Coverage for biobb_amber/sander/sander_mdrun.py: 50%
210 statements
« prev ^ index » next coverage.py v7.5.1, created at 2024-05-07 08:11 +0000
1#!/usr/bin/env python3
3"""Module containing the SanderMDRun class and the command line interface."""
4import argparse
5import shutil
6import re
7from pathlib import Path, PurePath
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.sander.common import check_input_path, check_output_path
15class SanderMDRun(BiobbObject):
16 """
17 | biobb_amber SanderMDRun
18 | Wrapper of the `AmberTools (AMBER MD Package) sander tool <https://ambermd.org/AmberTools.php>`_ module.
19 | Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools 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/sander/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/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).
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/sander/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/sander/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/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).
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/sander/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/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).
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/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).
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/sander/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/sander/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/sander/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*) - ({}) Sander MD run options specification. (Used if *input_mdin_path* is None)
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/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).
36 * **binary_path** (*str*) - ("sander") sander binary path to be used.
37 * **direct_mdin** (*bool*) - (False) Use input_mdin_path as it is, skip file parsing.
38 * **mpi_bin** (*str*) - (None) Path to the MPI runner. Usually "mpirun" or "srun".
39 * **mpi_np** (*int*) - (0) [0~1000|1] Number of MPI processes. Usually an integer bigger than 1.
40 * **mpi_flags** (*str*) - (None) Path to the MPI hostlist file.
41 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
42 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
43 * **container_path** (*str*) - (None) Container path definition.
44 * **container_image** (*str*) - ('afandiadib/ambertools:serial') Container image definition.
45 * **container_volume_path** (*str*) - ('/tmp') Container volume path definition.
46 * **container_working_dir** (*str*) - (None) Container working directory definition.
47 * **container_user_id** (*str*) - (None) Container user_id definition.
48 * **container_shell_path** (*str*) - ('/bin/bash') Path to default shell inside the container.
50 Examples:
51 This is a use example of how to use the building block from Python::
53 from biobb_amber.sander.sander_mdrun import sander_mdrun
54 prop = {
55 'simulation_type' : 'minimization',
56 'mdin' : {
57 'dt' : 0.002
58 }
59 }
60 sander_mdrun(input_top_path='/path/to/topology.top',
61 input_crd_path='/path/to/coordinates.crd',
62 output_traj_path='/path/to/newTrajectory.crd',
63 output_rst_path='/path/to/newRestart.rst',
64 output_log_path='/path/to/newAmberlog.log',
65 properties=prop)
67 Info:
68 * wrapped_software:
69 * name: AmberTools Sander
70 * version: >20.9
71 * license: LGPL 2.1
72 * multinode: mpi
73 * ontology:
74 * name: EDAM
75 * schema: http://edamontology.org/EDAM.owl
77 """
78 def __init__(self, input_top_path: str, input_crd_path: str, output_log_path: str, output_traj_path: str, output_rst_path: str,
79 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,
80 properties: dict = None, **kwargs) -> None:
82 properties = properties or {}
84 # Call parent class constructor
85 super().__init__(properties)
86 self.locals_var_dict = locals().copy()
88 # Input/Output files
89 self.io_dict = {
90 'in': {'input_top_path': input_top_path,
91 'input_crd_path': input_crd_path,
92 'input_mdin_path': input_mdin_path,
93 'input_ref_path': input_ref_path,
94 'input_cpin_path': input_cpin_path},
95 'out': {'output_log_path': output_log_path,
96 'output_traj_path': output_traj_path,
97 'output_rst_path': output_rst_path,
98 'output_cpout_path': output_cpout_path,
99 'output_cprst_path': output_cprst_path,
100 'output_mdinfo_path': output_mdinfo_path}
101 }
103 # Properties specific for BB
104 self.properties = properties
105 self.simulation_type = properties.get('simulation_type', "minimization")
106 self.binary_path = properties.get('binary_path', "sander")
108 self.direct_mdin = properties.get('direct_mdin', False)
109 self.mdin = {k: str(v) for k, v in properties.get('mdin', dict()).items()}
111 if 'restraintmask' in self.mdin and self.mdin['restraintmask'][0] != '"' and self.mdin['restraintmask'][-1] != '"':
112 self.mdin['restraintmask'] = "\"" + self.mdin['restraintmask'] + "\""
114 # Properties for MPI
115 self.mpi_bin = properties.get('mpi_bin')
116 self.mpi_np = properties.get('mpi_np')
117 self.mpi_flags = properties.get('mpi_flags')
119 # Check the properties
120 self.check_properties(properties)
121 self.check_arguments()
123 def check_data_params(self, out_log, out_err):
124 """ Checks input/output paths correctness """
126 # Check input(s)
127 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__)
128 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__)
129 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__)
130 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__)
131 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__)
133 # Check output(s)
134 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__)
135 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__)
136 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__)
137 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__)
138 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__)
139 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__)
141 def create_mdin(self, path: str = None) -> str:
142 """Creates an AMBER MD configuration file (mdin) using the properties file settings"""
143 mdin_list = []
144 mdin_firstPart = []
145 mdin_middlePart = []
146 mdin_lastPart = []
148 self.output_mdin_path = path
150 if self.io_dict['in']['input_mdin_path']:
151 # MDIN parameters read from an input mdin file
152 if (not self.direct_mdin):
153 mdin_firstPart.append("Mdin read from input file: " + self.stage_io_dict['in']['input_mdin_path'])
154 mdin_firstPart.append("and modified by the biobb_amber module from the BioBB library ")
155 with open(self.stage_io_dict['in']['input_mdin_path']) as input_params:
156 firstPart = True
157 secondPart = False
158 for line in input_params:
159 if '=' in line and not secondPart:
160 firstPart = False
161 mdin_middlePart.append(line.rstrip())
162 else:
163 if (firstPart):
164 mdin_firstPart.append(line.rstrip())
165 elif (secondPart):
166 mdin_lastPart.append(line.rstrip())
167 else:
168 secondPart = True
169 mdin_lastPart.append(line.rstrip())
171 for line in mdin_middlePart:
172 if ('!' in line or '#' in line) and not ('!@' in line or '!:' in line):
173 # Parsing lines with comments (#,!), e.g. :
174 # ntc=2, ntf=2, ! SHAKE, constrain lenghts of the bonds having H
175 params = re.split('!|#', line)
176 for param in params[0].split(','):
177 if param.strip():
178 mdin_list.append(" " + param.strip() + " ! " + params[1])
179 elif ('@' in line or ':' in line):
180 # Parsing masks, e.g. :
181 # restraintmask = ":1-40@P,O5',C5',C4',C3',O3'", restraint_wt = 0.5
182 mylist = re.findall(r'(?:[^,"]|"(?:\\.|[^"])*")+', line)
183 [mdin_list.append(" " + i.lstrip()) for i in mylist]
184 else:
185 for param in line.split(','):
186 if param.strip():
187 if not param.strip().startswith('!'):
188 mdin_list.append(" " + param.strip())
190 else:
191 # MDIN parameters added by the biobb_amber module
192 mdin_list.append("This mdin file has been created by the biobb_amber module from the BioBB library ")
194 sim_type = self.properties.get('simulation_type', 'minimization')
195 # sim_type = self.mdin.get('simulation_type', 'minimization')
196 minimization = (sim_type == 'minimization')
197 min_vacuo = (sim_type == 'min_vacuo')
198 heat = (sim_type == 'heat')
199 nvt = (sim_type == 'nvt')
200 npt = (sim_type == 'npt')
201 free = (sim_type == 'free')
202 md = (nvt or npt or free or heat)
204 mdin_list.append("Type of mdin: " + sim_type)
205 mdin_list.append("&cntrl")
207 # Pre-configured simulation type parameters
208 if minimization:
209 mdin_list.append(" imin = 1 ! BioBB simulation_type minimization")
210 if min_vacuo:
211 mdin_list.append(" imin = 1 ! BioBB simulation_type min_vacuo")
212 mdin_list.append(" ncyc = 250 ! BioBB simulation_type min_vacuo")
213 mdin_list.append(" ntb = 0 ! BioBB simulation_type min_vacuo")
214 mdin_list.append(" igb = 0 ! BioBB simulation_type min_vacuo")
215 mdin_list.append(" cut = 12 ! BioBB simulation_type min_vacuo")
216 if md:
217 mdin_list.append(" imin = 0 ! BioBB simulation_type nvt|npt|free|heat")
218 mdin_list.append(" cut = 10.0 ! BioBB simulation_type nvt|npt|free|heat")
219 mdin_list.append(" ntr = 0 ! BioBB simulation_type nvt|npt|free|heat")
220 mdin_list.append(" ntc = 2 ! BioBB simulation_type nvt|npt|free|heat")
221 mdin_list.append(" ntf = 2 ! BioBB simulation_type nvt|npt|free|heat")
222 mdin_list.append(" ntt = 3 ! BioBB simulation_type nvt|npt|free|heat")
223 mdin_list.append(" ig = -1 ! BioBB simulation_type nvt|npt|free|heat")
224 mdin_list.append(" ioutfm = 1 ! BioBB simulation_type nvt|npt|free|heat")
225 mdin_list.append(" iwrap = 1 ! BioBB simulation_type nvt|npt|free|heat")
226 mdin_list.append(" nstlim = 5000 ! BioBB simulation_type nvt|npt|free|heat")
227 mdin_list.append(" dt = 0.002 ! BioBB simulation_type nvt|npt|free|heat")
228 if npt:
229 mdin_list.append(" irest = 1 ! BioBB simulation_type npt")
230 mdin_list.append(" gamma_ln = 5.0 ! BioBB simulation_type npt")
231 mdin_list.append(" pres0 = 1.0 ! BioBB simulation_type npt")
232 mdin_list.append(" ntp = 1 ! BioBB simulation_type npt")
233 mdin_list.append(" taup = 2.0 ! BioBB simulation_type npt")
234 mdin_list.append(" ntx = 5 ! BioBB simulation_type npt")
235 if nvt:
236 mdin_list.append(" irest = 1 ! BioBB simulation_type nvt")
237 mdin_list.append(" gamma_ln = 5.0 ! BioBB simulation_type nvt")
238 mdin_list.append(" ntb = 1 ! BioBB simulation_type nvt")
239 mdin_list.append(" ntx = 5 ! BioBB simulation_type nvt")
240 if heat:
241 mdin_list.append(" tempi = 0.0 ! BioBB simulation_type heat")
242 mdin_list.append(" temp0 = 300.0 ! BioBB simulation_type heat")
243 mdin_list.append(" irest = 0 ! BioBB simulation_type heat")
244 mdin_list.append(" ntb = 1 ! BioBB simulation_type heat") # periodic boundaries
245 mdin_list.append(" gamma_ln = 1.0 ! BioBB simulation_type heat")
246 # mdin_list.append(" nmropt = 1 ! BioBB simulation_type heat")
248 # mdin_lastPart.append("/")
249 # mdin_lastPart.append("&wt")
250 # mdin_lastPart.append(" TYPE = 'TEMP0' ! BioBB simulation_type heat")
251 # mdin_lastPart.append(" ISTEP1 = 1 ! BioBB simulation_type heat")
252 # mdin_lastPart.append(" ISTEP2 = 4000 ! BioBB simulation_type heat")
253 # mdin_lastPart.append(" VALUE1 = 10.0 ! BioBB simulation_type heat")
254 # mdin_lastPart.append(" VALUE2 = 300.0 ! BioBB simulation_type heat")
255 # mdin_lastPart.append("/")
256 # mdin_lastPart.append("&wt")
257 # mdin_lastPart.append(" TYPE = 'END' ! BioBB simulation_type heat")
258 # mdin_lastPart.append("/")
260 if (not self.direct_mdin):
262 # Adding the rest of parameters in the config file to the mdin file
263 # if the parameter has already been added replace the value
264 parameter_keys = [parameter.split('=')[0].strip() for parameter in mdin_list]
265 for k, v in self.mdin.items():
266 config_parameter_key = str(k).strip()
267 if config_parameter_key in parameter_keys:
268 mdin_list[parameter_keys.index(config_parameter_key)] = ' ' + config_parameter_key + ' = ' + str(v) + ' ! BioBB property'
269 else:
270 mdin_list.append(' ' + config_parameter_key + ' = '+str(v) + ' ! BioBB property')
272 # Writing MD configuration file (mdin)
273 with open(self.output_mdin_path, 'w') as mdin:
274 # Start of file keyword(s)
275 if mdin_firstPart:
276 for line in mdin_firstPart:
277 mdin.write(line + '\n')
279 # MD config parameters
280 for line in mdin_list:
281 mdin.write(line + '\n')
283 # End of file keyword(s)
284 if mdin_lastPart:
285 for line in mdin_lastPart:
286 mdin.write(line + '\n')
287 else:
288 mdin.write("&end\n")
289 else:
290 # Copying generated output file to the final (user-given) file name
291 shutil.copy2(self.io_dict['in']['input_mdin_path'], self.output_mdin_path)
293 return self.output_mdin_path
295 @launchlogger
296 def launch(self):
297 """Launches the execution of the BuildLinearStructure module."""
299 # check input/output paths and parameters
300 self.check_data_params(self.out_log, self.err_log)
302 # Setup Biobb
303 if self.check_restart():
304 return 0
305 self.stage_files()
307 # Creating temporary folder
308 # self.tmp_folder = fu.create_unique_dir()
309 # fu.log('Creating %s temporary folder' % self.tmp_folder, self.out_log)
311 # if self.io_dict['in']['input_mdin_path']:
312 # self.output_mdin_path = self.io_dict['in']['input_mdin_path']
313 # else:
314 # self.output_mdin_path = self.create_mdin(path=str(Path(self.tmp_folder).joinpath("sander.mdin")))
315 # self.output_mdin_path = self.create_mdin(path=str(Path(self.tmp_folder).joinpath("sander.mdin")))
317 # Creating temporary folder & Sander configuration (instructions) file
318 if self.container_path:
319 # instructions_file = str(PurePath(self.stage_io_dict['unique_dir']).joinpath("leap.in"))
320 # instructions_file_path = str(PurePath(self.container_volume_path).joinpath("leap.in"))
321 instructions_file = self.create_mdin(path=str(Path(self.stage_io_dict['unique_dir']).joinpath("sander.mdin")))
322 self.output_mdin_path = str(PurePath(self.container_volume_path).joinpath(PurePath(instructions_file).name))
323 self.tmp_folder = None
324 else:
325 self.tmp_folder = fu.create_unique_dir()
326 fu.log('Creating %s temporary folder' % self.tmp_folder, self.out_log)
327 self.output_mdin_path = self.create_mdin(path=str(Path(self.tmp_folder).joinpath("sander.mdin")))
329 # Command line
330 # 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
331 self.cmd = [self.binary_path,
332 '-O',
333 '-i', self.output_mdin_path,
334 '-p', self.stage_io_dict['in']['input_top_path'],
335 '-c', self.stage_io_dict['in']['input_crd_path'],
336 '-r', self.stage_io_dict['out']['output_rst_path'],
337 '-o', self.stage_io_dict['out']['output_log_path'],
338 '-x', self.stage_io_dict['out']['output_traj_path']
339 ]
341 if self.io_dict['in']['input_ref_path']:
342 self.cmd.append('-ref')
343 self.cmd.append(self.stage_io_dict['in']['input_ref_path'])
345 if self.io_dict['in']['input_cpin_path']:
346 self.cmd.append('-cpin')
347 self.cmd.append(self.stage_io_dict['in']['input_cpin_path'])
349 if self.io_dict['out']['output_mdinfo_path']:
350 self.cmd.append('-inf')
351 self.cmd.append(self.stage_io_dict['out']['output_mdinfo_path'])
353 if self.io_dict['out']['output_cpout_path']:
354 self.cmd.append('-cpout')
355 self.cmd.append(self.stage_io_dict['out']['output_cpout_path'])
357 if self.io_dict['out']['output_cprst_path']:
358 self.cmd.append('-cprestrt')
359 self.cmd.append(self.stage_io_dict['out']['output_cprst_path'])
361 # general mpi properties
362 if self.mpi_bin:
363 mpi_cmd = [self.mpi_bin]
364 if self.mpi_np:
365 mpi_cmd.append('-n')
366 mpi_cmd.append(str(self.mpi_np))
367 if self.mpi_flags:
368 mpi_cmd.extend(self.mpi_flags)
369 self.cmd = mpi_cmd + self.cmd
371 # Run Biobb block
372 self.run_biobb()
374 # Copy files to host
375 self.copy_to_host()
377 # remove temporary folder(s)
378 '''if self.remove_tmp:
379 if self.container_path: self.tmp_files.append(self.stage_io_dict['unique_dir'])
380 else:
381 self.tmp_files.append(self.tmp_folder)
382 self.tmp_files.append("mdinfo")
383 self.remove_tmp_files()'''
385 self.tmp_files.extend([
386 self.stage_io_dict.get("unique_dir"),
387 "mdinfo",
388 self.tmp_folder
389 ])
390 self.remove_tmp_files()
392 self.check_arguments(output_files_created=True, raise_exception=False)
394 return self.return_code
397def sander_mdrun(input_top_path: str, input_crd_path: str,
398 output_log_path: str, output_traj_path: str, output_rst_path: str,
399 input_mdin_path: str = None, input_cpin_path: str = None,
400 output_cpout_path: str = None, output_cprst_path: str = None,
401 output_mdinfo_path: str = None, input_ref_path: str = None,
402 properties: dict = None, **kwargs) -> int:
403 """Create :class:`SanderMDRun <sander.sander_mdrun.SanderMDRun>`sander.sander_mdrun.SanderMDRun class and
404 execute :meth:`launch() <sander.sander_mdrun.SanderMDRun.launch>` method"""
406 return SanderMDRun(input_top_path=input_top_path,
407 input_crd_path=input_crd_path,
408 input_mdin_path=input_mdin_path,
409 input_cpin_path=input_cpin_path,
410 input_ref_path=input_ref_path,
411 output_log_path=output_log_path,
412 output_traj_path=output_traj_path,
413 output_rst_path=output_rst_path,
414 output_cpout_path=output_cpout_path,
415 output_cprst_path=output_cprst_path,
416 output_mdinfo_path=output_mdinfo_path,
417 properties=properties).launch()
420def main():
421 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))
422 parser.add_argument('--config', required=False, help='Configuration file')
424 # Specific args
425 required_args = parser.add_argument_group('required arguments')
426 required_args.add_argument('--input_top_path', required=True, help='Input topology file (AMBER ParmTop). Accepted formats: top, prmtop, parmtop.')
427 required_args.add_argument('--input_crd_path', required=True, help='Input coordinates file (AMBER crd). Accepted formats: crd, mdcrd.')
428 # required_args.add_argument('--input_mdin_path', required=False, help='Input configuration file (MD run options) (AMBER mdin). Accepted formats: mdin, in, txt.')
429 parser.add_argument('--input_mdin_path', required=False, help='Input configuration file (MD run options) (AMBER mdin). Accepted formats: mdin, in, txt.')
430 # required_args.add_argument('--input_cpin_path', required=False, help='Input constant pH file (AMBER cpin). Accepted formats: cpin.')
431 parser.add_argument('--input_cpin_path', required=False, help='Input constant pH file (AMBER cpin). Accepted formats: cpin.')
432 # required_args.add_argument('--input_ref_path', required=False, help='Input reference coordinates for position restraints. Accepted formats: rst, rst7.')
433 parser.add_argument('--input_ref_path', required=False, help='Input reference coordinates for position restraints. Accepted formats: rst, rst7.')
434 required_args.add_argument('--output_log_path', required=True, help='Output log file. Accepted formats: log, out, txt.')
435 required_args.add_argument('--output_traj_path', required=True, help='Output trajectory file. Accepted formats: trj, crd, mdcrd, x.')
436 required_args.add_argument('--output_rst_path', required=True, help='Output restart file. Accepted formats: rst, rst7.')
437 # required_args.add_argument('--output_cpout_path', required=False, help='Output constant pH file (AMBER cpout). Accepted formats: cpout.')
438 parser.add_argument('--output_cpout_path', required=False, help='Output constant pH file (AMBER cpout). Accepted formats: cpout.')
439 # required_args.add_argument('--output_cprst_path', required=False, help='Output constant pH restart file (AMBER rstout). Accepted formats: cprst.')
440 parser.add_argument('--output_cprst_path', required=False, help='Output constant pH restart file (AMBER rstout). Accepted formats: cprst.')
441 # required_args.add_argument('--output_mdinfo_path', required=False, help='Output MD info. Accepted formats: mdinfo.')
442 parser.add_argument('--output_mdinfo_path', required=False, help='Output MD info. Accepted formats: mdinfo.')
444 args = parser.parse_args()
445 # config = args.config if args.config else None
446 args.config = args.config or "{}"
447 # properties = settings.ConfReader(config=config).get_prop_dic()
448 properties = settings.ConfReader(config=args.config).get_prop_dic()
450 # Specific call
451 sander_mdrun(input_top_path=args.input_top_path,
452 input_crd_path=args.input_crd_path,
453 input_mdin_path=args.input_mdin_path,
454 input_cpin_path=args.input_cpin_path,
455 input_ref_path=args.input_ref_path,
456 output_log_path=args.output_log_path,
457 output_traj_path=args.output_traj_path,
458 output_rst_path=args.output_rst_path,
459 output_cpout_path=args.output_cpout_path,
460 output_cprst_path=args.output_cprst_path,
461 output_mdinfo_path=args.output_mdinfo_path,
462 properties=properties)
465if __name__ == '__main__':
466 main()