def rename_atoms_structure(self, pdbfile, gmx_path, forcefield):
"""
Create a subprocess to rename the atoms of the PDB input file using pdb2gmx
@type self: koala.RenameAtoms.RenameAtoms
@type pdbfile: file
@type gmx_path: string
@type forcefield: string
"""
delete_check_files(self.path_runs.get_path_execution())
program = os.path.join(gmx_path, "pdb2gmx")
process = Popen(
[program, "-f", pdbfile, "-o", pdbfile, "-p", "check.top", "-water", "none", "-ff", forcefield],
stdout=PIPE,
stderr=PIPE,
)
stdout, stderr = process.communicate()
process.wait()
delete_check_files(self.path_runs.get_path_execution())
def check_structue_by_pdb2gmx(self, pdbfile, gmx_path, forcefield):
"""
Create a subprocess to verify all the PDB input files
@type self: koala.CheckPDBStructure.CheckPDBStructure
@type pdbfile: file
@type gmx_path: string
@type forcefield: string
"""
try:
delete_check_files(self.path_runs.get_path_execution())
program = os.path.join(gmx_path, "pdb2gmx")
process = Popen([
program,
'-f',
pdbfile,
'-o',
'check.gro',
'-p',
'check.top',
'-water',
'none',
'-ff',
forcefield,
'-ignh'], stdout=PIPE, stderr=PIPE)
stdout, stderr = process.communicate()
process.wait()
# Checking output of pdb2gmx of pdbfile
if stderr.find('Fatal error') >= 0:
self.log_by_pdb2gmx(pdbfile, stderr)
self.move_structures(pdbfile)
delete_check_files(self.path_runs.get_path_execution())
except Exception, e:
show_error_message(str(e))