Coverage for biobb_analysis/ambertools/cpptraj_average.py: 83%
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1#!/usr/bin/env python3
3"""Module containing the Cpptraj Average 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, setup_structure, get_negative_mask, get_out_parameters, copy_instructions_file_to_container
14class CpptrajAverage(BiobbObject):
15 """
16 | biobb_analysis CpptrajAverage
17 | Wrapper of the Ambertools Cpptraj module for calculating a structure average of 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 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).
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_average import cpptraj_average
45 prop = {
46 'start': 1,
47 'end': -1,
48 'steps': 1,
49 'mask': 'c-alpha',
50 'format': 'pdb'
51 }
52 cpptraj_average(input_top_path='/path/to/myTopology.top',
53 input_traj_path='/path/to/myTrajectory.dcd',
54 output_cpptraj_path='/path/to/newStructure.pdb',
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 # Set up
122 instructions_list += setup_structure(self)
124 # mask
125 mask = self.in_parameters.get('mask', '')
126 if mask:
127 strip_mask = get_negative_mask(mask, out_log)
128 instructions_list.append('strip ' + strip_mask)
130 # output
131 out_params = get_out_parameters(self.out_parameters, out_log)
132 instructions_list.append('average ' + container_io_dict["out"]["output_cpptraj_path"] + ' ' + out_params)
134 # create .in file
135 with open(self.instructions_file, 'w') as mdp:
136 for line in instructions_list:
137 mdp.write(line.strip() + '\n')
139 return self.instructions_file
141 @launchlogger
142 def launch(self) -> int:
143 """Execute the :class:`CpptrajAverage <ambertools.cpptraj_average.CpptrajAverage>` ambertools.cpptraj_average.CpptrajAverage object."""
145 # check input/output paths and parameters
146 self.check_data_params(self.out_log, self.err_log)
148 # Setup Biobb
149 if self.check_restart():
150 return 0
151 self.stage_files()
153 # create instructions file
154 self.create_instructions_file(self.stage_io_dict, self.out_log, self.err_log)
156 # if container execution, copy intructions file to container
157 if self.container_path:
158 copy_instructions_file_to_container(self.instructions_file, self.stage_io_dict['unique_dir'])
160 # create cmd and launch execution
161 self.cmd = [self.binary_path, '-i', self.instructions_file]
163 # Run Biobb block
164 self.run_biobb()
166 # Copy files to host
167 self.copy_to_host()
169 # remove temporary folder(s)
170 self.tmp_files.extend([
171 self.stage_io_dict.get("unique_dir", ""),
172 str(PurePath(str(self.instructions_file)).parent)
173 ])
174 self.remove_tmp_files()
176 self.check_arguments(output_files_created=True, raise_exception=False)
178 return self.return_code
181def cpptraj_average(input_top_path: str, input_traj_path: str, output_cpptraj_path: str, properties: Optional[dict] = None, **kwargs) -> int:
182 """Execute the :class:`CpptrajAverage <ambertools.cpptraj_average.CpptrajAverage>` class and
183 execute the :meth:`launch() <ambertools.cpptraj_average.CpptrajAverage.launch>` method."""
185 return CpptrajAverage(input_top_path=input_top_path,
186 input_traj_path=input_traj_path,
187 output_cpptraj_path=output_cpptraj_path,
188 properties=properties, **kwargs).launch()
191def main():
192 """Command line execution of this building block. Please check the command line documentation."""
193 parser = argparse.ArgumentParser(description="Calculates a structure average of a given cpptraj compatible trajectory.", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
194 parser.add_argument('--config', required=False, help='Configuration file')
196 # Specific args of each building block
197 required_args = parser.add_argument_group('required arguments')
198 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.')
199 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.')
200 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.')
202 args = parser.parse_args()
203 args.config = args.config or "{}"
204 properties = settings.ConfReader(config=args.config).get_prop_dic()
206 # Specific call of each building block
207 cpptraj_average(input_top_path=args.input_top_path,
208 input_traj_path=args.input_traj_path,
209 output_cpptraj_path=args.output_cpptraj_path,
210 properties=properties)
213if __name__ == '__main__':
214 main()