def launch(self):
"""Launches the execution of the GROMACS solvate module.
"""
out_log, err_log = fu.get_logs(path=self.path, mutation=self.mutation, step=self.step)
self.output_top_path = fu.add_step_mutation_path_to_name(self.output_top_path, self.step, self.mutation)
# Unzip topology to topology_out
fu.unzip_top(zip_file=self.input_top_zip_path, top_file=self.output_top_path)
gmx = 'gmx' if self.gmx_path is None else self.gmx_path
cmd = [gmx, 'solvate',
'-cp', self.input_solute_gro_path,
'-cs', self.input_solvent_gro_path,
'-o', self.output_gro_path,
'-p', self.output_top_path]
if self.mpirun_np is not None:
cmd.insert(0, str(self.mpirun_np))
cmd.insert(0, '-np')
if self.mpirun:
cmd.insert(0, 'mpirun')
command = cmd_wrapper.CmdWrapper(cmd, out_log, err_log)
returncode = command.launch()
with open(self.output_top_path) as topology_file:
out_log.info('Last 5 lines of new top file: ')
lines = topology_file.readlines()
for index in [-i for i in range(5,0,-1)]:
out_log.info(lines[index])
# zip new_topology
fu.zip_top(self.output_top_path, self.output_top_zip_path, remove_files=True)
return returncode
def launch(self):
"""Launches the execution of the GROMACS genion module.
"""
if self.global_log is not None:
if self.concentration:
self.global_log.info(19 * ' ' + 'To reach up ' +
str(self.concentration) +
' mol/litre concentration')
out_log, err_log = fu.get_logs(path=self.path,
mutation=self.mutation,
step=self.step)
self.output_top_path = fu.add_step_mutation_path_to_name(
self.output_top_path, self.step, self.mutation)
# Unzip topology to topology_out
fu.unzip_top(zip_file=self.input_top_zip_path,
top_file=self.output_top_path)
gmx = 'gmx' if self.gmx_path is None else self.gmx_path
cmd = [
gmx, 'genion', '-s', self.input_tpr_path, '-o',
self.output_gro_path, '-p', self.output_top_path
]
if self.mpirun_np is not None:
cmd.insert(0, str(self.mpirun_np))
cmd.insert(0, '-np')
if self.mpirun:
cmd.insert(0, 'mpirun')
if self.neutral:
cmd.append('-neutral')
if self.concentration:
cmd.append('-conc')
cmd.append(str(self.concentration))
if self.seed is not None:
cmd.append('-seed')
cmd.append(str(self.seed))
if self.mpirun:
cmd.append('<<<')
cmd.append('\"' + self.replaced_group + '\"')
else:
cmd.insert(0, '|')
cmd.insert(0, '\"' + self.replaced_group + '\"')
cmd.insert(0, 'echo')
command = cmd_wrapper.CmdWrapper(cmd, out_log, err_log)
returncode = command.launch()
# zip new_topology
fu.zip_top(self.output_top_path,
self.output_top_zip_path,
remove_files=True)
return returncode
def launch(self):
"""Launches the execution of the GROMACS pdb2gmx module.
"""
out_log, err_log = fu.get_logs(path=self.path,
mutation=self.mutation,
step=self.step)
self.output_top_path = fu.add_step_mutation_path_to_name(
self.output_top_path, self.step, self.mutation)
gmx = "gmx" if self.gmx_path is None else self.gmx_path
cmd = [
gmx, "pdb2gmx", "-f", self.input_structure_pdb_path, "-o",
self.output_gro_path, "-p", self.output_top_path, "-water",
self.water_type, "-ff", self.force_field
]
if self.mpirun_np is not None:
cmd.insert(0, str(self.mpirun_np))
cmd.insert(0, '-np')
if self.mpirun:
cmd.insert(0, 'mpirun')
if self.output_itp_path is not None:
self.output_itp_path = self.output_itp_path if self.step is None else self.step + '_' + self.output_itp_path
self.output_itp_path = self.output_itp_path if self.mutation is None else self.mutation + '_' + self.output_itp_path
cmd.append("-i")
cmd.append(self.output_itp_path)
if self.ignh:
cmd.append("-ignh")
command = cmd_wrapper.CmdWrapper(cmd, out_log, err_log)
returncode = command.launch()
#Remove comment (first line) from gro file
with open(self.output_gro_path, 'r') as fin:
data = fin.read().splitlines(True)
data[0] = 'Created with pdb2gmx building block\n'
with open(self.output_gro_path, 'w') as fout:
fout.writelines(data)
# zip topology
fu.zip_top(self.output_top_path,
self.output_top_zip_path,
remove_files=True)
return returncode
def launch(self):
"""Launches the execution of the GROMACS pdb2gmx module.
"""
out_log, err_log = fu.get_logs(path=self.path,
mutation=self.mutation,
step=self.step)
self.output_top_path = fu.add_step_mutation_path_to_name(
self.output_top_path, self.step, self.mutation)
self.output_itp_path = fu.add_step_mutation_path_to_name(
self.output_itp_path, self.step, self.mutation)
gmx = "gmx" if self.gmx_path is None else self.gmx_path
cmd = [
gmx, "genrestr", "-f", self.input_structure_path, "-n",
self.input_ndx_path, "-o", self.output_itp_path, "-fc",
self.force_constants
]
if self.mpirun_np is not None:
cmd.insert(0, str(self.mpirun_np))
cmd.insert(0, '-np')
if self.mpirun:
cmd.insert(0, 'mpirun')
if self.mpirun:
cmd.append('<<<')
cmd.append('\"' + self.restricted_group + '\"')
else:
cmd.insert(0, '|')
cmd.insert(0, '\"' + self.restricted_group + '\"')
cmd.insert(0, 'echo')
command = cmd_wrapper.CmdWrapper(cmd, out_log, err_log)
returncode = command.launch()
fu.unzip_top(zip_file=self.input_top_zip_path,
top_file=self.output_top_path)
out_log.info('Unzip: ' + self.input_top_zip_path + ' to: ' +
self.output_top_path)
with open(self.output_top_path, 'r') as fin:
for line in fin:
if line.startswith('#ifdef POSRES'):
itp_name = re.findall('"([^"]*)"', fin.next())[0]
out_log.debug('itp_name: ' + itp_name)
break
# with open(self.output_top_path, 'r') as fin:
# data = fin.read().splitlines(True)
# index = data.index('#ifdef POSRES\n')
# data[index+2] = 'system\n'
# data.insert(index, '\n')
# data.insert(index, '#endif\n')
# data.insert(index, '#include "'+self.output_itp_path+'"\n')
# data.insert(index, '#ifdef CUSTOM_POSRES\n')
# data.insert(index, '; Include Position restraint file\n')
# # data.insert(index, '#include "'+self.output_itp_path+'"\n')
# # data.insert(index, '; Include genrestr generated itp\n')
# with open(self.output_top_path, 'w') as fout:
# fout.writelines(data)
with open(self.output_itp_path, 'r') as fin:
data = fin.read().splitlines(True)
# data.insert(0, '\n')
# data.insert(0, 'system 3\n')
# data.insert(0, ';Name nrexcl\n')
# data.insert(0, '[ system ]\n')
with open(itp_name, 'w') as fout:
fout.writelines(data)
os.remove(self.output_itp_path)
# zip topology
fu.zip_top(self.output_top_path,
self.output_top_zip_path,
remove_files=False)
out_log.info('Zip: ' + self.output_top_path + ' to: ' +
self.output_top_zip_path)
return returncode
def launch(self):
"""Launch the topology generation.
"""
out_log, err_log = fu.get_logs(path=self.path,
mutation=self.mutation,
step=self.step)
self.output_top_path = fu.add_step_mutation_path_to_name(
self.output_top_path, self.step, self.mutation)
fu.unzip_top(zip_file=self.input_top_zip_path,
top_file=self.output_top_path)
out_log.info('Unzip: ' + self.input_top_zip_path + ' to: ' +
self.output_top_path)
# Create index list of index file :)
index_dic = {}
lines = open(self.input_ndx_path, 'r').read().splitlines()
for index, line in enumerate(lines):
if line.startswith('['):
index_dic[line] = index,
if index > 0:
index_dic[label] = index_dic[label][0], index
label = line
index_dic[label] = index_dic[label][0], index
out_log.info('Index_dic: ' + str(index_dic))
self.ref_rest_chain_triplet_list = [
tuple(elem.strip(' ()').replace(' ', '').split(','))
for elem in self.ref_rest_chain_triplet_list.split('),')
]
for reference_group, restrain_group, chain in self.ref_rest_chain_triplet_list:
out_log.info('Reference group: ' + reference_group)
out_log.info('Restrain group: ' + restrain_group)
out_log.info('Chain: ' + chain)
self.output_itp_path = fu.add_step_mutation_path_to_name(
restrain_group + '.itp', self.step, self.mutation)
# Mapping atoms from absolute enumeration to Chain relative enumeration
out_log.info('reference_group_index: start_closed:' +
str(index_dic['[ ' + reference_group + ' ]'][0] + 1) +
' stop_open: ' +
str(index_dic['[ ' + reference_group + ' ]'][1]))
reference_group_list = [
int(elem)
for line in lines[index_dic['[ ' + reference_group + ' ]'][0] +
1:index_dic['[ ' + reference_group +
' ]'][1]]
for elem in line.split()
]
out_log.info('restrain_group_index: start_closed:' +
str(index_dic['[ ' + restrain_group + ' ]'][0] + 1) +
' stop_open: ' +
str(index_dic['[ ' + restrain_group + ' ]'][1]))
restrain_group_list = [
int(elem)
for line in lines[index_dic['[ ' + restrain_group + ' ]'][0] +
1:index_dic['[ ' + restrain_group + ' ]'][1]]
for elem in line.split()
]
selected_list = [
reference_group_list.index(atom) + 1
for atom in restrain_group_list
]
# Creating new ITP with restrictions
with open(self.output_itp_path, 'w') as f:
out_log.info('Creating: ' + str(f) +
' and adding the selected atoms force constants')
f.write('[ position_restraints ]\n')
f.write('; atom type fx fy fz\n')
for atom in selected_list:
f.write(
str(atom) + ' 1 ' + self.force_constants + '\n')
# Including new ITP in the corresponding ITP-chain file
for file_name in os.listdir('.'):
if not file_name.startswith(
"posre") and not file_name.endswith("_pr.itp"):
if fnmatch.fnmatch(file_name, "*_chain_" + chain + ".itp"):
with open(file_name, 'a') as f:
out_log.info(
'Opening: ' + str(f) +
' and adding the ifdef include statement')
f.write('\n')
f.write('; Include Position restraint file\n')
f.write('#ifdef CUSTOM_POSRES\n')
f.write('#include "' + self.output_itp_path +
'"\n')
f.write('#endif\n')
# zip topology
fu.zip_top(self.output_top_path,
self.output_top_zip_path,
remove_files=True)
out_log.info('Zip: ' + self.output_top_path + ' to: ' +
self.output_top_zip_path)
return 0