def load_complex_from_string(pdb_string, lig_id):
complex = PDBComplex() # plip molecule
complex.load_pdb(pdb_string, as_string=True)
lig_pdb_string = []
for line in pdb_string.split('\n'):
if line[17:20] == lig_id or line[:6] == 'CONECT':
lig_pdb_string.append(line)
lig_pdb_string = '\n'.join(lig_pdb_string)
lig = pybel.readstring('pdb', lig_pdb_string) # openbabel molecule
# lig = Chem.MolFromPDBBlock(lig_pdb_string, removeHs=False) # rdkit molecule
return complex, lig
def test_dna_rna(self):
"""Test if DNA and RNA is correctly processed as ligands"""
tmpmol = PDBComplex()
tmpmol.load_pdb('./pdb/1tf6.pdb')
bsid = 'DA:B:1'
# DNA ligand four times consisting of 31 parts (composite)
self.assertEqual([len(ligand.members) for ligand in tmpmol.ligands].count(31), 4)
for ligset in [set((x[0] for x in ligand.members)) for ligand in tmpmol.ligands]:
if len(ligset) == 4:
# DNA only contains four bases
self.assertEqual(ligset, set(['DG', 'DC', 'DA', 'DT']))
def plip_analysis(pdbpath, pdb_id):
''' run PLIP analysis for pdb file '''
mol = PDBComplex()
mol.load_pdb(pdbpath)
chain_id = pdb_id.split('_')[-1]
ligand_interactions_dict = {}
# invastigate only proteins with following ligands
ligand_whitelist = set([
'NAD', 'FAD', 'NDP', 'NAP', 'NAI', 'ADP', 'AMP', 'ATP', 'FMN', 'GTP',
'ADN', 'SAH', 'GDP', '5GP', 'ADX', 'LSS', '1ZZ', 'COA', 'ACO', '01A',
'HMG', 'SAI', 'GRA', 'ST9', 'MCA', 'SAM', 'HEM', 'CLA', 'BCB', 'BCL',
'HEA', 'HEC', 'HEB', 'HAS'
])
# plip analysis
ligand_list_from_mol = [x.hetid for x in mol.ligands]
print('=> ' + str(len(ligand_list_from_mol)) + ' ligands to process')
# if any ligand of interest present
# if not ligand_whitelist.intersection(set(ligand_list_from_mol)):
# print('=> No ligands of interest found')
# #print(ligand_list_from_mol)
# return ligand_interactions_dict
mol.analyze()
full_data_mol[pdb_id] = mol
for bsid in [
":".join([x.hetid, x.chain, str(x.position)]) for x in mol.ligands
]:
# for every ligand encountered in pdb
print bsid
#print '|',
interactions = mol.interaction_sets[
bsid] # Contains all interaction data
print interactions.interacting_res
interacting_residues = [
int(res[:-1]) for res in interactions.interacting_res
if res[-1] == chain_id
]
if interacting_residues:
ligand_interactions_dict[bsid] = interacting_residues
print '=> ' + str(
len(ligand_interactions_dict
)) + ' ligands interacting with chain ' + chain_id + ' found'
print
return ligand_interactions_dict
def test_4alw(self):
"""Binding of benzofuropyrimidinones compound 3 to PIM-1 (4alw)
Reference: Tsuhako et al. The design, synthesis, and biological evaluation of PIM kinase inhibitors.(2012)
"""
tmpmol = PDBComplex()
tmpmol.load_pdb('./pdb/4alw.pdb')
s = tmpmol.interaction_sets['HY7-A-1308']
# Hydrogen bonds to Asp186
hbonds = {hbond.resnr for hbond in s.hbonds_pdon}
self.assertTrue({186}.issubset(hbonds))
# Saltbridge to A186 and Glu171
saltb = {saltbridge.resnr for saltbridge in s.saltbridge_pneg}
self.assertTrue({186, 171}.issubset(saltb))
def test_1eve(self):
"""Binding of anti-Alzheimer drug E2020 to acetylcholinesterase from Torpedo californica (1eve)
Reference: Chakrabarti et al. Geometry of nonbonded interactions involving planar groups in proteins. (2007)
"""
tmpmol = PDBComplex()
tmpmol.load_pdb('./pdb/1eve.pdb')
s = tmpmol.interaction_sets['E20-A-2001']
# Aromatic stacking with Trp84 and Trp279
pistackres = {pistack.resnr for pistack in s.pistacking}
self.assertTrue({84, 279}.issubset(pistackres))
# Pi-Cation interaction of Phe330 with ligand
pication = {pication.resnr for pication in s.pication_paro}
self.assertTrue({330}.issubset(pication))
def test_4qnb(self):
"""Binding of (4qnb)
Reference: Bhattacharya et al. Structural basis of HIV-1 capsid recognition by PF74 and CPSF6(2014)
"""
tmpmol = PDBComplex()
tmpmol.load_pdb('./pdb/4qnb.pdb')
s = tmpmol.interaction_sets['1B0-A-301']
# Hydrogen bonds to Asn57 and Lys70
hbonds = {hbond.resnr for hbond in s.hbonds_pdon}
self.assertTrue({57, 70}.issubset(hbonds))
# Cation-pi interactions with Lys70
picat = {pication.resnr for pication in s.pication_laro}
self.assertEqual({70}, picat)
def test_1osn(self):
"""Binding of VZV-tk to BVDU-MP (2reg)
Reference: Bird et al. Crystal structures of Varicella Zoster Virus Thyrimidine Kinase. (2003)
"""
tmpmol = PDBComplex()
tmpmol.load_pdb('./pdb/1osn.pdb')
s = tmpmol.interaction_sets['BVP-A-500']
# Sandwiched pi-stacking involving Phe93 and Phe139
pistackres = {pistack.resnr for pistack in s.pistacking}
self.assertTrue({93, 139}.issubset(pistackres))
# Hydrogen bonding of Gln90
hbonds = {hbond.resnr for hbond in s.hbonds_pdon}
self.assertTrue({90}.issubset(hbonds))
def test_3thy(self):
"""Binding of ADP tp MutS(3thy)
Reference: Shikha et al. Mechanism of mismatch recognition revealed by human MutSβ bound to unpaired DNA loops.(2012)
"""
tmpmol = PDBComplex()
tmpmol.load_pdb('./pdb/3thy.pdb')
s = tmpmol.interaction_sets['ADP-A-935']
# Saltbridge to His295 and Lys675
saltb = {saltbridge.resnr for saltbridge in s.saltbridge_lneg}
self.assertTrue({675}.issubset(saltb))
# pi-stacking interaction with Tyr815
pistackres = {pistack.resnr for pistack in s.pistacking}
self.assertTrue({815}.issubset(pistackres))
def test_3OG7(self):
"""Inhibitor PLX4032 binding to B-RAF(V600E) (3og7)
Reference: Clinical efficacy of a RAF inhibitor needs broad target blockade in BRAF-mutant
melanoma (2010)
"""
tmpmol = PDBComplex()
tmpmol.load_pdb('./pdb/3og7.pdb')
s = tmpmol.interaction_sets['032-A-1']
# Hydrogen bonds
hbonds = {
str(hbond.resnr) + hbond.reschain
for hbond in s.hbonds_pdon + s.hbonds_ldon
}
self.assertTrue({'594A', '530A'}.issubset(hbonds))
def test_2efj(self):
"""Binding of teobromine to 1,7 dimethylxanthine methyltransferase(2efj)
Reference: McCarthy et al. The Structure of Two N-Methyltransferases from the Caffeine Biosynthetic
Pathway.(2007)
"""
tmpmol = PDBComplex()
tmpmol.load_pdb('./pdb/2efj.pdb')
s = tmpmol.interaction_sets['37T-A-502']
# Hydrogen bonds to Trp161, Ser237
hbonds = {hbond.resnr for hbond in s.hbonds_pdon}
self.assertTrue({161, 237}.issubset(hbonds))
# pi-stacking interaction with Tyr157
pistackres = {pistack.resnr for pistack in s.pistacking}
self.assertTrue({157}.issubset(pistackres))
def test_1p5e(self):
"""Binding of TBS to CDK2(1p5e)
Reference: De Moliner et al. Alternative binding modes of an inhibitor to two different kinases. (2003)
"""
tmpmol = PDBComplex()
tmpmol.load_pdb('./pdb/1p5e.pdb')
bsid = 'TBS:A:301'
for ligand in tmpmol.ligands:
if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid:
tmpmol.characterize_complex(ligand)
s = tmpmol.interaction_sets[bsid]
# Halogen Bonding of Ile10 and Leu83
halogens = {halogen.resnr for halogen in s.halogen_bonds}
self.assertTrue({10, 83}.issubset(halogens))
def test_2reg(self):
"""Binding of choline to ChoX (2reg)
Reference: Oswald et al. Crystal structures of the choline/acetylcholine substrate-binding protein ChoX
from Sinorhizobium meliloti in the liganded and unliganded-closed states. (2008)
"""
tmpmol = PDBComplex()
tmpmol.load_pdb('./pdb/2reg.pdb')
s = tmpmol.interaction_sets['CHT-A-1']
# Cation-pi interactions with Trp43, Trp90, Trp205, and Tyr119
picat = {pication.resnr for pication in s.pication_paro}
self.assertEqual({43, 90, 205, 119}, picat)
# Saltbridge to Asp45
saltb = {saltbridge.resnr for saltbridge in s.saltbridge_pneg}
self.assertEqual({45}, saltb)
def test_4pjt(self):
"""Binding of BMN 673 to catPARP1(4pj7)
Reference: Aoyagi-Scharber et al. Structural basis for the inhibition of poly(ADP-ribose) polymerases 1 and 2 by BMN
673, a potent inhibitor derived from dihydropyridophthalazinone.(2014)
"""
tmpmol = PDBComplex()
tmpmol.load_pdb('./pdb/4pjt.pdb')
s = tmpmol.interaction_sets['2YQ-D-1104']
# Hydrogen bonds to Gly863
hbonds = {hbond.resnr for hbond in s.hbonds_pdon}
self.assertTrue({863}.issubset(hbonds))
# pi-stacking interaction with Tyr889 and Tyr907
pistackres = {pistack.resnr for pistack in s.pistacking}
self.assertTrue({889, 907}.issubset(pistackres))
def test_1vsn(self):
"""Binding of NFT to Cathepsin K (1vsn)
Reference: Li et al. Identification of a potent and selective non-basic cathepsin K inhibitor. (2006)
"""
tmpmol = PDBComplex()
tmpmol.load_pdb('./pdb/1vsn.pdb')
bsid = 'NFT:A:283'
for ligand in tmpmol.ligands:
if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid:
tmpmol.characterize_complex(ligand)
s = tmpmol.interaction_sets[bsid]
# Hydrogen bonding to Gly66
hbonds = {hbond.resnr for hbond in s.hbonds_pdon}
self.assertTrue({66}.issubset(hbonds))
def test_3o1h(self):
"""Binding of TMAO to TorT-TorS system(3o1h)
Reference: Hendrickson et al. An Asymmetry-to-Symmetry Switch in Signal Transmission by the Histidine Kinase Receptor
for TMAO.(2013)
"""
tmpmol = PDBComplex()
tmpmol.load_pdb('./pdb/3o1h.pdb')
s = tmpmol.interaction_sets['TMO-B-1']
# Hydrogen bonds to Trp45
hbonds = {hbond.resnr for hbond in s.hbonds_pdon}
self.assertTrue({45}.issubset(hbonds))
# Water bridges to Trp45 not detected due to priorization of hydrogen bonds
# Cation-pi interactions with Tyr44
picat = {pication.resnr for pication in s.pication_paro}
self.assertEqual({44}, picat)
def test_3tah(self):
"""Binding of BGO to an an N11A mutant of the G-protein domain of FeoB.(3tah)
Reference: Ash et al. The structure of an N11A mutant of the G-protein domain of FeoB.(2011)
"""
tmpmol = PDBComplex()
tmpmol.load_pdb('./pdb/3tah.pdb')
s = tmpmol.interaction_sets['BGO-A-300']
# Hydrogen bonds to Ala11, Lys14, Thr15, Ser16, Asp113, Met114, Ala143 and Asp113
hbonds = {hbond.resnr for hbond in s.hbonds_pdon}
self.assertTrue({11, 13, 14, 15, 16, 113, 114, 143,
113}.issubset(hbonds))
# Water bridges to Ala11 not detected due to prioritization of hydrogen bonds
# Saltbridge to Asp116
saltb = {saltbridge.resnr for saltbridge in s.saltbridge_pneg}
self.assertTrue({116}.issubset(saltb))
def test_3OG7(self):
"""Inhibitor PLX4032 binding to B-RAF(V600E) (3og7)
Reference: Clinical efficacy of a RAF inhibitor needs broad target blockade in BRAF-mutant
melanoma (2010)
"""
tmpmol = PDBComplex()
tmpmol.load_pdb('./pdb/3og7.pdb')
bsid = '032:A:1'
for ligand in tmpmol.ligands:
if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid:
tmpmol.characterize_complex(ligand)
s = tmpmol.interaction_sets[bsid]
# Hydrogen bonds
hbonds = {str(hbond.resnr)+hbond.reschain for hbond in s.hbonds_pdon+s.hbonds_ldon}
self.assertTrue({'594A', '530A'}.issubset(hbonds))
def test_1acj(self):
"""Binding of Tacrine (THA) to active-site gorge of acetylcholinesterase (1acj)
Reference: Harel et al. Quaternary ligand binding to aromatic residues in the active-site gorge of
acetylcholinesterase.. (1993)
"""
tmpmol = PDBComplex()
tmpmol.load_pdb('./pdb/1acj.pdb')
bsid = 'THA:A:999'
for ligand in tmpmol.ligands:
if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid:
tmpmol.characterize_complex(ligand)
s = tmpmol.interaction_sets[bsid]
# pi-stacking interaction with Phe330 and Trp84
pistackres = {pistack.resnr for pistack in s.pistacking}
self.assertTrue({330, 84}.issubset(pistackres))
def test_2pvb(self):
"""Pike parvalbumin binding calcium (2pvb)
Reference: Harding. The architecture of metal coordination groups in proteins. (2004), Fig. 6
"""
tmpmol = PDBComplex()
tmpmol.load_pdb('./pdb/2pvb.pdb')
bsid = 'CA:A:110'
for ligand in tmpmol.ligands:
if ':'.join([ligand.hetid, ligand.chain,
str(ligand.position)]) == bsid:
tmpmol.characterize_complex(ligand)
s = tmpmol.interaction_sets[bsid]
# Ca atom with square pyramidal geometry (coordination number 5)
self.assertEqual(s.metal_complexes[0].coordination_num, 5)
self.assertEqual(s.metal_complexes[0].geometry, 'square.pyramidal')
def test_1h2t(self):
"""Binding of methylated guanosine to heterodimeric nuclear-cap binding complex (1h2t)
Reference: Chakrabarti et al. Geometry of nonbonded interactions involving planar groups in proteins. (2007)
"""
tmpmol = PDBComplex()
tmpmol.load_pdb('./pdb/1h2t.pdb')
s = tmpmol.interaction_sets['7MG-Z-1152']
# Sandwiched pi-stacking involving Tyr20 and Tyr43
pistackres = {pistack.resnr for pistack in s.pistacking}
self.assertTrue({20, 43}.issubset(pistackres))
# Hydrogen bond with R112
hbonds = {hbond.resnr for hbond in s.hbonds_pdon}
self.assertTrue({112}.issubset(hbonds))
# Salt bridge with D116
saltb = {saltbridge.resnr for saltbridge in s.saltbridge_pneg}
self.assertTrue({116}.issubset(saltb))
def __init__(self, protein, ligand, within=7.5):
self.protein = protein
self.ligand = ligand
genASite = GenActiveSite(within=within)
self.asite = genASite(self.protein, self.ligand)
renumberResidues(self.asite)
log(f'nAtoms of asite {self.asite.GetNumAtoms()}')
complex = Chem.CombineMols(self.asite, self.ligand)
self.pmol = PDBComplex()
cont = Chem.MolToPDBBlock(complex).replace('UNL 1', 'MOL 1')
self.pmol.load_pdb(cont, as_string=True)
self.pmol.analyze()
def test_3thy(self):
"""Binding of ADP tp MutS(3thy)
Reference: Shikha et al. Mechanism of mismatch recognition revealed by human MutSβ bound to unpaired DNA loops.(2012)
"""
tmpmol = PDBComplex()
tmpmol.load_pdb('./pdb/3thy.pdb')
bsid = 'ADP:A:935'
for ligand in tmpmol.ligands:
if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid:
tmpmol.characterize_complex(ligand)
s = tmpmol.interaction_sets[bsid]
# Saltbridge to His295 and Lys675
saltb = {saltbridge.resnr for saltbridge in s.saltbridge_lneg}
self.assertTrue({675}.issubset(saltb))
# pi-stacking interaction with Tyr815
pistackres = {pistack.resnr for pistack in s.pistacking}
self.assertTrue({815}.issubset(pistackres))
def test_4alw(self):
"""Binding of benzofuropyrimidinones compound 3 to PIM-1 (4alw)
Reference: Tsuhako et al. The design, synthesis, and biological evaluation of PIM kinase inhibitors.(2012)
"""
tmpmol = PDBComplex()
tmpmol.load_pdb('./pdb/4alw.pdb')
bsid = 'HY7:A:1308'
for ligand in tmpmol.ligands:
if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid:
tmpmol.characterize_complex(ligand)
s = tmpmol.interaction_sets[bsid]
# Hydrogen bonds to Asp186
hbonds = {hbond.resnr for hbond in s.hbonds_pdon}
self.assertTrue({186}.issubset(hbonds))
# Saltbridge to A186 and Glu171
saltb = {saltbridge.resnr for saltbridge in s.saltbridge_pneg}
self.assertTrue({186, 171}.issubset(saltb))
def test_1eve(self):
"""Binding of anti-Alzheimer drug E2020 to acetylcholinesterase from Torpedo californica (1eve)
Reference: Chakrabarti et al. Geometry of nonbonded interactions involving planar groups in proteins. (2007)
"""
tmpmol = PDBComplex()
tmpmol.load_pdb('./pdb/1eve.pdb')
bsid = 'E20:A:2001'
for ligand in tmpmol.ligands:
if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid:
tmpmol.characterize_complex(ligand)
s = tmpmol.interaction_sets[bsid]
# Aromatic stacking with Trp84 and Trp279
pistackres = {pistack.resnr for pistack in s.pistacking}
self.assertTrue({84, 279}.issubset(pistackres))
# Pi-Cation interaction of Phe330 with ligand
pication = {pication.resnr for pication in s.pication_paro}
self.assertTrue({330}.issubset(pication))
def test_4qnb(self):
"""Binding of (4qnb)
Reference: Bhattacharya et al. Structural basis of HIV-1 capsid recognition by PF74 and CPSF6(2014)
"""
tmpmol = PDBComplex()
tmpmol.load_pdb('./pdb/4qnb.pdb')
bsid = '1B0:A:301'
for ligand in tmpmol.ligands:
if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid:
tmpmol.characterize_complex(ligand)
s = tmpmol.interaction_sets[bsid]
# Hydrogen bonds to Asn57 and Lys70
hbonds = {hbond.resnr for hbond in s.hbonds_pdon}
self.assertTrue({57, 70}.issubset(hbonds))
# Cation-pi interactions with Lys70
picat = {pication.resnr for pication in s.pication_laro}
self.assertEqual({70}, picat)
def test_1osn(self):
"""Binding of VZV-tk to BVDU-MP (2reg)
Reference: Bird et al. Crystal structures of Varicella Zoster Virus Thyrimidine Kinase. (2003)
"""
tmpmol = PDBComplex()
tmpmol.load_pdb('./pdb/1osn.pdb')
bsid = 'BVP:A:500'
for ligand in tmpmol.ligands:
if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid:
tmpmol.characterize_complex(ligand)
s = tmpmol.interaction_sets[bsid]
# Sandwiched pi-stacking involving Phe93 and Phe139
pistackres = {pistack.resnr for pistack in s.pistacking}
self.assertTrue({93, 139}.issubset(pistackres))
# Hydrogen bonding of Gln90
hbonds = {hbond.resnr for hbond in s.hbonds_pdon}
self.assertTrue({90}.issubset(hbonds))
def test_1ay8(self):
"""Binding of PLP to aromatic amino acid aminotransferase(1ay8)
Reference: Okamoto et al. Crystal structures of Paracoccus denitrificans aromatic amino acid aminotransferase: a
substrate recognition site constructed by rearrangement of hydrogen bond network..(1998)
"""
tmpmol = PDBComplex()
tmpmol.load_pdb('./pdb/1ay8.pdb')
s = tmpmol.interaction_sets['PLP-A-413']
# Hydrogen bonds to Gly108, Thr109, Asn194 and Ser257
hbonds = {hbond.resnr for hbond in s.hbonds_pdon}
self.assertTrue({108, 109, 194, 257}.issubset(hbonds))
# Saltbridge to Ly258 and Arg266
saltb = {saltbridge.resnr for saltbridge in s.saltbridge_lneg}
self.assertTrue({258, 266}.issubset(saltb))
# pi-stacking interaction with Trp140
pistackres = {pistack.resnr for pistack in s.pistacking}
self.assertTrue({140}.issubset(pistackres))
def plip_analysis_targets(pdbpath, pdb_id, pi_helix_pdb_ids):
mol = PDBComplex()
mol.load_pdb(pdbpath)
chain_id = pdb_id.split('_')[-1]
ligand_interactions = []
# plip analysis
ligand_list_from_mol = [x.hetid for x in mol.ligands]
print('=> ' + str(len(ligand_list_from_mol)) + ' ligands to process')
mol.analyze()
full_data_mol[pdb_id] = mol
print(target_pdb_plip_data[pdb_id])
for bsid in [
":".join([x.hetid, x.chain, str(x.position)]) for x in mol.ligands
]:
# for every ligand encountered in pdb
print bsid
if bsid.split(':')[0] not in target_pdb_plip_data[pdb_id].keys():
print 'BSID not in PLIP data', bsid
continue
if (not target_pdb_plip_data[pdb_id][bsid.split(':')[0]]
or bsid.split(':')[1] != chain_id):
continue
print 'passed filters:', bsid
#print '|',
interactions = mol.interaction_sets[
bsid] # Contains all interaction data
pi_helix_pdb_ids_all = [res for reg in pi_helix_pdb_ids for res in reg]
#print pi_helix_pdb_ids
#print pi_helix_pdb_ids_all
for inter in interactions.all_itypes:
if inter.resnr in pi_helix_pdb_ids_all:
inter_type = str(type(inter)).strip('<>\'').split('.')[-1]
print inter_type, inter.resnr, inter.restype, inter.restype_l
ligand_interactions.append(inter)
return ligand_interactions
def process_pdb(pdbfile, outpath, as_string=False, outputprefix='report'):
"""Analysis of a single PDB file. Can generate textual reports XML, PyMOL session files and images as output."""
if not as_string:
startmessage = '\nStarting analysis of %s\n' % pdbfile.split('/')[-1]
else:
startmessage = "Starting analysis from stdin.\n"
write_message(startmessage)
write_message('='*len(startmessage)+'\n')
mol = PDBComplex()
mol.output_path = outpath
mol.load_pdb(pdbfile, as_string=as_string)
# #@todo Offers possibility for filter function from command line (by ligand chain, position, hetid)
for ligand in mol.ligands:
mol.characterize_complex(ligand)
create_folder_if_not_exists(outpath)
# Generate the report files
streport = StructureReport(mol, outputprefix=outputprefix)
config.MAXTHREADS = min(config.MAXTHREADS, len(mol.interaction_sets))
######################################
# PyMOL Visualization (parallelized) #
######################################
if config.PYMOL or config.PICS:
try:
from plip.modules.visualize import visualize_in_pymol
except ImportError:
from modules.visualize import visualize_in_pymol
complexes = [VisualizerData(mol, site) for site in sorted(mol.interaction_sets)
if not len(mol.interaction_sets[site].interacting_res) == 0]
if config.MAXTHREADS > 1:
write_message('\nGenerating visualizations in parallel on %i cores ...' % config.MAXTHREADS)
parfn = parallel_fn(visualize_in_pymol)
parfn(complexes, processes=config.MAXTHREADS)
else:
[visualize_in_pymol(plcomplex) for plcomplex in complexes]
if config.XML: # Generate report in xml format
streport.write_xml(as_string=config.STDOUT)
if config.TXT: # Generate report in txt (rst) format
streport.write_txt(as_string=config.STDOUT)
def test_1hii(self):
"""HIV-2 protease in complex with novel inhibitor CGP 53820 (1hii)
Reference: Comparative analysis of the X-ray structures of HIV-1 and HIV-2 proteases in complex
with CGP 53820, a novel pseudosymmetric inhibitor (1995)
"""
tmpmol = PDBComplex()
tmpmol.load_pdb('./pdb/1hii.pdb')
bsid = 'C20:B:101'
for ligand in tmpmol.ligands:
if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid:
tmpmol.characterize_complex(ligand)
s = tmpmol.interaction_sets[bsid]
# Water bridges
waterbridges = {str(wb.resnr)+wb.reschain for wb in s.water_bridges}
self.assertTrue({'50A', '50B'}.issubset(waterbridges)) # Bridging Ile-B50 and Ile-A50 with ligand
# Hydrogen bonds
hbonds = {str(hbond.resnr)+hbond.reschain for hbond in s.hbonds_pdon+s.hbonds_ldon}
self.assertTrue({'27A', '27B', '29A', '48A', '48B'}.issubset(hbonds))
