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 rms module.
"""
out_log, err_log = fu.get_logs(path=self.path,
mutation=self.mutation,
step=self.step)
gmx = 'gmx' if self.gmx_path is 'None' else self.gmx_path
cmd = [
gmx, 'rms', '-xvg', 'none', '-s', self.input_gro_path, '-f',
self.input_trr_path, '-o', self.output_xvg_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')
cmd.append('<<<')
cmd.append('\"' + "$'0\n0\n'" + '\"')
else:
cmd.insert(0, '|')
cmd.insert(0, '\"' + '0 0' + '\"')
cmd.insert(0, 'echo')
command = cmd_wrapper.CmdWrapper(cmd, out_log, err_log)
command.launch()
xvg = self.output_xvg_path if os.path.isfile(
self.output_xvg_path) else ntpath.basename(self.output_xvg_path)
self.mutation = '' if self.mutation is None else self.mutation
return {self.mutation: np.loadtxt(xvg)}
def launch(self):
# using cmd_wrapper
out_log, err_log = fu.get_logs(path=self.properties['path'],
step=self.properties['step'])
cmd = ["python ", self.script, self.res_lib, self.pdb_in, self.pdb_out]
command = cmd_wrapper.CmdWrapper(cmd, out_log, err_log)
command.launch()
def launch(self):
"""Launches the execution of the GROMACS editconf module.
"""
out_log, err_log = fu.get_logs(path=self.path,
mutation=self.mutation,
step=self.step)
gmx = 'gmx' if self.gmx_path is None else self.gmx_path
cmd = [
gmx, 'make_ndx', '-f', self.input_structure_path, '-o',
self.output_ndx_path
]
if self.mpirun_np is not None:
cmd.insert(0, str(self.mpirun_np))
cmd.insert(0, '-np')
if self.mpirun:
cmd.insert(0, 'mpirun')
if self.mpirun:
cmd.append('<<<')
cmd.append('\"' + self.selection + '\"')
else:
cmd.insert(0, '|')
cmd.insert(0, '\"' + self.selection + '\"')
cmd.insert(0, 'echo')
command = cmd_wrapper.CmdWrapper(cmd, out_log, err_log)
return command.launch()
def launch(self):
"""Launches the execution of the GROMACS rms module.
"""
out_log, err_log = fu.get_logs(path=self.path, mutation=self.mutation, step=self.step)
gmx = 'gmx' if self.gmx_path is 'None' else self.gmx_path
cmd = [gmx, 'cluster',
'-s', self.input_gro_path,
'-f', self.input_xtc_path,
'-cl', self.output_pdb_path,
'-cutoff', str(self.cutoff)]
if self.mpirun_np is not None:
cmd.insert(0, str(self.mpirun_np))
cmd.insert(0, '-np')
if self.mpirun:
cmd.insert(0, 'mpirun')
cmd.append('<<<')
cmd.append('\"'+"$'0\n0\n'"+'\"')
else:
cmd.insert(0, '|')
cmd.insert(0, '\"'+'1 1'+'\"')
cmd.insert(0, 'echo')
command = cmd_wrapper.CmdWrapper(cmd, out_log, err_log)
return command.launch()
def get_decoys_from_pdb(self):
"""
Returns the pdb_code decoys
"""
out_log, err_log = fu.get_logs(path=self.path,
mutation=self.mutation,
step=self.step)
out_log.info(self.pdb_code + ' not in target list checking cluster')
print 'hola'
if self.pdb_code in self.targets:
target = self.targets.get(self.pdb_code.lower())
else:
out_log.info(self.pdb_code +
' not in target list checking cluster')
print '2'
pdb_set = pdb.MmbPdb().get_cluster_pdb_codes(self.pdb_code.lower())
targets_set = set(self.targets.keys())
targets_pdb_set = pdb_set.intersection(targets_set)
target = self.targets.get(targets_pdb_set.pop()).lower()
print target
if not target:
return None
decoys_file_name = 'decoys_final.sdf.gz'
url = self.url + '/targets/' + target.lower() + '/' + decoys_file_name
print url
req = requests.get(url, allow_redirects=True)
with open(decoys_file_name, 'wb') as gz_file:
gz_file.write(req.content)
with gzip.open(decoys_file_name, 'rb') as gz_file:
with open(self.output_sdf_path, 'wb') as sdf_file:
sdf_file.write(gz_file.read())
return self.output_sdf_path
def launch(self):
"""Launches the execution of the GNUPLOT binary.
"""
out_log, err_log = fu.get_logs(path=self.path, mutation=self.mutation, step=self.step)
self.output_plotscript_path = fu.add_step_mutation_path_to_name(self.output_plotscript_path, self.step, self.mutation)
# Create the input script for gnuplot
xvg_file_list = []
with open(self.output_plotscript_path, 'w') as ps:
ps.write('set term '+self.term+'\n')
ps.write('set output "' + self.output_png_path + '"'+'\n')
ps.write('plot')
for k, v in self.input_xvg_path_dict.iteritems():
if isinstance(v, basestring) and os.path.isfile(v):
ps.write(' "' + v + '" u 1:3 w lp t "' + k + '",')
else:
xvg_file = fu.add_step_mutation_path_to_name(k + '.xvg', self.step, self.mutation)
np.savetxt(xvg_file, v, fmt='%4.7f')
out_log.info('Creating file: '+os.path.abspath(xvg_file))
xvg_file_list.append(os.path.abspath(xvg_file))
ps.write(' "' + xvg_file + '" u 0:2 w lp t "' + k + '", ')
gplot = 'gnuplot' if self.gnuplot_path is None else self.gnuplot_path
cmd = [gplot, self.output_plotscript_path]
command = cmd_wrapper.CmdWrapper(cmd, out_log, err_log)
returncode = command.launch()
return returncode
def launch(self):
"""Launches the execution of the MGLTools prepare_receptor module."""
out_log, err_log = fu.get_logs(path=self.path)
cmd = [self.executor_path, self.script_path,
'-r', self.input_receptor_pdb_path,
'-o', self.output_receptor_pdbqt_path]
command = cmd_wrapper.CmdWrapper(cmd, out_log, err_log)
return command.launch()
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 sdf2pdb module."""
out_log, err_log = fu.get_logs(path=self.path, mutation=self.mutation, step=self.step)
pdb_list = []
for mol_index, mol in enumerate(pybel.readfile("sdf", self.input_sdf_path)):
if mol_index >= self.max_pdbs and self.max_pdbs !=0 : break
fname=str(mol.title)+'.pdb'
mol.write("pdb", fname, overwrite=True)
pdb_list.append(os.path.abspath(fname))
return pdb_list
def launch(self):
"""Launches the execution of the SCWRL binary.
"""
out_log, err_log = fu.get_logs(path=self.path,
mutation=self.mut,
step=self.step)
if self.mutation is not None:
# Read structure with Biopython
parser = PDBParser(PERMISSIVE=1)
st = parser.get_structure(
's', self.input_pdb_path) # s random id never used
# Remove the side chain of the AA to be mutated
if self.mutation['chain'] != '*':
chains = [self.mutation['chain']]
else:
chains = [chain.id for chain in st[0]]
resnum = int(self.mutation['resnum'])
for chain in chains:
residue = st[0][chain][(' ', resnum, ' ')]
backbone_atoms = ['N', 'CA', 'C', 'O', 'CB']
not_backbone_atoms = []
# The following formula does not work. Biopython bug?
# for atom in residue:
# if atom.id not in backbone_atoms:
# residue.detach_child(atom.id)
for atom in residue:
if atom.id not in backbone_atoms:
not_backbone_atoms.append(atom)
for atom in not_backbone_atoms:
residue.detach_child(atom.id)
# Change residue name
residue.resname = self.mutation['mt'].upper()
# Write resultant structure
w = PDBIO()
w.set_structure(st)
prepared_file_path = self.mut + self.step + 'prepared.pdb'
w.save(prepared_file_path)
else:
prepared_file_path = self.input_pdb_path
scrwl = 'Scwrl4' if self.scwrl4_path is None else self.scwrl4_path
cmd = [scrwl, '-i', prepared_file_path, '-o', self.output_pdb_path]
command = cmd_wrapper.CmdWrapper(cmd, out_log, err_log)
return command.launch()
def launch(self, deleteTmpDir=True):
# using cmd_wrapper
self.out_log, self.err_log = fu.get_logs(path=self.properties['path'],
step=self.properties['step'])
command = cmd_wrapper.CmdWrapper(self.run.setup(), self.out_log,
self.err_log)
command.launch()
# using original CMIP execute
# self.result = self.run.execute
self.result = Result(self.run.tmpdir, self.run.files)
if deleteTmpDir:
self.run.rmTmpDir()
return self.result
def main():
start_time = time.time()
yaml_path=sys.argv[1]
system=sys.argv[2]
conf = settings.YamlReader(yaml_path, system)
workflow_path = conf.properties[system]['workflow_path']
fu.create_dir(os.path.abspath(workflow_path))
out_log, _ = fu.get_logs(path=workflow_path, console=True)
paths = conf.get_paths_dic()
prop = conf.get_prop_dic(global_log=out_log)
out_log.info('')
out_log.info('_______MD LAUNCH_______')
out_log.info('')
out_log.info('step1: gppeq ---- Preprocessing: Molecular dynamics')
fu.create_dir(prop['step1_gppeq']['path'])
grompp.Grompp(properties=prop['step1_gppeq'], **paths['step1_gppeq']).launch()
out_log.info('step2: mdeq ----- Running: Molecular dynamics')
fu.create_dir(prop['step2_mdeq']['path'])
mdrun.Mdrun(properties=prop['step2_mdeq'], **paths['step2_mdeq']).launch()
#Create setupfiles dir and copy files
mdfiles_path = os.path.join(workflow_path,'mdfiles')
fu.create_dir(mdfiles_path)
shutil.copy(paths['step2_mdeq']['input_tpr_path'], os.path.join(mdfiles_path, 'md.tpr'))
shutil.copy(paths['step2_mdeq']['output_cpt_path'], os.path.join(mdfiles_path, 'md.cpt'))
shutil.copy(paths['step2_mdeq']['output_gro_path'], os.path.join(mdfiles_path, 'md.gro'))
shutil.copy('_step2_mdeq_mdeq.xtc', os.path.join(mdfiles_path, 'md.xtc'))
removed_list = fu.remove_temp_files(['#', '.top', '.plotscript', '.edr', '.xtc', '.itp', '.top', '.log', '.pdb', '.cpt', '.mdp', '.trr'])
out_log.info('')
out_log.info('Removing unwanted files: ')
for removed_file in removed_list:
out_log.info(' X ' + removed_file)
elapsed_time = time.time() - start_time
out_log.info('')
out_log.info('')
out_log.info('Execution sucessful: ')
out_log.info(' Workflow_path: '+workflow_path)
out_log.info(' Config File: '+yaml_path)
out_log.info(' System: '+system)
if len(sys.argv) >= 4:
out_log.info(' Nodes: '+sys.argv[3])
out_log.info('')
out_log.info('Elapsed time: '+str(elapsed_time)+' seconds')
out_log.info('')
def launch(self):
"""Launches the execution of the GROMACS mdrun module.
"""
out_log, err_log = fu.get_logs(path=self.path,
mutation=self.mutation,
step=self.step)
gmx = 'gmx' if self.gmx_path is None else self.gmx_path
cmd = [
gmx, 'mdrun', '-s', self.input_tpr_path, '-c', self.output_gro_path
]
if self.output_trr_path is not None:
cmd.append('-o')
cmd.append(self.output_trr_path)
if self.output_xtc_path is not None:
cmd.append('-x')
cmd.append(self.output_xtc_path)
if self.output_edr_path is not None:
cmd.append('-e')
cmd.append(self.output_edr_path)
if self.output_cpt_path is not None:
cmd.append('-cpo')
cmd.append(self.output_cpt_path)
if self.output_log_path is not None:
cmd.append('-g')
cmd.append(self.output_log_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')
#Number of threads to run (0 is guess)
if not self.num_threads is None:
cmd.append('-nt')
cmd.append(str(self.num_threads))
if not self.ntmpi is None:
cmd.append('-ntmpi')
cmd.append(str(self.ntmpi))
if not self.ntomp is None:
cmd.append('-ntomp')
cmd.append(str(self.ntomp))
if not self.gpu_id is None:
cmd.append('-gpu_id')
cmd.append(str(self.gpu_id))
command = cmd_wrapper.CmdWrapper(cmd, out_log, err_log)
return command.launch()
def launch(self):
"""Launches the execution of the AutoDock Vina docking"""
out_log, err_log = fu.get_logs(path=self.path, step=self.step)
vina = 'vina' if self.vina_path is None else self.vina_path
x0, y0, z0, sidex, sidey, sidez = AutoDockVina._calculate_box(
self.box_path)
cmd = [
vina, '--ligand', self.ligand_pdbqt_path, '--receptor',
self.receptor_pdbqt_path, '--center_x=' + x0, '--center_y=' + y0,
'--center_z=' + z0, '--size_x=' + sidex, '--size_y=' + sidey,
'--size_z=' + sidez, '--out', self.output_path, '--log',
self.log_file
]
command = cmd_wrapper.CmdWrapper(cmd, out_log, err_log)
return command.launch()
def test_launch(self):
out_log, _ = fu.get_logs(path=self.properties['path'], console=True)
self.properties['global_log'] = out_log
output_tpr_path = opj(self.properties['path'],
self.properties['output_tpr_path'])
returncode = Grompp(
input_gro_path=opj(self.data_dir,
self.properties['input_gro_path']),
input_top_zip_path=opj(self.data_dir,
self.properties['input_top_zip_path']),
input_cpt_path=opj(self.data_dir,
self.properties['input_cpt_path']),
output_tpr_path=output_tpr_path,
properties=self.properties).launch()
assert fx.exe_success(returncode)
assert fx.not_empty(output_tpr_path)
def launch(self):
"""Launches the execution of the GROMACS grompp module.
"""
out_log, err_log = fu.get_logs(path=self.path,
mutation=self.mutation,
step=self.step)
mdp_file_path = self.create_mdp(
) if self.input_mdp_path is None else self.input_mdp_path
if self.global_log is not None:
md = self.mdp.get('type', 'minimization')
if md != 'index' and md != 'free':
self.global_log.info(22 * ' ' + 'Will run a ' + md +
' md of ' + str(self.nsteps) + ' steps')
elif md == 'index':
self.global_log.info(
22 * ' ' +
'Will create a TPR to be used as structure file')
else:
self.global_log.info(
22 * ' ' + 'Will run a ' + md + ' md of ' +
fu.human_readable_time(int(self.nsteps) * float(self.dt)))
# Unzip topology in de directory of the output_tpr_path and get the
# topology path
topology_path = fu.unzip_top(self.input_top_zip_path)
gmx = 'gmx' if self.gmx_path is None else self.gmx_path
cmd = [
gmx, 'grompp', '-f', mdp_file_path, '-c', self.input_gro_path,
'-p', topology_path, '-o', self.output_tpr_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.input_cpt_path is not None:
cmd.append('-t')
cmd.append(self.input_cpt_path)
if self.output_mdp_path is not None:
cmd.append('-po')
cmd.append(self.output_mdp_path)
command = cmd_wrapper.CmdWrapper(cmd, out_log, err_log)
return command.launch()
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 editconf module.
"""
out_log, err_log = fu.get_logs(path=self.path,
mutation=self.mutation,
step=self.step)
gmx = 'gmx' if self.gmx_path is None else self.gmx_path
cmd = [
gmx, 'editconf', '-f', self.input_gro_path, '-o',
self.output_gro_path, '-d',
str(self.distance_to_molecule), '-bt', self.box_type
]
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.center_molecule:
cmd.append('-c')
command = cmd_wrapper.CmdWrapper(cmd, out_log, err_log)
return command.launch()
def main():
from pycompss.api.api import compss_open
start_time = time.time()
yaml_path = sys.argv[1]
system = sys.argv[2]
conf = settings.YamlReader(yaml_path, system)
workflow_path = conf.properties[system]['workflow_path']
fu.create_dir(os.path.abspath(workflow_path))
out_log, _ = fu.get_logs(path=workflow_path, console=True)
paths_glob = conf.get_paths_dic()
prop_glob = conf.get_prop_dic()
out_log.info('')
out_log.info('_______GROMACS FULL WORKFLOW_______')
out_log.info('')
out_log.info('step1: mmbpdb -- Get PDB')
structure = conf.properties[system].get('initial_structure_pdb_path', None)
if structure is None or not os.path.isfile(structure):
out_log.info(' Selected PDB code: ' +
prop_glob['step1_mmbpdb']['pdb_code'])
fu.create_dir(prop_glob['step1_mmbpdb']['path'])
pdb.MmbPdb().get_pdb(prop_glob['step1_mmbpdb']['pdb_code'],
paths_glob['step1_mmbpdb']['output_pdb_path'])
structure = paths_glob['step1_mmbpdb']['output_pdb_path']
out_log.info('step2: mmbuniprot -- Get mutations')
mutations = conf.properties.get('input_mapped_mutations_list', None)
if mutations is None or len(mutations) < 7:
mmbuniprot = uniprot.MmbVariants(prop_glob['step1_mmbpdb']['pdb_code'])
mutations = mmbuniprot.get_pdb_variants()
if mutations is None or len(mutations) == 0: return
else:
mutations = [
m.strip() for m in conf.properties.get(
'input_mapped_mutations_list').split(',')
]
mutations_limit = min(
len(mutations), int(prop_glob.get('mutations_limit', len(mutations))))
out_log.info('')
out_log.info('Number of mutations to be modelled: ' + str(mutations_limit))
rms_list = []
mutations_counter = 0
for mut in mutations:
if mutations_counter == mutations_limit: break
mutations_counter += 1
paths = conf.get_paths_dic(mut)
prop = conf.get_prop_dic(mut)
out_log.info('')
out_log.info('-------------------------')
out_log.info(
str(mutations_counter) + '/' + str(mutations_limit) + ' ' + mut)
out_log.info('-------------------------')
out_log.info('')
out_log.info('step3: scw ------ Model mutation')
fu.create_dir(prop['step3_scw']['path'])
paths['step3_scw']['input_pdb_path'] = structure
scwrl_pc(properties=prop['step3_scw'], **paths['step3_scw'])
out_log.info('step4: p2g ------ Create gromacs topology')
fu.create_dir(prop['step4_p2g']['path'])
pdb2gmx_pc(properties=prop['step4_p2g'], **paths['step4_p2g'])
out_log.info('step5: ec ------- Define box dimensions')
fu.create_dir(prop['step5_ec']['path'])
editconf_pc(properties=prop['step5_ec'], **paths['step5_ec'])
out_log.info('step6: sol ------ Fill the box with water molecules')
fu.create_dir(prop['step6_sol']['path'])
solvate_pc(properties=prop['step6_sol'], **paths['step6_sol'])
out_log.info(
'step7: gppions -- Preprocessing: Adding monoatomic ions')
fu.create_dir(prop['step7_gppions']['path'])
grompp_pc(properties=prop['step7_gppions'], **paths['step7_gppions'])
out_log.info('step8: gio ------ Running: Adding monoatomic ions')
fu.create_dir(prop['step8_gio']['path'])
genion_pc(properties=prop['step8_gio'], **paths['step8_gio'])
out_log.info('step9: gppmin --- Preprocessing: Energy minimization')
fu.create_dir(prop['step9_gppmin']['path'])
grompp_pc(properties=prop['step9_gppmin'], **paths['step9_gppmin'])
out_log.info('step10: mdmin ---- Running: Energy minimization')
fu.create_dir(prop['step10_mdmin']['path'])
mdrun_pc(properties=prop['step10_mdmin'], **paths['step10_mdmin'])
out_log.info(
'step11: gppnvt --- Preprocessing: nvt constant number of molecules, volume and temp'
)
fu.create_dir(prop['step11_gppnvt']['path'])
grompp_pc(properties=prop['step11_gppnvt'], **paths['step11_gppnvt'])
out_log.info(
'step12: mdnvt ---- Running: nvt constant number of molecules, volume and temp'
)
fu.create_dir(prop['step12_mdnvt']['path'])
mdrun_pc_cpt(properties=prop['step12_mdnvt'], **paths['step12_mdnvt'])
out_log.info(
'step13: gppnpt --- Preprocessing: npt constant number of molecules, pressure and temp'
)
fu.create_dir(prop['step13_gppnpt']['path'])
grompp_pc_cpt(properties=prop['step13_gppnpt'],
**paths['step13_gppnpt'])
out_log.info(
'step14: mdnpt ---- Running: npt constant number of molecules, pressure and temp'
)
fu.create_dir(prop['step14_mdnpt']['path'])
mdrun_pc_cpt(properties=prop['step14_mdnpt'], **paths['step14_mdnpt'])
out_log.info(
'step15: gppeq ---- Preprocessing: 1ns Molecular dynamics Equilibration'
)
fu.create_dir(prop['step15_gppeq']['path'])
grompp_pc_cpt(properties=prop['step15_gppeq'], **paths['step15_gppeq'])
out_log.info(
'step16: mdeq ----- Running: 1ns Molecular dynamics Equilibration')
fu.create_dir(prop['step16_mdeq']['path'])
mdrun_pc(properties=prop['step16_mdeq'], **paths['step16_mdeq'])
out_log.info('step17: rmsd ----- Computing RMSD')
fu.create_dir(prop['step17_rmsd']['path'])
rms_list.append(
rms_pc(properties=prop['step17_rmsd'], **paths['step17_rmsd']))
xvg_dict = reduce(merge_dictionaries, rms_list)
out_log.info('step18: gnuplot ----- Creating RMSD plot')
fu.create_dir(prop_glob['step18_gnuplot']['path'])
output_png_path = paths_glob['step18_gnuplot']['output_png_path']
properties = prop_glob['step18_gnuplot']
gnuplot_pc(xvg_dict, output_png_path, properties)
png = compss_open(output_png_path)
elapsed_time = time.time() - start_time
with open(opj(workflow_path, 'time.txt'), 'a') as time_file:
time_file.write('Elapsed time: ')
time_file.write(str(elapsed_time))
time_file.write('\n')
time_file.write('Config File: ')
time_file.write(sys.argv[1])
time_file.write('\n')
time_file.write('Sytem: ')
time_file.write(sys.argv[2])
time_file.write('\n')
if len(sys.argv) >= 4:
time_file.write('Nodes: ')
time_file.write(sys.argv[3])
time_file.write('\n')
def main():
start_time = time.time()
yaml_path = sys.argv[1]
system = sys.argv[2]
conf = settings.YamlReader(yaml_path, system)
workflow_path = conf.properties[system]['workflow_path']
fu.create_dir(os.path.abspath(workflow_path))
out_log, _ = fu.get_logs(path=workflow_path, console=True)
paths = conf.get_paths_dic()
props = conf.get_prop_dic(global_log=out_log)
out_log.info('')
out_log.info('_______TEST CMIP TITRATION WORKFLOW_______')
out_log.info('')
stepid = 'step1_mmbpdb'
out_log.info(stepid)
props['step'] = stepid
# For testing only
fu.create_dir(props[stepid]['path'])
copyfile(paths['step1_mmbpdb']['input_test_pdb_path'],
paths['step1_mmbpdb']['output_pdb_path'])
out_log.info('Test input file copy from: ' +
paths['step1_mmbpdb']['input_test_pdb_path'] + ' to: ' +
paths['step1_mmbpdb']['output_pdb_path'])
stepid = 'step2_preppdbCMIP'
out_log.info(stepid)
props['step'] = stepid
fu.create_dir(props[stepid]['path'])
out_log.info('Step 2 prep pdb CMIP create dir: ' + props[stepid]['path'])
PPW.prepPDBWrapper(paths[stepid], props[stepid]).launch()
# stepid = 'step3_CMIPTitration'
# out_log.info(stepid)
# props['step'] = stepid
#
# fu.create_dir(props[stepid]['path'])
#
# cw = CW.CMIPWrapper(paths[stepid],props[stepid])
# #Delaying removal of temporary dir until output is processed
# cw.launch(False)
# out_log.debug ("Temp directory: "+ cw.run.tmpdir)
# out_log.info(stepid + " CMIP Output")
#
# if cw.result.errstr:
# out_log.error(cw.result.errstr)
# sys.exit(1)
# else:
# out_log.info(cw.result.output)
# out_log.info('')
#
# outpdbFn = cw.result.getFileName('outpdb')+".pdb"
# out_log.info('Building output pdb file at')
# out_log.info(paths[stepid]['output_pdb_path'])
#
# out_log.info('Base File: '+ paths[stepid]['input_pdb_path'])
# out_log.info('Titration File: '+ outpdbFn)
#
# outFh = open(paths[stepid]['output_pdb_path'],"w")
# baseFh = open(paths[stepid]['input_pdb_path'],"r")
# addFh = open(outpdbFn,"r")
#
# outFh.write(baseFh.read())
# baseFh.close()
# for line in addFh:
# if re.match('^ATOM',line):
# outFh.write(line)
# outFh.close()
# addFh.close()
#
# out_log.info('')
#
# cw.run.rmTmpDir()
#
elapsed_time = time.time() - start_time
out_log.info('')
out_log.info('')
out_log.info('Execution successful: ')
out_log.info(' Workflow_path: ' + workflow_path)
out_log.info(' Config File: ' + yaml_path)
out_log.info(' System: ' + system)
if len(sys.argv) >= 4:
out_log.info(' Nodes: ' + sys.argv[3])
out_log.info('')
out_log.info('Elapsed time: ' + str(elapsed_time) + ' seconds')
out_log.info('')
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 main():
start_time = time.time()
yaml_path = sys.argv[1]
system = sys.argv[2]
conf = settings.YamlReader(yaml_path, system)
workflow_path = conf.properties[system]['workflow_path']
fu.create_dir(os.path.abspath(workflow_path))
out_log, _ = fu.get_logs(path=workflow_path, console=True, level='DEBUG')
paths = conf.get_paths_dic()
prop = conf.get_prop_dic(global_log=out_log)
out_log.info('')
out_log.info('_______GROMACS FULL WORKFLOW_______')
out_log.info('')
out_log.info("Command Executed:")
out_log.info(" ".join(sys.argv))
out_log.info('Workflow_path: ' + workflow_path)
out_log.info('Config File: ' + yaml_path)
out_log.info('System: ' + system)
out_log.info('')
#Download initial structure
out_log.info('step1: mmbpdb -- Get PDB')
structure = conf.properties[system].get('initial_structure_pdb_path', None)
if structure is None or not os.path.isfile(structure):
out_log.info(' Selected PDB code: ' +
prop['step1_mmbpdb']['pdb_code'])
fu.create_dir(prop['step1_mmbpdb']['path'])
pdb.MmbPdb().get_pdb(prop['step1_mmbpdb']['pdb_code'],
paths['step1_mmbpdb']['output_pdb_path'],
"filter=:" + prop['step1_mmbpdb']['pdb_chain'])
structure = paths['step1_mmbpdb']['output_pdb_path']
decoys_sdf_path = conf.properties[system].get('decoys_sdf_path', None)
if not decoys_sdf_path:
#Dowload decoys
out_log.info('Downloading decoys from DUDe')
fu.create_dir(prop['dude']['path'])
out_log.debug('\nPaths:\n' + str(paths['dude']) + '\nProperties:\n' +
str(prop['dude']) + '\n')
decoys_sdf_path = dude.Dude(properties=prop['dude'],
**paths['dude']).get_decoys_from_pdb()
#SDF to PDB list
out_log.info('Converting sdf to pdb')
fu.create_dir(prop['sdf2pdb']['path'])
out_log.debug('\nPaths:\n' + str(paths['sdf2pdb']) + '\nProperties:\n' +
str(prop['sdf2pdb']) + '\n')
decoys_pdb_list = sdf2pdb.SDF2PDB(input_sdf_path=decoys_sdf_path,
properties=prop['sdf2pdb']).launch()
#Get Actives
actives_dir_path = conf.properties[system].get('actives_dir_path', None)
actives_pdb_list = []
if not actives_dir_path:
pass
for dirpath, _, filenames in os.walk(actives_dir_path):
for f in filenames:
actives_pdb_list.append(os.path.abspath(os.path.join(dirpath, f)))
#Merge actives and decoys
small_molecules_list = decoys_pdb_list + actives_pdb_list
#Get bindingsite
out_log.info('bindingsite')
fu.create_dir(prop['bindingsite']['path'])
out_log.debug('\nPaths:\n' + str(paths['bindingsite']) +
'\nProperties:\n' + str(prop['bindingsite']) + '\n')
bindingsite.BindingSite(properties=prop['bindingsite'],
**paths['bindingsite']).launch()
# Get Receptor pdb cluster
receptors_pdb_path = conf.properties[system].get('receptors_pdb_path',
None)
if not receptors_pdb_path:
out_log.info('md_clustering workflow')
fu.create_dir(prop['md_clustering']['path'])
out_log.debug('\nPaths:\n' + str(paths['md_clustering']) +
'\nProperties:\n' + str(prop['md_clustering']) + '\n')
receptors_pdb_path = md_cluster.MDCluster(
yaml_path=prop['md_clustering']['yaml_path'],
system=prop['md_clustering']['system'],
workflow_path=paths['md_clustering']['workflow_path'],
structure_pdb_path=structure).launch()
# Get BindingSite BOX
out_log.info('box')
fu.create_dir(prop['box']['path'])
out_log.debug('\nPaths:\n' + str(paths['box']) + '\nProperties:\n' +
str(prop['box']) + '\n')
box.Box(properties=prop['box'],
input_pdb_path=receptors_pdb_path,
**paths['box']).launch()
# Split receptor PDB into multiple PDBs
parser = Bio.PDB.PDBParser()
st = parser.get_structure('st', receptors_pdb_path)
receptors_list = []
for i in range(len(st)):
structure_tmp = st.copy()
for j in range(len(st)):
if j != i:
structure_tmp.detach_child(j)
io = Bio.PDB.PDBIO()
io.set_structure(structure_tmp)
receptor_name = 'receptor_' + str(i) + '.pdb'
io.save(receptor_name)
receptors_list.append(receptor_name)
max_receptors = conf.properties[system].get('max_receptors',
len(receptors_list))
max_ligands = conf.properties[system].get('max_ligands',
len(small_molecules_list))
for receptor_index, receptor_path in enumerate(receptors_list):
if receptor_index >= max_receptors: break
#Prepare receptor
out_log.info('Prepare receptor')
fu.create_dir(prop['prepare_receptor']['path'])
out_log.debug('\nPaths:\n' + str(paths['prepare_receptor']) +
'\nProperties:\n' + str(prop['prepare_receptor']) + '\n')
prepare_receptor.VinaPrepareReceptor(
properties=prop['prepare_receptor'],
input_receptor_pdb_path=receptor_path,
**paths['prepare_receptor']).launch()
for ligand_index, ligand_path in enumerate(small_molecules_list):
if ligand_index >= max_ligands: break
#Prepare Ligand
out_log.info('Prepare ligand')
fu.create_dir(prop['prepare_ligand']['path'])
out_log.debug('\nPaths:\n' + str(paths['prepare_ligand']) +
'\nProperties:\n' + str(prop['prepare_ligand']) +
'\n')
prepare_ligand.VinaPrepareLigand(
properties=prop['prepare_ligand'],
input_ligand_pdb_path=ligand_path,
**paths['prepare_ligand']).launch()
#Launch vina docking
paths['vina']['output_path'] = os.path.join(
prop['vina']['path'],
os.path.splitext(os.path.basename(receptor_path))[0] + '_' +
os.path.splitext(os.path.basename(ligand_path))[0] +
'_docking.pdbqt')
out_log.info('vina')
fu.create_dir(prop['vina']['path'])
out_log.debug('\nPaths:\n' + str(paths['vina']) +
'\nProperties:\n' + str(prop['vina']) + '\n')
vina.AutoDockVina(properties=prop['vina'],
**paths['vina']).launch()
#Docking to list
#Get top 10 ligands
elapsed_time = time.time() - start_time
out_log.info('')
out_log.info('')
out_log.info('Execution sucessful: ')
out_log.info(' Workflow_path: ' + workflow_path)
out_log.info(' Config File: ' + yaml_path)
out_log.info(' System: ' + system)
out_log.info('')
out_log.info('Elapsed time: ' + str(elapsed_time) + ' seconds')
out_log.info('')
def main():
from pycompss.api.api import compss_open, compss_barrier
start_time = time.time()
yaml_path = sys.argv[1]
system = sys.argv[2]
n_mutations = sys.argv[3]
conf = settings.YamlReader(yaml_path, system)
workflow_path = conf.properties[system]['workflow_path']
fu.create_dir(os.path.abspath(workflow_path))
out_log, _ = fu.get_logs(path=workflow_path, console=True, level='DEBUG')
paths_glob = conf.get_paths_dic()
prop_glob = conf.get_prop_dic()
out_log.info('')
out_log.info('_______GROMACS FULL WORKFLOW_______')
out_log.info('')
out_log.info("Command Executed:")
out_log.info(" ".join(sys.argv))
out_log.info('Workflow_path: ' + workflow_path)
out_log.info('Config File: ' + yaml_path)
out_log.info('System: ' + system)
out_log.info('Mutations limit: ' + n_mutations)
if len(sys.argv) >= 5:
out_log.info('Nodes: ' + sys.argv[4])
out_log.info('')
out_log.info('step1: mmbpdb -- Get PDB')
structure = conf.properties[system].get('initial_structure_pdb_path', None)
if structure is None or not os.path.isfile(structure):
out_log.info(22 * ' ' + 'Selected PDB code: ' +
prop_glob['step1_mmbpdb']['pdb_code'])
fu.create_dir(prop_glob['step1_mmbpdb']['path'])
pdb.MmbPdb().get_pdb(prop_glob['step1_mmbpdb']['pdb_code'],
paths_glob['step1_mmbpdb']['output_pdb_path'])
structure = paths_glob['step1_mmbpdb']['output_pdb_path']
else:
out_log.info(22 * ' ' + 'Selected PDB structure: ' + structure)
out_log.info('step2: mmbuniprot -- Get mutations')
mutations = conf.properties.get('input_mapped_mutations_list', None)
if mutations is None or len(mutations) < 7:
mmbuniprot = uniprot.MmbVariants(prop_glob['step1_mmbpdb']['pdb_code'])
mutations = mmbuniprot.get_pdb_variants()
if mutations is None or len(mutations) == 0:
return
else:
out_log.info(22 * ' ' + 'Number of obtained mutations: ' +
str(len(mutations)))
else:
mutations = [
m.strip() for m in conf.properties.get(
'input_mapped_mutations_list').split(',')
]
out_log.info(22 * ' ' + 'Number of mutations in list: ' +
str(len(mutations)))
mutations_limit = min(len(mutations), int(n_mutations))
out_log.info('')
out_log.info('Number of mutations to be modelled: ' + str(mutations_limit))
rms_list = []
mutations_counter = 0
for mut in mutations:
if mutations_counter == mutations_limit: break
mutations_counter += 1
mut = mut if not mut.startswith('*') else mut.replace('*', 'ALL')
paths = conf.get_paths_dic(mut)
prop = conf.get_prop_dic(mut)
out_log.info('')
out_log.info('-------------------------')
out_log.info(
str(mutations_counter) + '/' + str(mutations_limit) + ' ' + mut)
out_log.info('-------------------------')
out_log.info('')
out_log.info('step3: scw ---------- Model mutation')
fu.create_dir(prop['step3_scw']['path'])
paths['step3_scw']['input_pdb_path'] = structure
out_log.debug('Paths:')
out_log.debug(str(paths['step3_scw']))
out_log.debug('Properties:')
out_log.debug(str(prop['step3_scw']) + '\n')
scwrl_pc(properties=prop['step3_scw'], **paths['step3_scw'])
out_log.info('step4: p2g ---------- Create gromacs topology')
fu.create_dir(prop['step4_p2g']['path'])
out_log.debug('Paths:')
out_log.debug(str(paths['step4_p2g']))
out_log.debug('Properties:')
out_log.debug(str(prop['step4_p2g']) + '\n')
pdb2gmx_pc(properties=prop['step4_p2g'], **paths['step4_p2g'])
out_log.info('step5: ec ----------- Define box dimensions')
fu.create_dir(prop['step5_ec']['path'])
out_log.debug('Paths:')
out_log.debug(str(paths['step5_ec']))
out_log.debug('Properties:')
out_log.debug(str(prop['step5_ec']) + '\n')
editconf_pc(properties=prop['step5_ec'], **paths['step5_ec'])
out_log.info('step6: sol ---------- Fill the box with water molecules')
fu.create_dir(prop['step6_sol']['path'])
out_log.debug('Paths:')
out_log.debug(str(paths['step6_sol']))
out_log.debug('Properties:')
out_log.debug(str(prop['step6_sol']) + '\n')
solvate_pc(properties=prop['step6_sol'], **paths['step6_sol'])
out_log.info(
'step7: gppions ------ Preprocessing: Adding monoatomic ions')
fu.create_dir(prop['step7_gppions']['path'])
out_log.debug('Paths:')
out_log.debug(str(paths['step7_gppions']))
out_log.debug('Properties:')
out_log.debug(str(prop['step7_gppions']) + '\n')
grompp_pc(properties=prop['step7_gppions'], **paths['step7_gppions'])
out_log.info('step8: gio ---------- Running: Adding monoatomic ions')
fu.create_dir(prop['step8_gio']['path'])
out_log.debug('Paths:')
out_log.debug(str(paths['step8_gio']))
out_log.debug('Properties:')
out_log.debug(str(prop['step8_gio']) + '\n')
genion_pc(properties=prop['step8_gio'], **paths['step8_gio'])
out_log.info('Step9: gppndx ------- Preprocessing index creation')
fu.create_dir(prop['step9_gppndx']['path'])
out_log.debug('Paths:')
out_log.debug(str(paths['step9_gppndx']))
out_log.debug('Properties:')
out_log.debug(str(prop['step9_gppndx']) + '\n')
grompp_pc(properties=prop['step9_gppndx'], **paths['step9_gppndx'])
out_log.info('Step10: make_ndx ---- Create restrain index')
fu.create_dir(prop['step10_make_ndx']['path'])
out_log.debug('Paths:')
out_log.debug(str(paths['step10_make_ndx']))
out_log.debug('Properties:')
out_log.debug(str(prop['step10_make_ndx']) + '\n')
make_ndx_pc(properties=prop['step10_make_ndx'],
**paths['step10_make_ndx'])
out_log.info('Step11: ndx2resttop - Create restrain topology')
fu.create_dir(prop['step11_ndx2resttop']['path'])
out_log.debug('Paths:')
out_log.debug(str(paths['step11_ndx2resttop']))
out_log.debug('Properties:')
out_log.debug(str(prop['step11_ndx2resttop']) + '\n')
ndx2resttop_pc(properties=prop['step11_ndx2resttop'],
**paths['step11_ndx2resttop'])
out_log.info(
'step12: gppresmin --- Preprocessing: Mutated residue minimization'
)
fu.create_dir(prop['step12_gppresmin']['path'])
out_log.debug('Paths:')
out_log.debug(str(paths['step12_gppresmin']))
out_log.debug('Properties:')
out_log.debug(str(prop['step12_gppresmin']) + '\n')
grompp_pc(properties=prop['step12_gppresmin'],
**paths['step12_gppresmin'])
out_log.info(
'step13: mdresmin ---- Running: Mutated residue minimization')
fu.create_dir(prop['step13_mdresmin']['path'])
out_log.debug('Paths:')
out_log.debug(str(paths['step13_mdresmin']))
out_log.debug('Properties:')
out_log.debug(str(prop['step13_mdresmin']) + '\n')
mdrun_pc(properties=prop['step13_mdresmin'],
**paths['step13_mdresmin'])
out_log.info('Step14: ndx2resttop - Create restrain topology')
fu.create_dir(prop['step14_ndx2resttop']['path'])
out_log.debug('Paths:')
out_log.debug(str(paths['step14_ndx2resttop']))
out_log.debug('Properties:')
out_log.debug(str(prop['step14_ndx2resttop']) + '\n')
ndx2resttop_pc(properties=prop['step14_ndx2resttop'],
**paths['step14_ndx2resttop'])
out_log.info('step15: gppmin ------ Preprocessing: minimization')
fu.create_dir(prop['step15_gppmin']['path'])
out_log.debug('Paths:')
out_log.debug(str(paths['step15_gppmin']))
out_log.debug('Properties:')
out_log.debug(str(prop['step15_gppmin']) + '\n')
grompp_pc(properties=prop['step15_gppmin'], **paths['step15_gppmin'])
out_log.info('step16: mdmin ------- Running: minimization')
fu.create_dir(prop['step16_mdmin']['path'])
out_log.debug('Paths:')
out_log.debug(str(paths['step16_mdmin']))
out_log.debug('Properties:')
out_log.debug(str(prop['step16_mdmin']) + '\n')
mdrun_pc(properties=prop['step16_mdmin'], **paths['step16_mdmin'])
out_log.info('Step17: ndx2resttop - Create restrain topology')
fu.create_dir(prop['step17_ndx2resttop']['path'])
out_log.debug('Paths:')
out_log.debug(str(paths['step17_ndx2resttop']))
out_log.debug('Properties:')
out_log.debug(str(prop['step17_ndx2resttop']) + '\n')
ndx2resttop_pc(properties=prop['step17_ndx2resttop'],
**paths['step17_ndx2resttop'])
out_log.info(
'step18: gppsa ------- Preprocessing: simulated annealing')
fu.create_dir(prop['step18_gppsa']['path'])
out_log.debug('Paths:')
out_log.debug(str(paths['step18_gppsa']))
out_log.debug('Properties:')
out_log.debug(str(prop['step18_gppsa']) + '\n')
grompp_pc(properties=prop['step18_gppsa'], **paths['step18_gppsa'])
out_log.info('step19: mdsa -------- Running: simulated annealing')
fu.create_dir(prop['step19_mdsa']['path'])
out_log.debug('Paths:')
out_log.debug(str(paths['step19_mdsa']))
out_log.debug('Properties:')
out_log.debug(str(prop['step19_mdsa']) + '\n')
mdrun_pc_cpt(properties=prop['step19_mdsa'], **paths['step19_mdsa'])
out_log.info(
'step20: gppnvt_1000 - Preprocessing: nvt constant number of molecules, volume and temp'
)
fu.create_dir(prop['step20_gppnvt_1000']['path'])
out_log.debug('Paths:')
out_log.debug(str(paths['step20_gppnvt_1000']))
out_log.debug('Properties:')
out_log.debug(str(prop['step20_gppnvt_1000']) + '\n')
grompp_pc_cpt(properties=prop['step20_gppnvt_1000'],
**paths['step20_gppnvt_1000'])
out_log.info(
'step21: mdnvt_1000 -- Running: nvt constant number of molecules, volume and temp'
)
fu.create_dir(prop['step21_mdnvt_1000']['path'])
out_log.debug('Paths:')
out_log.debug(str(paths['step21_mdnvt_1000']))
out_log.debug('Properties:')
out_log.debug(str(prop['step21_mdnvt_1000']) + '\n')
mdrun_pc_cpt(properties=prop['step21_mdnvt_1000'],
**paths['step21_mdnvt_1000'])
out_log.info('Step22: ndx2resttop - Create restrain topology')
fu.create_dir(prop['step22_ndx2resttop']['path'])
out_log.debug('Paths:')
out_log.debug(str(paths['step22_ndx2resttop']))
out_log.debug('Properties:')
out_log.debug(str(prop['step22_ndx2resttop']) + '\n')
ndx2resttop_pc(properties=prop['step22_ndx2resttop'],
**paths['step22_ndx2resttop'])
out_log.info(
'step23: gppnvt_800 -- Preprocessing: nvt constant number of molecules, volume and temp'
)
fu.create_dir(prop['step23_gppnvt_800']['path'])
out_log.debug('Paths:')
out_log.debug(str(paths['step23_gppnvt_800']))
out_log.debug('Properties:')
out_log.debug(str(prop['step23_gppnvt_800']) + '\n')
grompp_pc_cpt(properties=prop['step23_gppnvt_800'],
**paths['step23_gppnvt_800'])
out_log.info(
'step24: mdnvt_800 --- Running: nvt constant number of molecules, volume and temp'
)
fu.create_dir(prop['step24_mdnvt_800']['path'])
out_log.debug('Paths:')
out_log.debug(str(paths['step24_mdnvt_800']))
out_log.debug('Properties:')
out_log.debug(str(prop['step24_mdnvt_800']) + '\n')
mdrun_pc_cpt(properties=prop['step24_mdnvt_800'],
**paths['step24_mdnvt_800'])
out_log.info('Step25: ndx2resttop - Create restrain topology')
fu.create_dir(prop['step25_ndx2resttop']['path'])
out_log.debug('Paths:')
out_log.debug(str(paths['step25_ndx2resttop']))
out_log.debug('Properties:')
out_log.debug(str(prop['step25_ndx2resttop']) + '\n')
ndx2resttop_pc(properties=prop['step25_ndx2resttop'],
**paths['step25_ndx2resttop'])
out_log.info(
'step26: gppnpt_500 -- Preprocessing: npt constant number of molecules, pressure and temp'
)
fu.create_dir(prop['step26_gppnpt_500']['path'])
out_log.debug('Paths:')
out_log.debug(str(paths['step26_gppnpt_500']))
out_log.debug('Properties:')
out_log.debug(str(prop['step26_gppnpt_500']) + '\n')
grompp_pc_cpt(properties=prop['step26_gppnpt_500'],
**paths['step26_gppnpt_500'])
out_log.info(
'step27: mdnpt_500 --- Running: npt constant number of molecules, pressure and temp'
)
fu.create_dir(prop['step27_mdnpt_500']['path'])
out_log.debug('Paths:')
out_log.debug(str(paths['step27_mdnpt_500']))
out_log.debug('Properties:')
out_log.debug(str(prop['step27_mdnpt_500']) + '\n')
mdrun_pc_cpt(properties=prop['step27_mdnpt_500'],
**paths['step27_mdnpt_500'])
out_log.info('Step28: ndx2resttop - Create restrain topology')
fu.create_dir(prop['step28_ndx2resttop']['path'])
out_log.debug('Paths:')
out_log.debug(str(paths['step28_ndx2resttop']))
out_log.debug('Properties:')
out_log.debug(str(prop['step28_ndx2resttop']) + '\n')
ndx2resttop_pc(properties=prop['step28_ndx2resttop'],
**paths['step28_ndx2resttop'])
out_log.info(
'step29: gppnpt_300 -- Preprocessing: npt constant number of molecules, pressure and temp'
)
fu.create_dir(prop['step29_gppnpt_300']['path'])
out_log.debug('Paths:')
out_log.debug(str(paths['step29_gppnpt_300']))
out_log.debug('Properties:')
out_log.debug(str(prop['step29_gppnpt_300']) + '\n')
grompp_pc_cpt(properties=prop['step29_gppnpt_300'],
**paths['step29_gppnpt_300'])
out_log.info(
'step30: mdnpt_300 --- Running: npt constant number of molecules, pressure and temp'
)
fu.create_dir(prop['step30_mdnpt_300']['path'])
out_log.debug('Paths:')
out_log.debug(str(paths['step30_mdnpt_300']))
out_log.debug('Properties:')
out_log.debug(str(prop['step30_mdnpt_300']) + '\n')
mdrun_pc_cpt(properties=prop['step30_mdnpt_300'],
**paths['step30_mdnpt_300'])
out_log.info('Step31: ndx2resttop - Create restrain topology')
fu.create_dir(prop['step31_ndx2resttop']['path'])
out_log.debug('Paths:')
out_log.debug(str(paths['step31_ndx2resttop']))
out_log.debug('Properties:')
out_log.debug(str(prop['step31_ndx2resttop']) + '\n')
ndx2resttop_pc(properties=prop['step31_ndx2resttop'],
**paths['step31_ndx2resttop'])
out_log.info(
'step32: gppnpt_200 -- Preprocessing: npt constant number of molecules, pressure and temp'
)
fu.create_dir(prop['step32_gppnpt_200']['path'])
out_log.debug('Paths:')
out_log.debug(str(paths['step32_gppnpt_200']))
out_log.debug('Properties:')
out_log.debug(str(prop['step32_gppnpt_200']) + '\n')
grompp_pc_cpt(properties=prop['step32_gppnpt_200'],
**paths['step32_gppnpt_200'])
out_log.info(
'step33: mdnpt_200 --- Running: npt constant number of molecules, pressure and temp'
)
fu.create_dir(prop['step33_mdnpt_200']['path'])
out_log.debug('Paths:')
out_log.debug(str(paths['step33_mdnpt_200']))
out_log.debug('Properties:')
out_log.debug(str(prop['step33_mdnpt_200']) + '\n')
mdrun_pc_cpt(properties=prop['step33_mdnpt_200'],
**paths['step33_mdnpt_200'])
out_log.info('Step34: ndx2resttop - Create restrain topology')
fu.create_dir(prop['step34_ndx2resttop']['path'])
out_log.debug('Paths:')
out_log.debug(str(paths['step34_ndx2resttop']))
out_log.debug('Properties:')
out_log.debug(str(prop['step34_ndx2resttop']) + '\n')
ndx2resttop_pc(properties=prop['step34_ndx2resttop'],
**paths['step34_ndx2resttop'])
out_log.info(
'step35: gppnpt_100 -- Preprocessing: npt constant number of molecules, pressure and temp'
)
fu.create_dir(prop['step35_gppnpt_100']['path'])
out_log.debug('Paths:')
out_log.debug(str(paths['step35_gppnpt_100']))
out_log.debug('Properties:')
out_log.debug(str(prop['step35_gppnpt_100']) + '\n')
grompp_pc_cpt(properties=prop['step35_gppnpt_100'],
**paths['step35_gppnpt_100'])
out_log.info(
'step36: mdnpt_100 --- Running: npt constant number of molecules, pressure and temp'
)
fu.create_dir(prop['step36_mdnpt_100']['path'])
out_log.debug('Paths:')
out_log.debug(str(paths['step36_mdnpt_100']))
out_log.debug('Properties:')
out_log.debug(str(prop['step36_mdnpt_100']) + '\n')
mdrun_pc_cpt(properties=prop['step36_mdnpt_100'],
**paths['step36_mdnpt_100'])
out_log.info('Step37: ndx2resttop - Create restrain topology')
fu.create_dir(prop['step37_ndx2resttop']['path'])
out_log.debug('Paths:')
out_log.debug(str(paths['step37_ndx2resttop']))
out_log.debug('Properties:')
out_log.debug(str(prop['step37_ndx2resttop']) + '\n')
ndx2resttop_pc(properties=prop['step37_ndx2resttop'],
**paths['step37_ndx2resttop'])
out_log.info(
'step38: gppnpt ------ Preprocessing: npt constant number of molecules, pressure and temp'
)
fu.create_dir(prop['step38_gppnpt']['path'])
out_log.debug('Paths:')
out_log.debug(str(paths['step38_gppnpt']))
out_log.debug('Properties:')
out_log.debug(str(prop['step38_gppnpt']) + '\n')
grompp_pc_cpt(properties=prop['step38_gppnpt'],
**paths['step38_gppnpt'])
out_log.info(
'step39: mdnpt ------- Running: npt constant number of molecules, pressure and temp'
)
fu.create_dir(prop['step39_mdnpt']['path'])
out_log.debug('Paths:')
out_log.debug(str(paths['step39_mdnpt']))
out_log.debug('Properties:')
out_log.debug(str(prop['step39_mdnpt']) + '\n')
mdrun_pc_cpt(properties=prop['step39_mdnpt'], **paths['step39_mdnpt'])
out_log.info(
'step40: gppmd ------- Preprocessing: Free Molecular dynamics')
fu.create_dir(prop['step40_gppmd']['path'])
out_log.debug('Paths:')
out_log.debug(str(paths['step40_gppmd']))
out_log.debug('Properties:')
out_log.debug(str(prop['step40_gppmd']) + '\n')
grompp_pc_cpt(properties=prop['step40_gppmd'], **paths['step40_gppmd'])
out_log.info('step41: md ---------- Running: Free Molecular dynamics')
fu.create_dir(prop['step41_md']['path'])
out_log.debug('Paths:')
out_log.debug(str(paths['step41_md']))
out_log.debug('Properties:')
out_log.debug(str(prop['step41_md']) + '\n')
mdrun_pc_cpt(properties=prop['step41_md'], **paths['step41_md'])
# out_log.info('step42: rmsd -------- Computing RMSD')
# fu.create_dir(prop['step42_rmsd']['path'])
# out_log.debug('Paths:')
# out_log.debug(str(paths['step42_rmsd']))
# out_log.debug('Properties:')
# out_log.debug(str(prop['step42_rmsd'])+'\n')
# rms_list.append(rms_pc(properties=prop['step42_rmsd'], **paths['step42_rmsd']))
# fu.remove_temp_files(['#', '.top', '.plotscript', '.edr', '.xtc', '.itp', '.top', '.log', '.pdb', '.cpt', '.mdp', '.xvg', '.seq'])
#
# xvg_dict = reduce(merge_dictionaries, rms_list)
#
# out_log.info('')
# out_log.info('step43: gnuplot ----- Creating RMSD plot')
# fu.create_dir(prop_glob['step43_gnuplot']['path'])
# output_png_path = paths_glob['step43_gnuplot']['output_png_path']
# properties = prop_glob['step43_gnuplot']
# gnuplot_pc(xvg_dict, output_png_path, properties)
#
# png = compss_open(output_png_path)
compss_barrier()
elapsed_time = time.time() - start_time
out_log.info('')
out_log.info('')
out_log.info('Execution sucessful: ')
out_log.info(' Workflow_path: ' + workflow_path)
out_log.info(' Config File: ' + yaml_path)
out_log.info(' System: ' + system)
if len(sys.argv) >= 5:
out_log.info(' Nodes: ' + sys.argv[4])
out_log.info('')
out_log.info('Elapsed time: ' + str(elapsed_time) + ' seconds')
out_log.info('')
def launch(self):
"""Launches the execution of the SCWRL binary.
"""
out_log, err_log = fu.get_logs(path=self.path,
mutation=self.mutation,
step=self.step)
if self.mutation is not None:
# Read structure with Biopython
parser = PDBParser(PERMISSIVE=1, QUIET=True)
st = parser.get_structure(
's', self.input_pdb_path) # s random id never used
if self.mut_dict['chain'] != 'ALL':
chains = [self.mut_dict['chain']]
else:
chains = [chain.id for chain in st[0]]
resnum = int(self.mut_dict['resnum'])
sequence = ''
for chain in chains:
residue = st[0][chain][(' ', resnum, ' ')]
backbone_atoms = ['N', 'CA', 'C', 'O', 'CB']
not_backbone_atoms = []
# The following formula does not work. Biopython bug?
# for atom in residue:
# if atom.id not in backbone_atoms:
# residue.detach_child(atom.id)
for atom in residue:
if atom.id not in backbone_atoms:
not_backbone_atoms.append(atom)
for atom in not_backbone_atoms:
residue.detach_child(atom.id)
# Change residue name
residue.resname = self.mut_dict['mt'].upper()
# Creating a sequence file where the lower case residues will
# remain untouched and the upper case residues will be modified
aa1c = {
'ALA': 'A',
'CYS': 'C',
'CYX': 'C',
'ASP': 'D',
'ASH': 'D',
'GLU': 'E',
'GLH': 'E',
'PHE': 'F',
'GLY': 'G',
'HIS': 'H',
'HID': 'H',
'HIE': 'H',
'HIP': 'H',
'ILE': 'I',
'LYS': 'K',
'LYP': 'K',
'LEU': 'L',
'MET': 'M',
'MSE': 'M',
'ASN': 'N',
'PRO': 'P',
'HYP': 'P',
'GLN': 'Q',
'ARG': 'R',
'SER': 'S',
'THR': 'T',
'VAL': 'V',
'TRP': 'W',
'TYR': 'Y'
}
for res in st[0][chain].get_residues():
if res.resname not in aa1c:
st[0][chain].detach_child(res.id)
elif (res.id == (' ', resnum, ' ')):
sequence += aa1c[res.resname].upper()
else:
sequence += aa1c[res.resname].lower()
# Write resultant sequence
sequence_file_path = fu.add_step_mutation_path_to_name(
"sequence.seq", self.step, self.mutation)
with open(sequence_file_path, 'w') as sqfile:
sqfile.write(sequence + "\n")
# Write resultant structure
w = PDBIO()
w.set_structure(st)
prepared_file_path = fu.add_step_mutation_path_to_name(
"prepared.pdb", self.step, self.mutation)
w.save(prepared_file_path)
else:
prepared_file_path = self.input_pdb_path
scrwl = 'Scwrl4' if self.scwrl4_path is None else self.scwrl4_path
cmd = [
scrwl, '-i', prepared_file_path, '-o', self.output_pdb_path, '-h',
'-t'
]
if self.mutation:
cmd.append('-s')
cmd.append(sequence_file_path)
command = cmd_wrapper.CmdWrapper(cmd, out_log, err_log)
return command.launch()
def main():
start_time = time.time()
yaml_path=sys.argv[1]
system=sys.argv[2]
n_mutations=sys.argv[3]
conf = settings.YamlReader(yaml_path, system)
workflow_path = conf.properties[system]['workflow_path']
fu.create_dir(os.path.abspath(workflow_path))
out_log, _ = fu.get_logs(path=workflow_path, console=True)
paths_glob = conf.get_paths_dic()
prop_glob = conf.get_prop_dic()
out_log.info('')
out_log.info('_______GROMACS FULL WORKFLOW_______')
out_log.info('')
out_log.info("Command Executed:")
out_log.info(" ".join(sys.argv))
out_log.info('Workflow_path: '+workflow_path)
out_log.info('Config File: '+yaml_path)
out_log.info('System: '+system)
out_log.info('Mutations limit: '+n_mutations)
if len(sys.argv) >= 5:
out_log.info('Nodes: '+sys.argv[4])
out_log.info('')
out_log.info( 'step1: mmbpdb -- Get PDB')
structure = conf.properties[system].get('initial_structure_pdb_path', None)
if structure is None or not os.path.isfile(structure):
out_log.info( ' Selected PDB code: ' + prop_glob['step1_mmbpdb']['pdb_code'])
fu.create_dir(prop_glob['step1_mmbpdb']['path'])
pdb.MmbPdb().get_pdb(prop_glob['step1_mmbpdb']['pdb_code'], paths_glob['step1_mmbpdb']['output_pdb_path'])
structure = paths_glob['step1_mmbpdb']['output_pdb_path']
out_log.info( 'step2: mmbuniprot -- Get mutations')
mutations = conf.properties.get('input_mapped_mutations_list', None)
if mutations is None or len(mutations) < 7:
mmbuniprot = uniprot.MmbVariants(prop_glob['step1_mmbpdb']['pdb_code'])
mutations = mmbuniprot.get_pdb_variants()
if mutations is None or len(mutations) == 0: return
else:
mutations = [m.strip() for m in conf.properties.get('input_mapped_mutations_list').split(',')]
mutations_limit = min(len(mutations), int(n_mutations))
out_log.info('')
out_log.info('Number of mutations to be modelled: ' + str(mutations_limit))
rms_list = []
mutations_counter = 0
for mut in mutations:
if mutations_counter == mutations_limit: break
mutations_counter += 1
mut = mut if not mut.startswith('*') else mut.replace('*', 'ALL')
paths = conf.get_paths_dic(mut)
prop = conf.get_prop_dic(mut, global_log=out_log)
out_log.info('')
out_log.info('-------------------------')
out_log.info(str(mutations_counter) + '/' + str(mutations_limit) + ' ' + mut)
out_log.info('-------------------------')
out_log.info('')
out_log.info('step3: scw --------- Model mutation')
fu.create_dir(prop['step3_scw']['path'])
paths['step3_scw']['input_pdb_path']=structure
scwrl.Scwrl4(properties=prop['step3_scw'], **paths['step3_scw']).launch()
out_log.info('step4: p2g --------- Create gromacs topology')
fu.create_dir(prop['step4_p2g']['path'])
pdb2gmx.Pdb2gmx(properties=prop['step4_p2g'], **paths['step4_p2g']).launch()
out_log.info('step5: ec ---------- Define box dimensions')
fu.create_dir(prop['step5_ec']['path'])
editconf.Editconf(properties=prop['step5_ec'], **paths['step5_ec']).launch()
out_log.info('step6: sol --------- Fill the box with water molecules')
fu.create_dir(prop['step6_sol']['path'])
solvate.Solvate(properties=prop['step6_sol'], **paths['step6_sol']).launch()
out_log.info('step7: gppions ----- Preprocessing: Adding monoatomic ions')
fu.create_dir(prop['step7_gppions']['path'])
grompp.Grompp(properties=prop['step7_gppions'], **paths['step7_gppions']).launch()
out_log.info('step8: gio --------- Running: Adding monoatomic ions')
fu.create_dir(prop['step8_gio']['path'])
genion.Genion(properties=prop['step8_gio'], **paths['step8_gio']).launch()
out_log.info('Step9: gppndx ------- Preprocessing index creation')
fu.create_dir(prop['step9_gppndx']['path'])
grompp.Grompp(properties=prop['step9_gppndx'], **paths['step9_gppndx']).launch()
out_log.info('Step10: make_ndx ---- Create restrain index')
fu.create_dir(prop['step10_make_ndx']['path'])
make_ndx.MakeNdx(properties=prop['step10_make_ndx'], **paths['step10_make_ndx']).launch()
out_log.info('Step11: ndx2resttop - Create restrain topology')
fu.create_dir(prop['step11_ndx2resttop']['path'])
ndx2resttop.Ndx2resttop(properties=prop['step11_ndx2resttop'], **paths['step11_ndx2resttop']).launch()
out_log.info('step12: gppresmin Preprocessing: Mutated residue minimization')
fu.create_dir(prop['step12_gppresmin']['path'])
grompp.Grompp(properties=prop['step12_gppresmin'], **paths['step12_gppresmin']).launch()
out_log.info('step13: mdresmin ---- Running: Mutated residue minimization')
fu.create_dir(prop['step13_mdresmin']['path'])
mdrun.Mdrun(properties=prop['step13_mdresmin'], **paths['step13_mdresmin']).launch()
out_log.info('Step14: ndx2resttop - Create restrain topology')
fu.create_dir(prop['step14_ndx2resttop']['path'])
ndx2resttop.Ndx2resttop(properties=prop['step14_ndx2resttop'], **paths['step14_ndx2resttop']).launch()
out_log.info('step15: gppmin Preprocessing: minimization')
fu.create_dir(prop['step15_gppmin']['path'])
grompp.Grompp(properties=prop['step15_gppmin'], **paths['step15_gppmin']).launch()
out_log.info('step16: mdmin ---- Running: minimization')
fu.create_dir(prop['step16_mdmin']['path'])
mdrun.Mdrun(properties=prop['step16_mdmin'], **paths['step16_mdmin']).launch()
out_log.info('Step17: ndx2resttop - Create restrain topology')
fu.create_dir(prop['step17_ndx2resttop']['path'])
ndx2resttop.Ndx2resttop(properties=prop['step17_ndx2resttop'], **paths['step17_ndx2resttop']).launch()
out_log.info('step18: gppsa Preprocessing: simulated annealing')
fu.create_dir(prop['step18_gppsa']['path'])
grompp.Grompp(properties=prop['step18_gppsa'], **paths['step18_gppsa']).launch()
out_log.info('step19: mdsa ---- Running: simulated annealing')
fu.create_dir(prop['step19_mdsa']['path'])
mdrun.Mdrun(properties=prop['step19_mdsa'], **paths['step19_mdsa']).launch()
out_log.info('step20: gppnvt_1000 Preprocessing: nvt constant number of molecules, volume and temp')
fu.create_dir(prop['step20_gppnvt_1000']['path'])
grompp.Grompp(properties=prop['step20_gppnvt_1000'], **paths['step20_gppnvt_1000']).launch()
out_log.info('step21: mdnvt_1000 ---- Running: nvt constant number of molecules, volume and temp')
fu.create_dir(prop['step21_mdnvt_1000']['path'])
mdrun.Mdrun(properties=prop['step21_mdnvt_1000'], **paths['step21_mdnvt_1000']).launch()
out_log.info('Step22: ndx2resttop - Create restrain topology')
fu.create_dir(prop['step22_ndx2resttop']['path'])
ndx2resttop.Ndx2resttop(properties=prop['step22_ndx2resttop'], **paths['step22_ndx2resttop']).launch()
out_log.info('step23: gppnvt_800 Preprocessing: nvt constant number of molecules, volume and temp')
fu.create_dir(prop['step23_gppnvt_800']['path'])
grompp.Grompp(properties=prop['step23_gppnvt_800'], **paths['step23_gppnvt_800']).launch()
out_log.info('step24: mdnvt_800 ---- Running: nvt constant number of molecules, volume and temp')
fu.create_dir(prop['step24_mdnvt_800']['path'])
mdrun.Mdrun(properties=prop['step24_mdnvt_800'], **paths['step24_mdnvt_800']).launch()
out_log.info('Step25: ndx2resttop - Create restrain topology')
fu.create_dir(prop['step25_ndx2resttop']['path'])
ndx2resttop.Ndx2resttop(properties=prop['step25_ndx2resttop'], **paths['step25_ndx2resttop']).launch()
out_log.info('step26: gppnpt_500 Preprocessing: npt constant number of molecules, pressure and temp')
fu.create_dir(prop['step26_gppnpt_500']['path'])
grompp.Grompp(properties=prop['step26_gppnpt_500'], **paths['step26_gppnpt_500']).launch()
out_log.info('step27: mdnpt_500 ---- Running: npt constant number of molecules, pressure and temp')
fu.create_dir(prop['step27_mdnpt_500']['path'])
mdrun.Mdrun(properties=prop['step27_mdnpt_500'], **paths['step27_mdnpt_500']).launch()
out_log.info('Step28: ndx2resttop - Create restrain topology')
fu.create_dir(prop['step28_ndx2resttop']['path'])
ndx2resttop.Ndx2resttop(properties=prop['step28_ndx2resttop'], **paths['step28_ndx2resttop']).launch()
out_log.info('step29: gppnpt_300 Preprocessing: npt constant number of molecules, pressure and temp')
fu.create_dir(prop['step29_gppnpt_300']['path'])
grompp.Grompp(properties=prop['step29_gppnpt_300'], **paths['step29_gppnpt_300']).launch()
out_log.info('step30: mdnpt_300 ---- Running: npt constant number of molecules, pressure and temp')
fu.create_dir(prop['step30_mdnpt_300']['path'])
mdrun.Mdrun(properties=prop['step30_mdnpt_300'], **paths['step30_mdnpt_300']).launch()
out_log.info('Step31: ndx2resttop - Create restrain topology')
fu.create_dir(prop['step31_ndx2resttop']['path'])
ndx2resttop.Ndx2resttop(properties=prop['step31_ndx2resttop'], **paths['step31_ndx2resttop']).launch()
out_log.info('step32: gppnpt_200 Preprocessing: npt constant number of molecules, pressure and temp')
fu.create_dir(prop['step32_gppnpt_200']['path'])
grompp.Grompp(properties=prop['step32_gppnpt_200'], **paths['step32_gppnpt_200']).launch()
out_log.info('step33: mdnpt_200 ---- Running: npt constant number of molecules, pressure and temp')
fu.create_dir(prop['step33_mdnpt_200']['path'])
mdrun.Mdrun(properties=prop['step33_mdnpt_200'], **paths['step33_mdnpt_200']).launch()
out_log.info('Step34: ndx2resttop - Create restrain topology')
fu.create_dir(prop['step34_ndx2resttop']['path'])
ndx2resttop.Ndx2resttop(properties=prop['step34_ndx2resttop'], **paths['step34_ndx2resttop']).launch()
out_log.info('step35: gppnpt_100 Preprocessing: npt constant number of molecules, pressure and temp')
fu.create_dir(prop['step35_gppnpt_100']['path'])
grompp.Grompp(properties=prop['step35_gppnpt_100'], **paths['step35_gppnpt_100']).launch()
out_log.info('step36: mdnpt_100 ---- Running: npt constant number of molecules, pressure and temp')
fu.create_dir(prop['step36_mdnpt_100']['path'])
mdrun.Mdrun(properties=prop['step36_mdnpt_100'], **paths['step36_mdnpt_100']).launch()
out_log.info('Step37: ndx2resttop - Create restrain topology')
fu.create_dir(prop['step37_ndx2resttop']['path'])
ndx2resttop.Ndx2resttop(properties=prop['step37_ndx2resttop'], **paths['step37_ndx2resttop']).launch()
out_log.info('step38: gppnpt - Preprocessing: npt constant number of molecules, pressure and temp')
fu.create_dir(prop['step38_gppnpt']['path'])
grompp.Grompp(properties=prop['step38_gppnpt'], **paths['step38_gppnpt']).launch()
out_log.info('step39: mdnpt ---- Running: npt constant number of molecules, pressure and temp')
fu.create_dir(prop['step39_mdnpt']['path'])
mdrun.Mdrun(properties=prop['step39_mdnpt'], **paths['step39_mdnpt']).launch()
fu.remove_temp_files(['#', '.top', '.plotscript', '.edr', '.xtc', '.itp', '.top', '.log', '.pdb', '.cpt', '.mdp', '.xvg', '.seq'])
elapsed_time = time.time() - start_time
out_log.info('')
out_log.info('')
out_log.info('Execution sucessful: ')
out_log.info(' Workflow_path: '+workflow_path)
out_log.info(' Config File: '+yaml_path)
out_log.info(' System: '+system)
if len(sys.argv) >= 5:
out_log.info(' Nodes: '+sys.argv[4])
out_log.info('')
out_log.info('Elapsed time: '+str(elapsed_time)+' seconds')
out_log.info('')
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
def main():
start_time = time.time()
yaml_path = sys.argv[1]
system = sys.argv[2]
conf = settings.YamlReader(yaml_path, system)
workflow_path = conf.properties[system]['workflow_path']
fu.create_dir(os.path.abspath(workflow_path))
out_log, _ = fu.get_logs(path=workflow_path, console=True, level='DEBUG')
paths = conf.get_paths_dic()
prop = conf.get_prop_dic(global_log=out_log)
out_log.info('')
out_log.info('_______GROMACS FULL WORKFLOW_______')
out_log.info('')
out_log.info("Command Executed:")
out_log.info(" ".join(sys.argv))
out_log.info('Workflow_path: ' + workflow_path)
out_log.info('Config File: ' + yaml_path)
out_log.info('System: ' + system)
out_log.info('')
out_log.info('step1: mmbpdb ------ Get PDB')
structure = conf.properties[system].get('initial_structure_pdb_path', None)
out_log.info(22 * ' ' + 'Selected PDB structure: ' + structure)
out_log.info('step2 and 3: scw --- Check and Repair PDB')
fu.create_dir(prop['step3_scw']['path'])
paths['step3_scw']['input_pdb_path'] = structure
out_log.debug('\nPaths:\n' + str(paths['step3_scw']) + '\nProperties:\n' +
str(prop['step3_scw']) + '\n')
scwrl.Scwrl4(properties=prop['step3_scw'], **paths['step3_scw']).launch()
out_log.info('step4: p2g --------- Create gromacs topology')
fu.create_dir(prop['step4_p2g']['path'])
out_log.debug('\nPaths:\n' + str(paths['step4_p2g']) + '\nProperties:\n' +
str(prop['step4_p2g']) + '\n')
pdb2gmx.Pdb2gmx(properties=prop['step4_p2g'],
**paths['step4_p2g']).launch()
out_log.info('step5: ec ---------- Define box dimensions')
fu.create_dir(prop['step5_ec']['path'])
out_log.debug('\nPaths:\n' + str(paths['step5_ec']) + '\nProperties:\n' +
str(prop['step5_ec']) + '\n')
editconf.Editconf(properties=prop['step5_ec'],
**paths['step5_ec']).launch()
out_log.info('step6: sol --------- Fill the box with water molecules')
fu.create_dir(prop['step6_sol']['path'])
out_log.debug('\nPaths:\n' + str(paths['step6_sol']) + '\nProperties:\n' +
str(prop['step6_sol']) + '\n')
solvate.Solvate(properties=prop['step6_sol'],
**paths['step6_sol']).launch()
out_log.info('step7: gppions ----- Preprocessing: Adding monoatomic ions')
fu.create_dir(prop['step7_gppions']['path'])
out_log.debug('\nPaths:\n' + str(paths['step7_gppions']) +
'\nProperties:\n' + str(prop['step7_gppions']) + '\n')
grompp.Grompp(properties=prop['step7_gppions'],
**paths['step7_gppions']).launch()
out_log.info('step8: gio --------- Running: Adding monoatomic ions')
fu.create_dir(prop['step8_gio']['path'])
out_log.debug('\nPaths:\n' + str(paths['step8_gio']) + '\nProperties:\n' +
str(prop['step8_gio']) + '\n')
genion.Genion(properties=prop['step8_gio'], **paths['step8_gio']).launch()
out_log.info('Step9: gppndx ------- Preprocessing index creation')
fu.create_dir(prop['step9_gppndx']['path'])
out_log.debug('\nPaths:\n' + str(paths['step9_gppndx']) +
'\nProperties:\n' + str(prop['step9_gppndx']) + '\n')
grompp.Grompp(properties=prop['step9_gppndx'],
**paths['step9_gppndx']).launch()
out_log.info('Step10: make_ndx ---- Create restrain index')
fu.create_dir(prop['step10_make_ndx']['path'])
out_log.debug('\nPaths:\n' + str(paths['step10_make_ndx']) +
'\nProperties:\n' + str(prop['step10_make_ndx']) + '\n')
make_ndx.MakeNdx(properties=prop['step10_make_ndx'],
**paths['step10_make_ndx']).launch()
out_log.info('Step11: genrest - Create restrain topology')
fu.create_dir(prop['step11_genrestr']['path'])
out_log.debug('\nPaths:\n' + str(paths['step11_genrestr']) +
'\nProperties:\n' + str(prop['step11_genrestr']) + '\n')
genrestr.Genrestr(properties=prop['step11_genrestr'],
**paths['step11_genrestr']).launch()
out_log.info('step15: gppmin ------ Preprocessing: minimization')
fu.create_dir(prop['step15_gppmin']['path'])
out_log.debug('\nPaths:\n' + str(paths['step15_gppmin']) +
'\nProperties:\n' + str(prop['step15_gppmin']) + '\n')
grompp.Grompp(properties=prop['step15_gppmin'],
**paths['step15_gppmin']).launch()
out_log.info('step16: mdmin ------- Running: minimization')
fu.create_dir(prop['step16_mdmin']['path'])
out_log.debug('\nPaths:\n' + str(paths['step16_mdmin']) +
'\nProperties:\n' + str(prop['step16_mdmin']) + '\n')
mdrun.Mdrun(properties=prop['step16_mdmin'],
**paths['step16_mdmin']).launch()
out_log.info('Step17: genrestr - Create restrain topology')
fu.create_dir(prop['step17_genrestr']['path'])
out_log.debug('\nPaths:\n' + str(paths['step17_genrestr']) +
'\nProperties:\n' + str(prop['step17_genrestr']) + '\n')
genrestr.Genrestr(properties=prop['step17_genrestr'],
**paths['step17_genrestr']).launch()
out_log.info('step18: gppsa ------- Preprocessing: simulated annealing')
fu.create_dir(prop['step18_gppsa']['path'])
out_log.debug('\nPaths:\n' + str(paths['step18_gppsa']) +
'\nProperties:\n' + str(prop['step18_gppsa']) + '\n')
grompp.Grompp(properties=prop['step18_gppsa'],
**paths['step18_gppsa']).launch()
out_log.info('step19: mdsa -------- Running: simulated annealing')
fu.create_dir(prop['step19_mdsa']['path'])
out_log.debug('\nPaths:\n' + str(paths['step19_mdsa']) +
'\nProperties:\n' + str(prop['step19_mdsa']) + '\n')
mdrun.Mdrun(properties=prop['step19_mdsa'],
**paths['step19_mdsa']).launch()
out_log.info(
'step20: gppnvt_1000 - Preprocessing: nvt constant number of molecules, volume and temp'
)
fu.create_dir(prop['step20_gppnvt_1000']['path'])
out_log.debug('\nPaths:\n' + str(paths['step20_gppnvt_1000']) +
'\nProperties:\n' + str(prop['step20_gppnvt_1000']) + '\n')
grompp.Grompp(properties=prop['step20_gppnvt_1000'],
**paths['step20_gppnvt_1000']).launch()
out_log.info(
'step21: mdnvt_1000 -- Running: nvt constant number of molecules, volume and temp'
)
fu.create_dir(prop['step21_mdnvt_1000']['path'])
out_log.debug('\nPaths:\n' + str(paths['step21_mdnvt_1000']) +
'\nProperties:\n' + str(prop['step21_mdnvt_1000']) + '\n')
mdrun.Mdrun(properties=prop['step21_mdnvt_1000'],
**paths['step21_mdnvt_1000']).launch()
out_log.info('Step22: genrestr - Create restrain topology')
fu.create_dir(prop['step22_genrestr']['path'])
out_log.debug('\nPaths:\n' + str(paths['step22_genrestr']) +
'\nProperties:\n' + str(prop['step22_genrestr']) + '\n')
genrestr.Genrestr(properties=prop['step22_genrestr'],
**paths['step22_genrestr']).launch()
out_log.info(
'step23: gppnvt_800 -- Preprocessing: nvt constant number of molecules, volume and temp'
)
fu.create_dir(prop['step23_gppnvt_800']['path'])
out_log.debug('\nPaths:\n' + str(paths['step23_gppnvt_800']) +
'\nProperties:\n' + str(prop['step23_gppnvt_800']) + '\n')
grompp.Grompp(properties=prop['step23_gppnvt_800'],
**paths['step23_gppnvt_800']).launch()
out_log.info(
'step24: mdnvt_800 --- Running: nvt constant number of molecules, volume and temp'
)
fu.create_dir(prop['step24_mdnvt_800']['path'])
out_log.debug('\nPaths:\n' + str(paths['step24_mdnvt_800']) +
'\nProperties:\n' + str(prop['step24_mdnvt_800']) + '\n')
mdrun.Mdrun(properties=prop['step24_mdnvt_800'],
**paths['step24_mdnvt_800']).launch()
out_log.info('Step25: genrestr - Create restrain topology')
fu.create_dir(prop['step25_genrestr']['path'])
out_log.debug('\nPaths:\n' + str(paths['step25_genrestr']) +
'\nProperties:\n' + str(prop['step25_genrestr']) + '\n')
genrestr.Genrestr(properties=prop['step25_genrestr'],
**paths['step25_genrestr']).launch()
out_log.info(
'step26: gppnpt_500 -- Preprocessing: npt constant number of molecules, pressure and temp'
)
fu.create_dir(prop['step26_gppnpt_500']['path'])
out_log.debug('\nPaths:\n' + str(paths['step26_gppnpt_500']) +
'\nProperties:\n' + str(prop['step26_gppnpt_500']) + '\n')
grompp.Grompp(properties=prop['step26_gppnpt_500'],
**paths['step26_gppnpt_500']).launch()
out_log.info(
'step27: mdnpt_500 --- Running: npt constant number of molecules, pressure and temp'
)
fu.create_dir(prop['step27_mdnpt_500']['path'])
out_log.debug('\nPaths:\n' + str(paths['step27_mdnpt_500']) +
'\nProperties:\n' + str(prop['step27_mdnpt_500']) + '\n')
mdrun.Mdrun(properties=prop['step27_mdnpt_500'],
**paths['step27_mdnpt_500']).launch()
out_log.info('Step28: genrestr - Create restrain topology')
fu.create_dir(prop['step28_genrestr']['path'])
out_log.debug('\nPaths:\n' + str(paths['step28_genrestr']) +
'\nProperties:\n' + str(prop['step28_genrestr']) + '\n')
genrestr.Genrestr(properties=prop['step28_genrestr'],
**paths['step28_genrestr']).launch()
out_log.info(
'step29: gppnpt_300 -- Preprocessing: npt constant number of molecules, pressure and temp'
)
fu.create_dir(prop['step29_gppnpt_300']['path'])
out_log.debug('\nPaths:\n' + str(paths['step29_gppnpt_300']) +
'\nProperties:\n' + str(prop['step29_gppnpt_300']) + '\n')
grompp.Grompp(properties=prop['step29_gppnpt_300'],
**paths['step29_gppnpt_300']).launch()
out_log.info(
'step30: mdnpt_300 --- Running: npt constant number of molecules, pressure and temp'
)
fu.create_dir(prop['step30_mdnpt_300']['path'])
out_log.debug('\nPaths:\n' + str(paths['step30_mdnpt_300']) +
'\nProperties:\n' + str(prop['step30_mdnpt_300']) + '\n')
mdrun.Mdrun(properties=prop['step30_mdnpt_300'],
**paths['step30_mdnpt_300']).launch()
out_log.info('Step31: genrestr - Create restrain topology')
fu.create_dir(prop['step31_genrestr']['path'])
out_log.debug('\nPaths:\n' + str(paths['step31_genrestr']) +
'\nProperties:\n' + str(prop['step31_genrestr']) + '\n')
genrestr.Genrestr(properties=prop['step31_genrestr'],
**paths['step31_genrestr']).launch()
out_log.info(
'step32: gppnpt_200 -- Preprocessing: npt constant number of molecules, pressure and temp'
)
fu.create_dir(prop['step32_gppnpt_200']['path'])
out_log.debug('\nPaths:\n' + str(paths['step32_gppnpt_200']) +
'\nProperties:\n' + str(prop['step32_gppnpt_200']) + '\n')
grompp.Grompp(properties=prop['step32_gppnpt_200'],
**paths['step32_gppnpt_200']).launch()
out_log.info(
'step33: mdnpt_200 --- Running: npt constant number of molecules, pressure and temp'
)
fu.create_dir(prop['step33_mdnpt_200']['path'])
out_log.debug('\nPaths:\n' + str(paths['step33_mdnpt_200']) +
'\nProperties:\n' + str(prop['step33_mdnpt_200']) + '\n')
mdrun.Mdrun(properties=prop['step33_mdnpt_200'],
**paths['step33_mdnpt_200']).launch()
out_log.info('Step34: genrestr - Create restrain topology')
fu.create_dir(prop['step34_genrestr']['path'])
out_log.debug('\nPaths:\n' + str(paths['step34_genrestr']) +
'\nProperties:\n' + str(prop['step34_genrestr']) + '\n')
genrestr.Genrestr(properties=prop['step34_genrestr'],
**paths['step34_genrestr']).launch()
out_log.info(
'step35: gppnpt_100 -- Preprocessing: npt constant number of molecules, pressure and temp'
)
fu.create_dir(prop['step35_gppnpt_100']['path'])
out_log.debug('\nPaths:\n' + str(paths['step35_gppnpt_100']) +
'\nProperties:\n' + str(prop['step35_gppnpt_100']) + '\n')
grompp.Grompp(properties=prop['step35_gppnpt_100'],
**paths['step35_gppnpt_100']).launch()
out_log.info(
'step36: mdnpt_100 --- Running: npt constant number of molecules, pressure and temp'
)
fu.create_dir(prop['step36_mdnpt_100']['path'])
out_log.debug('\nPaths:\n' + str(paths['step36_mdnpt_100']) +
'\nProperties:\n' + str(prop['step36_mdnpt_100']) + '\n')
mdrun.Mdrun(properties=prop['step36_mdnpt_100'],
**paths['step36_mdnpt_100']).launch()
out_log.info('Step37: genrestr - Create restrain topology')
fu.create_dir(prop['step37_genrestr']['path'])
out_log.debug('\nPaths:\n' + str(paths['step37_genrestr']) +
'\nProperties:\n' + str(prop['step37_genrestr']) + '\n')
genrestr.Genrestr(properties=prop['step37_genrestr'],
**paths['step37_genrestr']).launch()
out_log.info(
'step38: gppnpt ------ Preprocessing: npt constant number of molecules, pressure and temp'
)
fu.create_dir(prop['step38_gppnpt']['path'])
out_log.debug('\nPaths:\n' + str(paths['step38_gppnpt']) +
'\nProperties:\n' + str(prop['step38_gppnpt']) + '\n')
grompp.Grompp(properties=prop['step38_gppnpt'],
**paths['step38_gppnpt']).launch()
out_log.info(
'step39: mdnpt ------- Running: npt constant number of molecules, pressure and temp'
)
fu.create_dir(prop['step39_mdnpt']['path'])
out_log.debug('\nPaths:\n' + str(paths['step39_mdnpt']) +
'\nProperties:\n' + str(prop['step39_mdnpt']) + '\n')
mdrun.Mdrun(properties=prop['step39_mdnpt'],
**paths['step39_mdnpt']).launch()
out_log.info(
'step40: gppmd ------- Preprocessing: Free Molecular dynamics')
fu.create_dir(prop['step40_gppmd']['path'])
out_log.debug('\nPaths:\n' + str(paths['step40_gppmd']) +
'\nProperties:\n' + str(prop['step40_gppmd']) + '\n')
grompp.Grompp(properties=prop['step40_gppmd'],
**paths['step40_gppmd']).launch()
out_log.info('step41: md ---------- Running: Free Molecular dynamics')
fu.create_dir(prop['step41_md']['path'])
out_log.debug('\nPaths:\n' + str(paths['step41_md']) + '\nProperties:\n' +
str(prop['step41_md']) + '\n')
mdrun.Mdrun(properties=prop['step41_md'], **paths['step41_md']).launch()
fu.remove_temp_files([
'#', '.top', '.plotscript', '.edr', '.xtc', '.itp', '.top', '.log',
'.pdb', '.cpt', '.mdp', '.xvg', '.seq'
])
elapsed_time = time.time() - start_time
out_log.info('')
out_log.info('')
out_log.info('Execution sucessful: ')
out_log.info(' Workflow_path: ' + workflow_path)
out_log.info(' Config File: ' + yaml_path)
out_log.info(' System: ' + system)
if len(sys.argv) >= 5:
out_log.info(' Nodes: ' + sys.argv[4])
out_log.info('')
out_log.info('Elapsed time: ' + str(elapsed_time) + ' seconds')
out_log.info('')
def main():
start_time = time.time()
yaml_path = sys.argv[1]
system = sys.argv[2]
conf = settings.YamlReader(yaml_path, system)
workflow_path = conf.properties[system]['workflow_path']
fu.create_dir(os.path.abspath(workflow_path))
out_log, _ = fu.get_logs(path=workflow_path, console=True)
paths = conf.get_paths_dic()
prop = conf.get_prop_dic(global_log=out_log)
out_log.info('')
out_log.info('_______MD SETUP FULL WORKFLOW_______')
out_log.info('')
out_log.info('step1: mmbpdb --- Get PDB')
structure = conf.properties[system].get('initial_structure_pdb_path', None)
if structure is None or not os.path.isfile(structure):
out_log.info(' Selected PDB code: ' +
prop['step1_mmbpdb']['pdb_code'])
fu.create_dir(prop['step1_mmbpdb']['path'])
pdb.MmbPdb().get_pdb(prop['step1_mmbpdb']['pdb_code'],
paths['step1_mmbpdb']['output_pdb_path'])
structure = paths['step1_mmbpdb']['output_pdb_path']
out_log.info('step2: p2g ------ Create gromacs topology')
fu.create_dir(prop['step2_p2g']['path'])
pdb2gmx.Pdb2gmx(properties=prop['step2_p2g'],
**paths['step2_p2g']).launch()
out_log.info('step3: ec ------- Define box dimensions')
fu.create_dir(prop['step3_ec']['path'])
editconf.Editconf(properties=prop['step3_ec'],
**paths['step3_ec']).launch()
out_log.info('step4: sol ------ Fill the box with water molecules')
fu.create_dir(prop['step4_sol']['path'])
solvate.Solvate(properties=prop['step4_sol'],
**paths['step4_sol']).launch()
out_log.info('step5: gppions -- Preprocessing: Adding monoatomic ions')
fu.create_dir(prop['step5_gppions']['path'])
grompp.Grompp(properties=prop['step5_gppions'],
**paths['step5_gppions']).launch()
out_log.info('step6: gio ------ Running: Adding monoatomic ions')
fu.create_dir(prop['step6_gio']['path'])
genion.Genion(properties=prop['step6_gio'], **paths['step6_gio']).launch()
out_log.info('step7: gppmin --- Preprocessing: Energy minimization')
fu.create_dir(prop['step7_gppmin']['path'])
grompp.Grompp(properties=prop['step7_gppmin'],
**paths['step7_gppmin']).launch()
out_log.info('step8: mdmin ---- Running: Energy minimization')
fu.create_dir(prop['step8_mdmin']['path'])
mdrun.Mdrun(properties=prop['step8_mdmin'],
**paths['step8_mdmin']).launch()
out_log.info(
'step9: gppnvt --- Preprocessing: nvt constant number of molecules, volume and temp'
)
fu.create_dir(prop['step9_gppnvt']['path'])
grompp.Grompp(properties=prop['step9_gppnvt'],
**paths['step9_gppnvt']).launch()
out_log.info(
'step10: mdnvt ---- Running: nvt constant number of molecules, volume and temp'
)
fu.create_dir(prop['step10_mdnvt']['path'])
mdrun.Mdrun(properties=prop['step10_mdnvt'],
**paths['step10_mdnvt']).launch()
out_log.info(
'step11: gppnpt --- Preprocessing: npt constant number of molecules, pressure and temp'
)
fu.create_dir(prop['step11_gppnpt']['path'])
grompp.Grompp(properties=prop['step11_gppnpt'],
**paths['step11_gppnpt']).launch()
out_log.info(
'step12: mdnpt ---- Running: npt constant number of molecules, pressure and temp'
)
fu.create_dir(prop['step12_mdnpt']['path'])
mdrun.Mdrun(properties=prop['step12_mdnpt'],
**paths['step12_mdnpt']).launch()
out_log.info(
'step13: gppeq ---- Preprocessing: Molecular dynamics Equilibration')
fu.create_dir(prop['step13_gppeq']['path'])
grompp.Grompp(properties=prop['step13_gppeq'],
**paths['step13_gppeq']).launch()
out_log.info(
'step14: mdeq ----- Running: Molecular dynamics Equilibration')
fu.create_dir(prop['step14_mdeq']['path'])
mdrun.Mdrun(properties=prop['step14_mdeq'],
**paths['step14_mdeq']).launch()
#Create setupfiles dir and copy files
setupfiles_path = os.path.join(workflow_path, 'setupfiles')
fu.create_dir(setupfiles_path)
shutil.copy(paths['step14_mdeq']['output_gro_path'],
os.path.join(setupfiles_path, 'md_setup.gro'))
shutil.copy(paths['step14_mdeq']['output_cpt_path'],
os.path.join(setupfiles_path, 'md_setup.cpt'))
shutil.copy(paths['step6_gio']['output_top_zip_path'],
os.path.join(setupfiles_path, 'md_setup.zip'))
removed_list = fu.remove_temp_files([
'#', '.top', '.plotscript', '.edr', '.xtc', '.itp', '.top', '.log',
'.pdb', '.cpt', '.mdp'
])
out_log.info('')
out_log.info('Removing unwanted files: ')
for removed_file in removed_list:
out_log.info(' X ' + removed_file)
elapsed_time = time.time() - start_time
out_log.info('')
out_log.info('')
out_log.info('Execution sucessful: ')
out_log.info(' Workflow_path: ' + workflow_path)
out_log.info(' Config File: ' + yaml_path)
out_log.info(' System: ' + system)
if len(sys.argv) >= 4:
out_log.info(' Nodes: ' + sys.argv[3])
out_log.info('')
out_log.info('Elapsed time: ' + str(elapsed_time) + ' seconds')
out_log.info('')
def main():
start_time = time.time()
yaml_path=sys.argv[1]
system=sys.argv[2]
n_mutations=sys.argv[3]
conf = settings.YamlReader(yaml_path, system)
workflow_path = conf.properties[system]['workflow_path']
fu.create_dir(os.path.abspath(workflow_path))
out_log, _ = fu.get_logs(path=workflow_path, console=True)
paths_glob = conf.get_paths_dic()
prop_glob = conf.get_prop_dic()
out_log.info('')
out_log.info('_______GROMACS FULL WORKFLOW_______')
out_log.info('')
out_log.info("Command Executed:")
out_log.info(" ".join(sys.argv))
out_log.info('Workflow_path: '+workflow_path)
out_log.info('Config File: '+yaml_path)
out_log.info('System: '+system)
out_log.info('Mutations limit: '+n_mutations)
if len(sys.argv) >= 5:
out_log.info('Nodes: '+sys.argv[4])
out_log.info('')
out_log.info( 'step1: mmbpdb -- Get PDB')
structure = conf.properties[system].get('initial_structure_pdb_path', None)
if structure is None or not os.path.isfile(structure):
out_log.info( ' Selected PDB code: ' + prop_glob['step1_mmbpdb']['pdb_code'])
fu.create_dir(prop_glob['step1_mmbpdb']['path'])
pdb.MmbPdb().get_pdb(prop_glob['step1_mmbpdb']['pdb_code'], paths_glob['step1_mmbpdb']['output_pdb_path'])
structure = paths_glob['step1_mmbpdb']['output_pdb_path']
out_log.info( 'step2: mmbuniprot -- Get mutations')
mutations = conf.properties.get('input_mapped_mutations_list', None)
if mutations is None or len(mutations) < 7:
mmbuniprot = uniprot.MmbVariants(prop_glob['step1_mmbpdb']['pdb_code'])
mutations = mmbuniprot.get_pdb_variants()
if mutations is None or len(mutations) == 0: return
else:
mutations = [m.strip() for m in conf.properties.get('input_mapped_mutations_list').split(',')]
mutations_limit = min(len(mutations), int(n_mutations))
out_log.info('')
out_log.info('Number of mutations to be modelled: ' + str(mutations_limit))
rms_list = []
mutations_counter = 0
for mut in mutations:
if mutations_counter == mutations_limit: break
mutations_counter += 1
paths = conf.get_paths_dic(mut)
prop = conf.get_prop_dic(mut, global_log=out_log)
out_log.info('')
out_log.info('-------------------------')
out_log.info(str(mutations_counter) + '/' + str(mutations_limit) + ' ' + mut)
out_log.info('-------------------------')
out_log.info('')
out_log.info('step3: scw ------ Model mutation')
fu.create_dir(prop['step3_scw']['path'])
paths['step3_scw']['input_pdb_path']=structure
scwrl.Scwrl4(properties=prop['step3_scw'], **paths['step3_scw']).launch()
out_log.info('step4: p2g ------ Create gromacs topology')
fu.create_dir(prop['step4_p2g']['path'])
pdb2gmx.Pdb2gmx(properties=prop['step4_p2g'], **paths['step4_p2g']).launch()
out_log.info('step5: ec ------- Define box dimensions')
fu.create_dir(prop['step5_ec']['path'])
editconf.Editconf(properties=prop['step5_ec'], **paths['step5_ec']).launch()
out_log.info('step6: sol ------ Fill the box with water molecules')
fu.create_dir(prop['step6_sol']['path'])
solvate.Solvate(properties=prop['step6_sol'], **paths['step6_sol']).launch()
out_log.info('step7: gppions -- Preprocessing: Adding monoatomic ions')
fu.create_dir(prop['step7_gppions']['path'])
grompp.Grompp(properties=prop['step7_gppions'], **paths['step7_gppions']).launch()
out_log.info('step8: gio ------ Running: Adding monoatomic ions')
fu.create_dir(prop['step8_gio']['path'])
genion.Genion(properties=prop['step8_gio'], **paths['step8_gio']).launch()
out_log.info('step9: gppmin --- Preprocessing: Energy minimization')
fu.create_dir(prop['step9_gppmin']['path'])
grompp.Grompp(properties=prop['step9_gppmin'], **paths['step9_gppmin']).launch()
out_log.info('step10: mdmin ---- Running: Energy minimization')
fu.create_dir(prop['step10_mdmin']['path'])
mdrun.Mdrun(properties=prop['step10_mdmin'], **paths['step10_mdmin']).launch()
out_log.info('step11: gppnvt --- Preprocessing: nvt constant number of molecules, volume and temp')
fu.create_dir(prop['step11_gppnvt']['path'])
grompp.Grompp(properties=prop['step11_gppnvt'], **paths['step11_gppnvt']).launch()
out_log.info('step12: mdnvt ---- Running: nvt constant number of molecules, volume and temp')
fu.create_dir(prop['step12_mdnvt']['path'])
mdrun.Mdrun(properties=prop['step12_mdnvt'], **paths['step12_mdnvt']).launch()
out_log.info('step13: gppnpt --- Preprocessing: npt constant number of molecules, pressure and temp')
fu.create_dir(prop['step13_gppnpt']['path'])
grompp.Grompp(properties=prop['step13_gppnpt'], **paths['step13_gppnpt']).launch()
out_log.info('step14: mdnpt ---- Running: npt constant number of molecules, pressure and temp')
fu.create_dir(prop['step14_mdnpt']['path'])
mdrun.Mdrun(properties=prop['step14_mdnpt'], **paths['step14_mdnpt']).launch()
out_log.info('step15: gppeq ---- Preprocessing: 1ns Molecular dynamics Equilibration')
fu.create_dir(prop['step15_gppeq']['path'])
grompp.Grompp(properties=prop['step15_gppeq'], **paths['step15_gppeq']).launch()
out_log.info('step16: mdeq ----- Running: Free Molecular dynamics Equilibration')
fu.create_dir(prop['step16_mdeq']['path'])
mdrun.Mdrun(properties=prop['step16_mdeq'], **paths['step16_mdeq']).launch()
out_log.info('step17: rmsd ----- Computing RMSD')
fu.create_dir(prop['step17_rmsd']['path'])
rms_list.append(rms.Rms(properties=prop['step17_rmsd'], **paths['step17_rmsd']).launch())
removed_list = fu.remove_temp_files(['#', '.top', '.plotscript', '.edr', '.xtc', '.itp', '.top', '.log', '.pdb', '.cpt', '.mdp', '.xvg', '.grp', '.seq'])
xvg_dict=reduce(lambda a, b: dict(a, **b), rms_list)
out_log.info('step18: gnuplot ----- Creating RMSD plot')
fu.create_dir(prop_glob['step18_gnuplot']['path'])
gnuplot.Gnuplot(input_xvg_path_dict=xvg_dict, properties=prop_glob['step18_gnuplot'], **paths_glob['step18_gnuplot']).launch()
elapsed_time = time.time() - start_time
out_log.info('')
out_log.info('')
out_log.info('Execution sucessful: ')
out_log.info(' Workflow_path: '+workflow_path)
out_log.info(' Config File: '+yaml_path)
out_log.info(' System: '+system)
if len(sys.argv) >= 5:
out_log.info(' Nodes: '+sys.argv[4])
out_log.info('')
out_log.info('Elapsed time: '+str(elapsed_time)+' seconds')
out_log.info('')
