Coverage for biobb_vs / utils / box.py: 96%
72 statements
« prev ^ index » next coverage.py v7.13.0, created at 2025-12-22 13:24 +0000
1#!/usr/bin/env python3
3"""Module containing the Box class and the command line interface."""
4from pathlib import PurePath
5from typing import Optional
6import numpy as np
7from biobb_common.generic.biobb_object import BiobbObject
8from biobb_common.tools import file_utils as fu
9from biobb_common.tools.file_utils import launchlogger
11from biobb_vs.utils.common import (
12 check_input_path,
13 check_output_path,
14 get_box_coordinates,
15)
18class Box(BiobbObject):
19 """
20 | biobb_vs Box
21 | This class sets the center and the size of a rectangular parallelepiped box around a set of residues or a pocket.
22 | Sets the center and the size of a rectangular parallelepiped box around a set of residues from a given PDB or a pocket from a given PQR.
24 Args:
25 input_pdb_path (str): PDB file containing a selection of residue numbers or PQR file containing the pocket. File type: input. `Sample file <https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/data/utils/input_box.pqr>`_. Accepted formats: pdb (edam:format_1476), pqr (edam:format_1476).
26 output_pdb_path (str): PDB including the annotation of the box center and size as REMARKs. File type: output. `Sample file <https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/reference/utils/ref_output_box.pdb>`_. Accepted formats: pdb (edam:format_1476).
27 properties (dic - Python dictionary object containing the tool parameters, not input/output files):
28 * **offset** (*float*) - (2.0) [0.1~1000|0.1] Extra distance (Angstroms) between the last residue atom and the box boundary.
29 * **box_coordinates** (*bool*) - (False) Add box coordinates as 8 ATOM records.
30 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
31 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
32 * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
34 Examples:
35 This is a use example of how to use the building block from Python::
37 from biobb_vs.utils.box import box
38 prop = {
39 'offset': 2,
40 'box_coordinates': True
41 }
42 box(input_pdb_path='/path/to/myPocket.pqr',
43 output_pdb_path='/path/to/newBox.pdb',
44 properties=prop)
46 Info:
47 * wrapped_software:
48 * name: In house
49 * license: Apache-2.0
50 * ontology:
51 * name: EDAM
52 * schema: http://edamontology.org/EDAM.owl
54 """
56 def __init__(
57 self, input_pdb_path, output_pdb_path, properties=None, **kwargs
58 ) -> None:
59 properties = properties or {}
61 # Call parent class constructor
62 super().__init__(properties)
63 self.locals_var_dict = locals().copy()
65 # Input/Output files
66 self.io_dict = {
67 "in": {"input_pdb_path": input_pdb_path},
68 "out": {"output_pdb_path": output_pdb_path},
69 }
71 # Properties specific for BB
72 self.offset = float(properties.get("offset", 2.0))
73 self.box_coordinates = float(properties.get("box_coordinates", False))
74 self.properties = properties
76 # Check the properties
77 self.check_properties(properties)
78 self.check_arguments()
80 def check_data_params(self, out_log, err_log):
81 """Checks all the input/output paths and parameters"""
82 self.io_dict["in"]["input_pdb_path"] = check_input_path(
83 self.io_dict["in"]["input_pdb_path"],
84 "input_pdb_path",
85 self.out_log,
86 self.__class__.__name__,
87 )
88 self.io_dict["out"]["output_pdb_path"] = check_output_path(
89 self.io_dict["out"]["output_pdb_path"],
90 "output_pdb_path",
91 False,
92 self.out_log,
93 self.__class__.__name__,
94 )
96 @launchlogger
97 def launch(self) -> int:
98 """Execute the :class:`Box <utils.box.Box>` utils.box.Box object."""
100 # check input/output paths and parameters
101 self.check_data_params(self.out_log, self.err_log)
103 # Setup Biobb
104 if self.check_restart():
105 return 0
106 self.stage_files()
108 # check if cavity (pdb) or pocket (pqr)
109 input_type = PurePath(self.io_dict["in"]["input_pdb_path"]).suffix.lstrip(".")
110 if input_type == "pdb":
111 fu.log(
112 "Loading residue PDB selection from %s"
113 % (self.io_dict["in"]["input_pdb_path"]),
114 self.out_log,
115 self.global_log,
116 )
117 else:
118 fu.log(
119 "Loading pocket PQR selection from %s"
120 % (self.io_dict["in"]["input_pdb_path"]),
121 self.out_log,
122 self.global_log,
123 )
125 # get input_pdb_path atoms coordinates
126 selection_atoms_num = 0
127 x_coordslist = []
128 y_coordslist = []
129 z_coordslist = []
130 with open(self.io_dict["in"]["input_pdb_path"]) as infile:
131 for line in infile:
132 if line.startswith("HETATM") or line.startswith("ATOM"):
133 x_coordslist.append(float(line[31:38].strip()))
134 y_coordslist.append(float(line[39:46].strip()))
135 z_coordslist.append(float(line[47:54].strip()))
136 selection_atoms_num = selection_atoms_num + 1
138 # Compute binding site box size
140 # compute box center
141 selection_box_center = [
142 np.average(x_coordslist),
143 np.average(y_coordslist),
144 np.average(z_coordslist),
145 ]
146 fu.log(
147 "Binding site center (Angstroms): %10.3f%10.3f%10.3f"
148 % (
149 selection_box_center[0],
150 selection_box_center[1],
151 selection_box_center[2],
152 ),
153 self.out_log,
154 self.global_log,
155 )
157 # compute box size
158 selection_coords_max = np.amax(
159 [x_coordslist, y_coordslist, z_coordslist], axis=1
160 )
161 selection_box_size = selection_coords_max - selection_box_center
162 if self.offset:
163 fu.log(
164 "Adding %.1f Angstroms offset" % (self.offset),
165 self.out_log,
166 self.global_log,
167 )
168 selection_box_size = [c + self.offset for c in selection_box_size]
169 fu.log(
170 "Binding site size (Angstroms): %10.3f%10.3f%10.3f"
171 % (selection_box_size[0], selection_box_size[1], selection_box_size[2]),
172 self.out_log,
173 self.global_log,
174 )
176 # compute volume
177 vol = np.prod(selection_box_size) * 2**3
178 fu.log("Volume (cubic Angstroms): %.0f" % (vol), self.out_log, self.global_log)
180 # add box details as PDB remarks
181 remarks = "REMARK BOX CENTER:%10.3f%10.3f%10.3f" % (
182 selection_box_center[0],
183 selection_box_center[1],
184 selection_box_center[2],
185 )
186 remarks += " SIZE:%10.3f%10.3f%10.3f" % (
187 selection_box_size[0],
188 selection_box_size[1],
189 selection_box_size[2],
190 )
192 selection_box_coords_txt = ""
193 # add (optional) box coordinates as 8 ATOM records
194 if self.box_coordinates:
195 fu.log("Adding box coordinates", self.out_log, self.global_log)
196 selection_box_coords_txt = get_box_coordinates(
197 selection_box_center, selection_box_size
198 )
200 with open(self.io_dict["out"]["output_pdb_path"], "w") as f:
201 f.seek(0, 0)
202 f.write(remarks.rstrip("\r\n") + "\n" + selection_box_coords_txt)
204 fu.log(
205 "Saving output PDB file (with box setting annotations): %s"
206 % (self.io_dict["out"]["output_pdb_path"]),
207 self.out_log,
208 self.global_log,
209 )
211 # Copy files to host
212 self.copy_to_host()
213 self.remove_tmp_files()
215 self.check_arguments(output_files_created=True, raise_exception=False)
217 return 0
220def box(
221 input_pdb_path: str,
222 output_pdb_path: str,
223 properties: Optional[dict] = None,
224 **kwargs,
225) -> int:
226 """Create the :class:`Box <utils.box.Box>` class and
227 execute the :meth:`launch() <utils.box.Box.launch>` method."""
228 return Box(**dict(locals())).launch()
231box.__doc__ = Box.__doc__
232main = Box.get_main(box, "Sets the center and the size of a rectangular parallelepiped box around a set of residues from a given PDB or a pocket from a given PQR.")
235if __name__ == "__main__":
236 main()