Coverage for biobb_amber / process / process_mdout.py: 86%
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« prev ^ index » next coverage.py v7.14.0, created at 2026-05-12 10:52 +0000
1#!/usr/bin/env python3
3"""Module containing the ProcessMDOut class and the command line interface."""
5import shutil
6import os
7from pathlib import Path, PurePath
8from typing import Optional
10from biobb_common.generic.biobb_object import BiobbObject
11from biobb_common.tools import file_utils as fu
12from biobb_common.tools.file_utils import launchlogger
14from biobb_amber.process.common import (
15 _from_string_to_list,
16 check_input_path,
17 check_output_path,
18)
21class ProcessMDOut(BiobbObject):
22 """
23 | biobb_amber.process.process_mdout ProcessMDOut
24 | Wrapper of the `AmberTools (AMBER MD Package) process_mdout tool <https://ambermd.org/AmberTools.php>`_ module.
25 | Parses the AMBER (sander) md output file (log) and dumps statistics that can then be plotted. Using the process_mdout.pl tool from the AmberTools MD package.
27 Args:
28 input_log_path (str): AMBER (sander) MD output (log) file. File type: input. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/data/process/sander.heat.log>`_. Accepted formats: log (edam:format_2330), out (edam:format_2330), txt (edam:format_2330), o (edam:format_2330).
29 output_dat_path (str): Dat output file containing data from the specified terms along the minimization process. File type: output. `Sample file <https://github.com/bioexcel/biobb_amber/raw/master/biobb_amber/test/reference/process/sander.md.temp.dat>`_. Accepted formats: dat (edam:format_1637), txt (edam:format_2330), csv (edam:format_3752).
30 properties (dic - Python dictionary object containing the tool parameters, not input/output files):
31 * **terms** (*list*) - (["ETOT"]) Statistics descriptors. Values: VOLUME, TSOLVENT, TSOLUTE, TEMP, PRES, ETOT, ESCF, EPTOT, EKTOT, EKCMT, DENSITY.
32 * **binary_path** (*str*) - ("process_mdout.perl") Path to the process_mdout.perl executable binary.
33 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
34 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
35 * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
36 * **container_path** (*str*) - (None) Container path definition.
37 * **container_image** (*str*) - ('afandiadib/ambertools:serial') Container image definition.
38 * **container_volume_path** (*str*) - ('/tmp') Container volume path definition.
39 * **container_working_dir** (*str*) - (None) Container working directory definition.
40 * **container_user_id** (*str*) - (None) Container user_id definition.
41 * **container_shell_path** (*str*) - ('/bin/bash') Path to default shell inside the container.
43 Examples:
44 This is a use example of how to use the building block from Python::
46 from biobb_amber.process.process_mdout import process_mdout
47 prop = {
48 'terms' : ['TEMP','VOLUME','DENSITY']
49 }
50 process_mdout(input_log_path='/path/to/ambermd.log',
51 output_dat_path='/path/to/newFeature.dat',
52 properties=prop)
54 Info:
55 * wrapped_software:
56 * name: AmberTools process_mdout
57 * version: >20.9
58 * license: LGPL 2.1
59 * ontology:
60 * name: EDAM
61 * schema: http://edamontology.org/EDAM.owl
63 """
65 def __init__(self, input_log_path: str, output_dat_path: str, properties, **kwargs):
66 properties = properties or {}
68 # Call parent class constructor
69 super().__init__(properties)
70 self.locals_var_dict = locals().copy()
72 # Input/Output files
73 self.io_dict = {
74 "in": {"input_log_path": input_log_path},
75 "out": {"output_dat_path": output_dat_path},
76 }
78 # Properties specific for BB
79 self.properties = properties
80 self.terms = _from_string_to_list(properties.get("terms", ["ETOT"]))
81 self.binary_path = properties.get("binary_path", "process_mdout.perl")
83 # Check the properties
84 self.check_properties(properties)
85 self.check_arguments()
87 def check_data_params(self, out_log, err_log):
88 """Checks input/output paths correctness"""
90 # Check input(s)
91 self.io_dict["in"]["input_log_path"] = check_input_path(
92 self.io_dict["in"]["input_log_path"],
93 "input_log_path",
94 False,
95 out_log,
96 self.__class__.__name__,
97 )
99 # Check output(s)
100 self.io_dict["out"]["output_dat_path"] = check_output_path(
101 self.io_dict["out"]["output_dat_path"],
102 "output_dat_path",
103 False,
104 out_log,
105 self.__class__.__name__,
106 )
108 @launchlogger
109 def launch(self):
110 """Launches the execution of the ProcessMDOut module."""
112 # check input/output paths and parameters
113 self.check_data_params(self.out_log, self.err_log)
115 # Setup Biobb
116 if self.check_restart():
117 return 0
118 self.stage_files()
120 is_docker = self.container_path and os.path.basename(str(self.container_path)).lower() == 'docker'
122 if not self.container_path or not is_docker:
123 # No container or Singularity: cd to tmp_folder so summary.* files land there
124 tmp_folder = fu.create_unique_dir()
125 fu.log("Creating %s temporary folder" % tmp_folder, self.out_log)
126 self.cmd = [
127 "cd",
128 tmp_folder,
129 ";",
130 self.binary_path,
131 str(Path(self.stage_io_dict["in"]["input_log_path"]).resolve()),
132 ]
133 else:
134 # Docker: working dir is handled via container_working_dir
135 tmp_folder = None
136 self.cmd = [self.binary_path, self.stage_io_dict["in"]["input_log_path"]]
138 if self.container_path:
139 if not self.container_working_dir:
140 fu.log('WARNING: container_working_dir property was not set. Defining it with the same value as container_volume_path', self.out_log, self.global_log)
141 self.container_working_dir = self.container_volume_path
143 # Run Biobb block
144 self.run_biobb()
146 # Copy files to host
147 self.copy_to_host()
149 if len(self.terms) == 1:
150 if self.container_path and is_docker:
151 shutil.copy(
152 PurePath(self.stage_io_dict["unique_dir"]).joinpath(
153 "summary." + self.terms[0]
154 ),
155 self.io_dict["out"]["output_dat_path"],
156 )
157 else:
158 shutil.copy(
159 PurePath(str(tmp_folder)).joinpath("summary." + self.terms[0]),
160 self.io_dict["out"]["output_dat_path"],
161 )
162 else:
163 if self.container_path and is_docker:
164 tmp = self.stage_io_dict["unique_dir"]
165 else:
166 tmp = tmp_folder
168 ene_dict = {}
169 for term in self.terms:
170 with open(str(tmp) + "/summary." + term) as fp:
171 for line in fp:
172 x = line.split()
173 if x:
174 if len(x) > 1:
175 ene_dict.setdefault(float(x[0]), {})[term] = x[1]
176 else:
177 ene_dict.setdefault(float(x[0]), {})[term] = "-"
179 with open(self.io_dict["out"]["output_dat_path"], "w") as fp_out:
180 fp_out.write("# TIME ")
181 for term in self.terms:
182 fp_out.write(term + " ")
183 fp_out.write("\n")
184 for key in sorted(ene_dict.keys()):
185 fp_out.write(str(key) + " ")
186 for term in self.terms:
187 fp_out.write(ene_dict[key][term] + " ")
188 fp_out.write("\n")
190 # remove temporary folder(s)
191 self.tmp_files.extend([
192 str(tmp_folder)
193 ] + list(Path().glob("summary*"))
194 )
195 self.remove_tmp_files()
197 self.check_arguments(output_files_created=True, raise_exception=False)
199 return self.return_code
202def process_mdout(
203 input_log_path: str,
204 output_dat_path: str,
205 properties: Optional[dict] = None,
206 **kwargs,
207) -> int:
208 """Create :class:`ProcessMDOut <process.process_mdout.ProcessMDOut>`process.process_mdout.ProcessMDOut class and
209 execute :meth:`launch() <process.process_mdout.ProcessMDOut.launch>` method"""
210 return ProcessMDOut(**dict(locals())).launch()
213process_mdout.__doc__ = ProcessMDOut.__doc__
215main = ProcessMDOut.get_main(process_mdout, "Parses the AMBER (sander) MD output file (log) and dumps statistics that can then be plotted. Using the process_mdout.pl tool from the AmberTools MD package.")
217if __name__ == "__main__":
218 main()