Coverage for biobb_analysis/ambertools/cpptraj_image.py: 83%
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1#!/usr/bin/env python3
3"""Module containing the Cpptraj Image 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_mask, get_negative_mask, copy_instructions_file_to_container, get_out_parameters
14class CpptrajImage(BiobbObject):
15 """
16 | biobb_analysis CpptrajImage
17 | Wrapper of the Ambertools Cpptraj module for correcting periodicity (image) from a given cpptraj trajectory file.
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.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).
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), 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).
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_image import cpptraj_image
45 prop = {
46 'start': 1,
47 'end': -1,
48 'steps': 1,
49 'mask': 'c-alpha',
50 'format': 'netcdf'
51 }
52 cpptraj_image(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 # image
122 mask_atoms = get_mask('heavy-atoms', out_log)
123 instructions_list.append('center ' + mask_atoms + ' origin')
124 instructions_list.append('autoimage')
125 instructions_list.append('rms first ' + mask_atoms)
127 # mask
128 mask = self.in_parameters.get('mask', '')
129 if mask:
130 strip_mask = get_negative_mask(mask, out_log)
131 instructions_list.append('strip ' + strip_mask)
133 # trajout
134 out_params = get_out_parameters(self.out_parameters, out_log)
135 instructions_list.append('trajout ' + container_io_dict["out"]["output_cpptraj_path"] + ' ' + out_params)
137 # create .in file
138 with open(self.instructions_file, 'w') as mdp:
139 for line in instructions_list:
140 mdp.write(line.strip() + '\n')
142 return self.instructions_file
144 @launchlogger
145 def launch(self) -> int:
146 """Execute the :class:`CpptrajImage <ambertools.cpptraj_image.CpptrajImage>` ambertools.cpptraj_image.CpptrajImage object."""
148 # check input/output paths and parameters
149 self.check_data_params(self.out_log, self.err_log)
151 # Setup Biobb
152 if self.check_restart():
153 return 0
154 self.stage_files()
156 # create instructions file
157 self.create_instructions_file(self.stage_io_dict, self.out_log, self.err_log)
159 # if container execution, copy intructions file to container
160 if self.container_path:
161 copy_instructions_file_to_container(self.instructions_file, self.stage_io_dict['unique_dir'])
163 # create cmd and launch execution
164 self.cmd = [self.binary_path, '-i', self.instructions_file]
166 # Run Biobb block
167 self.run_biobb()
169 # Copy files to host
170 self.copy_to_host()
172 # remove temporary folder(s)
173 self.tmp_files.extend([
174 self.stage_io_dict.get("unique_dir", ""),
175 str(PurePath(self.instructions_file).parent)
176 ])
177 self.remove_tmp_files()
179 self.check_arguments(output_files_created=True, raise_exception=False)
181 return self.return_code
184def cpptraj_image(input_top_path: str, input_traj_path: str, output_cpptraj_path: str, properties: Optional[dict] = None, **kwargs) -> int:
185 """Execute the :class:`CpptrajImage <ambertools.cpptraj_image.CpptrajImage>` class and
186 execute the :meth:`launch() <ambertools.cpptraj_image.CpptrajImage.launch>` method."""
188 return CpptrajImage(input_top_path=input_top_path,
189 input_traj_path=input_traj_path,
190 output_cpptraj_path=output_cpptraj_path,
191 properties=properties, **kwargs).launch()
194def main():
195 """Command line execution of this building block. Please check the command line documentation."""
196 parser = argparse.ArgumentParser(description="Corrects periodicity (image) from a given cpptraj trajectory file.", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
197 parser.add_argument('--config', required=False, help='Configuration file')
199 # Specific args of each building block
200 required_args = parser.add_argument_group('required arguments')
201 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.')
202 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.')
203 required_args.add_argument('--output_cpptraj_path', required=True, help='Path to the output processed trajectory.')
205 args = parser.parse_args()
206 args.config = args.config or "{}"
207 properties = settings.ConfReader(config=args.config).get_prop_dic()
209 # Specific call of each building block
210 cpptraj_image(input_top_path=args.input_top_path,
211 input_traj_path=args.input_traj_path,
212 output_cpptraj_path=args.output_cpptraj_path,
213 properties=properties)
216if __name__ == '__main__':
217 main()