Coverage for biobb_analysis/ambertools/cpptraj_snapshot.py: 95%
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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 Snapshot 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.file_utils import launchlogger
9from biobb_analysis.ambertools.common import get_default_value, check_top_path, check_traj_path, check_out_path, get_binary_path, get_in_parameters, get_out_parameters, get_negative_mask
12class CpptrajSnapshot(BiobbObject):
13 """
14 | biobb_analysis CpptrajSnapshot
15 | Wrapper of the Ambertools Cpptraj module for extracting a particular snapshot from a given cpptraj compatible trajectory.
16 | 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>`_.
18 Args:
19 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).
20 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).
21 output_cpptraj_path (str): Path to the output processed structure. File type: output. `Sample file <https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/reference/ambertools/ref_cpptraj.snapshot.pdb>`_. 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).
22 properties (dic - Python dictionary object containing the tool parameters, not input/output files):
23 * **snapshot** (*int*) - (1) [1~100000|1] Frame to be captured for snapshot
24 * **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 `@*`).
25 * **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).
26 * **binary_path** (*str*) - ("cpptraj") Path to the cpptraj executable binary.
27 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
28 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
29 * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
30 * **container_path** (*str*) - (None) Container path definition.
31 * **container_image** (*str*) - ('afandiadib/ambertools:serial') Container image definition.
32 * **container_volume_path** (*str*) - ('/tmp') Container volume path definition.
33 * **container_working_dir** (*str*) - (None) Container working directory definition.
34 * **container_user_id** (*str*) - (None) Container user_id definition.
35 * **container_shell_path** (*str*) - ('/bin/bash') Path to default shell inside the container.
37 Examples:
38 This is a use example of how to use the building block from Python::
40 from biobb_analysis.ambertools.cpptraj_snapshot import cpptraj_snapshot
41 prop = {
42 'snapshot': 12,
43 'mask': 'c-alpha',
44 'format': 'pdb'
45 }
46 cpptraj_snapshot(input_top_path='/path/to/myTopology.top',
47 input_traj_path='/path/to/myTrajectory.dcd',
48 output_cpptraj_path='/path/to/newStructure.pdb',
49 properties=prop)
51 Info:
52 * wrapped_software:
53 * name: Ambertools Cpptraj
54 * version: >=22.5
55 * license: GNU
56 * ontology:
57 * name: EDAM
58 * schema: http://edamontology.org/EDAM.owl
60 """
62 def __init__(self, input_top_path, input_traj_path, output_cpptraj_path,
63 properties=None, **kwargs) -> None:
64 properties = properties or {}
66 # Call parent class constructor
67 super().__init__(properties)
68 self.locals_var_dict = locals().copy()
70 # Input/Output files
71 self.io_dict = {
72 "in": {"input_top_path": input_top_path, "input_traj_path": input_traj_path},
73 "out": {"output_cpptraj_path": output_cpptraj_path}
74 }
76 # Properties specific for BB
77 self.instructions_file = get_default_value('instructions_file')
78 self.snapshot = properties.get('snapshot', 1)
79 self.mask = properties.get('mask', 'all-atoms')
80 self.format = properties.get('format', 'netcdf')
81 self.properties = properties
82 self.binary_path = get_binary_path(properties, 'binary_path')
84 # Check the properties
85 self.check_init(properties)
87 def check_data_params(self, out_log, err_log):
88 """ Checks all the input/output paths and parameters """
89 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__)
90 self.io_dict["in"]["input_traj_path"] = check_traj_path(self.io_dict["in"]["input_traj_path"], out_log, self.__class__.__name__)
91 self.io_dict["out"]["output_cpptraj_path"] = check_out_path(self.io_dict["out"]["output_cpptraj_path"], out_log, self.__class__.__name__)
92 self.in_parameters = {'snapshot': self.snapshot, 'mask': self.mask}
93 self.out_parameters = {'format': self.format}
95 def create_instructions_file(self, container_io_dict, out_log, err_log):
96 """Creates an input file using the properties file settings"""
97 instructions_list = []
98 # different path if container execution or not
99 if self.container_path:
100 self.instructions_file = str(PurePath(self.container_volume_path).joinpath(self.instructions_file))
101 else:
102 self.instructions_file = self.create_tmp_file(self.instructions_file)
104 # parm
105 instructions_list.append('parm ' + container_io_dict["in"]["input_top_path"])
107 # trajin
108 in_params = get_in_parameters(self.in_parameters, out_log, 'snapshot')
109 instructions_list.append('trajin ' + container_io_dict["in"]["input_traj_path"] + ' ' + in_params)
111 # mask
112 mask = self.in_parameters.get('mask', '')
113 if mask:
114 strip_mask = get_negative_mask(mask, out_log)
115 instructions_list.append('strip ' + strip_mask)
117 # trajout
118 out_params = get_out_parameters(self.out_parameters, out_log)
119 instructions_list.append('trajout ' + container_io_dict["out"]["output_cpptraj_path"] + ' ' + out_params)
121 # create .in file
122 with open(self.instructions_file, 'w') as mdp:
123 for line in instructions_list:
124 mdp.write(line.strip() + '\n')
126 return self.instructions_file
128 @launchlogger
129 def launch(self) -> int:
130 """Execute the :class:`CpptrajSnapshot <ambertools.cpptraj_snapshot.CpptrajSnapshot>` object."""
132 # check input/output paths and parameters
133 self.check_data_params(self.out_log, self.err_log)
135 # Setup Biobb
136 if self.check_restart():
137 return 0
138 self.stage_files()
140 # create instructions file
141 self.create_instructions_file(self.stage_io_dict, self.out_log, self.err_log)
143 # create cmd and launch execution
144 self.cmd = [self.binary_path, '-i', self.instructions_file]
146 # Run Biobb block
147 self.run_biobb()
149 # Copy files to host
150 self.copy_to_host()
152 # remove temporary folder(s)
153 self.remove_tmp_files()
154 self.check_arguments(output_files_created=True, raise_exception=False)
156 return self.return_code
159def cpptraj_snapshot(input_top_path: str, input_traj_path: str, output_cpptraj_path: str, properties: Optional[dict] = None, **kwargs) -> int:
160 """Execute the :class:`CpptrajSnapshot <ambertools.cpptraj_snapshot.CpptrajSnapshot>` class and
161 execute the :meth:`launch() <ambertools.cpptraj_snapshot.CpptrajSnapshot.launch>` method."""
162 return CpptrajSnapshot(**dict(locals())).launch()
165cpptraj_snapshot.__doc__ = CpptrajSnapshot.__doc__
166main = CpptrajSnapshot.get_main(cpptraj_snapshot, "Extracts a particular snapshot from a given cpptraj compatible trajectory.")
168if __name__ == '__main__':
169 main()