from lxml import etree from urllib.request import urlopen class XMLStorage: """Generic class for storing XML data from PLIP XML files.""" def getdata(self, tree, location, force_string=False): """Gets XML data from a specific element and handles types.""" found = tree.xpath('%s/text()' % location) if not found: return None else: data = found[0] if force_string: return data if data == 'True': return True elif data == 'False': return False else: try: return int(data) except ValueError: try: return float(data) except ValueError: # It's a string return data 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)) 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') class HydrophobicInteraction(Interaction): """Stores information on a hydrophobic 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') class HydrogenBond(Interaction): """Stores information on a hydrogen bond 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.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) class WaterBridge(Interaction): """Stores information on a water bridge 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 = 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') class SaltBridge(Interaction): """Stores information on a salt bridge 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')] class PiStacking(Interaction): """Stores information on a pi stacking interaction""" def __init__(self, pistack_part): Interaction.__init__(self, pistack_part) 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')] class PiCation(Interaction): """Stores information on a pi cation 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')] class HalogenBond(Interaction): """Stores information on a halogen bond 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') class MetalComplex(Interaction): """Stores information on a metal complexe 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') class BSite(XMLStorage): """Stores all information about an specific binding site.""" def __init__(self, bindingsite, pdbid): self.bindingsite = bindingsite self.pdbid = pdbid 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) # Information on binding site members self.members = [] for member in bindingsite.xpath('identifiers/members/member'): self.members += member.xpath('text()') 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') # Binding Site residues self.bs_res = [] 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)} 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()') # 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) self.has_interactions = self.num_contacts > 0 self.get_atom_mapping() self.counts = self.get_counts() def get_atom_mapping(self): """Parses the ligand atom mapping.""" # Atom mappings 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} 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()} 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'] return counts class PlipXML(XMLStorage): """Parses and stores all information from a PLIP XML file.""" def __init__(self, xmlfile): 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()') # Parse binding site information 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)