def main(args):
arg_dict = parse_arguments(args)
if not confirm_arguments(arg_dict):
if args[0].split(os.path.sep)[-1] == "pdbseq.py":
print_usage(args)
return
# Flags and values
# Inputs:
# The PDB file name.
pdb_file = arg_dict[ARG_PDB_FILE]
# The PDB chains
# Many PDB files include multiple chains. The chain_identifier list includes those
# chains which correspond to the protein whose contacts are being evaluated.
# Most often, chain 'A' (in the case of multiple chains) or chain ' ' (only one chain)
# will be the appropriate choice.
if arg_dict.has_key(ARG_CHAINS):
chains = arg_dict[ARG_CHAINS]
if type(chains) is list:
chain_identifiers = chains + [' ']
else:
chain_identifiers = [chains, ' ']
else:
chain_identifiers = ['A', ' ']
# The file name for output.
if arg_dict.has_key(ARG_OUTPUT_FILE):
output_file = file(arg_dict[ARG_OUTPUT_FILE], 'w')
else:
output_file = sys.stdout
# Read in the PDB file to create a list of residues.
residues = pdb.File().read(file(pdb_file, 'r'))
# Filter residues not in selected chains
residue_seq = pdb.sequence(residues, chain_identifiers)
if residue_seq == '':
print "No residues found for chain(s) %s. Aborting..." % chain_identifiers
return
# Print it
output_file.write('# Residue sequence for chain(s) %s from PDB file %s\n%s' % \
(chain_identifiers, pdb_file, residue_seq))
if arg_dict.has_key(ARG_OUTPUT_FILE):
output_file.close()
def main(args):
arg_dict = parse_arguments(args)
if not confirm_arguments(arg_dict):
if args[0].split(os.path.sep)[-1] == "pdbseq.py":
print_usage(args)
return
# Flags and values
# Inputs:
# The PDB file name.
pdb_file = arg_dict[ARG_PDB_FILE]
# The PDB chains
# Many PDB files include multiple chains. The chain_identifier list includes those
# chains which correspond to the protein whose contacts are being evaluated.
# Most often, chain 'A' (in the case of multiple chains) or chain ' ' (only one chain)
# will be the appropriate choice.
if arg_dict.has_key(ARG_CHAINS):
chains = arg_dict[ARG_CHAINS]
if type(chains) is list:
chain_identifiers = chains + [' ']
else:
chain_identifiers = [chains, ' ']
else:
chain_identifiers = ['A',' ']
# The file name for output.
if arg_dict.has_key(ARG_OUTPUT_FILE):
output_file = file(arg_dict[ARG_OUTPUT_FILE], 'w')
else:
output_file = sys.stdout
# Read in the PDB file to create a list of residues.
residues = pdb.File().read(file(pdb_file, 'r'))
# Filter residues not in selected chains
residue_seq = pdb.sequence(residues, chain_identifiers)
if residue_seq == '':
print "No residues found for chain(s) %s. Aborting..." % chain_identifiers
return
# Print it
output_file.write('# Residue sequence for chain(s) %s from PDB file %s\n%s' % \
(chain_identifiers, pdb_file, residue_seq))
if arg_dict.has_key(ARG_OUTPUT_FILE):
output_file.close()
def main(args):
arg_dict = parse_arguments(args)
if not confirm_arguments(arg_dict):
if args[0].split(os.path.sep)[-1] == "schemacontacts.py":
print_usage(args)
return
# Flags and values
# Inputs:
# The PDB file name.
pdb_file = arg_dict[ARG_PDB_FILE]
# The alignment/fragment file name.
msa_file = arg_dict[ARG_MULTIPLE_SEQUENCE_ALIGNMENT_FILE]
# The alignment between the reference parent (indicated by reference_parent_index)
# and the target protein sequence in the provided PDB file. The amino acids in
# the aligned reference parent should correspond exactly to those in the
# msa_file above.
# If you don't provide a PDB alignment file, the program will assume that the ID of the PDB structure
# contained in the HEADER field corresponds to one of the sequence IDs in the MSA.
parent_pdb_alignment_file = None
if arg_dict.has_key(ARG_PDB_ALIGNMENT_FILE):
if not os.path.isfile(arg_dict[ARG_PDB_ALIGNMENT_FILE]):
print " Can't find PDB/parent alignment file %s" % arg_dict[
ARG_PDB_ALIGNMENT_FILE]
return
else:
parent_pdb_alignment_file = arg_dict[ARG_PDB_ALIGNMENT_FILE]
else:
pdb_key = pdb.File().getIDCode(file(pdb_file, 'r'))
# The PDB chains
# Many PDB files include multiple chains. The chain_identifier list includes those
# chains which correspond to the protein whose contacts are being evaluated.
# Most often, chain 'A' (in the case of multiple chains) or chain ' ' (only one chain)
# will be the appropriate choice.
if arg_dict.has_key(ARG_CHAINS):
chains = arg_dict[ARG_CHAINS]
if type(chains) is list:
chain_identifiers = chains + [' ']
else:
chain_identifiers = [chains, ' ']
else:
chain_identifiers = ['A', ' ']
# Read the alignment file to create a list of parents.
# The parents will appear in the list in the order in which they appear in the file.
parent_list = schema.readMultipleSequenceAlignmentFile(file(msa_file, 'r'))
parent_dict = dict(parent_list)
# Generate the contacts
# Read in the PDB file to create a list of residues.
residues = pdb.File().read(file(pdb_file, 'r'))
# Because the PDB file's residue sequence may differ from those of the parents, we
# must align the PDB residues to one parent.
if not parent_pdb_alignment_file: # Just get PDB sequence from the multiple sequence alignment
try:
aligned_pdb = parent_dict[pdb_key]
aligned_prot = parent_dict[pdb_key]
except KeyError:
print "Could not find sequence %s in the multiple sequence alignment file %s. Aborting..." % (
pdb_key, msa_file)
return
else: # Pull information from the parent/PDB alignment file.
# Our objective is to find the sequence with the same key in both the parent MSA file and
# the parent/PDB alignment file.
pdb_parent_seq_list = schema.readMultipleSequenceAlignmentFile(
file(parent_pdb_alignment_file, 'r'))
pdb_parent_seq_dict = dict(pdb_parent_seq_list)
# Bail out if there are fewer than 2 sequences.
if len(pdb_parent_seq_dict.keys()) < 2:
print "Only found one uniquely named sequence in the PDB/parent alignment, %s. Aborting..." % pdb_parent_seq_dict.keys(
)[0]
return
# Find the matching key
pdb_key = None
for k in parent_dict.keys():
if pdb_parent_seq_dict.has_key(k):
pdb_key = k
# Bail out if no matching key is found
if not pdb_key:
print "Could not find parents %s in PDB/parent aligned sequences %s. Aborting..." % (
parent_dict.keys(), )
return
aligned_prot = pdb_parent_seq_dict[pdb_key]
# Remove the sequence corresponding to the pdb_key, leaving only the parent sequence.
del pdb_parent_seq_dict[pdb_key]
# Take the first remaining sequence, which should be the parent sequence.
aligned_pdb = pdb_parent_seq_dict.values()[0]
# Check to make sure the parent sequence from both alignment files matches.
if aligned_prot.replace('-', '') != parent_dict[pdb_key].replace('-', ''):
print "The PDB-aligned parent and the named parent, %s, don't match! Aborting..." % (
pdb_key, )
return
# Check to ensure the aligned PDB sequence matches the residue sequence pulled directly from the PDB file.
if aligned_pdb.replace('-', '') != pdb.sequence(residues,
chain_identifiers):
print "The parent-aligned PDB sequence, %s, and the PDB file sequence, chain(s) %s in %s, don't match! Aborting..." % (
pdb_key, chain_identifiers, pdb_file)
return
#print aligned_prot
#print aligned_pdb
#print parent_dict[pdb_key]
#print pdb.sequence(residues)
# Align the residues with the parent protein.
try:
residues = schema.alignPDBResidues(residues, aligned_prot, aligned_pdb,
parent_dict[pdb_key],
chain_identifiers)
except ValueError, ve:
print ve
return
def main(args):
arg_dict = parse_arguments(args)
if not confirm_arguments(arg_dict):
if args[0].split(os.path.sep)[-1] == "schemacontacts.py":
print_usage(args)
return
# Flags and values
# Inputs:
# The PDB file name.
pdb_file = arg_dict[ARG_PDB_FILE]
# The alignment/fragment file name.
msa_file = arg_dict[ARG_MULTIPLE_SEQUENCE_ALIGNMENT_FILE]
# The alignment between the reference parent (indicated by reference_parent_index)
# and the target protein sequence in the provided PDB file. The amino acids in
# the aligned reference parent should correspond exactly to those in the
# msa_file above.
# If you don't provide a PDB alignment file, the program will assume that the ID of the PDB structure
# contained in the HEADER field corresponds to one of the sequence IDs in the MSA.
parent_pdb_alignment_file = None
if arg_dict.has_key(ARG_PDB_ALIGNMENT_FILE):
if not os.path.isfile(arg_dict[ARG_PDB_ALIGNMENT_FILE]):
print " Can't find PDB/parent alignment file %s" % arg_dict[ARG_PDB_ALIGNMENT_FILE]
return
else:
parent_pdb_alignment_file = arg_dict[ARG_PDB_ALIGNMENT_FILE]
else:
pdb_key = pdb.File().getIDCode(file(pdb_file,'r'))
# The PDB chains
# Many PDB files include multiple chains. The chain_identifier list includes those
# chains which correspond to the protein whose contacts are being evaluated.
# Most often, chain 'A' (in the case of multiple chains) or chain ' ' (only one chain)
# will be the appropriate choice.
if arg_dict.has_key(ARG_CHAINS):
chains = arg_dict[ARG_CHAINS]
if type(chains) is list:
chain_identifiers = chains + [' ']
else:
chain_identifiers = [chains, ' ']
else:
chain_identifiers = ['A',' ']
# Read the alignment file to create a list of parents.
# The parents will appear in the list in the order in which they appear in the file.
parent_list = schema.readMultipleSequenceAlignmentFile(file(msa_file, 'r'))
parent_dict = dict(parent_list)
# Generate the contacts
# Read in the PDB file to create a list of residues.
residues = pdb.File().read(file(pdb_file, 'r'))
# Because the PDB file's residue sequence may differ from those of the parents, we
# must align the PDB residues to one parent.
if not parent_pdb_alignment_file: # Just get PDB sequence from the multiple sequence alignment
try:
aligned_pdb = parent_dict[pdb_key]
aligned_prot = parent_dict[pdb_key]
except KeyError:
print "Could not find sequence %s in the multiple sequence alignment file %s. Aborting..." % (pdb_key, msa_file)
return
else: # Pull information from the parent/PDB alignment file.
# Our objective is to find the sequence with the same key in both the parent MSA file and
# the parent/PDB alignment file.
pdb_parent_seq_list = schema.readMultipleSequenceAlignmentFile(file(parent_pdb_alignment_file, 'r'))
pdb_parent_seq_dict = dict(pdb_parent_seq_list)
# Bail out if there are fewer than 2 sequences.
if len(pdb_parent_seq_dict.keys()) < 2:
print "Only found one uniquely named sequence in the PDB/parent alignment, %s. Aborting..." % pdb_parent_seq_dict.keys()[0]
return
# Find the matching key
pdb_key = None
for k in parent_dict.keys():
if pdb_parent_seq_dict.has_key(k):
pdb_key = k
# Bail out if no matching key is found
if not pdb_key:
print "Could not find parents %s in PDB/parent aligned sequences %s. Aborting..." % (parent_dict.keys(),)
return
aligned_prot = pdb_parent_seq_dict[pdb_key]
# Remove the sequence corresponding to the pdb_key, leaving only the parent sequence.
del pdb_parent_seq_dict[pdb_key]
# Take the first remaining sequence, which should be the parent sequence.
aligned_pdb = pdb_parent_seq_dict.values()[0]
# Check to make sure the parent sequence from both alignment files matches.
if aligned_prot.replace('-','') != parent_dict[pdb_key].replace('-',''):
print "The PDB-aligned parent and the named parent, %s, don't match! Aborting..." % (pdb_key,)
return
# Check to ensure the aligned PDB sequence matches the residue sequence pulled directly from the PDB file.
if aligned_pdb.replace('-','') != pdb.sequence(residues, chain_identifiers):
print "The parent-aligned PDB sequence, %s, and the PDB file sequence, chain(s) %s in %s, don't match! Aborting..." % (pdb_key, chain_identifiers, pdb_file)
return
#print aligned_prot
#print aligned_pdb
#print parent_dict[pdb_key]
#print pdb.sequence(residues)
# Align the residues with the parent protein.
try:
residues = schema.alignPDBResidues(residues, aligned_prot, aligned_pdb, parent_dict[pdb_key], chain_identifiers)
except ValueError, ve:
print ve
return
