Format code with Blackdeepsource-transform-b65b5545

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)