Source code for gromacs.gmx_trjconv_str_ens

#!/usr/bin/env python3

"""Module containing the GMX TrjConvStr class and the command line interface."""
import argparse
from biobb_common.generic.biobb_object import BiobbObject
from biobb_common.configuration import settings
from biobb_common.tools import file_utils as fu
from biobb_common.tools.file_utils import launchlogger
from biobb_analysis.gromacs.common import *


[docs]class GMXTrjConvStrEns(BiobbObject): """ | biobb_analysis GMXTrjConvStrEns | Wrapper of the GROMACS trjconv module for extracting an ensemble of frames containing a selection of atoms from GROMACS compatible trajectory files. | GROMACS trjconv module can convert trajectory files in many ways. See the `GROMACS trjconv <http://manual.gromacs.org/documentation/2018/onlinehelp/gmx-trjconv.html>`_ official documentation for further information. Args: input_traj_path (str): Path to the GROMACS trajectory file. File type: input. `Sample file <https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/gromacs/trajectory.trr>`_. Accepted formats: xtc (edam:format_3875), trr (edam:format_3910), cpt (edam:format_2333), gro (edam:format_2033), g96 (edam:format_2033), pdb (edam:format_1476), tng (edam:format_3876). input_top_path (str): Path to the GROMACS input topology file. File type: input. `Sample file <https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/gromacs/topology.tpr>`_. Accepted formats: tpr (edam:format_2333), gro (edam:format_2033), g96 (edam:format_2033), pdb (edam:format_1476), brk (edam:format_2033), ent (edam:format_1476). input_index_path (str) (Optional): Path to the GROMACS index file. File type: input. `Sample file <https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/gromacs/index.ndx>`_. Accepted formats: ndx (edam:format_2033). output_str_ens_path (str): Path to the output file. File type: output. `Sample file <https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/reference/gromacs/ref_trjconv.str.ens.zip>`_. Accepted formats: zip (edam:format_3987). properties (dic - Python dictionary object containing the tool parameters, not input/output files): * **selection** (*str*) - ("System") Group where the trjconv will be performed. If **input_index_path** provided, check the file for the accepted values. Values: System (all atoms in the system), Protein (all protein atoms), Protein-H (protein atoms excluding hydrogens), C-alpha (C-alpha atoms), Backbone (protein backbone atoms: N; C-alpha and C), MainChain (protein main chain atoms: N; C-alpha; C and O; including oxygens in C-terminus), MainChain+Cb (protein main chain atoms including C-beta), MainChain+H (protein main chain atoms including backbone amide hydrogens and hydrogens on the N-terminus), SideChain (protein side chain atoms: that is all atoms except N; C-alpha; C; O; backbone amide hydrogens and oxygens in C-terminus and hydrogens on the N-terminus), SideChain-H (protein side chain atoms excluding all hydrogens), Prot-Masses (protein atoms excluding dummy masses), non-Protein (all non-protein atoms), Water (water molecules), SOL (water molecules), non-Water (anything not covered by the Water group), Ion (any name matching an Ion entry in residuetypes.dat), NA (all NA atoms), CL (all CL atoms), Water_and_ions (combination of the Water and Ions groups). * **skip** (*int*) - (1) [0~10000|1] Only write every nr-th frame. * **start** (*int*) - (0) [0~10000|1] Time of first frame to read from trajectory (default unit ps). * **end** (*int*) - (0) [0~10000|1] Time of last frame to read from trajectory (default unit ps). * **dt** (*int*) - (0) [0~10000|1] Only write frame when t MOD dt = first time (ps). * **output_name** (*str*) - ("output") File name for ensemble of output files. * **output_type** (*str*) - ("pdb") File type for ensemble of output files. Values: gro (Contains a molecular structure in Gromos87 format), g96 (Can be a GROMOS-96 initial/final configuration file or a coordinate trajectory file or a combination of both), pdb (Molecular structure files in the protein databank file format). * **gmx_path** (*str*) - ("gmx") Path to the GROMACS executable binary. * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files. * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist. * **container_path** (*str*) - (None) Container path definition. * **container_image** (*str*) - ('gromacs/gromacs:latest') Container image definition. * **container_volume_path** (*str*) - ('/tmp') Container volume path definition. * **container_working_dir** (*str*) - (None) Container working directory definition. * **container_user_id** (*str*) - (None) Container user_id definition. * **container_shell_path** (*str*) - ('/bin/bash') Path to default shell inside the container. Examples: This is a use example of how to use the building block from Python:: from biobb_analysis.gromacs.gmx_trjconv_str_ens import gmx_trjconv_str_ens prop = { 'selection': 'System', 'start': 0, 'end': 10, 'dt': 1 } gmx_trjconv_str_ens(input_traj_path='/path/to/myStructure.trr', input_top_path='/path/to/myTopology.tpr', output_str_ens_path='/path/to/newStructureEnsemble.zip', input_index_path='/path/to/myIndex.ndx', properties=prop) Info: * wrapped_software: * name: GROMACS trjconv * version: >=2019.1 * license: LGPL 2.1 * ontology: * name: EDAM * schema: http://edamontology.org/EDAM.owl """ def __init__(self, input_traj_path, input_top_path, output_str_ens_path, input_index_path=None, properties=None, **kwargs) -> None: properties = properties or {} # Call parent class constructor super().__init__(properties) # Input/Output files self.io_dict = { "in": { "input_traj_path": input_traj_path, "input_top_path": input_top_path, "input_index_path": input_index_path }, "out": { "output_str_ens_path": output_str_ens_path } } # Properties specific for BB self.fit_selection = properties.get('fit_selection', "System") self.skip = properties.get('skip', 1) self.start = properties.get('start', 0) self.end = properties.get('end', 0) self.dt = properties.get('dt', 0) self.output_name = properties.get('output_name', "output") self.output_type = properties.get('output_type', "pdb") self.properties = properties # Properties common in all GROMACS BB self.gmx_path = get_binary_path(properties, 'gmx_path') # Check the properties self.check_properties(properties)
[docs] def check_data_params(self, out_log, err_log): """ Checks all the input/output paths and parameters """ self.io_dict["in"]["input_traj_path"] = check_traj_path(self.io_dict["in"]["input_traj_path"], out_log, self.__class__.__name__) self.io_dict["in"]["input_top_path"] = check_input_path(self.io_dict["in"]["input_top_path"], out_log, self.__class__.__name__) self.io_dict["in"]["input_index_path"] = check_index_path(self.io_dict["in"]["input_index_path"], out_log, self.__class__.__name__) self.io_dict["out"]["output_str_ens_path"] = check_out_str_ens_path(self.io_dict["out"]["output_str_ens_path"], out_log, self.__class__.__name__) if not self.io_dict["in"]["input_index_path"]: self.selection = get_selection(self.properties, out_log, self.__class__.__name__) else: self.selection = get_selection_index_file(self.properties, self.io_dict["in"]["input_index_path"], 'selection', out_log, self.__class__.__name__) self.skip = get_skip(self.properties, out_log, self.__class__.__name__) self.start = get_start(self.properties, out_log, self.__class__.__name__) self.end = get_end(self.properties, out_log, self.__class__.__name__) self.dt = get_dt(self.properties, out_log, self.__class__.__name__) self.output_name = self.properties.get('output_name', 'output') self.output_type = get_ot_str_ens(self.properties, out_log, self.__class__.__name__)
[docs] @launchlogger def launch(self) -> int: """Execute the :class:`GMXTrjConvStrEns <gromacs.gmx_trjconv_str_ens.GMXTrjConvStrEns>` gromacs.gmx_trjconv_str_ens.GMXTrjConvStrEns object.""" # check input/output paths and parameters self.check_data_params(self.out_log, self.err_log) # Setup Biobb if self.check_restart(): return 0 self.stage_files() # if container execution, output to container_volume_path, else create temporary folder to put zip output if self.container_path: output = self.container_volume_path + '/' + self.output_name + '.' + self.output_type else: # create temporary folder self.tmp_folder = fu.create_unique_dir() fu.log('Creating %s temporary folder' % self.tmp_folder, self.out_log) output = self.tmp_folder + '/' + self.output_name + '.' + self.output_type self.cmd = ['echo', '\"'+self.selection+'\"', '|', self.gmx_path, 'trjconv', '-f', self.stage_io_dict["in"]["input_traj_path"], '-s', self.stage_io_dict["in"]["input_top_path"], '-skip', self.skip, '-b', self.start, '-dt', self.dt, '-sep', '-o', output] # checking 'end' gromacs 'bug' if not str(self.end) =="0": self.cmd.append('-e') self.cmd.append(self.end) if self.stage_io_dict["in"]["input_index_path"]: self.cmd.extend(['-n', self.stage_io_dict["in"]["input_index_path"]]) # Run Biobb block self.run_biobb() # Copy files to host self.copy_to_host() if self.container_path: process_output_trjconv_str_ens(self.stage_io_dict['unique_dir'], self.remove_tmp, self.io_dict["out"]["output_str_ens_path"], self.output_name + '*', self.out_log) else: process_output_trjconv_str_ens(self.tmp_folder, self.remove_tmp, self.stage_io_dict["out"]["output_str_ens_path"], '*', self.out_log) return self.return_code
[docs]def gmx_trjconv_str_ens(input_traj_path: str, input_top_path: str, output_str_ens_path: str, input_index_path: str = None, properties: dict = None, **kwargs) -> int: """Execute the :class:`GMXTrjConvStrEns <gromacs.gmx_trjconv_str_ens.GMXTrjConvStrEns>` class and execute the :meth:`launch() <gromacs.gmx_trjconv_str_ens.GMXTrjConvStrEns.launch>` method.""" return GMXTrjConvStrEns(input_traj_path=input_traj_path, input_top_path = input_top_path, output_str_ens_path=output_str_ens_path, input_index_path=input_index_path, properties=properties).launch()
[docs]def main(): """Command line execution of this building block. Please check the command line documentation.""" parser = argparse.ArgumentParser(description="Extracts an ensemble of frames containing a selection of atoms from GROMACS compatible trajectory files.", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999)) parser.add_argument('--config', required=False, help='Configuration file') # Specific args of each building block required_args = parser.add_argument_group('required arguments') required_args.add_argument('--input_traj_path', required=True, help='Path to the GROMACS trajectory file. Accepted formats: xtc, trr, cpt, gro, g96, pdb, tng.') required_args.add_argument('--input_top_path', required=True, help='Path to the GROMACS input topology file. Accepted formats: tpr, gro, g96, pdb, brk, ent.') parser.add_argument('--input_index_path', required=False, help="Path to the GROMACS index file. Accepted formats: ndx.") required_args.add_argument('--output_str_ens_path', required=True, help='Path to the output file. Accepted formats: zip.') args = parser.parse_args() args.config = args.config or "{}" properties = settings.ConfReader(config=args.config).get_prop_dic() # Specific call of each building block gmx_trjconv_str_ens(input_traj_path=args.input_traj_path, input_top_path=args.input_top_path, output_str_ens_path=args.output_str_ens_path, input_index_path=args.input_index_path, properties=properties)
if __name__ == '__main__': main()