Coverage for biobb_flexdyn/flexdyn/imod_imove.py: 77%
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« prev ^ index » next coverage.py v7.6.4, created at 2024-11-04 11:11 +0000
« 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 ImodImove(BiobbObject):
15 """
16 | biobb_flexdyn imod_imove
17 | Wrapper of the imove tool
18 | Compute the normal modes of a macromolecule using the imove 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_pdb_path (str): Output multi-model PDB file with the generated animation by Principal Component. File type: output. `Sample file <https://github.com/bioexcel/biobb_flexdyn/raw/master/biobb_flexdyn/test/reference/flexdyn/imod_imove_output.pdb>`_. Accepted formats: pdb (edam:format_1476).
24 properties (dict - Python dictionary object containing the tool parameters, not input/output files):
25 * **pc** (*int*) - (1) Principal Component.
26 * **num_frames** (*int*) - (11) Number of frames to be generated
27 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
28 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
29 * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
31 Examples:
32 This is a use example of how to use the building block from Python::
34 from biobb_flexdyn.flexdyn.imod_imove import imod_imove
35 prop = {
36 'pc' : 1
37 }
38 imod_imove( input_pdb_path='/path/to/structure.pdb',
39 input_dat_path='/path/to/input_evecs.dat',
40 output_pdb_path='/path/to/output_anim.pdb',
41 properties=prop)
43 Info:
44 * wrapped_software:
45 * name: iMODS
46 * version: >=1.0.4
47 * license: other
48 * ontology:
49 * name: EDAM
50 * schema: http://edamontology.org/EDAM.owl
52 """
54 def __init__(self, input_pdb_path: str, input_dat_path: str, output_pdb_path: str,
55 properties: Optional[dict] = None, **kwargs) -> None:
57 properties = properties or {}
59 # Call parent class constructor
60 super().__init__(properties)
61 self.locals_var_dict = locals().copy()
63 # Input/Output files
64 self.io_dict = {
65 'in': {'input_pdb_path': input_pdb_path, 'input_dat_path': input_dat_path},
66 'out': {'output_pdb_path': output_pdb_path}
67 }
69 # Properties specific for BB
70 self.properties = properties
71 self.binary_path = properties.get('binary_path', 'imove')
73 self.pc = properties.get('pc', 1)
74 self.num_frames = properties.get('num_frames', 11)
76 # Check the properties
77 self.check_properties(properties)
78 self.check_arguments()
80 @launchlogger
81 def launch(self):
82 """Launches the execution of the FlexDyn iMOD imove module."""
84 # Setup Biobb
85 if self.check_restart():
86 return 0
87 # self.stage_files()
89 # Manually creating a Sandbox to avoid issues with input parameters buffer overflow:
90 # Long strings defining a file path makes Fortran or C compiled programs crash if the string
91 # declared is shorter than the input parameter path (string) length.
92 # Generating a temporary folder and working inside this folder (sandbox) fixes this problem.
93 # The problem was found in Galaxy executions, launching Singularity containers (May 2023).
95 # Creating temporary folder
96 self.tmp_folder = fu.create_unique_dir()
97 fu.log('Creating %s temporary folder' % self.tmp_folder, self.out_log)
99 shutil.copy2(self.io_dict["in"]["input_pdb_path"], self.tmp_folder)
100 shutil.copy2(self.io_dict["in"]["input_dat_path"], self.tmp_folder)
102 # Command line
103 # imove 1ake_backbone.pdb 1ake_backbone_evecs.dat -o 1ake_backbone.ensemble.pdb 1 -c 500
104 # self.cmd = [self.binary_path,
105 # str(Path(self.stage_io_dict["in"]["input_pdb_path"]).relative_to(Path.cwd())),
106 # str(Path(self.stage_io_dict["in"]["input_dat_path"]).relative_to(Path.cwd())),
107 # str(Path(self.stage_io_dict["out"]["output_pdb_path"]).relative_to(Path.cwd())),
108 # str(self.pc)
109 # ]
111 self.cmd = ['cd', self.tmp_folder, ';',
112 self.binary_path,
113 PurePath(self.io_dict["in"]["input_pdb_path"]).name,
114 PurePath(self.io_dict["in"]["input_dat_path"]).name,
115 PurePath(self.io_dict["out"]["output_pdb_path"]).name,
116 str(self.pc)
117 ]
119 # Properties
120 if self.num_frames:
121 self.cmd.append('-c')
122 self.cmd.append(str(self.num_frames))
124 # Run Biobb block
125 self.run_biobb()
127 # Copy outputs from temporary folder to output path
128 shutil.copy2(PurePath(self.tmp_folder).joinpath(PurePath(self.io_dict["out"]["output_pdb_path"]).name), PurePath(self.io_dict["out"]["output_pdb_path"]))
130 # Copy files to host
131 # self.copy_to_host()
133 # remove temporary folder(s)
134 self.tmp_files.extend([
135 # self.stage_io_dict.get("unique_dir", "")
136 self.tmp_folder
137 ])
138 self.remove_tmp_files()
140 self.check_arguments(output_files_created=True, raise_exception=False)
142 return self.return_code
145def imod_imove(input_pdb_path: str, input_dat_path: str, output_pdb_path: str,
146 properties: Optional[dict] = None, **kwargs) -> int:
147 """Create :class:`ImodImove <flexdyn.imod_imove.ImodImove>`flexdyn.imod_imove.ImodImove class and
148 execute :meth:`launch() <flexdyn.imod_imove.ImodImove.launch>` method"""
150 return ImodImove(input_pdb_path=input_pdb_path,
151 input_dat_path=input_dat_path,
152 output_pdb_path=output_pdb_path,
153 properties=properties).launch()
156def main():
157 parser = argparse.ArgumentParser(description='Animate the normal modes of a macromolecule using the imove tool from the iMODS package.', formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
158 parser.add_argument('--config', required=False, help='Configuration file')
160 # Specific args
161 required_args = parser.add_argument_group('required arguments')
162 required_args.add_argument('--input_pdb_path', required=True, help='Input structure file. Accepted formats: pdb')
163 required_args.add_argument('--input_dat_path', required=True, help='Input evecs file. Accepted formats: dat')
164 required_args.add_argument('--output_pdb_path', required=True, help='Output pdb file. Accepted formats: pdb.')
166 args = parser.parse_args()
167 args.config = args.config or "{}"
168 properties = settings.ConfReader(config=args.config).get_prop_dic()
170 # Specific call
171 imod_imove(input_pdb_path=args.input_pdb_path,
172 input_dat_path=args.input_dat_path,
173 output_pdb_path=args.output_pdb_path,
174 properties=properties)
177if __name__ == '__main__':
178 main()