def main(fasta_f, out_f='out.sdf'):
'''
Writes the sequences (with constraints) in fasta_f to a 3d SDF file, out_f.
'''
out_gen = (StructGen.constrained_peptide_smiles(*pair)
for pair in process_constraints(fasta_f))
#pdb.set_trace()
StructGen.write_library(out_gen, out_f,
write='structure', write_to_file=True)
def main(fasta_f, out_f='out.sdf'):
'''
Writes the sequences (with constraints) in fasta_f to a 3d SDF file, out_f.
'''
out_gen = (StructGen.constrained_peptide_smiles(*pair)
for pair in process_constraints(fasta_f))
#pdb.set_trace()
StructGen.write_library(out_gen,
out_f,
write='structure',
write_to_file=True)
def process_constraints(fasta_f):
'''
Processes the fasta file, and fills out incomplete constraint information
with a best guess.
'''
error_string = "%s is not a valid constraint for peptide %s"
constraint_functions = {
'SS': StructGen.can_ssbond,
'HT': StructGen.can_htbond,
'SCNT': StructGen.can_scntbond,
'SCCT': StructGen.can_scctbond,
'SCSC': StructGen.can_scscbond
}
for sequence, constraint in parse_fasta(fasta_f):
#Check if constraint is valid
if constraint.upper() in StructGen.what_constraints(sequence):
yield sequence, constraint
#If constraint does not specify a full pattern, only a type,
#try and generate the full pattern.
elif constraint.upper() in constraint_functions.keys():
result = constraint_functions[constraint.upper()](sequence)
if result:
yield result
else:
raise InvalidConstraintError(error_string %
(sequence, constraint))
elif constraint.upper() == 'SC':
#Try all the different side chain constraints, return the
#first one found
func_keys = [k for k in constraint_functions.keys() if 'SC' in k]
found = False
for k in func_keys:
result = constraint_functions[k](sequence)
if result:
yield result
found = True
break
if not found:
raise InvalidConstraintError(error_string %
(sequence, constraint))
elif not constraint:
#Generate linear peptide
yield sequence, ''
else:
raise InvalidConstraintError(error_string % (sequence, constraint))
def process_constraints(fasta_f):
'''
Processes the fasta file, and fills out incomplete constraint information
with a best guess.
'''
error_string = "%s is not a valid constraint for peptide %s"
constraint_functions = {'SS':StructGen.can_ssbond,
'HT':StructGen.can_htbond,
'SCNT':StructGen.can_scntbond,
'SCCT':StructGen.can_scctbond,
'SCSC':StructGen.can_scscbond}
for sequence, constraint in parse_fasta(fasta_f):
#Check if constraint is valid
if constraint.upper() in StructGen.what_constraints(sequence):
yield sequence, constraint
#If constraint does not specify a full pattern, only a type,
#try and generate the full pattern.
elif constraint.upper() in constraint_functions.keys():
result = constraint_functions[constraint.upper()](sequence)
if result:
yield result
else:
raise InvalidConstraintError(error_string % (sequence,
constraint))
elif constraint.upper() == 'SC':
#Try all the different side chain constraints, return the
#first one found
func_keys = [k for k in constraint_functions.keys() if 'SC' in k]
found = False
for k in func_keys:
result = constraint_functions[k](sequence)
if result:
yield result
found = True
break
if not found:
raise InvalidConstraintError(error_string % (sequence, constraint))
elif not constraint:
#Generate linear peptide
yield sequence, ''
else:
raise InvalidConstraintError(error_string % (sequence, constraint))
