diff options
Diffstat (limited to 'plip/exchange')
| -rw-r--r-- | plip/exchange/json.py | 2 | ||||
| -rw-r--r-- | plip/exchange/report.py | 786 | ||||
| -rw-r--r-- | plip/exchange/webservices.py | 40 | ||||
| -rw-r--r-- | plip/exchange/xml.py | 349 |
4 files changed, 807 insertions, 370 deletions
diff --git a/plip/exchange/json.py b/plip/exchange/json.py index 5c7ad5c..14febda 100644 --- a/plip/exchange/json.py +++ b/plip/exchange/json.py @@ -1 +1 @@ -# place holder for module to add Json support
\ No newline at end of file +# place holder for module to add Json support diff --git a/plip/exchange/report.py b/plip/exchange/report.py index a559bf8..edca1f1 100644 --- a/plip/exchange/report.py +++ b/plip/exchange/report.py @@ -11,7 +11,7 @@ from plip.structure.preparation import PDBComplex class StructureReport: """Creates reports (xml or txt) for one structure/""" - def __init__(self, mol: PDBComplex, outputprefix: str = 'report'): + def __init__(self, mol: PDBComplex, outputprefix: str = "report"): self.mol = mol self.excluded = self.mol.excluded self.xmlreport = self.construct_xml_tree() @@ -22,57 +22,75 @@ class StructureReport: def construct_xml_tree(self): """Construct the basic XML tree""" - report = et.Element('report') - plipversion = et.SubElement(report, 'plipversion') + report = et.Element("report") + plipversion = et.SubElement(report, "plipversion") plipversion.text = __version__ - date_of_creation = et.SubElement(report, 'date_of_creation') + date_of_creation = et.SubElement(report, "date_of_creation") date_of_creation.text = time.strftime("%Y/%m/%d") - citation_information = et.SubElement(report, 'citation_information') - citation_information.text = "Salentin,S. et al. PLIP: fully automated protein-ligand interaction profiler. " \ - "Nucl. Acids Res. (1 July 2015) 43 (W1): W443-W447. doi: 10.1093/nar/gkv315" + citation_information = et.SubElement(report, "citation_information") + citation_information.text = ( + "Salentin,S. et al. PLIP: fully automated protein-ligand interaction profiler. " + "Nucl. Acids Res. (1 July 2015) 43 (W1): W443-W447. doi: 10.1093/nar/gkv315" + ) - maintainer_information = et.SubElement(report, 'maintainer_information') + maintainer_information = et.SubElement(report, "maintainer_information") maintainer_information.text = config.__maintainer__ - mode = et.SubElement(report, 'mode') + mode = et.SubElement(report, "mode") if config.DNARECEPTOR: - mode.text = 'dna_receptor' + mode.text = "dna_receptor" else: - mode.text = 'default' - pdbid = et.SubElement(report, 'pdbid') + mode.text = "default" + pdbid = et.SubElement(report, "pdbid") pdbid.text = self.mol.pymol_name.upper() - filetype = et.SubElement(report, 'filetype') + filetype = et.SubElement(report, "filetype") filetype.text = self.mol.filetype.upper() - pdbfile = et.SubElement(report, 'pdbfile') - pdbfile.text = self.mol.sourcefiles['pdbcomplex'] - pdbfixes = et.SubElement(report, 'pdbfixes') - pdbfixes.text = str(self.mol.information['pdbfixes']) - filename = et.SubElement(report, 'filename') - filename.text = str(self.mol.sourcefiles.get('filename') or None) - exligs = et.SubElement(report, 'excluded_ligands') + pdbfile = et.SubElement(report, "pdbfile") + pdbfile.text = self.mol.sourcefiles["pdbcomplex"] + pdbfixes = et.SubElement(report, "pdbfixes") + pdbfixes.text = str(self.mol.information["pdbfixes"]) + filename = et.SubElement(report, "filename") + filename.text = str(self.mol.sourcefiles.get("filename") or None) + exligs = et.SubElement(report, "excluded_ligands") for i, exlig in enumerate(self.excluded): - e = et.SubElement(exligs, 'excluded_ligand', id=str(i + 1)) + e = et.SubElement(exligs, "excluded_ligand", id=str(i + 1)) e.text = exlig - covalent = et.SubElement(report, 'covlinkages') + covalent = et.SubElement(report, "covlinkages") for i, covlinkage in enumerate(self.mol.covalent): - e = et.SubElement(covalent, 'covlinkage', id=str(i + 1)) - f1 = et.SubElement(e, 'res1') - f2 = et.SubElement(e, 'res2') - f1.text = ":".join([covlinkage.id1, covlinkage.chain1, str(covlinkage.pos1)]) - f2.text = ":".join([covlinkage.id2, covlinkage.chain2, str(covlinkage.pos2)]) + e = et.SubElement(covalent, "covlinkage", id=str(i + 1)) + f1 = et.SubElement(e, "res1") + f2 = et.SubElement(e, "res2") + f1.text = ":".join( + [covlinkage.id1, covlinkage.chain1, str(covlinkage.pos1)] + ) + f2.text = ":".join( + [covlinkage.id2, covlinkage.chain2, str(covlinkage.pos2)] + ) return report def construct_txt_file(self): """Construct the header of the txt file""" - textlines = ['Prediction of noncovalent interactions for PDB structure %s' % self.mol.pymol_name.upper(), ] + textlines = [ + "Prediction of noncovalent interactions for PDB structure %s" + % self.mol.pymol_name.upper(), + ] textlines.append("=" * len(textlines[0])) - textlines.append('Created on %s using PLIP v%s\n' % (time.strftime("%Y/%m/%d"), __version__)) - textlines.append('If you are using PLIP in your work, please cite:') - textlines.append('Salentin,S. et al. PLIP: fully automated protein-ligand interaction profiler.') - textlines.append('Nucl. Acids Res. (1 July 2015) 43 (W1): W443-W447. doi: 10.1093/nar/gkv315\n') + textlines.append( + "Created on %s using PLIP v%s\n" % (time.strftime("%Y/%m/%d"), __version__) + ) + textlines.append("If you are using PLIP in your work, please cite:") + textlines.append( + "Salentin,S. et al. PLIP: fully automated protein-ligand interaction profiler." + ) + textlines.append( + "Nucl. Acids Res. (1 July 2015) 43 (W1): W443-W447. doi: 10.1093/nar/gkv315\n" + ) if len(self.excluded) != 0: - textlines.append('Excluded molecules as ligands: %s\n' % ','.join([lig for lig in self.excluded])) + textlines.append( + "Excluded molecules as ligands: %s\n" + % ",".join([lig for lig in self.excluded]) + ) if config.DNARECEPTOR: - textlines.append('DNA/RNA in structure was chosen as the receptor part.\n') + textlines.append("DNA/RNA in structure was chosen as the receptor part.\n") return textlines def get_bindingsite_data(self): @@ -80,21 +98,24 @@ class StructureReport: for i, site in enumerate(sorted(self.mol.interaction_sets)): s = self.mol.interaction_sets[site] bindingsite = BindingSiteReport(s).generate_xml() - bindingsite.set('id', str(i + 1)) - bindingsite.set('has_interactions', 'False') + bindingsite.set("id", str(i + 1)) + bindingsite.set("has_interactions", "False") self.xmlreport.insert(i + 1, bindingsite) for itype in BindingSiteReport(s).generate_txt(): self.txtreport.append(itype) if not s.no_interactions: - bindingsite.set('has_interactions', 'True') + bindingsite.set("has_interactions", "True") else: - self.txtreport.append('No interactions detected.') + self.txtreport.append("No interactions detected.") def write_xml(self, as_string=False): """Write the XML report""" if not as_string: - et.ElementTree(self.xmlreport).write('{}/{}.xml'.format(self.outpath, self.outputprefix), pretty_print=True, - xml_declaration=True) + et.ElementTree(self.xmlreport).write( + "{}/{}.xml".format(self.outpath, self.outputprefix), + pretty_print=True, + xml_declaration=True, + ) else: output = et.tostring(self.xmlreport, pretty_print=True) if config.RAWSTRING: @@ -104,10 +125,10 @@ class StructureReport: def write_txt(self, as_string=False): """Write the TXT report""" if not as_string: - with open('{}/{}.txt'.format(self.outpath, self.outputprefix), 'w') as f: - [f.write(textline + '\n') for textline in self.txtreport] + with open("{}/{}.txt".format(self.outpath, self.outputprefix), "w") as f: + [f.write(textline + "\n") for textline in self.txtreport] else: - output = '\n'.join(self.txtreport) + output = "\n".join(self.txtreport) if config.RAWSTRING: output = repr(output) print(output) @@ -126,7 +147,9 @@ class BindingSiteReport: self.ligand = self.complex.ligand self.bindingsite = self.complex.bindingsite self.output_path = self.complex.output_path - self.bsid = ':'.join([self.ligand.hetid, self.ligand.chain, str(self.ligand.position)]) + self.bsid = ":".join( + [self.ligand.hetid, self.ligand.chain, str(self.ligand.position)] + ) self.longname = self.ligand.longname self.ligtype = self.ligand.type self.bs_res = self.bindingsite.bs_res @@ -141,163 +164,408 @@ class BindingSiteReport: ############################ self.hydrophobic_features = ( - 'RESNR', 'RESTYPE', 'RESCHAIN', 'RESNR_LIG', 'RESTYPE_LIG', 'RESCHAIN_LIG', 'DIST', 'LIGCARBONIDX', - 'PROTCARBONIDX', 'LIGCOO', - 'PROTCOO') + "RESNR", + "RESTYPE", + "RESCHAIN", + "RESNR_LIG", + "RESTYPE_LIG", + "RESCHAIN_LIG", + "DIST", + "LIGCARBONIDX", + "PROTCARBONIDX", + "LIGCOO", + "PROTCOO", + ) self.hydrophobic_info = [] for hydroph in self.complex.hydrophobic_contacts: - self.hydrophobic_info.append((hydroph.resnr, hydroph.restype, hydroph.reschain, hydroph.resnr_l, - hydroph.restype_l, hydroph.reschain_l, '%.2f' % hydroph.distance, - hydroph.ligatom_orig_idx, hydroph.bsatom_orig_idx, hydroph.ligatom.coords, - hydroph.bsatom.coords)) + self.hydrophobic_info.append( + ( + hydroph.resnr, + hydroph.restype, + hydroph.reschain, + hydroph.resnr_l, + hydroph.restype_l, + hydroph.reschain_l, + "%.2f" % hydroph.distance, + hydroph.ligatom_orig_idx, + hydroph.bsatom_orig_idx, + hydroph.ligatom.coords, + hydroph.bsatom.coords, + ) + ) ################## # HYDROGEN BONDS # ################## self.hbond_features = ( - 'RESNR', 'RESTYPE', 'RESCHAIN', 'RESNR_LIG', 'RESTYPE_LIG', 'RESCHAIN_LIG', 'SIDECHAIN', 'DIST_H-A', - 'DIST_D-A', - 'DON_ANGLE', - 'PROTISDON', 'DONORIDX', 'DONORTYPE', 'ACCEPTORIDX', 'ACCEPTORTYPE', 'LIGCOO', 'PROTCOO') + "RESNR", + "RESTYPE", + "RESCHAIN", + "RESNR_LIG", + "RESTYPE_LIG", + "RESCHAIN_LIG", + "SIDECHAIN", + "DIST_H-A", + "DIST_D-A", + "DON_ANGLE", + "PROTISDON", + "DONORIDX", + "DONORTYPE", + "ACCEPTORIDX", + "ACCEPTORTYPE", + "LIGCOO", + "PROTCOO", + ) self.hbond_info = [] for hbond in self.complex.hbonds_pdon + self.complex.hbonds_ldon: - ligatom, protatom = (hbond.a, hbond.d) if hbond.protisdon else (hbond.d, hbond.a) - self.hbond_info.append((hbond.resnr, hbond.restype, hbond.reschain, hbond.resnr_l, hbond.restype_l, - hbond.reschain_l, hbond.sidechain, - '%.2f' % hbond.distance_ah, '%.2f' % hbond.distance_ad, '%.2f' % hbond.angle, - hbond.protisdon, hbond.d_orig_idx, hbond.dtype, hbond.a_orig_idx, hbond.atype, - ligatom.coords, protatom.coords)) + ligatom, protatom = ( + (hbond.a, hbond.d) if hbond.protisdon else (hbond.d, hbond.a) + ) + self.hbond_info.append( + ( + hbond.resnr, + hbond.restype, + hbond.reschain, + hbond.resnr_l, + hbond.restype_l, + hbond.reschain_l, + hbond.sidechain, + "%.2f" % hbond.distance_ah, + "%.2f" % hbond.distance_ad, + "%.2f" % hbond.angle, + hbond.protisdon, + hbond.d_orig_idx, + hbond.dtype, + hbond.a_orig_idx, + hbond.atype, + ligatom.coords, + protatom.coords, + ) + ) ################# # WATER-BRIDGES # ################# self.waterbridge_features = ( - 'RESNR', 'RESTYPE', 'RESCHAIN', 'RESNR_LIG', 'RESTYPE_LIG', 'RESCHAIN_LIG', 'DIST_A-W', 'DIST_D-W', - 'DON_ANGLE', - 'WATER_ANGLE', - 'PROTISDON', 'DONOR_IDX', 'DONORTYPE', 'ACCEPTOR_IDX', 'ACCEPTORTYPE', 'WATER_IDX', - 'LIGCOO', 'PROTCOO', 'WATERCOO') + "RESNR", + "RESTYPE", + "RESCHAIN", + "RESNR_LIG", + "RESTYPE_LIG", + "RESCHAIN_LIG", + "DIST_A-W", + "DIST_D-W", + "DON_ANGLE", + "WATER_ANGLE", + "PROTISDON", + "DONOR_IDX", + "DONORTYPE", + "ACCEPTOR_IDX", + "ACCEPTORTYPE", + "WATER_IDX", + "LIGCOO", + "PROTCOO", + "WATERCOO", + ) # The coordinate format is an exception here, since the interaction is not only between ligand and protein self.waterbridge_info = [] for wbridge in self.complex.water_bridges: - lig, prot = (wbridge.a, wbridge.d) if wbridge.protisdon else (wbridge.d, wbridge.a) - self.waterbridge_info.append((wbridge.resnr, wbridge.restype, wbridge.reschain, wbridge.resnr_l, - wbridge.restype_l, wbridge.reschain_l, - '%.2f' % wbridge.distance_aw, '%.2f' % wbridge.distance_dw, - '%.2f' % wbridge.d_angle, '%.2f' % wbridge.w_angle, wbridge.protisdon, - wbridge.d_orig_idx, wbridge.dtype, wbridge.a_orig_idx, wbridge.atype, - wbridge.water_orig_idx, lig.coords, prot.coords, wbridge.water.coords)) + lig, prot = ( + (wbridge.a, wbridge.d) if wbridge.protisdon else (wbridge.d, wbridge.a) + ) + self.waterbridge_info.append( + ( + wbridge.resnr, + wbridge.restype, + wbridge.reschain, + wbridge.resnr_l, + wbridge.restype_l, + wbridge.reschain_l, + "%.2f" % wbridge.distance_aw, + "%.2f" % wbridge.distance_dw, + "%.2f" % wbridge.d_angle, + "%.2f" % wbridge.w_angle, + wbridge.protisdon, + wbridge.d_orig_idx, + wbridge.dtype, + wbridge.a_orig_idx, + wbridge.atype, + wbridge.water_orig_idx, + lig.coords, + prot.coords, + wbridge.water.coords, + ) + ) ################ # SALT BRIDGES # ################ self.saltbridge_features = ( - 'RESNR', 'RESTYPE', 'RESCHAIN', 'RESNR_LIG', 'RESTYPE_LIG', 'RESCHAIN_LIG', 'DIST', 'PROTISPOS', - 'LIG_GROUP', - 'LIG_IDX_LIST', - 'LIGCOO', 'PROTCOO') + "RESNR", + "RESTYPE", + "RESCHAIN", + "RESNR_LIG", + "RESTYPE_LIG", + "RESCHAIN_LIG", + "DIST", + "PROTISPOS", + "LIG_GROUP", + "LIG_IDX_LIST", + "LIGCOO", + "PROTCOO", + ) self.saltbridge_info = [] for sb in self.complex.saltbridge_lneg + self.complex.saltbridge_pneg: if sb.protispos: - group, ids = sb.negative.fgroup, [str(x) for x in sb.negative.atoms_orig_idx] - self.saltbridge_info.append((sb.resnr, sb.restype, sb.reschain, sb.resnr_l, sb.restype_l, sb.reschain_l, - '%.2f' % sb.distance, sb.protispos, - group.capitalize(), ",".join(ids), - tuple(sb.negative.center), tuple(sb.positive.center))) + group, ids = ( + sb.negative.fgroup, + [str(x) for x in sb.negative.atoms_orig_idx], + ) + self.saltbridge_info.append( + ( + sb.resnr, + sb.restype, + sb.reschain, + sb.resnr_l, + sb.restype_l, + sb.reschain_l, + "%.2f" % sb.distance, + sb.protispos, + group.capitalize(), + ",".join(ids), + tuple(sb.negative.center), + tuple(sb.positive.center), + ) + ) else: - group, ids = sb.positive.fgroup, [str(x) for x in sb.positive.atoms_orig_idx] - self.saltbridge_info.append((sb.resnr, sb.restype, sb.reschain, sb.resnr_l, sb.restype_l, sb.reschain_l, - '%.2f' % sb.distance, sb.protispos, - group.capitalize(), ",".join(ids), - tuple(sb.positive.center), tuple(sb.negative.center))) + group, ids = ( + sb.positive.fgroup, + [str(x) for x in sb.positive.atoms_orig_idx], + ) + self.saltbridge_info.append( + ( + sb.resnr, + sb.restype, + sb.reschain, + sb.resnr_l, + sb.restype_l, + sb.reschain_l, + "%.2f" % sb.distance, + sb.protispos, + group.capitalize(), + ",".join(ids), + tuple(sb.positive.center), + tuple(sb.negative.center), + ) + ) ############### # PI-STACKING # ############### self.pistacking_features = ( - 'RESNR', 'RESTYPE', 'RESCHAIN', 'RESNR_LIG', 'RESTYPE_LIG', 'RESCHAIN_LIG', 'CENTDIST', 'ANGLE', 'OFFSET', - 'TYPE', - 'LIG_IDX_LIST', 'LIGCOO', 'PROTCOO') + "RESNR", + "RESTYPE", + "RESCHAIN", + "RESNR_LIG", + "RESTYPE_LIG", + "RESCHAIN_LIG", + "CENTDIST", + "ANGLE", + "OFFSET", + "TYPE", + "LIG_IDX_LIST", + "LIGCOO", + "PROTCOO", + ) self.pistacking_info = [] for stack in self.complex.pistacking: ids = [str(x) for x in stack.ligandring.atoms_orig_idx] - self.pistacking_info.append((stack.resnr, stack.restype, stack.reschain, stack.resnr_l, stack.restype_l, - stack.reschain_l, '%.2f' % stack.distance, - '%.2f' % stack.angle, '%.2f' % stack.offset, stack.type, ",".join(ids), - tuple(stack.ligandring.center), tuple(stack.proteinring.center))) + self.pistacking_info.append( + ( + stack.resnr, + stack.restype, + stack.reschain, + stack.resnr_l, + stack.restype_l, + stack.reschain_l, + "%.2f" % stack.distance, + "%.2f" % stack.angle, + "%.2f" % stack.offset, + stack.type, + ",".join(ids), + tuple(stack.ligandring.center), + tuple(stack.proteinring.center), + ) + ) ########################## # PI-CATION INTERACTIONS # ########################## self.pication_features = ( - 'RESNR', 'RESTYPE', 'RESCHAIN', 'RESNR_LIG', 'RESTYPE_LIG', 'RESCHAIN_LIG', 'DIST', 'OFFSET', 'PROTCHARGED', - 'LIG_GROUP', - 'LIG_IDX_LIST', 'LIGCOO', 'PROTCOO') + "RESNR", + "RESTYPE", + "RESCHAIN", + "RESNR_LIG", + "RESTYPE_LIG", + "RESCHAIN_LIG", + "DIST", + "OFFSET", + "PROTCHARGED", + "LIG_GROUP", + "LIG_IDX_LIST", + "LIGCOO", + "PROTCOO", + ) self.pication_info = [] for picat in self.complex.pication_laro + self.complex.pication_paro: if picat.protcharged: ids = [str(x) for x in picat.ring.atoms_orig_idx] - group = 'Aromatic' - self.pication_info.append((picat.resnr, picat.restype, picat.reschain, picat.resnr_l, picat.restype_l, - picat.reschain_l, '%.2f' % picat.distance, - '%.2f' % picat.offset, picat.protcharged, group, ",".join(ids), - tuple(picat.ring.center), tuple(picat.charge.center))) + group = "Aromatic" + self.pication_info.append( + ( + picat.resnr, + picat.restype, + picat.reschain, + picat.resnr_l, + picat.restype_l, + picat.reschain_l, + "%.2f" % picat.distance, + "%.2f" % picat.offset, + picat.protcharged, + group, + ",".join(ids), + tuple(picat.ring.center), + tuple(picat.charge.center), + ) + ) else: ids = [str(x) for x in picat.charge.atoms_orig_idx] group = picat.charge.fgroup - self.pication_info.append((picat.resnr, picat.restype, picat.reschain, picat.resnr_l, picat.restype_l, - picat.reschain_l, '%.2f' % picat.distance, - '%.2f' % picat.offset, picat.protcharged, group, ",".join(ids), - tuple(picat.charge.center), tuple(picat.ring.center))) + self.pication_info.append( + ( + picat.resnr, + picat.restype, + picat.reschain, + picat.resnr_l, + picat.restype_l, + picat.reschain_l, + "%.2f" % picat.distance, + "%.2f" % picat.offset, + picat.protcharged, + group, + ",".join(ids), + tuple(picat.charge.center), + tuple(picat.ring.center), + ) + ) ################# # HALOGEN BONDS # ################# self.halogen_features = ( - 'RESNR', 'RESTYPE', 'RESCHAIN', 'RESNR_LIG', 'RESTYPE_LIG', 'RESCHAIN_LIG', 'SIDECHAIN', 'DIST', - 'DON_ANGLE', - 'ACC_ANGLE', - 'DON_IDX', 'DONORTYPE', 'ACC_IDX', 'ACCEPTORTYPE', 'LIGCOO', 'PROTCOO') + "RESNR", + "RESTYPE", + "RESCHAIN", + "RESNR_LIG", + "RESTYPE_LIG", + "RESCHAIN_LIG", + "SIDECHAIN", + "DIST", + "DON_ANGLE", + "ACC_ANGLE", + "DON_IDX", + "DONORTYPE", + "ACC_IDX", + "ACCEPTORTYPE", + "LIGCOO", + "PROTCOO", + ) self.halogen_info = [] for halogen in self.complex.halogen_bonds: - self.halogen_info.append((halogen.resnr, halogen.restype, halogen.reschain, halogen.resnr_l, - halogen.restype_l, halogen.reschain_l, halogen.sidechain, - '%.2f' % halogen.distance, '%.2f' % halogen.don_angle, '%.2f' % halogen.acc_angle, - halogen.don_orig_idx, halogen.donortype, - halogen.acc_orig_idx, halogen.acctype, - halogen.acc.o.coords, halogen.don.x.coords)) + self.halogen_info.append( + ( + halogen.resnr, + halogen.restype, + halogen.reschain, + halogen.resnr_l, + halogen.restype_l, + halogen.reschain_l, + halogen.sidechain, + "%.2f" % halogen.distance, + "%.2f" % halogen.don_angle, + "%.2f" % halogen.acc_angle, + halogen.don_orig_idx, + halogen.donortype, + halogen.acc_orig_idx, + halogen.acctype, + halogen.acc.o.coords, + halogen.don.x.coords, + ) + ) ################### # METAL COMPLEXES # ################### self.metal_features = ( - 'RESNR', 'RESTYPE', 'RESCHAIN', 'RESNR_LIG', 'RESTYPE_LIG', 'RESCHAIN_LIG', 'METAL_IDX', 'METAL_TYPE', - 'TARGET_IDX', 'TARGET_TYPE', - 'COORDINATION', 'DIST', 'LOCATION', 'RMS', 'GEOMETRY', 'COMPLEXNUM', 'METALCOO', - 'TARGETCOO') + "RESNR", + "RESTYPE", + "RESCHAIN", + "RESNR_LIG", + "RESTYPE_LIG", + "RESCHAIN_LIG", + "METAL_IDX", + "METAL_TYPE", + "TARGET_IDX", + "TARGET_TYPE", + "COORDINATION", + "DIST", + "LOCATION", + "RMS", + "GEOMETRY", + "COMPLEXNUM", + "METALCOO", + "TARGETCOO", + ) self.metal_info = [] # Coordinate format here is non-standard since the interaction partner can be either ligand or protein for m in self.complex.metal_complexes: self.metal_info.append( - (m.resnr, m.restype, m.reschain, m.resnr_l, m.restype_l, m.reschain_l, m.metal_orig_idx, m.metal_type, - m.target_orig_idx, m.target_type, m.coordination_num, '%.2f' % m.distance, - m.location, '%.2f' % m.rms, m.geometry, str(m.complexnum), m.metal.coords, - m.target.atom.coords)) + ( + m.resnr, + m.restype, + m.reschain, + m.resnr_l, + m.restype_l, + m.reschain_l, + m.metal_orig_idx, + m.metal_type, + m.target_orig_idx, + m.target_type, + m.coordination_num, + "%.2f" % m.distance, + m.location, + "%.2f" % m.rms, + m.geometry, + str(m.complexnum), + m.metal.coords, + m.target.atom.coords, + ) + ) def write_section(self, name, features, info, f): """Provides formatting for one section (e.g. hydrogen bonds)""" if not len(info) == 0: - f.write('\n\n### %s ###\n' % name) - f.write('%s\n' % '\t'.join(features)) + f.write("\n\n### %s ###\n" % name) + f.write("%s\n" % "\t".join(features)) for line in info: - f.write('%s\n' % '\t'.join(map(str, line))) + f.write("%s\n" % "\t".join(map(str, line))) def rst_table(self, array): """Given an array, the function formats and returns and table in rST format.""" @@ -309,62 +577,77 @@ class BindingSiteReport: cell_dict[j] = [] cell_dict[j].append(val) for item in cell_dict: - cell_dict[item] = max([len(x) for x in cell_dict[item]]) + 1 # Contains adapted width for each column + cell_dict[item] = ( + max([len(x) for x in cell_dict[item]]) + 1 + ) # Contains adapted width for each column # Format top line num_cols = len(array[0]) - form = '+' + form = "+" for col in range(num_cols): - form += (cell_dict[col] + 1) * '-' - form += '+' - form += '\n' + form += (cell_dict[col] + 1) * "-" + form += "+" + form += "\n" # Format values for i, row in enumerate(array): - form += '| ' + form += "| " for j, val in enumerate(row): cell_width = cell_dict[j] - form += str(val) + (cell_width - len(val)) * ' ' + '| ' + form += str(val) + (cell_width - len(val)) * " " + "| " form.rstrip() - form += '\n' + form += "\n" # Seperation lines - form += '+' + form += "+" if i == 0: - sign = '=' + sign = "=" else: - sign = '-' + sign = "-" for col in range(num_cols): form += (cell_dict[col] + 1) * sign - form += '+' - form += '\n' + form += "+" + form += "\n" return form def generate_txt(self): """Generates an flat text report for a single binding site""" txt = [] - titletext = '%s (%s) - %s' % (self.bsid, self.longname, self.ligtype) + titletext = "%s (%s) - %s" % (self.bsid, self.longname, self.ligtype) txt.append(titletext) for i, member in enumerate(self.lig_members[1:]): - txt.append(' + %s' % ":".join(str(element) for element in member)) + txt.append(" + %s" % ":".join(str(element) for element in member)) txt.append("-" * len(titletext)) - txt.append("Interacting chain(s): %s\n" % ','.join([chain for chain in self.interacting_chains])) - for section in [['Hydrophobic Interactions', self.hydrophobic_features, self.hydrophobic_info], - ['Hydrogen Bonds', self.hbond_features, self.hbond_info], - ['Water Bridges', self.waterbridge_features, self.waterbridge_info], - ['Salt Bridges', self.saltbridge_features, self.saltbridge_info], - ['pi-Stacking', self.pistacking_features, self.pistacking_info], - ['pi-Cation Interactions', self.pication_features, self.pication_info], - ['Halogen Bonds', self.halogen_features, self.halogen_info], - ['Metal Complexes', self.metal_features, self.metal_info]]: + txt.append( + "Interacting chain(s): %s\n" + % ",".join([chain for chain in self.interacting_chains]) + ) + for section in [ + [ + "Hydrophobic Interactions", + self.hydrophobic_features, + self.hydrophobic_info, + ], + ["Hydrogen Bonds", self.hbond_features, self.hbond_info], + ["Water Bridges", self.waterbridge_features, self.waterbridge_info], + ["Salt Bridges", self.saltbridge_features, self.saltbridge_info], + ["pi-Stacking", self.pistacking_features, self.pistacking_info], + ["pi-Cation Interactions", self.pication_features, self.pication_info], + ["Halogen Bonds", self.halogen_features, self.halogen_info], + ["Metal Complexes", self.metal_features, self.metal_info], + ]: iname, features, interaction_information = section # Sort results first by res number, then by distance and finally ligand coordinates to get a unique order - interaction_information = sorted(interaction_information, key=itemgetter(0, 2, -2)) + interaction_information = sorted( + interaction_information, key=itemgetter(0, 2, -2) + ) if not len(interaction_information) == 0: - txt.append('\n**%s**' % iname) - table = [features, ] + txt.append("\n**%s**" % iname) + table = [ + features, + ] for single_contact in interaction_information: values = [] for x in single_contact: @@ -376,122 +659,185 @@ class BindingSiteReport: values.append(str(x)) table.append(values) txt.append(self.rst_table(table)) - txt.append('\n') + txt.append("\n") return txt def generate_xml(self): """Generates an XML-formatted report for a single binding site""" - report = et.Element('bindingsite') - identifiers = et.SubElement(report, 'identifiers') - longname = et.SubElement(identifiers, 'longname') - ligtype = et.SubElement(identifiers, 'ligtype') - hetid = et.SubElement(identifiers, 'hetid') - chain = et.SubElement(identifiers, 'chain') - position = et.SubElement(identifiers, 'position') - composite = et.SubElement(identifiers, 'composite') - members = et.SubElement(identifiers, 'members') - smiles = et.SubElement(identifiers, 'smiles') - inchikey = et.SubElement(identifiers, 'inchikey') + report = et.Element("bindingsite") + identifiers = et.SubElement(report, "identifiers") + longname = et.SubElement(identifiers, "longname") + ligtype = et.SubElement(identifiers, "ligtype") + hetid = et.SubElement(identifiers, "hetid") + chain = et.SubElement(identifiers, "chain") + position = et.SubElement(identifiers, "position") + composite = et.SubElement(identifiers, "composite") + members = et.SubElement(identifiers, "members") + smiles = et.SubElement(identifiers, "smiles") + inchikey = et.SubElement(identifiers, "inchikey") # Ligand properties. Number of (unpaired) functional atoms and rings. - lig_properties = et.SubElement(report, 'lig_properties') - num_heavy_atoms = et.SubElement(lig_properties, 'num_heavy_atoms') - num_hbd = et.SubElement(lig_properties, 'num_hbd') + lig_properties = et.SubElement(report, "lig_properties") + num_heavy_atoms = et.SubElement(lig_properties, "num_heavy_atoms") + num_hbd = et.SubElement(lig_properties, "num_hbd") num_hbd.text = str(self.ligand.num_hbd) - num_unpaired_hbd = et.SubElement(lig_properties, 'num_unpaired_hbd') + num_unpaired_hbd = et.SubElement(lig_properties, "num_unpaired_hbd") num_unpaired_hbd.text = str(self.complex.num_unpaired_hbd) - num_hba = et.SubElement(lig_properties, 'num_hba') + num_hba = et.SubElement(lig_properties, "num_hba") num_hba.text = str(self.ligand.num_hba) - num_unpaired_hba = et.SubElement(lig_properties, 'num_unpaired_hba') + num_unpaired_hba = et.SubElement(lig_properties, "num_unpaired_hba") num_unpaired_hba.text = str(self.complex.num_unpaired_hba) - num_hal = et.SubElement(lig_properties, 'num_hal') + num_hal = et.SubElement(lig_properties, "num_hal") num_hal.text = str(self.ligand.num_hal) - num_unpaired_hal = et.SubElement(lig_properties, 'num_unpaired_hal') + num_unpaired_hal = et.SubElement(lig_properties, "num_unpaired_hal") num_unpaired_hal.text = str(self.complex.num_unpaired_hal) - num_aromatic_rings = et.SubElement(lig_properties, 'num_aromatic_rings') + num_aromatic_rings = et.SubElement(lig_properties, "num_aromatic_rings") num_aromatic_rings.text = str(self.ligand.num_rings) - num_rot_bonds = et.SubElement(lig_properties, 'num_rotatable_bonds') + num_rot_bonds = et.SubElement(lig_properties, "num_rotatable_bonds") num_rot_bonds.text = str(self.ligand.num_rot_bonds) - molweight = et.SubElement(lig_properties, 'molweight') + molweight = et.SubElement(lig_properties, "molweight") molweight.text = str(self.ligand.molweight) - logp = et.SubElement(lig_properties, 'logp') + logp = et.SubElement(lig_properties, "logp") logp.text = str(self.ligand.logp) - ichains = et.SubElement(report, 'interacting_chains') - bsresidues = et.SubElement(report, 'bs_residues') + ichains = et.SubElement(report, "interacting_chains") + bsresidues = et.SubElement(report, "bs_residues") for i, ichain in enumerate(self.interacting_chains): - c = et.SubElement(ichains, 'interacting_chain', id=str(i + 1)) + c = et.SubElement(ichains, "interacting_chain", id=str(i + 1)) c.text = ichain for i, bsres in enumerate(self.bs_res): - contact = 'True' if bsres in self.bs_res_interacting else 'False' - distance = '%.1f' % self.min_dist[bsres][0] + contact = "True" if bsres in self.bs_res_interacting else "False" + distance = "%.1f" % self.min_dist[bsres][0] aatype = self.min_dist[bsres][1] - c = et.SubElement(bsresidues, 'bs_residue', id=str(i + 1), contact=contact, min_dist=distance, aa=aatype) + c = et.SubElement( + bsresidues, + "bs_residue", + id=str(i + 1), + contact=contact, + min_dist=distance, + aa=aatype, + ) c.text = bsres - hetid.text, chain.text, position.text = self.ligand.hetid, self.ligand.chain, str(self.ligand.position) - composite.text = 'True' if len(self.lig_members) > 1 else 'False' + hetid.text, chain.text, position.text = ( + self.ligand.hetid, + self.ligand.chain, + str(self.ligand.position), + ) + composite.text = "True" if len(self.lig_members) > 1 else "False" longname.text = self.longname ligtype.text = self.ligtype smiles.text = self.ligand.smiles inchikey.text = self.ligand.inchikey - num_heavy_atoms.text = str(self.ligand.heavy_atoms) # Number of heavy atoms in ligand + num_heavy_atoms.text = str( + self.ligand.heavy_atoms + ) # Number of heavy atoms in ligand for i, member in enumerate(self.lig_members): bsid = ":".join(str(element) for element in member) - m = et.SubElement(members, 'member', id=str(i + 1)) + m = et.SubElement(members, "member", id=str(i + 1)) m.text = bsid - interactions = et.SubElement(report, 'interactions') + interactions = et.SubElement(report, "interactions") def format_interactions(element_name, features, interaction_information): """Returns a formatted element with interaction information.""" interaction = et.Element(element_name) # Sort results first by res number, then by distance and finally ligand coordinates to get a unique order - interaction_information = sorted(interaction_information, key=itemgetter(0, 2, -2)) + interaction_information = sorted( + interaction_information, key=itemgetter(0, 2, -2) + ) for j, single_contact in enumerate(interaction_information): - if not element_name == 'metal_complexes': - new_contact = et.SubElement(interaction, element_name[:-1], id=str(j + 1)) + if not element_name == "metal_complexes": + new_contact = et.SubElement( + interaction, element_name[:-1], id=str(j + 1) + ) else: # Metal Complex[es] - new_contact = et.SubElement(interaction, element_name[:-2], id=str(j + 1)) + new_contact = et.SubElement( + interaction, element_name[:-2], id=str(j + 1) + ) for i, feature in enumerate(single_contact): # Just assign the value unless it's an atom list, use subelements in this case - if features[i] == 'LIG_IDX_LIST': + if features[i] == "LIG_IDX_LIST": feat = et.SubElement(new_contact, features[i].lower()) - for k, atm_idx in enumerate(feature.split(',')): - idx = et.SubElement(feat, 'idx', id=str(k + 1)) + for k, atm_idx in enumerate(feature.split(",")): + idx = et.SubElement(feat, "idx", id=str(k + 1)) idx.text = str(atm_idx) - elif features[i].endswith('COO'): + elif features[i].endswith("COO"): feat = et.SubElement(new_contact, features[i].lower()) xc, yc, zc = feature - xcoo = et.SubElement(feat, 'x') - xcoo.text = '%.3f' % xc - ycoo = et.SubElement(feat, 'y') - ycoo.text = '%.3f' % yc - zcoo = et.SubElement(feat, 'z') - zcoo.text = '%.3f' % zc + xcoo = et.SubElement(feat, "x") + xcoo.text = "%.3f" % xc + ycoo = et.SubElement(feat, "y") + ycoo.text = "%.3f" % yc + zcoo = et.SubElement(feat, "z") + zcoo.text = "%.3f" % zc else: feat = et.SubElement(new_contact, features[i].lower()) feat.text = str(feature) return interaction - interactions.append(format_interactions('hydrophobic_interactions', self.hydrophobic_features, - self.hydrophobic_info)) - interactions.append(format_interactions('hydrogen_bonds', self.hbond_features, self.hbond_info)) - interactions.append(format_interactions('water_bridges', self.waterbridge_features, self.waterbridge_info)) - interactions.append(format_interactions('salt_bridges', self.saltbridge_features, self.saltbridge_info)) - interactions.append(format_interactions('pi_stacks', self.pistacking_features, self.pistacking_info)) - interactions.append(format_interactions('pi_cation_interactions', self.pication_features, self.pication_info)) - interactions.append(format_interactions('halogen_bonds', self.halogen_features, self.halogen_info)) - interactions.append(format_interactions('metal_complexes', self.metal_features, self.metal_info)) + interactions.append( + format_interactions( + "hydrophobic_interactions", + self.hydrophobic_features, + self.hydrophobic_info, + ) + ) + interactions.append( + format_interactions("hydrogen_bonds", self.hbond_features, self.hbond_info) + ) + interactions.append( + format_interactions( + "water_bridges", self.waterbridge_features, self.waterbridge_info + ) + ) + interactions.append( + format_interactions( + "salt_bridges", self.saltbridge_features, self.saltbridge_info + ) + ) + interactions.append( + format_interactions( + "pi_stacks", self.pistacking_features, self.pistacking_info + ) + ) + interactions.append( + format_interactions( + "pi_cation_interactions", self.pication_features, self.pication_info + ) + ) + interactions.append( + format_interactions( + "halogen_bonds", self.halogen_features, self.halogen_info + ) + ) + interactions.append( + format_interactions("metal_complexes", self.metal_features, self.metal_info) + ) # Mappings - mappings = et.SubElement(report, 'mappings') - smiles_to_pdb = et.SubElement(mappings, 'smiles_to_pdb') # SMILES numbering to PDB file numbering (atoms) - bsid = ':'.join([self.ligand.hetid, self.ligand.chain, str(self.ligand.position)]) + mappings = et.SubElement(report, "mappings") + smiles_to_pdb = et.SubElement( + mappings, "smiles_to_pdb" + ) # SMILES numbering to PDB file numbering (atoms) + bsid = ":".join( + [self.ligand.hetid, self.ligand.chain, str(self.ligand.position)] + ) if self.ligand.atomorder is not None: - smiles_to_pdb_map = [(key, self.ligand.Mapper.mapid(self.ligand.can_to_pdb[key], - mtype='protein', bsid=bsid)) for key in - self.ligand.can_to_pdb] - smiles_to_pdb.text = ','.join([str(mapping[0]) + ':' + str(mapping[1]) for mapping in smiles_to_pdb_map]) + smiles_to_pdb_map = [ + ( + key, + self.ligand.Mapper.mapid( + self.ligand.can_to_pdb[key], mtype="protein", bsid=bsid + ), + ) + for key in self.ligand.can_to_pdb + ] + smiles_to_pdb.text = ",".join( + [ + str(mapping[0]) + ":" + str(mapping[1]) + for mapping in smiles_to_pdb_map + ] + ) else: - smiles_to_pdb.text = '' + smiles_to_pdb.text = "" return report diff --git a/plip/exchange/webservices.py b/plip/exchange/webservices.py index 0c8cd3e..61cb6f5 100644 --- a/plip/exchange/webservices.py +++ b/plip/exchange/webservices.py @@ -11,44 +11,50 @@ logger = logger.get_logger() def check_pdb_status(pdbid): """Returns the status and up-to-date entry in the PDB for a given PDB ID""" - url = 'http://www.rcsb.org/pdb/rest/idStatus?structureId=%s' % pdbid + url = "http://www.rcsb.org/pdb/rest/idStatus?structureId=%s" % pdbid xmlf = urlopen(url) xml = et.parse(xmlf) xmlf.close() status = None current_pdbid = pdbid - for df in xml.xpath('//record'): - status = df.attrib['status'] # Status of an entry can be either 'UNKWOWN', 'OBSOLETE', or 'CURRENT' - if status == 'OBSOLETE': - current_pdbid = df.attrib['replacedBy'] # Contains the up-to-date PDB ID for obsolete entries + for df in xml.xpath("//record"): + status = df.attrib[ + "status" + ] # Status of an entry can be either 'UNKWOWN', 'OBSOLETE', or 'CURRENT' + if status == "OBSOLETE": + current_pdbid = df.attrib[ + "replacedBy" + ] # Contains the up-to-date PDB ID for obsolete entries return [status, current_pdbid.lower()] def fetch_pdb(pdbid): """Get the newest entry from the RCSB server for the given PDB ID. Exits with '1' if PDB ID is invalid.""" pdbid = pdbid.lower() - logger.info(f'checking status of PDB-ID {pdbid}') + logger.info(f"checking status of PDB-ID {pdbid}") state, current_entry = check_pdb_status(pdbid) # Get state and current PDB ID - if state == 'OBSOLETE': - logger.info(f'entry is obsolete, getting {current_entry} instead') - elif state == 'CURRENT': - logger.info('entry is up-to-date') - elif state == 'UNKNOWN': - logger.error('invalid PDB-ID (entry does not exist on PDB server)') + if state == "OBSOLETE": + logger.info(f"entry is obsolete, getting {current_entry} instead") + elif state == "CURRENT": + logger.info("entry is up-to-date") + elif state == "UNKNOWN": + logger.error("invalid PDB-ID (entry does not exist on PDB server)") sys.exit(1) - logger.info('downloading file from PDB') + logger.info("downloading file from PDB") # get URL for current entry # @todo needs update to react properly on response codes of RCSB servers - pdburl = f'http://www.rcsb.org/pdb/files/{current_entry}.pdb' + pdburl = f"http://www.rcsb.org/pdb/files/{current_entry}.pdb" try: pdbfile = urlopen(pdburl).read().decode() # If no PDB file is available, a text is now shown with "We're sorry, but ..." # Could previously be distinguished by an HTTP error - if 'sorry' in pdbfile: - logger.error('no file in PDB format available from wwPDB for the given PDB ID.') + if "sorry" in pdbfile: + logger.error( + "no file in PDB format available from wwPDB for the given PDB ID." + ) sys.exit(1) except HTTPError: - logger.error('no file in PDB format available from wwPDB for the given PDB ID') + logger.error("no file in PDB format available from wwPDB for the given PDB ID") sys.exit(1) return [pdbfile, current_entry] diff --git a/plip/exchange/xml.py b/plip/exchange/xml.py index a5eee21..92399c2 100644 --- a/plip/exchange/xml.py +++ b/plip/exchange/xml.py @@ -8,16 +8,16 @@ class XMLStorage: def getdata(self, tree, location, force_string=False): """Gets XML data from a specific element and handles types.""" - found = tree.xpath('%s/text()' % location) + found = tree.xpath("%s/text()" % location) if not found: return None else: data = found[0] if force_string: return data - if data == 'True': + if data == "True": return True - elif data == 'False': + elif data == "False": return False else: try: @@ -31,22 +31,26 @@ class XMLStorage: def getcoordinates(self, tree, location): """Gets coordinates from a specific element in PLIP XML""" - return tuple(float(x) for x in tree.xpath('.//%s/*/text()' % location)) + return tuple(float(x) for x in tree.xpath(".//%s/*/text()" % location)) class Interaction(XMLStorage): """Stores information on a specific interaction type""" def __init__(self, interaction_part): - self.id = interaction_part.get('id') - self.resnr = self.getdata(interaction_part, 'resnr') - self.restype = self.getdata(interaction_part, 'restype', force_string=True) - self.reschain = self.getdata(interaction_part, 'reschain', force_string=True) - self.resnr_lig = self.getdata(interaction_part, 'resnr_lig') - self.restype_lig = self.getdata(interaction_part, 'restype_lig', force_string=True) - self.reschain_lig = self.getdata(interaction_part, 'reschain_lig', force_string=True) - self.ligcoo = self.getcoordinates(interaction_part, 'ligcoo') - self.protcoo = self.getcoordinates(interaction_part, 'protcoo') + self.id = interaction_part.get("id") + self.resnr = self.getdata(interaction_part, "resnr") + self.restype = self.getdata(interaction_part, "restype", force_string=True) + self.reschain = self.getdata(interaction_part, "reschain", force_string=True) + self.resnr_lig = self.getdata(interaction_part, "resnr_lig") + self.restype_lig = self.getdata( + interaction_part, "restype_lig", force_string=True + ) + self.reschain_lig = self.getdata( + interaction_part, "reschain_lig", force_string=True + ) + self.ligcoo = self.getcoordinates(interaction_part, "ligcoo") + self.protcoo = self.getcoordinates(interaction_part, "protcoo") class HydrophobicInteraction(Interaction): @@ -54,9 +58,9 @@ class HydrophobicInteraction(Interaction): def __init__(self, hydrophobic_part): Interaction.__init__(self, hydrophobic_part) - self.dist = self.getdata(hydrophobic_part, 'dist') - self.ligcarbonidx = self.getdata(hydrophobic_part, 'ligcarbonidx') - self.protcarbonidx = self.getdata(hydrophobic_part, 'protcarbonidx') + self.dist = self.getdata(hydrophobic_part, "dist") + self.ligcarbonidx = self.getdata(hydrophobic_part, "ligcarbonidx") + self.protcarbonidx = self.getdata(hydrophobic_part, "protcarbonidx") class HydrogenBond(Interaction): @@ -64,17 +68,17 @@ class HydrogenBond(Interaction): def __init__(self, hbond_part): Interaction.__init__(self, hbond_part) - self.sidechain = self.getdata(hbond_part, 'sidechain') - self.dist_h_a = self.getdata(hbond_part, 'dist_h-a') - self.dist_d_a = self.getdata(hbond_part, 'dist_d-a') + self.sidechain = self.getdata(hbond_part, "sidechain") + self.dist_h_a = self.getdata(hbond_part, "dist_h-a") + self.dist_d_a = self.getdata(hbond_part, "dist_d-a") self.dist = self.dist_d_a - self.don_angle = self.getdata(hbond_part, 'don_angle') - self.protisdon = self.getdata(hbond_part, 'protisdon') - self.donoridx = self.getdata(hbond_part, 'donoridx') - self.acceptoridx = self.getdata(hbond_part, 'acceptoridx') - self.donortype = self.getdata(hbond_part, 'donortype', force_string=True) - self.acceptortype = self.getdata(hbond_part, 'acceptortype', force_string=True) + self.don_angle = self.getdata(hbond_part, "don_angle") + self.protisdon = self.getdata(hbond_part, "protisdon") + self.donoridx = self.getdata(hbond_part, "donoridx") + self.acceptoridx = self.getdata(hbond_part, "acceptoridx") + self.donortype = self.getdata(hbond_part, "donortype", force_string=True) + self.acceptortype = self.getdata(hbond_part, "acceptortype", force_string=True) class WaterBridge(Interaction): @@ -82,19 +86,21 @@ class WaterBridge(Interaction): def __init__(self, wbridge_part): Interaction.__init__(self, wbridge_part) - self.dist_a_w = self.getdata(wbridge_part, 'dist_a-w') - self.dist_d_w = self.getdata(wbridge_part, 'dist_d-w') - self.don_angle = self.getdata(wbridge_part, 'don_angle') - self.water_angle = self.getdata(wbridge_part, 'water_angle') - self.protisdon = self.getdata(wbridge_part, 'protisdon') + self.dist_a_w = self.getdata(wbridge_part, "dist_a-w") + self.dist_d_w = self.getdata(wbridge_part, "dist_d-w") + self.don_angle = self.getdata(wbridge_part, "don_angle") + self.water_angle = self.getdata(wbridge_part, "water_angle") + self.protisdon = self.getdata(wbridge_part, "protisdon") self.dist = self.dist_a_w if self.protisdon else self.dist_d_w - self.donor_idx = self.getdata(wbridge_part, 'donor_idx') - self.acceptor_idx = self.getdata(wbridge_part, 'acceptor_idx') - self.donortype = self.getdata(wbridge_part, 'donortype', force_string=True) - self.acceptortype = self.getdata(wbridge_part, 'acceptortype', force_string=True) - self.water_idx = self.getdata(wbridge_part, 'water_idx') - self.watercoo = self.getcoordinates(wbridge_part, 'watercoo') + self.donor_idx = self.getdata(wbridge_part, "donor_idx") + self.acceptor_idx = self.getdata(wbridge_part, "acceptor_idx") + self.donortype = self.getdata(wbridge_part, "donortype", force_string=True) + self.acceptortype = self.getdata( + wbridge_part, "acceptortype", force_string=True + ) + self.water_idx = self.getdata(wbridge_part, "water_idx") + self.watercoo = self.getcoordinates(wbridge_part, "watercoo") class SaltBridge(Interaction): @@ -102,11 +108,12 @@ class SaltBridge(Interaction): def __init__(self, sbridge_part): Interaction.__init__(self, sbridge_part) - self.dist = self.getdata(sbridge_part, 'dist') - self.protispos = self.getdata(sbridge_part, 'protispos') - self.lig_group = self.getdata(sbridge_part, 'lig_group', force_string=True) - self.lig_idx_list = [int(tagpart.text) for tagpart in - sbridge_part.xpath('lig_idx_list/idx')] + self.dist = self.getdata(sbridge_part, "dist") + self.protispos = self.getdata(sbridge_part, "protispos") + self.lig_group = self.getdata(sbridge_part, "lig_group", force_string=True) + self.lig_idx_list = [ + int(tagpart.text) for tagpart in sbridge_part.xpath("lig_idx_list/idx") + ] class PiStacking(Interaction): @@ -114,13 +121,14 @@ class PiStacking(Interaction): def __init__(self, pistack_part): Interaction.__init__(self, pistack_part) - self.centdist = self.getdata(pistack_part, 'centdist') + self.centdist = self.getdata(pistack_part, "centdist") self.dist = self.centdist - self.angle = self.getdata(pistack_part, 'angle') - self.offset = self.getdata(pistack_part, 'offset') - self.type = self.getdata(pistack_part, 'type') - self.lig_idx_list = [int(tagpart.text) for tagpart in - pistack_part.xpath('lig_idx_list/idx')] + self.angle = self.getdata(pistack_part, "angle") + self.offset = self.getdata(pistack_part, "offset") + self.type = self.getdata(pistack_part, "type") + self.lig_idx_list = [ + int(tagpart.text) for tagpart in pistack_part.xpath("lig_idx_list/idx") + ] class PiCation(Interaction): @@ -128,11 +136,13 @@ class PiCation(Interaction): def __init__(self, pication_part): Interaction.__init__(self, pication_part) - self.dist = self.getdata(pication_part, 'dist') - self.offset = self.getdata(pication_part, 'offset') - self.protcharged = self.getdata(pication_part, 'protcharged') - self.lig_group = self.getdata(pication_part, 'lig_group') - self.lig_idx_list = [int(tag.text) for tag in pication_part.xpath('.//lig_idx_list/idx')] + self.dist = self.getdata(pication_part, "dist") + self.offset = self.getdata(pication_part, "offset") + self.protcharged = self.getdata(pication_part, "protcharged") + self.lig_group = self.getdata(pication_part, "lig_group") + self.lig_idx_list = [ + int(tag.text) for tag in pication_part.xpath(".//lig_idx_list/idx") + ] class HalogenBond(Interaction): @@ -140,14 +150,16 @@ class HalogenBond(Interaction): def __init__(self, halogen_part): Interaction.__init__(self, halogen_part) - self.dist = self.getdata(halogen_part, 'dist') - self.don_angle = self.getdata(halogen_part, 'don_angle') - self.acc_angle = self.getdata(halogen_part, 'acc_angle') - self.donortype = self.getdata(halogen_part, 'donortype', force_string=True) - self.acceptortype = self.getdata(halogen_part, 'acceptortype', force_string=True) - self.don_idx = self.getdata(halogen_part, 'don_idx') - self.acc_idx = self.getdata(halogen_part, 'acc_idx') - self.sidechain = self.getdata(halogen_part, 'sidechain') + self.dist = self.getdata(halogen_part, "dist") + self.don_angle = self.getdata(halogen_part, "don_angle") + self.acc_angle = self.getdata(halogen_part, "acc_angle") + self.donortype = self.getdata(halogen_part, "donortype", force_string=True) + self.acceptortype = self.getdata( + halogen_part, "acceptortype", force_string=True + ) + self.don_idx = self.getdata(halogen_part, "don_idx") + self.acc_idx = self.getdata(halogen_part, "acc_idx") + self.sidechain = self.getdata(halogen_part, "sidechain") class MetalComplex(Interaction): @@ -155,18 +167,22 @@ class MetalComplex(Interaction): def __init__(self, metalcomplex_part): Interaction.__init__(self, metalcomplex_part) - self.metal_idx = self.getdata(metalcomplex_part, 'metal_idx') - self.metal_type = self.getdata(metalcomplex_part, 'metal_type', force_string=True) - self.target_idx = self.getdata(metalcomplex_part, 'target_idx') - self.target_type = self.getdata(metalcomplex_part, 'target_type', force_string=True) - self.coordination = self.getdata(metalcomplex_part, 'coordination') - self.dist = self.getdata(metalcomplex_part, 'dist') - self.location = self.getdata(metalcomplex_part, 'location', force_string=True) - self.rms = self.getdata(metalcomplex_part, 'rms') - self.geometry = self.getdata(metalcomplex_part, 'geometry', force_string=True) - self.complexnum = self.getdata(metalcomplex_part, 'complexnum') - self.targetcoo = self.getcoordinates(metalcomplex_part, 'targetcoo') - self.metalcoo = self.getcoordinates(metalcomplex_part, 'metalcoo') + self.metal_idx = self.getdata(metalcomplex_part, "metal_idx") + self.metal_type = self.getdata( + metalcomplex_part, "metal_type", force_string=True + ) + self.target_idx = self.getdata(metalcomplex_part, "target_idx") + self.target_type = self.getdata( + metalcomplex_part, "target_type", force_string=True + ) + self.coordination = self.getdata(metalcomplex_part, "coordination") + self.dist = self.getdata(metalcomplex_part, "dist") + self.location = self.getdata(metalcomplex_part, "location", force_string=True) + self.rms = self.getdata(metalcomplex_part, "rms") + self.geometry = self.getdata(metalcomplex_part, "geometry", force_string=True) + self.complexnum = self.getdata(metalcomplex_part, "complexnum") + self.targetcoo = self.getcoordinates(metalcomplex_part, "targetcoo") + self.metalcoo = self.getcoordinates(metalcomplex_part, "metalcoo") class BSite(XMLStorage): @@ -175,63 +191,107 @@ class BSite(XMLStorage): def __init__(self, bindingsite, pdbid): self.bindingsite = bindingsite self.pdbid = pdbid - self.bsid = ":".join(bindingsite.xpath('identifiers/*/text()')[2:5]) + self.bsid = ":".join(bindingsite.xpath("identifiers/*/text()")[2:5]) self.uniqueid = ":".join([self.pdbid, self.bsid]) - self.hetid = self.getdata(bindingsite, 'identifiers/hetid', force_string=True) - self.longname = self.getdata(bindingsite, 'identifiers/longname', force_string=True) - self.ligtype = self.getdata(bindingsite, 'identifiers/ligtype', force_string=True) - self.smiles = self.getdata(bindingsite, 'identifiers/smiles', force_string=True) - self.inchikey = self.getdata(bindingsite, 'identifiers/inchikey', force_string=True) - self.position = self.getdata(bindingsite, 'identifiers/position') - self.chain = self.getdata(bindingsite, 'identifiers/chain', force_string=True) + self.hetid = self.getdata(bindingsite, "identifiers/hetid", force_string=True) + self.longname = self.getdata( + bindingsite, "identifiers/longname", force_string=True + ) + self.ligtype = self.getdata( + bindingsite, "identifiers/ligtype", force_string=True + ) + self.smiles = self.getdata(bindingsite, "identifiers/smiles", force_string=True) + self.inchikey = self.getdata( + bindingsite, "identifiers/inchikey", force_string=True + ) + self.position = self.getdata(bindingsite, "identifiers/position") + self.chain = self.getdata(bindingsite, "identifiers/chain", force_string=True) # Information on binding site members self.members = [] - for member in bindingsite.xpath('identifiers/members/member'): - self.members += member.xpath('text()') + for member in bindingsite.xpath("identifiers/members/member"): + self.members += member.xpath("text()") - self.composite = self.getdata(bindingsite, 'identifiers/composite') + self.composite = self.getdata(bindingsite, "identifiers/composite") # Ligand Properties - self.heavy_atoms = self.getdata(bindingsite, 'lig_properties/num_heavy_atoms') - self.hbd = self.getdata(bindingsite, 'lig_properties/num_hbd') - self.unpaired_hbd = self.getdata(bindingsite, 'lig_properties/num_unpaired_hbd') - self.hba = self.getdata(bindingsite, 'lig_properties/num_hba') - self.unpaired_hba = self.getdata(bindingsite, 'lig_properties/num_unpaired_hba') - self.hal = self.getdata(bindingsite, 'lig_properties/num_hal') - self.unpaired_hal = self.getdata(bindingsite, 'lig_properties/num_unpaired_hal') - self.molweight = self.getdata(bindingsite, 'lig_properties/molweight') - self.logp = self.getdata(bindingsite, 'lig_properties/logp') - self.rotatable_bonds = self.getdata(bindingsite, 'lig_properties/num_rotatable_bonds') - self.rings = self.getdata(bindingsite, 'lig_properties/num_aromatic_rings') + self.heavy_atoms = self.getdata(bindingsite, "lig_properties/num_heavy_atoms") + self.hbd = self.getdata(bindingsite, "lig_properties/num_hbd") + self.unpaired_hbd = self.getdata(bindingsite, "lig_properties/num_unpaired_hbd") + self.hba = self.getdata(bindingsite, "lig_properties/num_hba") + self.unpaired_hba = self.getdata(bindingsite, "lig_properties/num_unpaired_hba") + self.hal = self.getdata(bindingsite, "lig_properties/num_hal") + self.unpaired_hal = self.getdata(bindingsite, "lig_properties/num_unpaired_hal") + self.molweight = self.getdata(bindingsite, "lig_properties/molweight") + self.logp = self.getdata(bindingsite, "lig_properties/logp") + self.rotatable_bonds = self.getdata( + bindingsite, "lig_properties/num_rotatable_bonds" + ) + self.rings = self.getdata(bindingsite, "lig_properties/num_aromatic_rings") # Binding Site residues self.bs_res = [] - for tagpart in bindingsite.xpath('bs_residues/bs_residue'): + for tagpart in bindingsite.xpath("bs_residues/bs_residue"): resnumber, reschain = tagpart.text[:-1], tagpart.text[-1] - aa, contact, min_dist = tagpart.get('aa'), tagpart.get('contact'), tagpart.get('min_dist') - new_bs_res = {'resnr': int(resnumber), 'reschain': reschain, 'aa': aa, - 'contact': True if contact == 'True' else False, 'min_dist': float(min_dist)} + aa, contact, min_dist = ( + tagpart.get("aa"), + tagpart.get("contact"), + tagpart.get("min_dist"), + ) + new_bs_res = { + "resnr": int(resnumber), + "reschain": reschain, + "aa": aa, + "contact": True if contact == "True" else False, + "min_dist": float(min_dist), + } self.bs_res.append(new_bs_res) # Interacting chains self.interacting_chains = [] - for chain in bindingsite.xpath('interacting_chains/interacting_chain'): - self.interacting_chains += chain.xpath('text()') + for chain in bindingsite.xpath("interacting_chains/interacting_chain"): + self.interacting_chains += chain.xpath("text()") # Interactions - interactions = bindingsite.xpath('interactions')[0] - self.hydrophobics = [HydrophobicInteraction(x) for x in - interactions.xpath('hydrophobic_interactions/hydrophobic_interaction')] - self.hbonds = [HydrogenBond(x) for x in interactions.xpath('hydrogen_bonds/hydrogen_bond')] - self.wbridges = [WaterBridge(x) for x in interactions.xpath('water_bridges/water_bridge')] - self.sbridges = [SaltBridge(x) for x in interactions.xpath('salt_bridges/salt_bridge')] - self.pi_stacks = [PiStacking(x) for x in interactions.xpath('pi_stacks/pi_stack')] - self.pi_cations = [PiCation(x) for x in interactions.xpath('pi_cation_interactions/pi_cation_interaction')] - self.halogens = [HalogenBond(x) for x in interactions.xpath('halogen_bonds/halogen_bond')] - self.metal_complexes = [MetalComplex(x) for x in interactions.xpath('metal_complexes/metal_complex')] - self.num_contacts = len(self.hydrophobics) + len(self.hbonds) + len(self.wbridges) + len(self.sbridges) + \ - len(self.pi_stacks) + len(self.pi_cations) + len(self.halogens) + len(self.metal_complexes) + interactions = bindingsite.xpath("interactions")[0] + self.hydrophobics = [ + HydrophobicInteraction(x) + for x in interactions.xpath( + "hydrophobic_interactions/hydrophobic_interaction" + ) + ] + self.hbonds = [ + HydrogenBond(x) for x in interactions.xpath("hydrogen_bonds/hydrogen_bond") + ] + self.wbridges = [ + WaterBridge(x) for x in interactions.xpath("water_bridges/water_bridge") + ] + self.sbridges = [ + SaltBridge(x) for x in interactions.xpath("salt_bridges/salt_bridge") + ] + self.pi_stacks = [ + PiStacking(x) for x in interactions.xpath("pi_stacks/pi_stack") + ] + self.pi_cations = [ + PiCation(x) + for x in interactions.xpath("pi_cation_interactions/pi_cation_interaction") + ] + self.halogens = [ + HalogenBond(x) for x in interactions.xpath("halogen_bonds/halogen_bond") + ] + self.metal_complexes = [ + MetalComplex(x) for x in interactions.xpath("metal_complexes/metal_complex") + ] + self.num_contacts = ( + len(self.hydrophobics) + + len(self.hbonds) + + len(self.wbridges) + + len(self.sbridges) + + len(self.pi_stacks) + + len(self.pi_cations) + + len(self.halogens) + + len(self.metal_complexes) + ) self.has_interactions = self.num_contacts > 0 self.get_atom_mapping() @@ -240,25 +300,45 @@ class BSite(XMLStorage): def get_atom_mapping(self): """Parses the ligand atom mapping.""" # Atom mappings - smiles_to_pdb_mapping = self.bindingsite.xpath('mappings/smiles_to_pdb/text()') + smiles_to_pdb_mapping = self.bindingsite.xpath("mappings/smiles_to_pdb/text()") if not smiles_to_pdb_mapping: - self.mappings = {'smiles_to_pdb': None, 'pdb_to_smiles': None} + self.mappings = {"smiles_to_pdb": None, "pdb_to_smiles": None} else: - smiles_to_pdb_mapping = {int(y[0]): int(y[1]) for y in [x.split(':') - for x in smiles_to_pdb_mapping[0].split(',')]} - self.mappings = {'smiles_to_pdb': smiles_to_pdb_mapping} - self.mappings['pdb_to_smiles'] = {v: k for k, v in self.mappings['smiles_to_pdb'].items()} + smiles_to_pdb_mapping = { + int(y[0]): int(y[1]) + for y in [x.split(":") for x in smiles_to_pdb_mapping[0].split(",")] + } + self.mappings = {"smiles_to_pdb": smiles_to_pdb_mapping} + self.mappings["pdb_to_smiles"] = { + v: k for k, v in self.mappings["smiles_to_pdb"].items() + } def get_counts(self): """counts the interaction types and backbone hydrogen bonding in a binding site""" hbondsback = len([hb for hb in self.hbonds if not hb.sidechain]) - counts = {'hydrophobics': len(self.hydrophobics), 'hbonds': len(self.hbonds), - 'wbridges': len(self.wbridges), 'sbridges': len(self.sbridges), 'pistacks': len(self.pi_stacks), - 'pications': len(self.pi_cations), 'halogens': len(self.halogens), 'metal': len(self.metal_complexes), - 'hbond_back': hbondsback, 'hbond_nonback': (len(self.hbonds) - hbondsback)} - counts['total'] = counts['hydrophobics'] + counts['hbonds'] + counts['wbridges'] + \ - counts['sbridges'] + counts['pistacks'] + counts['pications'] + counts['halogens'] + counts['metal'] + counts = { + "hydrophobics": len(self.hydrophobics), + "hbonds": len(self.hbonds), + "wbridges": len(self.wbridges), + "sbridges": len(self.sbridges), + "pistacks": len(self.pi_stacks), + "pications": len(self.pi_cations), + "halogens": len(self.halogens), + "metal": len(self.metal_complexes), + "hbond_back": hbondsback, + "hbond_nonback": (len(self.hbonds) - hbondsback), + } + counts["total"] = ( + counts["hydrophobics"] + + counts["hbonds"] + + counts["wbridges"] + + counts["sbridges"] + + counts["pistacks"] + + counts["pications"] + + counts["halogens"] + + counts["metal"] + ) return counts @@ -269,17 +349,22 @@ class PlipXML(XMLStorage): self.load_data(xmlfile) # Parse general information - self.version = self.getdata(self.doc, '/report/plipversion/') - self.pdbid = self.getdata(self.doc, '/report/pdbid', force_string=True) - self.filetype = self.getdata(self.doc, '/report/filetype') - self.fixed = self.getdata(self.doc, '/report/pdbfixes/') - self.filename = self.getdata(self.doc, '/report/filename') - self.excluded = self.doc.xpath('/report/excluded_ligands/excluded_ligand/text()') + self.version = self.getdata(self.doc, "/report/plipversion/") + self.pdbid = self.getdata(self.doc, "/report/pdbid", force_string=True) + self.filetype = self.getdata(self.doc, "/report/filetype") + self.fixed = self.getdata(self.doc, "/report/pdbfixes/") + self.filename = self.getdata(self.doc, "/report/filename") + self.excluded = self.doc.xpath( + "/report/excluded_ligands/excluded_ligand/text()" + ) # Parse binding site information - self.bsites = {BSite(bs, self.pdbid).bsid: BSite(bs, self.pdbid) for bs in self.doc.xpath('//bindingsite')} + self.bsites = { + BSite(bs, self.pdbid).bsid: BSite(bs, self.pdbid) + for bs in self.doc.xpath("//bindingsite") + } self.num_bsites = len(self.bsites) def load_data(self, xmlfile): """Loads/parses an XML file and saves it as a tree if successful.""" - self.doc = etree.parse(xmlfile)
\ No newline at end of file + self.doc = etree.parse(xmlfile) |