Coverage for biobb_analysis/ambertools/cpptraj_slice.py: 82%
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1#!/usr/bin/env python3
3"""Module containing the Cpptraj Slice class and the command line interface."""
4import argparse
5from typing import Optional
6from pathlib import PurePath
7from biobb_common.generic.biobb_object import BiobbObject
8from biobb_common.configuration import settings
9from biobb_common.tools import file_utils as fu
10from biobb_common.tools.file_utils import launchlogger
11from 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, copy_instructions_file_to_container
14class CpptrajSlice(BiobbObject):
15 """
16 | biobb_analysis CpptrajSlice
17 | Wrapper of the Ambertools Cpptraj module for extracting a particular trajectory slice from a given cpptraj compatible trajectory.
18 | 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://amber-md.github.io/cpptraj/CPPTRAJ.xhtml>`_.
20 Args:
21 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).
22 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).
23 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.slice.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).
24 properties (dic - Python dictionary object containing the tool parameters, not input/output files):
25 * **start** (*int*) - (1) [1~100000|1] Starting frame for slicing.
26 * **end** (*int*) - (-1) [-1~100000|1] Ending frame for slicing.
27 * **steps** (*int*) - (1) [1~100000|1] Step for slicing.
28 * **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 `@*`).
29 * **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).
30 * **binary_path** (*str*) - ("cpptraj") Path to the cpptraj executable binary.
31 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
32 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
33 * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
34 * **container_path** (*str*) - (None) Container path definition.
35 * **container_image** (*str*) - ('afandiadib/ambertools:serial') Container image definition.
36 * **container_volume_path** (*str*) - ('/tmp') Container volume path definition.
37 * **container_working_dir** (*str*) - (None) Container working directory definition.
38 * **container_user_id** (*str*) - (None) Container user_id definition.
39 * **container_shell_path** (*str*) - ('/bin/bash') Path to default shell inside the container.
41 Examples:
42 This is a use example of how to use the building block from Python::
44 from biobb_analysis.ambertools.cpptraj_slice import cpptraj_slice
45 prop = {
46 'start': 1,
47 'end': -1,
48 'steps': 1,
49 'mask': 'c-alpha',
50 'format': 'netcdf'
51 }
52 cpptraj_slice(input_top_path='/path/to/myTopology.top',
53 input_traj_path='/path/to/myTrajectory.dcd',
54 output_cpptraj_path='/path/to/newTrajectory.netcdf',
55 properties=prop)
57 Info:
58 * wrapped_software:
59 * name: Ambertools Cpptraj
60 * version: >=20.0
61 * license: GNU
62 * ontology:
63 * name: EDAM
64 * schema: http://edamontology.org/EDAM.owl
66 """
68 def __init__(self, input_top_path, input_traj_path, output_cpptraj_path,
69 properties=None, **kwargs) -> None:
70 properties = properties or {}
72 # Call parent class constructor
73 super().__init__(properties)
74 self.locals_var_dict = locals().copy()
76 # Input/Output files
77 self.io_dict = {
78 "in": {"input_top_path": input_top_path, "input_traj_path": input_traj_path},
79 "out": {"output_cpptraj_path": output_cpptraj_path}
80 }
82 # Properties specific for BB
83 self.instructions_file = get_default_value('instructions_file')
84 self.start = properties.get('start', 1)
85 self.end = properties.get('end', -1)
86 self.steps = properties.get('steps', 1)
87 self.mask = properties.get('mask', 'all-atoms')
88 self.format = properties.get('format', 'netcdf')
89 self.properties = properties
90 self.binary_path = get_binary_path(properties, 'binary_path')
92 # Check the properties
93 self.check_properties(properties)
94 self.check_arguments()
96 def check_data_params(self, out_log, err_log):
97 """ Checks all the input/output paths and parameters """
98 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__)
99 self.io_dict["in"]["input_traj_path"] = check_traj_path(self.io_dict["in"]["input_traj_path"], out_log, self.__class__.__name__)
100 self.io_dict["out"]["output_cpptraj_path"] = check_out_path(self.io_dict["out"]["output_cpptraj_path"], out_log, self.__class__.__name__)
101 self.in_parameters = {'start': self.start, 'end': self.end, 'step': self.steps, 'mask': self.mask}
102 self.out_parameters = {'format': self.format}
104 def create_instructions_file(self, container_io_dict, out_log, err_log):
105 """Creates an input file using the properties file settings"""
106 instructions_list = []
107 # different path if container execution or not
108 if self.container_path:
109 self.instructions_file = str(PurePath(self.container_volume_path).joinpath(self.instructions_file))
110 else:
111 self.instructions_file = str(PurePath(fu.create_unique_dir()).joinpath(self.instructions_file))
112 fu.create_name(prefix=self.prefix, step=self.step, name=self.instructions_file)
114 # parm
115 instructions_list.append('parm ' + container_io_dict["in"]["input_top_path"])
117 # trajin
118 in_params = get_in_parameters(self.in_parameters, out_log)
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 mask:
124 strip_mask = get_negative_mask(mask, out_log)
125 instructions_list.append('strip ' + strip_mask)
127 # trajout
128 out_params = get_out_parameters(self.out_parameters, out_log)
129 instructions_list.append('trajout ' + container_io_dict["out"]["output_cpptraj_path"] + ' ' + out_params)
131 # create .in file
132 with open(self.instructions_file, 'w') as mdp:
133 for line in instructions_list:
134 mdp.write(line.strip() + '\n')
136 return self.instructions_file
138 @launchlogger
139 def launch(self) -> int:
140 """Execute the :class:`CpptrajSlice <ambertools.cpptraj_slice.CpptrajSlice>` ambertools.cpptraj_slice.CpptrajSlice object."""
142 # check input/output paths and parameters
143 self.check_data_params(self.out_log, self.err_log)
145 # Setup Biobb
146 if self.check_restart():
147 return 0
148 self.stage_files()
150 # create instructions file
151 self.create_instructions_file(self.stage_io_dict, self.out_log, self.err_log)
153 # if container execution, copy intructions file to container
154 if self.container_path:
155 copy_instructions_file_to_container(self.instructions_file, self.stage_io_dict['unique_dir'])
157 # create cmd and launch execution
158 self.cmd = [self.binary_path, '-i', self.instructions_file]
160 # Run Biobb block
161 self.run_biobb()
163 # Copy files to host
164 self.copy_to_host()
166 # remove temporary folder(s)
167 self.tmp_files.extend([
168 self.stage_io_dict.get("unique_dir", ""),
169 str(PurePath(self.instructions_file).parent)
170 ])
171 self.remove_tmp_files()
173 self.check_arguments(output_files_created=True, raise_exception=False)
175 return self.return_code
178def cpptraj_slice(input_top_path: str, input_traj_path: str, output_cpptraj_path: str, properties: Optional[dict] = None, **kwargs) -> int:
179 """Execute the :class:`CpptrajSlice <ambertools.cpptraj_slice.CpptrajSlice>` class and
180 execute the :meth:`launch() <ambertools.cpptraj_slice.CpptrajSlice.launch>` method."""
182 return CpptrajSlice(input_top_path=input_top_path,
183 input_traj_path=input_traj_path,
184 output_cpptraj_path=output_cpptraj_path,
185 properties=properties, **kwargs).launch()
188def main():
189 """Command line execution of this building block. Please check the command line documentation."""
190 parser = argparse.ArgumentParser(description="Extracts a particular trajectory slice from a given cpptraj compatible trajectory.", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
191 parser.add_argument('--config', required=False, help='Configuration file')
193 # Specific args of each building block
194 required_args = parser.add_argument_group('required arguments')
195 required_args.add_argument('--input_top_path', required=True, help='Path to the input structure or topology file. Accepted formats: top, pdb, prmtop, parmtop, zip.')
196 required_args.add_argument('--input_traj_path', required=True, help='Path to the input trajectory to be processed. Accepted formats: crd, cdf, netcdf, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib.')
197 required_args.add_argument('--output_cpptraj_path', required=True, help='Path to the output processed trajectory.')
199 args = parser.parse_args()
200 args.config = args.config or "{}"
201 properties = settings.ConfReader(config=args.config).get_prop_dic()
203 # Specific call of each building block
204 cpptraj_slice(input_top_path=args.input_top_path,
205 input_traj_path=args.input_traj_path,
206 output_cpptraj_path=args.output_cpptraj_path,
207 properties=properties)
210if __name__ == '__main__':
211 main()