from __future__ import absolute_import, division, print_function from iotbx.cns.crystal_symmetry_utils import \ re_sg_uc, crystal_symmetry_from_re_match from cctbx import crystal from cctbx import uctbx from cctbx import sgtbx from cctbx import adptbx from cctbx import xray import cctbx.eltbx.xray_scattering from cctbx import eltbx from libtbx import adopt_init_args from libtbx import easy_pickle import re import os from six.moves import range class sdb_site(object): def __init__(self, action, segid, type, x, y, z, b, q, g): adopt_init_args(self, locals()) def as_xray_scatterer(self, unit_cell=None): scattering_type = eltbx.xray_scattering.get_standard_label( label=self.type, exact=False, optional=True) if (scattering_type is None): scattering_type = eltbx.xray_scattering.get_standard_label( label=self.segid, exact=False, optional=True) if (scattering_type is None): scattering_type = "unknown" site = (self.x, self.y, self.z) if (unit_cell is not None): site = unit_cell.fractionalize(site) return xray.scatterer( label="_".join((self.segid, self.type)), site=site, u=adptbx.b_as_u(self.b), occupancy=self.q, scattering_type=scattering_type) class sdb_file(object): def __init__(self, file_name, unit_cell, space_group_info, sites): adopt_init_args(self, locals()) def crystal_symmetry(self): return crystal.symmetry( unit_cell=self.unit_cell, space_group_info=self.space_group_info) def as_xray_structure(self, crystal_symmetry=None, force_symmetry=False, min_distance_sym_equiv=0.5): crystal_symmetry = self.crystal_symmetry().join_symmetry( other_symmetry=crystal_symmetry, force=force_symmetry) assert crystal_symmetry.unit_cell() is not None assert crystal_symmetry.space_group_info() is not None structure = xray.structure(crystal.special_position_settings( crystal_symmetry=crystal_symmetry, min_distance_sym_equiv=min_distance_sym_equiv)) for site in self.sites: structure.add_scatterer(site.as_xray_scatterer(structure.unit_cell())) return structure def generic_add_str(m, buffer): if (not m): return seq_no = int(m.group(1)) assert seq_no == len(buffer) + 1 buffer.append(m.group(2)) def generic_add_float(m, buffer): if (not m): return seq_no = int(m.group(1)) assert seq_no == len(buffer) + 1 buffer.append(float(m.group(2))) class raw_parameters(object): def __init__(self, file_name): self.file_name = file_name self.unit_cell = None self.space_group_info = None self.action = [] self.segid = [] self.type = [] self.x = [] self.y = [] self.z = [] self.b = [] self.q = [] self.g = [] def add_action(self, m): generic_add_str(m, self.action) def add_segid(self, m): generic_add_str(m, self.segid) def add_type(self, m): generic_add_str(m, self.type) def add_x(self, m): generic_add_float(m, self.x) def add_y(self, m): generic_add_float(m, self.y) def add_z(self, m): generic_add_float(m, self.z) def add_b(self, m): generic_add_float(m, self.b) def add_q(self, m): generic_add_float(m, self.q) def add_g(self, m): generic_add_str(m, self.g) def as_sdb_sites(self): assert len(self.segid) == len(self.action) assert len(self.type) == len(self.action) assert len(self.x) == len(self.action) assert len(self.y) == len(self.action) assert len(self.z) == len(self.action) assert len(self.b) == len(self.action) assert len(self.q) == len(self.action) assert len(self.g) == len(self.action) sites = [] for i in range(len(self.x)): sites.append(sdb_site( self.action[i], self.segid[i], self.type[i], self.x[i], self.y[i], self.z[i], self.b[i], self.q[i], self.g[i])) return sdb_file( self.file_name, self.unit_cell, self.space_group_info, sites) def multi_sdb_parser(lines, file_name=None, max_characters=1000000): # Parser for one or more cns sdb files. # Lines interpreted: # {+ file: heavy_search_1.sdb +} # sg= P6 a= 116.097 b= 116.097 c= 44.175 alpha= 90 beta= 90 gamma= 120 # {===>} site.action_1="refine"; # {===>} site.segid_1="SITE"; site.type_1="SE"; # {===>} site.x_1=18.7869; site.y_1=12.1257; site.z_1=0.163635; # {===>} site.b_1=65.6408; site.q_1=1; site.g_1=""; # Sites must be sorted. sdb_files = [] block_name = None current_symmetry = None n_characters = 0 p = 0 for line in lines: if (max_characters != 0): n_characters += len(line) if (n_characters > max_characters): break m = re.search(r'\{\+\s+file:\s*(\S*)', line) if (m): block_name = m.group(1) m = re.match(re_sg_uc, line) if (m): current_symmetry = crystal_symmetry_from_re_match(m=m) m = re.search( r'\{\-\s+begin\s+block\s+parameter\s+definition\s+\-\}', line) if (m): if (block_name is None): i = len(sdb_files) + 1 if (p): i += 1 if (file_name is None): block_name = "block_%d" % i else: block_name = file_name + "_%d" % i if (p): sdb_files.append(p.as_sdb_sites()) p = raw_parameters(block_name) if (current_symmetry is None): p.unit_cell = None p.space_group_info = None else: p.unit_cell = current_symmetry.unit_cell() p.space_group_info = current_symmetry.space_group_info() current_symmetry = None block_name = None if (not p): continue m = re.match(r'\{===>\}\s*sg=\s*"(\S+)"\s*;', line) if (m): p.space_group_info = sgtbx.space_group_info(m.group(1)) p.add_action(re.search(r'site\.action_(\d+)\s*=\s*"([^"]*)"', line)) p.add_segid(re.search(r'site\.segid_(\d+)\s*=\s*"([^"]*)"', line)) p.add_type(re.search(r'site\.type_(\d+)\s*=\s*"([^"]*)"', line)) p.add_x(re.search(r'site\.x_(\d+)\s*=\s*([^\s;]*)', line)) p.add_y(re.search(r'site\.y_(\d+)\s*=\s*([^\s;]*)', line)) p.add_z(re.search(r'site\.z_(\d+)\s*=\s*([^\s;]*)', line)) p.add_b(re.search(r'site\.b_(\d+)\s*=\s*([^\s;]*)', line)) p.add_q(re.search(r'site\.q_(\d+)\s*=\s*([^\s;]*)', line)) p.add_g(re.search(r'site\.g_(\d+)\s*=\s*"([^"]*)"', line)) if (p): sdb_files.append(p.as_sdb_sites()) return sdb_files def run(args): show_raw = "--show_raw" in args write_pickle = "--pickle" in args unit_cell = None space_group_info = None for arg in args: if (arg.startswith("--unit_cell=")): params = arg.split("=", 1)[1] unit_cell = uctbx.unit_cell(params) elif (arg.startswith("--space_group=")): symbol = arg.split("=", 1)[1] space_group_info = sgtbx.space_group_info(symbol) for file_name in args: if (file_name.startswith("--")): continue f = open(file_name, "r") lines = f.readlines() f.close() sdb_files = multi_sdb_parser(lines, file_name) for sdb in sdb_files: if (unit_cell is not None): sdb.unit_cell = unit_cell if (space_group_info is not None): sdb.space_group_info=space_group_info print("file:", sdb.file_name) if (sdb.unit_cell is not None): print("unit cell:", sdb.unit_cell.parameters()) if (sdb.space_group_info is not None): print("space group:", sdb.space_group_info) if (show_raw): for site in sdb.sites: print(site.action, site.segid, site.type, site.g) print(" ", site.x, site.y, site.z, site.b, site.q) else: xray_structure = sdb.as_xray_structure() xray_structure.show_summary().show_scatterers() if (write_pickle): file_name_pickle = os.path.split(sdb.file_name)[1] + ".pickle" print("Writing:", file_name_pickle) easy_pickle.dump(file_name_pickle, xray_structure) print()