diff options
Diffstat (limited to 'plip/exchange/xml.py')
| -rw-r--r-- | plip/exchange/xml.py | 285 |
1 files changed, 0 insertions, 285 deletions
diff --git a/plip/exchange/xml.py b/plip/exchange/xml.py deleted file mode 100644 index a5eee21..0000000 --- a/plip/exchange/xml.py +++ /dev/null @@ -1,285 +0,0 @@ -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)
\ No newline at end of file |