Coverage for biobb_amber/leap/leap_add_ions.py: 59%
203 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 LeapAddIons class and the command line interface."""
4import argparse
5import shutil
6import re
7from decimal import Decimal
8from pathlib import PurePath
9from biobb_common.generic.biobb_object import BiobbObject
10from biobb_common.configuration import settings
11from biobb_common.tools import file_utils as fu
12from biobb_common.tools.file_utils import launchlogger
13from biobb_amber.leap.common import check_input_path, check_output_path
16class LeapAddIons(BiobbObject):
17 """
18 | biobb_amber LeapAddIons
19 | Wrapper of the `AmberTools (AMBER MD Package) leap tool <https://ambermd.org/AmberTools.php>`_ module.
20 | Adds counterions to a system box for an AMBER MD system using tLeap tool from the AmberTools MD package.
22 Args:
23 input_pdb_path (str): Input 3D structure PDB file. File type: input. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/leap/structure.solv.pdb>`_. Accepted formats: pdb (edam:format_1476).
24 input_lib_path (str) (Optional): Input ligand library parameters file. File type: input. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/leap/ligand.lib>`_. Accepted formats: lib (edam:format_3889), zip (edam:format_3987).
25 input_frcmod_path (str) (Optional): Input ligand frcmod parameters file. File type: input. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/leap/ligand.frcmod>`_. Accepted formats: frcmod (edam:format_3888), zip (edam:format_3987).
26 input_params_path (str) (Optional): Additional leap parameter files to load with loadAmberParams Leap command. File type: input. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/leap/frcmod.ionsdang_spce.txt>`_. Accepted formats: in (edam:format_2330), leapin (edam:format_2330), txt (edam:format_2330), zip (edam:format_3987).
27 input_source_path (str) (Optional): Additional leap command files to load with source Leap command. File type: input. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/leap/leaprc.water.spce.txt>`_. Accepted formats: in (edam:format_2330), leapin (edam:format_2330), txt (edam:format_2330), zip (edam:format_3987).
28 output_pdb_path (str): Output 3D structure PDB file matching the topology file. File type: output. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/reference/leap/structure.ions.pdb>`_. Accepted formats: pdb (edam:format_1476).
29 output_top_path (str): Output topology file (AMBER ParmTop). File type: output. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/reference/leap/structure.ions.top>`_. Accepted formats: top (edam:format_3881), parmtop (edam:format_3881), prmtop (edam:format_3881).
30 output_crd_path (str): Output coordinates file (AMBER crd). File type: output. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/reference/leap/structure.ions.crd>`_. Accepted formats: crd (edam:format_3878), mdcrd (edam:format_3878), inpcrd (edam:format_3878).
31 properties (dic - Python dictionary object containing the tool parameters, not input/output files):
32 * **forcefield** (*list*) - (["protein.ff14SB","DNA.bsc1","gaff"]) Forcefield to be used for the structure generation. Values: protein.ff14SB, protein.ff19SB, DNA.bsc1, DNA.OL15, RNA.OL3, gaff.
33 * **water_type** (*str*) - ("TIP3PBOX") Water molecule parameters to be used for the topology. Values: POL3BOX, QSPCFWBOX, SPCBOX, SPCFWBOX, TIP3PBOX, TIP3PFBOX, TIP4PBOX, TIP4PEWBOX, OPCBOX, OPC3BOX, TIP5PBOX.
34 * **box_type** (*str*) - ("truncated_octahedron") Type for the MD system box. Values: cubic, truncated_octahedron.
35 * **ions_type** (*str*) - ("ionsjc_tip3p") Ions type. Values: ionsjc_tip3p, ionsjc_spce, ionsff99_tip3p, ions_charmm22, ionsjc_tip4pew, None.
36 * **neutralise** (*bool*) - ("True") Energetically neutralise the system adding the necessary counterions.
37 * **ionic_concentration** (*float*) - (50) Additional ionic concentration to include in the system box. Units in Mol/L.
38 * **positive_ions_number** (*int*) - (0) Number of additional positive ions to include in the system box.
39 * **negative_ions_number** (*int*) - (0) Number of additional negative ions to include in the system box.
40 * **positive_ions_type** (*str*) - ("Na+") Type of additional positive ions to include in the system box. Values: Na+,K+.
41 * **negative_ions_type** (*str*) - ("Cl-") Type of additional negative ions to include in the system box. Values: Cl-.
42 * **binary_path** (*str*) - ("tleap") Path to the tleap executable binary.
43 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
44 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
45 * **container_path** (*str*) - (None) Container path definition.
46 * **container_image** (*str*) - ('afandiadib/ambertools:serial') Container image definition.
47 * **container_volume_path** (*str*) - ('/tmp') Container volume path definition.
48 * **container_working_dir** (*str*) - (None) Container working directory definition.
49 * **container_user_id** (*str*) - (None) Container user_id definition.
50 * **container_shell_path** (*str*) - ('/bin/bash') Path to default shell inside the container.
52 Examples:
53 This is a use example of how to use the building block from Python::
55 from biobb_amber.leap.leap_add_ions import leap_add_ions
56 prop = {
57 'forcefield': ['protein.ff14SB'],
58 'water_type': 'TIP3PBOX',
59 'neutralise' : True
60 }
61 leap_add_ions(input_pdb_path='/path/to/structure.pdb',
62 output_pdb_path='/path/to/newStructure.pdb',
63 output_top_path='/path/to/newTopology.top',
64 output_crd_path='/path/to/newCoordinates.crd',
65 properties=prop)
67 Info:
68 * wrapped_software:
69 * name: AmberTools tLeap
70 * version: >20.9
71 * license: LGPL 2.1
72 * ontology:
73 * name: EDAM
74 * schema: http://edamontology.org/EDAM.owl
76 """
78 def __init__(self, input_pdb_path: str,
79 output_pdb_path: str, output_top_path: str, output_crd_path: str,
80 input_lib_path: str = None, input_frcmod_path: str = None,
81 input_params_path: str = None, input_source_path: str = None,
82 properties: dict = None, **kwargs):
84 properties = properties or {}
86 # Call parent class constructor
87 super().__init__(properties)
88 self.locals_var_dict = locals().copy()
90 # Input/Output files
91 self.io_dict = {
92 'in': {'input_pdb_path': input_pdb_path,
93 'input_lib_path': input_lib_path,
94 'input_frcmod_path': input_frcmod_path,
95 'input_params_path': input_params_path,
96 'input_source_path': input_source_path},
97 'out': {'output_pdb_path': output_pdb_path,
98 'output_top_path': output_top_path,
99 'output_crd_path': output_crd_path}
100 }
102 # Ligand Parameter lists
103 self.ligands_lib_list = []
104 if input_lib_path:
105 self.ligands_lib_list.append(input_lib_path)
107 self.ligands_frcmod_list = []
108 if input_frcmod_path:
109 self.ligands_frcmod_list.append(input_frcmod_path)
111 # Properties specific for BB
112 self.properties = properties
113 self.forcefield = properties.get('forcefield', ["protein.ff14SB", "DNA.bsc1", "gaff"])
114 self.water_type = properties.get('water_type', "TIP3PBOX")
115 self.box_type = properties.get('box_type', "truncated_octahedron")
116 self.ions_type = properties.get('ions_type', "ionsjc_tip3p")
117 self.neutralise = properties.get('neutralise', True)
118 self.ionic_concentration = properties.get('ionic_concentration', 50)
119 self.positive_ions_number = properties.get('positive_ions_number', 0)
120 self.positive_ions_type = properties.get('positive_ions_type', "Na+")
121 self.negative_ions_number = properties.get('negative_ions_number', 0)
122 self.negative_ions_type = properties.get('negative_ions_type', "Cl-")
123 self.binary_path = properties.get('binary_path', 'tleap')
125 # Check the properties
126 self.check_properties(properties)
127 self.check_arguments()
129 def check_data_params(self, out_log, err_log):
130 """ Checks input/output paths correctness """
132 # Check input(s)
133 self.io_dict["in"]["input_pdb_path"] = check_input_path(self.io_dict["in"]["input_pdb_path"], "input_pdb_path", False, out_log, self.__class__.__name__)
134 self.io_dict["in"]["input_lib_path"] = check_input_path(self.io_dict["in"]["input_lib_path"], "input_lib_path", True, out_log, self.__class__.__name__)
135 self.io_dict["in"]["input_frcmod_path"] = check_input_path(self.io_dict["in"]["input_frcmod_path"], "input_frcmod_path", True, out_log, self.__class__.__name__)
136 # self.io_dict["in"]["input_params_path"] = check_input_path(self.io_dict["in"]["input_params_path"], "input_params_path", True, out_log, self.__class__.__name__)
137 # self.io_dict["in"]["input_source_path"] = check_input_path(self.io_dict["in"]["input_source_path"], "input_source_path", True, out_log, self.__class__.__name__)
139 # Check output(s)
140 self.io_dict["out"]["output_pdb_path"] = check_output_path(self.io_dict["out"]["output_pdb_path"], "output_pdb_path", False, out_log, self.__class__.__name__)
141 self.io_dict["out"]["output_top_path"] = check_output_path(self.io_dict["out"]["output_top_path"], "output_top_path", False, out_log, self.__class__.__name__)
142 self.io_dict["out"]["output_crd_path"] = check_output_path(self.io_dict["out"]["output_crd_path"], "output_crd_path", False, out_log, self.__class__.__name__)
144 def find_out_number_of_ions(self):
145 """ Computes the number of positive and negative ions from the input ionic
146 concentration and the number of water molecules in the system box."""
148 # Finding number of water molecules in the box
149 cnt = 0
150 with open(self.io_dict['in']['input_pdb_path']) as fp:
151 for line in fp:
152 # Water molecules are identified with different resids
153 # by different forcefields / MD packages
154 pq = re.compile((r'WAT|HOH|TP3|TIP3|SOL'), re.M)
155 if pq.search(line):
156 # Incrementing number of water molecules just in the water
157 # oxygen atom, ignoring hydrogen atoms
158 pq2 = re.compile(r"H", re.M)
159 if not pq2.search(line):
160 cnt = cnt + 1
162 # To get to X mM ions we need
163 # n(NaCl) = #waters / 55 Mol * X M
164 # where X M = X mM / 1000
165 self.nio = int((cnt / 55) * (self.ionic_concentration / 1000))
167 @launchlogger
168 def launch(self):
169 """Launches the execution of the LeapAddIons module."""
171 # check input/output paths and parameters
172 self.check_data_params(self.out_log, self.err_log)
174 # Setup Biobb
175 if self.check_restart():
176 return 0
177 self.stage_files()
179 # Water Type
180 # leaprc.water.tip4pew, tip4pd, tip3p, spceb, spce, opc, fb4, fb3
181 # Values: POL3BOX, QSPCFWBOX, SPCBOX, SPCFWBOX, TIP3PBOX, TIP3PFBOX, TIP4PBOX, TIP4PEWBOX, OPCBOX, OPC3BOX, TIP5PBOX.
182 source_wat_command = "source leaprc.water.tip3p"
183 if self.water_type == "TIP4PEWBOX":
184 source_wat_command = "leaprc.water.tip4pew"
185 if self.water_type == "TIP4PBOX":
186 source_wat_command = "leaprc.water.tip4pd"
187 if re.match(r"SPC", self.water_type):
188 source_wat_command = "source leaprc.water.spce"
189 if re.match(r"OPC", self.water_type):
190 source_wat_command = "source leaprc.water.opc"
192 # Counterions
193 ions_command = ""
194 if self.neutralise:
195 # ions_command = ions_command + "addions mol " + self.negative_ions_type + " 0 \n"
196 # ions_command = ions_command + "addions mol " + self.positive_ions_type + " 0 \n"
197 ions_command = ions_command + "addionsRand mol " + self.negative_ions_type + " 0 \n"
198 ions_command = ions_command + "addionsRand mol " + self.positive_ions_type + " 0 \n"
200 if self.ionic_concentration and self.negative_ions_number == 0 and self.positive_ions_number == 0:
201 self.find_out_number_of_ions()
202 nneg = self.nio # Update with function
203 npos = self.nio # Update with function
204 # ions_command = ions_command + "addions mol " + self.negative_ions_type + " " + str(nneg) + " \n"
205 # ions_command = ions_command + "addions mol " + self.positive_ions_type + " " + str(npos) + " \n"
206 ions_command = ions_command + "addionsRand mol " + self.negative_ions_type + " " + str(nneg) + " \n"
207 ions_command = ions_command + "addionsRand mol " + self.positive_ions_type + " " + str(npos) + " \n"
208 else:
209 if self.negative_ions_number != 0:
210 # ions_command = ions_command + "addions mol " + self.negative_ions_type + " " + str(self.negative_ions_number) + " \n"
211 ions_command = ions_command + "addionsRand mol " + self.negative_ions_type + " " + str(self.negative_ions_number) + " \n"
212 if self.positive_ions_number != 0:
213 # ions_command = ions_command + "addions mol " + self.positive_ions_type + " " + str(self.positive_ions_number) + " \n"
214 ions_command = ions_command + "addionsRand mol " + self.positive_ions_type + " " + str(self.positive_ions_number) + " \n"
216 # Creating temporary folder & Leap configuration (instructions) file
217 if self.container_path:
218 instructions_file = str(PurePath(self.stage_io_dict['unique_dir']).joinpath("leap.in"))
219 instructions_file_path = str(PurePath(self.container_volume_path).joinpath("leap.in"))
220 self.tmp_folder = None
221 else:
222 self.tmp_folder = fu.create_unique_dir()
223 instructions_file = str(PurePath(self.tmp_folder).joinpath("leap.in"))
224 fu.log('Creating %s temporary folder' % self.tmp_folder, self.out_log)
225 instructions_file_path = instructions_file
227 ligands_lib_list = []
228 if self.io_dict['in']['input_lib_path'] is not None:
229 if self.io_dict['in']['input_lib_path'].endswith('.zip'):
230 ligands_lib_list = fu.unzip_list(self.stage_io_dict['in']['input_lib_path'], dest_dir=self.tmp_folder, out_log=self.out_log)
231 else:
232 ligands_lib_list.append(self.stage_io_dict['in']['input_lib_path'])
234 ligands_frcmod_list = []
235 if self.io_dict['in']['input_frcmod_path'] is not None:
236 if self.io_dict['in']['input_frcmod_path'].endswith('.zip'):
237 ligands_frcmod_list = fu.unzip_list(self.stage_io_dict['in']['input_frcmod_path'], dest_dir=self.tmp_folder, out_log=self.out_log)
238 else:
239 ligands_frcmod_list.append(self.stage_io_dict['in']['input_frcmod_path'])
241 amber_params_list = []
242 if self.io_dict['in']['input_params_path'] is not None:
243 if self.io_dict['in']['input_params_path'].endswith('.zip'):
244 amber_params_list = fu.unzip_list(self.stage_io_dict['in']['input_params_path'], dest_dir=self.tmp_folder, out_log=self.out_log)
245 else:
246 amber_params_list.append(self.stage_io_dict['in']['input_params_path'])
248 leap_source_list = []
249 if self.io_dict['in']['input_source_path'] is not None:
250 if self.io_dict['in']['input_source_path'].endswith('.zip'):
251 leap_source_list = fu.unzip_list(self.stage_io_dict['in']['input_source_path'], dest_dir=self.tmp_folder, out_log=self.out_log)
252 else:
253 leap_source_list.append(self.stage_io_dict['in']['input_source_path'])
255 # instructions_file = str(PurePath(self.tmp_folder).joinpath("leap.in"))
256 with open(instructions_file, 'w') as leapin:
257 # Forcefields loaded by default:
258 # Protein: ff14SB (PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA)
259 # leapin.write("source leaprc.protein.ff14SB \n")
260 # DNA: parmBSC1 (ParmBSC1 (ff99 + bsc0 + bsc1) for DNA. Ivani et al. Nature Methods 13: 55, 2016)
261 # leapin.write("source leaprc.DNA.bsc1 \n")
262 # Ligands: GAFF (General Amber Force field, J. Comput. Chem. 2004 Jul 15;25(9):1157-74)
263 # leapin.write("source leaprc.gaff \n")
265 # Forcefields loaded from input forcefield property
266 for t in self.forcefield:
267 leapin.write("source leaprc.{}\n".format(t))
269 # Additional Leap commands
270 for leap_commands in leap_source_list:
271 leapin.write("source " + leap_commands + "\n")
273 # Water Model loaded from input water_model property
274 leapin.write(source_wat_command + " \n")
276 # Ions Type
277 if self.ions_type != "None":
278 leapin.write("loadamberparams frcmod." + self.ions_type + "\n")
280 # Additional Amber parameters
281 for amber_params in amber_params_list:
282 leapin.write("loadamberparams " + amber_params + "\n")
284 # Ligand(s) libraries (if any)
285 for amber_lib in ligands_lib_list:
286 leapin.write("loadOff " + amber_lib + "\n")
287 for amber_frcmod in ligands_frcmod_list:
288 leapin.write("loadamberparams " + amber_frcmod + "\n")
290 # Loading PDB file
291 leapin.write("mol = loadpdb " + self.stage_io_dict['in']['input_pdb_path'] + " \n")
293 # Adding ions
294 leapin.write(ions_command)
296 # Generating box
297 leapin.write("setBox mol vdw \n")
299 # Saving output PDB file, coordinates and topology
300 leapin.write("savepdb mol " + self.stage_io_dict['out']['output_pdb_path'] + " \n")
301 leapin.write("saveAmberParm mol " + self.stage_io_dict['out']['output_top_path'] + " " + self.stage_io_dict['out']['output_crd_path'] + "\n")
302 leapin.write("quit \n")
304 # Command line
305 self.cmd = [self.binary_path,
306 '-f', instructions_file_path
307 ]
309 # Run Biobb block
310 self.run_biobb()
312 # Copy files to host
313 self.copy_to_host()
315 if self.box_type != "cubic":
316 fu.log('Fixing truncated octahedron Box in the topology and coordinates files', self.out_log, self.global_log)
318 # Taking box info from input PDB file, CRYST1 tag (first line)
319 with open(self.io_dict['in']['input_pdb_path']) as file:
320 lines = file.readlines()
321 pdb_line = lines[0]
323 if 'OCTBOX' not in pdb_line:
324 fu.log('WARNING: box info not found in input PDB file (OCTBOX). Needed to correctly assign the octahedron box. Assuming cubic box.', self.out_log, self.global_log)
325 else:
326 # PDB info: CRYST1 86.316 86.316 86.316 109.47 109.47 109.47 P 1
327 # PDB info: OCTBOX 86.1942924 86.1942924 86.1942924 109.4712190 109.4712190 109.4712190
328 # regex_box = 'CRYST1\s*(\d+\.\d+)\s*(\d+\.\d+)\s*(\d+\.\d+)\s*(\d+\.\d+)\s*(\d+\.\d+)\s*(\d+\.\d+)\s*P 1'
329 regex_box = r'OCTBOX\s*(\d+\.\d+)\s*(\d+\.\d+)\s*(\d+\.\d+)\s*(\d+\.\d+)\s*(\d+\.\d+)\s*(\d+\.\d+)'
330 box = re.findall(regex_box, pdb_line)[0]
331 box_line = ""
332 for coord in box:
333 box_line += "{:12.7f}".format(float(coord))
335 # PRMTOP info: 1.09471219E+02 8.63157502E+01 8.63157502E+01 8.63157502E+01
336 top_box_line = ""
337 top_box_line += ' %.8E' % Decimal(float(box[3]))
338 top_box_line += ' %.8E' % Decimal(float(box[0]))
339 top_box_line += ' %.8E' % Decimal(float(box[1]))
340 top_box_line += ' %.8E' % Decimal(float(box[2]))
342 # Removing box generated by tleap from the crd file (last line)
343 with open(self.io_dict['out']['output_crd_path']) as file:
344 lines = file.readlines()
345 crd_lines = lines[:-1]
347 # Adding old box coordinates (taken from the input pdb)
348 crd_lines.append(box_line)
350 with open(self.io_dict['out']['output_crd_path'], 'w') as file:
351 for line in crd_lines:
352 file.write(str(line))
353 file.write("\n")
355 # Now fixing IFBOX param in prmtop.
356 box_flag = False
357 ifbox_flag = 0
358 # %FLAG BOX_DIMENSIONS
359 # %FORMAT(5E16.8)
360 # 1.09471219E+02 8.63157502E+01 8.63157502E+01 8.63157502E+01
362 tmp_parmtop = str(PurePath(self.tmp_folder).joinpath("top_temp.parmtop"))
363 shutil.copyfile(self.io_dict['out']['output_top_path'], tmp_parmtop)
365 with open(self.io_dict['out']['output_top_path'], 'w') as new_top:
366 with open(tmp_parmtop, 'r') as old_top:
367 for line in old_top:
368 if 'BOX_DIMENSIONS' in line:
369 box_flag = True
370 new_top.write(line)
371 elif box_flag and 'FORMAT' not in line:
372 new_top.write(top_box_line + "\n")
373 box_flag = False
374 elif 'FLAG POINTERS' in line or ifbox_flag == 1 or ifbox_flag == 2 or ifbox_flag == 3:
375 ifbox_flag += 1
376 new_top.write(line)
377 elif ifbox_flag == 4:
378 # new_top.write(top_box_line + "\n")
379 new_top.write(line[:56] + ' 2' + line[64:])
380 ifbox_flag += 1
381 else:
382 new_top.write(line)
384 # remove temporary folder(s)
385 self.tmp_files.extend([
386 self.stage_io_dict.get("unique_dir"),
387 self.tmp_folder,
388 "leap.log"
389 ])
390 self.remove_tmp_files()
392 self.check_arguments(output_files_created=True, raise_exception=False)
394 return self.return_code
397def leap_add_ions(input_pdb_path: str, output_pdb_path: str,
398 output_top_path: str, output_crd_path: str,
399 input_lib_path: str = None, input_frcmod_path: str = None,
400 input_params_path: str = None, input_source_path: str = None,
401 properties: dict = None, **kwargs) -> int:
402 """Create :class:`LeapAddIons <leap.leap_add_ions.LeapAddIons>`leap.leap_add_ions.LeapAddIons class and
403 execute :meth:`launch() <leap.leap_add_ions.LeapAddIons.launch>` method"""
405 return LeapAddIons(input_pdb_path=input_pdb_path,
406 input_lib_path=input_lib_path,
407 input_frcmod_path=input_frcmod_path,
408 input_params_path=input_params_path,
409 input_source_path=input_source_path,
410 output_pdb_path=output_pdb_path,
411 output_top_path=output_top_path,
412 output_crd_path=output_crd_path,
413 properties=properties).launch()
416def main():
417 parser = argparse.ArgumentParser(description='Adds counterions to a system box for an AMBER MD system using tLeap.', formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
418 parser.add_argument('--config', required=False, help='Configuration file')
420 # Specific args
421 required_args = parser.add_argument_group('required arguments')
422 required_args.add_argument('--input_pdb_path', required=True, help='Input 3D structure PDB file. Accepted formats: pdb.')
423 required_args.add_argument('--input_lib_path', required=False, help='Input ligand library parameters file. Accepted formats: lib, zip.')
424 required_args.add_argument('--input_frcmod_path', required=False, help='Input ligand frcmod parameters file. Accepted formats: frcmod, zip.')
425 required_args.add_argument('--input_params_path', required=False, help='Additional leap parameter files to load with loadAmberParams Leap command. Accepted formats: leapin, in, txt, zip.')
426 required_args.add_argument('--input_source_path', required=False, help='Additional leap command files to load with source Leap command. Accepted formats: leapin, in, txt, zip.')
427 required_args.add_argument('--output_pdb_path', required=True, help='Output 3D structure PDB file matching the topology file. Accepted formats: pdb.')
428 required_args.add_argument('--output_top_path', required=True, help='Output topology file (AMBER ParmTop). Accepted formats: top.')
429 required_args.add_argument('--output_crd_path', required=True, help='Output coordinates file (AMBER crd). Accepted formats: crd.')
431 args = parser.parse_args()
432 config = args.config if args.config else None
433 properties = settings.ConfReader(config=config).get_prop_dic()
435 # Specific call
436 leap_add_ions(input_pdb_path=args.input_pdb_path,
437 input_lib_path=args.input_lib_path,
438 input_frcmod_path=args.input_frcmod_path,
439 input_params_path=args.input_params_path,
440 input_source_path=args.input_source_path,
441 output_pdb_path=args.output_pdb_path,
442 output_top_path=args.output_top_path,
443 output_crd_path=args.output_crd_path,
444 properties=properties)
447if __name__ == '__main__':
448 main()