Coverage for biobb_flexdyn/flexdyn/imod_imc.py: 81%
62 statements
« prev ^ index » next coverage.py v7.6.4, created at 2024-11-04 11:11 +0000
1#!/usr/bin/env python3
3"""Module containing the imode class and the command line interface."""
4import argparse
5from typing import Optional
6import shutil
7from pathlib import PurePath
8from biobb_common.tools import file_utils as fu
9from biobb_common.generic.biobb_object import BiobbObject
10from biobb_common.configuration import settings
11from biobb_common.tools.file_utils import launchlogger
14class ImodImc(BiobbObject):
15 """
16 | biobb_flexdyn imod_imc
17 | Wrapper of the imc tool
18 | Compute a Monte-Carlo IC-NMA based conformational ensemble using the imc tool from the iMODS package.
20 Args:
21 input_pdb_path (str): Input PDB file. File type: input. `Sample file <https://github.com/bioexcel/biobb_flexdyn/raw/master/biobb_flexdyn/test/data/flexdyn/structure_cleaned.pdb>`_. Accepted formats: pdb (edam:format_1476).
22 input_dat_path (str): Input dat with normal modes. File type: input. `Sample file <https://github.com/bioexcel/biobb_flexdyn/raw/master/biobb_flexdyn/test/data/flexdyn/imod_imode_evecs.dat>`_. Accepted formats: dat (edam:format_1637), txt (edam:format_2330).
23 output_traj_path (str): Output multi-model PDB file with the generated ensemble. File type: output. `Sample file <https://github.com/bioexcel/biobb_flexdyn/raw/master/biobb_flexdyn/test/reference/flexdyn/imod_imc_output.pdb>`_. Accepted formats: pdb (edam:format_1476).
24 properties (dict - Python dictionary object containing the tool parameters, not input/output files):
25 * **num_structs** (*int*) - (500) Number of structures to be generated
26 * **num_modes** (*int*) - (5) Number of eigenvectors to be employed
27 * **amplitude** (*int*) - (1) Amplitude linear factor to scale motion
28 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
29 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
30 * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
32 Examples:
33 This is a use example of how to use the building block from Python::
35 from biobb_flexdyn.flexdyn.imod_imc import imod_imc
36 prop = {
37 'num_structs' : 500
38 }
39 imod_imc( input_pdb_path='/path/to/structure.pdb',
40 input_dat_path='/path/to/input_evecs.dat',
41 output_traj_path='/path/to/output_ensemble.pdb',
42 properties=prop)
44 Info:
45 * wrapped_software:
46 * name: iMODS
47 * version: >=1.0.4
48 * license: other
49 * ontology:
50 * name: EDAM
51 * schema: http://edamontology.org/EDAM.owl
53 """
55 def __init__(self, input_pdb_path: str, input_dat_path: str, output_traj_path: str,
56 properties: Optional[dict] = None, **kwargs) -> None:
58 properties = properties or {}
60 # Call parent class constructor
61 super().__init__(properties)
62 self.locals_var_dict = locals().copy()
64 # Input/Output files
65 self.io_dict = {
66 'in': {'input_pdb_path': input_pdb_path, 'input_dat_path': input_dat_path},
67 'out': {'output_traj_path': output_traj_path}
68 }
70 # Properties specific for BB
71 self.properties = properties
72 self.binary_path = properties.get('binary_path', 'imc')
74 self.num_structs = properties.get('num_structs', 500)
75 self.num_modes = properties.get('num_modes', 5)
76 self.amplitude = properties.get('amplitude', 1.0)
78 # Check the properties
79 self.check_properties(properties)
80 self.check_arguments()
82 @launchlogger
83 def launch(self):
84 """Launches the execution of the FlexDyn iMOD imc module."""
86 # Setup Biobb
87 if self.check_restart():
88 return 0
89 # self.stage_files()
91 # Manually creating a Sandbox to avoid issues with input parameters buffer overflow:
92 # Long strings defining a file path makes Fortran or C compiled programs crash if the string
93 # declared is shorter than the input parameter path (string) length.
94 # Generating a temporary folder and working inside this folder (sandbox) fixes this problem.
95 # The problem was found in Galaxy executions, launching Singularity containers (May 2023).
97 # Creating temporary folder
98 self.tmp_folder = fu.create_unique_dir()
99 fu.log('Creating %s temporary folder' % self.tmp_folder, self.out_log)
101 shutil.copy2(self.io_dict["in"]["input_pdb_path"], self.tmp_folder)
102 shutil.copy2(self.io_dict["in"]["input_dat_path"], self.tmp_folder)
104 # Output temporary file
105 # out_file_prefix = Path(self.stage_io_dict.get("unique_dir", "")).joinpath("imod_ensemble")
106 # out_file = Path(self.stage_io_dict.get("unique_dir", "")).joinpath("imod_ensemble.pdb")
107 out_file_prefix = "imod_ensemble" # Needed as imod is appending the .pdb extension
108 out_file = "imod_ensemble.pdb"
110 # Command line
111 # imc 1ake_backbone.pdb 1ake_backbone_evecs.dat -o 1ake_backbone.ensemble.pdb -c 500
112 # self.cmd = [self.binary_path,
113 # str(Path(self.stage_io_dict["in"]["input_pdb_path"]).relative_to(Path.cwd())),
114 # str(Path(self.stage_io_dict["in"]["input_dat_path"]).relative_to(Path.cwd())),
115 # "-o", str(out_file_prefix)
116 # ]
118 self.cmd = ['cd', self.tmp_folder, ';',
119 self.binary_path,
120 PurePath(self.io_dict["in"]["input_pdb_path"]).name,
121 PurePath(self.io_dict["in"]["input_dat_path"]).name,
122 '-o', out_file_prefix
123 ]
125 # Properties
126 if self.num_structs:
127 self.cmd.append('-c')
128 self.cmd.append(str(self.num_structs))
130 if self.num_modes:
131 self.cmd.append('-n')
132 self.cmd.append(str(self.num_modes))
134 if self.amplitude:
135 self.cmd.append('-a')
136 self.cmd.append(str(self.amplitude))
138 # Run Biobb block
139 self.run_biobb()
141 # Copying generated output file to the final (user-given) file name
142 # shutil.copy2(out_file, self.stage_io_dict["out"]["output_traj_path"])
144 # Copy outputs from temporary folder to output path
145 shutil.copy2(PurePath(self.tmp_folder).joinpath(out_file), PurePath(self.io_dict["out"]["output_traj_path"]))
147 # Copy files to host
148 # self.copy_to_host()
150 # remove temporary folder(s)
151 self.tmp_files.extend([
152 # self.stage_io_dict.get("unique_dir", "")
153 self.tmp_folder
154 ])
155 self.remove_tmp_files()
157 self.check_arguments(output_files_created=True, raise_exception=False)
159 return self.return_code
162def imod_imc(input_pdb_path: str, input_dat_path: str, output_traj_path: str,
163 properties: Optional[dict] = None, **kwargs) -> int:
164 """Create :class:`ImodImc <flexdyn.imod_imc.ImodImc>`flexdyn.imod_imc.ImodImc class and
165 execute :meth:`launch() <flexdyn.imod_imc.ImodImc.launch>` method"""
167 return ImodImc(input_pdb_path=input_pdb_path,
168 input_dat_path=input_dat_path,
169 output_traj_path=output_traj_path,
170 properties=properties).launch()
173def main():
174 parser = argparse.ArgumentParser(description='Compute a Monte-Carlo IC-NMA based conformational ensemble using the imc tool from the iMODS package.', formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
175 parser.add_argument('--config', required=False, help='Configuration file')
177 # Specific args
178 required_args = parser.add_argument_group('required arguments')
179 required_args.add_argument('--input_pdb_path', required=True, help='Input structure file. Accepted formats: pdb')
180 required_args.add_argument('--input_dat_path', required=True, help='Input evecs file. Accepted formats: dat')
181 required_args.add_argument('--output_traj_path', required=True, help='Output traj file. Accepted formats: pdb.')
183 args = parser.parse_args()
184 args.config = args.config or "{}"
185 properties = settings.ConfReader(config=args.config).get_prop_dic()
187 # Specific call
188 imod_imc(input_pdb_path=args.input_pdb_path,
189 input_dat_path=args.input_dat_path,
190 output_traj_path=args.output_traj_path,
191 properties=properties)
194if __name__ == '__main__':
195 main()