Coverage for biobb_amber/pmemd/pmemd_mdrun.py: 9%
200 statements
« prev ^ index » next coverage.py v7.6.10, created at 2025-01-28 08:28 +0000
1#!/usr/bin/env python3
3"""Module containing the PmemdMDRun class and the command line interface."""
4import argparse
5from typing import Optional
6import re
7from pathlib import Path
8from biobb_common.generic.biobb_object import BiobbObject
9from biobb_common.configuration import settings
10from biobb_common.tools import file_utils as fu
11from biobb_common.tools.file_utils import launchlogger
12from biobb_amber.pmemd.common import check_input_path, check_output_path
15class PmemdMDRun(BiobbObject):
16 """
17 | biobb_amber PmemdMDRun
18 | Wrapper of the `AmberTools (AMBER MD Package) pmemd tool <https://ambermd.org/AmberTools.php>`_ module.
19 | Runs molecular dynamics using pmemd tool from the AMBER MD package.
21 Args:
22 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/pmemd/cln025.prmtop>`_. Accepted formats: top (edam:format_3881), parmtop (edam:format_3881), prmtop (edam:format_3881).
23 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/pmemd/cln025.inpcrd>`_. Accepted formats: crd (edam:format_3878), mdcrd (edam:format_3878), inpcrd (edam:format_3878), rst (edam:format_3886), rst7 (edam:format_3886), netcdf (edam:format_3650), nc (edam:format_3650), ncrst (edam:format_3886).
24 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/pmemd/npt.mdin>`_. Accepted formats: mdin (edam:format_2330), in (edam:format_2330), txt (edam:format_2330).
25 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/pmemd/cln025.cpin>`_. Accepted formats: cpin (edam:format_2330).
26 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/pmemd/sander.rst>`_. Accepted formats: crd (edam:format_3878), mdcrd (edam:format_3878), inpcrd (edam:format_3878), rst (edam:format_3886), rst7 (edam:format_3886), netcdf (edam:format_3650), nc (edam:format_3650), ncrst (edam:format_3886).
27 output_log_path (str): Output log file. File type: output. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/reference/pmemd/sander.log>`_. Accepted formats: log (edam:format_2330), out (edam:format_2330), txt (edam:format_2330), o (edam:format_2330).
28 output_traj_path (str): Output trajectory file. File type: output. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/reference/pmemd/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).
29 output_rst_path (str): Output restart file. File type: output. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/reference/pmemd/sander.rst>`_. Accepted formats: rst (edam:format_3886), rst7 (edam:format_3886), netcdf (edam:format_3650), nc (edam:format_3650), ncrst (edam:format_3886).
30 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/pmemd/sander.cpout>`_. Accepted formats: cpout (edam:format_2330).
31 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/pmemd/sander.cprst>`_. Accepted formats: cprst (edam:format_3886), rst (edam:format_3886), rst7 (edam:format_3886).
32 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/pmemd/sander.mdinfo>`_. Accepted formats: mdinfo (edam:format_2330).
33 properties (dict - Python dictionary object containing the tool parameters, not input/output files):
34 * **mdin** (*dict*) - ({}) pmemd MD run options specification. (Used if *input_mdin_path* is None)
35 * **binary_path** (*str*) - ("pmemd") pmemd binary path to be used.
36 * **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/mdin/minimization.mdin>`_ (Runs an energy minimization), `min_vacuo <https://biobb-amber.readthedocs.io/en/latest/_static/mdin/min_vacuo.mdin>`_ (Runs an energy minimization in vacuo), `NVT <https://biobb-amber.readthedocs.io/en/latest/_static/mdin/NVT.mdin>`_ (Runs an NVT equilibration), `npt <https://biobb-amber.readthedocs.io/en/latest/_static/mdin/NPT.mdin>`_ (Runs an NPT equilibration), `free <https://biobb-amber.readthedocs.io/en/latest/_static/mdin/free.mdin>`_ (Runs a MD simulation).
37 * **mpi_bin** (*str*) - (None) Path to the MPI runner. Usually "mpirun" or "srun".
38 * **mpi_np** (*int*) - (0) [0~1000|1] Number of MPI processes. Usually an integer bigger than 1.
39 * **mpi_flags** (*str*) - (None) Path to the MPI hostlist file.
40 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
41 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
42 * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
44 Examples:
45 This is a use example of how to use the building block from Python::
47 from biobb_amber.pmemd.pmemd_mdrun import pmemd_mdrun
48 prop = {
49 'simulation_type' : 'npt',
50 'mdin' : {
51 'dt' : 0.002
52 }
53 }
54 pmemd_mdrun(input_top_path='/path/to/topology.top',
55 input_crd_path='/path/to/coordinates.crd',
56 output_traj_path='/path/to/newTrajectory.crd',
57 output_rst_path='/path/to/newRestart.rst',
58 output_log_path='/path/to/newAmberlog.log',
59 properties=prop)
61 Info:
62 * wrapped_software:
63 * name: AMBER pmemd
64 * version: >20
65 * license: other
66 * multinode: mpi
67 * ontology:
68 * name: EDAM
69 * schema: http://edamontology.org/EDAM.owl
71 """
73 def __init__(self, input_top_path: str, input_crd_path: str, output_log_path: str, output_traj_path: str, output_rst_path: str,
74 input_ref_path: Optional[str] = None, input_mdin_path: Optional[str] = None, input_cpin_path: Optional[str] = None, output_cpout_path: Optional[str] = None, output_cprst_path: Optional[str] = None, output_mdinfo_path: Optional[str] = None,
75 properties: Optional[dict] = None, **kwargs) -> None:
77 properties = properties or {}
79 # Call parent class constructor
80 super().__init__(properties)
81 self.locals_var_dict = locals().copy()
83 # Input/Output files
84 self.io_dict = {
85 'in': {'input_top_path': input_top_path,
86 'input_crd_path': input_crd_path,
87 'input_mdin_path': input_mdin_path,
88 'input_ref_path': input_ref_path,
89 'input_cpin_path': input_cpin_path},
90 'out': {'output_log_path': output_log_path,
91 'output_traj_path': output_traj_path,
92 'output_rst_path': output_rst_path,
93 'output_cpout_path': output_cpout_path,
94 'output_cprst_path': output_cprst_path,
95 'output_mdinfo_path': output_mdinfo_path}
96 }
98 # Properties specific for BB
99 self.properties = properties
100 self.simulation_type = properties.get('simulation_type', "minimization")
101 self.binary_path = properties.get('binary_path', "pmemd")
102 self.mdin = {k: str(v) for k, v in properties.get('mdin', dict()).items()}
104 # Properties for MPI
105 self.mpi_bin = properties.get('mpi_bin')
106 self.mpi_np = properties.get('mpi_np')
107 self.mpi_flags = properties.get('mpi_flags')
109 # Check the properties
110 self.check_properties(properties)
111 self.check_arguments()
113 def check_data_params(self, out_log, err_log):
114 """ Checks input/output paths correctness """
116 # Check input(s)
117 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__)
118 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__)
119 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__)
120 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__)
121 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__)
123 # Check output(s)
124 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__)
125 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__)
126 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__)
127 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__)
128 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__)
129 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__)
131 def create_mdin(self, path: Optional[str] = None) -> str:
132 """Creates an AMBER MD configuration file (mdin) using the properties file settings"""
133 mdin_list = []
134 mdin_firstPart = []
135 mdin_middlePart = []
136 mdin_lastPart = []
138 self.output_mdin_path = path
140 if self.io_dict['in']['input_mdin_path']:
141 # MDIN parameters read from an input mdin file
142 mdin_firstPart.append("Mdin read from input file: " + self.io_dict['in']['input_mdin_path'])
143 mdin_firstPart.append("and modified by the biobb_amber module from the BioBB library ")
144 with open(self.io_dict['in']['input_mdin_path']) as input_params:
145 firstPart = True
146 secondPart = False
147 for line in input_params:
148 if '=' in line and not secondPart:
149 firstPart = False
150 mdin_middlePart.append(line.rstrip())
151 else:
152 if (firstPart):
153 mdin_firstPart.append(line.rstrip())
154 elif (secondPart):
155 mdin_lastPart.append(line.rstrip())
156 else:
157 secondPart = True
158 mdin_lastPart.append(line.rstrip())
160 for line in mdin_middlePart:
161 if ('!' in line or '#' in line) and not ('!@' in line or '!:' in line):
162 # Parsing lines with comments (#,!), e.g. :
163 # ntc=2, ntf=2, ! SHAKE, constrain lenghts of the bonds having H
164 params = re.split('!|#', line)
165 for param in params[0].split(','):
166 if param.strip():
167 mdin_list.append(" " + param.strip() + " ! " + params[1])
168 elif ('@' in line or ':' in line):
169 # Parsing masks, e.g. :
170 # restraintmask = ":1-40@P,O5',C5',C4',C3',O3'", restraint_wt = 0.5
171 mylist = re.findall(r'(?:[^,"]|"(?:\\.|[^"])*")+', line)
172 [mdin_list.append(" " + i.lstrip()) for i in mylist] # type: ignore
173 else:
174 for param in line.split(','):
175 if param.strip():
176 if not param.strip().startswith('!'):
177 mdin_list.append(" " + param.strip())
179 else:
180 # MDIN parameters added by the biobb_amber module
181 mdin_list.append("This mdin file has been created by the biobb_amber module from the BioBB library ")
183 sim_type = self.properties.get('simulation_type', 'minimization')
184 # sim_type = self.mdin.get('simulation_type', 'minimization')
185 minimization = (sim_type == 'minimization')
186 min_vacuo = (sim_type == 'min_vacuo')
187 heat = (sim_type == 'heat')
188 nvt = (sim_type == 'nvt')
189 npt = (sim_type == 'npt')
190 free = (sim_type == 'free')
191 md = (nvt or npt or free or heat)
193 mdin_list.append("Type of mdin: " + sim_type)
194 mdin_list.append("&cntrl")
196 # Pre-configured simulation type parameters
197 if minimization:
198 mdin_list.append(" imin = 1 ! BioBB simulation_type minimization")
199 if min_vacuo:
200 mdin_list.append(" imin = 1 ! BioBB simulation_type min_vacuo")
201 mdin_list.append(" ncyc = 250 ! BioBB simulation_type min_vacuo")
202 mdin_list.append(" ntb = 0 ! BioBB simulation_type min_vacuo")
203 mdin_list.append(" igb = 0 ! BioBB simulation_type min_vacuo")
204 mdin_list.append(" cut = 12 ! BioBB simulation_type min_vacuo")
205 if md:
206 mdin_list.append(" imin = 0 ! BioBB simulation_type nvt|npt|free|heat")
207 mdin_list.append(" cut = 10.0 ! BioBB simulation_type nvt|npt|free|heat")
208 mdin_list.append(" ntr = 0 ! BioBB simulation_type nvt|npt|free|heat")
209 mdin_list.append(" ntc = 2 ! BioBB simulation_type nvt|npt|free|heat")
210 mdin_list.append(" ntf = 2 ! BioBB simulation_type nvt|npt|free|heat")
211 mdin_list.append(" ntt = 3 ! BioBB simulation_type nvt|npt|free|heat")
212 mdin_list.append(" ig = -1 ! BioBB simulation_type nvt|npt|free|heat")
213 mdin_list.append(" ioutfm = 1 ! BioBB simulation_type nvt|npt|free|heat")
214 mdin_list.append(" iwrap = 1 ! BioBB simulation_type nvt|npt|free|heat")
215 mdin_list.append(" nstlim = 5000 ! BioBB simulation_type nvt|npt|free|heat")
216 mdin_list.append(" dt = 0.002 ! BioBB simulation_type nvt|npt|free|heat")
217 if npt:
218 mdin_list.append(" irest = 1 ! BioBB simulation_type npt")
219 mdin_list.append(" gamma_ln = 5.0 ! BioBB simulation_type npt")
220 mdin_list.append(" pres0 = 1.0 ! BioBB simulation_type npt")
221 mdin_list.append(" ntp = 1 ! BioBB simulation_type npt")
222 mdin_list.append(" taup = 2.0 ! BioBB simulation_type npt")
223 mdin_list.append(" ntx = 5 ! BioBB simulation_type npt")
224 if nvt:
225 mdin_list.append(" irest = 1 ! BioBB simulation_type nvt")
226 mdin_list.append(" gamma_ln = 5.0 ! BioBB simulation_type nvt")
227 mdin_list.append(" ntb = 1 ! BioBB simulation_type nvt")
228 mdin_list.append(" ntx = 5 ! BioBB simulation_type nvt")
229 if heat:
230 mdin_list.append(" tempi = 0.0 ! BioBB simulation_type heat")
231 mdin_list.append(" temp0 = 300.0 ! BioBB simulation_type heat")
232 mdin_list.append(" irest = 0 ! BioBB simulation_type heat")
233 mdin_list.append(" ntb = 1 ! BioBB simulation_type heat") # periodic boundaries
234 mdin_list.append(" gamma_ln = 1.0 ! BioBB simulation_type heat")
235 # mdin_list.append(" nmropt = 1 ! BioBB simulation_type heat")
237 # mdin_lastPart.append("/")
238 # mdin_lastPart.append("&wt")
239 # mdin_lastPart.append(" TYPE = 'TEMP0' ! BioBB simulation_type heat")
240 # mdin_lastPart.append(" ISTEP1 = 1 ! BioBB simulation_type heat")
241 # mdin_lastPart.append(" ISTEP2 = 4000 ! BioBB simulation_type heat")
242 # mdin_lastPart.append(" VALUE1 = 10.0 ! BioBB simulation_type heat")
243 # mdin_lastPart.append(" VALUE2 = 300.0 ! BioBB simulation_type heat")
244 # mdin_lastPart.append("/")
245 # mdin_lastPart.append("&wt")
246 # mdin_lastPart.append(" TYPE = 'END' ! BioBB simulation_type heat")
247 # mdin_lastPart.append("/")
249 # Adding the rest of parameters in the config file to the mdin file
250 # if the parameter has already been added replace the value
251 parameter_keys = [parameter.split('=')[0].strip() for parameter in mdin_list]
252 for k, v in self.mdin.items():
253 config_parameter_key = str(k).strip()
254 if config_parameter_key in parameter_keys:
255 mdin_list[parameter_keys.index(config_parameter_key)] = ' ' + config_parameter_key + ' = ' + str(v) + ' ! BioBB property'
256 else:
257 mdin_list.append(' ' + config_parameter_key + ' = '+str(v) + ' ! BioBB property')
259 # Writing MD configuration file (mdin)
260 with open(str(self.output_mdin_path), 'w') as mdin:
261 # Start of file keyword(s)
262 if mdin_firstPart:
263 for line in mdin_firstPart:
264 mdin.write(line + '\n')
266 # MD config parameters
267 for line in mdin_list:
268 mdin.write(line + '\n')
270 # End of file keyword(s)
271 if mdin_lastPart:
272 for line in mdin_lastPart:
273 mdin.write(line + '\n')
274 else:
275 mdin.write("&end\n")
277 return str(self.output_mdin_path)
279 @launchlogger
280 def launch(self):
281 """Launches the execution of the PmemdMDRun module."""
283 # check input/output paths and parameters
284 self.check_data_params(self.out_log, self.err_log)
286 # Setup Biobb
287 if self.check_restart():
288 return 0
289 self.stage_files()
291 # Creating temporary folder
292 self.tmp_folder = fu.create_unique_dir()
293 fu.log('Creating %s temporary folder' % self.tmp_folder, self.out_log)
295 # if self.io_dict['in']['input_mdin_path']:
296 # self.output_mdin_path = self.io_dict['in']['input_mdin_path']
297 # else:
298 # self.output_mdin_path = self.create_mdin(path=str(Path(self.tmp_folder).joinpath("pmemd.mdin")))
299 self.output_mdin_path = self.create_mdin(path=str(Path(self.tmp_folder).joinpath("pmemd.mdin")))
301 # Command line
302 # pmemd -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
303 self.cmd = [self.binary_path,
304 '-O',
305 '-i', self.output_mdin_path,
306 '-p', self.io_dict['in']['input_top_path'],
307 '-c', self.io_dict['in']['input_crd_path'],
308 '-r', self.io_dict['out']['output_rst_path'],
309 '-o', self.io_dict['out']['output_log_path'],
310 '-x', self.io_dict['out']['output_traj_path']
311 ]
313 if self.io_dict['in']['input_ref_path']:
314 self.cmd.append('-ref')
315 self.cmd.append(self.io_dict['in']['input_ref_path'])
317 if self.io_dict['in']['input_cpin_path']:
318 self.cmd.append('-cpin')
319 self.cmd.append(self.io_dict['in']['input_cpin_path'])
321 if self.io_dict['out']['output_mdinfo_path']:
322 self.cmd.append('-inf')
323 self.cmd.append(self.io_dict['out']['output_mdinfo_path'])
325 if self.io_dict['out']['output_cpout_path']:
326 self.cmd.append('-cpout')
327 self.cmd.append(self.io_dict['out']['output_cpout_path'])
329 if self.io_dict['out']['output_cprst_path']:
330 self.cmd.append('-cprestrt')
331 self.cmd.append(self.io_dict['out']['output_cprst_path'])
333 # general mpi properties
334 if self.mpi_bin:
335 mpi_cmd = [self.mpi_bin]
336 if self.mpi_np:
337 mpi_cmd.append('-n')
338 mpi_cmd.append(str(self.mpi_np))
339 if self.mpi_flags:
340 mpi_cmd.extend(self.mpi_flags)
341 self.cmd = mpi_cmd + self.cmd
343 # Run Biobb block
344 self.run_biobb()
346 # Copy files to host
347 self.copy_to_host()
349 # remove temporary folder(s)
350 self.tmp_files.extend([
351 # self.stage_io_dict.get("unique_dir", ""),
352 self.tmp_folder,
353 "mdinfo"
354 ])
355 self.remove_tmp_files()
357 self.check_arguments(output_files_created=True, raise_exception=False)
359 return self.return_code
362def pmemd_mdrun(input_top_path: str, input_crd_path: str,
363 output_log_path: str, output_traj_path: str, output_rst_path: str,
364 input_mdin_path: Optional[str] = None, input_cpin_path: Optional[str] = None,
365 output_cpout_path: Optional[str] = None, output_cprst_path: Optional[str] = None,
366 output_mdinfo_path: Optional[str] = None, input_ref_path: Optional[str] = None,
367 properties: Optional[dict] = None, **kwargs) -> int:
368 """Create :class:`PmemdMDRun <pmemd.pmemd_mdrun.PmemdMDRun>`pmemd.pmemd_mdrun.PmemdMDRun class and
369 execute :meth:`launch() <pmemd.pmemd_mdrun.PmemdMDRun.launch>` method"""
371 return PmemdMDRun(input_top_path=input_top_path,
372 input_crd_path=input_crd_path,
373 input_mdin_path=input_mdin_path,
374 input_cpin_path=input_cpin_path,
375 input_ref_path=input_ref_path,
376 output_log_path=output_log_path,
377 output_traj_path=output_traj_path,
378 output_rst_path=output_rst_path,
379 output_cpout_path=output_cpout_path,
380 output_cprst_path=output_cprst_path,
381 output_mdinfo_path=output_mdinfo_path,
382 properties=properties).launch()
384 pmemd_mdrun.__doc__ = PmemdMDRun.__doc__
387def main():
388 parser = argparse.ArgumentParser(description='Running molecular dynamics using pmemd tool from the AMBER MD package.', formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
389 parser.add_argument('--config', required=False, help='Configuration file')
391 # Specific args
392 required_args = parser.add_argument_group('required arguments')
393 required_args.add_argument('--input_top_path', required=True, help='Input topology file (AMBER ParmTop). Accepted formats: top, prmtop, parmtop.')
394 required_args.add_argument('--input_crd_path', required=True, help='Input coordinates file (AMBER crd). Accepted formats: crd, mdcrd.')
395 required_args.add_argument('--input_mdin_path', required=False, help='Input configuration file (MD run options) (AMBER mdin). Accepted formats: mdin, in, txt.')
396 required_args.add_argument('--input_cpin_path', required=False, help='Input constant pH file (AMBER cpin). Accepted formats: cpin.')
397 required_args.add_argument('--input_ref_path', required=False, help='Input reference coordinates for position restraints. Accepted formats: rst, rst7.')
398 required_args.add_argument('--output_log_path', required=True, help='Output log file. Accepted formats: log, out, txt.')
399 required_args.add_argument('--output_traj_path', required=True, help='Output trajectory file. Accepted formats: trj, crd, mdcrd, x.')
400 required_args.add_argument('--output_rst_path', required=True, help='Output restart file. Accepted formats: rst, rst7.')
401 required_args.add_argument('--output_cpout_path', required=False, help='Output constant pH file (AMBER cpout). Accepted formats: cpout.')
402 required_args.add_argument('--output_cprst_path', required=False, help='Output constant pH restart file (AMBER rstout). Accepted formats: cprst.')
403 required_args.add_argument('--output_mdinfo_path', required=False, help='Output MD info. Accepted formats: mdinfo.')
405 args = parser.parse_args()
406 config = args.config if args.config else None
407 properties = settings.ConfReader(config=config).get_prop_dic()
409 # Specific call
410 pmemd_mdrun(input_top_path=args.input_top_path,
411 input_crd_path=args.input_crd_path,
412 input_mdin_path=args.input_mdin_path,
413 input_cpin_path=args.input_cpin_path,
414 input_ref_path=args.input_ref_path,
415 output_log_path=args.output_log_path,
416 output_traj_path=args.output_traj_path,
417 output_rst_path=args.output_rst_path,
418 output_cpout_path=args.output_cpout_path,
419 output_cprst_path=args.output_cprst_path,
420 output_mdinfo_path=args.output_mdinfo_path,
421 properties=properties)
424if __name__ == '__main__':
425 main()