#!/usr/bin/env python3
"""Module containing the Convert_tpr class and the command line interface."""
from pathlib import Path, PurePath
from typing import Optional
from biobb_common.generic.biobb_object import BiobbObject
from biobb_common.tools import file_utils as fu
from biobb_common.tools.file_utils import launchlogger
from biobb_gromacs.gromacs.common import get_gromacs_version
[docs]
class ConvertTpr(BiobbObject):
"""
| biobb_gromacs ConvertTpr
| Wrapper of the `GROMACS convert-tpr <https://manual.gromacs.org/current/onlinehelp/gmx-convert-tpr.html>`_ module.
| The GROMACS convert-tpr module can edit run input files (.tpr): modify the run length (extend/until/nsteps) or trim the tpr file to a subset of atoms defined in an index file (input_ndx_path). Note that GROMACS does not allow both operations in a single call, so when an index file is provided the extend/until/nsteps properties are ignored.
Args:
input_tpr_path (str): Path to the input portable binary run file TPR. File type: input. `Sample file <https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/reference/gromacs/ref_grompp.tpr>`_. Accepted formats: tpr (edam:format_2333).
output_tpr_path (str): Path to the output portable binary run file TPR. File type: output. `Sample file <https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/reference/gromacs/ref_grompp.tpr>`_. Accepted formats: tpr (edam:format_2333).
input_ndx_path (str) (Optional): Path to the input index NDX file, used to trim the tpr file to a subset of atoms. File type: input. Accepted formats: ndx (edam:format_2033).
properties (dict - Python dictionary object containing the tool parameters, not input/output files):
* **extend** (*int*) - (0) Extend the runtime by this amount (ps).
* **until** (*int*) - (0) Extend the runtime until this ending time (ps).
* **nsteps** (*int*) - (0) Change the number of steps remaining to be made.
* **output_group** (*str*) - ("System") Index group to write to the output tpr file when trimming to a subset of atoms. Only used when input_ndx_path is provided.
* **gmx_lib** (*str*) - (None) Path set GROMACS GMXLIB environment variable.
* **binary_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.
* **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
* **container_path** (*str*) - (None) Path to the binary executable of your container.
* **container_image** (*str*) - ("gromacs/gromacs:latest") Container Image identifier.
* **container_volume_path** (*str*) - ("/data") Path to an internal directory in the container.
* **container_working_dir** (*str*) - (None) Path to the internal CWD in the container.
* **container_user_id** (*str*) - (None) User number id to be mapped inside the container.
* **container_shell_path** (*str*) - ("/bin/bash") Path to the binary executable of the container shell.
Examples:
This is a use example of how to use the building block from Python::
from biobb_gromacs.gromacs.convert_tpr import convert_tpr
prop = { 'extend': 100000}
convert_tpr(input_tpr_path='/path/to/myStructure.tpr',
output_tpr_path='/path/to/newCompiledBin.tpr',
properties=prop)
# Trim the tpr file to a subset of atoms defined in an index file
prop = { 'output_group': 'Protein'}
convert_tpr(input_tpr_path='/path/to/myStructure.tpr',
output_tpr_path='/path/to/trimmedBin.tpr',
input_ndx_path='/path/to/myIndex.ndx',
properties=prop)
Info:
* wrapped_software:
* name: GROMACS Convert-tpr
* version: 2025.2
* license: LGPL 2.1
* ontology:
* name: EDAM
* schema: http://edamontology.org/EDAM.owl
"""
def __init__(self, input_tpr_path: str, output_tpr_path: str,
input_ndx_path: Optional[str] = None,
properties: Optional[dict] = None, **kwargs) -> None:
properties = properties or {}
# Call parent class constructor
super().__init__(properties)
self.locals_var_dict = locals().copy()
# Input/Output files
self.io_dict = {
"in": {"input_tpr_path": input_tpr_path, "input_ndx_path": input_ndx_path},
"out": {"output_tpr_path": output_tpr_path}
}
# Properties specific for BB
self.extend = properties.get('extend')
self.until = properties.get('until')
self.nsteps = properties.get('nsteps')
self.output_group = properties.get('output_group', 'System')
# Properties common in all GROMACS BB
self.gmx_lib = properties.get('gmx_lib', None)
self.binary_path = properties.get('binary_path', 'gmx')
self.gmx_nobackup = properties.get('gmx_nobackup', True)
self.gmx_nocopyright = properties.get('gmx_nocopyright', True)
if self.gmx_nobackup:
self.binary_path += ' -nobackup'
if self.gmx_nocopyright:
self.binary_path += ' -nocopyright'
if not self.container_path:
self.gmx_version = get_gromacs_version(self.binary_path)
# Check the properties
self.check_properties(properties)
self.check_arguments()
[docs]
@launchlogger
def launch(self) -> int:
"""Execute the :class:`ConvertTpr <gromacs.convert_tpr.ConvertTpr>` object."""
# Setup Biobb
if self.check_restart():
return 0
# When trimming to a subset (an index file is provided), GROMACS
# convert-tpr prompts for the output group; answer it via stdin.
if self.io_dict["in"].get("input_ndx_path"):
self.io_dict["in"]["stdin_file_path"] = fu.create_stdin_file(f"{self.output_group}")
self.stage_files()
if self.container_path:
working_dir = self.container_volume_path if self.container_volume_path else "/data"
else:
working_dir = self.stage_io_dict.get('unique_dir', '')
self.cmd = ["cd", working_dir, ";", self.binary_path, 'convert-tpr',
'-s', PurePath(self.stage_io_dict["in"]["input_tpr_path"]).name,
'-o', PurePath(self.stage_io_dict["out"]["output_tpr_path"]).name
]
trimming = bool(self.stage_io_dict["in"].get("input_ndx_path")) and \
Path(self.stage_io_dict["in"].get("input_ndx_path")).exists()
if trimming:
# Trim the tpr to the selected index group. GROMACS does not allow
# combining index-group extraction with runtime modification
# (-extend/-until/-nsteps) in a single convert-tpr call.
self.cmd.append('-n')
self.cmd.append(PurePath(self.stage_io_dict["in"].get("input_ndx_path")).name)
if self.extend or self.until or self.nsteps:
fu.log("Warning: extend, until and nsteps are ignored when trimming the tpr "
"file to an index group; GROMACS convert-tpr cannot do both in a single call.",
self.out_log, self.global_log)
else:
if self.extend:
self.cmd.extend(['-extend', str(self.extend)])
if self.until:
self.cmd.extend(['-until', str(self.until)])
if self.nsteps:
self.cmd.extend(['-nsteps', str(self.nsteps)])
# Add stdin input file to answer the output group prompt when trimming
if self.io_dict["in"].get("stdin_file_path"):
self.cmd.append('<')
self.cmd.append(PurePath(self.stage_io_dict["in"]["stdin_file_path"]).name)
if self.gmx_lib:
self.env_vars_dict['GMXLIB'] = self.gmx_lib
# Run Biobb block
self.run_biobb()
# Copy files to host
self.copy_to_host()
if self.io_dict["in"].get("stdin_file_path"):
self.tmp_files.append(str(self.io_dict["in"].get("stdin_file_path")))
self.remove_tmp_files()
self.check_arguments(output_files_created=True, raise_exception=False)
return self.return_code
[docs]
def convert_tpr(input_tpr_path: str, output_tpr_path: str, input_ndx_path: Optional[str] = None,
properties: Optional[dict] = None, **kwargs) -> int:
"""Create :class:`ConvertTpr <gromacs.convert_tpr.ConvertTpr>` class and
execute the :meth:`launch() <gromacs.convert_tpr.ConvertTpr.launch>` method."""
return ConvertTpr(**dict(locals())).launch()
convert_tpr.__doc__ = ConvertTpr.__doc__
main = ConvertTpr.get_main(
convert_tpr, "Wrapper of the GROMACS convert-tpr module.")
if __name__ == '__main__':
main()