diff options
Diffstat (limited to 'plip/exchange/xml.py')
| -rw-r--r-- | plip/exchange/xml.py | 349 |
1 files changed, 217 insertions, 132 deletions
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) |