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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)
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