Coverage for biobb_analysis/ambertools/cpptraj_dry.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 Dry 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_mask, get_negative_mask, copy_instructions_file_to_container, get_out_parameters
13class CpptrajDry(BiobbObject):
14 """
15 | biobb_analysis CpptrajDry
16 | Wrapper of the Ambertools Cpptraj module for dehydrating a given cpptraj compatible trajectory stripping out solvent molecules and ions.
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.dry.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_dry import cpptraj_dry
43 prop = {
44 'start': 1,
45 'end': -1,
46 'steps': 1,
47 'mask': 'c-alpha',
48 'format': 'netcdf'
49 }
50 cpptraj_dry(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 # dry
120 mask_dry1 = get_negative_mask('solute', out_log)
121 instructions_list.append('strip ' + mask_dry1)
122 mask_dry2 = get_mask('heavy-atoms', out_log)
123 instructions_list.append('strip ' + mask_dry2)
125 # mask
126 mask = self.in_parameters.get('mask', '')
127 if mask:
128 strip_mask = get_negative_mask(mask, out_log)
129 instructions_list.append('strip ' + strip_mask)
131 # trajout
132 out_params = get_out_parameters(self.out_parameters, out_log)
133 instructions_list.append('trajout ' + container_io_dict["out"]["output_cpptraj_path"] + ' ' + out_params)
135 # create .in file
136 with open(self.instructions_file, 'w') as mdp:
137 for line in instructions_list:
138 mdp.write(line.strip() + '\n')
140 return self.instructions_file
142 @launchlogger
143 def launch(self) -> int:
144 """Execute the :class:`CpptrajDry <ambertools.cpptraj_dry.CpptrajDry>` ambertools.cpptraj_dry.CpptrajDry object."""
146 # check input/output paths and parameters
147 self.check_data_params(self.out_log, self.err_log)
149 # Setup Biobb
150 if self.check_restart():
151 return 0
152 self.stage_files()
154 # create instructions file
155 self.create_instructions_file(self.stage_io_dict, self.out_log, self.err_log)
157 # if container execution, copy intructions file to container
158 if self.container_path:
159 copy_instructions_file_to_container(self.instructions_file, self.stage_io_dict['unique_dir'])
161 # create cmd and launch execution
162 self.cmd = [self.binary_path, '-i', self.instructions_file]
164 # Run Biobb block
165 self.run_biobb()
167 # Copy files to host
168 self.copy_to_host()
170 # remove temporary folder(s)
171 self.tmp_files.extend([
172 self.stage_io_dict.get("unique_dir"),
173 PurePath(self.instructions_file).parent
174 ])
175 self.remove_tmp_files()
177 self.check_arguments(output_files_created=True, raise_exception=False)
179 return self.return_code
182def cpptraj_dry(input_top_path: str, input_traj_path: str, output_cpptraj_path: str, properties: dict = None, **kwargs) -> int:
183 """Execute the :class:`CpptrajDry <ambertools.cpptraj_dry.CpptrajDry>` class and
184 execute the :meth:`launch() <ambertools.cpptraj_dry.CpptrajDry.launch>` method."""
186 return CpptrajDry(input_top_path=input_top_path,
187 input_traj_path=input_traj_path,
188 output_cpptraj_path=output_cpptraj_path,
189 properties=properties, **kwargs).launch()
192def main():
193 """Command line execution of this building block. Please check the command line documentation."""
194 parser = argparse.ArgumentParser(description="Dehydrates a given cpptraj compatible trajectory stripping out solvent molecules and ions.", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
195 parser.add_argument('--config', required=False, help='Configuration file')
197 # Specific args of each building block
198 required_args = parser.add_argument_group('required arguments')
199 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.')
200 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.')
201 required_args.add_argument('--output_cpptraj_path', required=True, help='Path to the output processed trajectory.')
203 args = parser.parse_args()
204 args.config = args.config or "{}"
205 properties = settings.ConfReader(config=args.config).get_prop_dic()
207 # Specific call of each building block
208 cpptraj_dry(input_top_path=args.input_top_path,
209 input_traj_path=args.input_traj_path,
210 output_cpptraj_path=args.output_cpptraj_path,
211 properties=properties)
214if __name__ == '__main__':
215 main()