import time from operator import itemgetter import lxml.etree as et from plip.basic import config from plip.basic.config import __version__ from plip.structure.preparation import PDBComplex class StructureReport: """Creates reports (xml or txt) for one structure/""" def __init__(self, mol: PDBComplex, outputprefix: str = 'report'): self.mol = mol self.excluded = self.mol.excluded self.xmlreport = self.construct_xml_tree() self.txtreport = self.construct_txt_file() self.get_bindingsite_data() self.outpath = mol.output_path self.outputprefix = outputprefix def construct_xml_tree(self): """Construct the basic XML tree""" report = et.Element('report') plipversion = et.SubElement(report, 'plipversion') plipversion.text = __version__ 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" maintainer_information = et.SubElement(report, 'maintainer_information') maintainer_information.text = config.__maintainer__ mode = et.SubElement(report, 'mode') if config.DNARECEPTOR: mode.text = 'dna_receptor' else: mode.text = 'default' pdbid = et.SubElement(report, 'pdbid') pdbid.text = self.mol.pymol_name.upper() 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') for i, exlig in enumerate(self.excluded): e = et.SubElement(exligs, 'excluded_ligand', id=str(i + 1)) e.text = exlig 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)]) 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.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') if len(self.excluded) != 0: 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') return textlines def get_bindingsite_data(self): """Get the additional data for the binding sites""" 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') 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') else: 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) else: output = et.tostring(self.xmlreport, pretty_print=True) print(output.decode('utf8')) 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] else: output = '\n'.join(self.txtreport) print(output) class BindingSiteReport: """Gather report data and generate reports for one binding site in different formats.""" def __init__(self, plcomplex): ################ # GENERAL DATA # ################ self.complex = plcomplex 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.longname = self.ligand.longname self.ligtype = self.ligand.type self.bs_res = self.bindingsite.bs_res self.min_dist = self.bindingsite.min_dist self.bs_res_interacting = self.complex.interacting_res self.pdbid = self.complex.pdbid.upper() self.lig_members = self.complex.lig_members self.interacting_chains = self.complex.interacting_chains ############################ # HYDROPHOBIC INTERACTIONS # ############################ self.hydrophobic_features = ( '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)) ################## # 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') 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)) ################# # 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') # 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)) ################ # SALT BRIDGES # ################ self.saltbridge_features = ( '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))) 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))) ############### # PI-STACKING # ############### self.pistacking_features = ( '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))) ########################## # 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') 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))) 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))) ################# # 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') 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)) ################### # 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') 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)) 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)) for line in info: 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.""" # Determine cell width for each column cell_dict = {} for i, row in enumerate(array): for j, val in enumerate(row): if j not in cell_dict: 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 # Format top line num_cols = len(array[0]) form = '+' for col in range(num_cols): form += (cell_dict[col] + 1) * '-' form += '+' form += '\n' # Format values for i, row in enumerate(array): form += '| ' for j, val in enumerate(row): cell_width = cell_dict[j] form += str(val) + (cell_width - len(val)) * ' ' + '| ' form.rstrip() form += '\n' # Seperation lines form += '+' if i == 0: sign = '=' else: sign = '-' for col in range(num_cols): form += (cell_dict[col] + 1) * sign 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) txt.append(titletext) for i, member in enumerate(self.lig_members[1:]): 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]]: 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)) if not len(interaction_information) == 0: txt.append('\n**%s**' % iname) table = [features, ] for single_contact in interaction_information: values = [] for x in single_contact: if type(x) == str: values.append(x) elif type(x) == tuple and len(x) == 3: # Coordinates values.append("%.3f, %.3f, %.3f" % x) else: values.append(str(x)) table.append(values) txt.append(self.rst_table(table)) 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') # 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') num_hbd.text = str(self.ligand.num_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.text = str(self.ligand.num_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.text = str(self.ligand.num_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.text = str(self.ligand.num_rings) 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.text = str(self.ligand.molweight) logp = et.SubElement(lig_properties, 'logp') logp.text = str(self.ligand.logp) 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.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] aatype = self.min_dist[bsres][1] 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' 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 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.text = bsid 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)) 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)) else: # Metal Complex[es] 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': 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)) idx.text = str(atm_idx) 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 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)) # 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)]) 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]) else: smiles_to_pdb.text = '' return report