Coverage for biobb_amber/leap/leap_solvate.py: 63%
182 statements
« prev ^ index » next coverage.py v7.6.10, created at 2025-01-28 08:28 +0000
1#!/usr/bin/env python3
3"""Module containing the LeapSolvate class and the command line interface."""
5import os
6import argparse
7import re
8from pathlib import PurePath
9from typing import List, Optional
11from biobb_common.configuration import settings
12from biobb_common.generic.biobb_object import BiobbObject
13from biobb_common.tools import file_utils as fu
14from biobb_common.tools.file_utils import launchlogger
16from biobb_amber.leap.common import _from_string_to_list
19class LeapSolvate(BiobbObject):
20 """
21 | biobb_amber LeapSolvate
22 | Wrapper of the `AmberTools (AMBER MD Package) leap tool <https://ambermd.org/AmberTools.php>`_ module.
23 | Creates and solvates a system box for an AMBER MD system using tLeap tool from the AmberTools MD package.
25 Args:
26 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.leap.pdb>`_. Accepted formats: pdb (edam:format_1476).
27 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).
28 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).
29 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).
30 input_prep_path (str) (Optional): Additional leap parameter files to load with loadAmberPrep Leap command. File type: input. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/leap/heme_all.in>`_. Accepted formats: in (edam:format_2330), leapin (edam:format_2330), txt (edam:format_2330), zip (edam:format_3987).
31 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).
32 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.solv.pdb>`_. Accepted formats: pdb (edam:format_1476).
33 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.solv.top>`_. Accepted formats: top (edam:format_3881), parmtop (edam:format_3881), prmtop (edam:format_3881).
34 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.solv.crd>`_. Accepted formats: crd (edam:format_3878), mdcrd (edam:format_3878), inpcrd (edam:format_3878).
35 properties (dic - Python dictionary object containing the tool parameters, not input/output files):
36 * **forcefield** (*list*) - (["protein.ff14SB","DNA.bsc1","gaff"]) Forcefields to be used for the structure generation. Each item should be either a path to a leaprc file or a string with the leaprc file name if the force field is included with Amber (e.g. "/path/to/leaprc.protein.ff14SB" or "protein.ff14SB"). Default values: ["protein.ff14SB","DNA.bsc1","gaff"].
37 * **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.
38 * **box_type** (*str*) - ("truncated_octahedron") Type for the MD system box. Values: cubic, truncated_octahedron.
39 * **ions_type** (*str*) - ("ionsjc_tip3p") Ions type. Values: ionsjc_tip3p, ionsjc_spce, ionsff99_tip3p, ions_charmm22, ionsjc_tip4pew, None.
40 * **neutralise** (*bool*) - ("False") Energetically neutralise the system adding the necessary counterions.
41 * **iso** (*bool*) - ("False") Make the box isometric.
42 * **positive_ions_number** (*int*) - (0) Number of additional positive ions to include in the system box.
43 * **negative_ions_number** (*int*) - (0) Number of additional negative ions to include in the system box.
44 * **positive_ions_type** (*str*) - ("Na+") Type of additional positive ions to include in the system box. Values: Na+,K+.
45 * **negative_ions_type** (*str*) - ("Cl-") Type of additional negative ions to include in the system box. Values: Cl-.
46 * **distance_to_molecule** (*float*) - ("8.0") Size for the MD system box -in Angstroms-, defined such as the minimum distance between any atom originally present in solute and the edge of the periodic box is given by this distance parameter.
47 * **closeness** (*float*) - ("1.0") How close, in Å, solvent ATOMs may come to solute ATOMs.
48 * **binary_path** (*str*) - ("tleap") Path to the tleap executable binary.
49 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
50 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
51 * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
52 * **container_path** (*str*) - (None) Container path definition.
53 * **container_image** (*str*) - ('afandiadib/ambertools:serial') Container image definition.
54 * **container_volume_path** (*str*) - ('/tmp') Container volume path definition.
55 * **container_working_dir** (*str*) - (None) Container working directory definition.
56 * **container_user_id** (*str*) - (None) Container user_id definition.
57 * **container_shell_path** (*str*) - ('/bin/bash') Path to default shell inside the container.
59 Examples:
60 This is a use example of how to use the building block from Python::
61 from biobb_amber.leap.leap_solvate import leap_solvate
62 prop = {
63 'forcefield': ['protein.ff14SB'],
64 'water_type': 'TIP3PBOX',
65 'box_type': 'truncated_octahedron',
66 'neutralise' : True
67 }
68 leap_solvate(input_pdb_path='/path/to/structure.pdb',
69 output_pdb_path='/path/to/newStructure.pdb',
70 output_top_path='/path/to/newTopology.top',
71 output_crd_path='/path/to/newCoordinates.crd',
72 properties=prop)
74 Info:
75 * wrapped_software:
76 * name: AmberTools tLeap
77 * version: >20.9
78 * license: LGPL 2.1
79 * ontology:
80 * name: EDAM
81 * schema: http://edamontology.org/EDAM.owl
83 """
85 def __init__(
86 self,
87 input_pdb_path: str,
88 output_pdb_path: str,
89 output_top_path: str,
90 output_crd_path: str,
91 input_lib_path: Optional[str] = None,
92 input_frcmod_path: Optional[str] = None,
93 input_params_path: Optional[str] = None,
94 input_prep_path: Optional[str] = None,
95 input_source_path: Optional[str] = None,
96 properties: Optional[dict] = None,
97 **kwargs,
98 ):
99 properties = properties or {}
101 # Call parent class constructor
102 super().__init__(properties)
103 self.locals_var_dict = locals().copy()
105 # Input/Output files
106 self.io_dict = {
107 "in": {
108 "input_pdb_path": input_pdb_path,
109 "input_lib_path": input_lib_path,
110 "input_frcmod_path": input_frcmod_path,
111 "input_params_path": input_params_path,
112 "input_prep_path": input_prep_path,
113 "input_source_path": input_source_path,
114 },
115 "out": {
116 "output_pdb_path": output_pdb_path,
117 "output_top_path": output_top_path,
118 "output_crd_path": output_crd_path,
119 },
120 }
122 # # Ligand Parameter lists
123 # self.ligands_lib_list = []
124 # if input_lib_path:
125 # self.ligands_lib_list.append(input_lib_path)
126 #
127 # self.ligands_frcmod_list = []
128 # if input_frcmod_path:
129 # self.ligands_frcmod_list.append(input_frcmod_path)
131 # Set default forcefields
132 amber_home_path = os.getenv("AMBERHOME")
133 protein_ff14SB_path = os.path.join(amber_home_path, 'dat', 'leap', 'cmd', 'leaprc.protein.ff14SB')
134 dna_bsc1_path = os.path.join(amber_home_path, 'dat', 'leap', 'cmd', 'leaprc.DNA.bsc1')
135 gaff_path = os.path.join(amber_home_path, 'dat', 'leap', 'cmd', 'leaprc.gaff')
137 # Properties specific for BB
138 self.properties = properties
139 self.forcefield = _from_string_to_list(
140 properties.get("forcefield", [protein_ff14SB_path, dna_bsc1_path, gaff_path])
141 )
142 # Find the paths of the leaprc files if only the force field names are provided
143 self.forcefield = self.find_leaprc_paths(self.forcefield)
144 self.water_type = properties.get("water_type", "TIP3PBOX")
145 self.box_type = properties.get("box_type", "truncated_octahedron")
146 self.ions_type = properties.get("ions_type", "ionsjc_tip3p")
147 self.neutralise = properties.get("neutralise", False)
148 self.iso = properties.get("iso", False)
149 self.positive_ions_number = properties.get("positive_ions_number", 0)
150 self.positive_ions_type = properties.get("positive_ions_type", "Na+")
151 self.negative_ions_number = properties.get("negative_ions_number", 0)
152 self.negative_ions_type = properties.get("negative_ions_type", "Cl-")
153 self.distance_to_molecule = properties.get("distance_to_molecule", 8.0)
154 self.closeness = properties.get("closeness", 1.0)
155 self.binary_path = properties.get("binary_path", "tleap")
157 # Check the properties
158 self.check_properties(properties)
159 self.check_arguments()
161 def find_leaprc_paths(self, forcefields: List[str]) -> List[str]:
162 """
163 Find the leaprc paths for the force fields provided.
165 For each item in the forcefields list, the function checks if the str is a path to an existing file.
166 If not, it tries to find the file in the $AMBERHOME/dat/leap/cmd/ directory or the $AMBERHOME/dat/leap/cmd/oldff/
167 directory with and without the leaprc prefix.
169 Args:
170 forcefields (List[str]): List of force fields to find the leaprc files for.
172 Returns:
173 List[str]: List of leaprc file paths.
174 """
176 leaprc_paths = []
178 for forcefield in forcefields:
180 num_paths = len(leaprc_paths)
182 # Check if the forcefield is a path to an existing file
183 if os.path.exists(forcefield):
184 leaprc_paths.append(forcefield)
185 continue
187 # Check if the forcefield is in the leaprc directory
188 leaprc_path = os.path.join(os.environ.get('AMBERHOME', ''), 'dat', 'leap', 'cmd', f"leaprc.{forcefield}")
189 if os.path.exists(leaprc_path):
190 leaprc_paths.append(leaprc_path)
191 continue
193 # Check if the forcefield is in the oldff directory
194 leaprc_path = os.path.join(os.environ.get('AMBERHOME', ''), 'dat', 'leap', 'cmd', 'oldff', f"leaprc.{forcefield}")
195 if os.path.exists(leaprc_path):
196 leaprc_paths.append(leaprc_path)
197 continue
199 # Check if the forcefield is in the leaprc directory without the leaprc prefix
200 leaprc_path = os.path.join(os.environ.get('AMBERHOME', ''), 'dat', 'leap', 'cmd', f"{forcefield}")
201 if os.path.exists(leaprc_path):
202 leaprc_paths.append(leaprc_path)
203 continue
205 # Check if the forcefield is in the oldff directory without the leaprc prefix
206 leaprc_path = os.path.join(os.environ.get('AMBERHOME', ''), 'dat', 'leap', 'cmd', 'oldff', f"{forcefield}")
207 if os.path.exists(leaprc_path):
208 leaprc_paths.append(leaprc_path)
209 continue
211 new_num_paths = len(leaprc_paths)
213 if new_num_paths == num_paths:
214 raise ValueError(f"Force field {forcefield} not found. Check the $AMBERHOME/dat/leap/cmd/ directory for available force fields or provide the path to an existing leaprc file.")
216 return leaprc_paths
218 # def check_data_params(self, out_log, err_log):
219 # """ Checks input/output paths correctness """
221 # # Check input(s)
222 # 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__)
223 # 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__)
224 # 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__)
225 # # 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__)
226 # # 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__)
228 # # Check output(s)
229 # 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__)
230 # 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__)
231 # 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__)
233 @launchlogger
234 def launch(self):
235 """Launches the execution of the LeapSolvate module."""
237 # check input/output paths and parameters
238 # self.check_data_params(self.out_log, self.err_log)
240 # Setup Biobb
241 if self.check_restart():
242 return 0
243 self.stage_files()
245 box_command = "solvateOct"
246 if self.box_type == "cubic":
247 box_command = "solvateBox"
249 # Forcefield
250 # source_ff_command = "source leaprc." + self.forcefield
252 # Water Type
253 # leaprc.water.tip4pew, tip4pd, tip3p, spceb, spce, opc, fb4, fb3
254 # Values: POL3BOX, QSPCFWBOX, SPCBOX, SPCFWBOX, TIP3PBOX, TIP3PFBOX, TIP4PBOX, TIP4PEWBOX, OPCBOX, OPC3BOX, TIP5PBOX.
255 source_wat_command = "source leaprc.water.tip3p"
256 if self.water_type == "TIP4PEWBOX":
257 source_wat_command = "leaprc.water.tip4pew"
258 if self.water_type == "TIP4PBOX":
259 source_wat_command = "leaprc.water.tip4pd"
260 if re.match(r"SPC", self.water_type):
261 source_wat_command = "source leaprc.water.spce"
262 if re.match(r"OPC", self.water_type):
263 source_wat_command = "source leaprc.water.opc"
265 # Counterions
266 ions_command = ""
267 if self.neutralise:
268 ions_command = (
269 ions_command + "addions mol " + self.negative_ions_type + " 0 \n"
270 )
271 ions_command = (
272 ions_command + "addions mol " + self.positive_ions_type + " 0 \n"
273 )
275 if self.negative_ions_number != 0:
276 ions_command = (
277 ions_command + "addions mol " + self.negative_ions_type + " " + str(self.negative_ions_number) + " \n"
278 )
279 if self.positive_ions_number != 0:
280 ions_command = (
281 ions_command + "addions mol " + self.positive_ions_type + " " + str(self.positive_ions_number) + " \n"
282 )
284 # Creating temporary folder & Leap configuration (instructions) file
285 if self.container_path:
286 instructions_file = str(
287 PurePath(self.stage_io_dict["unique_dir"]).joinpath("leap.in")
288 )
289 instructions_file_path = str(
290 PurePath(self.container_volume_path).joinpath("leap.in")
291 )
292 self.tmp_folder = None
293 else:
294 self.tmp_folder = fu.create_unique_dir()
295 instructions_file = str(PurePath(self.tmp_folder).joinpath("leap.in"))
296 fu.log("Creating %s temporary folder" % self.tmp_folder, self.out_log)
297 instructions_file_path = instructions_file
299 ligands_lib_list = []
300 if self.io_dict["in"]["input_lib_path"] is not None:
301 if self.io_dict["in"]["input_lib_path"].endswith(".zip"):
302 ligands_lib_list = fu.unzip_list(
303 self.stage_io_dict["in"]["input_lib_path"],
304 dest_dir=self.tmp_folder,
305 out_log=self.out_log,
306 )
307 else:
308 ligands_lib_list.append(self.stage_io_dict["in"]["input_lib_path"])
310 ligands_frcmod_list = []
311 if self.io_dict["in"]["input_frcmod_path"] is not None:
312 if self.io_dict["in"]["input_frcmod_path"].endswith(".zip"):
313 ligands_frcmod_list = fu.unzip_list(
314 self.stage_io_dict["in"]["input_frcmod_path"],
315 dest_dir=self.tmp_folder,
316 out_log=self.out_log,
317 )
318 else:
319 ligands_frcmod_list.append(
320 self.stage_io_dict["in"]["input_frcmod_path"]
321 )
323 amber_params_list = []
324 if self.io_dict["in"]["input_params_path"] is not None:
325 if self.io_dict["in"]["input_params_path"].endswith(".zip"):
326 amber_params_list = fu.unzip_list(
327 self.stage_io_dict["in"]["input_params_path"],
328 dest_dir=self.tmp_folder,
329 out_log=self.out_log,
330 )
331 else:
332 amber_params_list.append(self.stage_io_dict["in"]["input_params_path"])
334 amber_prep_list = []
335 if self.io_dict["in"]["input_prep_path"] is not None:
336 if self.io_dict["in"]["input_prep_path"].endswith(".zip"):
337 amber_prep_list = fu.unzip_list(
338 self.stage_io_dict["in"]["input_prep_path"],
339 dest_dir=self.tmp_folder,
340 out_log=self.out_log,
341 )
342 else:
343 amber_prep_list.append(self.stage_io_dict["in"]["input_prep_path"])
345 leap_source_list = []
346 if self.io_dict["in"]["input_source_path"] is not None:
347 if self.io_dict["in"]["input_source_path"].endswith(".zip"):
348 leap_source_list = fu.unzip_list(
349 self.stage_io_dict["in"]["input_source_path"],
350 dest_dir=self.tmp_folder,
351 out_log=self.out_log,
352 )
353 else:
354 leap_source_list.append(self.stage_io_dict["in"]["input_source_path"])
356 with open(instructions_file, "w") as leapin:
357 # Forcefields loaded by default:
358 # Protein: ff14SB (PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA)
359 # leapin.write("source leaprc.protein.ff14SB \n")
360 # DNA: parmBSC1 (ParmBSC1 (ff99 + bsc0 + bsc1) for DNA. Ivani et al. Nature Methods 13: 55, 2016)
361 # leapin.write("source leaprc.DNA.bsc1 \n")
362 # Ligands: GAFF (General Amber Force field, J. Comput. Chem. 2004 Jul 15;25(9):1157-74)
363 # leapin.write("source leaprc.gaff \n")
365 # Forcefields loaded from input forcefield property
366 for t in self.forcefield:
367 leapin.write("source {}\n".format(t))
369 # Additional Leap commands
370 for leap_commands in leap_source_list:
371 leapin.write("source " + leap_commands + "\n")
373 # Ions Type
374 if self.ions_type != "None":
375 leapin.write("loadamberparams frcmod." + self.ions_type + "\n")
377 # Additional Amber parameters
378 for amber_params in amber_params_list:
379 leapin.write("loadamberparams " + amber_params + "\n")
381 # Additional Amber prep files
382 for amber_prep in amber_prep_list:
383 leapin.write("loadamberprep " + amber_prep + "\n")
385 # Water Model loaded from input water_model property
386 leapin.write(source_wat_command + " \n")
388 # Ligand(s) libraries (if any)
389 for amber_lib in ligands_lib_list:
390 leapin.write("loadOff " + amber_lib + "\n")
391 for amber_frcmod in ligands_frcmod_list:
392 leapin.write("loadamberparams " + amber_frcmod + "\n")
394 # Loading PDB file
395 leapin.write(
396 "mol = loadpdb " + self.stage_io_dict["in"]["input_pdb_path"] + " \n"
397 )
399 # Generating box + adding water molecules
400 leapin.write(
401 box_command + " mol " + self.water_type + " " + str(self.distance_to_molecule)
402 )
403 leapin.write(
404 " iso " + str(self.closeness) + "\n"
405 ) if self.iso else leapin.write(" " + str(self.closeness) + "\n")
407 # Adding counterions
408 leapin.write(ions_command)
410 # Saving output PDB file, coordinates and topology
411 leapin.write(
412 "savepdb mol " + self.stage_io_dict["out"]["output_pdb_path"] + " \n"
413 )
414 leapin.write(
415 "saveAmberParm mol " + self.stage_io_dict["out"]["output_top_path"] + " " + self.stage_io_dict["out"]["output_crd_path"] + "\n"
416 )
417 leapin.write("quit \n")
419 # Command line
420 self.cmd = [self.binary_path, "-f", instructions_file_path]
422 # Run Biobb block
423 self.run_biobb()
425 # Copy files to host
426 self.copy_to_host()
428 # Saving octahedron box with all decimals in PDB file. Needed for the add_ions BB.
430 # Getting octahedron box from generated crd file
431 with open(self.io_dict["out"]["output_crd_path"], "r") as file:
432 for line in file:
433 pass
435 # Adding box as a first line in the generated pdb file with OCTBOX tag
436 octbox = "OCTBOX " + line
437 with open(self.io_dict["out"]["output_pdb_path"], "r+") as f:
438 content = f.read()
439 f.seek(0, 0)
440 f.write(octbox + content)
442 # remove temporary folder(s)
443 self.tmp_files.extend([
444 # self.stage_io_dict.get("unique_dir", ""),
445 str(self.tmp_folder), "leap.log"
446 ])
447 self.remove_tmp_files()
449 self.check_arguments(output_files_created=True, raise_exception=False)
451 return self.return_code
454def leap_solvate(
455 input_pdb_path: str,
456 output_pdb_path: str,
457 output_top_path: str,
458 output_crd_path: str,
459 input_lib_path: Optional[str] = None,
460 input_frcmod_path: Optional[str] = None,
461 input_params_path: Optional[str] = None,
462 input_prep_path: Optional[str] = None,
463 input_source_path: Optional[str] = None,
464 properties: Optional[dict] = None,
465 **kwargs,
466) -> int:
467 """Create :class:`LeapSolvate <leap.leap_solvate.LeapSolvate>`leap.leap_solvate.LeapSolvate class and
468 execute :meth:`launch() <leap.leap_solvate.LeapSolvate.launch>` method"""
470 return LeapSolvate(
471 input_pdb_path=input_pdb_path,
472 input_lib_path=input_lib_path,
473 input_frcmod_path=input_frcmod_path,
474 input_params_path=input_params_path,
475 input_prep_path=input_prep_path,
476 input_source_path=input_source_path,
477 output_pdb_path=output_pdb_path,
478 output_top_path=output_top_path,
479 output_crd_path=output_crd_path,
480 properties=properties,
481 ).launch()
483 leap_solvate.__doc__ = LeapSolvate.__doc__
486def main():
487 parser = argparse.ArgumentParser(
488 description="Generating and solvating a system box for an AMBER MD system. using tLeap program from AmberTools MD package.",
489 formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999),
490 )
491 parser.add_argument("--config", required=False, help="Configuration file")
493 # Specific args
494 required_args = parser.add_argument_group("required arguments")
495 required_args.add_argument(
496 "--input_pdb_path",
497 required=True,
498 help="Input 3D structure PDB file. Accepted formats: pdb.",
499 )
500 required_args.add_argument(
501 "--input_lib_path",
502 required=False,
503 help="Input ligand library parameters file. Accepted formats: lib, zip.",
504 )
505 required_args.add_argument(
506 "--input_frcmod_path",
507 required=False,
508 help="Input ligand frcmod parameters file. Accepted formats: frcmod, zip.",
509 )
510 required_args.add_argument(
511 "--input_params_path",
512 required=False,
513 help="Additional leap parameter files to load with loadAmberParams Leap command. Accepted formats: leapin, in, txt, zip.",
514 )
515 required_args.add_argument(
516 "--input_prep_path",
517 required=False,
518 help="Additional leap parameter files to load with loadAmberPrep Leap command. Accepted formats: leapin, in, txt, zip.",
519 )
520 required_args.add_argument(
521 "--input_source_path",
522 required=False,
523 help="Additional leap command files to load with source Leap command. Accepted formats: leapin, in, txt, zip.",
524 )
525 required_args.add_argument(
526 "--output_pdb_path",
527 required=True,
528 help="Output 3D structure PDB file matching the topology file. Accepted formats: pdb.",
529 )
530 required_args.add_argument(
531 "--output_top_path",
532 required=True,
533 help="Output topology file (AMBER ParmTop). Accepted formats: top.",
534 )
535 required_args.add_argument(
536 "--output_crd_path",
537 required=True,
538 help="Output coordinates file (AMBER crd). Accepted formats: crd.",
539 )
541 args = parser.parse_args()
542 config = args.config if args.config else None
543 properties = settings.ConfReader(config=config).get_prop_dic()
545 # Specific call
546 leap_solvate(
547 input_pdb_path=args.input_pdb_path,
548 input_lib_path=args.input_lib_path,
549 input_frcmod_path=args.input_frcmod_path,
550 input_params_path=args.input_params_path,
551 input_prep_path=args.input_prep_path,
552 input_source_path=args.input_source_path,
553 output_pdb_path=args.output_pdb_path,
554 output_top_path=args.output_top_path,
555 output_crd_path=args.output_crd_path,
556 properties=properties,
557 )
560if __name__ == "__main__":
561 main()