Coverage for biobb_analysis/ambertools/cpptraj_image.py: 96%
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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 Image 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_mask, get_negative_mask, get_out_parameters
12class CpptrajImage(BiobbObject):
13 """
14 | biobb_analysis CpptrajImage
15 | Wrapper of the Ambertools Cpptraj module for correcting periodicity (image) from a given cpptraj trajectory file.
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 trajectory. File type: output. `Sample file <https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/reference/ambertools/ref_cpptraj.image.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).
22 properties (dic - Python dictionary object containing the tool parameters, not input/output files):
23 * **start** (*int*) - (1) [1~100000|1] Starting frame for slicing.
24 * **end** (*int*) - (-1) [-1~100000|1] Ending frame for slicing.
25 * **steps** (*int*) - (1) [1~100000|1] Step for slicing.
26 * **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 `@*`).
27 * **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), nc (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), 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).
28 * **binary_path** (*str*) - ("cpptraj") Path to the cpptraj executable binary.
29 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
30 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
31 * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
32 * **container_path** (*str*) - (None) Container path definition.
33 * **container_image** (*str*) - ('afandiadib/ambertools:serial') Container image definition.
34 * **container_volume_path** (*str*) - ('/tmp') Container volume path definition.
35 * **container_working_dir** (*str*) - (None) Container working directory definition.
36 * **container_user_id** (*str*) - (None) Container user_id definition.
37 * **container_shell_path** (*str*) - ('/bin/bash') Path to default shell inside the container.
39 Examples:
40 This is a use example of how to use the building block from Python::
42 from biobb_analysis.ambertools.cpptraj_image import cpptraj_image
43 prop = {
44 'start': 1,
45 'end': -1,
46 'steps': 1,
47 'mask': 'c-alpha',
48 'format': 'netcdf'
49 }
50 cpptraj_image(input_top_path='/path/to/myTopology.top',
51 input_traj_path='/path/to/myTrajectory.dcd',
52 output_cpptraj_path='/path/to/newTrajectory.netcdf',
53 properties=prop)
55 Info:
56 * wrapped_software:
57 * name: Ambertools Cpptraj
58 * version: >=22.5
59 * license: GNU
60 * ontology:
61 * name: EDAM
62 * schema: http://edamontology.org/EDAM.owl
64 """
66 def __init__(self, input_top_path, input_traj_path, output_cpptraj_path,
67 properties=None, **kwargs) -> None:
68 properties = properties or {}
70 # Call parent class constructor
71 super().__init__(properties)
72 self.locals_var_dict = locals().copy()
74 # Input/Output files
75 self.io_dict = {
76 "in": {"input_top_path": input_top_path, "input_traj_path": input_traj_path},
77 "out": {"output_cpptraj_path": output_cpptraj_path}
78 }
80 # Properties specific for BB
81 self.instructions_file = get_default_value('instructions_file')
82 self.start = properties.get('start', 1)
83 self.end = properties.get('end', -1)
84 self.steps = properties.get('steps', 1)
85 self.mask = properties.get('mask', 'all-atoms')
86 self.format = properties.get('format', 'netcdf')
87 self.properties = properties
88 self.binary_path = get_binary_path(properties, 'binary_path')
90 # Check the properties
91 self.check_init(properties)
93 def check_data_params(self, out_log, err_log):
94 """ Checks all the input/output paths and parameters """
95 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__)
96 self.io_dict["in"]["input_traj_path"] = check_traj_path(self.io_dict["in"]["input_traj_path"], out_log, self.__class__.__name__)
97 self.io_dict["out"]["output_cpptraj_path"] = check_out_path(self.io_dict["out"]["output_cpptraj_path"], out_log, self.__class__.__name__)
98 self.in_parameters = {'start': self.start, 'end': self.end, 'step': self.steps, 'mask': self.mask}
99 self.out_parameters = {'format': self.format}
101 def create_instructions_file(self, container_io_dict, out_log, err_log):
102 """Creates an input file using the properties file settings"""
103 instructions_list = []
104 # different path if container execution or not
105 if self.container_path:
106 self.instructions_file = str(PurePath(self.container_volume_path).joinpath(self.instructions_file))
107 else:
108 self.instructions_file = self.create_tmp_file(self.instructions_file)
110 # parm
111 instructions_list.append('parm ' + container_io_dict["in"]["input_top_path"])
113 # trajin
114 in_params = get_in_parameters(self.in_parameters, out_log)
115 instructions_list.append('trajin ' + container_io_dict["in"]["input_traj_path"] + ' ' + in_params)
117 # image
118 mask_atoms = get_mask('heavy-atoms', out_log)
119 instructions_list.append('center ' + mask_atoms + ' origin')
120 instructions_list.append('autoimage')
121 instructions_list.append('rms first ' + mask_atoms)
123 # mask
124 mask = self.in_parameters.get('mask', '')
125 if mask:
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:`CpptrajImage <ambertools.cpptraj_image.CpptrajImage>` 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_image(input_top_path: str, input_traj_path: str, output_cpptraj_path: str, properties: Optional[dict] = None, **kwargs) -> int:
172 """Execute the :class:`CpptrajImage <ambertools.cpptraj_image.CpptrajImage>` class and
173 execute the :meth:`launch() <ambertools.cpptraj_image.CpptrajImage.launch>` method."""
174 return CpptrajImage(**dict(locals())).launch()
177cpptraj_image.__doc__ = CpptrajImage.__doc__
178main = CpptrajImage.get_main(cpptraj_image, "Corrects periodicity (image) from a given cpptraj trajectory file.")
180if __name__ == '__main__':
181 main()