Coverage for biobb_pmx / pmxbiobb / pmxgentop.py: 81%
86 statements
« prev ^ index » next coverage.py v7.13.0, created at 2025-12-22 17:32 +0000
1#!/usr/bin/env python3
3"""Module containing the PMX gentop class and the command line interface."""
5import os
6import shutil
7import sys
8from pathlib import Path
9from typing import Optional
11from biobb_common.generic.biobb_object import BiobbObject
12from biobb_common.tools import file_utils as fu
13from biobb_common.tools.file_utils import launchlogger
16class Pmxgentop(BiobbObject):
17 """
18 | biobb_pmx Pmxgentop
19 | Wrapper class for the `PMX gentop <https://github.com/deGrootLab/pmx>`_ module.
20 | Generate a topology file for a morphing simulation.
22 Args:
23 input_top_zip_path (str): Path the input GROMACS topology TOP and ITP files in zip format. File type: input. `Sample file <https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/data/pmx/topology.zip>`_. Accepted formats: zip (edam:format_3987).
24 output_top_zip_path (str): Path the output TOP topology in zip format. File type: output. `Sample file <https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/reference/pmx/ref_output_topology.zip>`_. Accepted formats: zip (edam:format_3987).
25 properties (dic):
26 * **force_field** (*str*) - ("amber99sb-star-ildn-mut") Force field to use. If **input_top_zip_path** is a top file, it's not necessary to specify the forcefield, as it will be determined automatically. If **input_top_zip_path** is an itp file, then it's needed.
27 * **split** (*bool*) - (False) Write separate topologies for the vdW and charge transformations.
28 * **scale_mass** (*bool*) - (False) Scale the masses of morphing atoms so that dummies have a mass of 1.
29 * **gmx_lib** (*str*) - ("$CONDA_PREFIX/lib/python3.7/site-packages/pmx/data/mutff/") Path to the GMXLIB folder in your computer.
30 * **binary_path** (*str*) - ("pmx") Path to the PMX command line interface.
31 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
32 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
33 * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
34 * **container_path** (*str*) - (None) Path to the binary executable of your container.
35 * **container_image** (*str*) - ("gromacs/gromacs:latest") Container Image identifier.
36 * **container_volume_path** (*str*) - ("/inout") Path to an internal directory in the container.
37 * **container_working_dir** (*str*) - (None) Path to the internal CWD in the container.
38 * **container_user_id** (*str*) - (None) User number id to be mapped inside the container.
39 * **container_shell_path** (*str*) - ("/bin/bash") Path to the binary executable of the container shell.
41 Examples:
42 This is a use example of how to use the building block from Python::
44 from biobb_pmx.pmxbiobb.pmxgentop import pmxgentop
45 prop = {
46 'gmx_lib': '/path/to/myGMXLIB/',
47 'force_field': 'amber99sb-star-ildn-mut'
48 }
49 pmxgentop(input_top_zip_path='/path/to/myTopology.zip',
50 output_top_zip_path='/path/to/newTopology.zip',
51 properties=prop)
53 Info:
54 * wrapped_software:
55 * name: PMX gentop
56 * version: >=1.0.1
57 * license: GNU
58 * ontology:
59 * name: EDAM
60 * schema: http://edamontology.org/EDAM.owl
62 """
64 def __init__(
65 self,
66 input_top_zip_path: str,
67 output_top_zip_path: str,
68 properties: Optional[dict] = None,
69 **kwargs,
70 ) -> None:
71 properties = properties or {}
73 # Call parent class constructor
74 super().__init__(properties)
75 self.locals_var_dict = locals().copy()
77 # Input/Output files
78 self.io_dict = {"in": {}, "out": {"output_top_zip_path": output_top_zip_path}}
79 # Should not be copied inside container
80 self.input_top_zip_path = input_top_zip_path
82 # Properties specific for BB
83 self.force_field = properties.get("force_field", "amber99sb-star-ildn-mut")
84 self.split = properties.get("split", False)
85 self.scale_mass = properties.get("scale_mass", False)
87 # Properties common in all PMX BB
88 self.gmx_lib = properties.get("gmx_lib", None)
89 if not self.gmx_lib and os.environ.get("CONDA_PREFIX", ""):
90 python_version = f"{sys.version_info.major}.{sys.version_info.minor}"
91 self.gmx_lib = str(
92 Path(os.environ.get("CONDA_PREFIX", "")).joinpath(
93 f"lib/python{python_version}/site-packages/pmx/data/mutff/"
94 )
95 )
96 if properties.get("container_path"):
97 self.gmx_lib = str(
98 Path("/usr/local/").joinpath(
99 "lib/python3.8/site-packages/pmx/data/mutff/"
100 )
101 )
102 self.binary_path = properties.get("binary_path", "pmx")
104 # Check the properties
105 self.check_properties(properties)
106 self.check_arguments()
108 @launchlogger
109 def launch(self) -> int:
110 """Execute the :class:`Pmxgentop <pmx.pmxgentop.Pmxgentop>` pmx.pmxgentop.Pmxgentop object."""
112 # Setup Biobb
113 if self.check_restart():
114 return 0
115 self.stage_files()
117 # Check if executable exists
118 if not self.container_path:
119 if not Path(self.binary_path).is_file():
120 if not shutil.which(self.binary_path):
121 raise FileNotFoundError(
122 "Executable %s not found. Check if it is installed in your system and correctly defined in the properties"
123 % self.binary_path
124 )
126 # Unzip topology to topology_out
127 top_file = fu.unzip_top(zip_file=self.input_top_zip_path, out_log=self.out_log)
128 top_dir = str(Path(top_file).parent)
130 # Copy extra files to container: topology folder
131 if self.container_path:
132 fu.log("Container execution enabled", self.out_log)
133 fu.log(f"Unique dir: {self.stage_io_dict['unique_dir']}", self.out_log)
134 fu.log(
135 f"{self.stage_io_dict['unique_dir']} files: {os.listdir(self.stage_io_dict['unique_dir'])}",
136 self.out_log,
137 )
138 fu.log(
139 f"Copy all files of the unzipped original topology to unique dir: {self.out_log}"
140 )
141 shutil.copytree(
142 top_dir,
143 str(
144 Path(self.stage_io_dict.get("unique_dir", "")).joinpath(
145 Path(top_dir).name
146 )
147 ),
148 )
149 top_file = str(
150 Path(self.container_volume_path).joinpath(
151 Path(top_dir).name, Path(top_file).name
152 )
153 )
155 output_file_name = fu.create_name(
156 prefix=self.prefix, step=self.step, name=str(Path(top_file).name)
157 )
158 u_dir = fu.create_unique_dir()
159 unique_dir_output_file = str(
160 Path(u_dir).joinpath(output_file_name)
161 )
162 fu.log(f"unique_dir_output_file: {unique_dir_output_file}", self.out_log)
164 if self.container_path:
165 fu.log("Change references for container:", self.out_log)
166 unique_dir_output_file = str(
167 Path(self.container_volume_path).joinpath(Path(output_file_name))
168 )
169 fu.log(
170 f" unique_dir_output_file: {unique_dir_output_file}", self.out_log
171 )
173 self.cmd = [
174 self.binary_path,
175 "gentop",
176 "-o",
177 str(Path(unique_dir_output_file)),
178 "-ff",
179 self.force_field,
180 "-p",
181 top_file,
182 ]
184 if self.split:
185 self.cmd.append("--split")
186 if self.scale_mass:
187 self.cmd.append("--scale_mass")
189 if self.gmx_lib:
190 self.env_vars_dict["GMXLIB"] = self.gmx_lib
192 # Run Biobb block
193 self.run_biobb()
195 # Copy files to host
196 self.copy_to_host()
198 if self.container_path:
199 unique_dir_output_file = str(
200 Path(self.stage_io_dict.get("unique_dir", "")).joinpath(
201 Path(unique_dir_output_file).name
202 )
203 )
205 # Remove paths from top file
206 with open(Path(unique_dir_output_file)) as top_fh:
207 top_lines = top_fh.readlines()
208 with open(Path(unique_dir_output_file), "w") as top_fh:
209 for line in top_lines:
210 top_fh.write(
211 line.replace(str(Path(unique_dir_output_file).parent) + "/", "")
212 )
213 # Copy the not modified itp files
214 for orig_itp_file in Path(top_dir).iterdir():
215 fu.log(
216 f"Check if {str(Path(unique_dir_output_file).parent.joinpath(Path(orig_itp_file).name))} exists",
217 self.out_log,
218 self.global_log,
219 )
220 if (
221 not Path(unique_dir_output_file)
222 .parent.joinpath(Path(orig_itp_file).name)
223 .exists()
224 ):
225 shutil.copy(orig_itp_file, Path(unique_dir_output_file).parent)
226 fu.log(
227 f"Copying {str(orig_itp_file)} to: {str(Path(unique_dir_output_file).parent)}",
228 self.out_log,
229 self.global_log,
230 )
232 # zip topology
233 fu.log(
234 "Compressing topology to: %s" % self.io_dict["out"]["output_top_zip_path"],
235 self.out_log,
236 self.global_log,
237 )
238 fu.zip_top(
239 zip_file=self.io_dict["out"]["output_top_zip_path"],
240 top_file=str(Path(unique_dir_output_file)),
241 out_log=self.out_log,
242 remove_original_files=self.remove_tmp
243 )
245 self.tmp_files.extend([top_dir, u_dir])
246 self.remove_tmp_files()
248 self.check_arguments(output_files_created=True, raise_exception=False)
249 return self.return_code
252def pmxgentop(
253 input_top_zip_path: str,
254 output_top_zip_path: str,
255 properties: Optional[dict] = None,
256 **kwargs,
257) -> int:
258 """Create the :class:`Pmxgentop <pmx.pmxgentop.Pmxgentop>` class and
259 execute the :meth:`launch() <pmx.pmxgentop.Pmxgentop.launch> method."""
260 return Pmxgentop(**dict(locals())).launch()
263pmxgentop.__doc__ = Pmxgentop.__doc__
264main = Pmxgentop.get_main(pmxgentop, "Wrapper class for the PMX gentop module")
266if __name__ == "__main__":
267 main()