Coverage for biobb_flexserv/pcasuite/pcz_collectivity.py: 94%
48 statements
« prev ^ index » next coverage.py v7.14.1, created at 2026-05-28 11:28 +0000
1#!/usr/bin/env python3
3"""Module containing the PCZcollectivity class and the command line interface."""
4from typing import Optional
5from pathlib import Path, PurePath
6import json
7from biobb_common.generic.biobb_object import BiobbObject
8from biobb_common.tools.file_utils import launchlogger
11class PCZcollectivity(BiobbObject):
12 """
13 | biobb_flexserv PCZcollectivity
14 | Extract PCA collectivity (numerical measure of how many atoms are affected by a given mode) from a compressed PCZ file.
15 | Wrapper of the pczdump tool from the PCAsuite FlexServ module.
17 Args:
18 input_pcz_path (str): Input compressed trajectory file. File type: input. `Sample file <https://github.com/bioexcel/biobb_flexserv/raw/master/biobb_flexserv/test/data/pcasuite/pcazip.pcz>`_. Accepted formats: pcz (edam:format_3874).
19 output_json_path (str): Output json file with PCA Collectivity indexes per mode. File type: output. `Sample file <https://github.com/bioexcel/biobb_flexserv/raw/master/biobb_flexserv/test/reference/pcasuite/pcz_collectivity.json>`_. Accepted formats: json (edam:format_3464).
20 properties (dict - Python dictionary object containing the tool parameters, not input/output files):
21 * **eigenvector** (*int*) - (0) PCA mode (eigenvector) from which to extract stiffness.
22 * **binary_path** (*str*) - ("pczdump") pczdump binary path to be used.
23 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
24 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
25 * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
26 * **container_path** (*str*) - (None) Container path definition.
27 * **container_image** (*str*) - ('afandiadib/ambertools:serial') Container image definition.
28 * **container_volume_path** (*str*) - ('/tmp') Container volume path definition.
29 * **container_working_dir** (*str*) - (None) Container working directory definition.
30 * **container_user_id** (*str*) - (None) Container user_id definition.
31 * **container_shell_path** (*str*) - ('/bin/bash') Path to default shell inside the container.
33 Examples:
34 This is a use example of how to use the building block from Python::
36 from biobb_flexserv.pcasuite.pcz_collectivity import pcz_collectivity
38 prop = {
39 'eigenvector': 1
40 }
42 pcz_collectivity( input_pcz_path='/path/to/pcazip_input.pcz',
43 output_json_path='/path/to/pcz_collectivity.json',
44 properties=prop)
46 Info:
47 * wrapped_software:
48 * name: FlexServ PCAsuite
49 * version: >=1.0
50 * license: Apache-2.0
51 * ontology:
52 * name: EDAM
53 * schema: http://edamontology.org/EDAM.owl
55 """
57 def __init__(self, input_pcz_path: str,
58 output_json_path: str, properties: Optional[dict] = None, **kwargs) -> None:
60 properties = properties or {}
62 # Call parent class constructor
63 super().__init__(properties)
64 self.locals_var_dict = locals().copy()
66 # Input/Output files
67 self.io_dict = {
68 'in': {'input_pcz_path': input_pcz_path},
69 'out': {'output_json_path': output_json_path}
70 }
72 # Properties specific for BB
73 self.properties = properties
74 self.binary_path = properties.get('binary_path', 'pczdump')
75 self.eigenvector = properties.get('eigenvector', 0)
77 # Check the properties
78 self.check_properties(properties)
79 self.check_arguments()
81 @launchlogger
82 def launch(self):
83 """Launches the execution of the FlexServ pcz_collectivity module."""
85 # Setup Biobb
86 if self.check_restart():
87 return 0
88 self.stage_files()
90 if self.container_path:
91 working_dir = self.container_volume_path if self.container_volume_path else "/data"
92 else:
93 working_dir = self.stage_io_dict.get("unique_dir", "")
95 unique_dir = Path(self.stage_io_dict.get("unique_dir", ""))
97 # Temporary output
98 # temp_out = str(Path(self.stage_io_dict.get("unique_dir", "")).joinpath("output.dat"))
99 temp_out = "output.dat"
100 temp_out_path = unique_dir.joinpath(temp_out)
101 staged_output_json_path = unique_dir.joinpath(Path(self.stage_io_dict["out"]["output_json_path"]).name)
103 # Command line
104 # pczdump -i structure.ca.std.pcz --collectivity -o pcz.collectivity
105 # self.cmd = [self.binary_path,
106 # "-i", input_pcz,
107 # "-o", temp_out,
108 # "--collectivity={}".format(self.eigenvector)
109 # ]
111 self.cmd = ['cd', working_dir, ';',
112 self.binary_path,
113 '-i', PurePath(self.stage_io_dict["in"]["input_pcz_path"]).name,
114 '-o', temp_out,
115 "--collectivity={}".format(self.eigenvector)
116 ]
118 # Run Biobb block
119 self.run_biobb()
121 # Parse output collectivity
122 # 0.132891
123 # 0.165089
124 # 0.147202
125 info_dict = {}
126 info_dict['collectivity'] = []
127 with open(temp_out_path, 'r') as file:
128 for line in file:
129 info = float(line.strip())
130 info_dict['collectivity'].append(info)
132 with open(staged_output_json_path, 'w') as out_file:
133 out_file.write(json.dumps(info_dict, indent=4))
135 # Copy files to host
136 self.copy_to_host()
138 # Remove temporary folder(s)
139 self.remove_tmp_files()
141 self.check_arguments(output_files_created=True, raise_exception=False)
143 return self.return_code
146def pcz_collectivity(input_pcz_path: str, output_json_path: str,
147 properties: Optional[dict] = None, **kwargs) -> int:
148 """Create :class:`PCZcollectivity <flexserv.pcasuite.pcz_collectivity>`flexserv.pcasuite.PCZcollectivity class and
149 execute :meth:`launch() <flexserv.pcasuite.pcz_collectivity.launch>` method"""
150 return PCZcollectivity(**dict(locals())).launch()
153pcz_collectivity.__doc__ = PCZcollectivity.__doc__
154main = PCZcollectivity.get_main(pcz_collectivity, "Extract PCA collectivity (numerical measure of how many atoms are affected by a given mode) from a compressed PCZ file.")
156if __name__ == '__main__':
157 main()