From 702e1bb1a48ba0f7a180bc097488ed7fb4038697 Mon Sep 17 00:00:00 2001 From: "deepsource-autofix[bot]" <62050782+deepsource-autofix[bot]@users.noreply.github.com> Date: Tue, 7 Jul 2020 15:19:11 +0000 Subject: Format code with Black --- plip/structure/preparation.py | 1823 ++++++++++++++++++++++++++++++----------- 1 file changed, 1328 insertions(+), 495 deletions(-) (limited to 'plip/structure') diff --git a/plip/structure/preparation.py b/plip/structure/preparation.py index c2631d3..32083c7 100644 --- a/plip/structure/preparation.py +++ b/plip/structure/preparation.py @@ -10,12 +10,39 @@ from openbabel import pybel from plip.basic import config, logger from plip.basic.supplemental import centroid, tilde_expansion, tmpfile, classify_by_name -from plip.basic.supplemental import cluster_doubles, is_lig, normalize_vector, vector, ring_is_planar -from plip.basic.supplemental import extract_pdbid, read_pdb, create_folder_if_not_exists, canonicalize +from plip.basic.supplemental import ( + cluster_doubles, + is_lig, + normalize_vector, + vector, + ring_is_planar, +) +from plip.basic.supplemental import ( + extract_pdbid, + read_pdb, + create_folder_if_not_exists, + canonicalize, +) from plip.basic.supplemental import read, nucleotide_linkage, sort_members_by_importance -from plip.basic.supplemental import whichchain, whichrestype, whichresnumber, euclidean3d, int32_to_negative -from plip.structure.detection import halogen, pication, water_bridges, metal_complexation -from plip.structure.detection import hydrophobic_interactions, pistacking, hbonds, saltbridge +from plip.basic.supplemental import ( + whichchain, + whichrestype, + whichresnumber, + euclidean3d, + int32_to_negative, +) +from plip.structure.detection import ( + halogen, + pication, + water_bridges, + metal_complexation, +) +from plip.structure.detection import ( + hydrophobic_interactions, + pistacking, + hbonds, + saltbridge, +) logger = logger.get_logger() @@ -25,8 +52,16 @@ class PDBParser: self.as_string = as_string self.pdbpath = pdbpath self.num_fixed_lines = 0 - self.covlinkage = namedtuple("covlinkage", "id1 chain1 pos1 conf1 id2 chain2 pos2 conf2") - self.proteinmap, self.modres, self.covalent, self.altconformations, self.corrected_pdb = self.parse_pdb() + self.covlinkage = namedtuple( + "covlinkage", "id1 chain1 pos1 conf1 id2 chain2 pos2 conf2" + ) + ( + self.proteinmap, + self.modres, + self.covalent, + self.altconformations, + self.corrected_pdb, + ) = self.parse_pdb() def parse_pdb(self): """Extracts additional information from PDB files. @@ -38,7 +73,9 @@ class PDBParser: IV. Alternative conformations """ if self.as_string: - fil = self.pdbpath.rstrip('\n').split('\n') # Removing trailing newline character + fil = self.pdbpath.rstrip("\n").split( + "\n" + ) # Removing trailing newline character else: f = read(self.pdbpath) fil = f.readlines() @@ -57,19 +94,23 @@ class PDBParser: lastnum = 0 # Atom numbering (has to be consecutive) other_models = False for line in fil: - if not other_models: # Only consider the first model in an NRM structure + if ( + not other_models + ): # Only consider the first model in an NRM structure corrected_line, newnum = self.fix_pdbline(line, lastnum) if corrected_line is not None: - if corrected_line.startswith('MODEL'): + if corrected_line.startswith("MODEL"): try: # Get number of MODEL (1,2,3) model_num = int(corrected_line[10:14]) if model_num > 1: # MODEL 2,3,4 etc. other_models = True except ValueError: - logger.debug(f'ignoring invalid MODEL entry: {corrected_line}') + logger.debug( + f"ignoring invalid MODEL entry: {corrected_line}" + ) corrected_lines.append(corrected_line) lastnum = newnum - corrected_pdb = ''.join(corrected_lines) + corrected_pdb = "".join(corrected_lines) else: corrected_pdb = self.pdbpath corrected_lines = fil @@ -81,8 +122,8 @@ class PDBParser: if line.startswith(("ATOM", "HETATM")): # Retrieve alternate conformations atomid, location = int(line[6:11]), line[16] - location = 'A' if location == ' ' else location - if location != 'A': + location = "A" if location == " " else location + if location != "A": alt.append(atomid) if not previous_ter: @@ -107,12 +148,18 @@ class PDBParser: def fix_pdbline(self, pdbline, lastnum): """Fix a PDB line if information is missing.""" pdbqt_conversion = { - "HD": "H", "HS": "H", "NA": "N", - "NS": "N", "OA": "O", "OS": "O", "SA": "S"} + "HD": "H", + "HS": "H", + "NA": "N", + "NS": "N", + "OA": "O", + "OS": "O", + "SA": "S", + } fixed = False new_num = 0 forbidden_characters = "[^a-zA-Z0-9_]" - pdbline = pdbline.strip('\n') + pdbline = pdbline.strip("\n") # Some MD / Docking tools produce empty lines, leading to segfaults if len(pdbline.strip()) == 0: self.num_fixed_lines += 1 @@ -121,9 +168,9 @@ class PDBParser: self.num_fixed_lines += 1 return None, lastnum # TER Entries also have continuing numbering, consider them as well - if pdbline.startswith('TER'): + if pdbline.startswith("TER"): new_num = lastnum + 1 - if pdbline.startswith('ATOM'): + if pdbline.startswith("ATOM"): new_num = lastnum + 1 current_num = int(pdbline[6:11]) resnum = pdbline[22:27].strip() @@ -132,73 +179,107 @@ class PDBParser: try: int(resnum) except ValueError: - pdbline = pdbline[:22] + ' 0 ' + pdbline[27:] + pdbline = pdbline[:22] + " 0 " + pdbline[27:] fixed = True # Invalid characters in residue name if re.match(forbidden_characters, resname.strip()): - pdbline = pdbline[:17] + 'UNK ' + pdbline[21:] + pdbline = pdbline[:17] + "UNK " + pdbline[21:] fixed = True if lastnum + 1 != current_num: - pdbline = pdbline[:6] + (5 - len(str(new_num))) * ' ' + str(new_num) + ' ' + pdbline[12:] + pdbline = ( + pdbline[:6] + + (5 - len(str(new_num))) * " " + + str(new_num) + + " " + + pdbline[12:] + ) fixed = True # No chain assigned - if pdbline[21] == ' ': - pdbline = pdbline[:21] + 'A' + pdbline[22:] + if pdbline[21] == " ": + pdbline = pdbline[:21] + "A" + pdbline[22:] fixed = True - if pdbline.endswith('H'): + if pdbline.endswith("H"): self.num_fixed_lines += 1 return None, lastnum # Sometimes, converted PDB structures contain PDBQT atom types. Fix that. for pdbqttype in pdbqt_conversion: if pdbline.strip().endswith(pdbqttype): - pdbline = pdbline.strip()[:-2] + ' ' + pdbqt_conversion[pdbqttype] + '\n' + pdbline = ( + pdbline.strip()[:-2] + " " + pdbqt_conversion[pdbqttype] + "\n" + ) self.num_fixed_lines += 1 - if pdbline.startswith('HETATM'): + if pdbline.startswith("HETATM"): new_num = lastnum + 1 try: current_num = int(pdbline[6:11]) except ValueError: current_num = None - logger.debug(f'invalid HETATM entry: {pdbline}') + logger.debug(f"invalid HETATM entry: {pdbline}") if lastnum + 1 != current_num: - pdbline = pdbline[:6] + (5 - len(str(new_num))) * ' ' + str(new_num) + ' ' + pdbline[12:] + pdbline = ( + pdbline[:6] + + (5 - len(str(new_num))) * " " + + str(new_num) + + " " + + pdbline[12:] + ) fixed = True # No chain assigned or number assigned as chain - if pdbline[21] == ' ': - pdbline = pdbline[:21] + 'Z' + pdbline[22:] + if pdbline[21] == " ": + pdbline = pdbline[:21] + "Z" + pdbline[22:] fixed = True # No residue number assigned - if pdbline[23:26] == ' ': - pdbline = pdbline[:23] + '999' + pdbline[26:] + if pdbline[23:26] == " ": + pdbline = pdbline[:23] + "999" + pdbline[26:] fixed = True # Non-standard Ligand Names ligname = pdbline[17:21].strip() if len(ligname) > 3: - pdbline = pdbline[:17] + ligname[:3] + ' ' + pdbline[21:] + pdbline = pdbline[:17] + ligname[:3] + " " + pdbline[21:] fixed = True if re.match(forbidden_characters, ligname.strip()): - pdbline = pdbline[:17] + 'LIG ' + pdbline[21:] + pdbline = pdbline[:17] + "LIG " + pdbline[21:] fixed = True if len(ligname.strip()) == 0: - pdbline = pdbline[:17] + 'LIG ' + pdbline[21:] + pdbline = pdbline[:17] + "LIG " + pdbline[21:] fixed = True - if pdbline.endswith('H'): + if pdbline.endswith("H"): self.num_fixed_lines += 1 return None, lastnum # Sometimes, converted PDB structures contain PDBQT atom types. Fix that. for pdbqttype in pdbqt_conversion: if pdbline.strip().endswith(pdbqttype): - pdbline = pdbline.strip()[:-2] + ' ' + pdbqt_conversion[pdbqttype] + ' ' + pdbline = ( + pdbline.strip()[:-2] + " " + pdbqt_conversion[pdbqttype] + " " + ) self.num_fixed_lines += 1 self.num_fixed_lines += 1 if fixed else 0 - return pdbline + '\n', max(new_num, lastnum) + return pdbline + "\n", max(new_num, lastnum) def get_linkage(self, line): """Get the linkage information from a LINK entry PDB line.""" - conf1, id1, chain1, pos1 = line[16].strip(), line[17:20].strip(), line[21].strip(), int(line[22:26]) - conf2, id2, chain2, pos2 = line[46].strip(), line[47:50].strip(), line[51].strip(), int(line[52:56]) - return self.covlinkage(id1=id1, chain1=chain1, pos1=pos1, conf1=conf1, - id2=id2, chain2=chain2, pos2=pos2, conf2=conf2) + conf1, id1, chain1, pos1 = ( + line[16].strip(), + line[17:20].strip(), + line[21].strip(), + int(line[22:26]), + ) + conf2, id2, chain2, pos2 = ( + line[46].strip(), + line[47:50].strip(), + line[51].strip(), + int(line[52:56]), + ) + return self.covlinkage( + id1=id1, + chain1=chain1, + pos1=pos1, + conf1=conf1, + id2=id2, + chain2=chain2, + pos2=pos2, + conf2=conf2, + ) class LigandFinder: @@ -212,15 +293,20 @@ class LigandFinder: self.covalent = covalent self.mapper = mapper self.ligands = self.getligs() - self.excluded = sorted(list(self.lignames_all.difference(set(self.lignames_kept)))) + self.excluded = sorted( + list(self.lignames_all.difference(set(self.lignames_kept))) + ) def getpeptides(self, chain): """If peptide ligand chains are defined via the command line options, try to extract the underlying ligand formed by all residues in the given chain without water """ - all_from_chain = [o for o in pybel.ob.OBResidueIter( - self.proteincomplex.OBMol) if o.GetChain() == chain] # All residues from chain + all_from_chain = [ + o + for o in pybel.ob.OBResidueIter(self.proteincomplex.OBMol) + if o.GetChain() == chain + ] # All residues from chain if len(all_from_chain) == 0: return None else: @@ -240,7 +326,9 @@ class LigandFinder: # Filter for ligands using lists ligand_residues, self.lignames_all, self.water = self.filter_for_ligands() - all_res_dict = {(a.GetName(), a.GetChain(), a.GetNum()): a for a in ligand_residues} + all_res_dict = { + (a.GetName(), a.GetChain(), a.GetNum()): a for a in ligand_residues + } self.lignames_kept = list(set([a.GetName() for a in ligand_residues])) if not config.BREAKCOMPOSITE: @@ -249,22 +337,35 @@ class LigandFinder: # Find fragment linked by covalent bonds res_kmers = self.identify_kmers(all_res_dict) else: - res_kmers = [[a, ] for a in ligand_residues] - logger.debug(f'{len(res_kmers)} ligand kmer(s) detected for closer inspection') - for kmer in res_kmers: # iterate over all ligands and extract molecules + information + res_kmers = [[a,] for a in ligand_residues] + logger.debug( + f"{len(res_kmers)} ligand kmer(s) detected for closer inspection" + ) + for ( + kmer + ) in ( + res_kmers + ): # iterate over all ligands and extract molecules + information if len(kmer) > config.MAX_COMPOSITE_LENGTH: logger.debug( - f'ligand kmer(s) filtered out with a length of {len(kmer)} fragments ({config.MAX_COMPOSITE_LENGTH} allowed)') + f"ligand kmer(s) filtered out with a length of {len(kmer)} fragments ({config.MAX_COMPOSITE_LENGTH} allowed)" + ) else: ligands.append(self.extract_ligand(kmer)) else: # Extract peptides from given chains - self.water = [o for o in pybel.ob.OBResidueIter(self.proteincomplex.OBMol) if o.GetResidueProperty(9)] + self.water = [ + o + for o in pybel.ob.OBResidueIter(self.proteincomplex.OBMol) + if o.GetResidueProperty(9) + ] if config.PEPTIDES: peptide_ligands = [self.getpeptides(chain) for chain in config.PEPTIDES] elif config.INTRA is not None: - peptide_ligands = [self.getpeptides(config.INTRA), ] + peptide_ligands = [ + self.getpeptides(config.INTRA), + ] ligands = [p for p in peptide_ligands if p is not None] self.covalent, self.lignames_kept, self.lignames_all = [], [], set() @@ -273,35 +374,50 @@ class LigandFinder: def extract_ligand(self, kmer): """Extract the ligand by copying atoms and bonds and assign all information necessary for later steps.""" - data = namedtuple('ligand', 'mol hetid chain position water members longname type atomorder can_to_pdb') - members = [(res.GetName(), res.GetChain(), int32_to_negative(res.GetNum())) for res in kmer] + data = namedtuple( + "ligand", + "mol hetid chain position water members longname type atomorder can_to_pdb", + ) + members = [ + (res.GetName(), res.GetChain(), int32_to_negative(res.GetNum())) + for res in kmer + ] members = sort_members_by_importance(members) rname, rchain, rnum = members[0] - logger.debug(f'finalizing extraction for ligand {rname}:{rchain}:{rnum} with {len(kmer)} elements') + logger.debug( + f"finalizing extraction for ligand {rname}:{rchain}:{rnum} with {len(kmer)} elements" + ) names = [x[0] for x in members] - longname = '-'.join([x[0] for x in members]) + longname = "-".join([x[0] for x in members]) if config.PEPTIDES: - ligtype = 'PEPTIDE' + ligtype = "PEPTIDE" elif config.INTRA is not None: - ligtype = 'INTRA' + ligtype = "INTRA" else: # Classify a ligand by its HETID(s) ligtype = classify_by_name(names) - logger.debug(f'ligand classified as {ligtype}') + logger.debug(f"ligand classified as {ligtype}") hetatoms = dict() for obresidue in kmer: - cur_hetatoms = {obatom.GetIdx(): obatom for obatom in pybel.ob.OBResidueAtomIter(obresidue) if - obatom.GetAtomicNum() != 1} + cur_hetatoms = { + obatom.GetIdx(): obatom + for obatom in pybel.ob.OBResidueAtomIter(obresidue) + if obatom.GetAtomicNum() != 1 + } if not config.ALTLOC: # Remove alternative conformations (standard -> True) - ids_to_remove = [atom_id for atom_id in hetatoms.keys() if - self.mapper.mapid(atom_id, mtype='protein', to='internal') in self.altconformations] + ids_to_remove = [ + atom_id + for atom_id in hetatoms.keys() + if self.mapper.mapid(atom_id, mtype="protein", to="internal") + in self.altconformations + ] for atom_id in ids_to_remove: del cur_hetatoms[atom_id] hetatoms.update(cur_hetatoms) - logger.debug(f'hetero atoms determined (n={len(hetatoms)})') + logger.debug(f"hetero atoms determined (n={len(hetatoms)})") lig = pybel.ob.OBMol() # new ligand mol neighbours = dict() @@ -309,15 +425,24 @@ class LigandFinder: idx = obatom.GetIdx() lig.AddAtom(obatom) # ids of all neighbours of obatom - neighbours[idx] = set([neighbour_atom.GetIdx() for neighbour_atom - in pybel.ob.OBAtomAtomIter(obatom)]) & set(hetatoms.keys()) - logger.debug(f'atom neighbours mapped') + neighbours[idx] = set( + [ + neighbour_atom.GetIdx() + for neighbour_atom in pybel.ob.OBAtomAtomIter(obatom) + ] + ) & set(hetatoms.keys()) + logger.debug(f"atom neighbours mapped") ############################################################## # map the old atom idx of OBMol to the new idx of the ligand # ############################################################## - newidx = dict(zip(hetatoms.keys(), [obatom.GetIdx() for obatom in pybel.ob.OBMolAtomIter(lig)])) + newidx = dict( + zip( + hetatoms.keys(), + [obatom.GetIdx() for obatom in pybel.ob.OBMolAtomIter(lig)], + ) + ) mapold = dict(zip(newidx.values(), newidx)) # copy the bonds for obatom in hetatoms: @@ -327,16 +452,16 @@ class LigandFinder: lig = pybel.Molecule(lig) # For kmers, the representative ids are chosen (first residue of kmer) - lig.data.update({'Name': rname, 'Chain': rchain, 'ResNr': rnum}) + lig.data.update({"Name": rname, "Chain": rchain, "ResNr": rnum}) # Check if a negative residue number is represented as a 32 bit integer if rnum > 10 ** 5: rnum = int32_to_negative(rnum) - lig.title = ':'.join((rname, rchain, str(rnum))) + lig.title = ":".join((rname, rchain, str(rnum))) self.mapper.ligandmaps[lig.title] = mapold - logger.debug('renumerated molecule generated') + logger.debug("renumerated molecule generated") if not config.NOPDBCANMAP: atomorder = canonicalize(lig) @@ -347,9 +472,18 @@ class LigandFinder: if atomorder is not None: can_to_pdb = {atomorder[key - 1]: mapold[key] for key in mapold} - ligand = data(mol=lig, hetid=rname, chain=rchain, position=rnum, water=self.water, - members=members, longname=longname, type=ligtype, atomorder=atomorder, - can_to_pdb=can_to_pdb) + ligand = data( + mol=lig, + hetid=rname, + chain=rchain, + position=rnum, + water=self.water, + members=members, + longname=longname, + type=ligtype, + atomorder=atomorder, + can_to_pdb=can_to_pdb, + ) return ligand def is_het_residue(self, obres): @@ -374,20 +508,35 @@ class LigandFinder: def filter_for_ligands(self): """Given an OpenBabel Molecule, get all ligands, their names, and water""" - candidates1 = [o for o in pybel.ob.OBResidueIter( - self.proteincomplex.OBMol) if not o.GetResidueProperty(9) and self.is_het_residue(o)] + candidates1 = [ + o + for o in pybel.ob.OBResidueIter(self.proteincomplex.OBMol) + if not o.GetResidueProperty(9) and self.is_het_residue(o) + ] if config.DNARECEPTOR: # If DNA is the receptor, don't consider DNA as a ligand - candidates1 = [res for res in candidates1 if res.GetName() not in config.DNA + config.RNA] + candidates1 = [ + res + for res in candidates1 + if res.GetName() not in config.DNA + config.RNA + ] all_lignames = set([a.GetName() for a in candidates1]) - water = [o for o in pybel.ob.OBResidueIter(self.proteincomplex.OBMol) if o.GetResidueProperty(9)] + water = [ + o + for o in pybel.ob.OBResidueIter(self.proteincomplex.OBMol) + if o.GetResidueProperty(9) + ] # Filter out non-ligands if not config.KEEPMOD: # Keep modified residues as ligands - candidates2 = [a for a in candidates1 if is_lig(a.GetName()) and a.GetName() not in self.modresidues] + candidates2 = [ + a + for a in candidates1 + if is_lig(a.GetName()) and a.GetName() not in self.modresidues + ] else: candidates2 = [a for a in candidates1 if is_lig(a.GetName())] - logger.debug(f'{len(candidates2)} ligand(s) after first filtering step') + logger.debug(f"{len(candidates2)} ligand(s) after first filtering step") ############################################ # Filtering by counting and artifacts list # @@ -396,7 +545,10 @@ class LigandFinder: unique_ligs = set(a.GetName() for a in candidates2) for ulig in unique_ligs: # Discard if appearing 15 times or more and is possible artifact - if ulig in config.biolip_list and [a.GetName() for a in candidates2].count(ulig) >= 15: + if ( + ulig in config.biolip_list + and [a.GetName() for a in candidates2].count(ulig) >= 15 + ): artifacts.append(ulig) selected_ligands = [a for a in candidates2 if a.GetName() not in artifacts] @@ -407,12 +559,19 @@ class LigandFinder: """Using the covalent linkage information, find out which fragments/subunits form a ligand.""" # Remove all those not considered by ligands and pairings including alternate conformations - ligdoubles = [[(link.id1, link.chain1, link.pos1), - (link.id2, link.chain2, link.pos2)] for link in - [c for c in self.covalent if c.id1 in self.lignames_kept and c.id2 in self.lignames_kept - and c.conf1 in ['A', ''] and c.conf2 in ['A', ''] - and (c.id1, c.chain1, c.pos1) in residues - and (c.id2, c.chain2, c.pos2) in residues]] + ligdoubles = [ + [(link.id1, link.chain1, link.pos1), (link.id2, link.chain2, link.pos2)] + for link in [ + c + for c in self.covalent + if c.id1 in self.lignames_kept + and c.id2 in self.lignames_kept + and c.conf1 in ["A", ""] + and c.conf2 in ["A", ""] + and (c.id1, c.chain1, c.pos1) in residues + and (c.id2, c.chain2, c.pos2) in residues + ] + ] kmers = cluster_doubles(ligdoubles) if not kmers: # No ligand kmers, just normal independent ligands return [[residues[res]] for res in residues] @@ -428,7 +587,9 @@ class LigandFinder: in_kmer.append((res.GetName(), res.GetChain(), res.GetNum())) for res in residues: if res not in in_kmer: - newres = [residues[res], ] + newres = [ + residues[res], + ] res_kmers.append(newres) return res_kmers @@ -437,26 +598,32 @@ class Mapper: """Provides functions for mapping atom IDs in the correct way""" def __init__(self): - self.proteinmap = None # Map internal atom IDs of protein residues to original PDB Atom IDs - self.ligandmaps = {} # Map IDs of new ligand molecules to internal IDs (or PDB IDs?) + self.proteinmap = ( + None # Map internal atom IDs of protein residues to original PDB Atom IDs + ) + self.ligandmaps = ( + {} + ) # Map IDs of new ligand molecules to internal IDs (or PDB IDs?) self.original_structure = None - def mapid(self, idx, mtype, bsid=None, to='original'): # Mapping to original IDs is standard for ligands - if mtype == 'reversed': # Needed to map internal ID back to original protein ID + def mapid( + self, idx, mtype, bsid=None, to="original" + ): # Mapping to original IDs is standard for ligands + if mtype == "reversed": # Needed to map internal ID back to original protein ID return self.reversed_proteinmap[idx] - if mtype == 'protein': + if mtype == "protein": return self.proteinmap[idx] - elif mtype == 'ligand': - if to == 'internal': + elif mtype == "ligand": + if to == "internal": return self.ligandmaps[bsid][idx] - elif to == 'original': + elif to == "original": return self.proteinmap[self.ligandmaps[bsid][idx]] def id_to_atom(self, idx): """Returns the atom for a given original ligand ID. To do this, the ID is mapped to the protein first and then the atom returned. """ - mapped_idx = self.mapid(idx, 'reversed') + mapped_idx = self.mapid(idx, "reversed") return pybel.Atom(self.original_structure.GetAtom(mapped_idx)) @@ -475,10 +642,15 @@ class Mol: def hydrophobic_atoms(self, all_atoms): """Select all carbon atoms which have only carbons and/or hydrogens as direct neighbors.""" atom_set = [] - data = namedtuple('hydrophobic', 'atom orig_atom orig_idx') - atm = [a for a in all_atoms if a.atomicnum == 6 and set([natom.GetAtomicNum() for natom - in pybel.ob.OBAtomAtomIter(a.OBAtom)]).issubset( - {1, 6})] + data = namedtuple("hydrophobic", "atom orig_atom orig_idx") + atm = [ + a + for a in all_atoms + if a.atomicnum == 6 + and set( + [natom.GetAtomicNum() for natom in pybel.ob.OBAtomAtomIter(a.OBAtom)] + ).issubset({1, 6}) + ] for atom in atm: orig_idx = self.Mapper.mapid(atom.idx, mtype=self.mtype, bsid=self.bsid) orig_atom = self.Mapper.id_to_atom(orig_idx) @@ -488,45 +660,88 @@ class Mol: def find_hba(self, all_atoms): """Find all possible hydrogen bond acceptors""" - data = namedtuple('hbondacceptor', 'a a_orig_atom a_orig_idx type') + data = namedtuple("hbondacceptor", "a a_orig_atom a_orig_idx type") a_set = [] for atom in filter(lambda at: at.OBAtom.IsHbondAcceptor(), all_atoms): - if atom.atomicnum not in [9, 17, 35, 53] and atom.idx not in self.altconf: # Exclude halogen atoms - a_orig_idx = self.Mapper.mapid(atom.idx, mtype=self.mtype, bsid=self.bsid) + if ( + atom.atomicnum not in [9, 17, 35, 53] and atom.idx not in self.altconf + ): # Exclude halogen atoms + a_orig_idx = self.Mapper.mapid( + atom.idx, mtype=self.mtype, bsid=self.bsid + ) a_orig_atom = self.Mapper.id_to_atom(a_orig_idx) - a_set.append(data(a=atom, a_orig_atom=a_orig_atom, a_orig_idx=a_orig_idx, type='regular')) + a_set.append( + data( + a=atom, + a_orig_atom=a_orig_atom, + a_orig_idx=a_orig_idx, + type="regular", + ) + ) a_set = sorted(a_set, key=lambda x: x.a_orig_idx) return a_set def find_hbd(self, all_atoms, hydroph_atoms): """Find all possible strong and weak hydrogen bonds donors (all hydrophobic C-H pairings)""" donor_pairs = [] - data = namedtuple('hbonddonor', 'd d_orig_atom d_orig_idx h type') - for donor in [a for a in all_atoms if a.OBAtom.IsHbondDonor() and a.idx not in self.altconf]: + data = namedtuple("hbonddonor", "d d_orig_atom d_orig_idx h type") + for donor in [ + a + for a in all_atoms + if a.OBAtom.IsHbondDonor() and a.idx not in self.altconf + ]: in_ring = False if not in_ring: - for adj_atom in [a for a in pybel.ob.OBAtomAtomIter(donor.OBAtom) if a.IsHbondDonorH()]: - d_orig_idx = self.Mapper.mapid(donor.idx, mtype=self.mtype, bsid=self.bsid) + for adj_atom in [ + a + for a in pybel.ob.OBAtomAtomIter(donor.OBAtom) + if a.IsHbondDonorH() + ]: + d_orig_idx = self.Mapper.mapid( + donor.idx, mtype=self.mtype, bsid=self.bsid + ) d_orig_atom = self.Mapper.id_to_atom(d_orig_idx) - donor_pairs.append(data(d=donor, d_orig_atom=d_orig_atom, d_orig_idx=d_orig_idx, - h=pybel.Atom(adj_atom), type='regular')) + donor_pairs.append( + data( + d=donor, + d_orig_atom=d_orig_atom, + d_orig_idx=d_orig_idx, + h=pybel.Atom(adj_atom), + type="regular", + ) + ) for carbon in hydroph_atoms: - for adj_atom in [a for a in pybel.ob.OBAtomAtomIter(carbon.atom.OBAtom) if a.GetAtomicNum() == 1]: - d_orig_idx = self.Mapper.mapid(carbon.atom.idx, mtype=self.mtype, bsid=self.bsid) + for adj_atom in [ + a + for a in pybel.ob.OBAtomAtomIter(carbon.atom.OBAtom) + if a.GetAtomicNum() == 1 + ]: + d_orig_idx = self.Mapper.mapid( + carbon.atom.idx, mtype=self.mtype, bsid=self.bsid + ) d_orig_atom = self.Mapper.id_to_atom(d_orig_idx) - donor_pairs.append(data(d=carbon, d_orig_atom=d_orig_atom, - d_orig_idx=d_orig_idx, h=pybel.Atom(adj_atom), type='weak')) + donor_pairs.append( + data( + d=carbon, + d_orig_atom=d_orig_atom, + d_orig_idx=d_orig_idx, + h=pybel.Atom(adj_atom), + type="weak", + ) + ) donor_pairs = sorted(donor_pairs, key=lambda x: (x.d_orig_idx, x.h.idx)) return donor_pairs def find_rings(self, mol, all_atoms): """Find rings and return only aromatic. Rings have to be sufficiently planar OR be detected by OpenBabel as aromatic.""" - data = namedtuple('aromatic_ring', 'atoms orig_atoms atoms_orig_idx normal obj center type') + data = namedtuple( + "aromatic_ring", "atoms orig_atoms atoms_orig_idx normal obj center type" + ) rings = [] - aromatic_amino = ['TYR', 'TRP', 'HIS', 'PHE'] + aromatic_amino = ["TYR", "TRP", "HIS", "PHE"] ring_candidates = mol.OBMol.GetSSSR() - logger.debug(f'number of aromatic ring candidates: {len(ring_candidates)}') + logger.debug(f"number of aromatic ring candidates: {len(ring_candidates)}") # Check here first for ligand rings not being detected as aromatic by Babel and check for planarity for ring in ring_candidates: r_atoms = [a for a in all_atoms if ring.IsMember(a.OBAtom)] @@ -534,28 +749,42 @@ class Mol: if 4 < len(r_atoms) <= 6: res = list(set([whichrestype(a) for a in r_atoms])) # re-sort ring atoms for only ligands, because HETATM numbering is not canonical in OpenBabel - if res[0] == 'UNL': - ligand_orig_idx = [self.Mapper.ligandmaps[self.bsid][a.idx] for a in r_atoms] + if res[0] == "UNL": + ligand_orig_idx = [ + self.Mapper.ligandmaps[self.bsid][a.idx] for a in r_atoms + ] sort_order = np.argsort(np.array(ligand_orig_idx)) r_atoms = [r_atoms[i] for i in sort_order] - if ring.IsAromatic() or res[0] in aromatic_amino or ring_is_planar(ring, r_atoms): + if ( + ring.IsAromatic() + or res[0] in aromatic_amino + or ring_is_planar(ring, r_atoms) + ): # Causes segfault with OpenBabel 2.3.2, so deactivated # typ = ring.GetType() if not ring.GetType() == '' else 'unknown' # Alternative typing - ring_type = '%s-membered' % len(r_atoms) - ring_atms = [r_atoms[a].coords for a in [0, 2, 4]] # Probe atoms for normals, assuming planarity + ring_type = "%s-membered" % len(r_atoms) + ring_atms = [ + r_atoms[a].coords for a in [0, 2, 4] + ] # Probe atoms for normals, assuming planarity ringv1 = vector(ring_atms[0], ring_atms[1]) ringv2 = vector(ring_atms[2], ring_atms[0]) - atoms_orig_idx = [self.Mapper.mapid(r_atom.idx, mtype=self.mtype, - bsid=self.bsid) for r_atom in r_atoms] + atoms_orig_idx = [ + self.Mapper.mapid(r_atom.idx, mtype=self.mtype, bsid=self.bsid) + for r_atom in r_atoms + ] orig_atoms = [self.Mapper.id_to_atom(idx) for idx in atoms_orig_idx] - rings.append(data(atoms=r_atoms, - orig_atoms=orig_atoms, - atoms_orig_idx=atoms_orig_idx, - normal=normalize_vector(np.cross(ringv1, ringv2)), - obj=ring, - center=centroid([ra.coords for ra in r_atoms]), - type=ring_type)) + rings.append( + data( + atoms=r_atoms, + orig_atoms=orig_atoms, + atoms_orig_idx=atoms_orig_idx, + normal=normalize_vector(np.cross(ringv1, ringv2)), + obj=ring, + center=centroid([ra.coords for ra in r_atoms]), + type=ring_type, + ) + ) return rings def get_hydrophobic_atoms(self): @@ -565,16 +794,24 @@ class Mol: return self.hbond_acc_atoms def get_hbd(self): - return [don_pair for don_pair in self.hbond_don_atom_pairs if don_pair.type == 'regular'] + return [ + don_pair + for don_pair in self.hbond_don_atom_pairs + if don_pair.type == "regular" + ] def get_weak_hbd(self): - return [don_pair for don_pair in self.hbond_don_atom_pairs if don_pair.type == 'weak'] + return [ + don_pair + for don_pair in self.hbond_don_atom_pairs + if don_pair.type == "weak" + ] def get_pos_charged(self): - return [charge for charge in self.charged if charge.type == 'positive'] + return [charge for charge in self.charged if charge.type == "positive"] def get_neg_charged(self): - return [charge for charge in self.charged if charge.type == 'negative'] + return [charge for charge in self.charged if charge.type == "negative"] class PLInteraction: @@ -591,65 +828,135 @@ class PLInteraction: self.altconf = protcomplex.altconf # #@todo Refactor code to combine different directionality - self.saltbridge_lneg = saltbridge(self.bindingsite.get_pos_charged(), self.ligand.get_neg_charged(), True) - self.saltbridge_pneg = saltbridge(self.ligand.get_pos_charged(), self.bindingsite.get_neg_charged(), False) - - self.all_hbonds_ldon = hbonds(self.bindingsite.get_hba(), - self.ligand.get_hbd(), False, 'strong') - self.all_hbonds_pdon = hbonds(self.ligand.get_hba(), - self.bindingsite.get_hbd(), True, 'strong') - - self.hbonds_ldon = self.refine_hbonds_ldon(self.all_hbonds_ldon, self.saltbridge_lneg, - self.saltbridge_pneg) - self.hbonds_pdon = self.refine_hbonds_pdon(self.all_hbonds_pdon, self.saltbridge_lneg, - self.saltbridge_pneg) + self.saltbridge_lneg = saltbridge( + self.bindingsite.get_pos_charged(), self.ligand.get_neg_charged(), True + ) + self.saltbridge_pneg = saltbridge( + self.ligand.get_pos_charged(), self.bindingsite.get_neg_charged(), False + ) + + self.all_hbonds_ldon = hbonds( + self.bindingsite.get_hba(), self.ligand.get_hbd(), False, "strong" + ) + self.all_hbonds_pdon = hbonds( + self.ligand.get_hba(), self.bindingsite.get_hbd(), True, "strong" + ) + + self.hbonds_ldon = self.refine_hbonds_ldon( + self.all_hbonds_ldon, self.saltbridge_lneg, self.saltbridge_pneg + ) + self.hbonds_pdon = self.refine_hbonds_pdon( + self.all_hbonds_pdon, self.saltbridge_lneg, self.saltbridge_pneg + ) self.pistacking = pistacking(self.bindingsite.rings, self.ligand.rings) - self.all_pi_cation_laro = pication(self.ligand.rings, self.bindingsite.get_pos_charged(), True) - self.pication_paro = pication(self.bindingsite.rings, self.ligand.get_pos_charged(), False) - - self.pication_laro = self.refine_pi_cation_laro(self.all_pi_cation_laro, self.pistacking) - - self.all_hydrophobic_contacts = hydrophobic_interactions(self.bindingsite.get_hydrophobic_atoms(), - self.ligand.get_hydrophobic_atoms()) - self.hydrophobic_contacts = self.refine_hydrophobic(self.all_hydrophobic_contacts, self.pistacking) - self.halogen_bonds = halogen(self.bindingsite.halogenbond_acc, self.ligand.halogenbond_don) - self.water_bridges = water_bridges(self.bindingsite.get_hba(), self.ligand.get_hba(), - self.bindingsite.get_hbd(), self.ligand.get_hbd(), - self.ligand.water) - - self.water_bridges = self.refine_water_bridges(self.water_bridges, self.hbonds_ldon, self.hbonds_pdon) - - self.metal_complexes = metal_complexation(self.ligand.metals, self.ligand.metal_binding, - self.bindingsite.metal_binding) + self.all_pi_cation_laro = pication( + self.ligand.rings, self.bindingsite.get_pos_charged(), True + ) + self.pication_paro = pication( + self.bindingsite.rings, self.ligand.get_pos_charged(), False + ) + + self.pication_laro = self.refine_pi_cation_laro( + self.all_pi_cation_laro, self.pistacking + ) + + self.all_hydrophobic_contacts = hydrophobic_interactions( + self.bindingsite.get_hydrophobic_atoms(), + self.ligand.get_hydrophobic_atoms(), + ) + self.hydrophobic_contacts = self.refine_hydrophobic( + self.all_hydrophobic_contacts, self.pistacking + ) + self.halogen_bonds = halogen( + self.bindingsite.halogenbond_acc, self.ligand.halogenbond_don + ) + self.water_bridges = water_bridges( + self.bindingsite.get_hba(), + self.ligand.get_hba(), + self.bindingsite.get_hbd(), + self.ligand.get_hbd(), + self.ligand.water, + ) + + self.water_bridges = self.refine_water_bridges( + self.water_bridges, self.hbonds_ldon, self.hbonds_pdon + ) + + self.metal_complexes = metal_complexation( + self.ligand.metals, + self.ligand.metal_binding, + self.bindingsite.metal_binding, + ) self.all_itypes = self.saltbridge_lneg + self.saltbridge_pneg + self.hbonds_pdon - self.all_itypes = self.all_itypes + self.hbonds_ldon + self.pistacking + self.pication_laro + self.pication_paro - self.all_itypes = self.all_itypes + self.hydrophobic_contacts + self.halogen_bonds + self.water_bridges + self.all_itypes = ( + self.all_itypes + + self.hbonds_ldon + + self.pistacking + + self.pication_laro + + self.pication_paro + ) + self.all_itypes = ( + self.all_itypes + + self.hydrophobic_contacts + + self.halogen_bonds + + self.water_bridges + ) self.all_itypes = self.all_itypes + self.metal_complexes self.no_interactions = all(len(i) == 0 for i in self.all_itypes) - self.unpaired_hba, self.unpaired_hbd, self.unpaired_hal = self.find_unpaired_ligand() - self.unpaired_hba_orig_idx = [self.Mapper.mapid(atom.idx, mtype='ligand', bsid=self.ligand.bsid) - for atom in self.unpaired_hba] - self.unpaired_hbd_orig_idx = [self.Mapper.mapid(atom.idx, mtype='ligand', bsid=self.ligand.bsid) - for atom in self.unpaired_hbd] - self.unpaired_hal_orig_idx = [self.Mapper.mapid(atom.idx, mtype='ligand', bsid=self.ligand.bsid) - for atom in self.unpaired_hal] - self.num_unpaired_hba, self.num_unpaired_hbd = len(self.unpaired_hba), len(self.unpaired_hbd) + ( + self.unpaired_hba, + self.unpaired_hbd, + self.unpaired_hal, + ) = self.find_unpaired_ligand() + self.unpaired_hba_orig_idx = [ + self.Mapper.mapid(atom.idx, mtype="ligand", bsid=self.ligand.bsid) + for atom in self.unpaired_hba + ] + self.unpaired_hbd_orig_idx = [ + self.Mapper.mapid(atom.idx, mtype="ligand", bsid=self.ligand.bsid) + for atom in self.unpaired_hbd + ] + self.unpaired_hal_orig_idx = [ + self.Mapper.mapid(atom.idx, mtype="ligand", bsid=self.ligand.bsid) + for atom in self.unpaired_hal + ] + self.num_unpaired_hba, self.num_unpaired_hbd = ( + len(self.unpaired_hba), + len(self.unpaired_hbd), + ) self.num_unpaired_hal = len(self.unpaired_hal) # Exclude empty chains (coming from ligand as a target, from metal complexes) - self.interacting_chains = sorted(list(set([i.reschain for i in self.all_itypes - if i.reschain not in [' ', None]]))) + self.interacting_chains = sorted( + list( + set( + [ + i.reschain + for i in self.all_itypes + if i.reschain not in [" ", None] + ] + ) + ) + ) # Get all interacting residues, excluding ligand and water molecules - self.interacting_res = list(set([''.join([str(i.resnr), str(i.reschain)]) for i in self.all_itypes - if i.restype not in ['LIG', 'HOH']])) + self.interacting_res = list( + set( + [ + "".join([str(i.resnr), str(i.reschain)]) + for i in self.all_itypes + if i.restype not in ["LIG", "HOH"] + ] + ) + ) if len(self.interacting_res) != 0: logger.info( - f'ligand interacts with {len(self.interacting_res)} binding site residue(s) in chain(s) {self.interacting_chains}') + f"ligand interacts with {len(self.interacting_res)} binding site residue(s) in chain(s) {self.interacting_chains}" + ) interactions_list = [] num_saltbridges = len(self.saltbridge_lneg + self.saltbridge_pneg) num_hbonds = len(self.hbonds_ldon + self.hbonds_pdon) @@ -658,34 +965,49 @@ class PLInteraction: num_halogen = len(self.halogen_bonds) num_waterbridges = len(self.water_bridges) if num_saltbridges != 0: - interactions_list.append('%i salt bridge(s)' % num_saltbridges) + interactions_list.append("%i salt bridge(s)" % num_saltbridges) if num_hbonds != 0: - interactions_list.append('%i hydrogen bond(s)' % num_hbonds) + interactions_list.append("%i hydrogen bond(s)" % num_hbonds) if num_pication != 0: - interactions_list.append('%i pi-cation interaction(s)' % num_pication) + interactions_list.append("%i pi-cation interaction(s)" % num_pication) if num_pistack != 0: - interactions_list.append('%i pi-stacking(s)' % num_pistack) + interactions_list.append("%i pi-stacking(s)" % num_pistack) if num_halogen != 0: - interactions_list.append('%i halogen bond(s)' % num_halogen) + interactions_list.append("%i halogen bond(s)" % num_halogen) if num_waterbridges != 0: - interactions_list.append('%i water bridge(s)' % num_waterbridges) + interactions_list.append("%i water bridge(s)" % num_waterbridges) if not len(interactions_list) == 0: - logger.info(f'complex uses {interactions_list}') + logger.info(f"complex uses {interactions_list}") else: - logger.info('no interactions for this ligand') + logger.info("no interactions for this ligand") def find_unpaired_ligand(self): """Identify unpaired functional in groups in ligands, involving H-Bond donors, acceptors, halogen bond donors. """ unpaired_hba, unpaired_hbd, unpaired_hal = [], [], [] # Unpaired hydrogen bond acceptors/donors in ligand (not used for hydrogen bonds/water, salt bridges/mcomplex) - involved_atoms = [hbond.a.idx for hbond in self.hbonds_pdon] + [hbond.d.idx for hbond in self.hbonds_ldon] - [[involved_atoms.append(atom.idx) for atom in sb.negative.atoms] for sb in self.saltbridge_lneg] - [[involved_atoms.append(atom.idx) for atom in sb.positive.atoms] for sb in self.saltbridge_pneg] + involved_atoms = [hbond.a.idx for hbond in self.hbonds_pdon] + [ + hbond.d.idx for hbond in self.hbonds_ldon + ] + [ + [involved_atoms.append(atom.idx) for atom in sb.negative.atoms] + for sb in self.saltbridge_lneg + ] + [ + [involved_atoms.append(atom.idx) for atom in sb.positive.atoms] + for sb in self.saltbridge_pneg + ] [involved_atoms.append(wb.a.idx) for wb in self.water_bridges if wb.protisdon] - [involved_atoms.append(wb.d.idx) for wb in self.water_bridges if not wb.protisdon] - [involved_atoms.append(mcomplex.target.atom.idx) for mcomplex in self.metal_complexes - if mcomplex.location == 'ligand'] + [ + involved_atoms.append(wb.d.idx) + for wb in self.water_bridges + if not wb.protisdon + ] + [ + involved_atoms.append(mcomplex.target.atom.idx) + for mcomplex in self.metal_complexes + if mcomplex.location == "ligand" + ] for atom in [hba.a for hba in self.ligand.get_hba()]: if atom.idx not in involved_atoms: unpaired_hba.append(atom) @@ -707,7 +1029,10 @@ class PLInteraction: # 1. Rings interacting via stacking can't have additional hydrophobic contacts between each other. for pistack, h in itertools.product(pistacks, all_h): h1, h2 = h.bsatom.idx, h.ligatom.idx - brs, lrs = [p1.idx for p1 in pistack.proteinring.atoms], [p2.idx for p2 in pistack.ligandring.atoms] + brs, lrs = ( + [p1.idx for p1 in pistack.proteinring.atoms], + [p2.idx for p2 in pistack.ligandring.atoms], + ) if h1 in brs and h2 in lrs: sel[(h1, h2)] = "EXCLUDE" hydroph = [h for h in all_h if not (h.bsatom.idx, h.ligatom.idx) in sel] @@ -726,7 +1051,9 @@ class PLInteraction: # 3. If a protein atom interacts with several neighboring ligand atoms, just keep the one with the closest dist for h in hydroph: if h.bsatom.idx not in bsclust: - bsclust[h.bsatom.idx] = [h, ] + bsclust[h.bsatom.idx] = [ + h, + ] else: bsclust[h.bsatom.idx].append(h) @@ -752,10 +1079,12 @@ class PLInteraction: tuples = list(set(tuples)) tuples = sorted(tuples, key=itemgetter(1)) - clusters = cluster_doubles(tuples) # Cluster connected atoms (i.e. find hydrophobic patches) + clusters = cluster_doubles( + tuples + ) # Cluster connected atoms (i.e. find hydrophobic patches) for cluster in clusters: - min_dist = float('inf') + min_dist = float("inf") min_h = None for atm_idx in cluster: h = idx_to_h[atm_idx] @@ -765,7 +1094,9 @@ class PLInteraction: hydroph_final.append(min_h) before, reduced = len(all_h), len(hydroph_final) if not before == 0 and not before == reduced: - logger.info(f'reduced number of hydrophobic contacts from {before} to {reduced}') + logger.info( + f"reduced number of hydrophobic contacts from {before} to {reduced}" + ) return hydroph_final def refine_hbonds_ldon(self, all_hbonds, salt_lneg, salt_pneg): @@ -774,11 +1105,17 @@ class PLInteraction: for hbond in all_hbonds: i_set[hbond] = False for salt in salt_pneg: - protidx, ligidx = [at.idx for at in salt.negative.atoms], [at.idx for at in salt.positive.atoms] + protidx, ligidx = ( + [at.idx for at in salt.negative.atoms], + [at.idx for at in salt.positive.atoms], + ) if hbond.d.idx in ligidx and hbond.a.idx in protidx: i_set[hbond] = True for salt in salt_lneg: - protidx, ligidx = [at.idx for at in salt.positive.atoms], [at.idx for at in salt.negative.atoms] + protidx, ligidx = ( + [at.idx for at in salt.positive.atoms], + [at.idx for at in salt.negative.atoms], + ) if hbond.d.idx in ligidx and hbond.a.idx in protidx: i_set[hbond] = True @@ -801,11 +1138,17 @@ class PLInteraction: for hbond in all_hbonds: i_set[hbond] = False for salt in salt_lneg: - protidx, ligidx = [at.idx for at in salt.positive.atoms], [at.idx for at in salt.negative.atoms] + protidx, ligidx = ( + [at.idx for at in salt.positive.atoms], + [at.idx for at in salt.negative.atoms], + ) if hbond.a.idx in ligidx and hbond.d.idx in protidx: i_set[hbond] = True for salt in salt_pneg: - protidx, ligidx = [at.idx for at in salt.negative.atoms], [at.idx for at in salt.positive.atoms] + protidx, ligidx = ( + [at.idx for at in salt.negative.atoms], + [at.idx for at in salt.positive.atoms], + ) if hbond.a.idx in ligidx and hbond.d.idx in protidx: i_set[hbond] = True @@ -829,7 +1172,10 @@ class PLInteraction: for picat in all_picat: exclude = False for stack in stacks: - if whichrestype(stack.proteinring.atoms[0]) == 'HIS' and picat.ring.obj == stack.ligandring.obj: + if ( + whichrestype(stack.proteinring.atoms[0]) == "HIS" + and picat.ring.obj == stack.ligandring.obj + ): exclude = True if not exclude: i_set.append(picat) @@ -848,18 +1194,27 @@ class PLInteraction: if (wbridge.water.idx, wbridge.a.idx) not in wb_dict: wb_dict[(wbridge.water.idx, wbridge.a.idx)] = wbridge else: - if abs(omega - wb_dict[(wbridge.water.idx, wbridge.a.idx)].w_angle) < abs(omega - wbridge.w_angle): + if abs( + omega - wb_dict[(wbridge.water.idx, wbridge.a.idx)].w_angle + ) < abs(omega - wbridge.w_angle): wb_dict[(wbridge.water.idx, wbridge.a.idx)] = wbridge for wb_tuple in wb_dict: water, acceptor = wb_tuple if water not in wb_dict2: - wb_dict2[water] = [(abs(omega - wb_dict[wb_tuple].w_angle), wb_dict[wb_tuple]), ] + wb_dict2[water] = [ + (abs(omega - wb_dict[wb_tuple].w_angle), wb_dict[wb_tuple]), + ] elif len(wb_dict2[water]) == 1: - wb_dict2[water].append((abs(omega - wb_dict[wb_tuple].w_angle), wb_dict[wb_tuple])) + wb_dict2[water].append( + (abs(omega - wb_dict[wb_tuple].w_angle), wb_dict[wb_tuple]) + ) wb_dict2[water] = sorted(wb_dict2[water], key=lambda x: x[0]) else: if wb_dict2[water][1][0] < abs(omega - wb_dict[wb_tuple].w_angle): - wb_dict2[water] = [wb_dict2[water][0], (wb_dict[wb_tuple].w_angle, wb_dict[wb_tuple])] + wb_dict2[water] = [ + wb_dict2[water][0], + (wb_dict[wb_tuple].w_angle, wb_dict[wb_tuple]), + ] filtered_wb = [] for fwbridges in wb_dict2.values(): @@ -870,12 +1225,19 @@ class PLInteraction: class BindingSite(Mol): def __init__(self, atoms, protcomplex, cclass, altconf, min_dist, mapper): """Find all relevant parts which could take part in interactions""" - Mol.__init__(self, altconf, mapper, mtype='protein', bsid=None) + Mol.__init__(self, altconf, mapper, mtype="protein", bsid=None) self.complex = cclass self.full_mol = protcomplex self.all_atoms = atoms self.min_dist = min_dist # Minimum distance of bs res to ligand - self.bs_res = list(set([''.join([str(whichresnumber(a)), whichchain(a)]) for a in self.all_atoms])) # e.g. 47A + self.bs_res = list( + set( + [ + "".join([str(whichresnumber(a)), whichchain(a)]) + for a in self.all_atoms + ] + ) + ) # e.g. 47A self.rings = self.find_rings(self.full_mol, self.all_atoms) self.hydroph_atoms = self.hydrophobic_atoms(self.all_atoms) self.hbond_acc_atoms = self.find_hba(self.all_atoms) @@ -886,118 +1248,228 @@ class BindingSite(Mol): def find_hal(self, atoms): """Look for halogen bond acceptors (Y-{O|P|N|S}, with Y=C,P,S)""" - data = namedtuple('hal_acceptor', 'o o_orig_idx y y_orig_idx') + data = namedtuple("hal_acceptor", "o o_orig_idx y y_orig_idx") a_set = [] # All oxygens, nitrogen, sulfurs with neighboring carbon, phosphor, nitrogen or sulfur for a in [at for at in atoms if at.atomicnum in [8, 7, 16]]: - n_atoms = [na for na in pybel.ob.OBAtomAtomIter(a.OBAtom) if na.GetAtomicNum() in [6, 7, 15, 16]] + n_atoms = [ + na + for na in pybel.ob.OBAtomAtomIter(a.OBAtom) + if na.GetAtomicNum() in [6, 7, 15, 16] + ] if len(n_atoms) == 1: # Proximal atom o_orig_idx = self.Mapper.mapid(a.idx, mtype=self.mtype, bsid=self.bsid) - y_orig_idx = self.Mapper.mapid(n_atoms[0].GetIdx(), mtype=self.mtype, bsid=self.bsid) - a_set.append(data(o=a, o_orig_idx=o_orig_idx, y=pybel.Atom(n_atoms[0]), y_orig_idx=y_orig_idx)) + y_orig_idx = self.Mapper.mapid( + n_atoms[0].GetIdx(), mtype=self.mtype, bsid=self.bsid + ) + a_set.append( + data( + o=a, + o_orig_idx=o_orig_idx, + y=pybel.Atom(n_atoms[0]), + y_orig_idx=y_orig_idx, + ) + ) return a_set def find_charged(self, mol): """Looks for positive charges in arginine, histidine or lysine, for negative in aspartic and glutamic acid.""" - data = namedtuple('pcharge', 'atoms atoms_orig_idx type center restype resnr reschain') + data = namedtuple( + "pcharge", "atoms atoms_orig_idx type center restype resnr reschain" + ) a_set = [] # Iterate through all residue, exclude those in chains defined as peptides - for res in [r for r in pybel.ob.OBResidueIter(mol.OBMol) if not r.GetChain() in config.PEPTIDES]: + for res in [ + r + for r in pybel.ob.OBResidueIter(mol.OBMol) + if not r.GetChain() in config.PEPTIDES + ]: if config.INTRA is not None: if res.GetChain() != config.INTRA: continue a_contributing = [] a_contributing_orig_idx = [] - if res.GetName() in ('ARG', 'HIS', 'LYS'): # Arginine, Histidine or Lysine have charged sidechains + if res.GetName() in ( + "ARG", + "HIS", + "LYS", + ): # Arginine, Histidine or Lysine have charged sidechains for a in pybel.ob.OBResidueAtomIter(res): - if a.GetType().startswith('N') and res.GetAtomProperty(a, 8) \ - and not self.Mapper.mapid(a.GetIdx(), mtype='protein') in self.altconf: + if ( + a.GetType().startswith("N") + and res.GetAtomProperty(a, 8) + and not self.Mapper.mapid(a.GetIdx(), mtype="protein") + in self.altconf + ): a_contributing.append(pybel.Atom(a)) - a_contributing_orig_idx.append(self.Mapper.mapid(a.GetIdx(), mtype='protein')) + a_contributing_orig_idx.append( + self.Mapper.mapid(a.GetIdx(), mtype="protein") + ) if not len(a_contributing) == 0: - a_set.append(data(atoms=a_contributing, - atoms_orig_idx=a_contributing_orig_idx, - type='positive', - center=centroid([ac.coords for ac in a_contributing]), - restype=res.GetName(), - resnr=res.GetNum(), - reschain=res.GetChain())) - if res.GetName() in ('GLU', 'ASP'): # Aspartic or Glutamic Acid + a_set.append( + data( + atoms=a_contributing, + atoms_orig_idx=a_contributing_orig_idx, + type="positive", + center=centroid([ac.coords for ac in a_contributing]), + restype=res.GetName(), + resnr=res.GetNum(), + reschain=res.GetChain(), + ) + ) + if res.GetName() in ("GLU", "ASP"): # Aspartic or Glutamic Acid for a in pybel.ob.OBResidueAtomIter(res): - if a.GetType().startswith('O') and res.GetAtomProperty(a, 8) \ - and not self.Mapper.mapid(a.GetIdx(), mtype='protein') in self.altconf: + if ( + a.GetType().startswith("O") + and res.GetAtomProperty(a, 8) + and not self.Mapper.mapid(a.GetIdx(), mtype="protein") + in self.altconf + ): a_contributing.append(pybel.Atom(a)) - a_contributing_orig_idx.append(self.Mapper.mapid(a.GetIdx(), mtype='protein')) + a_contributing_orig_idx.append( + self.Mapper.mapid(a.GetIdx(), mtype="protein") + ) if not len(a_contributing) == 0: - a_set.append(data(atoms=a_contributing, - atoms_orig_idx=a_contributing_orig_idx, - type='negative', - center=centroid([ac.coords for ac in a_contributing]), - restype=res.GetName(), - resnr=res.GetNum(), - reschain=res.GetChain())) + a_set.append( + data( + atoms=a_contributing, + atoms_orig_idx=a_contributing_orig_idx, + type="negative", + center=centroid([ac.coords for ac in a_contributing]), + restype=res.GetName(), + resnr=res.GetNum(), + reschain=res.GetChain(), + ) + ) return a_set def find_metal_binding(self, mol): """Looks for atoms that could possibly be involved in chelating a metal ion. This can be any main chain oxygen atom or oxygen, nitrogen and sulfur from specific amino acids""" - data = namedtuple('metal_binding', 'atom atom_orig_idx type restype resnr reschain location') + data = namedtuple( + "metal_binding", "atom atom_orig_idx type restype resnr reschain location" + ) a_set = [] for res in pybel.ob.OBResidueIter(mol.OBMol): - restype, reschain, resnr = res.GetName().upper(), res.GetChain(), res.GetNum() - if restype in ['ASP', 'GLU', 'SER', 'THR', 'TYR']: # Look for oxygens here + restype, reschain, resnr = ( + res.GetName().upper(), + res.GetChain(), + res.GetNum(), + ) + if restype in ["ASP", "GLU", "SER", "THR", "TYR"]: # Look for oxygens here for a in pybel.ob.OBResidueAtomIter(res): - if a.GetType().startswith('O') and res.GetAtomProperty(a, 8) \ - and not self.Mapper.mapid(a.GetIdx(), mtype='protein') in self.altconf: - atom_orig_idx = self.Mapper.mapid(a.GetIdx(), mtype=self.mtype, bsid=self.bsid) - a_set.append(data(atom=pybel.Atom(a), atom_orig_idx=atom_orig_idx, type='O', restype=restype, - resnr=resnr, reschain=reschain, - location='protein.sidechain')) - if restype == 'HIS': # Look for nitrogen here + if ( + a.GetType().startswith("O") + and res.GetAtomProperty(a, 8) + and not self.Mapper.mapid(a.GetIdx(), mtype="protein") + in self.altconf + ): + atom_orig_idx = self.Mapper.mapid( + a.GetIdx(), mtype=self.mtype, bsid=self.bsid + ) + a_set.append( + data( + atom=pybel.Atom(a), + atom_orig_idx=atom_orig_idx, + type="O", + restype=restype, + resnr=resnr, + reschain=reschain, + location="protein.sidechain", + ) + ) + if restype == "HIS": # Look for nitrogen here for a in pybel.ob.OBResidueAtomIter(res): - if a.GetType().startswith('N') and res.GetAtomProperty(a, 8) \ - and not self.Mapper.mapid(a.GetIdx(), mtype='protein') in self.altconf: - atom_orig_idx = self.Mapper.mapid(a.GetIdx(), mtype=self.mtype, bsid=self.bsid) - a_set.append(data(atom=pybel.Atom(a), atom_orig_idx=atom_orig_idx, type='N', restype=restype, - resnr=resnr, reschain=reschain, - location='protein.sidechain')) - if restype == 'CYS': # Look for sulfur here + if ( + a.GetType().startswith("N") + and res.GetAtomProperty(a, 8) + and not self.Mapper.mapid(a.GetIdx(), mtype="protein") + in self.altconf + ): + atom_orig_idx = self.Mapper.mapid( + a.GetIdx(), mtype=self.mtype, bsid=self.bsid + ) + a_set.append( + data( + atom=pybel.Atom(a), + atom_orig_idx=atom_orig_idx, + type="N", + restype=restype, + resnr=resnr, + reschain=reschain, + location="protein.sidechain", + ) + ) + if restype == "CYS": # Look for sulfur here for a in pybel.ob.OBResidueAtomIter(res): - if a.GetType().startswith('S') and res.GetAtomProperty(a, 8) \ - and not self.Mapper.mapid(a.GetIdx(), mtype='protein') in self.altconf: - atom_orig_idx = self.Mapper.mapid(a.GetIdx(), mtype=self.mtype, bsid=self.bsid) - a_set.append(data(atom=pybel.Atom(a), atom_orig_idx=atom_orig_idx, type='S', restype=restype, - resnr=resnr, reschain=reschain, - location='protein.sidechain')) + if ( + a.GetType().startswith("S") + and res.GetAtomProperty(a, 8) + and not self.Mapper.mapid(a.GetIdx(), mtype="protein") + in self.altconf + ): + atom_orig_idx = self.Mapper.mapid( + a.GetIdx(), mtype=self.mtype, bsid=self.bsid + ) + a_set.append( + data( + atom=pybel.Atom(a), + atom_orig_idx=atom_orig_idx, + type="S", + restype=restype, + resnr=resnr, + reschain=reschain, + location="protein.sidechain", + ) + ) for a in pybel.ob.OBResidueAtomIter(res): # All main chain oxygens - if a.GetType().startswith('O') and res.GetAtomProperty(a, 2) \ - and not self.Mapper.mapid(a.GetIdx(), mtype='protein') in self.altconf and restype != 'HOH': - atom_orig_idx = self.Mapper.mapid(a.GetIdx(), mtype=self.mtype, bsid=self.bsid) - a_set.append(data(atom=pybel.Atom(a), atom_orig_idx=atom_orig_idx, type='O', restype=res.GetName(), - resnr=res.GetNum(), reschain=res.GetChain(), - location='protein.mainchain')) + if ( + a.GetType().startswith("O") + and res.GetAtomProperty(a, 2) + and not self.Mapper.mapid(a.GetIdx(), mtype="protein") + in self.altconf + and restype != "HOH" + ): + atom_orig_idx = self.Mapper.mapid( + a.GetIdx(), mtype=self.mtype, bsid=self.bsid + ) + a_set.append( + data( + atom=pybel.Atom(a), + atom_orig_idx=atom_orig_idx, + type="O", + restype=res.GetName(), + resnr=res.GetNum(), + reschain=res.GetChain(), + location="protein.mainchain", + ) + ) return a_set class Ligand(Mol): def __init__(self, cclass, ligand): altconf = cclass.altconf - self.hetid, self.chain, self.position = ligand.hetid, ligand.chain, ligand.position - self.bsid = ':'.join([self.hetid, self.chain, str(self.position)]) - Mol.__init__(self, altconf, cclass.Mapper, mtype='ligand', bsid=self.bsid) + self.hetid, self.chain, self.position = ( + ligand.hetid, + ligand.chain, + ligand.position, + ) + self.bsid = ":".join([self.hetid, self.chain, str(self.position)]) + Mol.__init__(self, altconf, cclass.Mapper, mtype="ligand", bsid=self.bsid) self.members = ligand.members self.longname = ligand.longname self.type = ligand.type self.complex = cclass self.molecule = ligand.mol # Pybel Molecule - self.smiles = self.molecule.write(format='can') # SMILES String - self.inchikey = self.molecule.write(format='inchikey') + self.smiles = self.molecule.write(format="can") # SMILES String + self.inchikey = self.molecule.write(format="inchikey") self.can_to_pdb = ligand.can_to_pdb if not len(self.smiles) == 0: self.smiles = self.smiles.split()[0] else: - logger.warning(f'could not write SMILES for ligand {ligand}') - self.smiles = '' + logger.warning(f"could not write SMILES for ligand {ligand}") + self.smiles = "" self.heavy_atoms = self.molecule.OBMol.NumHvyAtoms() # Heavy atoms count self.all_atoms = self.molecule.atoms self.atmdict = {l.idx: l for l in self.all_atoms} @@ -1006,9 +1478,9 @@ class Ligand(Mol): self.hbond_acc_atoms = self.find_hba(self.all_atoms) self.num_rings = len(self.rings) if self.num_rings != 0: - logger.info(f'contains {self.num_rings} aromatic ring(s)') + logger.info(f"contains {self.num_rings} aromatic ring(s)") descvalues = self.molecule.calcdesc() - self.molweight, self.logp = float(descvalues['MW']), float(descvalues['logP']) + self.molweight, self.logp = float(descvalues["MW"]), float(descvalues["logP"]) self.num_rot_bonds = int(self.molecule.OBMol.NumRotors()) self.atomorder = ligand.atomorder @@ -1016,48 +1488,73 @@ class Ligand(Mol): # Special Case for hydrogen bond acceptor identification # ########################################################## - self.inverse_mapping = {v: k for k, v in self.Mapper.ligandmaps[self.bsid].items()} + self.inverse_mapping = { + v: k for k, v in self.Mapper.ligandmaps[self.bsid].items() + } self.pdb_to_idx_mapping = {v: k for k, v in self.Mapper.proteinmap.items()} self.hbond_don_atom_pairs = self.find_hbd(self.all_atoms, self.hydroph_atoms) ###### donor_pairs = [] - data = namedtuple('hbonddonor', 'd d_orig_atom d_orig_idx h type') + data = namedtuple("hbonddonor", "d d_orig_atom d_orig_idx h type") for donor in self.all_atoms: - pdbidx = self.Mapper.mapid(donor.idx, mtype='ligand', bsid=self.bsid, to='original') + pdbidx = self.Mapper.mapid( + donor.idx, mtype="ligand", bsid=self.bsid, to="original" + ) d = cclass.atoms[self.pdb_to_idx_mapping[pdbidx]] if d.OBAtom.IsHbondDonor(): - for adj_atom in [a for a in pybel.ob.OBAtomAtomIter(d.OBAtom) if a.IsHbondDonorH()]: + for adj_atom in [ + a for a in pybel.ob.OBAtomAtomIter(d.OBAtom) if a.IsHbondDonorH() + ]: d_orig_atom = self.Mapper.id_to_atom(pdbidx) - donor_pairs.append(data(d=donor, d_orig_atom=d_orig_atom, d_orig_idx=pdbidx, - h=pybel.Atom(adj_atom), type='regular')) + donor_pairs.append( + data( + d=donor, + d_orig_atom=d_orig_atom, + d_orig_idx=pdbidx, + h=pybel.Atom(adj_atom), + type="regular", + ) + ) self.hbond_don_atom_pairs = donor_pairs ####### self.charged = self.find_charged(self.all_atoms) self.centroid = centroid([a.coords for a in self.all_atoms]) - self.max_dist_to_center = max((euclidean3d(self.centroid, a.coords) for a in self.all_atoms)) + self.max_dist_to_center = max( + (euclidean3d(self.centroid, a.coords) for a in self.all_atoms) + ) self.water = [] - data = namedtuple('water', 'oxy oxy_orig_idx') + data = namedtuple("water", "oxy oxy_orig_idx") for hoh in ligand.water: oxy = None for at in pybel.ob.OBResidueAtomIter(hoh): if at.GetAtomicNum() == 8 and at.GetIdx() not in self.altconf: oxy = pybel.Atom(at) # There are some cases where there is no oxygen in a water residue, ignore those - if not set([at.GetAtomicNum() for at in pybel.ob.OBResidueAtomIter(hoh)]) == {1} and oxy is not None: - if euclidean3d(self.centroid, oxy.coords) < self.max_dist_to_center + config.BS_DIST: - oxy_orig_idx = self.Mapper.mapid(oxy.idx, mtype='protein') + if ( + not set([at.GetAtomicNum() for at in pybel.ob.OBResidueAtomIter(hoh)]) + == {1} + and oxy is not None + ): + if ( + euclidean3d(self.centroid, oxy.coords) + < self.max_dist_to_center + config.BS_DIST + ): + oxy_orig_idx = self.Mapper.mapid(oxy.idx, mtype="protein") self.water.append(data(oxy=oxy, oxy_orig_idx=oxy_orig_idx)) self.halogenbond_don = self.find_hal(self.all_atoms) self.metal_binding = self.find_metal_binding(self.all_atoms, self.water) self.metals = [] - data = namedtuple('metal', 'm orig_m m_orig_idx') + data = namedtuple("metal", "m orig_m m_orig_idx") for a in [a for a in self.all_atoms if a.type.upper() in config.METAL_IONS]: m_orig_idx = self.Mapper.mapid(a.idx, mtype=self.mtype, bsid=self.bsid) orig_m = self.Mapper.id_to_atom(m_orig_idx) self.metals.append(data(m=a, m_orig_idx=m_orig_idx, orig_m=orig_m)) - self.num_hba, self.num_hbd = len(self.hbond_acc_atoms), len(self.hbond_don_atom_pairs) + self.num_hba, self.num_hbd = ( + len(self.hbond_acc_atoms), + len(self.hbond_don_atom_pairs), + ) self.num_hal = len(self.halogenbond_don) def get_canonical_num(self, atomnum): @@ -1066,41 +1563,69 @@ class Ligand(Mol): def is_functional_group(self, atom, group): """Given a pybel atom, look up if it belongs to a function group""" - n_atoms = [a_neighbor.GetAtomicNum() for a_neighbor in pybel.ob.OBAtomAtomIter(atom.OBAtom)] + n_atoms = [ + a_neighbor.GetAtomicNum() + for a_neighbor in pybel.ob.OBAtomAtomIter(atom.OBAtom) + ] - if group in ['quartamine', 'tertamine'] and atom.atomicnum == 7: # Nitrogen + if group in ["quartamine", "tertamine"] and atom.atomicnum == 7: # Nitrogen # It's a nitrogen, so could be a protonated amine or quaternary ammonium - if '1' not in n_atoms and len(n_atoms) == 4: - return True if group == 'quartamine' else False # It's a quat. ammonium (N with 4 residues != H) + if "1" not in n_atoms and len(n_atoms) == 4: + return ( + True if group == "quartamine" else False + ) # It's a quat. ammonium (N with 4 residues != H) elif atom.OBAtom.GetHyb() == 3 and len(n_atoms) >= 3: - return True if group == 'tertamine' else False # It's sp3-hybridized, so could pick up an hydrogen + return ( + True if group == "tertamine" else False + ) # It's sp3-hybridized, so could pick up an hydrogen else: return False - if group in ['sulfonium', 'sulfonicacid', 'sulfate'] and atom.atomicnum == 16: # Sulfur - if '1' not in n_atoms and len(n_atoms) == 3: # It's a sulfonium (S with 3 residues != H) - return True if group == 'sulfonium' else False + if ( + group in ["sulfonium", "sulfonicacid", "sulfate"] and atom.atomicnum == 16 + ): # Sulfur + if ( + "1" not in n_atoms and len(n_atoms) == 3 + ): # It's a sulfonium (S with 3 residues != H) + return True if group == "sulfonium" else False elif n_atoms.count(8) == 3: # It's a sulfonate or sulfonic acid - return True if group == 'sulfonicacid' else False + return True if group == "sulfonicacid" else False elif n_atoms.count(8) == 4: # It's a sulfate - return True if group == 'sulfate' else False + return True if group == "sulfate" else False - if group == 'phosphate' and atom.atomicnum == 15: # Phosphor + if group == "phosphate" and atom.atomicnum == 15: # Phosphor if set(n_atoms) == {8}: # It's a phosphate return True - if group in ['carboxylate', 'guanidine'] and atom.atomicnum == 6: # It's a carbon atom - if n_atoms.count(8) == 2 and n_atoms.count(6) == 1: # It's a carboxylate group - return True if group == 'carboxylate' else False + if ( + group in ["carboxylate", "guanidine"] and atom.atomicnum == 6 + ): # It's a carbon atom + if ( + n_atoms.count(8) == 2 and n_atoms.count(6) == 1 + ): # It's a carboxylate group + return True if group == "carboxylate" else False elif n_atoms.count(7) == 3 and len(n_atoms) == 3: # It's a guanidine group nitro_partners = [] for nitro in pybel.ob.OBAtomAtomIter(atom.OBAtom): - nitro_partners.append(len([b_neighbor for b_neighbor in pybel.ob.OBAtomAtomIter(nitro)])) - if min(nitro_partners) == 1: # One nitrogen is only connected to the carbon, can pick up a H - return True if group == 'guanidine' else False - - if group == 'halocarbon' and atom.atomicnum in [9, 17, 35, 53]: # Halogen atoms - n_atoms = [na for na in pybel.ob.OBAtomAtomIter(atom.OBAtom) if na.GetAtomicNum() == 6] + nitro_partners.append( + len( + [ + b_neighbor + for b_neighbor in pybel.ob.OBAtomAtomIter(nitro) + ] + ) + ) + if ( + min(nitro_partners) == 1 + ): # One nitrogen is only connected to the carbon, can pick up a H + return True if group == "guanidine" else False + + if group == "halocarbon" and atom.atomicnum in [9, 17, 35, 53]: # Halogen atoms + n_atoms = [ + na + for na in pybel.ob.OBAtomAtomIter(atom.OBAtom) + if na.GetAtomicNum() == 6 + ] if len(n_atoms) == 1: # Halocarbon return True else: @@ -1108,18 +1633,32 @@ class Ligand(Mol): def find_hal(self, atoms): """Look for halogen bond donors (X-C, with X=F, Cl, Br, I)""" - data = namedtuple('hal_donor', 'x orig_x x_orig_idx c c_orig_idx') + data = namedtuple("hal_donor", "x orig_x x_orig_idx c c_orig_idx") a_set = [] for a in atoms: - if self.is_functional_group(a, 'halocarbon'): - n_atoms = [na for na in pybel.ob.OBAtomAtomIter(a.OBAtom) if na.GetAtomicNum() == 6] + if self.is_functional_group(a, "halocarbon"): + n_atoms = [ + na + for na in pybel.ob.OBAtomAtomIter(a.OBAtom) + if na.GetAtomicNum() == 6 + ] x_orig_idx = self.Mapper.mapid(a.idx, mtype=self.mtype, bsid=self.bsid) orig_x = self.Mapper.id_to_atom(x_orig_idx) - c_orig_idx = [self.Mapper.mapid(na.GetIdx(), mtype=self.mtype, bsid=self.bsid) for na in n_atoms] - a_set.append(data(x=a, orig_x=orig_x, x_orig_idx=x_orig_idx, - c=pybel.Atom(n_atoms[0]), c_orig_idx=c_orig_idx)) + c_orig_idx = [ + self.Mapper.mapid(na.GetIdx(), mtype=self.mtype, bsid=self.bsid) + for na in n_atoms + ] + a_set.append( + data( + x=a, + orig_x=orig_x, + x_orig_idx=x_orig_idx, + c=pybel.Atom(n_atoms[0]), + c_orig_idx=c_orig_idx, + ) + ) if len(a_set) != 0: - logger.info(f'ligand contains {len(a_set)} halogen atom(s)') + logger.info(f"ligand contains {len(a_set)} halogen atom(s)") return a_set def find_charged(self, all_atoms): @@ -1128,76 +1667,189 @@ class Ligand(Mol): as mentioned in 'Cation-pi interactions in ligand recognition and catalysis' (Zacharias et al., 2002)). Identify negatively charged groups in the ligand. """ - data = namedtuple('lcharge', 'atoms orig_atoms atoms_orig_idx type center fgroup') + data = namedtuple( + "lcharge", "atoms orig_atoms atoms_orig_idx type center fgroup" + ) a_set = [] for a in all_atoms: a_orig_idx = self.Mapper.mapid(a.idx, mtype=self.mtype, bsid=self.bsid) a_orig = self.Mapper.id_to_atom(a_orig_idx) - if self.is_functional_group(a, 'quartamine'): - a_set.append(data(atoms=[a, ], orig_atoms=[a_orig, ], atoms_orig_idx=[a_orig_idx, ], type='positive', - center=list(a.coords), fgroup='quartamine')) - elif self.is_functional_group(a, 'tertamine'): - a_set.append(data(atoms=[a, ], orig_atoms=[a_orig, ], atoms_orig_idx=[a_orig_idx, ], type='positive', - center=list(a.coords), - fgroup='tertamine')) - if self.is_functional_group(a, 'sulfonium'): - a_set.append(data(atoms=[a, ], orig_atoms=[a_orig, ], atoms_orig_idx=[a_orig_idx, ], type='positive', - center=list(a.coords), - fgroup='sulfonium')) - if self.is_functional_group(a, 'phosphate'): - a_contributing = [a, ] - a_contributing_orig_idx = [a_orig_idx, ] - [a_contributing.append(pybel.Atom(neighbor)) for neighbor in pybel.ob.OBAtomAtomIter(a.OBAtom)] - [a_contributing_orig_idx.append(self.Mapper.mapid(neighbor.idx, mtype=self.mtype, bsid=self.bsid)) - for neighbor in a_contributing] - orig_contributing = [self.Mapper.id_to_atom(idx) for idx in a_contributing_orig_idx] + if self.is_functional_group(a, "quartamine"): + a_set.append( + data( + atoms=[a,], + orig_atoms=[a_orig,], + atoms_orig_idx=[a_orig_idx,], + type="positive", + center=list(a.coords), + fgroup="quartamine", + ) + ) + elif self.is_functional_group(a, "tertamine"): a_set.append( - data(atoms=a_contributing, orig_atoms=orig_contributing, atoms_orig_idx=a_contributing_orig_idx, - type='negative', - center=a.coords, fgroup='phosphate')) - if self.is_functional_group(a, 'sulfonicacid'): - a_contributing = [a, ] - a_contributing_orig_idx = [a_orig_idx, ] - [a_contributing.append(pybel.Atom(neighbor)) for neighbor in pybel.ob.OBAtomAtomIter(a.OBAtom) if - neighbor.GetAtomicNum() == 8] - [a_contributing_orig_idx.append(self.Mapper.mapid(neighbor.idx, mtype=self.mtype, bsid=self.bsid)) - for neighbor in a_contributing] - orig_contributing = [self.Mapper.id_to_atom(idx) for idx in a_contributing_orig_idx] + data( + atoms=[a,], + orig_atoms=[a_orig,], + atoms_orig_idx=[a_orig_idx,], + type="positive", + center=list(a.coords), + fgroup="tertamine", + ) + ) + if self.is_functional_group(a, "sulfonium"): a_set.append( - data(atoms=a_contributing, orig_atoms=orig_contributing, atoms_orig_idx=a_contributing_orig_idx, - type='negative', - center=a.coords, fgroup='sulfonicacid')) - elif self.is_functional_group(a, 'sulfate'): - a_contributing = [a, ] - a_contributing_orig_idx = [a_orig_idx, ] - [a_contributing_orig_idx.append(self.Mapper.mapid(neighbor.idx, mtype=self.mtype, bsid=self.bsid)) - for neighbor in a_contributing] - [a_contributing.append(pybel.Atom(neighbor)) for neighbor in pybel.ob.OBAtomAtomIter(a.OBAtom)] - orig_contributing = [self.Mapper.id_to_atom(idx) for idx in a_contributing_orig_idx] + data( + atoms=[a,], + orig_atoms=[a_orig,], + atoms_orig_idx=[a_orig_idx,], + type="positive", + center=list(a.coords), + fgroup="sulfonium", + ) + ) + if self.is_functional_group(a, "phosphate"): + a_contributing = [ + a, + ] + a_contributing_orig_idx = [ + a_orig_idx, + ] + [ + a_contributing.append(pybel.Atom(neighbor)) + for neighbor in pybel.ob.OBAtomAtomIter(a.OBAtom) + ] + [ + a_contributing_orig_idx.append( + self.Mapper.mapid( + neighbor.idx, mtype=self.mtype, bsid=self.bsid + ) + ) + for neighbor in a_contributing + ] + orig_contributing = [ + self.Mapper.id_to_atom(idx) for idx in a_contributing_orig_idx + ] a_set.append( - data(atoms=a_contributing, orig_atoms=orig_contributing, atoms_orig_idx=a_contributing_orig_idx, - type='negative', - center=a.coords, fgroup='sulfate')) - if self.is_functional_group(a, 'carboxylate'): - a_contributing = [pybel.Atom(neighbor) for neighbor in pybel.ob.OBAtomAtomIter(a.OBAtom) - if neighbor.GetAtomicNum() == 8] - a_contributing_orig_idx = [self.Mapper.mapid(neighbor.idx, mtype=self.mtype, bsid=self.bsid) - for neighbor in a_contributing] - orig_contributing = [self.Mapper.id_to_atom(idx) for idx in a_contributing_orig_idx] + data( + atoms=a_contributing, + orig_atoms=orig_contributing, + atoms_orig_idx=a_contributing_orig_idx, + type="negative", + center=a.coords, + fgroup="phosphate", + ) + ) + if self.is_functional_group(a, "sulfonicacid"): + a_contributing = [ + a, + ] + a_contributing_orig_idx = [ + a_orig_idx, + ] + [ + a_contributing.append(pybel.Atom(neighbor)) + for neighbor in pybel.ob.OBAtomAtomIter(a.OBAtom) + if neighbor.GetAtomicNum() == 8 + ] + [ + a_contributing_orig_idx.append( + self.Mapper.mapid( + neighbor.idx, mtype=self.mtype, bsid=self.bsid + ) + ) + for neighbor in a_contributing + ] + orig_contributing = [ + self.Mapper.id_to_atom(idx) for idx in a_contributing_orig_idx + ] a_set.append( - data(atoms=a_contributing, orig_atoms=orig_contributing, atoms_orig_idx=a_contributing_orig_idx, - type='negative', - center=centroid([a.coords for a in a_contributing]), fgroup='carboxylate')) - elif self.is_functional_group(a, 'guanidine'): - a_contributing = [pybel.Atom(neighbor) for neighbor in pybel.ob.OBAtomAtomIter(a.OBAtom) - if neighbor.GetAtomicNum() == 7] - a_contributing_orig_idx = [self.Mapper.mapid(neighbor.idx, mtype=self.mtype, bsid=self.bsid) - for neighbor in a_contributing] - orig_contributing = [self.Mapper.id_to_atom(idx) for idx in a_contributing_orig_idx] + data( + atoms=a_contributing, + orig_atoms=orig_contributing, + atoms_orig_idx=a_contributing_orig_idx, + type="negative", + center=a.coords, + fgroup="sulfonicacid", + ) + ) + elif self.is_functional_group(a, "sulfate"): + a_contributing = [ + a, + ] + a_contributing_orig_idx = [ + a_orig_idx, + ] + [ + a_contributing_orig_idx.append( + self.Mapper.mapid( + neighbor.idx, mtype=self.mtype, bsid=self.bsid + ) + ) + for neighbor in a_contributing + ] + [ + a_contributing.append(pybel.Atom(neighbor)) + for neighbor in pybel.ob.OBAtomAtomIter(a.OBAtom) + ] + orig_contributing = [ + self.Mapper.id_to_atom(idx) for idx in a_contributing_orig_idx + ] a_set.append( - data(atoms=a_contributing, orig_atoms=orig_contributing, atoms_orig_idx=a_contributing_orig_idx, - type='positive', - center=a.coords, fgroup='guanidine')) + data( + atoms=a_contributing, + orig_atoms=orig_contributing, + atoms_orig_idx=a_contributing_orig_idx, + type="negative", + center=a.coords, + fgroup="sulfate", + ) + ) + if self.is_functional_group(a, "carboxylate"): + a_contributing = [ + pybel.Atom(neighbor) + for neighbor in pybel.ob.OBAtomAtomIter(a.OBAtom) + if neighbor.GetAtomicNum() == 8 + ] + a_contributing_orig_idx = [ + self.Mapper.mapid(neighbor.idx, mtype=self.mtype, bsid=self.bsid) + for neighbor in a_contributing + ] + orig_contributing = [ + self.Mapper.id_to_atom(idx) for idx in a_contributing_orig_idx + ] + a_set.append( + data( + atoms=a_contributing, + orig_atoms=orig_contributing, + atoms_orig_idx=a_contributing_orig_idx, + type="negative", + center=centroid([a.coords for a in a_contributing]), + fgroup="carboxylate", + ) + ) + elif self.is_functional_group(a, "guanidine"): + a_contributing = [ + pybel.Atom(neighbor) + for neighbor in pybel.ob.OBAtomAtomIter(a.OBAtom) + if neighbor.GetAtomicNum() == 7 + ] + a_contributing_orig_idx = [ + self.Mapper.mapid(neighbor.idx, mtype=self.mtype, bsid=self.bsid) + for neighbor in a_contributing + ] + orig_contributing = [ + self.Mapper.id_to_atom(idx) for idx in a_contributing_orig_idx + ] + a_set.append( + data( + atoms=a_contributing, + orig_atoms=orig_contributing, + atoms_orig_idx=a_contributing_orig_idx, + type="positive", + center=a.coords, + fgroup="guanidine", + ) + ) return a_set def find_metal_binding(self, lig_atoms, water_oxygens): @@ -1206,67 +1858,173 @@ class Ligand(Mol): nitrogen from imidazole; sulfur from thiolate. """ a_set = [] - data = namedtuple('metal_binding', 'atom orig_atom atom_orig_idx type fgroup restype resnr reschain location') + data = namedtuple( + "metal_binding", + "atom orig_atom atom_orig_idx type fgroup restype resnr reschain location", + ) for oxygen in water_oxygens: - a_set.append(data(atom=oxygen.oxy, atom_orig_idx=oxygen.oxy_orig_idx, type='O', fgroup='water', - restype=whichrestype(oxygen.oxy), resnr=whichresnumber(oxygen.oxy), - reschain=whichchain(oxygen.oxy), location='water', - orig_atom=self.Mapper.id_to_atom(oxygen.oxy_orig_idx))) + a_set.append( + data( + atom=oxygen.oxy, + atom_orig_idx=oxygen.oxy_orig_idx, + type="O", + fgroup="water", + restype=whichrestype(oxygen.oxy), + resnr=whichresnumber(oxygen.oxy), + reschain=whichchain(oxygen.oxy), + location="water", + orig_atom=self.Mapper.id_to_atom(oxygen.oxy_orig_idx), + ) + ) # #@todo Refactor code for a in lig_atoms: - a_orig_idx = self.Mapper.mapid(a.idx, mtype='ligand', bsid=self.bsid) + a_orig_idx = self.Mapper.mapid(a.idx, mtype="ligand", bsid=self.bsid) n_atoms = pybel.ob.OBAtomAtomIter(a.OBAtom) # Neighboring atoms # All atomic numbers of neighboring atoms - n_atoms_atomicnum = [n.GetAtomicNum() for n in pybel.ob.OBAtomAtomIter(a.OBAtom)] + n_atoms_atomicnum = [ + n.GetAtomicNum() for n in pybel.ob.OBAtomAtomIter(a.OBAtom) + ] if a.atomicnum == 8: # Oxygen - if n_atoms_atomicnum.count('1') == 1 and len(n_atoms_atomicnum) == 2: # Oxygen in alcohol (R-[O]-H) - a_set.append(data(atom=a, atom_orig_idx=a_orig_idx, type='O', fgroup='alcohol', - restype=self.hetid, resnr=self.position, reschain=self.chain, - location='ligand', orig_atom=self.Mapper.id_to_atom(a_orig_idx))) - if True in [n.IsAromatic() for n in n_atoms] and not a.OBAtom.IsAromatic(): # Phenolate oxygen - a_set.append(data(atom=a, atom_orig_idx=a_orig_idx, type='O', fgroup='phenolate', - restype=self.hetid, resnr=self.position, reschain=self.chain, - location='ligand', orig_atom=self.Mapper.id_to_atom(a_orig_idx))) + if ( + n_atoms_atomicnum.count("1") == 1 and len(n_atoms_atomicnum) == 2 + ): # Oxygen in alcohol (R-[O]-H) + a_set.append( + data( + atom=a, + atom_orig_idx=a_orig_idx, + type="O", + fgroup="alcohol", + restype=self.hetid, + resnr=self.position, + reschain=self.chain, + location="ligand", + orig_atom=self.Mapper.id_to_atom(a_orig_idx), + ) + ) + if ( + True in [n.IsAromatic() for n in n_atoms] + and not a.OBAtom.IsAromatic() + ): # Phenolate oxygen + a_set.append( + data( + atom=a, + atom_orig_idx=a_orig_idx, + type="O", + fgroup="phenolate", + restype=self.hetid, + resnr=self.position, + reschain=self.chain, + location="ligand", + orig_atom=self.Mapper.id_to_atom(a_orig_idx), + ) + ) if a.atomicnum == 6: # It's a carbon atom - if n_atoms_atomicnum.count(8) == 2 and n_atoms_atomicnum.count(6) == 1: # It's a carboxylate group + if ( + n_atoms_atomicnum.count(8) == 2 and n_atoms_atomicnum.count(6) == 1 + ): # It's a carboxylate group for neighbor in [n for n in n_atoms if n.GetAtomicNum() == 8]: - neighbor_orig_idx = self.Mapper.mapid(neighbor.GetIdx(), mtype='ligand', bsid=self.bsid) - a_set.append(data(atom=pybel.Atom(neighbor), atom_orig_idx=neighbor_orig_idx, type='O', - fgroup='carboxylate', - restype=self.hetid, - resnr=self.position, reschain=self.chain, - location='ligand', orig_atom=self.Mapper.id_to_atom(a_orig_idx))) + neighbor_orig_idx = self.Mapper.mapid( + neighbor.GetIdx(), mtype="ligand", bsid=self.bsid + ) + a_set.append( + data( + atom=pybel.Atom(neighbor), + atom_orig_idx=neighbor_orig_idx, + type="O", + fgroup="carboxylate", + restype=self.hetid, + resnr=self.position, + reschain=self.chain, + location="ligand", + orig_atom=self.Mapper.id_to_atom(a_orig_idx), + ) + ) if a.atomicnum == 15: # It's a phosphor atom if n_atoms_atomicnum.count(8) >= 3: # It's a phosphoryl for neighbor in [n for n in n_atoms if n.GetAtomicNum() == 8]: - neighbor_orig_idx = self.Mapper.mapid(neighbor.GetIdx(), mtype='ligand', bsid=self.bsid) - a_set.append(data(atom=pybel.Atom(neighbor), atom_orig_idx=neighbor_orig_idx, type='O', - fgroup='phosphoryl', - restype=self.hetid, - resnr=self.position, reschain=self.chain, - location='ligand', orig_atom=self.Mapper.id_to_atom(a_orig_idx))) - if n_atoms_atomicnum.count(8) == 2: # It's another phosphor-containing group #@todo (correct name?) + neighbor_orig_idx = self.Mapper.mapid( + neighbor.GetIdx(), mtype="ligand", bsid=self.bsid + ) + a_set.append( + data( + atom=pybel.Atom(neighbor), + atom_orig_idx=neighbor_orig_idx, + type="O", + fgroup="phosphoryl", + restype=self.hetid, + resnr=self.position, + reschain=self.chain, + location="ligand", + orig_atom=self.Mapper.id_to_atom(a_orig_idx), + ) + ) + if ( + n_atoms_atomicnum.count(8) == 2 + ): # It's another phosphor-containing group #@todo (correct name?) for neighbor in [n for n in n_atoms if n.GetAtomicNum() == 8]: - neighbor_orig_idx = self.Mapper.mapid(neighbor.GetIdx(), mtype='ligand', bsid=self.bsid) - a_set.append(data(atom=pybel.Atom(neighbor), atom_orig_idx=neighbor_orig_idx, type='O', - fgroup='phosphor.other', restype=self.hetid, - resnr=self.position, - reschain=self.chain, location='ligand', - orig_atom=self.Mapper.id_to_atom(a_orig_idx))) + neighbor_orig_idx = self.Mapper.mapid( + neighbor.GetIdx(), mtype="ligand", bsid=self.bsid + ) + a_set.append( + data( + atom=pybel.Atom(neighbor), + atom_orig_idx=neighbor_orig_idx, + type="O", + fgroup="phosphor.other", + restype=self.hetid, + resnr=self.position, + reschain=self.chain, + location="ligand", + orig_atom=self.Mapper.id_to_atom(a_orig_idx), + ) + ) if a.atomicnum == 7: # It's a nitrogen atom if n_atoms_atomicnum.count(6) == 2: # It's imidazole/pyrrole or similar - a_set.append(data(atom=a, atom_orig_idx=a_orig_idx, type='N', fgroup='imidazole/pyrrole', - restype=self.hetid, resnr=self.position, reschain=self.chain, - location='ligand', orig_atom=self.Mapper.id_to_atom(a_orig_idx))) + a_set.append( + data( + atom=a, + atom_orig_idx=a_orig_idx, + type="N", + fgroup="imidazole/pyrrole", + restype=self.hetid, + resnr=self.position, + reschain=self.chain, + location="ligand", + orig_atom=self.Mapper.id_to_atom(a_orig_idx), + ) + ) if a.atomicnum == 16: # It's a sulfur atom - if True in [n.IsAromatic() for n in n_atoms] and not a.OBAtom.IsAromatic(): # Thiolate - a_set.append(data(atom=a, atom_orig_idx=a_orig_idx, type='S', fgroup='thiolate', - restype=self.hetid, resnr=self.position, reschain=self.chain, - location='ligand', orig_atom=self.Mapper.id_to_atom(a_orig_idx))) + if ( + True in [n.IsAromatic() for n in n_atoms] + and not a.OBAtom.IsAromatic() + ): # Thiolate + a_set.append( + data( + atom=a, + atom_orig_idx=a_orig_idx, + type="S", + fgroup="thiolate", + restype=self.hetid, + resnr=self.position, + reschain=self.chain, + location="ligand", + orig_atom=self.Mapper.id_to_atom(a_orig_idx), + ) + ) if set(n_atoms_atomicnum) == {26}: # Sulfur in Iron sulfur cluster - a_set.append(data(atom=a, atom_orig_idx=a_orig_idx, type='S', fgroup='iron-sulfur.cluster', - restype=self.hetid, resnr=self.position, reschain=self.chain, - location='ligand', orig_atom=self.Mapper.id_to_atom(a_orig_idx))) + a_set.append( + data( + atom=a, + atom_orig_idx=a_orig_idx, + type="S", + fgroup="iron-sulfur.cluster", + restype=self.hetid, + resnr=self.position, + reschain=self.chain, + location="ligand", + orig_atom=self.Mapper.id_to_atom(a_orig_idx), + ) + ) return a_set @@ -1278,43 +2036,54 @@ class PDBComplex: """ def __init__(self): - self.interaction_sets = {} # Dictionary with site identifiers as keys and object as value + self.interaction_sets = ( + {} + ) # Dictionary with site identifiers as keys and object as value self.protcomplex = None self.filetype = None self.atoms = {} # Dictionary of Pybel atoms, accessible by their idx self.sourcefiles = {} self.information = {} - self.corrected_pdb = '' + self.corrected_pdb = "" self._output_path = tempfile.gettempdir() self.pymol_name = None self.modres = set() self.resis = [] self.altconf = [] # Atom idx of atoms with alternate conformations - self.covalent = [] # Covalent linkages between ligands and protein residues/other ligands + self.covalent = ( + [] + ) # Covalent linkages between ligands and protein residues/other ligands self.excluded = [] # Excluded ligands self.Mapper = Mapper() self.ligands = [] def __str__(self): - formatted_lig_names = [":".join([x.hetid, x.chain, str(x.position)]) for x in self.ligands] + formatted_lig_names = [ + ":".join([x.hetid, x.chain, str(x.position)]) for x in self.ligands + ] return "Protein structure %s with ligands:\n" % (self.pymol_name) + "\n".join( - [lig for lig in formatted_lig_names]) + [lig for lig in formatted_lig_names] + ) def load_pdb(self, pdbpath, as_string=False): """Loads a pdb file with protein AND ligand(s), separates and prepares them. If specified 'as_string', the input is a PDB string instead of a path.""" if as_string: - self.sourcefiles['pdbcomplex.original'] = None - self.sourcefiles['pdbcomplex'] = None - self.sourcefiles['pdbstring'] = pdbpath + self.sourcefiles["pdbcomplex.original"] = None + self.sourcefiles["pdbcomplex"] = None + self.sourcefiles["pdbstring"] = pdbpath else: - self.sourcefiles['pdbcomplex.original'] = pdbpath - self.sourcefiles['pdbcomplex'] = pdbpath - self.information['pdbfixes'] = False - pdbparser = PDBParser(pdbpath, as_string=as_string) # Parse PDB file to find errors and get additional data + self.sourcefiles["pdbcomplex.original"] = pdbpath + self.sourcefiles["pdbcomplex"] = pdbpath + self.information["pdbfixes"] = False + pdbparser = PDBParser( + pdbpath, as_string=as_string + ) # Parse PDB file to find errors and get additional data # #@todo Refactor and rename here self.Mapper.proteinmap = pdbparser.proteinmap - self.Mapper.reversed_proteinmap = {v: k for k, v in self.Mapper.proteinmap.items()} + self.Mapper.reversed_proteinmap = { + v: k for k, v in self.Mapper.proteinmap.items() + } self.modres = pdbparser.modres self.covalent = pdbparser.covalent self.altconf = pdbparser.altconformations @@ -1322,78 +2091,103 @@ class PDBComplex: if not config.PLUGIN_MODE: if pdbparser.num_fixed_lines > 0: - logger.info(f'{pdbparser.num_fixed_lines} lines automatically fixed in PDB input file') + logger.info( + f"{pdbparser.num_fixed_lines} lines automatically fixed in PDB input file" + ) # Save modified PDB file if not as_string: - basename = os.path.basename(pdbpath).split('.')[0] + basename = os.path.basename(pdbpath).split(".")[0] else: basename = "from_stdin" - pdbpath_fixed = tmpfile(prefix='plipfixed.' + basename + '_', direc=self.output_path) + pdbpath_fixed = tmpfile( + prefix="plipfixed." + basename + "_", direc=self.output_path + ) create_folder_if_not_exists(self.output_path) - self.sourcefiles['pdbcomplex'] = pdbpath_fixed - self.corrected_pdb = re.sub(r'[^\x00-\x7F]+', ' ', self.corrected_pdb) # Strip non-unicode chars - if not config.NOFIXFILE: # Only write to file if this option is not activated - with open(pdbpath_fixed, 'w') as f: + self.sourcefiles["pdbcomplex"] = pdbpath_fixed + self.corrected_pdb = re.sub( + r"[^\x00-\x7F]+", " ", self.corrected_pdb + ) # Strip non-unicode chars + if ( + not config.NOFIXFILE + ): # Only write to file if this option is not activated + with open(pdbpath_fixed, "w") as f: f.write(self.corrected_pdb) - self.information['pdbfixes'] = True + self.information["pdbfixes"] = True if not as_string: - self.sourcefiles['filename'] = os.path.basename(self.sourcefiles['pdbcomplex']) + self.sourcefiles["filename"] = os.path.basename( + self.sourcefiles["pdbcomplex"] + ) self.protcomplex, self.filetype = read_pdb(self.corrected_pdb, as_string=True) # Update the model in the Mapper class instance self.Mapper.original_structure = self.protcomplex.OBMol - logger.info('PDB structure successfully read') + logger.info("PDB structure successfully read") # Determine (temporary) PyMOL Name from Filename - self.pymol_name = pdbpath.split('/')[-1].split('.')[0] + '-Protein' + self.pymol_name = pdbpath.split("/")[-1].split(".")[0] + "-Protein" # Replace characters causing problems in PyMOL - self.pymol_name = self.pymol_name.replace(' ', '').replace('(', '').replace(')', '').replace('-', '_') + self.pymol_name = ( + self.pymol_name.replace(" ", "") + .replace("(", "") + .replace(")", "") + .replace("-", "_") + ) # But if possible, name it after PDBID in Header - if 'HEADER' in self.protcomplex.data: # If the PDB file has a proper header - potential_name = self.protcomplex.data['HEADER'][56:60].lower() - if extract_pdbid(potential_name) != 'UnknownProtein': + if "HEADER" in self.protcomplex.data: # If the PDB file has a proper header + potential_name = self.protcomplex.data["HEADER"][56:60].lower() + if extract_pdbid(potential_name) != "UnknownProtein": self.pymol_name = potential_name - logger.debug(f'PyMOL name set as: {self.pymol_name}') + logger.debug(f"PyMOL name set as: {self.pymol_name}") # Extract and prepare ligands - ligandfinder = LigandFinder(self.protcomplex, self.altconf, self.modres, self.covalent, self.Mapper) + ligandfinder = LigandFinder( + self.protcomplex, self.altconf, self.modres, self.covalent, self.Mapper + ) self.ligands = ligandfinder.ligands self.excluded = ligandfinder.excluded # decide whether to add polar hydrogens if not config.NOHYDRO: if not as_string: - basename = os.path.basename(pdbpath).split('.')[0] + basename = os.path.basename(pdbpath).split(".")[0] else: basename = "from_stdin" self.protcomplex.OBMol.AddPolarHydrogens() - output_path = os.path.join(self._output_path, f'{basename}_protonated.pdb') - self.protcomplex.write('pdb', output_path, overwrite=True) - logger.info(f'protonated structure written to {output_path}') + output_path = os.path.join(self._output_path, f"{basename}_protonated.pdb") + self.protcomplex.write("pdb", output_path, overwrite=True) + logger.info(f"protonated structure written to {output_path}") else: - logger.warning('no polar hydrogens will be assigned (make sure your structure contains hydrogens)') + logger.warning( + "no polar hydrogens will be assigned (make sure your structure contains hydrogens)" + ) for atm in self.protcomplex: self.atoms[atm.idx] = atm if len(self.excluded) != 0: - logger.info(f'excluded molecules as ligands: {self.excluded}') + logger.info(f"excluded molecules as ligands: {self.excluded}") if config.DNARECEPTOR: - self.resis = [obres for obres in pybel.ob.OBResidueIter( - self.protcomplex.OBMol) if obres.GetName() in config.DNA + config.RNA] + self.resis = [ + obres + for obres in pybel.ob.OBResidueIter(self.protcomplex.OBMol) + if obres.GetName() in config.DNA + config.RNA + ] else: - self.resis = [obres for obres in pybel.ob.OBResidueIter( - self.protcomplex.OBMol) if obres.GetResidueProperty(0)] + self.resis = [ + obres + for obres in pybel.ob.OBResidueIter(self.protcomplex.OBMol) + if obres.GetResidueProperty(0) + ] num_ligs = len(self.ligands) if num_ligs == 1: - logger.info('analyzing one ligand') + logger.info("analyzing one ligand") elif num_ligs > 1: - logger.info(f'analyzing {num_ligs} ligands') + logger.info(f"analyzing {num_ligs} ligands") else: - logger.info(f'structure contains no ligands') + logger.info(f"structure contains no ligands") def analyze(self): """Triggers analysis of all complexes in structure""" @@ -1405,42 +2199,66 @@ class PDBComplex: single_sites = [] for member in ligand.members: - single_sites.append(':'.join([str(x) for x in member])) - site = ' + '.join(single_sites) - site = site if not len(site) > 20 else site[:20] + '...' - longname = ligand.longname if not len(ligand.longname) > 20 else ligand.longname[:20] + '...' - ligtype = 'unspecified type' if ligand.type == 'UNSPECIFIED' else ligand.type - ligtext = f'{longname} [{ligtype}] -- {site}' - logger.info(f'processing ligand {ligtext}') - if ligtype == 'PEPTIDE': - logger.info(f'chain {ligand.chain} will be processed in [PEPTIDE / INTER-CHAIN] mode') - if ligtype == 'INTRA': - logger.info(f'chain {ligand.chain} will be processed in [INTRA-CHAIN] mode') - any_in_biolip = len(set([x[0] for x in ligand.members]).intersection(config.biolip_list)) != 0 - - if ligtype not in ['POLYMER', 'DNA', 'ION', 'DNA+ION', 'RNA+ION', 'SMALLMOLECULE+ION'] and any_in_biolip: - logger.info('may be biologically irrelevant') + single_sites.append(":".join([str(x) for x in member])) + site = " + ".join(single_sites) + site = site if not len(site) > 20 else site[:20] + "..." + longname = ( + ligand.longname + if not len(ligand.longname) > 20 + else ligand.longname[:20] + "..." + ) + ligtype = "unspecified type" if ligand.type == "UNSPECIFIED" else ligand.type + ligtext = f"{longname} [{ligtype}] -- {site}" + logger.info(f"processing ligand {ligtext}") + if ligtype == "PEPTIDE": + logger.info( + f"chain {ligand.chain} will be processed in [PEPTIDE / INTER-CHAIN] mode" + ) + if ligtype == "INTRA": + logger.info(f"chain {ligand.chain} will be processed in [INTRA-CHAIN] mode") + any_in_biolip = ( + len(set([x[0] for x in ligand.members]).intersection(config.biolip_list)) + != 0 + ) + + if ( + ligtype + not in ["POLYMER", "DNA", "ION", "DNA+ION", "RNA+ION", "SMALLMOLECULE+ION"] + and any_in_biolip + ): + logger.info("may be biologically irrelevant") lig_obj = Ligand(self, ligand) cutoff = lig_obj.max_dist_to_center + config.BS_DIST bs_res = self.extract_bs(cutoff, lig_obj.centroid, self.resis) # Get a list of all atoms belonging to the binding site, search by idx - bs_atoms = [self.atoms[idx] for idx in [i for i in self.atoms.keys() - if self.atoms[i].OBAtom.GetResidue().GetIdx() in bs_res] - if idx in self.Mapper.proteinmap and self.Mapper.mapid(idx, mtype='protein') not in self.altconf] - if ligand.type == 'PEPTIDE': + bs_atoms = [ + self.atoms[idx] + for idx in [ + i + for i in self.atoms.keys() + if self.atoms[i].OBAtom.GetResidue().GetIdx() in bs_res + ] + if idx in self.Mapper.proteinmap + and self.Mapper.mapid(idx, mtype="protein") not in self.altconf + ] + if ligand.type == "PEPTIDE": # If peptide, don't consider the peptide chain as part of the protein binding site - bs_atoms = [a for a in bs_atoms if a.OBAtom.GetResidue().GetChain() != lig_obj.chain] - if ligand.type == 'INTRA': + bs_atoms = [ + a for a in bs_atoms if a.OBAtom.GetResidue().GetChain() != lig_obj.chain + ] + if ligand.type == "INTRA": # Interactions within the chain - bs_atoms = [a for a in bs_atoms if a.OBAtom.GetResidue().GetChain() == lig_obj.chain] + bs_atoms = [ + a for a in bs_atoms if a.OBAtom.GetResidue().GetChain() == lig_obj.chain + ] bs_atoms_refined = [] # Create hash with BSRES -> (MINDIST_TO_LIG, AA_TYPE) # and refine binding site atom selection with exact threshold min_dist = {} for r in bs_atoms: - bs_res_id = ''.join([str(whichresnumber(r)), whichchain(r)]) + bs_res_id = "".join([str(whichresnumber(r)), whichchain(r)]) for l in ligand.mol.atoms: distance = euclidean3d(r.coords, l.coords) if bs_res_id not in min_dist: @@ -1450,25 +2268,40 @@ class PDBComplex: if distance <= config.BS_DIST and r not in bs_atoms_refined: bs_atoms_refined.append(r) num_bs_atoms = len(bs_atoms_refined) - logger.info(f'binding site atoms in vicinity ({config.BS_DIST} A max. dist: {num_bs_atoms})') - - bs_obj = BindingSite(bs_atoms_refined, self.protcomplex, self, self.altconf, min_dist, self.Mapper) + logger.info( + f"binding site atoms in vicinity ({config.BS_DIST} A max. dist: {num_bs_atoms})" + ) + + bs_obj = BindingSite( + bs_atoms_refined, + self.protcomplex, + self, + self.altconf, + min_dist, + self.Mapper, + ) pli_obj = PLInteraction(lig_obj, bs_obj, self) self.interaction_sets[ligand.mol.title] = pli_obj def extract_bs(self, cutoff, ligcentroid, resis): """Return list of ids from residues belonging to the binding site""" - return [obres.GetIdx() for obres in resis if self.res_belongs_to_bs(obres, cutoff, ligcentroid)] + return [ + obres.GetIdx() + for obres in resis + if self.res_belongs_to_bs(obres, cutoff, ligcentroid) + ] def res_belongs_to_bs(self, res, cutoff, ligcentroid): """Check for each residue if its centroid is within a certain distance to the ligand centroid. Additionally checks if a residue belongs to a chain restricted by the user (e.g. by defining a peptide chain)""" - rescentroid = centroid([(atm.x(), atm.y(), atm.z()) for atm in pybel.ob.OBResidueAtomIter(res)]) + rescentroid = centroid( + [(atm.x(), atm.y(), atm.z()) for atm in pybel.ob.OBResidueAtomIter(res)] + ) # Check geometry near_enough = True if euclidean3d(rescentroid, ligcentroid) < cutoff else False # Check chain membership restricted_chain = True if res.GetChain() in config.PEPTIDES else False - return (near_enough and not restricted_chain) + return near_enough and not restricted_chain def get_atom(self, idx): return self.atoms[idx] -- cgit v1.2.3