Coverage for biobb_amber / sander / sander_mdrun.py: 54%
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« prev ^ index » next coverage.py v7.13.0, created at 2025-12-22 10:27 +0000
1#!/usr/bin/env python3
3"""Module containing the SanderMDRun class and the command line interface."""
4from typing import Optional
5import shutil
6import re
7from pathlib import Path, PurePath
8from biobb_common.generic.biobb_object import BiobbObject
9from biobb_common.tools import file_utils as fu
10from biobb_common.tools.file_utils import launchlogger
11from biobb_amber.sander.common import check_input_path, check_output_path
14class SanderMDRun(BiobbObject):
15 """
16 | biobb_amber SanderMDRun
17 | Wrapper of the `AmberTools (AMBER MD Package) sander tool <https://ambermd.org/AmberTools.php>`_ module.
18 | Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools 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/sander/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/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), rst (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/sander/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/sander/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/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).
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/sander/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/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).
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/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).
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/sander/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/sander/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/sander/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*) - ({}) Sander MD run options specification. (Used if *input_mdin_path* is None)
34 * **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).
35 * **binary_path** (*str*) - ("sander") sander binary path to be used.
36 * **direct_mdin** (*bool*) - (False) Use input_mdin_path as it is, skip file parsing.
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.
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 """
79 def __init__(self, input_top_path: str, input_crd_path: str, output_log_path: str, output_traj_path: str, output_rst_path: str,
80 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,
81 properties: Optional[dict] = None, **kwargs) -> None:
83 properties = properties or {}
85 # Call parent class constructor
86 super().__init__(properties)
87 self.locals_var_dict = locals().copy()
89 # Input/Output files
90 self.io_dict = {
91 'in': {'input_top_path': input_top_path,
92 'input_crd_path': input_crd_path,
93 'input_mdin_path': input_mdin_path,
94 'input_ref_path': input_ref_path,
95 'input_cpin_path': input_cpin_path},
96 'out': {'output_log_path': output_log_path,
97 'output_traj_path': output_traj_path,
98 'output_rst_path': output_rst_path,
99 'output_cpout_path': output_cpout_path,
100 'output_cprst_path': output_cprst_path,
101 'output_mdinfo_path': output_mdinfo_path}
102 }
104 # Properties specific for BB
105 self.properties = properties
106 self.simulation_type = properties.get('simulation_type', "minimization")
107 self.binary_path = properties.get('binary_path', "sander")
109 self.direct_mdin = properties.get('direct_mdin', False)
110 self.mdin = {k: str(v) for k, v in properties.get('mdin', dict()).items()}
112 if 'restraintmask' in self.mdin and self.mdin['restraintmask'][0] != '"' and self.mdin['restraintmask'][-1] != '"':
113 self.mdin['restraintmask'] = "\"" + self.mdin['restraintmask'] + "\""
115 # Properties for MPI
116 self.mpi_bin = properties.get('mpi_bin')
117 self.mpi_np = properties.get('mpi_np')
118 self.mpi_flags = properties.get('mpi_flags')
120 # Check the properties
121 self.check_properties(properties)
122 self.check_arguments()
124 def check_data_params(self, out_log, out_err):
125 """ Checks input/output paths correctness """
127 # Check input(s)
128 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__)
129 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__)
130 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__)
131 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__)
132 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__)
134 # Check output(s)
135 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__)
136 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__)
137 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__)
138 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__)
139 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__)
140 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__)
142 def create_mdin(self, path: Optional[str] = None) -> str:
143 """Creates an AMBER MD configuration file (mdin) using the properties file settings"""
144 mdin_list = []
145 mdin_firstPart = []
146 mdin_middlePart = []
147 mdin_lastPart = []
149 self.output_mdin_path = path
151 if self.io_dict['in']['input_mdin_path']:
152 # MDIN parameters read from an input mdin file
153 if (not self.direct_mdin):
154 mdin_firstPart.append("Mdin read from input file: " + self.stage_io_dict['in']['input_mdin_path'])
155 mdin_firstPart.append("and modified by the biobb_amber module from the BioBB library ")
156 with open(self.stage_io_dict['in']['input_mdin_path']) as input_params:
157 firstPart = True
158 secondPart = False
159 for line in input_params:
160 if '=' in line and not secondPart:
161 firstPart = False
162 mdin_middlePart.append(line.rstrip())
163 else:
164 if (firstPart):
165 mdin_firstPart.append(line.rstrip())
166 elif (secondPart):
167 mdin_lastPart.append(line.rstrip())
168 else:
169 secondPart = True
170 mdin_lastPart.append(line.rstrip())
172 for line in mdin_middlePart:
173 if ('!' in line or '#' in line) and not ('!@' in line or '!:' in line):
174 # Parsing lines with comments (#,!), e.g. :
175 # ntc=2, ntf=2, ! SHAKE, constrain lenghts of the bonds having H
176 params = re.split('!|#', line)
177 for param in params[0].split(','):
178 if param.strip():
179 mdin_list.append(" " + param.strip() + " ! " + params[1])
180 elif ('@' in line or ':' in line):
181 # Parsing masks, e.g. :
182 # restraintmask = ":1-40@P,O5',C5',C4',C3',O3'", restraint_wt = 0.5
183 mylist = re.findall(r'(?:[^,"]|"(?:\\.|[^"])*")+', line)
184 [mdin_list.append(" " + i.lstrip()) for i in mylist] # type: ignore
185 else:
186 for param in line.split(','):
187 if param.strip():
188 if not param.strip().startswith('!'):
189 mdin_list.append(" " + param.strip())
191 else:
192 # MDIN parameters added by the biobb_amber module
193 mdin_list.append("This mdin file has been created by the biobb_amber module from the BioBB library ")
195 sim_type = self.properties.get('simulation_type', 'minimization')
196 # sim_type = self.mdin.get('simulation_type', 'minimization')
197 minimization = (sim_type == 'minimization')
198 min_vacuo = (sim_type == 'min_vacuo')
199 heat = (sim_type == 'heat')
200 nvt = (sim_type == 'nvt')
201 npt = (sim_type == 'npt')
202 free = (sim_type == 'free')
203 md = (nvt or npt or free or heat)
205 mdin_list.append("Type of mdin: " + sim_type)
206 mdin_list.append("&cntrl")
208 # Pre-configured simulation type parameters
209 if minimization:
210 mdin_list.append(" imin = 1 ! BioBB simulation_type minimization")
211 if min_vacuo:
212 mdin_list.append(" imin = 1 ! BioBB simulation_type min_vacuo")
213 mdin_list.append(" ncyc = 250 ! BioBB simulation_type min_vacuo")
214 mdin_list.append(" ntb = 0 ! BioBB simulation_type min_vacuo")
215 mdin_list.append(" igb = 0 ! BioBB simulation_type min_vacuo")
216 mdin_list.append(" cut = 12 ! BioBB simulation_type min_vacuo")
217 if md:
218 mdin_list.append(" imin = 0 ! BioBB simulation_type nvt|npt|free|heat")
219 mdin_list.append(" cut = 10.0 ! BioBB simulation_type nvt|npt|free|heat")
220 mdin_list.append(" ntr = 0 ! BioBB simulation_type nvt|npt|free|heat")
221 mdin_list.append(" ntc = 2 ! BioBB simulation_type nvt|npt|free|heat")
222 mdin_list.append(" ntf = 2 ! BioBB simulation_type nvt|npt|free|heat")
223 mdin_list.append(" ntt = 3 ! BioBB simulation_type nvt|npt|free|heat")
224 mdin_list.append(" ig = -1 ! BioBB simulation_type nvt|npt|free|heat")
225 mdin_list.append(" ioutfm = 1 ! BioBB simulation_type nvt|npt|free|heat")
226 mdin_list.append(" iwrap = 1 ! BioBB simulation_type nvt|npt|free|heat")
227 mdin_list.append(" nstlim = 5000 ! BioBB simulation_type nvt|npt|free|heat")
228 mdin_list.append(" dt = 0.002 ! BioBB simulation_type nvt|npt|free|heat")
229 if npt:
230 mdin_list.append(" irest = 1 ! BioBB simulation_type npt")
231 mdin_list.append(" gamma_ln = 5.0 ! BioBB simulation_type npt")
232 mdin_list.append(" pres0 = 1.0 ! BioBB simulation_type npt")
233 mdin_list.append(" ntp = 1 ! BioBB simulation_type npt")
234 mdin_list.append(" taup = 2.0 ! BioBB simulation_type npt")
235 mdin_list.append(" ntx = 5 ! BioBB simulation_type npt")
236 if nvt:
237 mdin_list.append(" irest = 1 ! BioBB simulation_type nvt")
238 mdin_list.append(" gamma_ln = 5.0 ! BioBB simulation_type nvt")
239 mdin_list.append(" ntb = 1 ! BioBB simulation_type nvt")
240 mdin_list.append(" ntx = 5 ! BioBB simulation_type nvt")
241 if heat:
242 mdin_list.append(" tempi = 0.0 ! BioBB simulation_type heat")
243 mdin_list.append(" temp0 = 300.0 ! BioBB simulation_type heat")
244 mdin_list.append(" irest = 0 ! BioBB simulation_type heat")
245 mdin_list.append(" ntb = 1 ! BioBB simulation_type heat") # periodic boundaries
246 mdin_list.append(" gamma_ln = 1.0 ! BioBB simulation_type heat")
247 # mdin_list.append(" nmropt = 1 ! BioBB simulation_type heat")
249 # mdin_lastPart.append("/")
250 # mdin_lastPart.append("&wt")
251 # mdin_lastPart.append(" TYPE = 'TEMP0' ! BioBB simulation_type heat")
252 # mdin_lastPart.append(" ISTEP1 = 1 ! BioBB simulation_type heat")
253 # mdin_lastPart.append(" ISTEP2 = 4000 ! BioBB simulation_type heat")
254 # mdin_lastPart.append(" VALUE1 = 10.0 ! BioBB simulation_type heat")
255 # mdin_lastPart.append(" VALUE2 = 300.0 ! BioBB simulation_type heat")
256 # mdin_lastPart.append("/")
257 # mdin_lastPart.append("&wt")
258 # mdin_lastPart.append(" TYPE = 'END' ! BioBB simulation_type heat")
259 # mdin_lastPart.append("/")
261 if (not self.direct_mdin):
263 # Adding the rest of parameters in the config file to the mdin file
264 # if the parameter has already been added replace the value
265 parameter_keys = [parameter.split('=')[0].strip() for parameter in mdin_list]
266 for k, v in self.mdin.items():
267 config_parameter_key = str(k).strip()
268 if config_parameter_key in parameter_keys:
269 mdin_list[parameter_keys.index(config_parameter_key)] = ' ' + config_parameter_key + ' = ' + str(v) + ' ! BioBB property'
270 else:
271 mdin_list.append(' ' + config_parameter_key + ' = '+str(v) + ' ! BioBB property')
273 # Writing MD configuration file (mdin)
274 with open(str(self.output_mdin_path), 'w') as mdin:
275 # Start of file keyword(s)
276 if mdin_firstPart:
277 for line in mdin_firstPart:
278 mdin.write(line + '\n')
280 # MD config parameters
281 for line in mdin_list:
282 mdin.write(line + '\n')
284 # End of file keyword(s)
285 if mdin_lastPart:
286 for line in mdin_lastPart:
287 mdin.write(line + '\n')
288 else:
289 mdin.write("&end\n")
290 else:
291 # Copying generated output file to the final (user-given) file name
292 shutil.copy2(self.io_dict['in']['input_mdin_path'], str(self.output_mdin_path))
294 return str(self.output_mdin_path)
296 @launchlogger
297 def launch(self):
298 """Launches the execution of the BuildLinearStructure module."""
300 # check input/output paths and parameters
301 self.check_data_params(self.out_log, self.err_log)
303 # Setup Biobb
304 if self.check_restart():
305 return 0
306 self.stage_files()
308 # Creating temporary folder
309 # tmp_folder = fu.create_unique_dir()
310 # fu.log('Creating %s temporary folder' % tmp_folder, self.out_log)
312 # if self.io_dict['in']['input_mdin_path']:
313 # self.output_mdin_path = self.io_dict['in']['input_mdin_path']
314 # else:
315 # self.output_mdin_path = self.create_mdin(path=str(Path(tmp_folder).joinpath("sander.mdin")))
316 # self.output_mdin_path = self.create_mdin(path=str(Path(tmp_folder).joinpath("sander.mdin")))
318 # Creating temporary folder & Sander configuration (instructions) file
319 if self.container_path:
320 # instructions_file = str(PurePath(self.stage_io_dict['unique_dir']).joinpath("leap.in"))
321 # instructions_file_path = str(PurePath(self.container_volume_path).joinpath("leap.in"))
322 instructions_file = self.create_mdin(path=str(Path(self.stage_io_dict['unique_dir']).joinpath("sander.mdin")))
323 self.output_mdin_path = str(PurePath(self.container_volume_path).joinpath(PurePath(instructions_file).name))
324 tmp_folder = None
325 else:
326 tmp_folder = fu.create_unique_dir()
327 fu.log('Creating %s temporary folder' % tmp_folder, self.out_log)
328 self.output_mdin_path = self.create_mdin(path=str(Path(tmp_folder).joinpath("sander.mdin")))
330 # Command line
331 # 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
332 self.cmd = [self.binary_path,
333 '-O',
334 '-i', self.output_mdin_path,
335 '-p', self.stage_io_dict['in']['input_top_path'],
336 '-c', self.stage_io_dict['in']['input_crd_path'],
337 '-r', self.stage_io_dict['out']['output_rst_path'],
338 '-o', self.stage_io_dict['out']['output_log_path'],
339 '-x', self.stage_io_dict['out']['output_traj_path']
340 ]
342 if self.io_dict['in']['input_ref_path']:
343 self.cmd.append('-ref')
344 self.cmd.append(self.stage_io_dict['in']['input_ref_path'])
346 if self.io_dict['in']['input_cpin_path']:
347 self.cmd.append('-cpin')
348 self.cmd.append(self.stage_io_dict['in']['input_cpin_path'])
350 if self.io_dict['out']['output_mdinfo_path']:
351 self.cmd.append('-inf')
352 self.cmd.append(self.stage_io_dict['out']['output_mdinfo_path'])
354 if self.io_dict['out']['output_cpout_path']:
355 self.cmd.append('-cpout')
356 self.cmd.append(self.stage_io_dict['out']['output_cpout_path'])
358 if self.io_dict['out']['output_cprst_path']:
359 self.cmd.append('-cprestrt')
360 self.cmd.append(self.stage_io_dict['out']['output_cprst_path'])
362 # general mpi properties
363 if self.mpi_bin:
364 mpi_cmd = [self.mpi_bin]
365 if self.mpi_np:
366 mpi_cmd.append('-n')
367 mpi_cmd.append(str(self.mpi_np))
368 if self.mpi_flags:
369 mpi_cmd.extend(self.mpi_flags)
370 self.cmd = mpi_cmd + self.cmd
372 # Run Biobb block
373 self.run_biobb()
375 # Copy files to host
376 self.copy_to_host()
378 # remove temporary folder(s)
379 self.tmp_files.extend(["mdinfo", str(tmp_folder)])
380 self.remove_tmp_files()
382 self.check_arguments(output_files_created=True, raise_exception=False)
384 return self.return_code
387def sander_mdrun(input_top_path: str, input_crd_path: str,
388 output_log_path: str, output_traj_path: str, output_rst_path: str,
389 input_mdin_path: Optional[str] = None, input_cpin_path: Optional[str] = None,
390 output_cpout_path: Optional[str] = None, output_cprst_path: Optional[str] = None,
391 output_mdinfo_path: Optional[str] = None, input_ref_path: Optional[str] = None,
392 properties: Optional[dict] = None, **kwargs) -> int:
393 """Create :class:`SanderMDRun <sander.sander_mdrun.SanderMDRun>`sander.sander_mdrun.SanderMDRun class and
394 execute :meth:`launch() <sander.sander_mdrun.SanderMDRun.launch>` method"""
395 return SanderMDRun(**dict(locals())).launch()
398sander_mdrun.__doc__ = SanderMDRun.__doc__
399main = SanderMDRun.get_main(sander_mdrun, "Running energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package.")
401if __name__ == '__main__':
402 main()