Coverage for biobb_flexdyn/flexdyn/prody_anm.py: 80%
54 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 prody_anm class and the command line interface."""
4import argparse
5from typing import Optional
6import prody # type: ignore
7from biobb_common.generic.biobb_object import BiobbObject
8from biobb_common.configuration import settings
9from biobb_common.tools.file_utils import launchlogger
12class ProdyANM(BiobbObject):
13 """
14 | biobb_flexdyn ProdyANM
15 | Wrapper of the ANM tool from the Prody package.
16 | Generate an ensemble of structures using the Prody Anisotropic Network Model (ANM), for coarse-grained NMA.
18 Args:
19 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.pdb>`_. Accepted formats: pdb (edam:format_1476).
20 output_pdb_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/prody/prody_output.pdb>`_. Accepted formats: pdb (edam:format_1476).
21 properties (dict - Python dictionary object containing the tool parameters, not input/output files):
22 * **num_structs** (*int*) - (500) Number of structures to be generated
23 * **selection** (*str*) - (calpha) Atoms selection (Prody syntax: http://prody.csb.pitt.edu/manual/reference/atomic/select.html)
24 * **cutoff** (*float*) - (15.0) Cutoff distance (Å) for pairwise interactions, minimum is 4.0 Å
25 * **gamma** (*float*) - (1.0) Spring constant
26 * **rmsd** (*float*) - (1.0) Average RMSD that the conformations will have with respect to the initial conformation
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.prody_anm import prody_anm
35 prop = {
36 'num_structs' : 20,
37 'rmsd' : 4.0
38 }
39 prody_anm( input_pdb_path='/path/to/structure.pdb',
40 output_pdb_path='/path/to/output.pdb',
41 properties=prop)
43 Info:
44 * wrapped_software:
45 * name: Prody
46 * version: >=2.2.0
47 * license: MIT
48 * ontology:
49 * name: EDAM
50 * schema: http://edamontology.org/EDAM.owl
52 """
54 def __init__(self, input_pdb_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},
66 'out': {'output_pdb_path': output_pdb_path}
67 }
69 # Properties specific for BB
70 self.properties = properties
72 self.num_structs = properties.get('num_structs', 500)
73 self.selection = properties.get('selection', 'calpha')
74 self.cutoff = properties.get('cutoff', 15.0)
75 self.gamma = properties.get('gamma', 1.0)
76 self.rmsd = properties.get('rmsd', 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 ConcoordDist module."""
86 # Setup Biobb
87 if self.check_restart():
88 return 0
89 self.stage_files()
91 prot = prody.parsePDB(self.stage_io_dict["in"]["input_pdb_path"],)
93 # http://prody.csb.pitt.edu/manual/reference/atomic/select.html
94 prot_sel = prot.select(self.selection) # type: ignore
96 enm = prody.ANM('BioBB_flexdyn Prody ANM ensemble generator')
98 enm.buildHessian(prot_sel, cutoff=self.cutoff, gamma=self.gamma)
100 enm.calcModes()
102 bb_enm, bb_atoms = prody.extendModel(enm, prot_sel, prot_sel)
104 ensemble = prody.sampleModes(bb_enm[:3], bb_atoms, n_confs=self.num_structs, rmsd=self.rmsd)
106 nmastruct = bb_atoms.copy()
107 nmastruct.addCoordset(ensemble)
109 prody.writePDB(self.stage_io_dict["out"]["output_pdb_path"], nmastruct)
111 # Copy files to host
112 self.copy_to_host()
114 # remove temporary folder(s)
115 self.tmp_files.extend([
116 self.stage_io_dict.get("unique_dir", "")
117 ])
118 self.remove_tmp_files()
120 self.check_arguments(output_files_created=True, raise_exception=False)
122 return self.return_code
125def prody_anm(input_pdb_path: str, output_pdb_path: str,
126 properties: Optional[dict] = None, **kwargs) -> int:
127 """Create :class:`ProdyANM <flexdyn.prody_anm.ProdyANM>`flexdyn.prody_anm.ProdyANM class and
128 execute :meth:`launch() <flexdyn.prody_anm.ProdyANM.launch>` method"""
130 return ProdyANM(input_pdb_path=input_pdb_path,
131 output_pdb_path=output_pdb_path,
132 properties=properties).launch()
135def main():
136 parser = argparse.ArgumentParser(description='Generate an ensemble of structures using the Prody Anisotropic Network Model (ANM), for coarse-grained NMA.', formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
137 parser.add_argument('--config', required=False, help='Configuration file')
139 # Specific args
140 required_args = parser.add_argument_group('required arguments')
141 required_args.add_argument('--input_pdb_path', required=True, help='Input structure file. Accepted formats: pdb')
142 required_args.add_argument('--output_pdb_path', required=True, help='Output pdb file. Accepted formats: pdb.')
144 args = parser.parse_args()
145 args.config = args.config or "{}"
146 properties = settings.ConfReader(config=args.config).get_prop_dic()
148 # Specific call
149 prody_anm(input_pdb_path=args.input_pdb_path,
150 output_pdb_path=args.output_pdb_path,
151 properties=properties)
154if __name__ == '__main__':
155 main()