: assert not show_diff(str(e), """\ invalid residue sequence number: ATOM 1A NaMelrNmCh 18AI 0.000 0.000 0.000 0.00 0.00 ^^^^""") else: raise Exception_expected # h = pdb.input(source_info=None, lines=flex.split_lines("""\ ATOM 1B """)).construct_hierarchy(sort_atoms=False) for r in [h.only_residue_group(), h.only_residue()]: try: r.resseq_as_int() except (RuntimeError, ValueError) as e: assert not show_diff(str(e), """\ invalid residue sequence number: ATOM 1B 0.000 0.000 0.000 0.00 0.00 ^^^^""") else: raise Exception_expected # ch = pdb.hierarchy.chain(id="C") ch.append_residue_group(pdb.hierarchy.residue_group(resseq=" 1C")) ch.residue_groups()[0].append_atom_group(pdb.hierarchy.atom_group()) for r in[ch.only_residue_group(), ch.only_conformer().only_residue()]: try: r.resseq_as_int() except (RuntimeError, ValueError) as e: assert not show_diff(str(e), 'invalid residue sequence number: " 1C"') else: raise Exception_expected # pdb_inp = pdb.input(source_info=None, lines=flex.split_lines("""\ MODEL 0 ATOM 1 C MET A 1 ATOM 2 CA AMET A 1 BREAK ATOM 3 N GLY A 2 ATOM 4 CA AGLY A 2 ENDMDL MODEL 1 ATOM 1 N MET A 1 ATOM 2 CA AMET A 1 ATOM 3 N ALA B 2 ATOM 4 CA AALA B 2 ENDMDL """)) hierarchy = pdb_inp.construct_hierarchy() for obj in [hierarchy, pdb_inp]: for fmt in ["format_atom_record_group", "format_atom_record_group"]: sio = StringIO() for awl in obj.atoms_with_labels(): assert awl.parent(optional=False) is not None awlc = awl.detached_copy() assert awlc.parent() is None try: awlc.parent(optional=False) except RuntimeError as e: assert not show_diff(str(e), "atom has no parent atom_group") else: raise Exception_expected print(getattr(awl, fmt)(), \ int(awl.is_first_in_chain), \ int(awl.is_first_after_break), \ awl.model_id, file=sio) assert not show_diff(sio.getvalue(), """\ ATOM 1 C MET A 1 0.000 0.000 0.000 0.00 0.00 1 0 0 ATOM 2 CA AMET A 1 0.000 0.000 0.000 0.00 0.00 0 0 0 ATOM 3 N GLY A 2 0.000 0.000 0.000 0.00 0.00 0 1 0 ATOM 4 CA AGLY A 2 0.000 0.000 0.000 0.00 0.00 0 0 0 ATOM 1 N MET A 1 0.000 0.000 0.000 0.00 0.00 1 0 1 ATOM 2 CA AMET A 1 0.000 0.000 0.000 0.00 0.00 0 0 1 ATOM 3 N ALA B 2 0.000 0.000 0.000 0.00 0.00 1 0 1 ATOM 4 CA AALA B 2 0.000 0.000 0.000 0.00 0.00 0 0 1 """) # expected = """\ MODEL 0 ATOM 1 C MET A 1 0.000 0.000 0.000 0.00 0.00 ATOM 2 CA AMET A 1 0.000 0.000 0.000 0.00 0.00 BREAK ATOM 3 N GLY A 2 0.000 0.000 0.000 0.00 0.00 ATOM 4 CA AGLY A 2 0.000 0.000 0.000 0.00 0.00 TER ENDMDL MODEL 1 ATOM 1 N MET A 1 0.000 0.000 0.000 0.00 0.00 ATOM 2 CA AMET A 1 0.000 0.000 0.000 0.00 0.00 TER ATOM 3 N ALA B 2 0.000 0.000 0.000 0.00 0.00 ATOM 4 CA AALA B 2 0.000 0.000 0.000 0.00 0.00 TER ENDMDL """ for append_end in [False, True]: if (append_end): expected += "END\n" assert not show_diff(pdb_inp.as_pdb_string(append_end=append_end),expected) pdb_inp.write_pdb_file(file_name="tmp_tst_hierarchy.pdb", append_end=append_end) with open("tmp_tst_hierarchy.pdb") as f: lines = f.read() assert not show_diff(lines, expected) # lines = flex.split_lines("""\ MODEL SKDI HETATMB1234 NaMeLResChUvwqI 1.300 2.100 3.200 0.40 4.80 sEgIElcH ENDMDL """) pdb_inp = pdb.input(source_info=None, lines=lines) hierarchy = pdb_inp.construct_hierarchy(sort_atoms=False) awl = hierarchy.atoms()[0].fetch_labels() assert not show_diff(awl.format_atom_record(), lines[1]) assert awl.model_id == "SKDI" assert not awl.is_first_in_chain assert not awl.is_first_after_break awl_pkl = pickle.dumps(awl) awl_unpkl = pickle.loads(awl_pkl) assert not show_diff(awl.format_atom_record(), awl_unpkl.format_atom_record()) def exercise_transfer_chains_from_other(): atoms_x = """\ ATOM 1 X1 A ATOM 2 X2 A ATOM 3 X1 B ATOM 4 X2 B""" pdb_inp = pdb.input(source_info=None, lines=flex.split_lines("""\ MODEL 1 %s ENDMDL MODEL 2 %s ENDMDL """ % (atoms_x, atoms_x.replace("X","Y")))) hierarchy = pdb_inp.construct_hierarchy() models = hierarchy.models() assert [md.chains_size() for md in models] == [2, 2] models[0].transfer_chains_from_other(other=models[1]) assert [md.chains_size() for md in models] == [4, 0] hierarchy.remove_model(model=models[1]) trailing = " 0.000 0.000 0.000 0.00 0.00" check_wpf(hierarchy, trailing=trailing, expected="""\ ATOM 1 X1 A ATOM 2 X2 A ATOM 3 X1 B ATOM 4 X2 B ATOM 1 Y1 A ATOM 2 Y2 A ATOM 3 Y1 B ATOM 4 Y2 B """) # for suffixes in [Auto, "FG"]: roots = [ pdb.input(source_info=None, lines=flex.split_lines(lines)) .construct_hierarchy() for lines in [atoms_x, atoms_x.replace("X","Y")]] joined = pdb.hierarchy.join_roots( roots=roots, chain_id_suffixes=suffixes) if (suffixes is Auto): f,g = "1", "2" else: f,g = "F", "G" trailing = " 0.000 0.000 0.000 0.00 0.00" check_wpf(joined, trailing=trailing, expected="""\ ATOM 1 X1 A%s ATOM 2 X2 A%s ATOM 3 X1 B%s ATOM 4 X2 B%s ATOM 1 Y1 A%s ATOM 2 Y2 A%s ATOM 3 Y1 B%s ATOM 4 Y2 B%s """ % (f,f,f,f,g,g,g,g)) # roots = [pdb_inp.construct_hierarchy() for pdb_inp in [ pdb.input(source_info=None, lines=flex.split_lines("""\ MODEL 1 %s ENDMDL MODEL 1 %s ENDMDL MODEL 1 %s ENDMDL """ % (atoms_x, atoms_x.replace("X","Y"), atoms_x.replace("X","Z")))), pdb.input(source_info=None, lines=flex.split_lines("""\ MODEL 3 %s ENDMDL MODEL 3 %s ENDMDL """ % (atoms_x.replace("X","P"), atoms_x.replace("X","Q"))))]] joined = pdb.hierarchy.join_roots(roots=roots) trailing = " 0.000 0.000 0.000 0.00 0.00" check_wpf(joined, trailing=trailing, expected="""\ MODEL 1 ATOM 1 X1 A1 ATOM 2 X2 A1 ATOM 3 X1 B1 ATOM 4 X2 B1 ATOM 1 P1 A2 ATOM 2 P2 A2 ATOM 3 P1 B2 ATOM 4 P2 B2 ENDMDL MODEL 2 ATOM 1 Y1 A1 ATOM 2 Y2 A1 ATOM 3 Y1 B1 ATOM 4 Y2 B1 ATOM 1 Q1 A2 ATOM 2 Q2 A2 ATOM 3 Q1 B2 ATOM 4 Q2 B2 ENDMDL MODEL 3 ATOM 1 Z1 A1 ATOM 2 Z2 A1 ATOM 3 Z1 B1 ATOM 4 Z2 B1 ENDMDL """) def exercise_root_select(n_trials=100): h_all = pdb.input(source_info=None, lines=flex.split_lines("""\ MODEL 1 ATOM 1 ATOM 2 ATOM 3 ATOM 4 ATOM 5 ATOM 6 ATOM 7 ATOM 8 ENDMDL MODEL 2 ATOM 11 ATOM 12 ATOM 13 ATOM 14 ATOM 15 ATOM 16 ATOM 17 ATOM 18 ENDMDL """)).construct_hierarchy(sort_atoms=False) try: h_all.select(atom_selection=flex.bool()) except (ValueError, RuntimeError) as e: assert str(e) == "atom_selection array too short." else: raise Exception_expected try: h_all.select(atom_selection=flex.bool(17, False)) except (ValueError, RuntimeError) as e: assert str(e) == "atom_selection array too large." else: raise Exception_expected try: h_all.select(atom_selection=flex.size_t([1,0])) except (ValueError, RuntimeError) as e: assert str(e) == "atom_selection indices not in strictly ascending order." else: raise Exception_expected try: h_all.select(atom_selection=flex.size_t([16])) except (ValueError, RuntimeError) as e: assert str(e) \ == "atom_selection indices greater than or equal to number of atoms." else: raise Exception_expected for atom_selections in [[flex.bool(16, False), flex.bool()], [flex.size_t(), flex.size_t()]]: h_sel = h_all.select(atom_selection=atom_selections[0]) assert h_sel.models_size() == 0 assert h_sel.select(atom_selection=atom_selections[1]).models_size() == 0 try: h_sel.select(atom_selection=flex.bool(1, False)) except (ValueError, RuntimeError) as e: assert str(e) == "atom_selection array too large." else: raise Exception_expected try: h_sel.select(atom_selection=flex.size_t([0])) except (ValueError, RuntimeError) as e: assert str(e) \ == "atom_selection indices greater than or equal to number of atoms." else: raise Exception_expected for atom_selection in [flex.bool(16, True), flex.size_t_range(16)]: h_sel = h_all.select(atom_selection=atom_selection) assert h_sel.is_similar_hierarchy(other=h_all) assert h_all.is_similar_hierarchy(other=h_sel) for atom_selection in [flex.bool([True]*8+[False]*8), flex.size_t_range(8)]: h_sel = h_all.select(atom_selection=atom_selection) assert h_sel.models_size() == 1 assert h_sel.only_model().is_identical_hierarchy( other=h_all.models()[0]) assert not h_sel.only_model().is_identical_hierarchy( other=h_all.models()[1]) for atom_selection in [flex.bool([False]*8+[True]*8), flex.size_t_range(8,16)]: h_sel = h_all.select(atom_selection=atom_selection) assert h_sel.models_size() == 1 assert not h_sel.only_model().is_identical_hierarchy( other=h_all.models()[0]) assert h_sel.only_model().is_identical_hierarchy( other=h_all.models()[1]) for atom_selection in [flex.bool([False,True]*8), flex.size_t_range(1,16,2)]: h_sel = h_all.select(atom_selection=atom_selection) assert [a.serial.lstrip() for a in h_sel.atoms()] \ == ["2", "4", "6", "8", "12", "14", "16", "18"] for atom_selection in [flex.bool([True,False]*8), flex.size_t_range(0,16,2)]: h_sel = h_all.select(atom_selection=atom_selection) assert [a.serial.lstrip() for a in h_sel.atoms()] \ == ["1", "3", "5", "7", "11", "13", "15", "17"] a_all = h_all.atoms() a_all.reset_i_seq() sentinel = a_all.reset_tmp(first_value=1, increment=0) for copy_atoms in [False, True]: for i_trial in range(n_trials): sel = flex.random_bool(size=16, threshold=0.5) a_sel = a_all.select(sel) h_sel = h_all.select(sel, copy_atoms=copy_atoms) assert h_sel.atoms_size() == sel.count(True) def check(h_sel): for a,b in zip(a_sel, h_sel.atoms()): assert a.serial == b.serial if (copy_atoms): assert a.memory_id() != b.memory_id() assert a.tmp == 1 assert b.tmp == 0 assert b.i_seq == 0 else: assert a.memory_id() == b.memory_id() check(h_sel) h_isel = h_all.select(sel.iselection(), copy_atoms=copy_atoms) check(h_isel) assert h_isel.is_similar_hierarchy(h_sel) assert h_sel.is_similar_hierarchy(h_isel) assert h_sel.as_pdb_string() == h_isel.as_pdb_string() def exercise_root_altloc_indices(n_trials=10): lines = flex.split_lines("""\ ATOM 1 N ATOM 2 CB A ATOM 3 CA ATOM 4 CB B ATOM 5 CG ATOM 6 CG A ATOM 7 CD A ATOM 8 C ATOM 9 CD B ATOM 10 O """) for i_trial in range(n_trials): pdb_inp = pdb.input( source_info=None, lines=lines.select(flex.random_permutation(size=lines.size()))) hierarchy = pdb_inp.construct_hierarchy(sort_atoms=False) atoms = hierarchy.atoms() ai = dict([(k,sorted([int(atoms[i].serial) for i in v])) for k,v in hierarchy.altloc_indices().items()]) assert ai == { "": [1, 3, 8, 10], " ": [5], "A": [2, 6, 7], "B": [4, 9]} def exercise_root_pickling(): # XXX fp, fdp? pdb_inp = pdb.input(source_info=None, lines="""\ MODEL 1 ATOM 1 N MET A 1 6.215 22.789 24.067 1.00 0.00 N ATOM 2 CA MET A 1 6.963 22.789 22.822 1.00 0.00 C BREAK HETATM 3 C MET A 2 7.478 21.387 22.491 1.00 0.00 C ATOM 4 O MET A 2 8.406 20.895 23.132 1.00 0.00 O ENDMDL MODEL 3 HETATM 9 2H3 MPR B 5 16.388 0.289 6.613 1.00 0.08 SIGATM 9 2H3 MPR B 5 0.155 0.175 0.155 0.00 0.05 ANISOU 9 2H3 MPR B 5 848 848 848 0 0 0 SIGUIJ 9 2H3 MPR B 5 510 510 510 0 0 0 TER ATOM 10 N CYSCH 6 14.270 2.464 3.364 1.00 0.07 SIGATM 10 N CYSCH 6 0.012 0.012 0.011 0.00 0.00 ANISOU 10 N CYSCH 6 788 626 677 -344 621 -232 SIGUIJ 10 N CYSCH 6 3 13 4 11 6 13 TER ENDMDL """) hierarchy = pdb_inp.construct_hierarchy() hierarchy.info.append("a") hierarchy.info.append("b") s = pickle.dumps(hierarchy, 1) l = pickle.loads(s) assert not show_diff("\n".join(l.info), "\n".join(hierarchy.info)) assert not show_diff(l.as_pdb_string(), hierarchy.as_pdb_string()) def exercise_residue_pickling(): # XXX fp, fdp? pdb_inp = pdb.input(source_info=None, lines="""\ ATOM 1 N GLY A 1 -9.009 4.612 6.102 1.00 16.77 N ATOM 2 CA GLY A 1 -9.052 4.207 4.651 1.00 16.57 C ANISOU 2 CA GLY A 1 788 626 677 -344 621 -232 C ATOM 3 C GLY A 1 -8.015 3.140 4.419 1.00 16.16 C ATOM 4 O GLY A 1 -7.523 2.521 5.381 1.00 16.78 O ATOM 5 N ASN A 2 -7.656 2.923 3.155 1.00 15.02 N ATOM 6 CA ASN A 2 -6.522 2.038 2.831 1.00 14.10 C ATOM 7 C ASN A 2 -5.241 2.537 3.427 1.00 13.13 C ATOM 8 O ASN A 2 -4.978 3.742 3.426 1.00 11.91 O ATOM 9 N ASN A 3 -4.438 1.590 3.905 1.00 12.26 N SIGATM 9 N ASN A 3 0.012 0.012 0.011 0.00 0.00 N ATOM 10 CA ASN A 3 -3.193 1.904 4.589 1.00 11.74 C ATOM 11 C ASN A 3 -1.955 1.332 3.895 1.00 11.10 C ATOM 12 O ASN A 3 -1.872 0.119 3.648 1.00 10.42 O """) hierarchy = pdb_inp.construct_hierarchy() hierarchy.atoms().reset_i_seq() conformer = hierarchy.only_conformer() for residue in conformer.residues(): eps = hierarchy.select(residue.atoms().extract_i_seq()).as_pdb_string() rsc = residue.standalone_copy() assert not show_diff(rsc.root().as_pdb_string(), eps) for rp in [residue, rsc]: for i_pass in range(2): s = pickle.dumps(rp, 1) l = pickle.loads(s) assert not show_diff(l.root().as_pdb_string(), eps) rp = l def exercise_hierarchy_input(): pdb_obj = pdb.hierarchy.input(pdb_string=pdb_2izq_220) i_atoms = pdb_obj.input.atoms() h_atoms = pdb_obj.hierarchy.atoms() assert i_atoms.size() == 70 assert h_atoms.size() == 70 h_i_perm = pdb_obj.hierarchy_to_input_atom_permutation() i_h_perm = pdb_obj.input_to_hierarchy_atom_permutation() def check(atoms, atoms_perm): for a,ap in zip(atoms, atoms_perm): assert ap.memory_id() == a.memory_id() check(h_atoms.select(h_i_perm), i_atoms) check(i_atoms.select(i_h_perm), h_atoms) def exercise_other(): # XXX Nat's utility functions pdb_inp = pdb.input(source_info=None, lines="""\ CRYST1 2.000 3.000 4.000 90.00 80.00 90.00 P 2 5 ATOM 0 S SO4 0 3.302 8.419 8.560 1.00 10.00 S ANISOU 0 S SO4 0 1000 2000 3000 400 -500 600 ATOM 1 O1 SO4 0 3.497 8.295 7.118 1.00 10.00 O ATOM 4 O3 SO4 0 4.481 9.037 9.159 1.00 20.00 O ATOM 5 O4 SO4 0 2.131 9.251 8.823 1.00 30.00 O ATOM 2 O2 ASO4 0 3.098 7.095 9.140 0.80 40.00 O ATOM 3 O2 BSO4 0 3.498 7.495 9.440 0.20 50.00 O TER END """) hierarchy = pdb_inp.construct_hierarchy(sort_atoms=False) assert hierarchy.first_resseq_as_int() == 0 assert hierarchy.last_resseq_as_int() == 0 xray_structure = hierarchy.extract_xray_structure() assert xray_structure.sites_cart().size() == hierarchy.atoms().size() xray_structure.scale_adps(2.0) ag = hierarchy.only_model().only_chain().residue_groups()[0].atom_groups()[0] assert (ag.id_str() == ' SO4 0 ') atoms = hierarchy.atoms() atoms.set_adps_from_scatterers(xray_structure.scatterers(), xray_structure.unit_cell()) assert approx_equal(atoms.extract_uij(), [(0.2, 0.4, 0.6, 0.08, -0.1, 0.12), (-1,-1,-1,-1,-1,-1), (-1,-1,-1,-1,-1,-1), (-1,-1,-1,-1,-1,-1), (-1,-1,-1,-1,-1,-1), (-1,-1,-1,-1,-1,-1)]) assert approx_equal(atoms.extract_b(), [31.5827341, 20.0, 40.0, 60.0, 80.0, 100.0]) xray_structure.convert_to_isotropic() atoms.set_adps_from_scatterers(xray_structure.scatterers(), xray_structure.unit_cell()) assert approx_equal(atoms.extract_uij(), [(-1,-1,-1,-1,-1,-1)]*6) assert approx_equal(atoms.extract_b(), [31.5827341, 20.0, 40.0, 60.0, 80.0, 100.0]) pdb_inp = pdb.input(source_info=None, lines="""\ ATOM 1 N GLY A 1 -9.009 4.612 6.102 1.00 16.77 N ATOM 2 CA GLY A 1 -9.052 4.207 4.651 1.00 16.57 C ANISOU 2 CA GLY A 1 788 626 677 -344 621 -232 C ATOM 3 C GLY A 1 -8.015 3.140 4.419 1.00 16.16 C ATOM 4 O GLY A 1 -7.523 2.521 5.381 1.00 16.78 O ATOM 5 N ASN B 2 -7.656 2.923 3.155 1.00 15.02 N ATOM 6 CA ASN B 2 -6.522 2.038 2.831 1.00 14.10 C ATOM 7 C ASN B 2 -5.241 2.537 3.427 1.00 13.13 C ATOM 8 O ASN B 2 -4.978 3.742 3.426 1.00 11.91 O ATOM 9 N ASN B 3 -4.438 1.590 3.905 1.00 12.26 N ATOM 10 CA ASN B 3 -3.193 1.904 4.589 1.00 11.74 C ATOM 11 C ASN B 3 -1.955 1.332 3.895 1.00 11.10 C ATOM 12 O ASN B 3 -1.872 0.119 3.648 1.00 10.42 O ATOM 0 S SO4 C 4 3.302 8.419 8.560 1.00 10.00 S ATOM 1 O1 SO4 C 4 3.497 8.295 7.118 1.00 10.00 O ATOM 4 O3 SO4 C 4 4.481 9.037 9.159 1.00 10.00 O ATOM 5 O4 SO4 C 4 2.131 9.251 8.823 1.00 10.00 O """) hierarchy = pdb_inp.construct_hierarchy(sort_atoms=False) assert hierarchy.first_resseq_as_int() == 1 assert hierarchy.last_resseq_as_int() == 4 pdb_inp_new = pdb.input(source_info=None, lines="""\ ATOM 5 N ASN B 2 -7.656 2.923 3.155 1.00 15.02 N ATOM 6 CA ASN B 2 -6.522 2.038 2.831 1.00 14.10 C ATOM 7 C ASN B 2 -5.241 2.537 3.427 1.00 13.13 C ATOM 8 O ASN B 2 -4.978 3.742 3.426 1.00 11.91 O ATOM 9 N AASN B 3 -4.438 1.590 3.905 1.00 12.26 N ATOM 10 CA AASN B 3 -3.193 1.904 4.589 1.00 11.74 C ATOM 11 C AASN B 3 -1.955 1.332 3.895 1.00 11.10 C ATOM 12 O AASN B 3 -1.872 0.119 3.648 1.00 10.42 O ATOM 9 N BASN B 3 -4.438 1.590 3.905 1.00 12.26 N ATOM 10 CA BASN B 3 -3.193 1.904 4.589 1.00 11.74 C ATOM 11 C BASN B 3 -1.955 1.332 3.895 1.00 11.10 C ATOM 12 O BASN B 3 -1.872 0.119 3.648 1.00 10.42 O """) h2 = pdb_inp_new.construct_hierarchy(sort_atoms=False) chain_b = h2.models()[0].chains()[0] partial_hierarchy = pdb.hierarchy.new_hierarchy_from_chain(chain_b) assert not show_diff(partial_hierarchy.as_pdb_string(), h2.as_pdb_string()) pdb.hierarchy.find_and_replace_chains(hierarchy, partial_hierarchy) assert not show_diff(hierarchy.as_pdb_string(), """\ ATOM 1 N GLY A 1 -9.009 4.612 6.102 1.00 16.77 N ATOM 2 CA GLY A 1 -9.052 4.207 4.651 1.00 16.57 C ANISOU 2 CA GLY A 1 788 626 677 -344 621 -232 C ATOM 3 C GLY A 1 -8.015 3.140 4.419 1.00 16.16 C ATOM 4 O GLY A 1 -7.523 2.521 5.381 1.00 16.78 O TER ATOM 5 N ASN B 2 -7.656 2.923 3.155 1.00 15.02 N ATOM 6 CA ASN B 2 -6.522 2.038 2.831 1.00 14.10 C ATOM 7 C ASN B 2 -5.241 2.537 3.427 1.00 13.13 C ATOM 8 O ASN B 2 -4.978 3.742 3.426 1.00 11.91 O ATOM 9 N AASN B 3 -4.438 1.590 3.905 1.00 12.26 N ATOM 10 CA AASN B 3 -3.193 1.904 4.589 1.00 11.74 C ATOM 11 C AASN B 3 -1.955 1.332 3.895 1.00 11.10 C ATOM 12 O AASN B 3 -1.872 0.119 3.648 1.00 10.42 O ATOM 9 N BASN B 3 -4.438 1.590 3.905 1.00 12.26 N ATOM 10 CA BASN B 3 -3.193 1.904 4.589 1.00 11.74 C ATOM 11 C BASN B 3 -1.955 1.332 3.895 1.00 11.10 C ATOM 12 O BASN B 3 -1.872 0.119 3.648 1.00 10.42 O TER ATOM 0 S SO4 C 4 3.302 8.419 8.560 1.00 10.00 S ATOM 1 O1 SO4 C 4 3.497 8.295 7.118 1.00 10.00 O ATOM 4 O3 SO4 C 4 4.481 9.037 9.159 1.00 10.00 O ATOM 5 O4 SO4 C 4 2.131 9.251 8.823 1.00 10.00 O """) # distance-based connectivity pdb_hierarchy = pdb.input(source_info=None, lines="""\ ATOM 1 C01 LIG A 1 -2.986 0.015 1.643 1.00 20.00 A C ATOM 2 N02 LIG A 1 -1.545 0.015 1.643 1.00 20.00 A N ATOM 3 C03 LIG A 1 -0.733 0.015 2.801 1.00 20.00 A C ATOM 4 N04 LIG A 1 0.593 0.015 2.395 1.00 20.00 A N ATOM 5 C05 LIG A 1 0.618 0.015 1.034 1.00 20.00 A C ATOM 6 N06 LIG A 1 1.758 0.015 0.102 1.00 20.00 A N ATOM 7 C07 LIG A 1 3.092 -0.060 0.694 1.00 20.00 A C ATOM 8 C08 LIG A 1 1.525 0.015 -1.360 1.00 20.00 A C ATOM 9 O09 LIG A 1 2.489 -0.024 -2.139 1.00 20.00 A O ATOM 10 N10 LIG A 1 0.158 0.015 -1.888 1.00 20.00 A N ATOM 11 C11 LIG A 1 -0.025 0.024 -3.330 1.00 20.00 A C ATOM 12 C12 LIG A 1 -0.986 0.015 -0.959 1.00 20.00 A C ATOM 13 O13 LIG A 1 -2.155 0.008 -1.408 1.00 20.00 A O ATOM 14 C14 LIG A 1 -0.733 0.015 0.565 1.00 20.00 A C ATOM 15 H011 LIG A 1 -3.346 0.016 2.662 1.00 20.00 A H ATOM 16 H012 LIG A 1 -3.347 0.896 1.133 1.00 20.00 A H ATOM 17 H013 LIG A 1 -3.347 -0.868 1.136 1.00 20.00 A H ATOM 18 H031 LIG A 1 -1.083 0.020 3.822 1.00 20.00 A H ATOM 19 H071 LIG A 1 3.184 -0.975 1.260 1.00 20.00 A H ATOM 20 H072 LIG A 1 3.245 0.785 1.348 1.00 20.00 A H ATOM 21 H073 LIG A 1 3.835 -0.047 -0.090 1.00 20.00 A H ATOM 22 H111 LIG A 1 0.508 0.861 -3.756 1.00 20.00 A H ATOM 23 H112 LIG A 1 -1.076 0.113 -3.560 1.00 20.00 A H ATOM 24 H113 LIG A 1 0.358 -0.896 -3.748 1.00 20.00 A H """).construct_hierarchy(sort_atoms=False) bonds = pdb_hierarchy.distance_based_simple_two_way_bond_sets() assert bonds.size() == pdb_hierarchy.atoms().size() #print list(bonds[0]) assert list(bonds[0]) == [1, 14, 15, 16] pdb_hierarchy = pdb.input(source_info=None, lines="""\ ATOM 1 C1 EOH 1 3.108 0.653 -8.526 1.00 0.00 C ATOM 2 C2 EOH 1 4.597 0.674 -8.132 1.00 0.00 C ATOM 3 1H1 EOH 1 2.815 -0.349 -8.761 1.00 0.00 H ATOM 4 2H1 EOH 1 2.517 1.015 -7.711 1.00 0.00 H ATOM 5 3H1 EOH 1 2.956 1.278 -9.381 1.00 0.00 H ATOM 6 1H2 AEOH 1 5.210 0.503 -9.017 1.00 0.00 H ATOM 7 2H2 AEOH 1 4.790 -0.110 -7.400 1.00 0.00 H ATOM 8 OH AEOH 1 4.922 1.945 -7.565 1.00 0.00 O ATOM 9 HH AEOH 1 5.850 1.958 -7.320 1.00 0.00 H ATOM 10 1H2 BEOH 1 5.198 0.305 -8.963 1.00 0.00 H ATOM 11 2H2 BEOH 1 4.751 0.037 -7.261 1.00 0.00 H ATOM 12 OH BEOH 1 4.988 2.012 -7.818 1.00 0.00 O ATOM 13 HH BEOH 1 5.916 2.025 -7.573 1.00 0.00 H """).construct_hierarchy(sort_atoms=False) pdb_hierarchy.atoms().reset_i_seq() bonds = pdb_hierarchy.distance_based_simple_two_way_bond_sets() assert (list(bonds[7]) == [1,8]) assert (list(bonds[10]) == [1]) assert (list(bonds[11]) == [1,12]) assert (list(bonds[12]) == [11]) pdb_file = libtbx.env.find_in_repositories( relative_path="phenix_regression/pdb/2hr0.pdb", test=os.path.isfile) if (pdb_file is not None): (n_res,n_frag,n_wat)=pdb.hierarchy.get_residue_and_fragment_count(pdb_file) assert (n_res == 1548) and (n_frag == 7) and (n_wat == 708) # pdb_hierarchy = pdb.input(source_info=None, lines="""\ HETATM 0 PA ANP A 1 27.977 39.209 67.441 1.00 26.15 P HETATM 1 O2A ANP A 1 28.552 39.588 68.829 1.00 27.12 O HETATM 2 MN MN B 1 28.911 38.079 64.440 1.00 24.79 Mn """).construct_hierarchy() bond_sets = pdb_hierarchy.distance_based_simple_two_way_bond_sets() assert [list(bond) for bond in bond_sets] == [[1], [0], []] # the following tests check order of xray scatterers vs. hierarchy atoms pdb_str = """\ ATOM 1 C1 EOH 1 3.108 0.653 -8.526 1.00 0.00 C ATOM 2 C2 EOH 1 4.597 0.674 -8.132 1.00 0.00 C ATOM 3 1H1 EOH 1 2.815 -0.349 -8.761 1.00 0.00 H ATOM 4 2H1 EOH 1 2.517 1.015 -7.711 1.00 0.00 H ATOM 5 3H1 EOH 1 2.956 1.278 -9.381 1.00 0.00 H ATOM 6 1H2 AEOH 1 5.210 0.503 -9.017 1.00 0.00 H ATOM 7 1H2 BEOH 1 5.198 0.305 -8.963 1.00 0.00 H ATOM 8 2H2 AEOH 1 4.790 -0.110 -7.400 1.00 0.00 H ATOM 9 2H2 BEOH 1 4.751 0.037 -7.261 1.00 0.00 H ATOM 10 OH AEOH 1 4.922 1.945 -7.565 1.00 0.00 O ATOM 11 OH BEOH 1 4.988 2.012 -7.818 1.00 0.00 O ATOM 12 HH AEOH 1 5.850 1.958 -7.320 1.00 0.00 H ATOM 13 HH BEOH 1 5.916 2.025 -7.573 1.00 0.00 H """ # This does not guaranteed pdb_in = pdb.hierarchy.input(pdb_string=pdb_str) xrs = pdb_in.xray_structure_simple() assert (xrs.sites_cart().size() == 13) # assert (approx_equal(xrs.sites_cart()[-3][-1], -7.261, eps=0.0001)) pdb_in = pdb.input(source_info=None, lines=pdb_str) hierarchy = pdb_in.construct_hierarchy(sort_atoms=False) xrs = hierarchy.extract_xray_structure( crystal_symmetry=pdb_in.crystal_symmetry()) assert (xrs.sites_cart().size() == 13) assert (approx_equal(xrs.sites_cart()[-3][-1], -7.261, eps=0.0001)) # sequence extraction pdb_hierarchy = pdb.input(source_info=None, lines="""\ ATOM 2 CA GLY A 3 -9.052 4.207 4.651 1.00 16.57 C ATOM 6 CA ASN A 4 -6.522 2.038 2.831 1.00 14.10 C ATOM 14 CA ASN A 5 -3.193 1.904 4.589 1.00 11.74 C ATOM 22 CA GLN A 6 0.384 1.888 3.199 1.00 10.53 C ATOM 31 CA GLN A 7 3.270 2.361 5.640 1.00 11.39 C ATOM 40 CA ASN A 8 6.831 2.310 4.318 1.00 12.30 C ATOM 48 CA TYR A 9 9.159 2.144 7.299 1.00 15.18 C """).construct_hierarchy() main_conf = pdb_hierarchy.models()[0].chains()[0].conformers()[0] assert main_conf.get_residue_names_and_classes() == ( ['GLY', 'ASN', 'ASN', 'GLN', 'GLN', 'ASN', 'TYR'], {'common_amino_acid': 7}) assert main_conf.as_sequence() == ['G', 'N', 'N', 'Q', 'Q', 'N', 'Y'] assert (main_conf.as_padded_sequence() == "XXGNNQQNY") # duplicate of tests above but for chain methods chain = pdb_hierarchy.models()[0].chains()[0] assert chain.get_residue_names_and_classes() == ( ['GLY', 'ASN', 'ASN', 'GLN', 'GLN', 'ASN', 'TYR'], {'common_amino_acid': 7}) assert chain.as_sequence() == ['G', 'N', 'N', 'Q', 'Q', 'N', 'Y'] dd = chain.as_dict_of_resseq_as_int_residue_names() keys = list(dd.keys()) keys.sort() values = [dd[key] for key in keys] assert [keys, values] == [[3, 4, 5, 6, 7, 8, 9], ['GLY', 'ASN', 'ASN', 'GLN', 'GLN', 'ASN', 'TYR']], [keys, values] assert chain.as_new_hierarchy().as_pdb_string().splitlines()[0].strip() == \ "ATOM 1 CA GLY A 3 -9.052 4.207 4.651 1.00 16.57 C" assert chain.as_new_hierarchy().as_pdb_string() == \ chain.as_new_hierarchy().as_model_manager(pdb_in.crystal_symmetry() ).get_hierarchy().as_pdb_string() assert chain.as_new_hierarchy().as_model_manager(pdb_in.crystal_symmetry() ).as_model_manager_each_chain()[0].get_hierarchy().as_pdb_string() == \ chain.as_new_hierarchy().as_pdb_string() assert chain.as_padded_sequence() == "XXGNNQQNY" assert (chain.is_protein()) and (not chain.is_na()) assert pdb_hierarchy.chain_types() == ['PROTEIN'] assert pdb_hierarchy.chain_type() == 'PROTEIN' assert pdb_hierarchy.contains_protein() assert not pdb_hierarchy.contains_nucleic_acid() assert not pdb_hierarchy.contains_rna() assert not pdb_hierarchy.contains_dna() assert pdb_hierarchy.as_sequence() == ['G', 'N', 'N', 'Q', 'Q', 'N', 'Y'] assert pdb_hierarchy.as_sequence(as_string = True) == 'GNNQQNY' dd = pdb_hierarchy.as_dict_of_resseq_as_int_residue_names() keys = list(dd.keys()) keys.sort() values = [dd[key] for key in keys] assert [keys, values] == [['A'], [{3: 'GLY', 4: 'ASN', 5: 'ASN', 6: 'GLN', 7: 'GLN', 8: 'ASN', 9: 'TYR'}]], [keys, values] assert pdb_hierarchy.format_fasta() == ['> chain " A"', 'GNNQQNY'] assert pdb_hierarchy.format_fasta(as_string = True) == \ """> chain " A" GNNQQNY""" pdb_hierarchy = pdb.input(source_info=None, lines="""\ ATOM 1282 P U A 75 8.046 10.090 17.379 1.00 20.97 P ATOM 1302 P A A 76 3.836 12.353 14.321 1.00 22.14 P ATOM 1324 P U A 77 -0.490 11.589 11.092 1.00 27.25 P ATOM 1344 P G A 78 -4.128 7.571 8.789 1.00 29.69 P ATOM 1367 P U A 79 -6.043 2.064 7.771 1.00 35.59 P ATOM 1387 P C A 80 -6.888 -3.348 8.809 1.00 52.93 P ATOM 1407 P C A 81 -6.452 -7.275 14.101 1.00 67.04 P """).construct_hierarchy() assert pdb_hierarchy.chain_types() == ['RNA'] assert pdb_hierarchy.chain_type() == 'RNA' assert pdb_hierarchy.contains_nucleic_acid() assert pdb_hierarchy.contains_rna() assert not pdb_hierarchy.contains_dna() assert pdb_hierarchy.as_sequence() == ['U', 'A', 'U', 'G', 'U', 'C', 'C'] assert pdb_hierarchy.as_sequence(as_string = True) == 'UAUGUCC' assert pdb_hierarchy.format_fasta() == ['> chain " A"', 'UAUGUCC'] assert pdb_hierarchy.format_fasta(as_string = True) == \ """> chain " A" UAUGUCC""" pdb_hierarchy = pdb.input(source_info=None, lines="""\ ATOM 590 P DG B 19 0.025 6.958 12.325 1.00 0.00 P ATOM 623 P DC B 20 -6.245 5.331 12.090 1.00 0.00 P ATOM 653 P DC B 21 -10.927 0.678 11.688 1.00 0.00 P ATOM 683 P DG B 22 -13.972 -4.787 13.859 1.00 0.00 P ATOM 716 P DA B 23 -14.817 -10.233 18.166 1.00 0.00 P ATOM 748 P DG B 24 -15.074 -12.316 24.830 1.00 0.00 P """).construct_hierarchy() assert pdb_hierarchy.contains_nucleic_acid() assert not pdb_hierarchy.contains_rna() assert pdb_hierarchy.contains_dna() assert pdb_hierarchy.chain_types() == ['DNA'] assert pdb_hierarchy.chain_type() == 'DNA' assert pdb_hierarchy.as_sequence() == ['G', 'C', 'C', 'G', 'A', 'G'] assert pdb_hierarchy.as_sequence(as_string = True) == 'GCCGAG' assert pdb_hierarchy.format_fasta() == ['> chain " B"', 'GCCGAG'] assert pdb_hierarchy.format_fasta(as_string = True) == \ """> chain " B" GCCGAG""" pdb_hierarchy = pdb.input(source_info=None, lines="""\ ATOM 1282 P U A 75 8.046 10.090 17.379 1.00 20.97 P ATOM 1302 P A A 76 3.836 12.353 14.321 1.00 22.14 P ATOM 1324 P U A 77 -0.490 11.589 11.092 1.00 27.25 P ATOM 1344 P G A 78 -4.128 7.571 8.789 1.00 29.69 P ATOM 1367 P U A 79 -6.043 2.064 7.771 1.00 35.59 P ATOM 1387 P C A 80 -6.888 -3.348 8.809 1.00 52.93 P ATOM 590 P DG B 19 0.025 6.958 12.325 1.00 0.00 P ATOM 623 P DC B 20 -6.245 5.331 12.090 1.00 0.00 P ATOM 653 P DC B 21 -10.927 0.678 11.688 1.00 0.00 P ATOM 683 P DG B 22 -13.972 -4.787 13.859 1.00 0.00 P ATOM 716 P DA B 23 -14.817 -10.233 18.166 1.00 0.00 P ATOM 748 P DG B 24 -15.074 -12.316 24.830 1.00 0.00 P """).construct_hierarchy() assert pdb_hierarchy.contains_nucleic_acid() assert pdb_hierarchy.contains_rna() assert pdb_hierarchy.contains_dna() assert pdb_hierarchy.chain_types() == ['DNA','RNA'] assert pdb_hierarchy.chain_type() == None assert pdb_hierarchy.as_sequence() == ['U', 'A', 'U', 'G', 'U', 'C', 'G', 'C', 'C', 'G', 'A', 'G'] assert pdb_hierarchy.as_sequence(as_string = True) == 'UAUGUCGCCGAG' assert pdb_hierarchy.format_fasta() == ['> chain " A"', 'UAUGUC','> chain " B"','GCCGAG'] assert pdb_hierarchy.format_fasta(as_string = True) == \ """> chain " A" UAUGUC > chain " B" GCCGAG""" pdb_hierarchy = pdb.input(source_info=None, lines="""\ ATOM 2 CA UNK A 3 -9.052 4.207 4.651 1.00 16.57 C ATOM 6 CA UNK A 4 -6.522 2.038 2.831 1.00 14.10 C ATOM 14 CA UNK A 5 -3.193 1.904 4.589 1.00 11.74 C ATOM 22 CA UNK A 6 0.384 1.888 3.199 1.00 10.53 C ATOM 31 CA UNK A 7 3.270 2.361 5.640 1.00 11.39 C ATOM 40 CA UNK A 8 6.831 2.310 4.318 1.00 12.30 C ATOM 48 CA UNK A 9 9.159 2.144 7.299 1.00 15.18 C HETATM 48 O HOH A 10 0.000 20.000 7.299 1.00 15.18 O HETATM 48 O HOH A 11 2.000 16.000 7.299 1.00 15.18 O HETATM 48 O HOH A 12 4.000 12.000 7.299 1.00 15.18 O HETATM 48 O HOH A 13 6.000 8.000 7.299 1.00 15.18 O HETATM 48 O HOH A 14 8.000 4.000 7.299 1.00 15.18 O HETATM 48 O HOH A 15 10.000 0.000 7.299 1.00 15.18 O """).construct_hierarchy() assert pdb_hierarchy.only_model().only_chain().is_protein() assert not pdb_hierarchy.only_model().only_chain().is_protein( ignore_water=False) assert pdb_hierarchy.as_sequence() == [] assert pdb_hierarchy.as_sequence(as_string = True) == '' print(pdb_hierarchy.format_fasta()) assert pdb_hierarchy.format_fasta() == [] assert pdb_hierarchy.format_fasta(as_string = True) == '' pdb_hierarchy = pdb.input(source_info=None, lines="""\ HETATM 48 O HOH A 10 0.000 20.000 7.299 1.00 15.18 O HETATM 48 O HOH A 11 2.000 16.000 7.299 1.00 15.18 O HETATM 48 O HOH A 12 4.000 12.000 7.299 1.00 15.18 O HETATM 48 O HOH A 13 6.000 8.000 7.299 1.00 15.18 O HETATM 48 O HOH A 14 8.000 4.000 7.299 1.00 15.18 O HETATM 48 O HOH A 15 10.000 0.000 7.299 1.00 15.18 O """).construct_hierarchy() assert not pdb_hierarchy.only_model().only_chain().is_protein() assert not pdb_hierarchy.only_model().only_chain().is_protein( ignore_water=False) pdb_hierarchy = pdb.input(source_info=None, lines="""\ ATOM 2 CA GLY A -2 -9.052 4.207 4.651 1.00 16.57 C ATOM 6 CA ASN A -1 -6.522 2.038 2.831 1.00 14.10 C ATOM 14 CA ASN A 0 -3.193 1.904 4.589 1.00 11.74 C ATOM 22 CA GLN A 1 0.384 1.888 3.199 1.00 10.53 C ATOM 31 CA GLN A 4 3.270 2.361 5.640 1.00 11.39 C ATOM 40 CA ASN A 5 6.831 2.310 4.318 1.00 12.30 C ATOM 48 CA TYR A 6 9.159 2.144 7.299 1.00 15.18 C """).construct_hierarchy() main_conf = pdb_hierarchy.models()[0].chains()[0].conformers()[0] assert main_conf.as_sequence() == ['G', 'N', 'N', 'Q', 'Q', 'N', 'Y'] assert main_conf.as_padded_sequence() == "GNNQXXQNY" chain = pdb_hierarchy.models()[0].chains()[0] assert chain.as_sequence() == ['G', 'N', 'N', 'Q', 'Q', 'N', 'Y'] assert chain.as_padded_sequence() == "GNNQXXQNY" pdb_hierarchy = pdb.input(source_info=None, lines="""\ ATOM 2 CA GLY A 3 -9.052 4.207 4.651 1.00 16.57 C ATOM 6 CA ASN A 4 -6.522 2.038 2.831 1.00 14.10 C ATOM 14 CA ASN A 5 -3.193 1.904 4.589 1.00 11.74 C ATOM 22 CA GLN A 6 0.384 1.888 3.199 1.00 10.53 C ATOM 22 CA ALA A 6A 0.384 1.888 3.199 1.00 10.53 C ATOM 22 CA GLY A 6B 0.384 1.888 3.199 1.00 10.53 C ATOM 31 CA GLN A 7 3.270 2.361 5.640 1.00 11.39 C ATOM 40 CA ASN A 8 6.831 2.310 4.318 1.00 12.30 C ATOM 48 CA TYR A 9 9.159 2.144 7.299 1.00 15.18 C """).construct_hierarchy() main_conf = pdb_hierarchy.models()[0].chains()[0].conformers()[0] assert main_conf.get_residue_names_and_classes() == ( ['GLY', 'ASN', 'ASN', 'GLN', 'ALA', 'GLY', 'GLN', 'ASN', 'TYR'], {'common_amino_acid': 9}) assert main_conf.as_sequence() == ['G', 'N', 'N', 'Q', 'A', 'G', 'Q', 'N', 'Y'] assert (main_conf.as_padded_sequence() == "XXGNNQAGQNY") assert (main_conf.as_padded_sequence(skip_insertions=True) == "XXGNNQQNY") assert pdb_hierarchy.as_sequence() == ['G', 'N', 'N', 'Q', 'A', 'G', 'Q', 'N', 'Y'] resids = main_conf.get_residue_ids() assert (len(resids) == 11) assert (resids[0] == resids[1] == None) assert (resids[-4].strip() == "6B") resnames = main_conf.get_residue_names_padded() assert len(resnames) == 11 assert resnames == [ None, None, 'GLY', 'ASN', 'ASN', 'GLN', 'ALA', 'GLY', 'GLN', 'ASN', 'TYR'] assert len(main_conf.get_residue_names_padded(pad_at_start=False)) == 9 # duplicate of tests above but for chain methods chain = pdb_hierarchy.models()[0].chains()[0] assert chain.get_residue_names_and_classes() == ( ['GLY', 'ASN', 'ASN', 'GLN', 'ALA', 'GLY', 'GLN', 'ASN', 'TYR'], {'common_amino_acid': 9}) assert chain.as_sequence() == ['G', 'N', 'N', 'Q', 'A', 'G', 'Q', 'N', 'Y'] assert (chain.as_padded_sequence() == "XXGNNQAGQNY") assert (chain.as_padded_sequence(skip_insertions=True) == "XXGNNQQNY") resids = chain.get_residue_ids() assert (len(resids) == 11) assert (resids[0] == resids[1] == None) assert (resids[-4].strip() == "6B") resnames = chain.get_residue_names_padded() assert len(resnames) == 11 assert resnames == [ None, None, 'GLY', 'ASN', 'ASN', 'GLN', 'ALA', 'GLY', 'GLN', 'ASN', 'TYR'] assert len(chain.get_residue_names_padded(pad_at_start=False)) == 9 # this next example comes from PDB ID 3ty2, demonstrating why it is better to # determine the sequence using residue_groups rather than looking at the first # conformer. If we get the sequence from main_conf, then the second MSE is # is 'lost' from the sequence because it is only present as B and C altlocs pdb_hierarchy = pdb.input(source_info=None, lines="""\ ATOM 450 CA ASN A 1 37.242 41.665 44.160 1.00 35.89 C ATOM 458 CA GLY A 2 37.796 38.269 42.523 1.00 30.13 C HETATM 463 CA AMSE A 3 35.878 39.005 39.326 0.54 22.83 C HETATM 464 CA BMSE A 3 35.892 39.018 39.323 0.46 22.96 C ATOM 478 CA ILE A 4 37.580 38.048 36.061 1.00 22.00 C ATOM 486 CA SER A 5 37.593 40.843 33.476 1.00 18.73 C ATOM 819 CA ALA A 8 25.982 34.781 27.220 1.00 18.43 C ATOM 824 CA ALA A 9 23.292 32.475 28.614 1.00 19.60 C HETATM 830 CA BMSE A 10 22.793 30.814 25.223 0.41 22.60 C HETATM 831 CA CMSE A 10 22.801 30.850 25.208 0.59 22.54 C ATOM 845 CA GLU A 11 26.504 30.054 24.966 1.00 25.19 C ATOM 854 CA GLY A 12 25.907 28.394 28.320 1.00 38.88 C """).construct_hierarchy() main_conf = pdb_hierarchy.models()[0].chains()[0].conformers()[0] assert main_conf.get_residue_names_and_classes() == ( ['ASN', 'GLY', 'MSE', 'ILE', 'SER', 'ALA', 'ALA', 'GLU', 'GLY'], {'common_amino_acid': 9}) assert main_conf.as_sequence() == ['N', 'G', 'M', 'I', 'S', 'A', 'A', 'E', 'G'] assert main_conf.as_padded_sequence() == 'NGMISXXAAXEG' assert main_conf.get_residue_ids() == [ ' 1 ', ' 2 ', ' 3 ', ' 4 ', ' 5 ', None, None, ' 8 ', ' 9 ', None, ' 11 ', ' 12 '] assert main_conf.get_residue_names_padded() == [ 'ASN', 'GLY', 'MSE', 'ILE', 'SER', None, None, 'ALA', 'ALA', None, 'GLU', 'GLY'] # now the chain methods should give different (more correct) answers chain = pdb_hierarchy.models()[0].chains()[0] assert chain.get_residue_names_and_classes() == ( ['ASN', 'GLY', 'MSE', 'ILE', 'SER', 'ALA', 'ALA', 'MSE', 'GLU', 'GLY'], {'common_amino_acid': 10}) assert chain.as_sequence() == ['N', 'G', 'M', 'I', 'S', 'A', 'A', 'M', 'E', 'G'] assert chain.as_padded_sequence() == 'NGMISXXAAMEG' print(pdb_hierarchy.as_sequence()) assert "".join(pdb_hierarchy.as_sequence()) == 'NGMISAAMEG' assert chain.get_residue_ids() == [ ' 1 ', ' 2 ', ' 3 ', ' 4 ', ' 5 ', None, None, ' 8 ', ' 9 ', ' 10 ', ' 11 ', ' 12 '] assert chain.get_residue_names_padded() == [ 'ASN', 'GLY', 'MSE', 'ILE', 'SER', None, None, 'ALA', 'ALA', 'MSE', 'GLU', 'GLY'] # test modified AA pdb_hierarchy = pdb.input(source_info=None, lines="""\ ATOM 2 CA GLY A 3 -9.052 4.207 4.651 1.00 16.57 C ATOM 6 CA ASN A 4 -6.522 2.038 2.831 1.00 14.10 C ATOM 14 CA ASN A 5 -3.193 1.904 4.589 1.00 11.74 C ATOM 22 CA GLN A 6 0.384 1.888 3.199 1.00 10.53 C ATOM 22 CA ALA A 6A 0.384 1.888 3.199 1.00 10.53 C ATOM 22 CA GLY A 6B 0.384 1.888 3.199 1.00 10.53 C ATOM 31 CA GLN A 7 3.270 2.361 5.640 1.00 11.39 C ATOM 40 CA ASN A 8 6.831 2.310 4.318 1.00 12.30 C ATOM 48 CA PTR A 9 9.159 2.144 7.299 1.00 15.18 C """).construct_hierarchy() main_conf = pdb_hierarchy.models()[0].chains()[0].conformers()[0] assert (main_conf.as_padded_sequence() == "XXGNNQAGQNY") # Ligand with big resid pdb_hierarchy = pdb.input(source_info=None, lines="""\ ATOM 2 CA GLY A 3 -9.052 4.207 4.651 1.00 16.57 C ATOM 6 CA ASN A 4 -6.522 2.038 2.831 1.00 14.10 C ATOM 14 CA ASN A 5 -3.193 1.904 4.589 1.00 11.74 C ATOM 22 CA GLN A 6 0.384 1.888 3.199 1.00 10.53 C ATOM 31 CA GLN A 7 3.270 2.361 5.640 1.00 11.39 C ATOM 40 CA ASN A 8 6.831 2.310 4.318 1.00 12.30 C ATOM 48 CA TYR A 9 9.159 2.144 7.299 1.00 15.18 C HETATM45571 NB CLA A1401 10.336 10.558 15.466 1.00 79.02 k N """).construct_hierarchy() ch = pdb_hierarchy.models()[0].chains()[0] # assert ch.as_sequence() == ['G', 'N', 'N', 'Q', 'Q', 'N', 'Y'] # assert ch.as_padded_sequence() == "XXGNNQQNY" # sites_diff hierarchy_1 = pdb.input(source_info=None, lines="""\ ATOM 0 O WAT B 1 17.523 2.521 10.381 1.10 16.78 O ATOM 1 N GLY A 1 -9.009 4.612 6.102 1.00 16.77 N ATOM 2 CA GLY A 1 -9.052 4.207 4.651 1.00 16.57 C ATOM 3 C GLY A 1 -8.015 3.140 4.419 1.00 16.16 C ATOM 4 O GLY A 1 -7.523 2.521 5.381 1.00 16.78 O TER ATOM 5 O HOH S 1 -7.523 2.521 10.381 0.10 6.78 O """).construct_hierarchy() hierarchy_2 = pdb.input(source_info=None, lines="""\ ATOM 1 N GLY A 1 -9.009 4.612 7.102 1.00 16.77 N ATOM 2 CA GLY A 1 -9.052 4.207 5.651 1.00 16.57 C ATOM 3 C GLY A 1 -8.015 3.140 5.419 1.00 16.16 C ATOM 4 O GLY A 1 -6.523 3.521 6.381 1.00 16.78 O TER ATOM 5 O HOH S 1 -9.523 5.521 11.381 0.10 6.78 O """).construct_hierarchy() hierarchy_new = pdb.hierarchy.sites_diff(hierarchy_1, hierarchy_2) assert approx_equal(hierarchy_new.atoms().extract_b(), [1.0, 1.0, 1.0, 1.7320508, -1.0]) deltas = pdb.hierarchy.sites_diff(hierarchy_1, hierarchy_2, exclude_waters=False, return_hierarchy=False) assert approx_equal(deltas, [1.0, 1.0, 1.0, 1.7320508, 3.7416574]) # show_file_summary out = StringIO() pdb_file = libtbx.env.find_in_repositories( relative_path="phenix_regression/pdb/2C30.pdb", test=os.path.isfile) if (pdb_file is None): return pdb_in = pdb.input(file_name=pdb_file) info = pdb.show_file_summary(pdb_in, out=out) expected = """\ Number of atoms: 2691 Number of chains: 3 Chain IDs: A, Z Alternate conformations: 2 Amino acid residues: 289 Water molecules: 350 Elemental ions: 1 ( CL) Other molecules: 1 (PO4) Mean isotropic B-factor: 22.10 (range: 10.58 - 55.34) Space group: P 21 21 21 Unit cell: 59.781 66.674 96.999 90 90 90 """ assert (out.getvalue() == expected), "\n"+out.getvalue() # get_contiguous_ranges pdb_hierarchy = pdb.input(source_info=None, lines="""\ ATOM 2 CA GLY A -1 -9.052 4.207 4.651 1.00 16.57 C ATOM 6 CA ASN A 0 -6.522 2.038 2.831 1.00 14.10 C ATOM 14 CA ASN A 1 -3.193 1.904 4.589 1.00 11.74 C ATOM 22 CA GLN A 2 0.384 1.888 3.199 1.00 10.53 C ATOM 22 CA ALA A 2A 0.384 1.888 3.199 1.00 10.53 C ATOM 22 CA GLY A 2B 0.384 1.888 3.199 1.00 10.53 C ATOM 31 CA GLN A 4 3.270 2.361 5.640 1.00 11.39 C ATOM 40 CA ASN A 5 6.831 2.310 4.318 1.00 12.30 C ATOM 48 CA TYR A 6 9.159 2.144 7.299 1.00 15.18 C TER ATOM 5 O HOH S 1 -9.523 5.521 11.381 0.10 6.78 O """).construct_hierarchy() selections = pdb.hierarchy.get_contiguous_ranges(pdb_hierarchy) assert (selections == [ "chain 'A' and ((resid -1 through 2B) or (resid 4 through 6 ))", "chain 'S' and ((resid 1 ))"]) # root.remove_hd() hierarchy = pdb.input(source_info=None, lines="""\ ATOM 39 N ASN A 6 5.514 2.664 4.856 1.00 11.99 N ATOM 40 CA ASN A 6 6.831 2.310 4.318 1.00 12.30 C ATOM 41 C ASN A 6 7.854 2.761 5.324 1.00 13.40 C ATOM 42 O ASN A 6 8.219 3.943 5.374 1.00 13.92 O ATOM 43 CB ASN A 6 7.065 3.016 2.993 1.00 12.13 C ATOM 44 CG ASN A 6 5.961 2.735 2.003 1.00 12.77 C ATOM 45 OD1 ASN A 6 5.798 1.604 1.551 1.00 14.27 O ATOM 46 ND2 ASN A 6 5.195 3.747 1.679 1.00 10.07 N ATOM 0 H ASN A 6 5.376 3.649 4.962 1.00 11.99 H ATOM 0 HA ASN A 6 6.900 1.226 4.142 1.00 12.30 H ATOM 0 1HB ASN A 6 7.137 4.100 3.163 1.00 12.13 H ATOM 0 2HB ASN A 6 8.027 2.692 2.570 1.00 12.13 H ATOM 0 1HD2 ASN A 6 4.439 3.617 1.038 1.00 10.07 H ATOM 0 2HD2 ASN A 6 5.366 4.650 2.073 1.00 10.07 H TER ATOM 60 H ASN B 1 5.376 3.649 4.962 1.00 11.99 H END """).construct_hierarchy() assert (hierarchy.remove_hd() == 7) assert hierarchy.only_model().only_chain() def exercise_equality_and_hashing(): root = pdb.hierarchy.root() model = pdb.hierarchy.model() root.append_model( model ) chain = pdb.hierarchy.chain() model.append_chain( chain ) rg = pdb.hierarchy.residue_group() chain.append_residue_group( rg ) ag = pdb.hierarchy.atom_group() rg.append_atom_group( ag ) atom = pdb.hierarchy.atom() ag.append_atom( atom ) collection = set( [ root, model, chain, rg, ag, atom ] ) # Root pr = model.parent() assert pr is not root assert pr == root assert pr in collection # Model pm = chain.parent() assert pm is not model assert pm == model assert pm in collection # Chain pc = rg.parent() assert pc is not chain assert pc == chain assert pc in collection # Residue group prg = ag.parent() assert prg is not rg assert prg == rg assert prg in collection # Atom group pag = atom.parent() assert pag is not ag assert pag == ag assert pag in collection # Atom pa = ag.atoms()[0] assert pa is not atom assert pa == atom assert pa in collection def exercise_atom_is_in_same_conformer_as(): pdb_hierarchy = pdb.input(source_info=None, lines="""\ MODEL 1 ATOM 0 N MET ATOM 1 CA AMET ATOM 2 CA BMET ENDMDL MODEL 2 ATOM 3 N MET ATOM 4 CA MET ATOM 5 CA BMET ENDMDL END """).construct_hierarchy() atoms = pdb_hierarchy.atoms() for first in [0,3]: for i in range(3): assert atoms[first].is_in_same_conformer_as(atoms[first+i]) assert not atoms[first+1].is_in_same_conformer_as(atoms[first+2]) for i in range(3): for j in range(3,6): assert not atoms[i].is_in_same_conformer_as(atoms[j]) def get_phenix_regression_pdb_file_names(): pdb_dir = libtbx.env.find_in_repositories("phenix_regression/pdb") if (pdb_dir is None): return None result = [] for node in os.listdir(pdb_dir): if (not (node.endswith(".pdb") or node.endswith(".ent"))): continue result.append(os.path.join(pdb_dir, node)) assert len(result) != 0 return result def exercise_adopt_xray_structure(): from cctbx import adptbx pdb_inp = pdb.input(source_info=None, lines="""\ CRYST1 12.000 13.000 14.000 80.00 90.00 100.00 P 1 ATOM 0 O WAT B 1 17.523 2.521 10.381 1.10 16.78 O ATOM 1 N GLY A 1 -9.009 4.612 6.102 1.00 16.77 N ATOM 2 CA GLY A 1 -9.052 4.207 4.651 1.00 16.57 C ANISOU 2 CA GLY A 1 788 626 677 -344 621 -232 C ATOM 3 C GLY A 1 -8.015 3.140 4.419 1.00 16.16 C ATOM 4 O GLY A 1 -7.523 2.521 5.381 1.00 16.78 O TER ATOM 5 O HOH S 1 -7.523 2.521 10.381 0.10 6.78 O TER ATOM 6 O HOH 1 10.523 2.521 5.381 1.00 16.78 O ANISOU 6 O HOH 1 788 626 677 -344 621 -232 O """) hierarchy = pdb_inp.construct_hierarchy() xrs = pdb_inp.xray_structure_simple() xrs_new1 = xrs.deep_copy_scatterers() xrs_new1.shake_adp() xrs_new1.shake_occupancies() xrs_new1.shake_sites_in_place(rms_difference=0.5) hierarchy.adopt_xray_structure(xray_structure = xrs_new1) xrs_new2 = hierarchy.extract_xray_structure(crystal_symmetry = xrs.crystal_symmetry()) uc = xrs.unit_cell() orth = uc.orthogonalize for s1,s2 in zip(xrs_new1.scatterers(), xrs_new2.scatterers()): assert approx_equal(orth(s1.site), orth(s2.site), 1.e-3) assert approx_equal(adptbx.u_as_b(s1.u_iso), adptbx.u_as_b(s2.u_iso), 1.e-2) assert approx_equal(s1.occupancy, s2.occupancy, 1.e-2) assert approx_equal(s1.u_star, s2.u_star) assert s1.scattering_type == s2.scattering_type xrs_new3 = xrs.concatenate(other = xrs_new1) try: hierarchy.adopt_xray_structure(xray_structure = xrs_new3) except RuntimeError as e: assert str(e) == "Incompatible size of hierarchy and scatterers array." xrs_new4 = xrs.deep_copy_scatterers() xrs_new4.set_inelastic_form_factors(photon=1.4, table="sasaki") for atom in hierarchy.atoms(): assert atom.fp == 0 assert atom.fdp == 0 hierarchy.adopt_xray_structure(xray_structure=xrs_new4) expected_fp = [0.0389, 0.0241, 0.0139, 0.0139, 0.0389, 0.0389, 0.0389] expected_fdp = [0.0264, 0.0147, 0.0073, 0.0073, 0.0264, 0.0264, 0.0264] assert approx_equal([atom.fp for atom in hierarchy.atoms()], expected_fp) assert approx_equal([atom.fdp for atom in hierarchy.atoms()], expected_fdp) #xrs_new5 = hierarchy.extract_xray_structure( #crystal_symmetry=xrs.crystal_symmetry()) #assert xrs_new5 is not xrs_new4 #assert xrs_new5.scatterers() is not xrs_new4.scatterers() #assert approx_equal([sc.fp for sc in xrs_new5.scatterers()], expected_fp) #assert approx_equal([sc.fdp for sc in xrs_new5.scatterers()], expected_fdp) hierarchy.adopt_xray_structure(xray_structure=xrs_new1) for model in hierarchy.models(): for chain in model.chains(): if chain.id == "A": chain.id = "C" try: hierarchy.adopt_xray_structure(xray_structure=xrs) except Exception as e: pass else: raise Exception_expected hierarchy.adopt_xray_structure( xray_structure=xrs, assert_identical_id_str=False) xrs_new5 = hierarchy.extract_xray_structure( crystal_symmetry=xrs.crystal_symmetry()) for s1,s2 in zip(xrs.scatterers(), xrs_new5.scatterers()): assert approx_equal(orth(s1.site), orth(s2.site), 1.e-3) assert approx_equal(adptbx.u_as_b(s1.u_iso), adptbx.u_as_b(s2.u_iso), 1.e-2) assert approx_equal(s1.occupancy, s2.occupancy, 1.e-2) assert approx_equal(s1.u_star, s2.u_star) assert s1.scattering_type == s2.scattering_type def exercise_adopt_xray_structure2(): p1 = pdb.input(source_info=None, lines="""\ CRYST1 12.000 13.000 14.000 80.00 90.00 100.00 P 1 ATOM 1134 MG MG A1002 46.207 95.853 116.979 1.00 40.88 Mg """) h1 = p1.construct_hierarchy() xrs1 = p1.xray_structure_simple() # p2 = pdb.input(source_info=None, lines="""\ CRYST1 12.000 13.000 14.000 80.00 90.00 100.00 P 1 HETATM 1135 MG MG A1002 46.279 95.897 117.018 1.00 40.88 Mg """) h2 = p2.construct_hierarchy() xrs2 = p2.xray_structure_simple() # h2.adopt_xray_structure(xrs1) def exercise_substitute_atom_group(): hierarchy1 = pdb.input(source_info=None, lines="""\ ATOM 39 N ASN A 6 5.514 2.664 4.856 1.00 11.99 N ATOM 40 CA ASN A 6 6.831 2.310 4.318 1.00 12.30 C ATOM 41 C ASN A 6 7.854 2.761 5.324 1.00 13.40 C ATOM 42 O ASN A 6 8.219 3.943 5.374 1.00 13.92 O ATOM 43 CB ASN A 6 7.065 3.016 2.993 1.00 12.13 C ATOM 44 CG ASN A 6 5.961 2.735 2.003 1.00 12.77 C ATOM 45 OD1 ASN A 6 5.798 1.604 1.551 1.00 14.27 O ATOM 46 ND2 ASN A 6 5.195 3.747 1.679 1.00 10.07 N ATOM 0 H ASN A 6 5.376 3.649 4.962 1.00 11.99 H ATOM 0 HA ASN A 6 6.900 1.226 4.142 1.00 12.30 H ATOM 0 1HB ASN A 6 7.137 4.100 3.163 1.00 12.13 H ATOM 0 2HB ASN A 6 8.027 2.692 2.570 1.00 12.13 H ATOM 0 1HD2 ASN A 6 4.439 3.617 1.038 1.00 10.07 H ATOM 0 2HD2 ASN A 6 5.366 4.650 2.073 1.00 10.07 H """).construct_hierarchy(sort_atoms=False) hierarchy1.write_pdb_file(file_name="hierarchy1.pdb") hierarchy2 = pdb.input(source_info=None, lines="""\ ATOM 47 N TYR A 7 8.292 1.817 6.147 1.00 14.70 N ATOM 48 CA TYR A 7 9.159 2.144 7.299 1.00 15.18 C ATOM 49 C TYR A 7 10.603 2.331 6.885 1.00 15.91 C ATOM 50 O TYR A 7 11.041 1.811 5.855 1.00 15.76 O ATOM 51 CB TYR A 7 9.061 1.065 8.369 1.00 15.35 C ATOM 52 CG TYR A 7 7.665 0.929 8.902 1.00 14.45 C ATOM 53 CD1 TYR A 7 6.771 0.021 8.327 1.00 15.68 C ATOM 54 CD2 TYR A 7 7.210 1.756 9.920 1.00 14.80 C ATOM 55 CE1 TYR A 7 5.480 -0.094 8.796 1.00 13.46 C ATOM 56 CE2 TYR A 7 5.904 1.649 10.416 1.00 14.33 C ATOM 57 CZ TYR A 7 5.047 0.729 9.831 1.00 15.09 C ATOM 58 OH TYR A 7 3.766 0.589 10.291 1.00 14.39 O ATOM 59 OXT TYR A 7 11.358 2.999 7.612 1.00 17.49 O """).construct_hierarchy(sort_atoms=False) hierarchy2.write_pdb_file(file_name="hierarchy2.pdb") chain1 = hierarchy1.models()[0].chains()[0] chain2 = hierarchy2.models()[0].chains()[0] current_group = chain1.residue_groups()[0].atom_groups()[0] new_group = chain2.residue_groups()[0].atom_groups()[0] pdb.hierarchy.substitute_atom_group( current_group=current_group, new_group=new_group) hierarchy1.write_pdb_file(file_name="moved.pdb") print(hierarchy1.as_pdb_string()) assert not show_diff(hierarchy1.as_pdb_string(), """\ ATOM 39 N TYR A 6 5.514 2.664 4.856 1.00 11.99 N ATOM 40 CA TYR A 6 6.831 2.310 4.318 1.00 12.30 C ATOM 41 C TYR A 6 7.854 2.761 5.324 1.00 13.40 C ATOM 42 O TYR A 6 8.219 3.943 5.374 1.00 13.92 O ATOM 51 CB TYR A 6 7.068 3.009 2.992 1.00 12.13 C ATOM 52 CG TYR A 6 6.101 2.535 1.948 1.00 12.77 C ATOM 53 CD1 TYR A 6 4.898 3.215 1.734 1.00 12.11 C ATOM 54 CD2 TYR A 6 6.343 1.371 1.232 1.00 12.11 C ATOM 55 CE1 TYR A 6 3.994 2.773 0.792 1.00 12.11 C ATOM 56 CE2 TYR A 6 5.440 0.910 0.265 1.00 12.11 C ATOM 57 CZ TYR A 6 4.262 1.615 0.069 1.00 12.11 C ATOM 58 OH TYR A 6 3.358 1.201 -0.871 1.00 12.11 O ATOM 59 OXT TYR A 6 9.015 2.205 5.262 1.00 12.11 O TER """) def exercise_get_peptide_c_alpha_selection(): pdb_inp = pdb.input(source_info=None, lines=flex.split_lines("""\ MODEL 0 ATOM 1 C MET A 1 ATOM 2 CA AMET A 1 BREAK ATOM 3 N GLY A 2 ATOM 4 CA AGLY A 2 ENDMDL MODEL 1 ATOM 1 N MET A 1 ATOM 2 CA AMET A 1 ATOM 3 N ALA B 2 ATOM 4 CA AALA B 2 ENDMDL MODEL 2 HETATM 6 CA AION B 1 32.360 11.092 17.308 0.92 35.96 CA2+ HETATM 7 CA ION B 2 30.822 10.665 17.190 1.00 36.87 ENDMDL """)) h = pdb_inp.construct_hierarchy() h.atoms().reset_i_seq() assert list(h.get_peptide_c_alpha_selection()) == [1, 3, 5, 7] # pdb_inp = pdb.input(source_info=None, lines=flex.split_lines("""\ ATOM 1 N THR A 2 -3.791 -8.769 29.092 1.00 24.15 N ATOM 2 CA THR A 2 -3.627 -7.675 28.090 1.00 25.97 C ATOM 3 C THR A 2 -2.202 -7.127 28.152 1.00 24.18 C ATOM 4 O THR A 2 -1.633 -6.984 29.233 1.00 24.71 O ATOM 5 CB THR A 2 -4.627 -6.527 28.357 1.00 26.50 C ATOM 6 OG1 THR A 2 -5.961 -7.056 28.404 1.00 28.79 O ATOM 7 CG2 THR A 2 -4.548 -5.486 27.255 1.00 27.05 C ATOM 8 N LYS A 3 -1.629 -6.832 26.988 1.00 24.44 N ATOM 10 C LYS A 3 -0.196 -4.896 27.485 1.00 23.66 C ATOM 11 O LYS A 3 -1.094 -4.084 27.265 1.00 23.75 O ATOM 12 CB LYS A 3 0.199 -6.262 25.438 1.00 26.61 C ATOM 9 CA ALYS A 3 -0.266 -6.307 26.901 1.00 25.16 C ATOM 13 CG ALYS A 3 0.312 -7.619 24.754 0.50 27.88 C ATOM 15 CD ALYS A 3 1.436 -8.454 25.347 0.50 27.58 C ATOM 17 CE ALYS A 3 1.585 -9.783 24.621 0.50 28.69 C ATOM 19 NZ ALYS A 3 0.362 -10.624 24.732 0.50 28.63 N ATOM 9 CA BLYS A 3 -0.266 -6.307 26.901 1.00 25.16 C ATOM 14 CG BLYS A 3 0.201 -7.603 24.718 0.50 27.66 C ATOM 16 CD BLYS A 3 1.205 -8.570 25.325 0.50 27.30 C ATOM 18 CE BLYS A 3 1.213 -9.893 24.575 0.50 28.17 C ATOM 20 NZ BLYS A 3 2.149 -10.873 25.188 0.50 27.40 N ATOM 21 N LYS A 4 0.873 -4.612 28.225 1.00 22.24 N ATOM 22 CA LYS A 4 1.068 -3.295 28.826 1.00 21.81 C ATOM 23 C LYS A 4 2.337 -2.642 28.295 1.00 19.26 C ATOM 24 O LYS A 4 3.417 -3.243 28.310 1.00 18.66 O ATOM 25 CB LYS A 4 1.156 -3.398 30.354 1.00 23.29 C ATOM 26 CG LYS A 4 -0.170 -3.685 31.031 1.00 27.60 C ATOM 27 CD LYS A 4 -0.049 -3.681 32.551 1.00 32.16 C ATOM 28 CE LYS A 4 0.797 -4.842 33.052 1.00 33.04 C ATOM 29 NZ LYS A 4 0.827 -4.892 34.541 1.00 36.05 N """)) h = pdb_inp.construct_hierarchy() h.atoms().reset_i_seq() assert list(h.get_peptide_c_alpha_selection()) == [1, 11, 16, 22] def exercise_chunk_selections(): # multiple altlocs pdb_inp = pdb.input(source_info=None, lines=flex.split_lines("""\ ATOM 0 N THR A 2 -3.791 -8.769 29.092 1.00 24.15 N ATOM 1 CA THR A 2 -3.627 -7.675 28.090 1.00 25.97 C ATOM 2 C THR A 2 -2.202 -7.127 28.152 1.00 24.18 C ATOM 3 O THR A 2 -1.633 -6.984 29.233 1.00 24.71 O ATOM 4 CB THR A 2 -4.627 -6.527 28.357 1.00 26.50 C ATOM 5 OG1 THR A 2 -5.961 -7.056 28.404 1.00 28.79 O ATOM 6 CG2 THR A 2 -4.548 -5.486 27.255 1.00 27.05 C ATOM 7 N LYS A 3 -1.629 -6.832 26.988 1.00 24.44 N ATOM 8 C LYS A 3 -0.196 -4.896 27.485 1.00 23.66 C ATOM 9 O LYS A 3 -1.094 -4.084 27.265 1.00 23.75 O ATOM 10 CB LYS A 3 0.199 -6.262 25.438 1.00 26.61 C ATOM 11 CA ALYS A 3 -0.266 -6.307 26.901 1.00 25.16 C ATOM 12 CG ALYS A 3 0.312 -7.619 24.754 0.50 27.88 C ATOM 13 CD ALYS A 3 1.436 -8.454 25.347 0.50 27.58 C ATOM 14 CE ALYS A 3 1.585 -9.783 24.621 0.50 28.69 C ATOM 15 NZ ALYS A 3 0.362 -10.624 24.732 0.50 28.63 N ATOM 16 CA BLYS A 3 -0.266 -6.307 26.901 1.00 25.16 C ATOM 17 CG BLYS A 3 0.201 -7.603 24.718 0.50 27.66 C ATOM 18 CD BLYS A 3 1.205 -8.570 25.325 0.50 27.30 C ATOM 19 CE BLYS A 3 1.213 -9.893 24.575 0.50 28.17 C ATOM 20 NZ BLYS A 3 2.149 -10.873 25.188 0.50 27.40 N ATOM 21 N LYS A 4 0.873 -4.612 28.225 1.00 22.24 N ATOM 22 CA LYS A 4 1.068 -3.295 28.826 1.00 21.81 C ATOM 23 C LYS A 4 2.337 -2.642 28.295 1.00 19.26 C ATOM 24 O LYS A 4 3.417 -3.243 28.310 1.00 18.66 O ATOM 25 CB LYS A 4 1.156 -3.398 30.354 1.00 23.29 C ATOM 26 CG LYS A 4 -0.170 -3.685 31.031 1.00 27.60 C ATOM 27 CD LYS A 4 -0.049 -3.681 32.551 1.00 32.16 C ATOM 28 CE LYS A 4 0.797 -4.842 33.052 1.00 33.04 C ATOM 29 NZ LYS A 4 0.827 -4.892 34.541 1.00 36.05 N """)) h = pdb_inp.construct_hierarchy() h.atoms().reset_i_seq() sites_cart = h.extract_xray_structure().sites_cart() # css = h.chunk_selections(residues_per_chunk=0) assert len(css)==0 # css = h.chunk_selections(residues_per_chunk=1) assert list(css[0]) == [0, 1, 2, 3, 4, 5, 6] assert list(css[1]) == [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] assert list(css[2]) == [21, 22, 23, 24, 25, 26, 27, 28, 29] assert len(css)==3 for cs in css: assert approx_equal(sites_cart.select(cs), h.select(cs).extract_xray_structure().sites_cart()) # css = h.chunk_selections(residues_per_chunk=2) assert list(css[0]) == [0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19, 20] assert list(css[1]) == [21, 22, 23, 24, 25, 26, 27, 28, 29] assert len(css)==2 for cs in css: assert approx_equal(sites_cart.select(cs), h.select(cs).extract_xray_structure().sites_cart()) # css = h.chunk_selections(residues_per_chunk=3) assert list(css[0]) == [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29] assert len(css)==1 for cs in css: assert approx_equal(sites_cart.select(cs), h.select(cs).extract_xray_structure().sites_cart()) # multiple chains pdb_inp = pdb.input(source_info=None, lines=flex.split_lines("""\ ATOM 0 N ASP A 1 49.347 -62.804 60.380 1.00 34.60 N ATOM 1 CA ASP A 1 47.975 -63.194 59.946 1.00 33.86 C ATOM 2 C ASP A 1 47.122 -63.665 61.114 1.00 34.02 C ATOM 3 O ASP A 1 47.573 -64.451 61.947 1.00 32.23 O ATOM 4 N VAL A 2 45.889 -63.176 61.175 1.00 31.94 N ATOM 5 CA VAL A 2 44.978 -63.576 62.233 1.00 29.81 C ATOM 6 C VAL A 2 44.472 -64.973 61.900 1.00 28.28 C ATOM 7 O VAL A 2 43.989 -65.221 60.796 1.00 27.24 O ATOM 8 N GLN A 3 44.585 -65.878 62.864 1.00 25.93 N ATOM 9 CA GLN A 3 44.166 -67.262 62.686 1.00 24.46 C ATOM 10 C GLN A 3 42.730 -67.505 63.153 1.00 23.33 C ATOM 11 O GLN A 3 42.389 -67.234 64.302 1.00 20.10 O ATOM 12 N MET A 4 41.894 -68.026 62.256 1.00 24.27 N ATOM 13 CA MET A 4 40.497 -68.318 62.576 1.00 22.89 C ATOM 14 C MET A 4 40.326 -69.824 62.795 1.00 21.48 C ATOM 15 O MET A 4 40.633 -70.625 61.911 1.00 23.73 O TER ATOM 16 N THR B 5 39.836 -70.208 63.971 1.00 20.55 N ATOM 17 CA THR B 5 39.652 -71.626 64.301 1.00 20.64 C ATOM 18 C THR B 5 38.188 -72.004 64.496 1.00 20.08 C ATOM 19 O THR B 5 37.534 -71.507 65.409 1.00 20.87 O ATOM 20 N GLN B 6 37.680 -72.891 63.643 1.00 21.97 N ATOM 21 CA GLN B 6 36.288 -73.325 63.743 1.00 25.11 C ATOM 22 C GLN B 6 36.147 -74.705 64.370 1.00 25.56 C ATOM 23 O GLN B 6 36.912 -75.622 64.064 1.00 26.32 O ATOM 24 N THR B 7 35.141 -74.839 65.229 1.00 27.28 N ATOM 25 CA THR B 7 34.842 -76.087 65.919 1.00 29.94 C ATOM 26 C THR B 7 33.332 -76.282 65.861 1.00 30.28 C ATOM 27 O THR B 7 32.576 -75.339 66.091 1.00 30.65 O ATOM 28 N PRO B 8 32.867 -77.502 65.555 1.00 29.43 N ATOM 29 CA PRO B 8 33.636 -78.711 65.256 1.00 27.63 C ATOM 30 C PRO B 8 33.982 -78.790 63.773 1.00 27.58 C ATOM 31 O PRO B 8 33.634 -77.895 63.000 1.00 28.53 O ATOM 32 N LEU B 9 34.669 -79.856 63.373 1.00 27.41 N ATOM 33 CA LEU B 9 35.035 -80.024 61.969 1.00 25.92 C ATOM 34 C LEU B 9 33.808 -80.409 61.159 1.00 23.43 C ATOM 35 O LEU B 9 33.602 -79.903 60.059 1.00 22.17 O TER """)) h = pdb_inp.construct_hierarchy() h.atoms().reset_i_seq() sites_cart = h.extract_xray_structure().sites_cart() # css = h.chunk_selections(residues_per_chunk=3) for cs in css: assert approx_equal(sites_cart.select(cs), h.select(cs).extract_xray_structure().sites_cart()) # assert list(css[0]) == [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11] assert list(css[1]) == [12, 13, 14, 15] assert list(css[2]) == [16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27] assert list(css[3]) == [28, 29, 30, 31, 32, 33, 34, 35] assert len(css)==4 def exercise_atom_xyz_9999(): """ When one atom have all 3 xyz coordinates > 9999 an exception should be thrown. 2 such coordinates are fine for unknown reasons. Such files could be originated from CNS where those are handled as "unknown coordinates" """ pdb_inp = pdb.input(source_info=None, lines=flex.split_lines("""\ ATOM 10849 C ILE A1445 50.977 77.127 41.547 1.00129.33 A ATOM 10850 O ILE A1445 50.257 76.569 42.421 1.00129.33 A ATOM 10851 OXT ILE A1445 50.752 78.273 41.078 1.00189.50 A ATOM 27953 ZN ZN A1506 50.7529999.9999999.999 1.00166.17 A """)) pdb_inp = pdb.input(source_info=None, lines=flex.split_lines("""\ ATOM 10849 C ILE A1445 50.977 77.127 41.547 1.00129.33 A ATOM 10850 O ILE A1445 50.257 76.569 42.421 1.00129.33 A ATOM 10851 OXT ILE A1445 50.752 78.273 41.078 1.00189.50 A ATOM 27953 ZN ZN A1506 50.752 78.2739999.999 1.00166.17 A """)) try: pdb_inp = pdb.input(source_info=None, lines=flex.split_lines("""\ ATOM 10849 C ILE A1445 50.977 77.127 41.547 1.00129.33 A ATOM 10850 O ILE A1445 50.257 76.569 42.421 1.00129.33 A ATOM 10851 OXT ILE A1445 50.752 78.273 41.078 1.00189.50 A ATOM 27953 ZN ZN A1506 9999.9999999.9999999.999 1.00166.17 A ATOM 27954 ZN ZN A1508 9999.9999999.9999999.999 1.00166.17 A """)) except RuntimeError as e: assert str(e).find( "IOTBX_ASSERT(! (xyz[0]>9999 && xyz[1]>9999 && xyz[2]>9999)) failure.") >0 else: raise Exception_expected def exercise_is_pure_main_conf(): """ This test is to illustrate what is 'is_pure_main_conf' parameter. It is turned off. """ pdb_inp = pdb.input(source_info=None, lines=flex.split_lines("""\ ATOM 1904 N GLU M 7 22.484 46.518 1.826 1.00 38.08 N ATOM 1905 CA AGLU M 7 22.261 45.290 1.052 0.50 37.74 C ATOM 1906 CA BGLU M 7 22.222 45.269 1.113 0.50 37.74 C ATOM 1907 C GLU M 7 23.326 44.233 1.331 1.00 37.38 C ATOM 1908 O GLU M 7 23.020 43.060 1.550 1.00 37.42 O ATOM 1909 CB AGLU M 7 22.249 45.622 -0.449 0.50 37.75 C ATOM 1910 CB BGLU M 7 21.980 45.510 -0.378 0.50 37.76 C ATOM 1911 CG AGLU M 7 22.567 44.444 -1.378 0.50 37.91 C ATOM 1912 CG BGLU M 7 21.408 44.296 -1.097 0.50 37.93 C ATOM 1913 CD AGLU M 7 23.700 44.738 -2.358 0.50 38.10 C ATOM 1914 CD BGLU M 7 21.008 44.592 -2.523 0.50 38.25 C ATOM 1915 OE1AGLU M 7 24.714 45.352 -1.953 0.50 38.05 O ATOM 1916 OE1BGLU M 7 20.006 45.310 -2.724 0.50 38.27 O ATOM 1917 OE2AGLU M 7 23.582 44.336 -3.534 0.50 37.92 O ATOM 1918 OE2BGLU M 7 21.690 44.096 -3.443 0.50 38.22 O ATOM 1919 N THR M 8 24.587 44.665 1.271 1.00 36.83 N ATOM 1920 CA BTHR M 8 25.711 43.853 1.726 0.50 36.29 C ATOM 1921 CA CTHR M 8 25.700 43.848 1.745 0.50 36.39 C ATOM 1922 C THR M 8 26.210 44.451 3.041 1.00 35.92 C ATOM 1923 O THR M 8 26.572 45.630 3.097 1.00 35.88 O ATOM 1924 CB BTHR M 8 26.847 43.800 0.679 0.50 36.40 C ATOM 1925 CB CTHR M 8 26.854 43.708 0.703 0.50 36.51 C ATOM 1926 OG1BTHR M 8 26.323 43.348 -0.576 0.50 36.54 O ATOM 1927 OG1CTHR M 8 27.904 44.642 0.990 0.50 36.90 O ATOM 1928 CG2BTHR M 8 27.956 42.852 1.124 0.50 36.27 C ATOM 1929 CG2CTHR M 8 26.350 43.915 -0.725 0.50 36.69 C """)) h = pdb_inp.construct_hierarchy() print("*"*50) for conf in h.only_chain().conformers(): print("conf altloc '%s'" % conf.altloc) for res in conf.residues(): print("residue:", res.id_str(), "is_pure_main_conf:", res.is_pure_main_conf) for atom in res.atoms(): print(" ", atom.id_str()) print("*"*50) print("*"*50) for rg in h.only_chain().residue_groups(): print("rg ", rg.resseq, rg.have_conformers()) for ag in rg.atom_groups(): print("ag:", ag.resname, ag.altloc) for atom in ag.atoms(): print(" ", atom.id_str()) # assert not h.only_chain().conformers()[2].residues()[0].is_pure_main_conf # assert not h.only_chain().conformers()[2].residues()[1].is_pure_main_conf r0_pmc = h.only_chain().conformers()[2].residues()[0].is_pure_main_conf r1_pmc = h.only_chain().conformers()[2].residues()[1].is_pure_main_conf print("Residue 0 is", r0_pmc) print("Residue 1 is", r1_pmc) def exercise_selection_and_deep_copy(): """ This test illustrates strange behavior while executing selections and assigning the result to the same variable. In partucular, the atoms in resulting hierarchy miss their parents. Otherwise, hierarchy seems to be functional. """ def show_atoms(h): for a in h.atoms(): print(a.id_str()) pdb_inp = pdb.input(source_info=None, lines=flex.split_lines("""\ ATOM 0 N ASP A 1 49.347 -62.804 60.380 1.00 34.60 N ATOM 1 CA ASP A 1 47.975 -63.194 59.946 1.00 33.86 C ATOM 2 C ASP A 1 47.122 -63.665 61.114 1.00 34.02 C ATOM 3 O ASP A 1 47.573 -64.451 61.947 1.00 32.23 O ATOM 4 N VAL A 2 45.889 -63.176 61.175 1.00 31.94 N ATOM 5 CA VAL A 2 44.978 -63.576 62.233 1.00 29.81 C ATOM 6 C VAL A 2 44.472 -64.973 61.900 1.00 28.28 C ATOM 7 O VAL A 2 43.989 -65.221 60.796 1.00 27.24 O ATOM 8 N GLN A 3 44.585 -65.878 62.864 1.00 25.93 N ATOM 9 CA GLN A 3 44.166 -67.262 62.686 1.00 24.46 C ATOM 10 C GLN A 3 42.730 -67.505 63.153 1.00 23.33 C ATOM 11 O GLN A 3 42.389 -67.234 64.302 1.00 20.10 O ATOM 12 N MET A 4 41.894 -68.026 62.256 1.00 24.27 N ATOM 13 CA MET A 4 40.497 -68.318 62.576 1.00 22.89 C ATOM 14 C MET A 4 40.326 -69.824 62.795 1.00 21.48 C ATOM 15 O MET A 4 40.633 -70.625 61.911 1.00 23.73 O """)) pdb_h = pdb_inp.construct_hierarchy() assert pdb_h.atoms()[0].parent() is not None # example 1, everything is normal h1 = pdb_h.deep_copy() assert h1.atoms()[0].parent() is not None h1 = h1.deep_copy() assert h1.atoms()[0].parent() is not None print("example 2") h2 = pdb_h.deep_copy() sel = h2.atom_selection_cache().selection("resid 3") h2 = h2.select(sel) # assert h2.atoms()[0].parent() is not None # FAILURE show_atoms(h2) # in this printout information about residue and chain is missing print("===============") # example 3 - same as 2, but using separate variable for asc to make it work print("example 3") h2 = pdb_h.deep_copy() asc = h2.atom_selection_cache() sel = asc.selection("resid 3") h2 = h2.select(sel) assert h2.atoms()[0].parent() is not None # WORKING!!! show_atoms(h2) print("===============") # example 4 - same as 2, but using variable for hierarchy to make it work print("example 4") h2 = pdb_h.deep_copy() sel = h2.atom_selection_cache().selection("resid 3") h3 = h2.select(sel) assert h3.atoms()[0].parent() is not None # WORKING!!! show_atoms(h3) def exercise_is_ca_only(): pdb_inp = pdb.input(source_info=None, lines=flex.split_lines("""\ ATOM 0 N ASP A 1 49.347 -62.804 60.380 1.00 34.60 N ATOM 1 CA ASP A 1 47.975 -63.194 59.946 1.00 33.86 C ATOM 2 C ASP A 1 47.122 -63.665 61.114 1.00 34.02 C ATOM 3 O ASP A 1 47.573 -64.451 61.947 1.00 32.23 O ATOM 4 N VAL A 2 45.889 -63.176 61.175 1.00 31.94 N ATOM 5 CA VAL A 2 44.978 -63.576 62.233 1.00 29.81 C ATOM 6 C VAL A 2 44.472 -64.973 61.900 1.00 28.28 C ATOM 7 O VAL A 2 43.989 -65.221 60.796 1.00 27.24 O ATOM 8 N GLN B 3 44.585 -65.878 62.864 1.00 25.93 N ATOM 9 CA GLN B 3 44.166 -67.262 62.686 1.00 24.46 C ATOM 10 C GLN B 3 42.730 -67.505 63.153 1.00 23.33 C ATOM 11 O GLN B 3 42.389 -67.234 64.302 1.00 20.10 O ATOM 12 N MET B 4 41.894 -68.026 62.256 1.00 24.27 N ATOM 13 CA MET B 4 40.497 -68.318 62.576 1.00 22.89 C ATOM 14 C MET B 4 40.326 -69.824 62.795 1.00 21.48 C ATOM 15 O MET B 4 40.633 -70.625 61.911 1.00 23.73 O """)) pdb_h = pdb_inp.construct_hierarchy() for chain in pdb_h.only_model().chains(): assert not chain.is_ca_only() pdb_inp = pdb.input(source_info=None, lines=flex.split_lines("""\ ATOM 1 CA ASP A 1 47.975 -63.194 59.946 1.00 33.86 C ATOM 5 CA VAL A 2 44.978 -63.576 62.233 1.00 29.81 C ATOM 8 N GLN B 3 44.585 -65.878 62.864 1.00 25.93 N ATOM 9 CA GLN B 3 44.166 -67.262 62.686 1.00 24.46 C ATOM 10 C GLN B 3 42.730 -67.505 63.153 1.00 23.33 C ATOM 11 O GLN B 3 42.389 -67.234 64.302 1.00 20.10 O ATOM 12 N MET B 4 41.894 -68.026 62.256 1.00 24.27 N ATOM 13 CA MET B 4 40.497 -68.318 62.576 1.00 22.89 C ATOM 14 C MET B 4 40.326 -69.824 62.795 1.00 21.48 C ATOM 15 O MET B 4 40.633 -70.625 61.911 1.00 23.73 O """)) pdb_h = pdb_inp.construct_hierarchy() result = [chain.is_ca_only() for chain in pdb_h.only_model().chains()] assert result == [True, False], result def exercise_expand_to_p1(): pdb_str = """ CRYST1 194.707 61.015 92.246 90.00 116.65 90.00 C 1 2 1 8 ATOM 1 N ASP L 1 52.015 9.560 31.693 1.00 25.58 N END """ pdb_inp = pdb.input(source_info=None, lines=pdb_str) cs = pdb_inp.crystal_symmetry() ph = pdb_inp.construct_hierarchy() assert len(ph.atoms())==1 xyz_p1 = ph.extract_xray_structure( crystal_symmetry=cs).expand_to_p1().sites_cart() p1 = ph.expand_to_p1(crystal_symmetry=cs) assert len(p1.atoms())==4 assert approx_equal(xyz_p1, p1.atoms().extract_xyz()) def exercise_convert_met_to_semet(): pdb_str_met1 = """ ATOM 1 N MET B 37 7.525 5.296 6.399 1.00 10.00 N ATOM 2 CA MET B 37 6.533 6.338 6.634 1.00 10.00 C ATOM 3 C MET B 37 6.175 7.044 5.330 1.00 10.00 C ATOM 4 O MET B 37 5.000 7.200 5.000 1.00 10.00 O ATOM 5 CB MET B 37 7.051 7.351 7.655 1.00 10.00 C ATOM 6 CG MET B 37 7.377 6.750 9.013 1.00 10.00 C ATOM 7 SD MET B 37 8.647 5.473 8.922 1.00 10.00 S ATOM 8 CE MET B 37 8.775 5.000 10.645 1.00 10.00 C TER END """ pdb_str_met2 = """ ATOM 1 N AMET B 37 7.525 5.296 6.399 1.00 10.00 N ATOM 2 CA AMET B 37 6.533 6.338 6.634 1.00 10.00 C ATOM 3 C AMET B 37 6.175 7.044 5.330 1.00 10.00 C ATOM 4 O AMET B 37 5.000 7.200 5.000 1.00 10.00 O ATOM 5 CB AMET B 37 7.051 7.351 7.655 1.00 10.00 C ATOM 6 CG AMET B 37 7.377 6.750 9.013 1.00 10.00 C ATOM 7 SD AMET B 37 8.647 5.473 8.922 1.00 10.00 S ATOM 8 CE AMET B 37 8.775 5.000 10.645 1.00 10.00 C ATOM 1 N BMET B 37 7.525 5.296 6.399 1.00 10.00 N ATOM 2 CA BMET B 37 6.533 6.338 6.634 1.00 10.00 C ATOM 3 C BMET B 37 6.175 7.044 5.330 1.00 10.00 C ATOM 4 O BMET B 37 5.000 7.200 5.000 1.00 10.00 O ATOM 5 CB BMET B 37 7.051 7.351 7.655 1.00 10.00 C ATOM 6 CG BMET B 37 7.377 6.750 9.013 1.00 10.00 C ATOM 7 SD BMET B 37 8.647 5.473 8.922 1.00 10.00 S ATOM 8 CE BMET B 37 8.775 5.000 10.645 1.00 10.00 C TER END """ for pdb_str in [pdb_str_met1, pdb_str_met2]: pi = pdb.input(source_info=None, lines=pdb_str) ph_met_in = pi.construct_hierarchy() ph_met_in.convert_met_to_semet() for rg in ph_met_in.residue_groups(): for rn in rg.unique_resnames(): assert rn=="MSE" ph_met_in.convert_semet_to_met() for rg in ph_met_in.residue_groups(): for rn in rg.unique_resnames(): assert rn=="MET" def exercise_truncate_to_polyala(): pdb_str = """ ATOM 1 N AMET B 37 7.525 5.296 6.399 1.00 10.00 N ATOM 2 CA AMET B 37 6.533 6.338 6.634 1.00 10.00 C ATOM 3 C AMET B 37 6.175 7.044 5.330 1.00 10.00 C ATOM 4 O AMET B 37 5.000 7.200 5.000 1.00 10.00 O ATOM 5 CB AMET B 37 7.051 7.351 7.655 1.00 10.00 C ATOM 6 CG AMET B 37 7.377 6.750 9.013 1.00 10.00 C ATOM 7 SD AMET B 37 8.647 5.473 8.922 1.00 10.00 S ATOM 8 CE AMET B 37 8.775 5.000 10.645 1.00 10.00 C ATOM 1 N BMET B 37 7.525 5.296 6.399 1.00 10.00 N ATOM 2 CA BMET B 37 6.533 6.338 6.634 1.00 10.00 C ATOM 3 C BMET B 37 6.175 7.044 5.330 1.00 10.00 C ATOM 4 O BMET B 37 5.000 7.200 5.000 1.00 10.00 O ATOM 5 CB BMET B 37 7.051 7.351 7.655 1.00 10.00 C ATOM 6 CG BMET B 37 7.377 6.750 9.013 1.00 10.00 C ATOM 7 SD BMET B 37 8.647 5.473 8.922 1.00 10.00 S ATOM 8 CE BMET B 37 8.775 5.000 10.645 1.00 10.00 C TER END """ pi = pdb.input(source_info=None, lines=pdb_str) ph_in = pi.construct_hierarchy() ph_in.truncate_to_poly_gly() for a in ph_in.atoms(): assert a.name in [" N ", " CA ", " C ", " O ", " CB "] def exercise_set_atomic_charge(): pdb_str = """ ATOM 1 CL CL X 1 0.000 0.000 0.000 1.00 20.00 CL END """ pi = pdb.input(source_info=None, lines=pdb_str) ph = pi.construct_hierarchy() ph.set_atomic_charge(iselection=flex.size_t([0]), charge=-1) xrs = ph.extract_xray_structure() assert (xrs.scatterers()[0].scattering_type == 'Cl1-') assert (ph.atoms()[0].charge == '1-') def exercise_remove_atoms(): random.seed(1) flex.set_random_seed(1) pdb_str = """ ATOM 1 N AMET B 37 7.525 5.296 6.399 1.00 10.00 N ATOM 2 CA AMET B 37 6.533 6.338 6.634 1.00 10.00 C ATOM 3 C AMET B 37 6.175 7.044 5.330 1.00 10.00 C ATOM 4 O AMET B 37 5.000 7.200 5.000 1.00 10.00 O ATOM 5 CB AMET B 37 7.051 7.351 7.655 1.00 10.00 C ATOM 6 CG AMET B 37 7.377 6.750 9.013 1.00 10.00 C ATOM 7 SD AMET B 37 8.647 5.473 8.922 1.00 10.00 S ATOM 8 CE AMET B 37 8.775 5.000 10.645 1.00 10.00 C ATOM 1 N BMET B 37 7.525 5.296 6.399 1.00 10.00 N ATOM 2 CA BMET B 37 6.533 6.338 6.634 1.00 10.00 C ATOM 3 C BMET B 37 6.175 7.044 5.330 1.00 10.00 C ATOM 4 O BMET B 37 5.000 7.200 5.000 1.00 10.00 O ATOM 5 CB BMET B 37 7.051 7.351 7.655 1.00 10.00 C ATOM 6 CG BMET B 37 7.377 6.750 9.013 1.00 10.00 C ATOM 7 SD BMET B 37 8.647 5.473 8.922 1.00 10.00 S ATOM 8 CE BMET B 37 8.775 5.000 10.645 1.00 10.00 C ATOM 1 N AMET B 38 7.525 5.296 6.399 1.00 10.00 N ATOM 2 CA AMET B 38 6.533 6.338 6.634 1.00 10.00 C ATOM 3 C AMET B 38 6.175 7.044 5.330 1.00 10.00 C ATOM 4 O AMET B 38 5.000 7.200 5.000 1.00 10.00 O ATOM 5 CB AMET B 38 7.051 7.351 7.655 1.00 10.00 C ATOM 6 CG AMET B 38 7.377 6.750 9.013 1.00 10.00 C ATOM 7 SD AMET B 38 8.647 5.473 8.922 1.00 10.00 S ATOM 8 CE AMET B 38 8.775 5.000 10.645 1.00 10.00 C ATOM 1 N BMET B 38 7.525 5.296 6.399 1.00 10.00 N ATOM 2 CA BMET B 38 6.533 6.338 6.634 1.00 10.00 C ATOM 3 C BMET B 38 6.175 7.044 5.330 1.00 10.00 C ATOM 4 O BMET B 38 5.000 7.200 5.000 1.00 10.00 O ATOM 5 CB BMET B 38 7.051 7.351 7.655 1.00 10.00 C ATOM 6 CG BMET B 38 7.377 6.750 9.013 1.00 10.00 C ATOM 7 SD BMET B 38 8.647 5.473 8.922 1.00 10.00 S ATOM 8 CE BMET B 38 8.775 5.000 10.645 1.00 10.00 C ATOM 1 N AMET B 39 7.525 5.296 6.399 1.00 10.00 N ATOM 2 CA AMET B 39 6.533 6.338 6.634 1.00 10.00 C ATOM 3 C AMET B 39 6.175 7.044 5.330 1.00 10.00 C ATOM 4 O AMET B 39 5.000 7.200 5.000 1.00 10.00 O ATOM 5 CB AMET B 39 7.051 7.351 7.655 1.00 10.00 C ATOM 6 CG AMET B 39 7.377 6.750 9.013 1.00 10.00 C ATOM 7 SD AMET B 39 8.647 5.473 8.922 1.00 10.00 S ATOM 8 CE AMET B 39 8.775 5.000 10.645 1.00 10.00 C ATOM 1 N BMET B 39 7.525 5.296 6.399 1.00 10.00 N ATOM 2 CA BMET B 39 6.533 6.338 6.634 1.00 10.00 C ATOM 3 C BMET B 39 6.175 7.044 5.330 1.00 10.00 C ATOM 4 O BMET B 39 5.000 7.200 5.000 1.00 10.00 O ATOM 5 CB BMET B 39 7.051 7.351 7.655 1.00 10.00 C ATOM 6 CG BMET B 39 7.377 6.750 9.013 1.00 10.00 C ATOM 7 SD BMET B 39 8.647 5.473 8.922 1.00 10.00 S ATOM 8 CE BMET B 39 8.775 5.000 10.645 1.00 10.00 C TER END """ pi = pdb.input(source_info=None, lines=pdb_str) ph_in = pi.construct_hierarchy() s1 = ph_in.atoms_size() ph = ph_in.remove_atoms(fraction=0.1) s2 = ph.atoms_size() f = s2*100./s1 assert f>90 and f<100 def exercise_set_atomic_charge(): pdb_str = """ ATOM 1 CL CL X 1 0.000 0.000 0.000 1.00 20.00 CL END """ pi = pdb.input(source_info=None, lines=pdb_str) ph = pi.construct_hierarchy() ph.set_atomic_charge(iselection=flex.size_t([0]), charge=-1) xrs = ph.extract_xray_structure() assert (xrs.scatterers()[0].scattering_type == 'Cl1-') assert (ph.atoms()[0].charge == '1-') def exercise_rename_chain_id(): pdb_str = """ ATOM 1 N AMET B 37 7.525 5.296 6.399 1.00 10.00 N ATOM 2 CA AMET B 37 6.533 6.338 6.634 1.00 10.00 C ATOM 3 C AMET B 37 6.175 7.044 5.330 1.00 10.00 C ATOM 4 O AMET B 37 5.000 7.200 5.000 1.00 10.00 O ATOM 5 CB AMET B 37 7.051 7.351 7.655 1.00 10.00 C ATOM 6 CG AMET B 37 7.377 6.750 9.013 1.00 10.00 C ATOM 7 SD AMET B 37 8.647 5.473 8.922 1.00 10.00 S ATOM 8 CE AMET B 37 8.775 5.000 10.645 1.00 10.00 C TER ATOM 1 N BMET C 37 7.525 5.296 6.399 1.00 10.00 N ATOM 2 CA BMET C 37 6.533 6.338 6.634 1.00 10.00 C ATOM 3 C BMET C 37 6.175 7.044 5.330 1.00 10.00 C ATOM 4 O BMET C 37 5.000 7.200 5.000 1.00 10.00 O ATOM 5 CB BMET C 37 7.051 7.351 7.655 1.00 10.00 C ATOM 6 CG BMET C 37 7.377 6.750 9.013 1.00 10.00 C ATOM 7 SD BMET C 37 8.647 5.473 8.922 1.00 10.00 S ATOM 8 CE BMET C 37 8.775 5.000 10.645 1.00 10.00 C TER END """ pi = pdb.input(source_info=None, lines=pdb_str) ph_in = pi.construct_hierarchy() ph_in.rename_chain_id(old_id="C", new_id="A") assert [c.id.strip() for c in ph_in.chains()] == ["B","A"] def exercise_shift_to_origin(): pdb_inp = pdb.input(source_info=None, lines="""\ CRYST1 10.000 10.000 10.000 90.00 90.00 90.00 P 1 HETATM 1135 MG MG A1002 15.000 25.000 35.000 1.00 40.88 Mg """) ph = pdb_inp.construct_hierarchy() ph.shift_to_origin(crystal_symmetry=pdb_inp.crystal_symmetry()) assert approx_equal(list(ph.atoms().extract_xyz())[0],[5,5,5]) def exercise_remove_residue_groups_with_atoms_on_special_positions_selective(): pdb_inp = pdb.input(source_info=None, lines="""\ CRYST1 63.163 63.163 63.163 90.00 90.00 90.00 P 43 3 2 24 ATOM 1 N ASN A 157 24.727 56.381 3.666 1.00 91.06 N ATOM 2 CA ASN A 157 25.810 56.034 2.749 1.00 80.09 C ATOM 3 C ASN A 157 26.430 54.639 2.977 1.00 78.36 C ATOM 4 O ASN A 157 26.317 54.040 4.054 1.00 63.78 O ATOM 5 CB ASN A 157 26.887 57.131 2.745 1.00101.42 C ATOM 6 CG ASN A 157 28.150 56.719 1.991 1.00118.14 C ATOM 7 OD1 ASN A 157 29.118 56.232 2.602 1.00 77.94 O ATOM 8 ND2 ASN A 157 28.130 56.863 0.656 1.00100.46 N TER HETATM 143 S SO4 A 201 35.546 59.209 3.956 0.18 60.16 S HETATM 144 O1 SO4 A 201 35.886 60.613 4.197 0.18 51.29 O HETATM 145 O2 SO4 A 201 35.779 58.873 2.549 0.18 51.29 O HETATM 146 O3 SO4 A 201 36.392 58.365 4.792 0.18 51.09 O HETATM 147 O4 SO4 A 201 34.143 58.969 4.301 0.18 51.29 O HETATM 148 O HOH A 301 34.726 50.417 -2.119 1.00 57.37 O HETATM 153 O HOH A 306 40.659 54.085 9.078 0.33 44.83 O HETATM 154 O HOH A 307 38.574 47.757 2.362 1.00 63.80 O END """) cs = pdb_inp.crystal_symmetry() ph = pdb_inp.construct_hierarchy() removed = ph.remove_residue_groups_with_atoms_on_special_positions_selective( crystal_symmetry=cs) assert removed == ['A, 201 ,SO4', 'A, 306 ,HOH'] removed = ph.remove_residue_groups_with_atoms_on_special_positions_selective( crystal_symmetry=cs) assert removed == [] def exercise_occupancy_counts(): pdb_inp = pdb.input(source_info=None, lines="""\ ATOM 0 N THR A 2 -3.791 -8.769 29.092 1.20 24.15 N ATOM 1 CA THR A 2 -3.627 -7.675 28.090 1.00 25.97 C ATOM 2 C THR A 2 -2.202 -7.127 28.152 0.00 24.18 C ATOM 3 O THR A 2 -1.633 -6.984 29.233 1.00 24.71 O ATOM 4 CB THR A 2 -4.627 -6.527 28.357 1.00 26.50 C ATOM 5 OG1 THR A 2 -5.961 -7.056 28.404 -1.00 28.79 O ATOM 6 CG2 THR A 2 -4.548 -5.486 27.255 -0.50 27.05 C ATOM 7 N LYS A 3 -1.629 -6.832 26.988 1.00 24.44 N ATOM 8 C LYS A 3 -0.196 -4.896 27.485 0.00 23.66 C ATOM 9 O LYS A 3 -1.094 -4.084 27.265 1.00 23.75 O ATOM 10 CB LYS A 3 0.199 -6.262 25.438 1.00 26.61 C ATOM 11 CA ALYS A 3 -0.266 -6.307 26.901 1.00 25.16 C ATOM 12 CG ALYS A 3 0.312 -7.619 24.754 0.50 27.88 C ATOM 13 CD ALYS A 3 1.436 -8.454 25.347 0.50 27.58 C ATOM 14 CE ALYS A 3 1.585 -9.783 24.621 0.50 28.69 C ATOM 15 NZ ALYS A 3 0.362 -10.624 24.732 0.50 28.63 N ATOM 16 CA BLYS A 3 -0.266 -6.307 26.901 1.00 25.16 C ATOM 17 CG BLYS A 3 0.201 -7.603 24.718 0.50 27.66 C ATOM 18 CD BLYS A 3 1.205 -8.570 25.325 0.50 27.30 C ATOM 19 CE BLYS A 3 1.213 -9.893 24.575 0.50 28.17 C ATOM 20 NZ BLYS A 3 2.149 -10.873 25.188 0.50 27.40 N ATOM 21 N LYS A 4 0.873 -4.612 28.225 1.00 22.24 N ATOM 22 CA LYS A 4 1.068 -3.295 28.826 1.00 21.81 C ATOM 23 C LYS A 4 2.337 -2.642 28.295 1.00 19.26 C ATOM 24 O LYS A 4 3.417 -3.243 28.310 0.00 18.66 O ATOM 25 CB LYS A 4 1.156 -3.398 30.354 1.00 23.29 C ATOM 26 CG LYS A 4 -0.170 -3.685 31.031 1.00 27.60 C ATOM 27 CD LYS A 4 -0.049 -3.681 32.551 1.00 32.16 C ATOM 28 CE LYS A 4 0.797 -4.842 33.052 0.40 33.04 C ATOM 29 NZ LYS A 4 0.827 -4.892 34.541 1.10 36.05 N """) ph = pdb_inp.construct_hierarchy() oc = ph.occupancy_counts() eps = 1.e-6 assert (approx_equal(oc.mean, 0.64, eps=eps)) assert (approx_equal(oc.negative, 2, eps=eps)) assert (approx_equal(oc.zero_count, 3, eps=eps)) assert (approx_equal(oc.zero_fraction, 10, eps=eps)) assert (approx_equal(oc.equal_to_1_count, 14, eps=eps)) assert (approx_equal(oc.equal_to_1_fraction, 14*100/30, eps=eps)) assert (approx_equal(oc.between_0_and_1_count, 9, eps=eps)) assert (approx_equal(oc.between_0_and_1_fraction, 30, eps=eps)) assert (approx_equal(oc.greater_than_1_count, 2, eps=eps)) assert (approx_equal(oc.greater_than_1_fraction, 2*100/30, eps=eps)) assert (approx_equal(oc.alt_conf_frac, 100/3, eps=eps)) def exercise(args): comprehensive = "--comprehensive" in args forever = "--forever" in args print("iotbx.pdb.hierarchy.atom.sizeof_data():", \ pdb.hierarchy.atom.sizeof_data()) offsets = pdb.hierarchy.atom.data_offsets() if (comprehensive): print("iotbx.pdb.hierarchy.atom.data_offsets():") prev = 0 for key,value in sorted(offsets.items()): print(" %+3d %3d %s" % (key-prev, key, value)) prev = key phenix_regression_pdb_file_names = get_phenix_regression_pdb_file_names() while True: exercise_remove_residue_groups_with_atoms_on_special_positions_selective() exercise_shift_to_origin() exercise_rename_chain_id() exercise_convert_met_to_semet() exercise_truncate_to_polyala() exercise_set_atomic_charge() exercise_remove_atoms() exercise_expand_to_p1() exercise_chunk_selections() exercise_set_i_seq() exercise_get_peptide_c_alpha_selection() exercise_adopt_xray_structure() exercise_adopt_xray_structure2() exercise_atom() exercise_atom_group() exercise_residue_group() exercise_chain() exercise_model() exercise_root() exercise_atom_id_str() exercise_format_atom_record() exercise_construct_hierarchy() exercise_convenience_generators() exercise_only() exercise_merge_atom_groups() exercise_merge_residue_groups() exercise_chain_merge_residue_groups() exercise_edit_blank_altloc() exercise_find_pure_altloc_ranges() exercise_occupancy_groups_simple() exercise_conformers() exercise_residue() exercise_is_identical_hierarchy() exercise_is_similar_hierarchy() exercise_atoms() exercise_atoms_interleaved_conf() exercise_as_pdb_string( pdb_file_names=phenix_regression_pdb_file_names, comprehensive=comprehensive) exercise_atom_with_labels() exercise_transfer_chains_from_other() exercise_root_select() exercise_root_altloc_indices() exercise_root_pickling() exercise_residue_pickling() exercise_hierarchy_input() exercise_other() exercise_equality_and_hashing() exercise_atom_is_in_same_conformer_as() exercise_substitute_atom_group() exercise_atom_xyz_9999() # exercise_is_pure_main_conf() exercise_selection_and_deep_copy() exercise_is_ca_only() exercise_occupancy_counts() if (not forever): break print(format_cpu_times()) if (__name__ == "__main__"): exercise(sys.argv[1:])