""" Test for mmtbx.ncs.ligands module and associated command-line tool mmtbx.apply_ncs_to_ligands (used in phenix.ligand_pipeline) """ from __future__ import absolute_import, division, print_function from iotbx import file_reader from libtbx import easy_run from libtbx.utils import null_out import os.path as op import os def make_inputs(prefix="tst_ligand_ncs"): pdb_raw = """\ CRYST1 25.000 10.000 25.477 90.00 107.08 90.00 P 1 ATOM 1 N GLY A 1 9.010 0.535 -6.096 1.00 16.23 N ATOM 2 CA GLY A 1 9.052 0.053 -4.707 1.00 16.20 C ATOM 3 C GLY A 1 8.015 -1.161 -4.448 1.00 15.91 C ATOM 4 O GLY A 1 7.563 -1.905 -5.385 1.00 16.11 O ATOM 5 N ASN A 2 7.642 -1.374 -3.185 1.00 15.02 N ATOM 6 CA ASN A 2 6.537 -2.383 -2.848 1.00 13.92 C ATOM 7 C ASN A 2 5.231 -1.825 -3.428 1.00 12.24 C ATOM 8 O ASN A 2 4.965 -0.471 -3.432 1.00 11.42 O ATOM 9 CB ASN A 2 6.391 -2.550 -1.340 1.00 14.42 C ATOM 10 CG ASN A 2 7.639 -3.142 -0.697 1.00 13.92 C ATOM 11 ND2 ASN A 2 8.253 -2.228 0.168 1.00 12.78 N ATOM 12 OD1 ASN A 2 8.062 -4.416 -0.978 1.00 14.39 O ATOM 13 N ASN A 3 4.414 -2.880 -3.904 1.00 12.20 N ATOM 14 CA ASN A 3 3.168 -2.511 -4.594 1.00 11.81 C ATOM 15 C ASN A 3 1.927 -3.147 -3.910 1.00 10.59 C ATOM 16 O ASN A 3 1.840 -4.501 -3.653 1.00 10.32 O ATOM 17 CB ASN A 3 3.235 -3.076 -6.046 1.00 12.51 C ATOM 18 CG ASN A 3 1.973 -2.713 -6.848 1.00 12.59 C ATOM 19 ND2 ASN A 3 1.258 -3.883 -7.268 1.00 12.39 N ATOM 20 OD1 ASN A 3 1.661 -1.397 -7.106 1.00 13.64 O ATOM 21 N GLN A 4 0.973 -2.158 -3.608 1.00 10.34 N ATOM 22 CA GLN A 4 -0.369 -2.634 -3.208 1.00 10.00 C ATOM 23 C GLN A 4 -1.409 -1.846 -4.085 1.00 10.21 C ATOM 24 O GLN A 4 -1.521 -0.467 -4.070 1.00 8.99 O ATOM 25 CB GLN A 4 -0.659 -2.286 -1.736 1.00 10.00 C ATOM 26 CG GLN A 4 -1.933 -3.051 -1.229 1.00 10.50 C ATOM 27 CD GLN A 4 -2.488 -2.371 0.060 1.00 11.36 C ATOM 28 NE2 GLN A 4 -2.690 -3.328 1.055 1.00 10.43 N ATOM 29 OE1 GLN A 4 -2.751 -1.015 0.151 1.00 12.29 O ATOM 30 N GLN A 5 -2.163 -2.714 -4.857 1.00 10.48 N ATOM 31 CA GLN A 5 -3.260 -2.063 -5.630 1.00 11.24 C ATOM 32 C GLN A 5 -4.607 -2.687 -5.178 1.00 11.40 C ATOM 33 O GLN A 5 -4.805 -4.059 -5.092 1.00 11.94 O ATOM 34 CB GLN A 5 -3.037 -2.282 -7.129 1.00 11.14 C ATOM 35 CG GLN A 5 -1.863 -1.378 -7.653 1.00 10.65 C ATOM 36 CD GLN A 5 -1.348 -1.972 -8.965 1.00 10.73 C ATOM 37 NE2 GLN A 5 -1.523 -1.092 -10.027 1.00 11.31 N ATOM 38 OE1 GLN A 5 -0.803 -3.209 -9.028 1.00 10.14 O ATOM 39 N ASN A 6 -5.522 -1.659 -4.872 1.00 11.56 N ATOM 40 CA ASN A 6 -6.830 -2.073 -4.359 1.00 12.07 C ATOM 41 C ASN A 6 -7.880 -1.587 -5.353 1.00 13.18 C ATOM 42 O ASN A 6 -8.282 -0.283 -5.362 1.00 13.64 O ATOM 43 CB ASN A 6 -7.073 -1.296 -3.017 1.00 12.12 C ATOM 44 CG ASN A 6 -5.983 -1.631 -1.998 1.00 12.31 C ATOM 45 ND2 ASN A 6 -5.212 -0.477 -1.645 1.00 11.88 N ATOM 46 OD1 ASN A 6 -5.849 -2.909 -1.517 1.00 13.43 O ATOM 47 N TYR A 7 -8.324 -2.630 -6.193 1.00 14.34 N ATOM 48 CA TYR A 7 -9.191 -2.233 -7.317 1.00 15.00 C ATOM 49 C TYR A 7 -10.635 -2.021 -6.893 1.00 15.64 C ATOM 50 O TYR A 7 -11.045 -2.569 -5.838 1.00 15.68 O ATOM 51 CB TYR A 7 -9.093 -3.430 -8.412 1.00 15.31 C ATOM 52 CG TYR A 7 -7.683 -3.606 -8.931 1.00 15.06 C ATOM 53 CD1 TYR A 7 -6.809 -4.645 -8.368 1.00 15.24 C ATOM 54 CD2 TYR A 7 -7.219 -2.707 -9.960 1.00 14.96 C ATOM 55 CE1 TYR A 7 -5.510 -4.797 -8.830 1.00 14.94 C ATOM 56 CE2 TYR A 7 -5.928 -2.849 -10.429 1.00 15.13 C ATOM 57 CZ TYR A 7 -5.075 -3.892 -9.861 1.00 14.97 C ATOM 58 OH TYR A 7 -3.785 -4.029 -10.335 1.00 14.93 O ATOM 59 OXT TYR A 7 -11.413 -1.296 -7.601 1.00 15.89 O1- TER 59 TYR A 7 HETATM 60 C ACT A 8 -0.915 -6.207 -5.572 1.00 18.56 C HETATM 61 O ACT A 8 0.141 -6.081 -6.241 1.00 19.26 O HETATM 62 CH3 ACT A 8 -1.548 -7.692 -5.404 1.00 18.08 C HETATM 63 OXT ACT A 8 -1.457 -5.087 -5.051 1.00 18.36 O HETATM 64 O HOH A 9 -10.495 -2.647 -3.168 1.00 17.57 O HETATM 65 O HOH A 10 6.480 1.219 -7.070 1.00 21.27 O HETATM 66 O HOH A 11 -11.846 0.122 -9.956 1.00 27.52 O HETATM 67 O HOH A 12 1.576 -3.897 -11.035 1.00 44.76 O TER 68 HOH A 12 ATOM 69 N GLY B 1 -9.010 5.535 6.096 1.00 16.23 N ATOM 70 CA GLY B 1 -9.052 5.053 4.707 1.00 16.20 C ATOM 71 C GLY B 1 -8.015 3.839 4.448 1.00 15.91 C ATOM 72 O GLY B 1 -7.563 3.095 5.385 1.00 16.11 O ATOM 73 N ASN B 2 -7.642 3.626 3.185 1.00 15.02 N ATOM 74 CA ASN B 2 -6.537 2.617 2.848 1.00 13.92 C ATOM 75 C ASN B 2 -5.231 3.175 3.428 1.00 12.24 C ATOM 76 O ASN B 2 -4.965 4.529 3.432 1.00 11.42 O ATOM 77 CB ASN B 2 -6.391 2.450 1.340 1.00 14.42 C ATOM 78 CG ASN B 2 -7.639 1.858 0.697 1.00 13.92 C ATOM 79 ND2 ASN B 2 -8.253 2.772 -0.168 1.00 12.78 N ATOM 80 OD1 ASN B 2 -8.062 0.584 0.978 1.00 14.39 O ATOM 81 N ASN B 3 -4.414 2.120 3.904 1.00 12.20 N ATOM 82 CA ASN B 3 -3.168 2.489 4.594 1.00 11.81 C ATOM 83 C ASN B 3 -1.927 1.853 3.910 1.00 10.59 C ATOM 84 O ASN B 3 -1.840 0.499 3.653 1.00 10.32 O ATOM 85 CB ASN B 3 -3.235 1.924 6.046 1.00 12.51 C ATOM 86 CG ASN B 3 -1.973 2.287 6.848 1.00 12.59 C ATOM 87 ND2 ASN B 3 -1.258 1.117 7.268 1.00 12.39 N ATOM 88 OD1 ASN B 3 -1.661 3.603 7.106 1.00 13.64 O ATOM 89 N GLN B 4 -0.973 2.842 3.608 1.00 10.34 N ATOM 90 CA GLN B 4 0.369 2.366 3.208 1.00 10.00 C ATOM 91 C GLN B 4 1.409 3.154 4.085 1.00 10.21 C ATOM 92 O GLN B 4 1.521 4.533 4.070 1.00 8.99 O ATOM 93 CB GLN B 4 0.659 2.714 1.736 1.00 10.00 C ATOM 94 CG GLN B 4 1.933 1.949 1.229 1.00 10.50 C ATOM 95 CD GLN B 4 2.488 2.629 -0.060 1.00 11.36 C ATOM 96 NE2 GLN B 4 2.690 1.672 -1.055 1.00 10.43 N ATOM 97 OE1 GLN B 4 2.751 3.985 -0.151 1.00 12.29 O ATOM 98 N GLN B 5 2.163 2.286 4.857 1.00 10.48 N ATOM 99 CA GLN B 5 3.260 2.937 5.630 1.00 11.24 C ATOM 100 C GLN B 5 4.607 2.313 5.178 1.00 11.40 C ATOM 101 O GLN B 5 4.805 0.941 5.092 1.00 11.94 O ATOM 102 CB GLN B 5 3.037 2.718 7.129 1.00 11.14 C ATOM 103 CG GLN B 5 1.863 3.622 7.653 1.00 10.65 C ATOM 104 CD GLN B 5 1.348 3.028 8.965 1.00 10.73 C ATOM 105 NE2 GLN B 5 1.523 3.908 10.027 1.00 11.31 N ATOM 106 OE1 GLN B 5 0.803 1.791 9.028 1.00 10.14 O ATOM 107 N ASN B 6 5.522 3.341 4.872 1.00 11.56 N ATOM 108 CA ASN B 6 6.830 2.927 4.359 1.00 12.07 C ATOM 109 C ASN B 6 7.880 3.413 5.353 1.00 13.18 C ATOM 110 O ASN B 6 8.282 4.717 5.362 1.00 13.64 O ATOM 111 CB ASN B 6 7.073 3.704 3.017 1.00 12.12 C ATOM 112 CG ASN B 6 5.983 3.369 1.998 1.00 12.31 C ATOM 113 ND2 ASN B 6 5.212 4.523 1.645 1.00 11.88 N ATOM 114 OD1 ASN B 6 5.849 2.091 1.517 1.00 13.43 O ATOM 115 N TYR B 7 8.324 2.370 6.193 1.00 14.34 N ATOM 116 CA TYR B 7 9.191 2.767 7.317 1.00 15.00 C ATOM 117 C TYR B 7 10.635 2.979 6.893 1.00 15.64 C ATOM 118 O TYR B 7 11.045 2.431 5.838 1.00 15.68 O ATOM 119 CB TYR B 7 9.093 1.570 8.412 1.00 15.31 C ATOM 120 CG TYR B 7 7.683 1.394 8.931 1.00 15.06 C ATOM 121 CD1 TYR B 7 6.809 0.355 8.368 1.00 15.24 C ATOM 122 CD2 TYR B 7 7.219 2.293 9.960 1.00 14.96 C ATOM 123 CE1 TYR B 7 5.510 0.203 8.830 1.00 14.94 C ATOM 124 CE2 TYR B 7 5.928 2.151 10.429 1.00 15.13 C ATOM 125 CZ TYR B 7 5.075 1.108 9.861 1.00 14.97 C ATOM 126 OH TYR B 7 3.785 0.971 10.335 1.00 14.93 O ATOM 127 OXT TYR B 7 11.413 3.704 7.601 1.00 15.89 O1- TER 128 TYR B 7 HETATM 133 C ACT B 8 1.032 -1.120 5.864 1.00 23.56 C HETATM 134 O ACT B 8 -0.050 -0.928 6.472 1.00 24.26 O HETATM 135 CH3 ACT B 8 1.698 -2.599 5.925 1.00 23.08 C HETATM 136 OXT ACT B 8 1.573 -0.070 5.213 1.00 23.36 O HETATM 129 O HOH B 9 10.495 2.353 3.168 1.00 17.57 O HETATM 130 O HOH B 10 -6.480 6.219 7.070 1.00 21.27 O HETATM 131 O HOH B 11 11.846 5.122 9.956 1.00 27.52 O HETATM 132 O HOH B 12 -1.576 1.103 11.035 1.00 44.76 O END """ pdb_in = prefix + "_in.pdb" with open(pdb_in, "w") as f: f.write(pdb_raw) mtz_in = prefix + "_in.mtz" params = """ high_resolution = 1.75 r_free_flags_fraction = 0.1 add_sigmas = True pdb_file = %s random_seed = 12345 output { label = F type = *real complex file_name = %s } """ % (pdb_in, mtz_in) with open("%s_fmodel.eff" % prefix, "w") as f: f.write(params) assert (easy_run.fully_buffered( "phenix.fmodel %s_fmodel.eff" % prefix ).raise_if_errors().return_code == 0) return pdb_in, mtz_in def exercise(): # # Test command-line program # pdb_in, mtz_in = make_inputs() pdb_file = file_reader.any_file(pdb_in, force_type="pdb") hierarchy = pdb_file.file_object.hierarchy old_ligand = None for chain in hierarchy.only_model().chains(): if (chain.id != "B") : continue for residue_group in chain.residue_groups(): atom_group = residue_group.only_atom_group() if (atom_group.resname == "ACT"): old_ligand = atom_group.detached_copy() residue_group.remove_atom_group(atom_group) break assert old_ligand is not None with open("tst_ligand_ncs_start.pdb", "w") as f: f.write(hierarchy.as_pdb_string( crystal_symmetry=pdb_file.file_object.crystal_symmetry())) args = [ "tst_ligand_ncs_start.pdb", mtz_in, "ligand_code=ACT", ] from mmtbx.command_line import apply_ncs_to_ligand if op.isfile("ncs_ligands.pdb"): os.remove("ncs_ligands.pdb") result = apply_ncs_to_ligand.run(args=args, out=null_out()) assert result.n_ligands_new == 1 assert op.isfile("ncs_ligands.pdb") pdb_out = file_reader.any_file("ncs_ligands.pdb", force_type="pdb") hierarchy_new = pdb_out.file_object.hierarchy new_ligand = None for chain in hierarchy_new.only_model().chains(): if (chain.id != "B") : continue for residue_group in chain.residue_groups(): atom_group = residue_group.only_atom_group() if (atom_group.resname == "ACT"): new_ligand = atom_group.detached_copy() assert new_ligand is not None rmsd = old_ligand.atoms().extract_xyz().rms_difference( new_ligand.atoms().extract_xyz()) assert (rmsd < 0.5) # # Unit tests # # Excessive testing of NCS search machinery although with ligands. May be removed. import iotbx.ncs ncs_obj = iotbx.ncs.input(hierarchy=hierarchy, log=null_out()) nrgl = ncs_obj.get_ncs_restraints_group_list() assert len(nrgl) == 1, len(nrgl) assert len(nrgl[0].master_iselection) == 59, len(nrgl[0].master_iselection) if (__name__ == "__main__"): exercise() print("OK")