#!/usr/bin/env python3
"""Module containing the SanderMDRun class and the command line interface."""
import argparse
import shutil
import re
from pathlib import Path, PurePath
from biobb_common.generic.biobb_object import BiobbObject
from biobb_common.configuration import settings
from biobb_common.tools import file_utils as fu
from biobb_common.tools.file_utils import launchlogger
from biobb_amber.sander.common import check_input_path, check_output_path
[docs]class SanderMDRun(BiobbObject):
"""
| biobb_amber SanderMDRun
| Wrapper of the `AmberTools (AMBER MD Package) sander tool <https://ambermd.org/AmberTools.php>`_ module.
| Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package.
Args:
input_top_path (str): Input topology file (AMBER ParmTop). File type: input. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/sander/cln025.prmtop>`_. Accepted formats: top (edam:format_3881), parmtop (edam:format_3881), prmtop (edam:format_3881).
input_crd_path (str): Input coordinates file (AMBER crd). File type: input. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/sander/cln025.inpcrd>`_. Accepted formats: crd (edam:format_3878), mdcrd (edam:format_3878), inpcrd (edam:format_3878), netcdf (edam:format_3650), nc (edam:format_3650), ncrst (edam:format_3886).
input_mdin_path (str) (Optional): Input configuration file (MD run options) (AMBER mdin). File type: input. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/sander/npt.mdin>`_. Accepted formats: mdin (edam:format_2330), in (edam:format_2330), txt (edam:format_2330).
input_cpin_path (str) (Optional): Input constant pH file (AMBER cpin). File type: input. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/sander/cln025.cpin>`_. Accepted formats: cpin (edam:format_2330).
input_ref_path (str) (Optional): Input reference coordinates for position restraints. File type: input. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/sander/sander.rst>`_. Accepted formats: rst (edam:format_3886), rst7 (edam:format_3886), netcdf (edam:format_3650), nc (edam:format_3650), ncrst (edam:format_3886), crd (edam:format_3878).
output_log_path (str): Output log file. File type: output. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/reference/sander/sander.log>`_. Accepted formats: log (edam:format_2330), out (edam:format_2330), txt (edam:format_2330), o (edam:format_2330).
output_traj_path (str): Output trajectory file. File type: output. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/reference/sander/sander.x>`_. Accepted formats: trj (edam:format_3878), crd (edam:format_3878), mdcrd (edam:format_3878), x (edam:format_3878), netcdf (edam:format_3650), nc (edam:format_3650).
output_rst_path (str): Output restart file. File type: output. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/reference/sander/sander.rst>`_. Accepted formats: rst (edam:format_3886), rst7 (edam:format_3886), netcdf (edam:format_3650), nc (edam:format_3650), ncrst (edam:format_3886).
output_cpout_path (str) (Optional): Output constant pH file (AMBER cpout). File type: output. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/reference/sander/sander.cpout>`_. Accepted formats: cpout (edam:format_2330).
output_cprst_path (str) (Optional): Output constant pH restart file (AMBER rstout). File type: output. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/reference/sander/sander.cprst>`_. Accepted formats: cprst (edam:format_3886), rst (edam:format_3886), rst7 (edam:format_3886).
output_mdinfo_path (str) (Optional): Output MD info. File type: output. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/reference/sander/sander.mdinfo>`_. Accepted formats: mdinfo (edam:format_2330).
properties (dict - Python dictionary object containing the tool parameters, not input/output files):
* **mdin** (*dict*) - ({}) Sander MD run options specification. (Used if *input_mdin_path* is None)
* **simulation_type** (*str*) - ("minimization") Default options for the mdin file. Each creates a different mdin file. Values: `minimization <https://biobb-amber.readthedocs.io/en/latest/_static/mdins/min.mdin>`_ (Runs an energy minimization), `min_vacuo <https://biobb-amber.readthedocs.io/en/latest/_static/mdins/min_vacuo.mdin>`_ (Runs an energy minimization in vacuo), `NVT <https://biobb-amber.readthedocs.io/en/latest/_static/mdins/nvt.mdin>`_ (Runs an NVT equilibration), `npt <https://biobb-amber.readthedocs.io/en/latest/_static/mdins/npt.mdin>`_ (Runs an NPT equilibration), `free <https://biobb-amber.readthedocs.io/en/latest/_static/mdins/free.mdin>`_ (Runs a MD simulation), `heat <https://biobb-amber.readthedocs.io/en/latest/_static/mdins/heat.mdin>`_ (Heats the MD system).
* **binary_path** (*str*) - ("sander") sander binary path to be used.
* **direct_mdin** (*bool*) - (False) Use input_mdin_path as it is, skip file parsing.
* **mpi_bin** (*str*) - (None) Path to the MPI runner. Usually "mpirun" or "srun".
* **mpi_np** (*int*) - (0) [0~1000|1] Number of MPI processes. Usually an integer bigger than 1.
* **mpi_flags** (*str*) - (None) Path to the MPI hostlist file.
* **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
* **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
* **container_path** (*str*) - (None) Container path definition.
* **container_image** (*str*) - ('afandiadib/ambertools:serial') Container image definition.
* **container_volume_path** (*str*) - ('/tmp') Container volume path definition.
* **container_working_dir** (*str*) - (None) Container working directory definition.
* **container_user_id** (*str*) - (None) Container user_id definition.
* **container_shell_path** (*str*) - ('/bin/bash') Path to default shell inside the container.
Examples:
This is a use example of how to use the building block from Python::
from biobb_amber.sander.sander_mdrun import sander_mdrun
prop = {
'simulation_type' : 'minimization',
'mdin' : {
'dt' : 0.002
}
}
sander_mdrun(input_top_path='/path/to/topology.top',
input_crd_path='/path/to/coordinates.crd',
output_traj_path='/path/to/newTrajectory.crd',
output_rst_path='/path/to/newRestart.rst',
output_log_path='/path/to/newAmberlog.log',
properties=prop)
Info:
* wrapped_software:
* name: AmberTools Sander
* version: >20.9
* license: LGPL 2.1
* multinode: mpi
* ontology:
* name: EDAM
* schema: http://edamontology.org/EDAM.owl
"""
def __init__(self, input_top_path: str, input_crd_path: str, output_log_path: str, output_traj_path: str, output_rst_path: str,
input_ref_path: str = None, input_mdin_path: str = None, input_cpin_path: str = None, output_cpout_path: str = None, output_cprst_path: str = None, output_mdinfo_path: str = None,
properties: dict = None, **kwargs) -> None:
properties = properties or {}
# Call parent class constructor
super().__init__(properties)
self.locals_var_dict = locals().copy()
# Input/Output files
self.io_dict = {
'in': {'input_top_path': input_top_path,
'input_crd_path': input_crd_path,
'input_mdin_path': input_mdin_path,
'input_ref_path': input_ref_path,
'input_cpin_path': input_cpin_path},
'out': {'output_log_path': output_log_path,
'output_traj_path': output_traj_path,
'output_rst_path': output_rst_path,
'output_cpout_path': output_cpout_path,
'output_cprst_path': output_cprst_path,
'output_mdinfo_path': output_mdinfo_path}
}
# Properties specific for BB
self.properties = properties
self.simulation_type = properties.get('simulation_type', "minimization")
self.binary_path = properties.get('binary_path', "sander")
self.direct_mdin = properties.get('direct_mdin', False)
self.mdin = {k: str(v) for k, v in properties.get('mdin', dict()).items()}
if 'restraintmask' in self.mdin and self.mdin['restraintmask'][0] != '"' and self.mdin['restraintmask'][-1] != '"':
self.mdin['restraintmask'] = "\"" + self.mdin['restraintmask'] + "\""
# Properties for MPI
self.mpi_bin = properties.get('mpi_bin')
self.mpi_np = properties.get('mpi_np')
self.mpi_flags = properties.get('mpi_flags')
# Check the properties
self.check_properties(properties)
self.check_arguments()
[docs] def check_data_params(self, out_log, out_err):
""" Checks input/output paths correctness """
# Check input(s)
self.io_dict["in"]["input_top_path"] = check_input_path(self.io_dict["in"]["input_top_path"], "input_top_path", False, out_log, self.__class__.__name__)
self.io_dict["in"]["input_crd_path"] = check_input_path(self.io_dict["in"]["input_crd_path"], "input_crd_path", False, out_log, self.__class__.__name__)
self.io_dict["in"]["input_mdin_path"] = check_input_path(self.io_dict["in"]["input_mdin_path"], "input_mdin_path", True, out_log, self.__class__.__name__)
self.io_dict["in"]["input_cpin_path"] = check_input_path(self.io_dict["in"]["input_cpin_path"], "input_cpin_path", True, out_log, self.__class__.__name__)
self.io_dict["in"]["input_ref_path"] = check_input_path(self.io_dict["in"]["input_ref_path"], "input_ref_path", True, out_log, self.__class__.__name__)
# Check output(s)
self.io_dict["out"]["output_log_path"] = check_output_path(self.io_dict["out"]["output_log_path"], "output_log_path", False, out_log, self.__class__.__name__)
self.io_dict["out"]["output_traj_path"] = check_output_path(self.io_dict["out"]["output_traj_path"], "output_traj_path", False, out_log, self.__class__.__name__)
self.io_dict["out"]["output_rst_path"] = check_output_path(self.io_dict["out"]["output_rst_path"], "output_rst_path", False, out_log, self.__class__.__name__)
self.io_dict["out"]["output_cpout_path"] = check_output_path(self.io_dict["out"]["output_cpout_path"], "output_cpout_path", True, out_log, self.__class__.__name__)
self.io_dict["out"]["output_cprst_path"] = check_output_path(self.io_dict["out"]["output_cprst_path"], "output_cprst_path", True, out_log, self.__class__.__name__)
self.io_dict["out"]["output_mdinfo_path"] = check_output_path(self.io_dict["out"]["output_mdinfo_path"], "output_mdinfo_path", True, out_log, self.__class__.__name__)
[docs] def create_mdin(self, path: str = None) -> str:
"""Creates an AMBER MD configuration file (mdin) using the properties file settings"""
mdin_list = []
mdin_firstPart = []
mdin_middlePart = []
mdin_lastPart = []
self.output_mdin_path = path
if self.io_dict['in']['input_mdin_path']:
# MDIN parameters read from an input mdin file
if (not self.direct_mdin):
mdin_firstPart.append("Mdin read from input file: " + self.stage_io_dict['in']['input_mdin_path'])
mdin_firstPart.append("and modified by the biobb_amber module from the BioBB library ")
with open(self.stage_io_dict['in']['input_mdin_path']) as input_params:
firstPart = True
secondPart = False
for line in input_params:
if '=' in line and not secondPart:
firstPart = False
mdin_middlePart.append(line.rstrip())
else:
if (firstPart):
mdin_firstPart.append(line.rstrip())
elif (secondPart):
mdin_lastPart.append(line.rstrip())
else:
secondPart = True
mdin_lastPart.append(line.rstrip())
for line in mdin_middlePart:
if ('!' in line or '#' in line) and not ('!@' in line or '!:' in line):
# Parsing lines with comments (#,!), e.g. :
# ntc=2, ntf=2, ! SHAKE, constrain lenghts of the bonds having H
params = re.split('!|#', line)
for param in params[0].split(','):
if param.strip():
mdin_list.append(" " + param.strip() + " ! " + params[1])
elif ('@' in line or ':' in line):
# Parsing masks, e.g. :
# restraintmask = ":1-40@P,O5',C5',C4',C3',O3'", restraint_wt = 0.5
mylist = re.findall(r'(?:[^,"]|"(?:\\.|[^"])*")+', line)
[mdin_list.append(" " + i.lstrip()) for i in mylist]
else:
for param in line.split(','):
if param.strip():
if not param.strip().startswith('!'):
mdin_list.append(" " + param.strip())
else:
# MDIN parameters added by the biobb_amber module
mdin_list.append("This mdin file has been created by the biobb_amber module from the BioBB library ")
sim_type = self.properties.get('simulation_type', 'minimization')
# sim_type = self.mdin.get('simulation_type', 'minimization')
minimization = (sim_type == 'minimization')
min_vacuo = (sim_type == 'min_vacuo')
heat = (sim_type == 'heat')
nvt = (sim_type == 'nvt')
npt = (sim_type == 'npt')
free = (sim_type == 'free')
md = (nvt or npt or free or heat)
mdin_list.append("Type of mdin: " + sim_type)
mdin_list.append("&cntrl")
# Pre-configured simulation type parameters
if minimization:
mdin_list.append(" imin = 1 ! BioBB simulation_type minimization")
if min_vacuo:
mdin_list.append(" imin = 1 ! BioBB simulation_type min_vacuo")
mdin_list.append(" ncyc = 250 ! BioBB simulation_type min_vacuo")
mdin_list.append(" ntb = 0 ! BioBB simulation_type min_vacuo")
mdin_list.append(" igb = 0 ! BioBB simulation_type min_vacuo")
mdin_list.append(" cut = 12 ! BioBB simulation_type min_vacuo")
if md:
mdin_list.append(" imin = 0 ! BioBB simulation_type nvt|npt|free|heat")
mdin_list.append(" cut = 10.0 ! BioBB simulation_type nvt|npt|free|heat")
mdin_list.append(" ntr = 0 ! BioBB simulation_type nvt|npt|free|heat")
mdin_list.append(" ntc = 2 ! BioBB simulation_type nvt|npt|free|heat")
mdin_list.append(" ntf = 2 ! BioBB simulation_type nvt|npt|free|heat")
mdin_list.append(" ntt = 3 ! BioBB simulation_type nvt|npt|free|heat")
mdin_list.append(" ig = -1 ! BioBB simulation_type nvt|npt|free|heat")
mdin_list.append(" ioutfm = 1 ! BioBB simulation_type nvt|npt|free|heat")
mdin_list.append(" iwrap = 1 ! BioBB simulation_type nvt|npt|free|heat")
mdin_list.append(" nstlim = 5000 ! BioBB simulation_type nvt|npt|free|heat")
mdin_list.append(" dt = 0.002 ! BioBB simulation_type nvt|npt|free|heat")
if npt:
mdin_list.append(" irest = 1 ! BioBB simulation_type npt")
mdin_list.append(" gamma_ln = 5.0 ! BioBB simulation_type npt")
mdin_list.append(" pres0 = 1.0 ! BioBB simulation_type npt")
mdin_list.append(" ntp = 1 ! BioBB simulation_type npt")
mdin_list.append(" taup = 2.0 ! BioBB simulation_type npt")
mdin_list.append(" ntx = 5 ! BioBB simulation_type npt")
if nvt:
mdin_list.append(" irest = 1 ! BioBB simulation_type nvt")
mdin_list.append(" gamma_ln = 5.0 ! BioBB simulation_type nvt")
mdin_list.append(" ntb = 1 ! BioBB simulation_type nvt")
mdin_list.append(" ntx = 5 ! BioBB simulation_type nvt")
if heat:
mdin_list.append(" tempi = 0.0 ! BioBB simulation_type heat")
mdin_list.append(" temp0 = 300.0 ! BioBB simulation_type heat")
mdin_list.append(" irest = 0 ! BioBB simulation_type heat")
mdin_list.append(" ntb = 1 ! BioBB simulation_type heat") # periodic boundaries
mdin_list.append(" gamma_ln = 1.0 ! BioBB simulation_type heat")
# mdin_list.append(" nmropt = 1 ! BioBB simulation_type heat")
# mdin_lastPart.append("/")
# mdin_lastPart.append("&wt")
# mdin_lastPart.append(" TYPE = 'TEMP0' ! BioBB simulation_type heat")
# mdin_lastPart.append(" ISTEP1 = 1 ! BioBB simulation_type heat")
# mdin_lastPart.append(" ISTEP2 = 4000 ! BioBB simulation_type heat")
# mdin_lastPart.append(" VALUE1 = 10.0 ! BioBB simulation_type heat")
# mdin_lastPart.append(" VALUE2 = 300.0 ! BioBB simulation_type heat")
# mdin_lastPart.append("/")
# mdin_lastPart.append("&wt")
# mdin_lastPart.append(" TYPE = 'END' ! BioBB simulation_type heat")
# mdin_lastPart.append("/")
if (not self.direct_mdin):
# Adding the rest of parameters in the config file to the mdin file
# if the parameter has already been added replace the value
parameter_keys = [parameter.split('=')[0].strip() for parameter in mdin_list]
for k, v in self.mdin.items():
config_parameter_key = str(k).strip()
if config_parameter_key in parameter_keys:
mdin_list[parameter_keys.index(config_parameter_key)] = ' ' + config_parameter_key + ' = ' + str(v) + ' ! BioBB property'
else:
mdin_list.append(' ' + config_parameter_key + ' = '+str(v) + ' ! BioBB property')
# Writing MD configuration file (mdin)
with open(self.output_mdin_path, 'w') as mdin:
# Start of file keyword(s)
if mdin_firstPart:
for line in mdin_firstPart:
mdin.write(line + '\n')
# MD config parameters
for line in mdin_list:
mdin.write(line + '\n')
# End of file keyword(s)
if mdin_lastPart:
for line in mdin_lastPart:
mdin.write(line + '\n')
else:
mdin.write("&end\n")
else:
# Copying generated output file to the final (user-given) file name
shutil.copy2(self.io_dict['in']['input_mdin_path'], self.output_mdin_path)
return self.output_mdin_path
[docs] @launchlogger
def launch(self):
"""Launches the execution of the BuildLinearStructure module."""
# check input/output paths and parameters
self.check_data_params(self.out_log, self.err_log)
# Setup Biobb
if self.check_restart():
return 0
self.stage_files()
# Creating temporary folder
# self.tmp_folder = fu.create_unique_dir()
# fu.log('Creating %s temporary folder' % self.tmp_folder, self.out_log)
# if self.io_dict['in']['input_mdin_path']:
# self.output_mdin_path = self.io_dict['in']['input_mdin_path']
# else:
# self.output_mdin_path = self.create_mdin(path=str(Path(self.tmp_folder).joinpath("sander.mdin")))
# self.output_mdin_path = self.create_mdin(path=str(Path(self.tmp_folder).joinpath("sander.mdin")))
# Creating temporary folder & Sander configuration (instructions) file
if self.container_path:
# instructions_file = str(PurePath(self.stage_io_dict['unique_dir']).joinpath("leap.in"))
# instructions_file_path = str(PurePath(self.container_volume_path).joinpath("leap.in"))
instructions_file = self.create_mdin(path=str(Path(self.stage_io_dict['unique_dir']).joinpath("sander.mdin")))
self.output_mdin_path = str(PurePath(self.container_volume_path).joinpath(PurePath(instructions_file).name))
self.tmp_folder = None
else:
self.tmp_folder = fu.create_unique_dir()
fu.log('Creating %s temporary folder' % self.tmp_folder, self.out_log)
self.output_mdin_path = self.create_mdin(path=str(Path(self.tmp_folder).joinpath("sander.mdin")))
# Command line
# sander -O -i mdin/min.mdin -p $1.cpH.prmtop -c ph$i/$1.inpcrd -r ph$i/$1.min.rst7 -o ph$i/$1.min.o
self.cmd = [self.binary_path,
'-O',
'-i', self.output_mdin_path,
'-p', self.stage_io_dict['in']['input_top_path'],
'-c', self.stage_io_dict['in']['input_crd_path'],
'-r', self.stage_io_dict['out']['output_rst_path'],
'-o', self.stage_io_dict['out']['output_log_path'],
'-x', self.stage_io_dict['out']['output_traj_path']
]
if self.io_dict['in']['input_ref_path']:
self.cmd.append('-ref')
self.cmd.append(self.stage_io_dict['in']['input_ref_path'])
if self.io_dict['in']['input_cpin_path']:
self.cmd.append('-cpin')
self.cmd.append(self.stage_io_dict['in']['input_cpin_path'])
if self.io_dict['out']['output_mdinfo_path']:
self.cmd.append('-inf')
self.cmd.append(self.stage_io_dict['out']['output_mdinfo_path'])
if self.io_dict['out']['output_cpout_path']:
self.cmd.append('-cpout')
self.cmd.append(self.stage_io_dict['out']['output_cpout_path'])
if self.io_dict['out']['output_cprst_path']:
self.cmd.append('-cprestrt')
self.cmd.append(self.stage_io_dict['out']['output_cprst_path'])
# general mpi properties
if self.mpi_bin:
mpi_cmd = [self.mpi_bin]
if self.mpi_np:
mpi_cmd.append('-n')
mpi_cmd.append(str(self.mpi_np))
if self.mpi_flags:
mpi_cmd.extend(self.mpi_flags)
self.cmd = mpi_cmd + self.cmd
# Run Biobb block
self.run_biobb()
# Copy files to host
self.copy_to_host()
# remove temporary folder(s)
'''if self.remove_tmp:
if self.container_path: self.tmp_files.append(self.stage_io_dict['unique_dir'])
else:
self.tmp_files.append(self.tmp_folder)
self.tmp_files.append("mdinfo")
self.remove_tmp_files()'''
self.tmp_files.extend([
self.stage_io_dict.get("unique_dir"),
"mdinfo",
self.tmp_folder
])
self.remove_tmp_files()
self.check_arguments(output_files_created=True, raise_exception=False)
return self.return_code
[docs]def sander_mdrun(input_top_path: str, input_crd_path: str,
output_log_path: str, output_traj_path: str, output_rst_path: str,
input_mdin_path: str = None, input_cpin_path: str = None,
output_cpout_path: str = None, output_cprst_path: str = None,
output_mdinfo_path: str = None, input_ref_path: str = None,
properties: dict = None, **kwargs) -> int:
"""Create :class:`SanderMDRun <sander.sander_mdrun.SanderMDRun>`sander.sander_mdrun.SanderMDRun class and
execute :meth:`launch() <sander.sander_mdrun.SanderMDRun.launch>` method"""
return SanderMDRun(input_top_path=input_top_path,
input_crd_path=input_crd_path,
input_mdin_path=input_mdin_path,
input_cpin_path=input_cpin_path,
input_ref_path=input_ref_path,
output_log_path=output_log_path,
output_traj_path=output_traj_path,
output_rst_path=output_rst_path,
output_cpout_path=output_cpout_path,
output_cprst_path=output_cprst_path,
output_mdinfo_path=output_mdinfo_path,
properties=properties).launch()
[docs]def main():
parser = argparse.ArgumentParser(description='Running energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package.', formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
parser.add_argument('--config', required=False, help='Configuration file')
# Specific args
required_args = parser.add_argument_group('required arguments')
required_args.add_argument('--input_top_path', required=True, help='Input topology file (AMBER ParmTop). Accepted formats: top, prmtop, parmtop.')
required_args.add_argument('--input_crd_path', required=True, help='Input coordinates file (AMBER crd). Accepted formats: crd, mdcrd.')
# required_args.add_argument('--input_mdin_path', required=False, help='Input configuration file (MD run options) (AMBER mdin). Accepted formats: mdin, in, txt.')
parser.add_argument('--input_mdin_path', required=False, help='Input configuration file (MD run options) (AMBER mdin). Accepted formats: mdin, in, txt.')
# required_args.add_argument('--input_cpin_path', required=False, help='Input constant pH file (AMBER cpin). Accepted formats: cpin.')
parser.add_argument('--input_cpin_path', required=False, help='Input constant pH file (AMBER cpin). Accepted formats: cpin.')
# required_args.add_argument('--input_ref_path', required=False, help='Input reference coordinates for position restraints. Accepted formats: rst, rst7.')
parser.add_argument('--input_ref_path', required=False, help='Input reference coordinates for position restraints. Accepted formats: rst, rst7.')
required_args.add_argument('--output_log_path', required=True, help='Output log file. Accepted formats: log, out, txt.')
required_args.add_argument('--output_traj_path', required=True, help='Output trajectory file. Accepted formats: trj, crd, mdcrd, x.')
required_args.add_argument('--output_rst_path', required=True, help='Output restart file. Accepted formats: rst, rst7.')
# required_args.add_argument('--output_cpout_path', required=False, help='Output constant pH file (AMBER cpout). Accepted formats: cpout.')
parser.add_argument('--output_cpout_path', required=False, help='Output constant pH file (AMBER cpout). Accepted formats: cpout.')
# required_args.add_argument('--output_cprst_path', required=False, help='Output constant pH restart file (AMBER rstout). Accepted formats: cprst.')
parser.add_argument('--output_cprst_path', required=False, help='Output constant pH restart file (AMBER rstout). Accepted formats: cprst.')
# required_args.add_argument('--output_mdinfo_path', required=False, help='Output MD info. Accepted formats: mdinfo.')
parser.add_argument('--output_mdinfo_path', required=False, help='Output MD info. Accepted formats: mdinfo.')
args = parser.parse_args()
# config = args.config if args.config else None
args.config = args.config or "{}"
# properties = settings.ConfReader(config=config).get_prop_dic()
properties = settings.ConfReader(config=args.config).get_prop_dic()
# Specific call
sander_mdrun(input_top_path=args.input_top_path,
input_crd_path=args.input_crd_path,
input_mdin_path=args.input_mdin_path,
input_cpin_path=args.input_cpin_path,
input_ref_path=args.input_ref_path,
output_log_path=args.output_log_path,
output_traj_path=args.output_traj_path,
output_rst_path=args.output_rst_path,
output_cpout_path=args.output_cpout_path,
output_cprst_path=args.output_cprst_path,
output_mdinfo_path=args.output_mdinfo_path,
properties=properties)
if __name__ == '__main__':
main()