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authordeepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com>2020-07-07 14:55:17 +0000
committerGitHub <noreply@github.com>2020-07-07 14:55:17 +0000
commit0d135d611506e81d322596c7827b08bbfd3b7c08 (patch)
treea281b8e1f140ad3de77d818747fce03bcfa5b77b /plip/exchange/xml.py
parent7059ee2a4ced23e467741cc846eb185886ffca38 (diff)
Format code with Blackdeepsource-transform-b65b5545
Diffstat (limited to 'plip/exchange/xml.py')
-rw-r--r--plip/exchange/xml.py349
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)