def get_molecule(path):
"""
Reads a molecular structure with Open Babel.
"""
if os.path.exists(path):
# DETERMINE FILE FORMAT
filename, filetype = os.path.splitext(path)
try:
molecule = pybel.readfile(filetype[1:], path).next()
except StopIteration:
logger.error("cannot read molecule {}: StopIteration.".format(path))
sys.exit(1)
return molecule
else:
logger.error('cannot not load molecule: the file {} does not exist.'.format(path))
sys.exit(1)
def get_molecule(path):
"""
Reads a molecular structure with Open Babel.
"""
if os.path.exists(path):
# DETERMINE FILE FORMAT
filename, filetype = os.path.splitext(path)
try:
molecule = pybel.readfile(filetype[1:], path).next()
except StopIteration:
logger.error(
"cannot read molecule {}: StopIteration.".format(path))
sys.exit(1)
return molecule
else:
logger.error(
'cannot not load molecule: the file {} does not exist.'.format(
path))
sys.exit(1)
def main():
'''
'''
options = parse_options()
# THIS OPTION WILL PRODUCE MORE VERBOSE OUTPUT
if options.debug: logger.setLevel(logging.DEBUG)
pdbbindconf = config['standard']
data = parse_index(options.pdbbind, options.index)
if options.output: fh = open(options.output, 'wb')
else: fh = sys.stdout
# CHOOSE HOW THE OUPTPUT DATA WILL BE WRITTEN
if options.format == 'csv':
writer = csv.writer(fh,
delimiter=',',
quotechar='"',
quoting=csv.QUOTE_MINIMAL)
HEADER = True
# ITERATE THROUGH ALL PROTEIN-LIGAND COMPLEXES
for pdb in data:
# NORMALISE ACTIVITY TO NANOMOLAR
pkd = get_pkd(float(data[pdb]['value']), data[pdb]['unit'])
# THE PDBBIND DIRECTORY CONTAINING ALL THE STRUCTURES FOR THIS PDB ENTRY
entry_dir = os.path.join(options.pdbbind, pdb)
# CHECK IF THE DIRECTORY ACTUALLY EXISTS
if not os.path.exists(entry_dir):
logger.error(
"The PDBbind directory for PDB entry {0} does not exist.".
format(pdb))
continue
# CREATE THE PATHS TO THE PROTEIN AND LIGAND USING THE SPECIFIC _<POCKET,PROTEIN,LIGAND,ZINC> LABEL
prot_path = os.path.join(
entry_dir, '{0}_{1}.pdb'.format(pdb, pdbbindconf['protein']))
lig_path = os.path.join(
entry_dir, '{0}_{1}.mol2'.format(pdb, pdbbindconf['ligand']))
if not os.path.exists(prot_path):
logger.error(
"The protein pocket structure for PDB entry {0} cannot be found."
.format(pdb))
continue
elif not os.path.exists(lig_path):
logger.error(
"The ligand structure for PDB entry {0} cannot be found.".
format(pdb))
continue
protein = get_molecule(prot_path)
ligand = get_molecule(lig_path)
# CALCULATE DESCRIPTOR USING STRUCTURAL INTERACTION FINGERPRINTS
if options.descriptor == 'credo':
# GET THE PROTEIN-LIGAND STRUCTURAL INTERACTION FINGERPRINT
descriptor, labels = contacts.sift_descriptor(
protein, ligand, binsize=options.binsize)
# CALCULATE DESCRIPTOR BASED ON THE SUM OF INTERACTING ELEMENT PAIRS
elif options.descriptor == 'elements':
# CALCULATE ELEMENT PAIR DESCRIPTOR FOR THIS COMPLEX
descriptor, labels = contacts.element_descriptor(
protein, ligand, binsize=options.binsize)
# CALCULATE DESCRIPTOR BASED ON THE SUM OF INTERACTING ELEMENT PAIRS
elif options.descriptor == 'sybyl':
# CALCULATE ELEMENT PAIR DESCRIPTOR FOR THIS COMPLEX
descriptor, labels = contacts.sybyl_atom_type_descriptor(
protein, ligand, binsize=options.binsize)
if HEADER:
# UPDATE COLUMN LABELS
labels.insert(0, 'pKd/pKi')
labels.append('pdb')
writer.writerow(labels)
HEADER = False
if options.format == 'csv':
# KEEP ONLY THE TWO MOST SIGNIFICANT BITS
pkdstring = "{0:.2f}".format(pkd)
# FIRST COLUMN OF OUTPUT ROW
row = [pkdstring] + descriptor.tolist() + [pdb]
writer.writerow(row)
def parse_options():
'''
'''
# PARSE COMMAND LINE
usage = "%prog [options]"
parser = OptionParser(usage=usage)
parser.add_option("--debug",
action = "store_true",
dest = "debug",
default = False,
help = 'Set logging level to debug and print more verbose output.')
parser.add_option("-B", "--binsize",
dest = "binsize",
type = float,
default = 0.0,
help = "Bin size (in Angstrom) to use for binning contacts based on inter-atomic distance.")
parser.add_option("-F", "--format",
dest = "format",
default = 'csv',
help = "Format to use for writing the SIFt of the protein-ligand complex.")
parser.add_option("-O", "--output",
dest = "output",
default = None,
help = "File to which the data will be written (default=STDOUT).")
parser.add_option("-P", "--pdbbind-dir",
dest = "pdbbind",
default = None,
help = "PDBbind directory.")
parser.add_option("-I", "--index",
dest = "index",
default = None,
help = "PDBbind data index file for a specific data set (core,refined,general).")
parser.add_option("-D", "--descriptor",
dest = "descriptor",
default = 'credo',
help = "Descriptor to use. Valid descriptors are 'credo', 'elements' and 'sybyl'.")
# GET COMMAND LINE OPTIONS
(options, args) = parser.parse_args()
if not options.pdbbind:
logger.error("The PDBbind directory must be provided.")
parser.print_help()
sys.exit(1)
elif not os.path.exists(options.pdbbind):
logger.fatal("The specified PDBbind directory does not exist.")
sys.exit(1)
if not options.index:
logger.error("A path to a PDBbind data index file must be provided.")
parser.print_help()
sys.exit(1)
elif not os.path.exists(options.index):
logger.fatal("The specified PDBbind data index file does not exist.")
sys.exit(1)
if options.descriptor not in ('elements', 'credo', 'sybyl'):
logger.fatal("Invalid descriptor: {0}.".format(options.descriptor))
parser.print_help()
sys.exit(1)
return options
def parse_options():
'''
'''
# PARSE COMMAND LINE
usage = "%prog [options]"
parser = OptionParser(usage=usage)
parser.add_option("--debug",
action = "store_true",
dest = "debug",
default = False,
help = 'Set logging level to debug and print more verbose output.')
parser.add_option("-B", "--binsize",
dest = "binsize",
type = float,
default = 0.0,
help = "Bin size (in Angstrom) to use for binning contacts based on inter-atomic distance.")
parser.add_option("-F", "--format",
dest = "format",
default = 'csv',
help = "Format to use for writing the SIFt of the protein-ligand complex.")
parser.add_option("-O", "--output",
dest = "output",
default = "/home/dat/WORK/DB/DESCRIPTORS/CASF2014-refined_SIFt_RMSD.csv",#None,
help = "File to which the data will be written (default=STDOUT).")
parser.add_option("-P", "--pdbbind-dir",
dest = "pdbbind",
default = "/home/dat/WORK/DB/PDBbind/v2014-refined/",#None,
help = "PDBbind directory.")
parser.add_option("-I", "--index",
dest = "index",
default = "/home/dat/WORK/DB/PDBbind/v2014-refined/INDEX_refined_data.2014",#None,
help = "PDBbind data index file for a specific data set (core,refined,general).")
parser.add_option("-D", "--descriptor",
dest = "descriptor",
default = 'credo',
help = "Descriptor to use. Valid descriptors are 'credo', 'elements' and 'sybyl'.")
# GET COMMAND LINE OPTIONS
(options, args) = parser.parse_args()
if not options.pdbbind:
logger.error("The PDBbind directory must be provided.")
parser.print_help()
sys.exit(1)
elif not os.path.exists(options.pdbbind):
logger.fatal("The specified PDBbind directory does not exist.")
sys.exit(1)
if not options.index:
logger.error("A path to a PDBbind data index file must be provided.")
parser.print_help()
sys.exit(1)
elif not os.path.exists(options.index):
logger.fatal("The specified PDBbind data index file does not exist.")
sys.exit(1)
if options.descriptor not in ('elements', 'credo', 'sybyl'):
logger.fatal("Invalid descriptor: {0}.".format(options.descriptor))
parser.print_help()
sys.exit(1)
return options
def main():
'''
'''
options = parse_options()
# THIS OPTION WILL PRODUCE MORE VERBOSE OUTPUT
if options.debug: logger.setLevel(logging.DEBUG)
pdbbindconf = config['pdbbind']
data = parse_index(options.pdbbind, options.index)
if options.output: fh = open(options.output,'wb')
else: fh = sys.stdout
# CHOOSE HOW THE OUPTPUT DATA WILL BE WRITTEN
if options.format == 'csv':
writer = csv.writer(fh, delimiter=',', quotechar='"', quoting=csv.QUOTE_MINIMAL)
HEADER = True
counter = 0
# ITERATE THROUGH ALL PROTEIN-LIGAND COMPLEXES
for pdb in data:
# THE PDBBIND DIRECTORY CONTAINING ALL THE STRUCTURES FOR THIS PDB ENTRY
entry_dir = os.path.join(options.pdbbind,pdb)
# CHECK IF THE DIRECTORY ACTUALLY EXISTS
if not os.path.exists(entry_dir):
logger.error("The PDBbind directory for PDB entry {0} does not exist.".format(pdb))
continue
# CREATE THE PATHS TO THE PROTEIN AND LIGAND USING THE SPECIFIC _<POCKET,PROTEIN,LIGAND,ZINC> LABEL
prot_path = os.path.join(entry_dir,'{0}_{1}.pdb'.format(pdb,pdbbindconf['protein']))
ref_lig_path = os.path.join(entry_dir,'{0}_{1}.mol2'.format(pdb,pdbbindconf['ligand']))
#for each protein, the ligand gets generated docking poses from x docking methods,
#
if not os.path.exists(prot_path):
logger.error("The protein pocket structure for PDB entry {0} cannot be found.".format(pdb))
continue
for score in dockingMethods:
pose_path = os.path.join(posesDir, score, pdb)
# \TODO: add pattern for each docking method, right now only works with gold
lig_pattern = "gold_soln"
# RMSD dict for all poses
counter = counter + 1
print("Calculating RMSDs for ligand " + pdb + ", docking method " + score)
RMSDs = calcRMSDPoses(ref_lig_path, pose_path, lig_pattern)
for pose in listFiles(pose_path, lig_pattern):
lig_path = os.path.join(posesDir, score, pdb, pose)
poseRMSD = RMSDs[pose]
poseID = pose.split('.')[0] + '_' + score
if not os.path.exists(lig_path):
logger.error("The ligand structure for PDB entry {0} cannot be found.".format(pdb))
continue
protein = get_molecule(prot_path)
ligand = get_molecule(lig_path)
# CALCULATE DESCRIPTOR USING STRUCTURAL INTERACTION FINGERPRINTS
if options.descriptor == 'credo':
# GET THE PROTEIN-LIGAND STRUCTURAL INTERACTION FINGERPRINT
descriptor, labels = contacts.sift_descriptor(protein, ligand, binsize=options.binsize)
# CALCULATE DESCRIPTOR BASED ON THE SUM OF INTERACTING ELEMENT PAIRS
elif options.descriptor == 'elements':
# CALCULATE ELEMENT PAIR DESCRIPTOR FOR THIS COMPLEX
descriptor, labels = contacts.element_descriptor(protein, ligand, binsize=options.binsize)
# CALCULATE DESCRIPTOR BASED ON THE SUM OF INTERACTING ELEMENT PAIRS
elif options.descriptor == 'sybyl':
# CALCULATE ELEMENT PAIR DESCRIPTOR FOR THIS COMPLEX
descriptor, labels = contacts.sybyl_atom_type_descriptor(protein, ligand, binsize=options.binsize)
if HEADER:
# UPDATE COLUMN LABELS
labels.insert(0,'RMSD')
labels.append('ligandID')
writer.writerow(labels)
HEADER = False
if options.format == 'csv':
# KEEP ONLY THE TWO MOST SIGNIFICANT BITS
#pkdstring = "{0:.2f}".format(pkd)
# FIRST COLUMN OF OUTPUT ROW
row = [poseRMSD] + descriptor.tolist() + [poseID]
writer.writerow(row)