Coverage for biobb_analysis/ambertools/cpptraj_slice.py: 82%
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« prev ^ index » next coverage.py v7.5.1, created at 2024-05-06 15:22 +0000
1#!/usr/bin/env python3
3"""Module containing the Cpptraj Slice class and the command line interface."""
4import argparse
5from pathlib import PurePath
6from biobb_common.generic.biobb_object import BiobbObject
7from biobb_common.configuration import settings
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_out_parameters, get_negative_mask, copy_instructions_file_to_container
13class CpptrajSlice(BiobbObject):
14 """
15 | biobb_analysis CpptrajSlice
16 | Wrapper of the Ambertools Cpptraj module for extracting a particular trajectory slice 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://amber-md.github.io/cpptraj/CPPTRAJ.xhtml>`_.
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.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).
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 * **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_slice import cpptraj_slice
43 prop = {
44 'start': 1,
45 'end': -1,
46 'steps': 1,
47 'mask': 'c-alpha',
48 'format': 'netcdf'
49 }
50 cpptraj_slice(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: >=20.0
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_properties(properties)
92 self.check_arguments()
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 = str(PurePath(fu.create_unique_dir()).joinpath(self.instructions_file))
110 fu.create_name(prefix=self.prefix, step=self.step, name=self.instructions_file)
112 # parm
113 instructions_list.append('parm ' + container_io_dict["in"]["input_top_path"])
115 # trajin
116 in_params = get_in_parameters(self.in_parameters, out_log)
117 instructions_list.append('trajin ' + container_io_dict["in"]["input_traj_path"] + ' ' + in_params)
119 # mask
120 mask = self.in_parameters.get('mask', '')
121 if mask:
122 strip_mask = get_negative_mask(mask, out_log)
123 instructions_list.append('strip ' + strip_mask)
125 # trajout
126 out_params = get_out_parameters(self.out_parameters, out_log)
127 instructions_list.append('trajout ' + container_io_dict["out"]["output_cpptraj_path"] + ' ' + out_params)
129 # create .in file
130 with open(self.instructions_file, 'w') as mdp:
131 for line in instructions_list:
132 mdp.write(line.strip() + '\n')
134 return self.instructions_file
136 @launchlogger
137 def launch(self) -> int:
138 """Execute the :class:`CpptrajSlice <ambertools.cpptraj_slice.CpptrajSlice>` ambertools.cpptraj_slice.CpptrajSlice object."""
140 # check input/output paths and parameters
141 self.check_data_params(self.out_log, self.err_log)
143 # Setup Biobb
144 if self.check_restart():
145 return 0
146 self.stage_files()
148 # create instructions file
149 self.create_instructions_file(self.stage_io_dict, self.out_log, self.err_log)
151 # if container execution, copy intructions file to container
152 if self.container_path:
153 copy_instructions_file_to_container(self.instructions_file, self.stage_io_dict['unique_dir'])
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.tmp_files.extend([
166 self.stage_io_dict.get("unique_dir"),
167 PurePath(self.instructions_file).parent
168 ])
169 self.remove_tmp_files()
171 self.check_arguments(output_files_created=True, raise_exception=False)
173 return self.return_code
176def cpptraj_slice(input_top_path: str, input_traj_path: str, output_cpptraj_path: str, properties: dict = None, **kwargs) -> int:
177 """Execute the :class:`CpptrajSlice <ambertools.cpptraj_slice.CpptrajSlice>` class and
178 execute the :meth:`launch() <ambertools.cpptraj_slice.CpptrajSlice.launch>` method."""
180 return CpptrajSlice(input_top_path=input_top_path,
181 input_traj_path=input_traj_path,
182 output_cpptraj_path=output_cpptraj_path,
183 properties=properties, **kwargs).launch()
186def main():
187 """Command line execution of this building block. Please check the command line documentation."""
188 parser = argparse.ArgumentParser(description="Extracts a particular trajectory slice from a given cpptraj compatible trajectory.", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
189 parser.add_argument('--config', required=False, help='Configuration file')
191 # Specific args of each building block
192 required_args = parser.add_argument_group('required arguments')
193 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.')
194 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.')
195 required_args.add_argument('--output_cpptraj_path', required=True, help='Path to the output processed trajectory.')
197 args = parser.parse_args()
198 args.config = args.config or "{}"
199 properties = settings.ConfReader(config=args.config).get_prop_dic()
201 # Specific call of each building block
202 cpptraj_slice(input_top_path=args.input_top_path,
203 input_traj_path=args.input_traj_path,
204 output_cpptraj_path=args.output_cpptraj_path,
205 properties=properties)
208if __name__ == '__main__':
209 main()