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authorNavan Chauhan <navanchauhan@gmail.com>2020-07-02 20:48:33 +0530
committerNavan Chauhan <navanchauhan@gmail.com>2020-07-02 20:48:33 +0530
commit4be08f7bdd77991e9e453c1cda863c3f20c338d5 (patch)
tree083e8e91622221185a28fd50754abc2f86b1df43 /plip/exchange
initial commit
Diffstat (limited to 'plip/exchange')
-rw-r--r--plip/exchange/__init__.py0
-rw-r--r--plip/exchange/json.py1
-rw-r--r--plip/exchange/report.py497
-rw-r--r--plip/exchange/webservices.py54
-rw-r--r--plip/exchange/xml.py285
5 files changed, 837 insertions, 0 deletions
diff --git a/plip/exchange/__init__.py b/plip/exchange/__init__.py
new file mode 100644
index 0000000..e69de29
--- /dev/null
+++ b/plip/exchange/__init__.py
diff --git a/plip/exchange/json.py b/plip/exchange/json.py
new file mode 100644
index 0000000..5c7ad5c
--- /dev/null
+++ b/plip/exchange/json.py
@@ -0,0 +1 @@
+# place holder for module to add Json support \ No newline at end of file
diff --git a/plip/exchange/report.py b/plip/exchange/report.py
new file mode 100644
index 0000000..a559bf8
--- /dev/null
+++ b/plip/exchange/report.py
@@ -0,0 +1,497 @@
+import time
+from operator import itemgetter
+
+import lxml.etree as et
+
+from plip.basic import config
+from plip.basic.config import __version__
+from plip.structure.preparation import PDBComplex
+
+
+class StructureReport:
+ """Creates reports (xml or txt) for one structure/"""
+
+ def __init__(self, mol: PDBComplex, outputprefix: str = 'report'):
+ self.mol = mol
+ self.excluded = self.mol.excluded
+ self.xmlreport = self.construct_xml_tree()
+ self.txtreport = self.construct_txt_file()
+ self.get_bindingsite_data()
+ self.outpath = mol.output_path
+ self.outputprefix = outputprefix
+
+ def construct_xml_tree(self):
+ """Construct the basic XML tree"""
+ report = et.Element('report')
+ plipversion = et.SubElement(report, 'plipversion')
+ plipversion.text = __version__
+ date_of_creation = et.SubElement(report, 'date_of_creation')
+ date_of_creation.text = time.strftime("%Y/%m/%d")
+ citation_information = et.SubElement(report, 'citation_information')
+ citation_information.text = "Salentin,S. et al. PLIP: fully automated protein-ligand interaction profiler. " \
+ "Nucl. Acids Res. (1 July 2015) 43 (W1): W443-W447. doi: 10.1093/nar/gkv315"
+
+ maintainer_information = et.SubElement(report, 'maintainer_information')
+ maintainer_information.text = config.__maintainer__
+ mode = et.SubElement(report, 'mode')
+ if config.DNARECEPTOR:
+ mode.text = 'dna_receptor'
+ else:
+ mode.text = 'default'
+ pdbid = et.SubElement(report, 'pdbid')
+ pdbid.text = self.mol.pymol_name.upper()
+ filetype = et.SubElement(report, 'filetype')
+ filetype.text = self.mol.filetype.upper()
+ pdbfile = et.SubElement(report, 'pdbfile')
+ pdbfile.text = self.mol.sourcefiles['pdbcomplex']
+ pdbfixes = et.SubElement(report, 'pdbfixes')
+ pdbfixes.text = str(self.mol.information['pdbfixes'])
+ filename = et.SubElement(report, 'filename')
+ filename.text = str(self.mol.sourcefiles.get('filename') or None)
+ exligs = et.SubElement(report, 'excluded_ligands')
+ for i, exlig in enumerate(self.excluded):
+ e = et.SubElement(exligs, 'excluded_ligand', id=str(i + 1))
+ e.text = exlig
+ covalent = et.SubElement(report, 'covlinkages')
+ for i, covlinkage in enumerate(self.mol.covalent):
+ e = et.SubElement(covalent, 'covlinkage', id=str(i + 1))
+ f1 = et.SubElement(e, 'res1')
+ f2 = et.SubElement(e, 'res2')
+ f1.text = ":".join([covlinkage.id1, covlinkage.chain1, str(covlinkage.pos1)])
+ f2.text = ":".join([covlinkage.id2, covlinkage.chain2, str(covlinkage.pos2)])
+ return report
+
+ def construct_txt_file(self):
+ """Construct the header of the txt file"""
+ textlines = ['Prediction of noncovalent interactions for PDB structure %s' % self.mol.pymol_name.upper(), ]
+ textlines.append("=" * len(textlines[0]))
+ textlines.append('Created on %s using PLIP v%s\n' % (time.strftime("%Y/%m/%d"), __version__))
+ textlines.append('If you are using PLIP in your work, please cite:')
+ textlines.append('Salentin,S. et al. PLIP: fully automated protein-ligand interaction profiler.')
+ textlines.append('Nucl. Acids Res. (1 July 2015) 43 (W1): W443-W447. doi: 10.1093/nar/gkv315\n')
+ if len(self.excluded) != 0:
+ textlines.append('Excluded molecules as ligands: %s\n' % ','.join([lig for lig in self.excluded]))
+ if config.DNARECEPTOR:
+ textlines.append('DNA/RNA in structure was chosen as the receptor part.\n')
+ return textlines
+
+ def get_bindingsite_data(self):
+ """Get the additional data for the binding sites"""
+ for i, site in enumerate(sorted(self.mol.interaction_sets)):
+ s = self.mol.interaction_sets[site]
+ bindingsite = BindingSiteReport(s).generate_xml()
+ bindingsite.set('id', str(i + 1))
+ bindingsite.set('has_interactions', 'False')
+ self.xmlreport.insert(i + 1, bindingsite)
+ for itype in BindingSiteReport(s).generate_txt():
+ self.txtreport.append(itype)
+ if not s.no_interactions:
+ bindingsite.set('has_interactions', 'True')
+ else:
+ self.txtreport.append('No interactions detected.')
+
+ def write_xml(self, as_string=False):
+ """Write the XML report"""
+ if not as_string:
+ et.ElementTree(self.xmlreport).write('{}/{}.xml'.format(self.outpath, self.outputprefix), pretty_print=True,
+ xml_declaration=True)
+ else:
+ output = et.tostring(self.xmlreport, pretty_print=True)
+ if config.RAWSTRING:
+ output = repr(output)
+ print(output)
+
+ def write_txt(self, as_string=False):
+ """Write the TXT report"""
+ if not as_string:
+ with open('{}/{}.txt'.format(self.outpath, self.outputprefix), 'w') as f:
+ [f.write(textline + '\n') for textline in self.txtreport]
+ else:
+ output = '\n'.join(self.txtreport)
+ if config.RAWSTRING:
+ output = repr(output)
+ print(output)
+
+
+class BindingSiteReport:
+ """Gather report data and generate reports for one binding site in different formats."""
+
+ def __init__(self, plcomplex):
+
+ ################
+ # GENERAL DATA #
+ ################
+
+ self.complex = plcomplex
+ self.ligand = self.complex.ligand
+ self.bindingsite = self.complex.bindingsite
+ self.output_path = self.complex.output_path
+ self.bsid = ':'.join([self.ligand.hetid, self.ligand.chain, str(self.ligand.position)])
+ self.longname = self.ligand.longname
+ self.ligtype = self.ligand.type
+ self.bs_res = self.bindingsite.bs_res
+ self.min_dist = self.bindingsite.min_dist
+ self.bs_res_interacting = self.complex.interacting_res
+ self.pdbid = self.complex.pdbid.upper()
+ self.lig_members = self.complex.lig_members
+ self.interacting_chains = self.complex.interacting_chains
+
+ ############################
+ # HYDROPHOBIC INTERACTIONS #
+ ############################
+
+ self.hydrophobic_features = (
+ 'RESNR', 'RESTYPE', 'RESCHAIN', 'RESNR_LIG', 'RESTYPE_LIG', 'RESCHAIN_LIG', 'DIST', 'LIGCARBONIDX',
+ 'PROTCARBONIDX', 'LIGCOO',
+ 'PROTCOO')
+ self.hydrophobic_info = []
+ for hydroph in self.complex.hydrophobic_contacts:
+ self.hydrophobic_info.append((hydroph.resnr, hydroph.restype, hydroph.reschain, hydroph.resnr_l,
+ hydroph.restype_l, hydroph.reschain_l, '%.2f' % hydroph.distance,
+ hydroph.ligatom_orig_idx, hydroph.bsatom_orig_idx, hydroph.ligatom.coords,
+ hydroph.bsatom.coords))
+
+ ##################
+ # HYDROGEN BONDS #
+ ##################
+
+ self.hbond_features = (
+ 'RESNR', 'RESTYPE', 'RESCHAIN', 'RESNR_LIG', 'RESTYPE_LIG', 'RESCHAIN_LIG', 'SIDECHAIN', 'DIST_H-A',
+ 'DIST_D-A',
+ 'DON_ANGLE',
+ 'PROTISDON', 'DONORIDX', 'DONORTYPE', 'ACCEPTORIDX', 'ACCEPTORTYPE', 'LIGCOO', 'PROTCOO')
+ self.hbond_info = []
+ for hbond in self.complex.hbonds_pdon + self.complex.hbonds_ldon:
+ ligatom, protatom = (hbond.a, hbond.d) if hbond.protisdon else (hbond.d, hbond.a)
+ self.hbond_info.append((hbond.resnr, hbond.restype, hbond.reschain, hbond.resnr_l, hbond.restype_l,
+ hbond.reschain_l, hbond.sidechain,
+ '%.2f' % hbond.distance_ah, '%.2f' % hbond.distance_ad, '%.2f' % hbond.angle,
+ hbond.protisdon, hbond.d_orig_idx, hbond.dtype, hbond.a_orig_idx, hbond.atype,
+ ligatom.coords, protatom.coords))
+
+ #################
+ # WATER-BRIDGES #
+ #################
+
+ self.waterbridge_features = (
+ 'RESNR', 'RESTYPE', 'RESCHAIN', 'RESNR_LIG', 'RESTYPE_LIG', 'RESCHAIN_LIG', 'DIST_A-W', 'DIST_D-W',
+ 'DON_ANGLE',
+ 'WATER_ANGLE',
+ 'PROTISDON', 'DONOR_IDX', 'DONORTYPE', 'ACCEPTOR_IDX', 'ACCEPTORTYPE', 'WATER_IDX',
+ 'LIGCOO', 'PROTCOO', 'WATERCOO')
+ # The coordinate format is an exception here, since the interaction is not only between ligand and protein
+ self.waterbridge_info = []
+ for wbridge in self.complex.water_bridges:
+ lig, prot = (wbridge.a, wbridge.d) if wbridge.protisdon else (wbridge.d, wbridge.a)
+ self.waterbridge_info.append((wbridge.resnr, wbridge.restype, wbridge.reschain, wbridge.resnr_l,
+ wbridge.restype_l, wbridge.reschain_l,
+ '%.2f' % wbridge.distance_aw, '%.2f' % wbridge.distance_dw,
+ '%.2f' % wbridge.d_angle, '%.2f' % wbridge.w_angle, wbridge.protisdon,
+ wbridge.d_orig_idx, wbridge.dtype, wbridge.a_orig_idx, wbridge.atype,
+ wbridge.water_orig_idx, lig.coords, prot.coords, wbridge.water.coords))
+
+ ################
+ # SALT BRIDGES #
+ ################
+
+ self.saltbridge_features = (
+ 'RESNR', 'RESTYPE', 'RESCHAIN', 'RESNR_LIG', 'RESTYPE_LIG', 'RESCHAIN_LIG', 'DIST', 'PROTISPOS',
+ 'LIG_GROUP',
+ 'LIG_IDX_LIST',
+ 'LIGCOO', 'PROTCOO')
+ self.saltbridge_info = []
+ for sb in self.complex.saltbridge_lneg + self.complex.saltbridge_pneg:
+ if sb.protispos:
+ group, ids = sb.negative.fgroup, [str(x) for x in sb.negative.atoms_orig_idx]
+ self.saltbridge_info.append((sb.resnr, sb.restype, sb.reschain, sb.resnr_l, sb.restype_l, sb.reschain_l,
+ '%.2f' % sb.distance, sb.protispos,
+ group.capitalize(), ",".join(ids),
+ tuple(sb.negative.center), tuple(sb.positive.center)))
+ else:
+ group, ids = sb.positive.fgroup, [str(x) for x in sb.positive.atoms_orig_idx]
+ self.saltbridge_info.append((sb.resnr, sb.restype, sb.reschain, sb.resnr_l, sb.restype_l, sb.reschain_l,
+ '%.2f' % sb.distance, sb.protispos,
+ group.capitalize(), ",".join(ids),
+ tuple(sb.positive.center), tuple(sb.negative.center)))
+
+ ###############
+ # PI-STACKING #
+ ###############
+
+ self.pistacking_features = (
+ 'RESNR', 'RESTYPE', 'RESCHAIN', 'RESNR_LIG', 'RESTYPE_LIG', 'RESCHAIN_LIG', 'CENTDIST', 'ANGLE', 'OFFSET',
+ 'TYPE',
+ 'LIG_IDX_LIST', 'LIGCOO', 'PROTCOO')
+ self.pistacking_info = []
+ for stack in self.complex.pistacking:
+ ids = [str(x) for x in stack.ligandring.atoms_orig_idx]
+ self.pistacking_info.append((stack.resnr, stack.restype, stack.reschain, stack.resnr_l, stack.restype_l,
+ stack.reschain_l, '%.2f' % stack.distance,
+ '%.2f' % stack.angle, '%.2f' % stack.offset, stack.type, ",".join(ids),
+ tuple(stack.ligandring.center), tuple(stack.proteinring.center)))
+
+ ##########################
+ # PI-CATION INTERACTIONS #
+ ##########################
+
+ self.pication_features = (
+ 'RESNR', 'RESTYPE', 'RESCHAIN', 'RESNR_LIG', 'RESTYPE_LIG', 'RESCHAIN_LIG', 'DIST', 'OFFSET', 'PROTCHARGED',
+ 'LIG_GROUP',
+ 'LIG_IDX_LIST', 'LIGCOO', 'PROTCOO')
+ self.pication_info = []
+ for picat in self.complex.pication_laro + self.complex.pication_paro:
+ if picat.protcharged:
+ ids = [str(x) for x in picat.ring.atoms_orig_idx]
+ group = 'Aromatic'
+ self.pication_info.append((picat.resnr, picat.restype, picat.reschain, picat.resnr_l, picat.restype_l,
+ picat.reschain_l, '%.2f' % picat.distance,
+ '%.2f' % picat.offset, picat.protcharged, group, ",".join(ids),
+ tuple(picat.ring.center), tuple(picat.charge.center)))
+ else:
+ ids = [str(x) for x in picat.charge.atoms_orig_idx]
+ group = picat.charge.fgroup
+ self.pication_info.append((picat.resnr, picat.restype, picat.reschain, picat.resnr_l, picat.restype_l,
+ picat.reschain_l, '%.2f' % picat.distance,
+ '%.2f' % picat.offset, picat.protcharged, group, ",".join(ids),
+ tuple(picat.charge.center), tuple(picat.ring.center)))
+
+ #################
+ # HALOGEN BONDS #
+ #################
+
+ self.halogen_features = (
+ 'RESNR', 'RESTYPE', 'RESCHAIN', 'RESNR_LIG', 'RESTYPE_LIG', 'RESCHAIN_LIG', 'SIDECHAIN', 'DIST',
+ 'DON_ANGLE',
+ 'ACC_ANGLE',
+ 'DON_IDX', 'DONORTYPE', 'ACC_IDX', 'ACCEPTORTYPE', 'LIGCOO', 'PROTCOO')
+ self.halogen_info = []
+ for halogen in self.complex.halogen_bonds:
+ self.halogen_info.append((halogen.resnr, halogen.restype, halogen.reschain, halogen.resnr_l,
+ halogen.restype_l, halogen.reschain_l, halogen.sidechain,
+ '%.2f' % halogen.distance, '%.2f' % halogen.don_angle, '%.2f' % halogen.acc_angle,
+ halogen.don_orig_idx, halogen.donortype,
+ halogen.acc_orig_idx, halogen.acctype,
+ halogen.acc.o.coords, halogen.don.x.coords))
+
+ ###################
+ # METAL COMPLEXES #
+ ###################
+
+ self.metal_features = (
+ 'RESNR', 'RESTYPE', 'RESCHAIN', 'RESNR_LIG', 'RESTYPE_LIG', 'RESCHAIN_LIG', 'METAL_IDX', 'METAL_TYPE',
+ 'TARGET_IDX', 'TARGET_TYPE',
+ 'COORDINATION', 'DIST', 'LOCATION', 'RMS', 'GEOMETRY', 'COMPLEXNUM', 'METALCOO',
+ 'TARGETCOO')
+ self.metal_info = []
+ # Coordinate format here is non-standard since the interaction partner can be either ligand or protein
+ for m in self.complex.metal_complexes:
+ self.metal_info.append(
+ (m.resnr, m.restype, m.reschain, m.resnr_l, m.restype_l, m.reschain_l, m.metal_orig_idx, m.metal_type,
+ m.target_orig_idx, m.target_type, m.coordination_num, '%.2f' % m.distance,
+ m.location, '%.2f' % m.rms, m.geometry, str(m.complexnum), m.metal.coords,
+ m.target.atom.coords))
+
+ def write_section(self, name, features, info, f):
+ """Provides formatting for one section (e.g. hydrogen bonds)"""
+ if not len(info) == 0:
+ f.write('\n\n### %s ###\n' % name)
+ f.write('%s\n' % '\t'.join(features))
+ for line in info:
+ f.write('%s\n' % '\t'.join(map(str, line)))
+
+ def rst_table(self, array):
+ """Given an array, the function formats and returns and table in rST format."""
+ # Determine cell width for each column
+ cell_dict = {}
+ for i, row in enumerate(array):
+ for j, val in enumerate(row):
+ if j not in cell_dict:
+ cell_dict[j] = []
+ cell_dict[j].append(val)
+ for item in cell_dict:
+ cell_dict[item] = max([len(x) for x in cell_dict[item]]) + 1 # Contains adapted width for each column
+
+ # Format top line
+ num_cols = len(array[0])
+ form = '+'
+ for col in range(num_cols):
+ form += (cell_dict[col] + 1) * '-'
+ form += '+'
+ form += '\n'
+
+ # Format values
+ for i, row in enumerate(array):
+ form += '| '
+ for j, val in enumerate(row):
+ cell_width = cell_dict[j]
+ form += str(val) + (cell_width - len(val)) * ' ' + '| '
+ form.rstrip()
+ form += '\n'
+
+ # Seperation lines
+ form += '+'
+ if i == 0:
+ sign = '='
+ else:
+ sign = '-'
+ for col in range(num_cols):
+ form += (cell_dict[col] + 1) * sign
+ form += '+'
+ form += '\n'
+ return form
+
+ def generate_txt(self):
+ """Generates an flat text report for a single binding site"""
+
+ txt = []
+ titletext = '%s (%s) - %s' % (self.bsid, self.longname, self.ligtype)
+ txt.append(titletext)
+ for i, member in enumerate(self.lig_members[1:]):
+ txt.append(' + %s' % ":".join(str(element) for element in member))
+ txt.append("-" * len(titletext))
+ txt.append("Interacting chain(s): %s\n" % ','.join([chain for chain in self.interacting_chains]))
+ for section in [['Hydrophobic Interactions', self.hydrophobic_features, self.hydrophobic_info],
+ ['Hydrogen Bonds', self.hbond_features, self.hbond_info],
+ ['Water Bridges', self.waterbridge_features, self.waterbridge_info],
+ ['Salt Bridges', self.saltbridge_features, self.saltbridge_info],
+ ['pi-Stacking', self.pistacking_features, self.pistacking_info],
+ ['pi-Cation Interactions', self.pication_features, self.pication_info],
+ ['Halogen Bonds', self.halogen_features, self.halogen_info],
+ ['Metal Complexes', self.metal_features, self.metal_info]]:
+ iname, features, interaction_information = section
+ # Sort results first by res number, then by distance and finally ligand coordinates to get a unique order
+ interaction_information = sorted(interaction_information, key=itemgetter(0, 2, -2))
+ if not len(interaction_information) == 0:
+
+ txt.append('\n**%s**' % iname)
+ table = [features, ]
+ for single_contact in interaction_information:
+ values = []
+ for x in single_contact:
+ if type(x) == str:
+ values.append(x)
+ elif type(x) == tuple and len(x) == 3: # Coordinates
+ values.append("%.3f, %.3f, %.3f" % x)
+ else:
+ values.append(str(x))
+ table.append(values)
+ txt.append(self.rst_table(table))
+ txt.append('\n')
+ return txt
+
+ def generate_xml(self):
+ """Generates an XML-formatted report for a single binding site"""
+ report = et.Element('bindingsite')
+ identifiers = et.SubElement(report, 'identifiers')
+ longname = et.SubElement(identifiers, 'longname')
+ ligtype = et.SubElement(identifiers, 'ligtype')
+ hetid = et.SubElement(identifiers, 'hetid')
+ chain = et.SubElement(identifiers, 'chain')
+ position = et.SubElement(identifiers, 'position')
+ composite = et.SubElement(identifiers, 'composite')
+ members = et.SubElement(identifiers, 'members')
+ smiles = et.SubElement(identifiers, 'smiles')
+ inchikey = et.SubElement(identifiers, 'inchikey')
+
+ # Ligand properties. Number of (unpaired) functional atoms and rings.
+ lig_properties = et.SubElement(report, 'lig_properties')
+ num_heavy_atoms = et.SubElement(lig_properties, 'num_heavy_atoms')
+ num_hbd = et.SubElement(lig_properties, 'num_hbd')
+ num_hbd.text = str(self.ligand.num_hbd)
+ num_unpaired_hbd = et.SubElement(lig_properties, 'num_unpaired_hbd')
+ num_unpaired_hbd.text = str(self.complex.num_unpaired_hbd)
+ num_hba = et.SubElement(lig_properties, 'num_hba')
+ num_hba.text = str(self.ligand.num_hba)
+ num_unpaired_hba = et.SubElement(lig_properties, 'num_unpaired_hba')
+ num_unpaired_hba.text = str(self.complex.num_unpaired_hba)
+ num_hal = et.SubElement(lig_properties, 'num_hal')
+ num_hal.text = str(self.ligand.num_hal)
+ num_unpaired_hal = et.SubElement(lig_properties, 'num_unpaired_hal')
+ num_unpaired_hal.text = str(self.complex.num_unpaired_hal)
+ num_aromatic_rings = et.SubElement(lig_properties, 'num_aromatic_rings')
+ num_aromatic_rings.text = str(self.ligand.num_rings)
+ num_rot_bonds = et.SubElement(lig_properties, 'num_rotatable_bonds')
+ num_rot_bonds.text = str(self.ligand.num_rot_bonds)
+ molweight = et.SubElement(lig_properties, 'molweight')
+ molweight.text = str(self.ligand.molweight)
+ logp = et.SubElement(lig_properties, 'logp')
+ logp.text = str(self.ligand.logp)
+
+ ichains = et.SubElement(report, 'interacting_chains')
+ bsresidues = et.SubElement(report, 'bs_residues')
+ for i, ichain in enumerate(self.interacting_chains):
+ c = et.SubElement(ichains, 'interacting_chain', id=str(i + 1))
+ c.text = ichain
+ for i, bsres in enumerate(self.bs_res):
+ contact = 'True' if bsres in self.bs_res_interacting else 'False'
+ distance = '%.1f' % self.min_dist[bsres][0]
+ aatype = self.min_dist[bsres][1]
+ c = et.SubElement(bsresidues, 'bs_residue', id=str(i + 1), contact=contact, min_dist=distance, aa=aatype)
+ c.text = bsres
+ hetid.text, chain.text, position.text = self.ligand.hetid, self.ligand.chain, str(self.ligand.position)
+ composite.text = 'True' if len(self.lig_members) > 1 else 'False'
+ longname.text = self.longname
+ ligtype.text = self.ligtype
+ smiles.text = self.ligand.smiles
+ inchikey.text = self.ligand.inchikey
+ num_heavy_atoms.text = str(self.ligand.heavy_atoms) # Number of heavy atoms in ligand
+ for i, member in enumerate(self.lig_members):
+ bsid = ":".join(str(element) for element in member)
+ m = et.SubElement(members, 'member', id=str(i + 1))
+ m.text = bsid
+ interactions = et.SubElement(report, 'interactions')
+
+ def format_interactions(element_name, features, interaction_information):
+ """Returns a formatted element with interaction information."""
+ interaction = et.Element(element_name)
+ # Sort results first by res number, then by distance and finally ligand coordinates to get a unique order
+ interaction_information = sorted(interaction_information, key=itemgetter(0, 2, -2))
+ for j, single_contact in enumerate(interaction_information):
+ if not element_name == 'metal_complexes':
+ new_contact = et.SubElement(interaction, element_name[:-1], id=str(j + 1))
+ else: # Metal Complex[es]
+ new_contact = et.SubElement(interaction, element_name[:-2], id=str(j + 1))
+ for i, feature in enumerate(single_contact):
+ # Just assign the value unless it's an atom list, use subelements in this case
+ if features[i] == 'LIG_IDX_LIST':
+ feat = et.SubElement(new_contact, features[i].lower())
+ for k, atm_idx in enumerate(feature.split(',')):
+ idx = et.SubElement(feat, 'idx', id=str(k + 1))
+ idx.text = str(atm_idx)
+ elif features[i].endswith('COO'):
+ feat = et.SubElement(new_contact, features[i].lower())
+ xc, yc, zc = feature
+ xcoo = et.SubElement(feat, 'x')
+ xcoo.text = '%.3f' % xc
+ ycoo = et.SubElement(feat, 'y')
+ ycoo.text = '%.3f' % yc
+ zcoo = et.SubElement(feat, 'z')
+ zcoo.text = '%.3f' % zc
+ else:
+ feat = et.SubElement(new_contact, features[i].lower())
+ feat.text = str(feature)
+ return interaction
+
+ interactions.append(format_interactions('hydrophobic_interactions', self.hydrophobic_features,
+ self.hydrophobic_info))
+ interactions.append(format_interactions('hydrogen_bonds', self.hbond_features, self.hbond_info))
+ interactions.append(format_interactions('water_bridges', self.waterbridge_features, self.waterbridge_info))
+ interactions.append(format_interactions('salt_bridges', self.saltbridge_features, self.saltbridge_info))
+ interactions.append(format_interactions('pi_stacks', self.pistacking_features, self.pistacking_info))
+ interactions.append(format_interactions('pi_cation_interactions', self.pication_features, self.pication_info))
+ interactions.append(format_interactions('halogen_bonds', self.halogen_features, self.halogen_info))
+ interactions.append(format_interactions('metal_complexes', self.metal_features, self.metal_info))
+
+ # Mappings
+ mappings = et.SubElement(report, 'mappings')
+ smiles_to_pdb = et.SubElement(mappings, 'smiles_to_pdb') # SMILES numbering to PDB file numbering (atoms)
+ bsid = ':'.join([self.ligand.hetid, self.ligand.chain, str(self.ligand.position)])
+ if self.ligand.atomorder is not None:
+ smiles_to_pdb_map = [(key, self.ligand.Mapper.mapid(self.ligand.can_to_pdb[key],
+ mtype='protein', bsid=bsid)) for key in
+ self.ligand.can_to_pdb]
+ smiles_to_pdb.text = ','.join([str(mapping[0]) + ':' + str(mapping[1]) for mapping in smiles_to_pdb_map])
+ else:
+ smiles_to_pdb.text = ''
+
+ return report
diff --git a/plip/exchange/webservices.py b/plip/exchange/webservices.py
new file mode 100644
index 0000000..0c8cd3e
--- /dev/null
+++ b/plip/exchange/webservices.py
@@ -0,0 +1,54 @@
+import sys
+from urllib.error import HTTPError
+from urllib.request import urlopen
+
+import lxml.etree as et
+
+from plip.basic import logger
+
+logger = logger.get_logger()
+
+
+def check_pdb_status(pdbid):
+ """Returns the status and up-to-date entry in the PDB for a given PDB ID"""
+ url = 'http://www.rcsb.org/pdb/rest/idStatus?structureId=%s' % pdbid
+ xmlf = urlopen(url)
+ xml = et.parse(xmlf)
+ xmlf.close()
+ status = None
+ current_pdbid = pdbid
+ for df in xml.xpath('//record'):
+ status = df.attrib['status'] # Status of an entry can be either 'UNKWOWN', 'OBSOLETE', or 'CURRENT'
+ if status == 'OBSOLETE':
+ current_pdbid = df.attrib['replacedBy'] # Contains the up-to-date PDB ID for obsolete entries
+ return [status, current_pdbid.lower()]
+
+
+def fetch_pdb(pdbid):
+ """Get the newest entry from the RCSB server for the given PDB ID. Exits with '1' if PDB ID is invalid."""
+ pdbid = pdbid.lower()
+ logger.info(f'checking status of PDB-ID {pdbid}')
+ state, current_entry = check_pdb_status(pdbid) # Get state and current PDB ID
+
+ if state == 'OBSOLETE':
+ logger.info(f'entry is obsolete, getting {current_entry} instead')
+ elif state == 'CURRENT':
+ logger.info('entry is up-to-date')
+ elif state == 'UNKNOWN':
+ logger.error('invalid PDB-ID (entry does not exist on PDB server)')
+ sys.exit(1)
+ logger.info('downloading file from PDB')
+ # get URL for current entry
+ # @todo needs update to react properly on response codes of RCSB servers
+ pdburl = f'http://www.rcsb.org/pdb/files/{current_entry}.pdb'
+ try:
+ pdbfile = urlopen(pdburl).read().decode()
+ # If no PDB file is available, a text is now shown with "We're sorry, but ..."
+ # Could previously be distinguished by an HTTP error
+ if 'sorry' in pdbfile:
+ logger.error('no file in PDB format available from wwPDB for the given PDB ID.')
+ sys.exit(1)
+ except HTTPError:
+ logger.error('no file in PDB format available from wwPDB for the given PDB ID')
+ sys.exit(1)
+ return [pdbfile, current_entry]
diff --git a/plip/exchange/xml.py b/plip/exchange/xml.py
new file mode 100644
index 0000000..a5eee21
--- /dev/null
+++ b/plip/exchange/xml.py
@@ -0,0 +1,285 @@
+from lxml import etree
+
+from urllib.request import urlopen
+
+
+class XMLStorage:
+ """Generic class for storing XML data from PLIP XML files."""
+
+ def getdata(self, tree, location, force_string=False):
+ """Gets XML data from a specific element and handles types."""
+ found = tree.xpath('%s/text()' % location)
+ if not found:
+ return None
+ else:
+ data = found[0]
+ if force_string:
+ return data
+ if data == 'True':
+ return True
+ elif data == 'False':
+ return False
+ else:
+ try:
+ return int(data)
+ except ValueError:
+ try:
+ return float(data)
+ except ValueError:
+ # It's a string
+ return data
+
+ def getcoordinates(self, tree, location):
+ """Gets coordinates from a specific element in PLIP XML"""
+ return tuple(float(x) for x in tree.xpath('.//%s/*/text()' % location))
+
+
+class Interaction(XMLStorage):
+ """Stores information on a specific interaction type"""
+
+ def __init__(self, interaction_part):
+ self.id = interaction_part.get('id')
+ self.resnr = self.getdata(interaction_part, 'resnr')
+ self.restype = self.getdata(interaction_part, 'restype', force_string=True)
+ self.reschain = self.getdata(interaction_part, 'reschain', force_string=True)
+ self.resnr_lig = self.getdata(interaction_part, 'resnr_lig')
+ self.restype_lig = self.getdata(interaction_part, 'restype_lig', force_string=True)
+ self.reschain_lig = self.getdata(interaction_part, 'reschain_lig', force_string=True)
+ self.ligcoo = self.getcoordinates(interaction_part, 'ligcoo')
+ self.protcoo = self.getcoordinates(interaction_part, 'protcoo')
+
+
+class HydrophobicInteraction(Interaction):
+ """Stores information on a hydrophobic interaction"""
+
+ def __init__(self, hydrophobic_part):
+ Interaction.__init__(self, hydrophobic_part)
+ self.dist = self.getdata(hydrophobic_part, 'dist')
+ self.ligcarbonidx = self.getdata(hydrophobic_part, 'ligcarbonidx')
+ self.protcarbonidx = self.getdata(hydrophobic_part, 'protcarbonidx')
+
+
+class HydrogenBond(Interaction):
+ """Stores information on a hydrogen bond interaction"""
+
+ def __init__(self, hbond_part):
+ Interaction.__init__(self, hbond_part)
+ self.sidechain = self.getdata(hbond_part, 'sidechain')
+ self.dist_h_a = self.getdata(hbond_part, 'dist_h-a')
+ self.dist_d_a = self.getdata(hbond_part, 'dist_d-a')
+ self.dist = self.dist_d_a
+
+ self.don_angle = self.getdata(hbond_part, 'don_angle')
+ self.protisdon = self.getdata(hbond_part, 'protisdon')
+ self.donoridx = self.getdata(hbond_part, 'donoridx')
+ self.acceptoridx = self.getdata(hbond_part, 'acceptoridx')
+ self.donortype = self.getdata(hbond_part, 'donortype', force_string=True)
+ self.acceptortype = self.getdata(hbond_part, 'acceptortype', force_string=True)
+
+
+class WaterBridge(Interaction):
+ """Stores information on a water bridge interaction"""
+
+ def __init__(self, wbridge_part):
+ Interaction.__init__(self, wbridge_part)
+ self.dist_a_w = self.getdata(wbridge_part, 'dist_a-w')
+ self.dist_d_w = self.getdata(wbridge_part, 'dist_d-w')
+ self.don_angle = self.getdata(wbridge_part, 'don_angle')
+ self.water_angle = self.getdata(wbridge_part, 'water_angle')
+ self.protisdon = self.getdata(wbridge_part, 'protisdon')
+ self.dist = self.dist_a_w if self.protisdon else self.dist_d_w
+
+ self.donor_idx = self.getdata(wbridge_part, 'donor_idx')
+ self.acceptor_idx = self.getdata(wbridge_part, 'acceptor_idx')
+ self.donortype = self.getdata(wbridge_part, 'donortype', force_string=True)
+ self.acceptortype = self.getdata(wbridge_part, 'acceptortype', force_string=True)
+ self.water_idx = self.getdata(wbridge_part, 'water_idx')
+ self.watercoo = self.getcoordinates(wbridge_part, 'watercoo')
+
+
+class SaltBridge(Interaction):
+ """Stores information on a salt bridge interaction"""
+
+ def __init__(self, sbridge_part):
+ Interaction.__init__(self, sbridge_part)
+ self.dist = self.getdata(sbridge_part, 'dist')
+ self.protispos = self.getdata(sbridge_part, 'protispos')
+ self.lig_group = self.getdata(sbridge_part, 'lig_group', force_string=True)
+ self.lig_idx_list = [int(tagpart.text) for tagpart in
+ sbridge_part.xpath('lig_idx_list/idx')]
+
+
+class PiStacking(Interaction):
+ """Stores information on a pi stacking interaction"""
+
+ def __init__(self, pistack_part):
+ Interaction.__init__(self, pistack_part)
+ self.centdist = self.getdata(pistack_part, 'centdist')
+ self.dist = self.centdist
+ self.angle = self.getdata(pistack_part, 'angle')
+ self.offset = self.getdata(pistack_part, 'offset')
+ self.type = self.getdata(pistack_part, 'type')
+ self.lig_idx_list = [int(tagpart.text) for tagpart in
+ pistack_part.xpath('lig_idx_list/idx')]
+
+
+class PiCation(Interaction):
+ """Stores information on a pi cation interaction"""
+
+ def __init__(self, pication_part):
+ Interaction.__init__(self, pication_part)
+ self.dist = self.getdata(pication_part, 'dist')
+ self.offset = self.getdata(pication_part, 'offset')
+ self.protcharged = self.getdata(pication_part, 'protcharged')
+ self.lig_group = self.getdata(pication_part, 'lig_group')
+ self.lig_idx_list = [int(tag.text) for tag in pication_part.xpath('.//lig_idx_list/idx')]
+
+
+class HalogenBond(Interaction):
+ """Stores information on a halogen bond interaction"""
+
+ def __init__(self, halogen_part):
+ Interaction.__init__(self, halogen_part)
+ self.dist = self.getdata(halogen_part, 'dist')
+ self.don_angle = self.getdata(halogen_part, 'don_angle')
+ self.acc_angle = self.getdata(halogen_part, 'acc_angle')
+ self.donortype = self.getdata(halogen_part, 'donortype', force_string=True)
+ self.acceptortype = self.getdata(halogen_part, 'acceptortype', force_string=True)
+ self.don_idx = self.getdata(halogen_part, 'don_idx')
+ self.acc_idx = self.getdata(halogen_part, 'acc_idx')
+ self.sidechain = self.getdata(halogen_part, 'sidechain')
+
+
+class MetalComplex(Interaction):
+ """Stores information on a metal complexe interaction"""
+
+ def __init__(self, metalcomplex_part):
+ Interaction.__init__(self, metalcomplex_part)
+ self.metal_idx = self.getdata(metalcomplex_part, 'metal_idx')
+ self.metal_type = self.getdata(metalcomplex_part, 'metal_type', force_string=True)
+ self.target_idx = self.getdata(metalcomplex_part, 'target_idx')
+ self.target_type = self.getdata(metalcomplex_part, 'target_type', force_string=True)
+ self.coordination = self.getdata(metalcomplex_part, 'coordination')
+ self.dist = self.getdata(metalcomplex_part, 'dist')
+ self.location = self.getdata(metalcomplex_part, 'location', force_string=True)
+ self.rms = self.getdata(metalcomplex_part, 'rms')
+ self.geometry = self.getdata(metalcomplex_part, 'geometry', force_string=True)
+ self.complexnum = self.getdata(metalcomplex_part, 'complexnum')
+ self.targetcoo = self.getcoordinates(metalcomplex_part, 'targetcoo')
+ self.metalcoo = self.getcoordinates(metalcomplex_part, 'metalcoo')
+
+
+class BSite(XMLStorage):
+ """Stores all information about an specific binding site."""
+
+ def __init__(self, bindingsite, pdbid):
+ self.bindingsite = bindingsite
+ self.pdbid = pdbid
+ self.bsid = ":".join(bindingsite.xpath('identifiers/*/text()')[2:5])
+ self.uniqueid = ":".join([self.pdbid, self.bsid])
+ self.hetid = self.getdata(bindingsite, 'identifiers/hetid', force_string=True)
+ self.longname = self.getdata(bindingsite, 'identifiers/longname', force_string=True)
+ self.ligtype = self.getdata(bindingsite, 'identifiers/ligtype', force_string=True)
+ self.smiles = self.getdata(bindingsite, 'identifiers/smiles', force_string=True)
+ self.inchikey = self.getdata(bindingsite, 'identifiers/inchikey', force_string=True)
+ self.position = self.getdata(bindingsite, 'identifiers/position')
+ self.chain = self.getdata(bindingsite, 'identifiers/chain', force_string=True)
+
+ # Information on binding site members
+ self.members = []
+ for member in bindingsite.xpath('identifiers/members/member'):
+ self.members += member.xpath('text()')
+
+ self.composite = self.getdata(bindingsite, 'identifiers/composite')
+
+ # Ligand Properties
+ self.heavy_atoms = self.getdata(bindingsite, 'lig_properties/num_heavy_atoms')
+ self.hbd = self.getdata(bindingsite, 'lig_properties/num_hbd')
+ self.unpaired_hbd = self.getdata(bindingsite, 'lig_properties/num_unpaired_hbd')
+ self.hba = self.getdata(bindingsite, 'lig_properties/num_hba')
+ self.unpaired_hba = self.getdata(bindingsite, 'lig_properties/num_unpaired_hba')
+ self.hal = self.getdata(bindingsite, 'lig_properties/num_hal')
+ self.unpaired_hal = self.getdata(bindingsite, 'lig_properties/num_unpaired_hal')
+ self.molweight = self.getdata(bindingsite, 'lig_properties/molweight')
+ self.logp = self.getdata(bindingsite, 'lig_properties/logp')
+ self.rotatable_bonds = self.getdata(bindingsite, 'lig_properties/num_rotatable_bonds')
+ self.rings = self.getdata(bindingsite, 'lig_properties/num_aromatic_rings')
+
+ # Binding Site residues
+ self.bs_res = []
+ for tagpart in bindingsite.xpath('bs_residues/bs_residue'):
+ resnumber, reschain = tagpart.text[:-1], tagpart.text[-1]
+ aa, contact, min_dist = tagpart.get('aa'), tagpart.get('contact'), tagpart.get('min_dist')
+ new_bs_res = {'resnr': int(resnumber), 'reschain': reschain, 'aa': aa,
+ 'contact': True if contact == 'True' else False, 'min_dist': float(min_dist)}
+ self.bs_res.append(new_bs_res)
+
+ # Interacting chains
+ self.interacting_chains = []
+ for chain in bindingsite.xpath('interacting_chains/interacting_chain'):
+ self.interacting_chains += chain.xpath('text()')
+
+ # Interactions
+ interactions = bindingsite.xpath('interactions')[0]
+ self.hydrophobics = [HydrophobicInteraction(x) for x in
+ interactions.xpath('hydrophobic_interactions/hydrophobic_interaction')]
+ self.hbonds = [HydrogenBond(x) for x in interactions.xpath('hydrogen_bonds/hydrogen_bond')]
+ self.wbridges = [WaterBridge(x) for x in interactions.xpath('water_bridges/water_bridge')]
+ self.sbridges = [SaltBridge(x) for x in interactions.xpath('salt_bridges/salt_bridge')]
+ self.pi_stacks = [PiStacking(x) for x in interactions.xpath('pi_stacks/pi_stack')]
+ self.pi_cations = [PiCation(x) for x in interactions.xpath('pi_cation_interactions/pi_cation_interaction')]
+ self.halogens = [HalogenBond(x) for x in interactions.xpath('halogen_bonds/halogen_bond')]
+ self.metal_complexes = [MetalComplex(x) for x in interactions.xpath('metal_complexes/metal_complex')]
+ self.num_contacts = len(self.hydrophobics) + len(self.hbonds) + len(self.wbridges) + len(self.sbridges) + \
+ len(self.pi_stacks) + len(self.pi_cations) + len(self.halogens) + len(self.metal_complexes)
+ self.has_interactions = self.num_contacts > 0
+
+ self.get_atom_mapping()
+ self.counts = self.get_counts()
+
+ def get_atom_mapping(self):
+ """Parses the ligand atom mapping."""
+ # Atom mappings
+ smiles_to_pdb_mapping = self.bindingsite.xpath('mappings/smiles_to_pdb/text()')
+ if not smiles_to_pdb_mapping:
+ self.mappings = {'smiles_to_pdb': None, 'pdb_to_smiles': None}
+ else:
+ smiles_to_pdb_mapping = {int(y[0]): int(y[1]) for y in [x.split(':')
+ for x in smiles_to_pdb_mapping[0].split(',')]}
+ self.mappings = {'smiles_to_pdb': smiles_to_pdb_mapping}
+ self.mappings['pdb_to_smiles'] = {v: k for k, v in self.mappings['smiles_to_pdb'].items()}
+
+ def get_counts(self):
+ """counts the interaction types and backbone hydrogen bonding in a binding site"""
+
+ hbondsback = len([hb for hb in self.hbonds if not hb.sidechain])
+ counts = {'hydrophobics': len(self.hydrophobics), 'hbonds': len(self.hbonds),
+ 'wbridges': len(self.wbridges), 'sbridges': len(self.sbridges), 'pistacks': len(self.pi_stacks),
+ 'pications': len(self.pi_cations), 'halogens': len(self.halogens), 'metal': len(self.metal_complexes),
+ 'hbond_back': hbondsback, 'hbond_nonback': (len(self.hbonds) - hbondsback)}
+ counts['total'] = counts['hydrophobics'] + counts['hbonds'] + counts['wbridges'] + \
+ counts['sbridges'] + counts['pistacks'] + counts['pications'] + counts['halogens'] + counts['metal']
+ return counts
+
+
+class PlipXML(XMLStorage):
+ """Parses and stores all information from a PLIP XML file."""
+
+ def __init__(self, xmlfile):
+ self.load_data(xmlfile)
+
+ # Parse general information
+ self.version = self.getdata(self.doc, '/report/plipversion/')
+ self.pdbid = self.getdata(self.doc, '/report/pdbid', force_string=True)
+ self.filetype = self.getdata(self.doc, '/report/filetype')
+ self.fixed = self.getdata(self.doc, '/report/pdbfixes/')
+ self.filename = self.getdata(self.doc, '/report/filename')
+ self.excluded = self.doc.xpath('/report/excluded_ligands/excluded_ligand/text()')
+
+ # Parse binding site information
+ self.bsites = {BSite(bs, self.pdbid).bsid: BSite(bs, self.pdbid) for bs in self.doc.xpath('//bindingsite')}
+ self.num_bsites = len(self.bsites)
+
+ def load_data(self, xmlfile):
+ """Loads/parses an XML file and saves it as a tree if successful."""
+ self.doc = etree.parse(xmlfile) \ No newline at end of file