def check_structure_and_run_ndx_pc(
ensemble, output_structure_path, input_structure_path, output_ndx_path,
properties_makendx, input_gro_path, input_top_zip_path,
output_tpr_path, properties_grompp, output_trr_path, output_gro_path,
output_edr_path, output_xtc_path, output_log_path, properties_mdrun,
**kwargs):
try:
dummy = bool(os.path.getsize(output_structure_path))
if not dummy:
#if ensemble == "stateA":
from shutil import copyfile
copyfile(input_gro_path, output_gro_path)
fu.write_failed_output(output_ndx_path)
fu.write_failed_output(output_tpr_path)
fu.write_failed_output(output_trr_path)
fu.write_failed_output(output_edr_path)
fu.write_failed_output(output_xtc_path)
fu.write_failed_output(output_log_path)
else:
# step4_gmx_makendx
make_ndx_pc(input_structure_path=input_structure_path,
output_ndx_path=output_ndx_path,
properties=properties_makendx)
# step5_gmx_grompp
grompp_ndx_pc(input_gro_path=input_gro_path,
input_top_zip_path=input_top_zip_path,
output_tpr_path=output_tpr_path,
input_ndx_path=output_ndx_path,
properties=properties_grompp)
# step6_gmx_mdrun
mdrun_pc(input_tpr_path=output_tpr_path,
output_trr_path=output_trr_path,
output_gro_path=output_gro_path,
output_edr_path=output_edr_path,
output_xtc_path=output_xtc_path,
output_log_path=output_log_path,
properties=properties_mdrun)
except Exception as e:
raise Exception(
"Error ocurred while checking the file containing dummy atoms")
def main(config, system=None):
start_time = time.time()
conf = settings.ConfReader(config, system)
global_log, _ = fu.get_logs(path=conf.get_working_dir_path(),
light_format=True)
global_prop = conf.get_prop_dic()
global_paths = conf.get_paths_dic()
for structure in conf.properties['input_structures'].split(','):
prefix_str = os.path.basename(structure)
prefix_str = prefix_str.replace('.', '_')
mut_prop = conf.get_prop_dic(prefix=prefix_str)
mut_paths = conf.get_paths_dic(prefix=prefix_str)
global_log.info("Starting setup process for PDB: " + prefix_str)
mut_paths['step1_pdb2gmx']['input_pdb_path'] = structure
global_log.info("step1_pdb2gmx: Generate the topology")
pdb2gmx_pc(**mut_paths["step1_pdb2gmx"],
properties=mut_prop["step1_pdb2gmx"])
global_log.info("step2_editconf: Create the solvent box")
editconf_pc(**mut_paths["step2_editconf"],
properties=mut_prop["step2_editconf"])
global_log.info(
"step3_solvate: Fill the solvent box with water molecules")
solvate_pc(**mut_paths["step3_solvate"],
properties=mut_prop["step3_solvate"])
global_log.info("step4_grompp_genion: Preprocess ion generation")
grompp_pc(**mut_paths["step4_grompp_genion"],
properties=mut_prop["step4_grompp_genion"])
global_log.info("step5_genion: Ion generation")
genion_pc(**mut_paths["step5_genion"],
properties=mut_prop["step5_genion"])
global_log.info("step6_grompp_min: Preprocess energy minimization")
grompp_pc(**mut_paths["step6_grompp_min"],
properties=mut_prop["step6_grompp_min"])
global_log.info("step7_mdrun_min: Execute energy minimization")
mdrun_pc(**mut_paths["step7_mdrun_min"],
properties=mut_prop["step7_mdrun_min"])
global_log.info("step8_make_ndx: Generate GROMACS index file")
make_ndx_pc(**mut_paths["step8_make_ndx"],
properties=mut_prop["step8_make_ndx"])
global_log.info(
"step9_grompp_nvt: Preprocess system temperature equilibration")
grompp_ndx_pc(**mut_paths["step9_grompp_nvt"],
properties=mut_prop["step9_grompp_nvt"])
global_log.info(
"step10_mdrun_nvt: Execute system temperature equilibration")
mdrun_pc(**mut_paths["step10_mdrun_nvt"],
properties=mut_prop["step10_mdrun_nvt"])
global_log.info(
"step11_grompp_npt: Preprocess system pressure equilibration")
grompp_ndx_pc(**mut_paths["step11_grompp_npt"],
properties=mut_prop["step11_grompp_npt"])
global_log.info(
"step12_mdrun_npt: Execute system pressure equilibration")
mdrun_pc(**mut_paths["step12_mdrun_npt"],
properties=mut_prop["step12_mdrun_npt"])
global_log.info("step13_grompp_md: Preprocess free dynamics")
grompp_ndx_pc(**mut_paths["step13_grompp_md"],
properties=mut_prop["step13_grompp_md"])
global_log.info(
"step14_mdrun_md: Execute free molecular dynamics simulation")
mdrun_pc(**mut_paths["step14_mdrun_md"],
properties=mut_prop["step14_mdrun_md"])
elapsed_time = time.time() - start_time
global_log.info('')
global_log.info('')
global_log.info('Execution successful: ')
global_log.info(' Workflow_path: %s' % conf.get_working_dir_path())
global_log.info(' Config File: %s' % config)
if system:
global_log.info(' System: %s' % system)
global_log.info('')
global_log.info('Elapsed time: %.1f minutes' % (elapsed_time / 60))
global_log.info('')
def main(config, system=None):
start_time = time.time()
conf = settings.ConfReader(config, system)
global_log, _ = fu.get_logs(path=conf.get_working_dir_path(),
light_format=True)
global_prop = conf.get_prop_dic()
global_paths = conf.get_paths_dic()
dhdl_paths_listA = []
dhdl_paths_listB = []
for ensemble, mutation in conf.properties['mutations'].items():
ensemble_prop = conf.get_prop_dic(prefix=ensemble)
ensemble_paths = conf.get_paths_dic(prefix=ensemble)
# step0_image
global_log.info(
ensemble +
" Step 0: gmx image: Imaging trajectories to remove PBC issues")
ensemble_paths['step0_image']['input_traj_path'] = conf.properties[
'input_trajs'][ensemble]['input_traj_path']
ensemble_paths['step0_image']['input_top_path'] = conf.properties[
'input_trajs'][ensemble]['input_tpr_path']
gmx_image_pc(**ensemble_paths["step0_image"],
properties=ensemble_prop["step0_image"])
# step1_trjconv
global_log.info(
ensemble +
" Step 1: gmx trjconv: Extract snapshots from equilibrium trajectories"
)
ensemble_paths['step1_trjconv_' +
ensemble]['input_top_path'] = conf.properties[
'input_trajs'][ensemble]['input_tpr_path']
gmx_trjconv_str_ens_pc(**ensemble_paths['step1_trjconv_' + ensemble],
properties=ensemble_prop['step1_trjconv_' +
ensemble])
for ensemble, mutation in conf.properties['mutations'].items():
ensemble_prop = conf.get_prop_dic(prefix=ensemble)
ensemble_paths = conf.get_paths_dic(prefix=ensemble)
compss_wait_on_file(ensemble_paths['step1_trjconv_' +
ensemble]["output_str_ens_path"])
with zipfile.ZipFile(
ensemble_paths['step1_trjconv_' +
ensemble]["output_str_ens_path"]) as zip_f:
unique_dir = os.path.abspath(
fu.create_unique_dir(
prefix=ensemble_prop['step1_trjconv_' +
ensemble]['working_dir_path'] + '/' +
ensemble + '/'))
zip_f.extractall(unique_dir)
state_pdb_list = [
os.path.join(unique_dir, name) for name in zip_f.namelist()
]
for pdb_path in state_pdb_list:
pdb_name = os.path.splitext(os.path.basename(pdb_path))[0]
prop = conf.get_prop_dic(prefix=os.path.join(ensemble, pdb_name))
paths = conf.get_paths_dic(prefix=os.path.join(ensemble, pdb_name))
# Fixing terminal residues
newpdb2 = pdb_path + ".term.gro"
#cmd2 = "sed 's/600ASN /600NASN/g' " + pdb_path + "| sed 's/ 1SER / 1NSER /g' | sed 's/597ASP /597CASP/g' | sed 's/793PRO /793CPRO/g' | sed 's/HIS /HIE /g' > " + newpdb2
cmd2 = "sed 's/600ASN /600NASN/g' " + pdb_path + "| sed 's/ 1SER / 1NSER /g' | sed 's/597ASP /597CASP/g' | sed 's/793PRO /793CPRO/g' > " + newpdb2
subprocess.call(cmd2, shell=True)
paths['step1_pmx_mutate']['input_structure_path'] = newpdb2
# step1_pmx_mutate
global_log.info(ensemble + " " + pdb_name +
" Step 1: pmx mutate: Generate Hybrid Structure")
prop['step1_pmx_mutate']['mutation_list'] = mutation
mutate_pc(**paths["step1_pmx_mutate"],
properties=prop["step1_pmx_mutate"])
# step1.1_check_dummies
global_log.info(ensemble + " " + pdb_name +
" Step 1.1 Check for dummy atoms")
extract_atoms_pc(**paths['step1.1_check_dummies'],
properties=prop['step1.1_check_dummies'])
compss_wait_on_file(
paths['step1.1_check_dummies']['output_structure_path'])
try:
dummy = bool(
os.path.getsize(paths['step1.1_check_dummies']
['output_structure_path']))
except:
global_log.info(
"Error ocurred while checking the file containing dummy atoms"
)
global_log.info(sys.exc_info()[0])
# step1.2_remove_ligand
#global_log.info(ensemble + " " + pdb_name + " Step 1.2 Remove ligand")
#remove_ligand_pc(**paths['step1.2_remove_ligand'], properties=prop['step1.2_remove_ligand'])
# step2_gmx_pdb2gmx
global_log.info(ensemble + " " + pdb_name +
" Step 2: gmx pdb2gmx: Generate Topology")
pdb2gmx_pc(**paths["step2_gmx_pdb2gmx"],
properties=prop["step2_gmx_pdb2gmx"])
# step2.1_sort_gro
#global_log.info(ensemble + " " + pdb_name + " Step 2.1 Sort gro residues")
#sort_gro_residues_pc(**paths['step2.1_sort_gro'], properties=prop['step2.1_sort_gro'])
# step2.2_lig_gmx_appendLigand
#global_log.info(ensemble + " " + pdb_name +" Step 2.2_lig: gmx appendLigand: Append a ligand to a GROMACS topology")
#append_ligand_pc(**paths["step2.2_lig_gmx_appendLigand"], properties=prop["step2.2_lig_gmx_appendLigand"])
# step3_pmx_gentop
global_log.info(ensemble + " " + pdb_name +
" Step 3: pmx gentop: Generate Hybrid Topology")
gentop_pc(**paths["step3_pmx_gentop"],
properties=prop["step3_pmx_gentop"])
if not dummy:
paths['step7_gmx_grompp']['input_gro_path'] = paths[
'step2_gmx_pdb2gmx']['output_gro_path']
else:
# step4_gmx_makendx
global_log.info(
ensemble + " " + pdb_name +
" Step 4 (Dummies): gmx make_ndx: Generate Gromacs Index file to select atoms to freeze"
)
make_ndx_pc(**paths["step4_gmx_makendx"],
properties=prop["step4_gmx_makendx"])
# step5_gmx_grompp
global_log.info(
ensemble + " " + pdb_name +
" Step 5 (Dummies): gmx grompp: Creating portable binary run file for energy minimization"
)
grompp_ndx_pc(**paths["step5_gmx_grompp"],
properties=prop["step5_gmx_grompp"])
# step6_gmx_mdrun
global_log.info(
ensemble + " " + pdb_name +
" Step 6 (Dummies): gmx mdrun: Running energy minimization"
)
mdrun_pc(**paths["step6_gmx_mdrun"],
properties=prop["step6_gmx_mdrun"])
# step7_gmx_grompp
global_log.info(
ensemble + " " + pdb_name +
" Step 7: gmx grompp: Creating portable binary run file for system equilibration"
)
grompp_pc(**paths["step7_gmx_grompp"],
properties=prop["step7_gmx_grompp"])
# step8_gmx_mdrun
global_log.info(ensemble + " " + pdb_name +
" Step 8: gmx mdrun: Running system equilibration")
mdrun_pc(**paths["step8_gmx_mdrun"],
properties=prop["step8_gmx_mdrun"])
# step9_gmx_grompp
global_log.info(
ensemble + " " + pdb_name +
" Step 9: Creating portable binary run file for thermodynamic integration (ti)"
)
grompp_pc(**paths["step9_gmx_grompp"],
properties=prop["step9_gmx_grompp"])
# step10_gmx_mdrun
global_log.info(
ensemble + " " + pdb_name +
" Step 10: gmx mdrun: Running thermodynamic integration")
mdrun_dhdl_pc(**paths["step10_gmx_mdrun"],
properties=prop["step10_gmx_mdrun"])
if ensemble == "stateA":
dhdl_paths_listA.append(
paths["step10_gmx_mdrun"]["output_dhdl_path"])
elif ensemble == "stateB":
dhdl_paths_listB.append(
paths["step10_gmx_mdrun"]["output_dhdl_path"])
# Creating zip file containing all the dhdl files
dhdlA_path = os.path.join(
global_prop["step11_pmx_analyse"]['working_dir_path'], 'dhdlA.zip')
dhdlB_path = os.path.join(
global_prop["step11_pmx_analyse"]['working_dir_path'], 'dhdlB.zip')
for dhdl_file in dhdl_paths_listA:
compss_wait_on_file(dhdl_file)
for dhdl_file in dhdl_paths_listB:
compss_wait_on_file(dhdl_file)
fu.zip_list(dhdlA_path, dhdl_paths_listA)
fu.zip_list(dhdlB_path, dhdl_paths_listB)
# step11_pmx_analyse
global_log.info(
ensemble +
" Step 11: pmx analyse: Calculate free energies from fast growth thermodynamic integration simulations"
)
global_paths["step11_pmx_analyse"]["input_a_xvg_zip_path"] = dhdlA_path
global_paths["step11_pmx_analyse"]["input_b_xvg_zip_path"] = dhdlB_path
analyse_pc(**global_paths["step11_pmx_analyse"],
properties=global_prop["step11_pmx_analyse"])
elapsed_time = time.time() - start_time
global_log.info('')
global_log.info('')
global_log.info('Execution successful: ')
global_log.info(' Workflow_path: %s' % conf.get_working_dir_path())
global_log.info(' Config File: %s' % config)
if system:
global_log.info(' System: %s' % system)
global_log.info('')
global_log.info('Elapsed time: %.1f minutes' % (elapsed_time / 60))
global_log.info('')
def main(config, imaged_traj_available):
start_time = time.time()
conf = settings.ConfReader(config)
global_log, _ = fu.get_logs(path=conf.get_working_dir_path(),
light_format=True)
global_prop = conf.get_prop_dic()
global_paths = conf.get_paths_dic()
dhdl_paths_listA = []
dhdl_paths_listB = []
for ensemble, mutation in conf.properties['mutations'].items():
ensemble_prop = conf.get_prop_dic(prefix=ensemble)
ensemble_paths = conf.get_paths_dic(prefix=ensemble)
if not imaged_traj_available:
# step0_image There isn't an imaged trajectory
global_log.info(
ensemble +
" Step 0: gmx image: Imaging trajectories to remove PBC issues"
)
ensemble_paths['step0_image']['input_top_path'] = conf.properties[
'input_trajs'][ensemble]['input_tpr_path']
ensemble_paths['step0_image']['input_traj_path'] = conf.properties[
'input_trajs'][ensemble]['input_traj_path']
gmx_image_pc(**ensemble_paths["step0_image"],
properties=ensemble_prop["step0_image"])
else:
# An imaged trajectory is available
ensemble_paths['step1_trjconv_' +
ensemble]['input_traj_path'] = conf.properties[
'input_trajs'][ensemble]['input_traj_path']
# step1_trjconv
global_log.info(
ensemble +
" Step 1: gmx trjconv: Extract snapshots from equilibrium trajectories"
)
ensemble_paths['step1_trjconv_' +
ensemble]['input_top_path'] = conf.properties[
'input_trajs'][ensemble]['input_tpr_path']
gmx_trjconv_str_ens_pc(**ensemble_paths['step1_trjconv_' + ensemble],
properties=ensemble_prop['step1_trjconv_' +
ensemble])
for ensemble, mutation in conf.properties['mutations'].items():
ensemble_prop = conf.get_prop_dic(prefix=ensemble)
ensemble_paths = conf.get_paths_dic(prefix=ensemble)
compss_wait_on_file(ensemble_paths['step1_trjconv_' +
ensemble]["output_str_ens_path"])
with zipfile.ZipFile(
ensemble_paths['step1_trjconv_' +
ensemble]["output_str_ens_path"]) as zip_f:
unique_dir = os.path.abspath(
fu.create_unique_dir(
prefix=ensemble_prop['step1_trjconv_' +
ensemble]['working_dir_path'] + '/' +
ensemble + '/'))
zip_f.extractall(unique_dir)
state_pdb_list = [
os.path.join(unique_dir, name) for name in zip_f.namelist()
]
for pdb_path in state_pdb_list:
pdb_name = os.path.splitext(os.path.basename(pdb_path))[0]
prop = conf.get_prop_dic(prefix=os.path.join(ensemble, pdb_name))
paths = conf.get_paths_dic(prefix=os.path.join(ensemble, pdb_name))
# step2_pmx_mutate
global_log.info(ensemble + " " + pdb_name +
" Step 2: pmx mutate: Generate Hybrid Structure")
paths['step2_pmx_mutate']['input_structure_path'] = pdb_path
prop['step2_pmx_mutate']['mutation_list'] = mutation
mutate_pc(**paths["step2_pmx_mutate"],
properties=prop["step2_pmx_mutate"])
# step3_check_dummies
global_log.info(ensemble + " " + pdb_name +
" Step 3 Check for dummy atoms")
extract_atoms_pc(**paths['step3_check_dummies'],
properties=prop['step3_check_dummies'])
compss_wait_on_file(
paths['step3_check_dummies']['output_structure_path'])
try:
dummy = bool(
os.path.getsize(
paths['step3_check_dummies']['output_structure_path']))
except:
global_log.info(
"Error ocurred while checking the file containing dummy atoms"
)
global_log.info(sys.exc_info()[0])
# step4_gmx_pdb2gmx
global_log.info(ensemble + " " + pdb_name +
" Step 4: gmx pdb2gmx: Generate Topology")
pdb2gmx_pc(**paths["step4_gmx_pdb2gmx"],
properties=prop["step4_gmx_pdb2gmx"])
# step5_pmx_gentop
global_log.info(ensemble + " " + pdb_name +
" Step 5: pmx gentop: Generate Hybrid Topology")
gentop_pc(**paths["step5_pmx_gentop"],
properties=prop["step5_pmx_gentop"])
if not dummy:
paths['step9_gmx_grompp']['input_gro_path'] = paths[
'step4_gmx_pdb2gmx']['output_gro_path']
else:
# step6_gmx_makendx
global_log.info(
ensemble + " " + pdb_name +
" Step 6: (Dummies): gmx make_ndx: Generate Gromacs Index file to select atoms to freeze"
)
make_ndx_pc(**paths["step6_gmx_makendx"],
properties=prop["step6_gmx_makendx"])
# step7_gmx_grompp
global_log.info(
ensemble + " " + pdb_name +
" Step 7: (Dummies): gmx grompp: Creating portable binary run file for energy minimization"
)
grompp_ndx_pc(**paths["step7_gmx_grompp"],
properties=prop["step7_gmx_grompp"])
# step8_gmx_mdrun
global_log.info(
ensemble + " " + pdb_name +
" Step 8: (Dummies): gmx mdrun: Running energy minimization"
)
mdrun_pc(**paths["step8_gmx_mdrun"],
properties=prop["step8_gmx_mdrun"])
# step9_gmx_grompp
global_log.info(
ensemble + " " + pdb_name +
" Step 9: gmx grompp: Creating portable binary run file for system equilibration"
)
grompp_pc(**paths["step9_gmx_grompp"],
properties=prop["step9_gmx_grompp"])
# step10_gmx_mdrun
global_log.info(
ensemble + " " + pdb_name +
" Step 10: gmx mdrun: Running system equilibration")
mdrun_pc(**paths["step10_gmx_mdrun"],
properties=prop["step10_gmx_mdrun"])
# step11_gmx_grompp
global_log.info(
ensemble + " " + pdb_name +
" Step 11: Creating portable binary run file for thermodynamic integration (ti)"
)
grompp_pc(**paths["step11_gmx_grompp"],
properties=prop["step11_gmx_grompp"])
# step12_gmx_mdrun
global_log.info(
ensemble + " " + pdb_name +
" Step 12: gmx mdrun: Running thermodynamic integration")
mdrun_dhdl_pc(**paths["step12_gmx_mdrun"],
properties=prop["step12_gmx_mdrun"])
if ensemble == "stateA":
dhdl_paths_listA.append(
paths["step12_gmx_mdrun"]["output_dhdl_path"])
elif ensemble == "stateB":
dhdl_paths_listB.append(
paths["step12_gmx_mdrun"]["output_dhdl_path"])
# Creating zip file containing all the dhdl files
dhdlA_path = os.path.join(
global_prop["step13_pmx_analyse"]['working_dir_path'], 'dhdlA.zip')
dhdlB_path = os.path.join(
global_prop["step13_pmx_analyse"]['working_dir_path'], 'dhdlB.zip')
for dhdl_file in dhdl_paths_listA:
compss_wait_on_file(dhdl_file)
for dhdl_file in dhdl_paths_listB:
compss_wait_on_file(dhdl_file)
fu.zip_list(dhdlA_path, dhdl_paths_listA)
fu.zip_list(dhdlB_path, dhdl_paths_listB)
# step13_pmx_analyse
global_log.info(
ensemble +
" Step 13: pmx analyse: Calculate free energies from fast growth thermodynamic integration simulations"
)
global_paths["step13_pmx_analyse"]["input_a_xvg_zip_path"] = dhdlA_path
global_paths["step13_pmx_analyse"]["input_b_xvg_zip_path"] = dhdlB_path
analyse_pc(**global_paths["step13_pmx_analyse"],
properties=global_prop["step13_pmx_analyse"])
elapsed_time = time.time() - start_time
global_log.info('')
global_log.info('')
global_log.info('Execution successful: ')
global_log.info(' Workflow_path: %s' % conf.get_working_dir_path())
global_log.info(' Config File: %s' % config)
global_log.info('')
global_log.info('Elapsed time: %.1f minutes' % (elapsed_time / 60))
global_log.info('')