Coverage for biobb_analysis/ambertools/cpptraj_snapshot.py: 94%
63 statements
« prev ^ index » next coverage.py v7.14.1, created at 2026-06-02 08:53 +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.stage_io_dict['unique_dir']).joinpath("cpptraj.in"))
101 self.instructions_file_path = str(PurePath(self.container_volume_path).joinpath("cpptraj.in"))
102 else:
103 self.instructions_file = self.create_tmp_file(self.instructions_file)
104 self.instructions_file_path = self.instructions_file
106 # parm
107 instructions_list.append('parm ' + container_io_dict["in"]["input_top_path"])
109 # trajin
110 in_params = get_in_parameters(self.in_parameters, out_log, 'snapshot')
111 instructions_list.append('trajin ' + container_io_dict["in"]["input_traj_path"] + ' ' + in_params)
113 # mask
114 mask = self.in_parameters.get('mask', '')
115 if mask:
116 strip_mask = get_negative_mask(mask, out_log)
117 instructions_list.append('strip ' + strip_mask)
119 # trajout
120 out_params = get_out_parameters(self.out_parameters, out_log)
121 instructions_list.append('trajout ' + container_io_dict["out"]["output_cpptraj_path"] + ' ' + out_params)
123 # create .in file
124 with open(self.instructions_file, 'w') as mdp:
125 for line in instructions_list:
126 mdp.write(line.strip() + '\n')
128 return self.instructions_file_path
130 @launchlogger
131 def launch(self) -> int:
132 """Execute the :class:`CpptrajSnapshot <ambertools.cpptraj_snapshot.CpptrajSnapshot>` object."""
134 # check input/output paths and parameters
135 self.check_data_params(self.out_log, self.err_log)
137 # Setup Biobb
138 if self.check_restart():
139 return 0
140 self.stage_files()
142 # create instructions file
143 self.create_instructions_file(self.stage_io_dict, self.out_log, self.err_log)
145 # create cmd and launch execution
146 self.cmd = [self.binary_path, '-i', self.instructions_file_path]
148 # Run Biobb block
149 self.run_biobb()
151 # Copy files to host
152 self.copy_to_host()
154 # remove temporary folder(s)
155 self.remove_tmp_files()
156 self.check_arguments(output_files_created=True, raise_exception=False)
158 return self.return_code
161def cpptraj_snapshot(input_top_path: str, input_traj_path: str, output_cpptraj_path: str, properties: Optional[dict] = None, **kwargs) -> int:
162 """Create the :class:`CpptrajSnapshot <ambertools.cpptraj_snapshot.CpptrajSnapshot>` class and
163 execute the :meth:`launch() <ambertools.cpptraj_snapshot.CpptrajSnapshot.launch>` method."""
164 return CpptrajSnapshot(**dict(locals())).launch()
167cpptraj_snapshot.__doc__ = CpptrajSnapshot.__doc__
168main = CpptrajSnapshot.get_main(cpptraj_snapshot, "Extracts a particular snapshot from a given cpptraj compatible trajectory.")
170if __name__ == '__main__':
171 main()