Coverage for biobb_mem/mdanalysis_biobb/mda_hole.py: 57%
104 statements
« prev ^ index » next coverage.py v7.6.11, created at 2025-02-10 11:25 +0000
1#!/usr/bin/env python3
3"""Module containing the MDAnalysis HOLE class and the command line interface."""
4import re
5import os
6import argparse
7import numpy as np
8import pandas as pd
9from biobb_common.generic.biobb_object import BiobbObject
10from biobb_common.configuration import settings
11from biobb_common.tools.file_utils import launchlogger
12import MDAnalysis as mda
13from mdahole2.analysis import HoleAnalysis
16class MDAHole(BiobbObject):
17 """
18 | biobb_mem MDAHole
19 | Wrapper of the MDAnalysis HOLE module for analyzing ion channel pores or transporter pathways.
20 | MDAnalysis HOLE provides an interface to the HOLE suite of tools to analyze pore dimensions and properties along a channel or transporter pathway. The parameter names and defaults follow the `MDAnalysis HOLE <https://www.mdanalysis.org/mdahole2/api.html>`_ implementation.
22 Args:
23 input_top_path (str): Path to the input structure or topology file. File type: input. `Sample file <https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/data/A01JD/A01JD.pdb>`_. Accepted formats: crd (edam:3878), gro (edam:2033), mdcrd (edam:3878), mol2 (edam:3816), pdb (edam:1476), pdbqt (edam:1476), prmtop (edam:3881), psf (edam:3882), top (edam:3881), tpr (edam:2333), xml (edam:2332), xyz (edam:3887).
24 input_traj_path (str): Path to the input trajectory to be processed. File type: input. `Sample file <https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/data/A01JD/A01JD.xtc>`_. Accepted formats: arc (edam:2333), crd (edam:3878), dcd (edam:3878), ent (edam:1476), gro (edam:2033), inpcrd (edam:3878), mdcrd (edam:3878), mol2 (edam:3816), nc (edam:3650), pdb (edam:1476), pdbqt (edam:1476), restrt (edam:3886), tng (edam:3876), trr (edam:3910), xtc (edam:3875), xyz (edam:3887).
25 output_hole_path (str): Path to the output HOLE analysis results. File type: output. `Sample file <https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/reference/mdanalysis_biobb/hole.vmd>`_. Accepted formats: vmd (edam:format_2330).
26 output_csv_path (str): Path to the output CSV file containing the radius and coordinates of the pore. File type: output. `Sample file <https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/reference/mdanalysis_biobb/hole_profile.csv>`_. Accepted formats: csv.
27 properties (dic - Python dictionary object containing the tool parameters, not input/output files):
28 * **start** (*int*) - (None) Starting frame for slicing.
29 * **stop** (*int*) - (None) Ending frame for slicing.
30 * **steps** (*int*) - (None) Step for slicing.
31 * **executable** (*str*) - ("hole") Path to the HOLE executable.
32 * **select** (*str*) - ("protein") The selection string to create an atom selection that the HOLE analysis is applied to.
33 * **cpoint** (*list*) - (None) Coordinates of a point inside the pore (Å). If None, tries to guess based on the geometry.
34 * **cvect** (*list*) - (None) Search direction vector. If None, tries to guess based on the geometry.
35 * **sample** (*float*) - (0.2) Distance of sample points in Å. This value determines how many points in the pore profile are calculated.
36 * **end_radius** (*float*) - (22) Radius in Å, which is considered to be the end of the pore.
37 * **dot_density** (*int*) - (15) [5~35] Density of facets for generating a 3D pore representation.
38 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
39 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
40 * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
42 Examples:
43 This is a use example of how to use the building block from Python::
45 from biobb_mem.mdanalysis_biobb.mda_hole import mda_hole
46 prop = {
47 'select': 'protein',
48 'executable': 'hole'
49 }
50 mda_hole(input_top_path='/path/to/myTopology.pdb',
51 input_traj_path='/path/to/myTrajectory.xtc',
52 output_hole_path='/path/to/hole_analysis.csv',
53 output_hole_path='/path/to/hole_profile.csv',
54 properties=prop)
56 Info:
57 * wrapped_software:
58 * name: MDAnalysis
59 * version: 2.7.0
60 * license: GNU
61 * ontology:
62 * name: EDAM
63 * schema: http://edamontology.org/EDAM.owl
64 """
66 def __init__(self, input_top_path, input_traj_path, output_hole_path, output_csv_path=None,
67 properties=None, **kwargs) -> None:
68 properties = properties or {}
70 # Call parent class constructor
71 super().__init__(properties)
72 self.locals_var_dict = locals().copy()
74 # Input/Output files
75 self.io_dict = {
76 "in": {"input_top_path": input_top_path, "input_traj_path": input_traj_path},
77 "out": {"output_hole_path": output_hole_path, "output_csv_path": output_csv_path}
78 }
80 # Properties specific for MDAHole
81 self.start = properties.get('start', None)
82 self.stop = properties.get('stop', None)
83 self.steps = properties.get('steps', None)
84 self.executable = properties.get('executable', 'hole')
85 self.select = properties.get('select', 'protein')
86 self.cpoint = properties.get('cpoint', None)
87 self.cvect = properties.get('cvect', None)
88 self.sample = properties.get('sample', 0.2)
89 self.end_radius = properties.get('end_radius', 22)
90 self.dot_density = properties.get('dot_density', 15)
91 self.properties = properties
93 # Check the properties
94 self.check_properties(properties)
95 self.check_arguments()
97 @launchlogger
98 def launch(self) -> int:
99 """Execute the :class:`MDAHole <mdanalysis_biobb.mda_hole.MDAHole>` class."""
101 # Setup Biobb
102 if self.check_restart():
103 return 0
104 self.stage_files()
106 # Load the universe
107 u = mda.Universe(self.stage_io_dict["in"]["input_top_path"],
108 self.stage_io_dict["in"]["input_traj_path"])
109 # save current directory and move to temporary
110 cwd = os.getcwd()
111 os.chdir(self.stage_io_dict.get("unique_dir"))
112 # Create HoleAnalysis object
113 hole = HoleAnalysis(
114 universe=u,
115 select=self.select,
116 cpoint=self.cpoint,
117 cvect=self.cvect,
118 sample=self.sample,
119 executable=self.executable,
120 end_radius=self.end_radius
121 )
122 # Run the analysis with step parameter
123 hole.run(
124 start=self.start,
125 stop=self.stop,
126 step=self.steps
127 )
128 # Save the results to a CSV file
129 all_frames = []
130 for frame in hole.results.profiles.keys():
131 rxn_coord = hole.results.profiles[frame].rxn_coord
132 radius = hole.results.profiles[frame].radius
133 df_frame = pd.DataFrame({'Frame': frame, 'Pore Coordinate': rxn_coord, 'Radius': radius})
134 all_frames.append(df_frame)
135 # Concatenate all frames into a single DataFrame
136 df_all_frames = pd.concat(all_frames, ignore_index=True)
137 df_all_frames.to_csv(self.stage_io_dict["out"]["output_csv_path"], index=False)
139 hole.create_vmd_surface(
140 self.stage_io_dict["out"]["output_hole_path"],
141 dot_density=self.dot_density
142 )
143 hole.delete_temporary_files()
144 # move back to original directory
145 os.chdir(cwd)
146 # Copy files to host
147 self.copy_to_host()
148 # remove temporary folder(s)
149 self.tmp_files.extend([
150 self.stage_io_dict.get("unique_dir")
151 ])
152 self.remove_tmp_files()
154 self.check_arguments(output_files_created=True, raise_exception=False)
156 return self.return_code
159def mda_hole(input_top_path: str, input_traj_path: str, output_hole_path: str, output_csv_path: str, properties: dict = None, **kwargs) -> int:
160 """Execute the :class:`MDAHole <mdanalysis_biobb.mda_hole.MDAHole>` class and
161 execute the :meth:`launch() <mdanalysis_biobb.mda_hole.MDAHole.launch>` method."""
163 return MDAHole(input_top_path=input_top_path,
164 input_traj_path=input_traj_path,
165 output_hole_path=output_hole_path,
166 output_csv_path=output_csv_path,
167 properties=properties, **kwargs).launch()
170def main():
171 """Command line execution of this building block. Please check the command line documentation."""
172 parser = argparse.ArgumentParser(description="Analyze ion channel pores or transporter pathways.", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
173 parser.add_argument('--config', required=False, help='Configuration file')
175 # Specific args of each building block
176 required_args = parser.add_argument_group('required arguments')
177 required_args.add_argument('--input_top_path', required=True, help='Path to the input structure or topology file. Accepted formats: crd, gro, mdcrd, mol2, pdb, pdbqt, prmtop, psf, top, tpr, xml, xyz.')
178 required_args.add_argument('--input_traj_path', required=True, help='Path to the input trajectory to be processed. Accepted formats: arc, crd, dcd, ent, gro, inpcrd, mdcrd, mol2, nc, pdb, pdbqt, restrt, tng, trr, xtc, xyz.')
179 required_args.add_argument('--output_hole_path', required=True, help='Path to the output HOLE analysis results. Accepted formats: vmd.')
180 required_args.add_argument('--output_csv_path', required=True, help='Path to the output CSV file containing the radius and coordinates of the pore. Accepted formats: csv.')
182 args = parser.parse_args()
183 args.config = args.config or "{}"
184 properties = settings.ConfReader(config=args.config).get_prop_dic()
186 # Specific call of each building block
187 mda_hole(input_top_path=args.input_top_path,
188 input_traj_path=args.input_traj_path,
189 output_hole_path=args.output_hole_path,
190 output_csv_path=args.output_csv_path,
191 properties=properties)
194def display_hole(input_top_path: str, input_traj_path: str,
195 output_hole_path: str = 'hole.vmd',
196 frame: int = 0, opacity: float = 0.9):
197 """
198 Visualize a channel using NGLView from a VMD file.
200 Args:
201 input_top_path (str): Path to the input topology file.
202 output_hole_path (str, optional): Path to the VMD file containing the channel data. Default is 'hole.vmd'.
203 frame (int, optional): Frame index to visualize. Default is 0.
204 opacity (float, optional): Opacity of the visualization. Default is 0.9.
205 Returns:
206 nglview.NGLWidget: NGLView widget for visualizing the channel.
207 """
209 try:
210 import nglview as nv
211 except ImportError:
212 raise ImportError('Please install the nglview package to visualize the channel.')
214 # Read the VMD file and parse triangles
215 with open(output_hole_path, 'r') as f:
216 lines = f.readlines()
218 # Find lines with triangle coordinates
219 trinorms = []
220 for i, line in enumerate(lines):
221 if i > 3 and 'set triangle' in line:
222 vmd_set = re.sub(r'set triangles\(\d+\)', '', line) # Remove set triangles(i)
223 vmd_set = re.sub(r'\{(\s*-?\d[^\s]*)(\s*-?\d[^\s]*)(\s*-?\d[^}]*)\}', r'[\1,\2,\3]', vmd_set) # Convert { x y z } to [x,y,z]
224 vmd_set = vmd_set.replace('{', '[').replace('}', ']') # Convert { to [ and } to ]
225 vmd_set = re.sub(r'\]\s*\[', '], [', vmd_set) # Add commas between brackets
226 vmd_set = eval(vmd_set.strip()) # Evaluate string as list
227 # different hole colors
228 trinorms.append(vmd_set)
229 # Create a list of positions, colors, and normals
230 colors = np.array([[1, 0, 0], # red
231 [0, 1, 0], # green
232 [0, 0, 1]]) # blue
233 poss, cols, nors = [], [], []
234 for i, color in enumerate(colors):
235 if len(trinorms[frame][i]) > 0:
236 col_dat = np.array(trinorms[frame][i])
237 poss.append(col_dat[:, :3, :].flatten()) # 3 first elements are positions
238 cols.append((np.zeros(col_dat.shape[0]*18).reshape(-1, 3) + color).flatten()) # 3 colors for each vertex
239 nors.append(col_dat[:, 3:, :].flatten()) # 3 last elements are normals
240 poss = np.concatenate(poss)
241 cols = np.concatenate(cols)
242 nors = np.concatenate(nors)
243 # Create NGLView widget
244 u = mda.Universe(input_top_path, input_traj_path)
245 view = nv.show_mdanalysis(u)
246 # view.clear_representations()
247 mesh = ('mesh', poss, cols)
248 view._add_shape([mesh], name='my_shape')
249 view.update_representation(component=1, repr_index=0, opacity=opacity)
250 return view
253if __name__ == '__main__':
254 main()