Coverage for biobb_analysis/ambertools/cpptraj_mask.py: 93%
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« prev ^ index » next coverage.py v7.10.6, created at 2025-09-08 10:47 +0000
1#!/usr/bin/env python3
3"""Module containing the Cpptraj Mask class and the command line interface."""
5from typing import Optional
6from pathlib import PurePath
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
10from biobb_analysis.ambertools.common import get_default_value, check_top_path, check_traj_path, check_out_path, get_binary_path, get_in_parameters, get_negative_mask, get_out_parameters
13class CpptrajMask(BiobbObject):
14 """
15 | biobb_analysis CpptrajMask
16 | Wrapper of the Ambertools Cpptraj module for extracting a selection of atoms from a given cpptraj compatible trajectory.
17 | Cpptraj (the successor to ptraj) is the main program in Ambertools for processing coordinate trajectories and data files. The parameter names and defaults are the same as the ones in the official `Cpptraj manual <https://raw.githubusercontent.com/Amber-MD/cpptraj/master/doc/CpptrajManual.pdf>`_.
19 Args:
20 input_top_path (str): Path to the input structure or topology file. File type: input. `Sample file <https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/ambertools/cpptraj.parm.top>`_. Accepted formats: top (edam:format_3881), pdb (edam:format_1476), prmtop (edam:format_3881), parmtop (edam:format_3881), zip (edam:format_3987).
21 input_traj_path (str): Path to the input trajectory to be processed. File type: input. `Sample file <https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd>`_. Accepted formats: mdcrd (edam:format_3878), crd (edam:format_3878), cdf (edam:format_3650), netcdf (edam:format_3650), nc (edam:format_3650), restart (edam:format_3886), ncrestart (edam:format_3886), restartnc (edam:format_3886), dcd (edam:format_3878), charmm (edam:format_3887), cor (edam:format_2033), pdb (edam:format_1476), mol2 (edam:format_3816), trr (edam:format_3910), gro (edam:format_2033), binpos (edam:format_3885), xtc (edam:format_3875), cif (edam:format_1477), arc (edam:format_2333), sqm (edam:format_2033), sdf (edam:format_3814), conflib (edam:format_2033).
22 output_cpptraj_path (str): Path to the output processed trajectory. File type: output. `Sample file <https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/reference/ambertools/ref_cpptraj.mask.netcdf>`_. Accepted formats: mdcrd (edam:format_3878), crd (edam:format_3878), netcdf (edam:format_3650), nc (edam:format_3650), rst7 (edam:format_3886), ncrst (edam:format_2033), dcd (edam:format_3878), pdb (edam:format_1476), mol2 (edam:format_3816), binpos (edam:format_3885), trr (edam:format_3910), xtc (edam:format_3875), sqm (edam:format_2033).
23 properties (dic - Python dictionary object containing the tool parameters, not input/output files):
24 * **start** (*int*) - (1) [1~100000|1] Starting frame for slicing.
25 * **end** (*int*) - (-1) [-1~100000|1] Ending frame for slicing.
26 * **steps** (*int*) - (1) [1~100000|1] Step for slicing.
27 * **mask** (*str*) - ("all-atoms") Mask definition. Values: c-alpha (All c-alpha atoms; protein only), backbone (Backbone atoms), all-atoms (All system atoms), heavy-atoms (System heavy atoms; not hydrogen), side-chain (All not backbone atoms), solute (All system atoms except solvent atoms), ions (All ion molecules), solvent (All solvent atoms), AnyAmberFromatMask (Amber atom selection syntax like `@*`).
28 * **format** (*str*) - ("netcdf") Output trajectory format. Values: crd (AMBER trajectory format), cdf (Format used by netCDF software library for writing and reading chromatography-MS data files), netcdf (Format used by netCDF software library for writing and reading chromatography-MS data files), nc (Format used by netCDF software library for writing and reading chromatography-MS data files), restart (AMBER coordinate/restart file with 6 coordinates per line), ncrestart (AMBER coordinate/restart file with 6 coordinates per line), restartnc (AMBER coordinate/restart file with 6 coordinates per line), dcd (AMBER trajectory format), charmm (Format of CHARMM Residue Topology Files (RTF)), cor (Charmm COR), pdb (Protein Data Bank format), mol2 (Complete and portable representation of a SYBYL molecule), trr (Trajectory of a simulation experiment used by GROMACS), gro (GROMACS structure), binpos (Translation of the ASCII atom coordinate format to binary code), xtc (Portable binary format for trajectories produced by GROMACS package), cif (Entry format of PDB database in mmCIF format), arc (Tinker ARC), sqm (SQM Input), sdf (One of a family of chemical-data file formats developed by MDL Information Systems), conflib (LMOD Conflib).
29 * **binary_path** (*str*) - ("cpptraj") Path to the cpptraj executable binary.
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.
33 * **container_path** (*str*) - (None) Container path definition.
34 * **container_image** (*str*) - ('afandiadib/ambertools:serial') Container image definition.
35 * **container_volume_path** (*str*) - ('/tmp') Container volume path definition.
36 * **container_working_dir** (*str*) - (None) Container working directory definition.
37 * **container_user_id** (*str*) - (None) Container user_id definition.
38 * **container_shell_path** (*str*) - ('/bin/bash') Path to default shell inside the container.
40 Examples:
41 This is a use example of how to use the building block from Python::
43 from biobb_analysis.ambertools.cpptraj_mask import cpptraj_mask
44 prop = {
45 'start': 1,
46 'end': -1,
47 'steps': 1,
48 'mask': 'c-alpha',
49 'format': 'netcdf'
50 }
51 cpptraj_mask(input_top_path='/path/to/myTopology.top',
52 input_traj_path='/path/to/myTrajectory.dcd',
53 output_cpptraj_path='/path/to/newTrajectory.netcdf',
54 properties=prop)
56 Info:
57 * wrapped_software:
58 * name: Ambertools Cpptraj
59 * version: >=22.5
60 * license: GNU
61 * ontology:
62 * name: EDAM
63 * schema: http://edamontology.org/EDAM.owl
65 """
67 def __init__(self, input_top_path, input_traj_path, output_cpptraj_path,
68 properties=None, **kwargs) -> None:
69 properties = properties or {}
71 # Call parent class constructor
72 super().__init__(properties)
73 self.locals_var_dict = locals().copy()
75 # Input/Output files
76 self.io_dict = {
77 "in": {"input_top_path": input_top_path, "input_traj_path": input_traj_path},
78 "out": {"output_cpptraj_path": output_cpptraj_path}
79 }
81 # Properties specific for BB
82 self.instructions_file = get_default_value('instructions_file')
83 self.start = properties.get('start', 1)
84 self.end = properties.get('end', -1)
85 self.steps = properties.get('steps', 1)
86 self.mask = properties.get('mask', 'all-atoms')
87 self.format = properties.get('format', 'netcdf')
88 self.properties = properties
89 self.binary_path = get_binary_path(properties, 'binary_path')
91 # Check the properties
92 self.check_init(properties)
94 def check_data_params(self, out_log, err_log):
95 """ Checks all the input/output paths and parameters """
96 self.io_dict["in"]["input_top_path"], self.input_top_path_orig = check_top_path(self.io_dict["in"]["input_top_path"], out_log, self.__class__.__name__)
97 self.io_dict["in"]["input_traj_path"] = check_traj_path(self.io_dict["in"]["input_traj_path"], out_log, self.__class__.__name__)
98 self.io_dict["out"]["output_cpptraj_path"] = check_out_path(self.io_dict["out"]["output_cpptraj_path"], out_log, self.__class__.__name__)
99 self.in_parameters = {'start': self.start, 'end': self.end, 'step': self.steps, 'mask': self.mask}
100 self.out_parameters = {'format': self.format}
102 def create_instructions_file(self, container_io_dict, out_log, err_log):
103 """Creates an input file using the properties file settings"""
104 instructions_list = []
105 # different path if container execution or not
106 if self.container_path:
107 self.instructions_file = str(PurePath(self.container_volume_path).joinpath(self.instructions_file))
108 else:
109 self.instructions_file = self.create_tmp_file(self.instructions_file)
111 # parm
112 instructions_list.append('parm ' + container_io_dict["in"]["input_top_path"])
114 # trajin
115 in_parameters = self.in_parameters
116 in_params = ''
117 if in_parameters:
118 in_params = get_in_parameters(self.in_parameters, out_log, 'mask')
119 instructions_list.append('trajin ' + container_io_dict["in"]["input_traj_path"] + ' ' + in_params)
121 # mask
122 mask = self.in_parameters.get('mask', '')
123 if not mask or mask == 'None':
124 fu.log('No mask provided, exiting', out_log, self.global_log)
125 raise SystemExit('Mask parameter is mandatory')
126 strip_mask = get_negative_mask(mask, out_log)
127 instructions_list.append('strip ' + strip_mask)
129 # trajout
130 out_params = get_out_parameters(self.out_parameters, out_log)
131 instructions_list.append('trajout ' + container_io_dict["out"]["output_cpptraj_path"] + ' ' + out_params)
133 # create .in file
134 with open(self.instructions_file, 'w') as mdp:
135 for line in instructions_list:
136 mdp.write(line.strip() + '\n')
138 return self.instructions_file
140 @launchlogger
141 def launch(self) -> int:
142 """Execute the :class:`CpptrajMask <ambertools.cpptraj_mask.CpptrajMask>` object."""
144 # check input/output paths and parameters
145 self.check_data_params(self.out_log, self.err_log)
147 # Setup Biobb
148 if self.check_restart():
149 return 0
150 self.stage_files()
152 # create instructions file
153 self.create_instructions_file(self.stage_io_dict, self.out_log, self.err_log)
155 # create cmd and launch execution
156 self.cmd = [self.binary_path, '-i', self.instructions_file]
158 # Run Biobb block
159 self.run_biobb()
161 # Copy files to host
162 self.copy_to_host()
164 # remove temporary folder(s)
165 self.remove_tmp_files()
166 self.check_arguments(output_files_created=True, raise_exception=False)
168 return self.return_code
171def cpptraj_mask(input_top_path: str, input_traj_path: str, output_cpptraj_path: str, properties: Optional[dict] = None, **kwargs) -> int:
172 """Execute the :class:`CpptrajMask <ambertools.cpptraj_mask.CpptrajMask>` class and
173 execute the :meth:`launch() <ambertools.cpptraj_mask.CpptrajMask.launch>` method."""
174 return CpptrajMask(**dict(locals())).launch()
177cpptraj_mask.__doc__ = CpptrajMask.__doc__
178main = CpptrajMask.get_main(cpptraj_mask, "Extracts a selection of atoms from a given cpptraj compatible trajectory.")
180if __name__ == '__main__':
181 main()