Format code with Blackdeepsource-transform-b65b5545

4 files changed, 807 insertions, 370 deletions

diff --git a/plip/exchange/json.py b/plip/exchange/json.py
index 5c7ad5c..14febda 100644
--- a/plip/exchange/json.py
+++ b/plip/exchange/json.py
@@ -1 +1 @@
-# place holder for module to add Json support
\ No newline at end of file
+# place holder for module to add Json support
diff --git a/plip/exchange/report.py b/plip/exchange/report.py
index a559bf8..edca1f1 100644
--- a/plip/exchange/report.py
+++ b/plip/exchange/report.py
@@ -11,7 +11,7 @@ from plip.structure.preparation import PDBComplex
 class StructureReport:
     """Creates reports (xml or txt) for one structure/"""
 
-    def __init__(self, mol: PDBComplex, outputprefix: str = 'report'):
+    def __init__(self, mol: PDBComplex, outputprefix: str = "report"):
         self.mol = mol
         self.excluded = self.mol.excluded
         self.xmlreport = self.construct_xml_tree()
@@ -22,57 +22,75 @@ class StructureReport:
 
     def construct_xml_tree(self):
         """Construct the basic XML tree"""
-        report = et.Element('report')
-        plipversion = et.SubElement(report, 'plipversion')
+        report = et.Element("report")
+        plipversion = et.SubElement(report, "plipversion")
         plipversion.text = __version__
-        date_of_creation = et.SubElement(report, 'date_of_creation')
+        date_of_creation = et.SubElement(report, "date_of_creation")
         date_of_creation.text = time.strftime("%Y/%m/%d")
-        citation_information = et.SubElement(report, 'citation_information')
-        citation_information.text = "Salentin,S. et al. PLIP: fully automated protein-ligand interaction profiler. " \
-                                    "Nucl. Acids Res. (1 July 2015) 43 (W1): W443-W447. doi: 10.1093/nar/gkv315"
+        citation_information = et.SubElement(report, "citation_information")
+        citation_information.text = (
+            "Salentin,S. et al. PLIP: fully automated protein-ligand interaction profiler. "
+            "Nucl. Acids Res. (1 July 2015) 43 (W1): W443-W447. doi: 10.1093/nar/gkv315"
+        )
 
-        maintainer_information = et.SubElement(report, 'maintainer_information')
+        maintainer_information = et.SubElement(report, "maintainer_information")
         maintainer_information.text = config.__maintainer__
-        mode = et.SubElement(report, 'mode')
+        mode = et.SubElement(report, "mode")
         if config.DNARECEPTOR:
-            mode.text = 'dna_receptor'
+            mode.text = "dna_receptor"
         else:
-            mode.text = 'default'
-        pdbid = et.SubElement(report, 'pdbid')
+            mode.text = "default"
+        pdbid = et.SubElement(report, "pdbid")
         pdbid.text = self.mol.pymol_name.upper()
-        filetype = et.SubElement(report, 'filetype')
+        filetype = et.SubElement(report, "filetype")
         filetype.text = self.mol.filetype.upper()
-        pdbfile = et.SubElement(report, 'pdbfile')
-        pdbfile.text = self.mol.sourcefiles['pdbcomplex']
-        pdbfixes = et.SubElement(report, 'pdbfixes')
-        pdbfixes.text = str(self.mol.information['pdbfixes'])
-        filename = et.SubElement(report, 'filename')
-        filename.text = str(self.mol.sourcefiles.get('filename') or None)
-        exligs = et.SubElement(report, 'excluded_ligands')
+        pdbfile = et.SubElement(report, "pdbfile")
+        pdbfile.text = self.mol.sourcefiles["pdbcomplex"]
+        pdbfixes = et.SubElement(report, "pdbfixes")
+        pdbfixes.text = str(self.mol.information["pdbfixes"])
+        filename = et.SubElement(report, "filename")
+        filename.text = str(self.mol.sourcefiles.get("filename") or None)
+        exligs = et.SubElement(report, "excluded_ligands")
         for i, exlig in enumerate(self.excluded):
-            e = et.SubElement(exligs, 'excluded_ligand', id=str(i + 1))
+            e = et.SubElement(exligs, "excluded_ligand", id=str(i + 1))
             e.text = exlig
-        covalent = et.SubElement(report, 'covlinkages')
+        covalent = et.SubElement(report, "covlinkages")
         for i, covlinkage in enumerate(self.mol.covalent):
-            e = et.SubElement(covalent, 'covlinkage', id=str(i + 1))
-            f1 = et.SubElement(e, 'res1')
-            f2 = et.SubElement(e, 'res2')
-            f1.text = ":".join([covlinkage.id1, covlinkage.chain1, str(covlinkage.pos1)])
-            f2.text = ":".join([covlinkage.id2, covlinkage.chain2, str(covlinkage.pos2)])
+            e = et.SubElement(covalent, "covlinkage", id=str(i + 1))
+            f1 = et.SubElement(e, "res1")
+            f2 = et.SubElement(e, "res2")
+            f1.text = ":".join(
+                [covlinkage.id1, covlinkage.chain1, str(covlinkage.pos1)]
+            )
+            f2.text = ":".join(
+                [covlinkage.id2, covlinkage.chain2, str(covlinkage.pos2)]
+            )
         return report
 
     def construct_txt_file(self):
         """Construct the header of the txt file"""
-        textlines = ['Prediction of noncovalent interactions for PDB structure %s' % self.mol.pymol_name.upper(), ]
+        textlines = [
+            "Prediction of noncovalent interactions for PDB structure %s"
+            % self.mol.pymol_name.upper(),
+        ]
         textlines.append("=" * len(textlines[0]))
-        textlines.append('Created on %s using PLIP v%s\n' % (time.strftime("%Y/%m/%d"), __version__))
-        textlines.append('If you are using PLIP in your work, please cite:')
-        textlines.append('Salentin,S. et al. PLIP: fully automated protein-ligand interaction profiler.')
-        textlines.append('Nucl. Acids Res. (1 July 2015) 43 (W1): W443-W447. doi: 10.1093/nar/gkv315\n')
+        textlines.append(
+            "Created on %s using PLIP v%s\n" % (time.strftime("%Y/%m/%d"), __version__)
+        )
+        textlines.append("If you are using PLIP in your work, please cite:")
+        textlines.append(
+            "Salentin,S. et al. PLIP: fully automated protein-ligand interaction profiler."
+        )
+        textlines.append(
+            "Nucl. Acids Res. (1 July 2015) 43 (W1): W443-W447. doi: 10.1093/nar/gkv315\n"
+        )
         if len(self.excluded) != 0:
-            textlines.append('Excluded molecules as ligands: %s\n' % ','.join([lig for lig in self.excluded]))
+            textlines.append(
+                "Excluded molecules as ligands: %s\n"
+                % ",".join([lig for lig in self.excluded])
+            )
         if config.DNARECEPTOR:
-            textlines.append('DNA/RNA in structure was chosen as the receptor part.\n')
+            textlines.append("DNA/RNA in structure was chosen as the receptor part.\n")
         return textlines
 
     def get_bindingsite_data(self):
@@ -80,21 +98,24 @@ class StructureReport:
         for i, site in enumerate(sorted(self.mol.interaction_sets)):
             s = self.mol.interaction_sets[site]
             bindingsite = BindingSiteReport(s).generate_xml()
-            bindingsite.set('id', str(i + 1))
-            bindingsite.set('has_interactions', 'False')
+            bindingsite.set("id", str(i + 1))
+            bindingsite.set("has_interactions", "False")
             self.xmlreport.insert(i + 1, bindingsite)
             for itype in BindingSiteReport(s).generate_txt():
                 self.txtreport.append(itype)
             if not s.no_interactions:
-                bindingsite.set('has_interactions', 'True')
+                bindingsite.set("has_interactions", "True")
             else:
-                self.txtreport.append('No interactions detected.')
+                self.txtreport.append("No interactions detected.")
 
     def write_xml(self, as_string=False):
         """Write the XML report"""
         if not as_string:
-            et.ElementTree(self.xmlreport).write('{}/{}.xml'.format(self.outpath, self.outputprefix), pretty_print=True,
-                                                 xml_declaration=True)
+            et.ElementTree(self.xmlreport).write(
+                "{}/{}.xml".format(self.outpath, self.outputprefix),
+                pretty_print=True,
+                xml_declaration=True,
+            )
         else:
             output = et.tostring(self.xmlreport, pretty_print=True)
             if config.RAWSTRING:
@@ -104,10 +125,10 @@ class StructureReport:
     def write_txt(self, as_string=False):
         """Write the TXT report"""
         if not as_string:
-            with open('{}/{}.txt'.format(self.outpath, self.outputprefix), 'w') as f:
-                [f.write(textline + '\n') for textline in self.txtreport]
+            with open("{}/{}.txt".format(self.outpath, self.outputprefix), "w") as f:
+                [f.write(textline + "\n") for textline in self.txtreport]
         else:
-            output = '\n'.join(self.txtreport)
+            output = "\n".join(self.txtreport)
             if config.RAWSTRING:
                 output = repr(output)
             print(output)
@@ -126,7 +147,9 @@ class BindingSiteReport:
         self.ligand = self.complex.ligand
         self.bindingsite = self.complex.bindingsite
         self.output_path = self.complex.output_path
-        self.bsid = ':'.join([self.ligand.hetid, self.ligand.chain, str(self.ligand.position)])
+        self.bsid = ":".join(
+            [self.ligand.hetid, self.ligand.chain, str(self.ligand.position)]
+        )
         self.longname = self.ligand.longname
         self.ligtype = self.ligand.type
         self.bs_res = self.bindingsite.bs_res
@@ -141,163 +164,408 @@ class BindingSiteReport:
         ############################
 
         self.hydrophobic_features = (
-            'RESNR', 'RESTYPE', 'RESCHAIN', 'RESNR_LIG', 'RESTYPE_LIG', 'RESCHAIN_LIG', 'DIST', 'LIGCARBONIDX',
-            'PROTCARBONIDX', 'LIGCOO',
-            'PROTCOO')
+            "RESNR",
+            "RESTYPE",
+            "RESCHAIN",
+            "RESNR_LIG",
+            "RESTYPE_LIG",
+            "RESCHAIN_LIG",
+            "DIST",
+            "LIGCARBONIDX",
+            "PROTCARBONIDX",
+            "LIGCOO",
+            "PROTCOO",
+        )
         self.hydrophobic_info = []
         for hydroph in self.complex.hydrophobic_contacts:
-            self.hydrophobic_info.append((hydroph.resnr, hydroph.restype, hydroph.reschain, hydroph.resnr_l,
-                                          hydroph.restype_l, hydroph.reschain_l, '%.2f' % hydroph.distance,
-                                          hydroph.ligatom_orig_idx, hydroph.bsatom_orig_idx, hydroph.ligatom.coords,
-                                          hydroph.bsatom.coords))
+            self.hydrophobic_info.append(
+                (
+                    hydroph.resnr,
+                    hydroph.restype,
+                    hydroph.reschain,
+                    hydroph.resnr_l,
+                    hydroph.restype_l,
+                    hydroph.reschain_l,
+                    "%.2f" % hydroph.distance,
+                    hydroph.ligatom_orig_idx,
+                    hydroph.bsatom_orig_idx,
+                    hydroph.ligatom.coords,
+                    hydroph.bsatom.coords,
+                )
+            )
 
         ##################
         # HYDROGEN BONDS #
         ##################
 
         self.hbond_features = (
-            'RESNR', 'RESTYPE', 'RESCHAIN', 'RESNR_LIG', 'RESTYPE_LIG', 'RESCHAIN_LIG', 'SIDECHAIN', 'DIST_H-A',
-            'DIST_D-A',
-            'DON_ANGLE',
-            'PROTISDON', 'DONORIDX', 'DONORTYPE', 'ACCEPTORIDX', 'ACCEPTORTYPE', 'LIGCOO', 'PROTCOO')
+            "RESNR",
+            "RESTYPE",
+            "RESCHAIN",
+            "RESNR_LIG",
+            "RESTYPE_LIG",
+            "RESCHAIN_LIG",
+            "SIDECHAIN",
+            "DIST_H-A",
+            "DIST_D-A",
+            "DON_ANGLE",
+            "PROTISDON",
+            "DONORIDX",
+            "DONORTYPE",
+            "ACCEPTORIDX",
+            "ACCEPTORTYPE",
+            "LIGCOO",
+            "PROTCOO",
+        )
         self.hbond_info = []
         for hbond in self.complex.hbonds_pdon + self.complex.hbonds_ldon:
-            ligatom, protatom = (hbond.a, hbond.d) if hbond.protisdon else (hbond.d, hbond.a)
-            self.hbond_info.append((hbond.resnr, hbond.restype, hbond.reschain, hbond.resnr_l, hbond.restype_l,
-                                    hbond.reschain_l, hbond.sidechain,
-                                    '%.2f' % hbond.distance_ah, '%.2f' % hbond.distance_ad, '%.2f' % hbond.angle,
-                                    hbond.protisdon, hbond.d_orig_idx, hbond.dtype, hbond.a_orig_idx, hbond.atype,
-                                    ligatom.coords, protatom.coords))
+            ligatom, protatom = (
+                (hbond.a, hbond.d) if hbond.protisdon else (hbond.d, hbond.a)
+            )
+            self.hbond_info.append(
+                (
+                    hbond.resnr,
+                    hbond.restype,
+                    hbond.reschain,
+                    hbond.resnr_l,
+                    hbond.restype_l,
+                    hbond.reschain_l,
+                    hbond.sidechain,
+                    "%.2f" % hbond.distance_ah,
+                    "%.2f" % hbond.distance_ad,
+                    "%.2f" % hbond.angle,
+                    hbond.protisdon,
+                    hbond.d_orig_idx,
+                    hbond.dtype,
+                    hbond.a_orig_idx,
+                    hbond.atype,
+                    ligatom.coords,
+                    protatom.coords,
+                )
+            )
 
         #################
         # WATER-BRIDGES #
         #################
 
         self.waterbridge_features = (
-            'RESNR', 'RESTYPE', 'RESCHAIN', 'RESNR_LIG', 'RESTYPE_LIG', 'RESCHAIN_LIG', 'DIST_A-W', 'DIST_D-W',
-            'DON_ANGLE',
-            'WATER_ANGLE',
-            'PROTISDON', 'DONOR_IDX', 'DONORTYPE', 'ACCEPTOR_IDX', 'ACCEPTORTYPE', 'WATER_IDX',
-            'LIGCOO', 'PROTCOO', 'WATERCOO')
+            "RESNR",
+            "RESTYPE",
+            "RESCHAIN",
+            "RESNR_LIG",
+            "RESTYPE_LIG",
+            "RESCHAIN_LIG",
+            "DIST_A-W",
+            "DIST_D-W",
+            "DON_ANGLE",
+            "WATER_ANGLE",
+            "PROTISDON",
+            "DONOR_IDX",
+            "DONORTYPE",
+            "ACCEPTOR_IDX",
+            "ACCEPTORTYPE",
+            "WATER_IDX",
+            "LIGCOO",
+            "PROTCOO",
+            "WATERCOO",
+        )
         # The coordinate format is an exception here, since the interaction is not only between ligand and protein
         self.waterbridge_info = []
         for wbridge in self.complex.water_bridges:
-            lig, prot = (wbridge.a, wbridge.d) if wbridge.protisdon else (wbridge.d, wbridge.a)
-            self.waterbridge_info.append((wbridge.resnr, wbridge.restype, wbridge.reschain, wbridge.resnr_l,
-                                          wbridge.restype_l, wbridge.reschain_l,
-                                          '%.2f' % wbridge.distance_aw, '%.2f' % wbridge.distance_dw,
-                                          '%.2f' % wbridge.d_angle, '%.2f' % wbridge.w_angle, wbridge.protisdon,
-                                          wbridge.d_orig_idx, wbridge.dtype, wbridge.a_orig_idx, wbridge.atype,
-                                          wbridge.water_orig_idx, lig.coords, prot.coords, wbridge.water.coords))
+            lig, prot = (
+                (wbridge.a, wbridge.d) if wbridge.protisdon else (wbridge.d, wbridge.a)
+            )
+            self.waterbridge_info.append(
+                (
+                    wbridge.resnr,
+                    wbridge.restype,
+                    wbridge.reschain,
+                    wbridge.resnr_l,
+                    wbridge.restype_l,
+                    wbridge.reschain_l,
+                    "%.2f" % wbridge.distance_aw,
+                    "%.2f" % wbridge.distance_dw,
+                    "%.2f" % wbridge.d_angle,
+                    "%.2f" % wbridge.w_angle,
+                    wbridge.protisdon,
+                    wbridge.d_orig_idx,
+                    wbridge.dtype,
+                    wbridge.a_orig_idx,
+                    wbridge.atype,
+                    wbridge.water_orig_idx,
+                    lig.coords,
+                    prot.coords,
+                    wbridge.water.coords,
+                )
+            )
 
         ################
         # SALT BRIDGES #
         ################
 
         self.saltbridge_features = (
-            'RESNR', 'RESTYPE', 'RESCHAIN', 'RESNR_LIG', 'RESTYPE_LIG', 'RESCHAIN_LIG', 'DIST', 'PROTISPOS',
-            'LIG_GROUP',
-            'LIG_IDX_LIST',
-            'LIGCOO', 'PROTCOO')
+            "RESNR",
+            "RESTYPE",
+            "RESCHAIN",
+            "RESNR_LIG",
+            "RESTYPE_LIG",
+            "RESCHAIN_LIG",
+            "DIST",
+            "PROTISPOS",
+            "LIG_GROUP",
+            "LIG_IDX_LIST",
+            "LIGCOO",
+            "PROTCOO",
+        )
         self.saltbridge_info = []
         for sb in self.complex.saltbridge_lneg + self.complex.saltbridge_pneg:
             if sb.protispos:
-                group, ids = sb.negative.fgroup, [str(x) for x in sb.negative.atoms_orig_idx]
-                self.saltbridge_info.append((sb.resnr, sb.restype, sb.reschain, sb.resnr_l, sb.restype_l, sb.reschain_l,
-                                             '%.2f' % sb.distance, sb.protispos,
-                                             group.capitalize(), ",".join(ids),
-                                             tuple(sb.negative.center), tuple(sb.positive.center)))
+                group, ids = (
+                    sb.negative.fgroup,
+                    [str(x) for x in sb.negative.atoms_orig_idx],
+                )
+                self.saltbridge_info.append(
+                    (
+                        sb.resnr,
+                        sb.restype,
+                        sb.reschain,
+                        sb.resnr_l,
+                        sb.restype_l,
+                        sb.reschain_l,
+                        "%.2f" % sb.distance,
+                        sb.protispos,
+                        group.capitalize(),
+                        ",".join(ids),
+                        tuple(sb.negative.center),
+                        tuple(sb.positive.center),
+                    )
+                )
             else:
-                group, ids = sb.positive.fgroup, [str(x) for x in sb.positive.atoms_orig_idx]
-                self.saltbridge_info.append((sb.resnr, sb.restype, sb.reschain, sb.resnr_l, sb.restype_l, sb.reschain_l,
-                                             '%.2f' % sb.distance, sb.protispos,
-                                             group.capitalize(), ",".join(ids),
-                                             tuple(sb.positive.center), tuple(sb.negative.center)))
+                group, ids = (
+                    sb.positive.fgroup,
+                    [str(x) for x in sb.positive.atoms_orig_idx],
+                )
+                self.saltbridge_info.append(
+                    (
+                        sb.resnr,
+                        sb.restype,
+                        sb.reschain,
+                        sb.resnr_l,
+                        sb.restype_l,
+                        sb.reschain_l,
+                        "%.2f" % sb.distance,
+                        sb.protispos,
+                        group.capitalize(),
+                        ",".join(ids),
+                        tuple(sb.positive.center),
+                        tuple(sb.negative.center),
+                    )
+                )
 
         ###############
         # PI-STACKING #
         ###############
 
         self.pistacking_features = (
-            'RESNR', 'RESTYPE', 'RESCHAIN', 'RESNR_LIG', 'RESTYPE_LIG', 'RESCHAIN_LIG', 'CENTDIST', 'ANGLE', 'OFFSET',
-            'TYPE',
-            'LIG_IDX_LIST', 'LIGCOO', 'PROTCOO')
+            "RESNR",
+            "RESTYPE",
+            "RESCHAIN",
+            "RESNR_LIG",
+            "RESTYPE_LIG",
+            "RESCHAIN_LIG",
+            "CENTDIST",
+            "ANGLE",
+            "OFFSET",
+            "TYPE",
+            "LIG_IDX_LIST",
+            "LIGCOO",
+            "PROTCOO",
+        )
         self.pistacking_info = []
         for stack in self.complex.pistacking:
             ids = [str(x) for x in stack.ligandring.atoms_orig_idx]
-            self.pistacking_info.append((stack.resnr, stack.restype, stack.reschain, stack.resnr_l, stack.restype_l,
-                                         stack.reschain_l, '%.2f' % stack.distance,
-                                         '%.2f' % stack.angle, '%.2f' % stack.offset, stack.type, ",".join(ids),
-                                         tuple(stack.ligandring.center), tuple(stack.proteinring.center)))
+            self.pistacking_info.append(
+                (
+                    stack.resnr,
+                    stack.restype,
+                    stack.reschain,
+                    stack.resnr_l,
+                    stack.restype_l,
+                    stack.reschain_l,
+                    "%.2f" % stack.distance,
+                    "%.2f" % stack.angle,
+                    "%.2f" % stack.offset,
+                    stack.type,
+                    ",".join(ids),
+                    tuple(stack.ligandring.center),
+                    tuple(stack.proteinring.center),
+                )
+            )
 
         ##########################
         # PI-CATION INTERACTIONS #
         ##########################
 
         self.pication_features = (
-            'RESNR', 'RESTYPE', 'RESCHAIN', 'RESNR_LIG', 'RESTYPE_LIG', 'RESCHAIN_LIG', 'DIST', 'OFFSET', 'PROTCHARGED',
-            'LIG_GROUP',
-            'LIG_IDX_LIST', 'LIGCOO', 'PROTCOO')
+            "RESNR",
+            "RESTYPE",
+            "RESCHAIN",
+            "RESNR_LIG",
+            "RESTYPE_LIG",
+            "RESCHAIN_LIG",
+            "DIST",
+            "OFFSET",
+            "PROTCHARGED",
+            "LIG_GROUP",
+            "LIG_IDX_LIST",
+            "LIGCOO",
+            "PROTCOO",
+        )
         self.pication_info = []
         for picat in self.complex.pication_laro + self.complex.pication_paro:
             if picat.protcharged:
                 ids = [str(x) for x in picat.ring.atoms_orig_idx]
-                group = 'Aromatic'
-                self.pication_info.append((picat.resnr, picat.restype, picat.reschain, picat.resnr_l, picat.restype_l,
-                                           picat.reschain_l, '%.2f' % picat.distance,
-                                           '%.2f' % picat.offset, picat.protcharged, group, ",".join(ids),
-                                           tuple(picat.ring.center), tuple(picat.charge.center)))
+                group = "Aromatic"
+                self.pication_info.append(
+                    (
+                        picat.resnr,
+                        picat.restype,
+                        picat.reschain,
+                        picat.resnr_l,
+                        picat.restype_l,
+                        picat.reschain_l,
+                        "%.2f" % picat.distance,
+                        "%.2f" % picat.offset,
+                        picat.protcharged,
+                        group,
+                        ",".join(ids),
+                        tuple(picat.ring.center),
+                        tuple(picat.charge.center),
+                    )
+                )
             else:
                 ids = [str(x) for x in picat.charge.atoms_orig_idx]
                 group = picat.charge.fgroup
-                self.pication_info.append((picat.resnr, picat.restype, picat.reschain, picat.resnr_l, picat.restype_l,
-                                           picat.reschain_l, '%.2f' % picat.distance,
-                                           '%.2f' % picat.offset, picat.protcharged, group, ",".join(ids),
-                                           tuple(picat.charge.center), tuple(picat.ring.center)))
+                self.pication_info.append(
+                    (
+                        picat.resnr,
+                        picat.restype,
+                        picat.reschain,
+                        picat.resnr_l,
+                        picat.restype_l,
+                        picat.reschain_l,
+                        "%.2f" % picat.distance,
+                        "%.2f" % picat.offset,
+                        picat.protcharged,
+                        group,
+                        ",".join(ids),
+                        tuple(picat.charge.center),
+                        tuple(picat.ring.center),
+                    )
+                )
 
         #################
         # HALOGEN BONDS #
         #################
 
         self.halogen_features = (
-            'RESNR', 'RESTYPE', 'RESCHAIN', 'RESNR_LIG', 'RESTYPE_LIG', 'RESCHAIN_LIG', 'SIDECHAIN', 'DIST',
-            'DON_ANGLE',
-            'ACC_ANGLE',
-            'DON_IDX', 'DONORTYPE', 'ACC_IDX', 'ACCEPTORTYPE', 'LIGCOO', 'PROTCOO')
+            "RESNR",
+            "RESTYPE",
+            "RESCHAIN",
+            "RESNR_LIG",
+            "RESTYPE_LIG",
+            "RESCHAIN_LIG",
+            "SIDECHAIN",
+            "DIST",
+            "DON_ANGLE",
+            "ACC_ANGLE",
+            "DON_IDX",
+            "DONORTYPE",
+            "ACC_IDX",
+            "ACCEPTORTYPE",
+            "LIGCOO",
+            "PROTCOO",
+        )
         self.halogen_info = []
         for halogen in self.complex.halogen_bonds:
-            self.halogen_info.append((halogen.resnr, halogen.restype, halogen.reschain, halogen.resnr_l,
-                                      halogen.restype_l, halogen.reschain_l, halogen.sidechain,
-                                      '%.2f' % halogen.distance, '%.2f' % halogen.don_angle, '%.2f' % halogen.acc_angle,
-                                      halogen.don_orig_idx, halogen.donortype,
-                                      halogen.acc_orig_idx, halogen.acctype,
-                                      halogen.acc.o.coords, halogen.don.x.coords))
+            self.halogen_info.append(
+                (
+                    halogen.resnr,
+                    halogen.restype,
+                    halogen.reschain,
+                    halogen.resnr_l,
+                    halogen.restype_l,
+                    halogen.reschain_l,
+                    halogen.sidechain,
+                    "%.2f" % halogen.distance,
+                    "%.2f" % halogen.don_angle,
+                    "%.2f" % halogen.acc_angle,
+                    halogen.don_orig_idx,
+                    halogen.donortype,
+                    halogen.acc_orig_idx,
+                    halogen.acctype,
+                    halogen.acc.o.coords,
+                    halogen.don.x.coords,
+                )
+            )
 
         ###################
         # METAL COMPLEXES #
         ###################
 
         self.metal_features = (
-            'RESNR', 'RESTYPE', 'RESCHAIN', 'RESNR_LIG', 'RESTYPE_LIG', 'RESCHAIN_LIG', 'METAL_IDX', 'METAL_TYPE',
-            'TARGET_IDX', 'TARGET_TYPE',
-            'COORDINATION', 'DIST', 'LOCATION', 'RMS', 'GEOMETRY', 'COMPLEXNUM', 'METALCOO',
-            'TARGETCOO')
+            "RESNR",
+            "RESTYPE",
+            "RESCHAIN",
+            "RESNR_LIG",
+            "RESTYPE_LIG",
+            "RESCHAIN_LIG",
+            "METAL_IDX",
+            "METAL_TYPE",
+            "TARGET_IDX",
+            "TARGET_TYPE",
+            "COORDINATION",
+            "DIST",
+            "LOCATION",
+            "RMS",
+            "GEOMETRY",
+            "COMPLEXNUM",
+            "METALCOO",
+            "TARGETCOO",
+        )
         self.metal_info = []
         # Coordinate format here is non-standard since the interaction partner can be either ligand or protein
         for m in self.complex.metal_complexes:
             self.metal_info.append(
-                (m.resnr, m.restype, m.reschain, m.resnr_l, m.restype_l, m.reschain_l, m.metal_orig_idx, m.metal_type,
-                 m.target_orig_idx, m.target_type, m.coordination_num, '%.2f' % m.distance,
-                 m.location, '%.2f' % m.rms, m.geometry, str(m.complexnum), m.metal.coords,
-                 m.target.atom.coords))
+                (
+                    m.resnr,
+                    m.restype,
+                    m.reschain,
+                    m.resnr_l,
+                    m.restype_l,
+                    m.reschain_l,
+                    m.metal_orig_idx,
+                    m.metal_type,
+                    m.target_orig_idx,
+                    m.target_type,
+                    m.coordination_num,
+                    "%.2f" % m.distance,
+                    m.location,
+                    "%.2f" % m.rms,
+                    m.geometry,
+                    str(m.complexnum),
+                    m.metal.coords,
+                    m.target.atom.coords,
+                )
+            )
 
     def write_section(self, name, features, info, f):
         """Provides formatting for one section (e.g. hydrogen bonds)"""
         if not len(info) == 0:
-            f.write('\n\n### %s ###\n' % name)
-            f.write('%s\n' % '\t'.join(features))
+            f.write("\n\n### %s ###\n" % name)
+            f.write("%s\n" % "\t".join(features))
             for line in info:
-                f.write('%s\n' % '\t'.join(map(str, line)))
+                f.write("%s\n" % "\t".join(map(str, line)))
 
     def rst_table(self, array):
         """Given an array, the function formats and returns and table in rST format."""
@@ -309,62 +577,77 @@ class BindingSiteReport:
                     cell_dict[j] = []
                 cell_dict[j].append(val)
         for item in cell_dict:
-            cell_dict[item] = max([len(x) for x in cell_dict[item]]) + 1  # Contains adapted width for each column
+            cell_dict[item] = (
+                max([len(x) for x in cell_dict[item]]) + 1
+            )  # Contains adapted width for each column
 
         # Format top line
         num_cols = len(array[0])
-        form = '+'
+        form = "+"
         for col in range(num_cols):
-            form += (cell_dict[col] + 1) * '-'
-            form += '+'
-        form += '\n'
+            form += (cell_dict[col] + 1) * "-"
+            form += "+"
+        form += "\n"
 
         # Format values
         for i, row in enumerate(array):
-            form += '| '
+            form += "| "
             for j, val in enumerate(row):
                 cell_width = cell_dict[j]
-                form += str(val) + (cell_width - len(val)) * ' ' + '| '
+                form += str(val) + (cell_width - len(val)) * " " + "| "
             form.rstrip()
-            form += '\n'
+            form += "\n"
 
             # Seperation lines
-            form += '+'
+            form += "+"
             if i == 0:
-                sign = '='
+                sign = "="
             else:
-                sign = '-'
+                sign = "-"
             for col in range(num_cols):
                 form += (cell_dict[col] + 1) * sign
-                form += '+'
-            form += '\n'
+                form += "+"
+            form += "\n"
         return form
 
     def generate_txt(self):
         """Generates an flat text report for a single binding site"""
 
         txt = []
-        titletext = '%s (%s) - %s' % (self.bsid, self.longname, self.ligtype)
+        titletext = "%s (%s) - %s" % (self.bsid, self.longname, self.ligtype)
         txt.append(titletext)
         for i, member in enumerate(self.lig_members[1:]):
-            txt.append('  + %s' % ":".join(str(element) for element in member))
+            txt.append("  + %s" % ":".join(str(element) for element in member))
         txt.append("-" * len(titletext))
-        txt.append("Interacting chain(s): %s\n" % ','.join([chain for chain in self.interacting_chains]))
-        for section in [['Hydrophobic Interactions', self.hydrophobic_features, self.hydrophobic_info],
-                        ['Hydrogen Bonds', self.hbond_features, self.hbond_info],
-                        ['Water Bridges', self.waterbridge_features, self.waterbridge_info],
-                        ['Salt Bridges', self.saltbridge_features, self.saltbridge_info],
-                        ['pi-Stacking', self.pistacking_features, self.pistacking_info],
-                        ['pi-Cation Interactions', self.pication_features, self.pication_info],
-                        ['Halogen Bonds', self.halogen_features, self.halogen_info],
-                        ['Metal Complexes', self.metal_features, self.metal_info]]:
+        txt.append(
+            "Interacting chain(s): %s\n"
+            % ",".join([chain for chain in self.interacting_chains])
+        )
+        for section in [
+            [
+                "Hydrophobic Interactions",
+                self.hydrophobic_features,
+                self.hydrophobic_info,
+            ],
+            ["Hydrogen Bonds", self.hbond_features, self.hbond_info],
+            ["Water Bridges", self.waterbridge_features, self.waterbridge_info],
+            ["Salt Bridges", self.saltbridge_features, self.saltbridge_info],
+            ["pi-Stacking", self.pistacking_features, self.pistacking_info],
+            ["pi-Cation Interactions", self.pication_features, self.pication_info],
+            ["Halogen Bonds", self.halogen_features, self.halogen_info],
+            ["Metal Complexes", self.metal_features, self.metal_info],
+        ]:
             iname, features, interaction_information = section
             # Sort results first by res number, then by distance and finally ligand coordinates to get a unique order
-            interaction_information = sorted(interaction_information, key=itemgetter(0, 2, -2))
+            interaction_information = sorted(
+                interaction_information, key=itemgetter(0, 2, -2)
+            )
             if not len(interaction_information) == 0:
 
-                txt.append('\n**%s**' % iname)
-                table = [features, ]
+                txt.append("\n**%s**" % iname)
+                table = [
+                    features,
+                ]
                 for single_contact in interaction_information:
                     values = []
                     for x in single_contact:
@@ -376,122 +659,185 @@ class BindingSiteReport:
                             values.append(str(x))
                     table.append(values)
                 txt.append(self.rst_table(table))
-        txt.append('\n')
+        txt.append("\n")
         return txt
 
     def generate_xml(self):
         """Generates an XML-formatted report for a single binding site"""
-        report = et.Element('bindingsite')
-        identifiers = et.SubElement(report, 'identifiers')
-        longname = et.SubElement(identifiers, 'longname')
-        ligtype = et.SubElement(identifiers, 'ligtype')
-        hetid = et.SubElement(identifiers, 'hetid')
-        chain = et.SubElement(identifiers, 'chain')
-        position = et.SubElement(identifiers, 'position')
-        composite = et.SubElement(identifiers, 'composite')
-        members = et.SubElement(identifiers, 'members')
-        smiles = et.SubElement(identifiers, 'smiles')
-        inchikey = et.SubElement(identifiers, 'inchikey')
+        report = et.Element("bindingsite")
+        identifiers = et.SubElement(report, "identifiers")
+        longname = et.SubElement(identifiers, "longname")
+        ligtype = et.SubElement(identifiers, "ligtype")
+        hetid = et.SubElement(identifiers, "hetid")
+        chain = et.SubElement(identifiers, "chain")
+        position = et.SubElement(identifiers, "position")
+        composite = et.SubElement(identifiers, "composite")
+        members = et.SubElement(identifiers, "members")
+        smiles = et.SubElement(identifiers, "smiles")
+        inchikey = et.SubElement(identifiers, "inchikey")
 
         # Ligand properties. Number of (unpaired) functional atoms and rings.
-        lig_properties = et.SubElement(report, 'lig_properties')
-        num_heavy_atoms = et.SubElement(lig_properties, 'num_heavy_atoms')
-        num_hbd = et.SubElement(lig_properties, 'num_hbd')
+        lig_properties = et.SubElement(report, "lig_properties")
+        num_heavy_atoms = et.SubElement(lig_properties, "num_heavy_atoms")
+        num_hbd = et.SubElement(lig_properties, "num_hbd")
         num_hbd.text = str(self.ligand.num_hbd)
-        num_unpaired_hbd = et.SubElement(lig_properties, 'num_unpaired_hbd')
+        num_unpaired_hbd = et.SubElement(lig_properties, "num_unpaired_hbd")
         num_unpaired_hbd.text = str(self.complex.num_unpaired_hbd)
-        num_hba = et.SubElement(lig_properties, 'num_hba')
+        num_hba = et.SubElement(lig_properties, "num_hba")
         num_hba.text = str(self.ligand.num_hba)
-        num_unpaired_hba = et.SubElement(lig_properties, 'num_unpaired_hba')
+        num_unpaired_hba = et.SubElement(lig_properties, "num_unpaired_hba")
         num_unpaired_hba.text = str(self.complex.num_unpaired_hba)
-        num_hal = et.SubElement(lig_properties, 'num_hal')
+        num_hal = et.SubElement(lig_properties, "num_hal")
         num_hal.text = str(self.ligand.num_hal)
-        num_unpaired_hal = et.SubElement(lig_properties, 'num_unpaired_hal')
+        num_unpaired_hal = et.SubElement(lig_properties, "num_unpaired_hal")
         num_unpaired_hal.text = str(self.complex.num_unpaired_hal)
-        num_aromatic_rings = et.SubElement(lig_properties, 'num_aromatic_rings')
+        num_aromatic_rings = et.SubElement(lig_properties, "num_aromatic_rings")
         num_aromatic_rings.text = str(self.ligand.num_rings)
-        num_rot_bonds = et.SubElement(lig_properties, 'num_rotatable_bonds')
+        num_rot_bonds = et.SubElement(lig_properties, "num_rotatable_bonds")
         num_rot_bonds.text = str(self.ligand.num_rot_bonds)
-        molweight = et.SubElement(lig_properties, 'molweight')
+        molweight = et.SubElement(lig_properties, "molweight")
         molweight.text = str(self.ligand.molweight)
-        logp = et.SubElement(lig_properties, 'logp')
+        logp = et.SubElement(lig_properties, "logp")
         logp.text = str(self.ligand.logp)
 
-        ichains = et.SubElement(report, 'interacting_chains')
-        bsresidues = et.SubElement(report, 'bs_residues')
+        ichains = et.SubElement(report, "interacting_chains")
+        bsresidues = et.SubElement(report, "bs_residues")
         for i, ichain in enumerate(self.interacting_chains):
-            c = et.SubElement(ichains, 'interacting_chain', id=str(i + 1))
+            c = et.SubElement(ichains, "interacting_chain", id=str(i + 1))
             c.text = ichain
         for i, bsres in enumerate(self.bs_res):
-            contact = 'True' if bsres in self.bs_res_interacting else 'False'
-            distance = '%.1f' % self.min_dist[bsres][0]
+            contact = "True" if bsres in self.bs_res_interacting else "False"
+            distance = "%.1f" % self.min_dist[bsres][0]
             aatype = self.min_dist[bsres][1]
-            c = et.SubElement(bsresidues, 'bs_residue', id=str(i + 1), contact=contact, min_dist=distance, aa=aatype)
+            c = et.SubElement(
+                bsresidues,
+                "bs_residue",
+                id=str(i + 1),
+                contact=contact,
+                min_dist=distance,
+                aa=aatype,
+            )
             c.text = bsres
-        hetid.text, chain.text, position.text = self.ligand.hetid, self.ligand.chain, str(self.ligand.position)
-        composite.text = 'True' if len(self.lig_members) > 1 else 'False'
+        hetid.text, chain.text, position.text = (
+            self.ligand.hetid,
+            self.ligand.chain,
+            str(self.ligand.position),
+        )
+        composite.text = "True" if len(self.lig_members) > 1 else "False"
         longname.text = self.longname
         ligtype.text = self.ligtype
         smiles.text = self.ligand.smiles
         inchikey.text = self.ligand.inchikey
-        num_heavy_atoms.text = str(self.ligand.heavy_atoms)  # Number of heavy atoms in ligand
+        num_heavy_atoms.text = str(
+            self.ligand.heavy_atoms
+        )  # Number of heavy atoms in ligand
         for i, member in enumerate(self.lig_members):
             bsid = ":".join(str(element) for element in member)
-            m = et.SubElement(members, 'member', id=str(i + 1))
+            m = et.SubElement(members, "member", id=str(i + 1))
             m.text = bsid
-        interactions = et.SubElement(report, 'interactions')
+        interactions = et.SubElement(report, "interactions")
 
         def format_interactions(element_name, features, interaction_information):
             """Returns a formatted element with interaction information."""
             interaction = et.Element(element_name)
             # Sort results first by res number, then by distance and finally ligand coordinates to get a unique order
-            interaction_information = sorted(interaction_information, key=itemgetter(0, 2, -2))
+            interaction_information = sorted(
+                interaction_information, key=itemgetter(0, 2, -2)
+            )
             for j, single_contact in enumerate(interaction_information):
-                if not element_name == 'metal_complexes':
-                    new_contact = et.SubElement(interaction, element_name[:-1], id=str(j + 1))
+                if not element_name == "metal_complexes":
+                    new_contact = et.SubElement(
+                        interaction, element_name[:-1], id=str(j + 1)
+                    )
                 else:  # Metal Complex[es]
-                    new_contact = et.SubElement(interaction, element_name[:-2], id=str(j + 1))
+                    new_contact = et.SubElement(
+                        interaction, element_name[:-2], id=str(j + 1)
+                    )
                 for i, feature in enumerate(single_contact):
                     # Just assign the value unless it's an atom list, use subelements in this case
-                    if features[i] == 'LIG_IDX_LIST':
+                    if features[i] == "LIG_IDX_LIST":
                         feat = et.SubElement(new_contact, features[i].lower())
-                        for k, atm_idx in enumerate(feature.split(',')):
-                            idx = et.SubElement(feat, 'idx', id=str(k + 1))
+                        for k, atm_idx in enumerate(feature.split(",")):
+                            idx = et.SubElement(feat, "idx", id=str(k + 1))
                             idx.text = str(atm_idx)
-                    elif features[i].endswith('COO'):
+                    elif features[i].endswith("COO"):
                         feat = et.SubElement(new_contact, features[i].lower())
                         xc, yc, zc = feature
-                        xcoo = et.SubElement(feat, 'x')
-                        xcoo.text = '%.3f' % xc
-                        ycoo = et.SubElement(feat, 'y')
-                        ycoo.text = '%.3f' % yc
-                        zcoo = et.SubElement(feat, 'z')
-                        zcoo.text = '%.3f' % zc
+                        xcoo = et.SubElement(feat, "x")
+                        xcoo.text = "%.3f" % xc
+                        ycoo = et.SubElement(feat, "y")
+                        ycoo.text = "%.3f" % yc
+                        zcoo = et.SubElement(feat, "z")
+                        zcoo.text = "%.3f" % zc
                     else:
                         feat = et.SubElement(new_contact, features[i].lower())
                         feat.text = str(feature)
             return interaction
 
-        interactions.append(format_interactions('hydrophobic_interactions', self.hydrophobic_features,
-                                                self.hydrophobic_info))
-        interactions.append(format_interactions('hydrogen_bonds', self.hbond_features, self.hbond_info))
-        interactions.append(format_interactions('water_bridges', self.waterbridge_features, self.waterbridge_info))
-        interactions.append(format_interactions('salt_bridges', self.saltbridge_features, self.saltbridge_info))
-        interactions.append(format_interactions('pi_stacks', self.pistacking_features, self.pistacking_info))
-        interactions.append(format_interactions('pi_cation_interactions', self.pication_features, self.pication_info))
-        interactions.append(format_interactions('halogen_bonds', self.halogen_features, self.halogen_info))
-        interactions.append(format_interactions('metal_complexes', self.metal_features, self.metal_info))
+        interactions.append(
+            format_interactions(
+                "hydrophobic_interactions",
+                self.hydrophobic_features,
+                self.hydrophobic_info,
+            )
+        )
+        interactions.append(
+            format_interactions("hydrogen_bonds", self.hbond_features, self.hbond_info)
+        )
+        interactions.append(
+            format_interactions(
+                "water_bridges", self.waterbridge_features, self.waterbridge_info
+            )
+        )
+        interactions.append(
+            format_interactions(
+                "salt_bridges", self.saltbridge_features, self.saltbridge_info
+            )
+        )
+        interactions.append(
+            format_interactions(
+                "pi_stacks", self.pistacking_features, self.pistacking_info
+            )
+        )
+        interactions.append(
+            format_interactions(
+                "pi_cation_interactions", self.pication_features, self.pication_info
+            )
+        )
+        interactions.append(
+            format_interactions(
+                "halogen_bonds", self.halogen_features, self.halogen_info
+            )
+        )
+        interactions.append(
+            format_interactions("metal_complexes", self.metal_features, self.metal_info)
+        )
 
         # Mappings
-        mappings = et.SubElement(report, 'mappings')
-        smiles_to_pdb = et.SubElement(mappings, 'smiles_to_pdb')  # SMILES numbering to PDB file numbering (atoms)
-        bsid = ':'.join([self.ligand.hetid, self.ligand.chain, str(self.ligand.position)])
+        mappings = et.SubElement(report, "mappings")
+        smiles_to_pdb = et.SubElement(
+            mappings, "smiles_to_pdb"
+        )  # SMILES numbering to PDB file numbering (atoms)
+        bsid = ":".join(
+            [self.ligand.hetid, self.ligand.chain, str(self.ligand.position)]
+        )
         if self.ligand.atomorder is not None:
-            smiles_to_pdb_map = [(key, self.ligand.Mapper.mapid(self.ligand.can_to_pdb[key],
-                                                                mtype='protein', bsid=bsid)) for key in
-                                 self.ligand.can_to_pdb]
-            smiles_to_pdb.text = ','.join([str(mapping[0]) + ':' + str(mapping[1]) for mapping in smiles_to_pdb_map])
+            smiles_to_pdb_map = [
+                (
+                    key,
+                    self.ligand.Mapper.mapid(
+                        self.ligand.can_to_pdb[key], mtype="protein", bsid=bsid
+                    ),
+                )
+                for key in self.ligand.can_to_pdb
+            ]
+            smiles_to_pdb.text = ",".join(
+                [
+                    str(mapping[0]) + ":" + str(mapping[1])
+                    for mapping in smiles_to_pdb_map
+                ]
+            )
         else:
-            smiles_to_pdb.text = ''
+            smiles_to_pdb.text = ""
 
         return report
diff --git a/plip/exchange/webservices.py b/plip/exchange/webservices.py
index 0c8cd3e..61cb6f5 100644
--- a/plip/exchange/webservices.py
+++ b/plip/exchange/webservices.py
@@ -11,44 +11,50 @@ logger = logger.get_logger()
 
 def check_pdb_status(pdbid):
     """Returns the status and up-to-date entry in the PDB for a given PDB ID"""
-    url = 'http://www.rcsb.org/pdb/rest/idStatus?structureId=%s' % pdbid
+    url = "http://www.rcsb.org/pdb/rest/idStatus?structureId=%s" % pdbid
     xmlf = urlopen(url)
     xml = et.parse(xmlf)
     xmlf.close()
     status = None
     current_pdbid = pdbid
-    for df in xml.xpath('//record'):
-        status = df.attrib['status']  # Status of an entry can be either 'UNKWOWN', 'OBSOLETE', or 'CURRENT'
-        if status == 'OBSOLETE':
-            current_pdbid = df.attrib['replacedBy']  # Contains the up-to-date PDB ID for obsolete entries
+    for df in xml.xpath("//record"):
+        status = df.attrib[
+            "status"
+        ]  # Status of an entry can be either 'UNKWOWN', 'OBSOLETE', or 'CURRENT'
+        if status == "OBSOLETE":
+            current_pdbid = df.attrib[
+                "replacedBy"
+            ]  # Contains the up-to-date PDB ID for obsolete entries
     return [status, current_pdbid.lower()]
 
 
 def fetch_pdb(pdbid):
     """Get the newest entry from the RCSB server for the given PDB ID. Exits with '1' if PDB ID is invalid."""
     pdbid = pdbid.lower()
-    logger.info(f'checking status of PDB-ID {pdbid}')
+    logger.info(f"checking status of PDB-ID {pdbid}")
     state, current_entry = check_pdb_status(pdbid)  # Get state and current PDB ID
 
-    if state == 'OBSOLETE':
-        logger.info(f'entry is obsolete, getting {current_entry} instead')
-    elif state == 'CURRENT':
-        logger.info('entry is up-to-date')
-    elif state == 'UNKNOWN':
-        logger.error('invalid PDB-ID (entry does not exist on PDB server)')
+    if state == "OBSOLETE":
+        logger.info(f"entry is obsolete, getting {current_entry} instead")
+    elif state == "CURRENT":
+        logger.info("entry is up-to-date")
+    elif state == "UNKNOWN":
+        logger.error("invalid PDB-ID (entry does not exist on PDB server)")
         sys.exit(1)
-    logger.info('downloading file from PDB')
+    logger.info("downloading file from PDB")
     # get URL for current entry
     # @todo needs update to react properly on response codes of RCSB servers
-    pdburl = f'http://www.rcsb.org/pdb/files/{current_entry}.pdb'
+    pdburl = f"http://www.rcsb.org/pdb/files/{current_entry}.pdb"
     try:
         pdbfile = urlopen(pdburl).read().decode()
         # If no PDB file is available, a text is now shown with "We're sorry, but ..."
         # Could previously be distinguished by an HTTP error
-        if 'sorry' in pdbfile:
-            logger.error('no file in PDB format available from wwPDB for the given PDB ID.')
+        if "sorry" in pdbfile:
+            logger.error(
+                "no file in PDB format available from wwPDB for the given PDB ID."
+            )
             sys.exit(1)
     except HTTPError:
-        logger.error('no file in PDB format available from wwPDB for the given PDB ID')
+        logger.error("no file in PDB format available from wwPDB for the given PDB ID")
         sys.exit(1)
     return [pdbfile, current_entry]
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)