Coverage for biobb_amber/pmemd/pmemd_mdrun.py: 0%
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1#!/usr/bin/env python3
3"""Module containing the PmemdMDRun class and the command line interface."""
4import argparse
5import re
6from pathlib import Path
7from biobb_common.generic.biobb_object import BiobbObject
8from biobb_common.configuration import settings
9from biobb_common.tools import file_utils as fu
10from biobb_common.tools.file_utils import launchlogger
11from biobb_amber.pmemd.common import check_input_path, check_output_path
14class PmemdMDRun(BiobbObject):
15 """
16 | biobb_amber PmemdMDRun
17 | Wrapper of the `AmberTools (AMBER MD Package) pmemd tool <https://ambermd.org/AmberTools.php>`_ module.
18 | Runs molecular dynamics using pmemd tool from the AMBER MD package.
20 Args:
21 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).
22 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).
23 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).
24 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).
25 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).
26 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).
27 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).
28 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).
29 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).
30 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).
31 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).
32 properties (dict - Python dictionary object containing the tool parameters, not input/output files):
33 * **mdin** (*dict*) - ({}) pmemd MD run options specification. (Used if *input_mdin_path* is None)
34 * **binary_path** (*str*) - ("pmemd") pmemd binary path to be used.
35 * **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).
36 * **mpi_bin** (*str*) - (None) Path to the MPI runner. Usually "mpirun" or "srun".
37 * **mpi_np** (*int*) - (0) [0~1000|1] Number of MPI processes. Usually an integer bigger than 1.
38 * **mpi_flags** (*str*) - (None) Path to the MPI hostlist file.
39 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
40 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
42 Examples:
43 This is a use example of how to use the building block from Python::
45 from biobb_amber.pmemd.pmemd_mdrun import pmemd_mdrun
46 prop = {
47 'simulation_type' : 'npt',
48 'mdin' : {
49 'dt' : 0.002
50 }
51 }
52 pmemd_mdrun(input_top_path='/path/to/topology.top',
53 input_crd_path='/path/to/coordinates.crd',
54 output_traj_path='/path/to/newTrajectory.crd',
55 output_rst_path='/path/to/newRestart.rst',
56 output_log_path='/path/to/newAmberlog.log',
57 properties=prop)
59 Info:
60 * wrapped_software:
61 * name: AMBER pmemd
62 * version: >20
63 * license: other
64 * multinode: mpi
65 * ontology:
66 * name: EDAM
67 * schema: http://edamontology.org/EDAM.owl
69 """
70 def __init__(self, input_top_path: str, input_crd_path: str, output_log_path: str, output_traj_path: str, output_rst_path: str,
71 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,
72 properties: dict = None, **kwargs) -> None:
74 properties = properties or {}
76 # Call parent class constructor
77 super().__init__(properties)
78 self.locals_var_dict = locals().copy()
80 # Input/Output files
81 self.io_dict = {
82 'in': {'input_top_path': input_top_path,
83 'input_crd_path': input_crd_path,
84 'input_mdin_path': input_mdin_path,
85 'input_ref_path': input_ref_path,
86 'input_cpin_path': input_cpin_path},
87 'out': {'output_log_path': output_log_path,
88 'output_traj_path': output_traj_path,
89 'output_rst_path': output_rst_path,
90 'output_cpout_path': output_cpout_path,
91 'output_cprst_path': output_cprst_path,
92 'output_mdinfo_path': output_mdinfo_path}
93 }
95 # Properties specific for BB
96 self.properties = properties
97 self.simulation_type = properties.get('simulation_type', "minimization")
98 self.binary_path = properties.get('binary_path', "pmemd")
99 self.mdin = {k: str(v) for k, v in properties.get('mdin', dict()).items()}
101 # Properties for MPI
102 self.mpi_bin = properties.get('mpi_bin')
103 self.mpi_np = properties.get('mpi_np')
104 self.mpi_flags = properties.get('mpi_flags')
106 # Check the properties
107 self.check_properties(properties)
108 self.check_arguments()
110 def check_data_params(self, out_log, err_log):
111 """ Checks input/output paths correctness """
113 # Check input(s)
114 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__)
115 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__)
116 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__)
117 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__)
118 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__)
120 # Check output(s)
121 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__)
122 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__)
123 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__)
124 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__)
125 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__)
126 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__)
128 def create_mdin(self, path: str = None) -> str:
129 """Creates an AMBER MD configuration file (mdin) using the properties file settings"""
130 mdin_list = []
131 mdin_firstPart = []
132 mdin_middlePart = []
133 mdin_lastPart = []
135 self.output_mdin_path = path
137 if self.io_dict['in']['input_mdin_path']:
138 # MDIN parameters read from an input mdin file
139 mdin_firstPart.append("Mdin read from input file: " + self.io_dict['in']['input_mdin_path'])
140 mdin_firstPart.append("and modified by the biobb_amber module from the BioBB library ")
141 with open(self.io_dict['in']['input_mdin_path']) as input_params:
142 firstPart = True
143 secondPart = False
144 for line in input_params:
145 if '=' in line and not secondPart:
146 firstPart = False
147 mdin_middlePart.append(line.rstrip())
148 else:
149 if (firstPart):
150 mdin_firstPart.append(line.rstrip())
151 elif (secondPart):
152 mdin_lastPart.append(line.rstrip())
153 else:
154 secondPart = True
155 mdin_lastPart.append(line.rstrip())
157 for line in mdin_middlePart:
158 if ('!' in line or '#' in line) and not ('!@' in line or '!:' in line):
159 # Parsing lines with comments (#,!), e.g. :
160 # ntc=2, ntf=2, ! SHAKE, constrain lenghts of the bonds having H
161 params = re.split('!|#', line)
162 for param in params[0].split(','):
163 if param.strip():
164 mdin_list.append(" " + param.strip() + " ! " + params[1])
165 elif ('@' in line or ':' in line):
166 # Parsing masks, e.g. :
167 # restraintmask = ":1-40@P,O5',C5',C4',C3',O3'", restraint_wt = 0.5
168 mylist = re.findall(r'(?:[^,"]|"(?:\\.|[^"])*")+', line)
169 [mdin_list.append(" " + i.lstrip()) for i in mylist]
170 else:
171 for param in line.split(','):
172 if param.strip():
173 if not param.strip().startswith('!'):
174 mdin_list.append(" " + param.strip())
176 else:
177 # MDIN parameters added by the biobb_amber module
178 mdin_list.append("This mdin file has been created by the biobb_amber module from the BioBB library ")
180 sim_type = self.properties.get('simulation_type', 'minimization')
181 # sim_type = self.mdin.get('simulation_type', 'minimization')
182 minimization = (sim_type == 'minimization')
183 min_vacuo = (sim_type == 'min_vacuo')
184 heat = (sim_type == 'heat')
185 nvt = (sim_type == 'nvt')
186 npt = (sim_type == 'npt')
187 free = (sim_type == 'free')
188 md = (nvt or npt or free or heat)
190 mdin_list.append("Type of mdin: " + sim_type)
191 mdin_list.append("&cntrl")
193 # Pre-configured simulation type parameters
194 if minimization:
195 mdin_list.append(" imin = 1 ! BioBB simulation_type minimization")
196 if min_vacuo:
197 mdin_list.append(" imin = 1 ! BioBB simulation_type min_vacuo")
198 mdin_list.append(" ncyc = 250 ! BioBB simulation_type min_vacuo")
199 mdin_list.append(" ntb = 0 ! BioBB simulation_type min_vacuo")
200 mdin_list.append(" igb = 0 ! BioBB simulation_type min_vacuo")
201 mdin_list.append(" cut = 12 ! BioBB simulation_type min_vacuo")
202 if md:
203 mdin_list.append(" imin = 0 ! BioBB simulation_type nvt|npt|free|heat")
204 mdin_list.append(" cut = 10.0 ! BioBB simulation_type nvt|npt|free|heat")
205 mdin_list.append(" ntr = 0 ! BioBB simulation_type nvt|npt|free|heat")
206 mdin_list.append(" ntc = 2 ! BioBB simulation_type nvt|npt|free|heat")
207 mdin_list.append(" ntf = 2 ! BioBB simulation_type nvt|npt|free|heat")
208 mdin_list.append(" ntt = 3 ! BioBB simulation_type nvt|npt|free|heat")
209 mdin_list.append(" ig = -1 ! BioBB simulation_type nvt|npt|free|heat")
210 mdin_list.append(" ioutfm = 1 ! BioBB simulation_type nvt|npt|free|heat")
211 mdin_list.append(" iwrap = 1 ! BioBB simulation_type nvt|npt|free|heat")
212 mdin_list.append(" nstlim = 5000 ! BioBB simulation_type nvt|npt|free|heat")
213 mdin_list.append(" dt = 0.002 ! BioBB simulation_type nvt|npt|free|heat")
214 if npt:
215 mdin_list.append(" irest = 1 ! BioBB simulation_type npt")
216 mdin_list.append(" gamma_ln = 5.0 ! BioBB simulation_type npt")
217 mdin_list.append(" pres0 = 1.0 ! BioBB simulation_type npt")
218 mdin_list.append(" ntp = 1 ! BioBB simulation_type npt")
219 mdin_list.append(" taup = 2.0 ! BioBB simulation_type npt")
220 mdin_list.append(" ntx = 5 ! BioBB simulation_type npt")
221 if nvt:
222 mdin_list.append(" irest = 1 ! BioBB simulation_type nvt")
223 mdin_list.append(" gamma_ln = 5.0 ! BioBB simulation_type nvt")
224 mdin_list.append(" ntb = 1 ! BioBB simulation_type nvt")
225 mdin_list.append(" ntx = 5 ! BioBB simulation_type nvt")
226 if heat:
227 mdin_list.append(" tempi = 0.0 ! BioBB simulation_type heat")
228 mdin_list.append(" temp0 = 300.0 ! BioBB simulation_type heat")
229 mdin_list.append(" irest = 0 ! BioBB simulation_type heat")
230 mdin_list.append(" ntb = 1 ! BioBB simulation_type heat") # periodic boundaries
231 mdin_list.append(" gamma_ln = 1.0 ! BioBB simulation_type heat")
232 # mdin_list.append(" nmropt = 1 ! BioBB simulation_type heat")
234 # mdin_lastPart.append("/")
235 # mdin_lastPart.append("&wt")
236 # mdin_lastPart.append(" TYPE = 'TEMP0' ! BioBB simulation_type heat")
237 # mdin_lastPart.append(" ISTEP1 = 1 ! BioBB simulation_type heat")
238 # mdin_lastPart.append(" ISTEP2 = 4000 ! BioBB simulation_type heat")
239 # mdin_lastPart.append(" VALUE1 = 10.0 ! BioBB simulation_type heat")
240 # mdin_lastPart.append(" VALUE2 = 300.0 ! BioBB simulation_type heat")
241 # mdin_lastPart.append("/")
242 # mdin_lastPart.append("&wt")
243 # mdin_lastPart.append(" TYPE = 'END' ! BioBB simulation_type heat")
244 # mdin_lastPart.append("/")
246 # Adding the rest of parameters in the config file to the mdin file
247 # if the parameter has already been added replace the value
248 parameter_keys = [parameter.split('=')[0].strip() for parameter in mdin_list]
249 for k, v in self.mdin.items():
250 config_parameter_key = str(k).strip()
251 if config_parameter_key in parameter_keys:
252 mdin_list[parameter_keys.index(config_parameter_key)] = ' ' + config_parameter_key + ' = ' + str(v) + ' ! BioBB property'
253 else:
254 mdin_list.append(' ' + config_parameter_key + ' = '+str(v) + ' ! BioBB property')
256 # Writing MD configuration file (mdin)
257 with open(self.output_mdin_path, 'w') as mdin:
258 # Start of file keyword(s)
259 if mdin_firstPart:
260 for line in mdin_firstPart:
261 mdin.write(line + '\n')
263 # MD config parameters
264 for line in mdin_list:
265 mdin.write(line + '\n')
267 # End of file keyword(s)
268 if mdin_lastPart:
269 for line in mdin_lastPart:
270 mdin.write(line + '\n')
271 else:
272 mdin.write("&end\n")
274 return self.output_mdin_path
276 @launchlogger
277 def launch(self):
278 """Launches the execution of the PmemdMDRun module."""
280 # check input/output paths and parameters
281 self.check_data_params(self.out_log, self.err_log)
283 # Setup Biobb
284 if self.check_restart():
285 return 0
286 self.stage_files()
288 # Creating temporary folder
289 self.tmp_folder = fu.create_unique_dir()
290 fu.log('Creating %s temporary folder' % self.tmp_folder, self.out_log)
292 # if self.io_dict['in']['input_mdin_path']:
293 # self.output_mdin_path = self.io_dict['in']['input_mdin_path']
294 # else:
295 # self.output_mdin_path = self.create_mdin(path=str(Path(self.tmp_folder).joinpath("pmemd.mdin")))
296 self.output_mdin_path = self.create_mdin(path=str(Path(self.tmp_folder).joinpath("pmemd.mdin")))
298 # Command line
299 # 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
300 self.cmd = [self.binary_path,
301 '-O',
302 '-i', self.output_mdin_path,
303 '-p', self.io_dict['in']['input_top_path'],
304 '-c', self.io_dict['in']['input_crd_path'],
305 '-r', self.io_dict['out']['output_rst_path'],
306 '-o', self.io_dict['out']['output_log_path'],
307 '-x', self.io_dict['out']['output_traj_path']
308 ]
310 if self.io_dict['in']['input_ref_path']:
311 self.cmd.append('-ref')
312 self.cmd.append(self.io_dict['in']['input_ref_path'])
314 if self.io_dict['in']['input_cpin_path']:
315 self.cmd.append('-cpin')
316 self.cmd.append(self.io_dict['in']['input_cpin_path'])
318 if self.io_dict['out']['output_mdinfo_path']:
319 self.cmd.append('-inf')
320 self.cmd.append(self.io_dict['out']['output_mdinfo_path'])
322 if self.io_dict['out']['output_cpout_path']:
323 self.cmd.append('-cpout')
324 self.cmd.append(self.io_dict['out']['output_cpout_path'])
326 if self.io_dict['out']['output_cprst_path']:
327 self.cmd.append('-cprestrt')
328 self.cmd.append(self.io_dict['out']['output_cprst_path'])
330 # general mpi properties
331 if self.mpi_bin:
332 mpi_cmd = [self.mpi_bin]
333 if self.mpi_np:
334 mpi_cmd.append('-n')
335 mpi_cmd.append(str(self.mpi_np))
336 if self.mpi_flags:
337 mpi_cmd.extend(self.mpi_flags)
338 self.cmd = mpi_cmd + self.cmd
340 # Run Biobb block
341 self.run_biobb()
343 # Copy files to host
344 self.copy_to_host()
346 # remove temporary folder(s)
347 self.tmp_files.extend([
348 self.stage_io_dict.get("unique_dir"),
349 self.tmp_folder,
350 "mdinfo"
351 ])
352 self.remove_tmp_files()
354 self.check_arguments(output_files_created=True, raise_exception=False)
356 return self.return_code
359def pmemd_mdrun(input_top_path: str, input_crd_path: str,
360 output_log_path: str, output_traj_path: str, output_rst_path: str,
361 input_mdin_path: str = None, input_cpin_path: str = None,
362 output_cpout_path: str = None, output_cprst_path: str = None,
363 output_mdinfo_path: str = None, input_ref_path: str = None,
364 properties: dict = None, **kwargs) -> int:
365 """Create :class:`PmemdMDRun <pmemd.pmemd_mdrun.PmemdMDRun>`pmemd.pmemd_mdrun.PmemdMDRun class and
366 execute :meth:`launch() <pmemd.pmemd_mdrun.PmemdMDRun.launch>` method"""
368 return PmemdMDRun(input_top_path=input_top_path,
369 input_crd_path=input_crd_path,
370 input_mdin_path=input_mdin_path,
371 input_cpin_path=input_cpin_path,
372 input_ref_path=input_ref_path,
373 output_log_path=output_log_path,
374 output_traj_path=output_traj_path,
375 output_rst_path=output_rst_path,
376 output_cpout_path=output_cpout_path,
377 output_cprst_path=output_cprst_path,
378 output_mdinfo_path=output_mdinfo_path,
379 properties=properties).launch()
382def main():
383 parser = argparse.ArgumentParser(description='Running molecular dynamics using pmemd tool from the AMBER MD package.', formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
384 parser.add_argument('--config', required=False, help='Configuration file')
386 # Specific args
387 required_args = parser.add_argument_group('required arguments')
388 required_args.add_argument('--input_top_path', required=True, help='Input topology file (AMBER ParmTop). Accepted formats: top, prmtop, parmtop.')
389 required_args.add_argument('--input_crd_path', required=True, help='Input coordinates file (AMBER crd). Accepted formats: crd, mdcrd.')
390 required_args.add_argument('--input_mdin_path', required=False, help='Input configuration file (MD run options) (AMBER mdin). Accepted formats: mdin, in, txt.')
391 required_args.add_argument('--input_cpin_path', required=False, help='Input constant pH file (AMBER cpin). Accepted formats: cpin.')
392 required_args.add_argument('--input_ref_path', required=False, help='Input reference coordinates for position restraints. Accepted formats: rst, rst7.')
393 required_args.add_argument('--output_log_path', required=True, help='Output log file. Accepted formats: log, out, txt.')
394 required_args.add_argument('--output_traj_path', required=True, help='Output trajectory file. Accepted formats: trj, crd, mdcrd, x.')
395 required_args.add_argument('--output_rst_path', required=True, help='Output restart file. Accepted formats: rst, rst7.')
396 required_args.add_argument('--output_cpout_path', required=False, help='Output constant pH file (AMBER cpout). Accepted formats: cpout.')
397 required_args.add_argument('--output_cprst_path', required=False, help='Output constant pH restart file (AMBER rstout). Accepted formats: cprst.')
398 required_args.add_argument('--output_mdinfo_path', required=False, help='Output MD info. Accepted formats: mdinfo.')
400 args = parser.parse_args()
401 config = args.config if args.config else None
402 properties = settings.ConfReader(config=config).get_prop_dic()
404 # Specific call
405 pmemd_mdrun(input_top_path=args.input_top_path,
406 input_crd_path=args.input_crd_path,
407 input_mdin_path=args.input_mdin_path,
408 input_cpin_path=args.input_cpin_path,
409 input_ref_path=args.input_ref_path,
410 output_log_path=args.output_log_path,
411 output_traj_path=args.output_traj_path,
412 output_rst_path=args.output_rst_path,
413 output_cpout_path=args.output_cpout_path,
414 output_cprst_path=args.output_cprst_path,
415 output_mdinfo_path=args.output_mdinfo_path,
416 properties=properties)
419if __name__ == '__main__':
420 main()