Coverage for biobb_analysis/ambertools/cpptraj_average.py: 83%
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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 Average 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, setup_structure, get_negative_mask, get_out_parameters, copy_instructions_file_to_container
13class CpptrajAverage(BiobbObject):
14 """
15 | biobb_analysis CpptrajAverage
16 | Wrapper of the Ambertools Cpptraj module for calculating a structure average of 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 structure. File type: output. `Sample file <https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/reference/ambertools/ref_cpptraj.average.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).
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_average import cpptraj_average
43 prop = {
44 'start': 1,
45 'end': -1,
46 'steps': 1,
47 'mask': 'c-alpha',
48 'format': 'pdb'
49 }
50 cpptraj_average(input_top_path='/path/to/myTopology.top',
51 input_traj_path='/path/to/myTrajectory.dcd',
52 output_cpptraj_path='/path/to/newStructure.pdb',
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 # Set up
120 instructions_list += setup_structure(self)
122 # mask
123 mask = self.in_parameters.get('mask', '')
124 if mask:
125 strip_mask = get_negative_mask(mask, out_log)
126 instructions_list.append('strip ' + strip_mask)
128 # output
129 out_params = get_out_parameters(self.out_parameters, out_log)
130 instructions_list.append('average ' + container_io_dict["out"]["output_cpptraj_path"] + ' ' + out_params)
132 # create .in file
133 with open(self.instructions_file, 'w') as mdp:
134 for line in instructions_list:
135 mdp.write(line.strip() + '\n')
137 return self.instructions_file
139 @launchlogger
140 def launch(self) -> int:
141 """Execute the :class:`CpptrajAverage <ambertools.cpptraj_average.CpptrajAverage>` ambertools.cpptraj_average.CpptrajAverage object."""
143 # check input/output paths and parameters
144 self.check_data_params(self.out_log, self.err_log)
146 # Setup Biobb
147 if self.check_restart():
148 return 0
149 self.stage_files()
151 # create instructions file
152 self.create_instructions_file(self.stage_io_dict, self.out_log, self.err_log)
154 # if container execution, copy intructions file to container
155 if self.container_path:
156 copy_instructions_file_to_container(self.instructions_file, self.stage_io_dict['unique_dir'])
158 # create cmd and launch execution
159 self.cmd = [self.binary_path, '-i', self.instructions_file]
161 # Run Biobb block
162 self.run_biobb()
164 # Copy files to host
165 self.copy_to_host()
167 # remove temporary folder(s)
168 self.tmp_files.extend([
169 self.stage_io_dict.get("unique_dir"),
170 PurePath(self.instructions_file).parent
171 ])
172 self.remove_tmp_files()
174 self.check_arguments(output_files_created=True, raise_exception=False)
176 return self.return_code
179def cpptraj_average(input_top_path: str, input_traj_path: str, output_cpptraj_path: str, properties: dict = None, **kwargs) -> int:
180 """Execute the :class:`CpptrajAverage <ambertools.cpptraj_average.CpptrajAverage>` class and
181 execute the :meth:`launch() <ambertools.cpptraj_average.CpptrajAverage.launch>` method."""
183 return CpptrajAverage(input_top_path=input_top_path,
184 input_traj_path=input_traj_path,
185 output_cpptraj_path=output_cpptraj_path,
186 properties=properties, **kwargs).launch()
189def main():
190 """Command line execution of this building block. Please check the command line documentation."""
191 parser = argparse.ArgumentParser(description="Calculates a structure average of a given cpptraj compatible trajectory.", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
192 parser.add_argument('--config', required=False, help='Configuration file')
194 # Specific args of each building block
195 required_args = parser.add_argument_group('required arguments')
196 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.')
197 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.')
198 required_args.add_argument('--output_cpptraj_path', required=True, help='Path to the output processed structure. Accepted formats: crd, netcdf, rst7, ncrst, dcd, pdb, mol2, binpos, trr, xtc, sqm.')
200 args = parser.parse_args()
201 args.config = args.config or "{}"
202 properties = settings.ConfReader(config=args.config).get_prop_dic()
204 # Specific call of each building block
205 cpptraj_average(input_top_path=args.input_top_path,
206 input_traj_path=args.input_traj_path,
207 output_cpptraj_path=args.output_cpptraj_path,
208 properties=properties)
211if __name__ == '__main__':
212 main()