biobb-mem 5.0.0__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- biobb_mem-5.0.0/LICENSE +202 -0
- biobb_mem-5.0.0/PKG-INFO +133 -0
- biobb_mem-5.0.0/README.md +110 -0
- biobb_mem-5.0.0/biobb_mem/__init__.py +3 -0
- biobb_mem-5.0.0/biobb_mem/ambertools/__init__.py +2 -0
- biobb_mem-5.0.0/biobb_mem/ambertools/cpptraj_density.py +188 -0
- biobb_mem-5.0.0/biobb_mem/chap/__init__.py +2 -0
- biobb_mem-5.0.0/biobb_mem/chap/chap_run.py +294 -0
- biobb_mem-5.0.0/biobb_mem/lipyphilicBB/__init__.py +2 -0
- biobb_mem-5.0.0/biobb_mem/lipyphilicBB/assign_leaflets.py +176 -0
- biobb_mem-5.0.0/biobb_mem/py.typed +0 -0
- biobb_mem-5.0.0/biobb_mem/test/__init__.py +0 -0
- biobb_mem-5.0.0/biobb_mem.egg-info/PKG-INFO +133 -0
- biobb_mem-5.0.0/biobb_mem.egg-info/SOURCES.txt +18 -0
- biobb_mem-5.0.0/biobb_mem.egg-info/dependency_links.txt +1 -0
- biobb_mem-5.0.0/biobb_mem.egg-info/entry_points.txt +4 -0
- biobb_mem-5.0.0/biobb_mem.egg-info/requires.txt +1 -0
- biobb_mem-5.0.0/biobb_mem.egg-info/top_level.txt +1 -0
- biobb_mem-5.0.0/setup.cfg +4 -0
- biobb_mem-5.0.0/setup.py +41 -0
biobb_mem-5.0.0/LICENSE
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biobb_mem-5.0.0/PKG-INFO
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Metadata-Version: 2.1
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Name: biobb_mem
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Version: 5.0.0
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Summary: Biobb_mem is a complete code template to promote and facilitate the creation of new Biobbs by the community.
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Home-page: https://github.com/bioexcel/biobb_mem
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Author: Biobb developers
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Author-email: ruben.chaves@irbbarcelona.org
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Project-URL: Documentation, http://biobb-mem.readthedocs.io/en/latest/
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Project-URL: Bioexcel, https://bioexcel.eu/
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Keywords: Bioinformatics Workflows BioExcel Compatibility
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Classifier: Development Status :: 5 - Production/Stable
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Classifier: Programming Language :: Python :: 3.9
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Classifier: Programming Language :: Python :: 3.10
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Classifier: Programming Language :: Python :: 3.11
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Classifier: License :: OSI Approved :: Apache Software License
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Classifier: Operating System :: MacOS :: MacOS X
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Classifier: Operating System :: POSIX
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Classifier: Operating System :: Unix
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Requires-Python: >=3.9
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Description-Content-Type: text/markdown
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License-File: LICENSE
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Requires-Dist: biobb_common==5.0.0
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[](https://GitHub.com/bioexcel/biobb_mem/tags/)
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[](https://pypi.python.org/pypi/biobb-mem/)
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[](https://anaconda.org/bioconda/biobb_mem)
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[](https://anaconda.org/bioconda/biobb_mem)
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[](https://quay.io/repository/biocontainers/biobb_mem?tab=tags)
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[](https://depot.galaxyproject.org/singularity/biobb_mem:5.0.0--pyhdfd78af_0)
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[](https://github.com/bioexcel/biobb_mem)
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[](https://pypi.org/project/biobb-mem/)
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[](https://opensource.org/licenses/Apache-2.0)
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[](https://github.com/bioexcel/biobb_mem)
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[](https://biobb-mem.readthedocs.io/en/latest/?badge=latest)
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[](https://mmb.irbbarcelona.org/biobb/)
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[](https://www.youtube.com/@BioExcelCoE/search?query=biobb)
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[](https://doi.org/10.1038/s41597-019-0177-4)
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[](https://www.nature.com/articles/s41597-019-0177-4#citeas)
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[](https://docs.bioexcel.eu/biobb_mem/junit/report.html)
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[](https://docs.bioexcel.eu/biobb_mem/coverage/)
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[](https://docs.bioexcel.eu/biobb_mem/flake8/)
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[](https://github.com/bioexcel/biobb_mem/commits/master)
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[](https://GitHub.com/bioexcel/biobb_mem/issues/)
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[](https://fair-software.eu)
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[](https://www.bestpractices.dev/projects/8847)
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[](https://bestpractices.coreinfrastructure.org/projects/8847/badge)
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[//]: # (The previous line invisible link is for compatibility with the howfairis script https://github.com/fair-software/howfairis-github-action/tree/main wich uses the old bestpractices URL)
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# biobb_mem
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### Introduction
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biobb_mem is a BioBB category for membrane analysis and manipulation.
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biobb_mem allows analysis of membrane properties and manipulation of membrane systems using tools like MDAnalysis and LiPyphilic.
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Biobb (BioExcel building blocks) packages are Python building blocks that
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create new layer of compatibility and interoperability over popular
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bioinformatics tools.
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The latest documentation of this package can be found in our readthedocs site:
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[latest API documentation](http://biobb-mem.readthedocs.io/en/latest/).
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### Version
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* Installation:
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* Usage: [Python API documentation](https://biobb-mem.readthedocs.io/en/latest/modules.html)
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* Usage: With conda installation BioBBs can be used with the [Python API documentation](https://biobb-mem.readthedocs.io/en/latest/modules.html) and the [Command Line documentation](https://biobb-mem.readthedocs.io/en/latest/command_line.html)
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**MacOS users**: it's strongly recommended to avoid Singularity and use **Docker** as containerization system.
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* Usage:
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The command list and specification can be found at the [Command Line documentation](https://biobb-mem.readthedocs.io/en/latest/command_line.html).
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### Copyright & Licensing
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This software has been developed in the [MMB group](http://mmb.irbbarcelona.org) at the [BSC](http://www.bsc.es/) & [IRB](https://www.irbbarcelona.org/) for the [European BioExcel](http://bioexcel.eu/), funded by the European Commission (EU H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)).
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* (c) 2015-2024 [Barcelona Supercomputing Center](https://www.bsc.es/)
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* (c) 2015-2024 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)
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Licensed under the
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[Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file LICENSE for details.
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[](https://GitHub.com/bioexcel/biobb_mem/tags/)
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[](https://pypi.python.org/pypi/biobb-mem/)
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[](https://anaconda.org/bioconda/biobb_mem)
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[](https://anaconda.org/bioconda/biobb_mem)
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[](https://quay.io/repository/biocontainers/biobb_mem?tab=tags)
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[](https://pypi.org/project/biobb-mem/)
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[](https://github.com/bioexcel/biobb_mem)
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[](https://biobb-mem.readthedocs.io/en/latest/?badge=latest)
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[](https://mmb.irbbarcelona.org/biobb/)
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[](https://www.youtube.com/@BioExcelCoE/search?query=biobb)
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[](https://doi.org/10.1038/s41597-019-0177-4)
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[](https://www.nature.com/articles/s41597-019-0177-4#citeas)
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[](https://docs.bioexcel.eu/biobb_mem/junit/report.html)
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[](https://docs.bioexcel.eu/biobb_mem/coverage/)
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[](https://docs.bioexcel.eu/biobb_mem/flake8/)
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[](https://github.com/bioexcel/biobb_mem/commits/master)
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[](https://GitHub.com/bioexcel/biobb_mem/issues/)
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[](https://fair-software.eu)
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[](https://www.bestpractices.dev/projects/8847)
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[](https://bestpractices.coreinfrastructure.org/projects/8847/badge)
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[//]: # (The previous line invisible link is for compatibility with the howfairis script https://github.com/fair-software/howfairis-github-action/tree/main wich uses the old bestpractices URL)
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# biobb_mem
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### Introduction
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biobb_mem is a BioBB category for membrane analysis and manipulation.
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biobb_mem allows analysis of membrane properties and manipulation of membrane systems using tools like MDAnalysis and LiPyphilic.
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Biobb (BioExcel building blocks) packages are Python building blocks that
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create new layer of compatibility and interoperability over popular
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bioinformatics tools.
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The latest documentation of this package can be found in our readthedocs site:
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[latest API documentation](http://biobb-mem.readthedocs.io/en/latest/).
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### Version
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### Installation
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Using PIP:
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> **Important:** PIP only installs the package. All the dependencies must be installed separately. To perform a complete installation, please use ANACONDA or DOCKER.
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* Installation:
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* Usage: [Python API documentation](https://biobb-mem.readthedocs.io/en/latest/modules.html)
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* Usage: With conda installation BioBBs can be used with the [Python API documentation](https://biobb-mem.readthedocs.io/en/latest/modules.html) and the [Command Line documentation](https://biobb-mem.readthedocs.io/en/latest/command_line.html)
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Using SINGULARITY:
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**MacOS users**: it's strongly recommended to avoid Singularity and use **Docker** as containerization system.
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* Usage:
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The command list and specification can be found at the [Command Line documentation](https://biobb-mem.readthedocs.io/en/latest/command_line.html).
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### Copyright & Licensing
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This software has been developed in the [MMB group](http://mmb.irbbarcelona.org) at the [BSC](http://www.bsc.es/) & [IRB](https://www.irbbarcelona.org/) for the [European BioExcel](http://bioexcel.eu/), funded by the European Commission (EU H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)).
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#!/usr/bin/env python3
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"""Module containing the Cpptraj Density class and the command line interface."""
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import argparse
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from pathlib import PurePath
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from biobb_common.generic.biobb_object import BiobbObject
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from biobb_common.configuration import settings
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from biobb_common.tools import file_utils as fu
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from biobb_common.tools.file_utils import launchlogger
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class CpptrajDensity(BiobbObject):
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"""
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| biobb_mem CpptrajDensity
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| Wrapper of the Ambertools Cpptraj module for calculating density profile along an axis of a given cpptraj compatible trajectory.
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| 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://raw.githubusercontent.com/Amber-MD/cpptraj/master/doc/CpptrajManual.pdf>`_.
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Args:
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input_top_path (str): Path to the input structure or topology file. File type: input. `Sample file <https://github.com/bioexcel/biobb_mem/raw/master/biobb_mem/test/data/ambertools/topology.top>`_. Accepted formats: top (edam:format_3881), pdb (edam:format_1476), prmtop (edam:format_3881), parmtop (edam:format_3881), zip (edam:format_3987).
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input_traj_path (str): Path to the input trajectory to be processed. File type: input. `Sample file <https://github.com/bioexcel/biobb_mem/raw/master/biobb_mem/test/data/ambertools/trajectory.xtc>`_. 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).
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output_cpptraj_path (str): Path to the output processed density analysis. File type: output. `Sample file <https://github.com/bioexcel/biobb_mem/raw/master/biobb_mem/test/reference/ambertools/reference/density_default.dat>`_. Accepted formats: dat (edam:format_1637), agr (edam:format_2033), xmgr (edam:format_2033), gnu (edam:format_2033).
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output_traj_path (str) (Optional): Path to the output processed trajectory. File type: output. `Sample file <https://github.com/bioexcel/biobb_mem/raw/master/biobb_mem/test/reference/ambertools/trajectory_out.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).
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properties (dic - Python dictionary object containing the tool parameters, not input/output files):
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* **start** (*int*) - (1) [1~100000|1] Starting frame for slicing
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* **end** (*int*) - (-1) [-1~100000|1] Ending frame for slicing
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* **steps** (*int*) - (1) [1~100000|1] Step for slicing
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* **density_type** (*str*) - ("number") Number, mass, partial charge (q) or electron (Ne - q) density. Electron density will be converted to e-/Å3 by dividing the average area spanned by the other two dimensions.
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* **mask** (*str*) - ("*") Arbitrary number of masks for atom selection; a dataset is created and the output will contain entries for each mask.. Default: all atoms.
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* **delta** (*float*) - (0.25) Resolution, i.e. determines number of slices (i.e. histogram bins).
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* **axis** (*str*) - ("z") Coordinate (axis) for density calculation. Vales: x, y, z.
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* **bintype** (*str*) - ("bincenter") Determine whether histogram bin coordinates will be based on bin center (default) or bin edges. Values: bicenter, binedge.
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* **restrict** (*str*) - (None) If specified, only calculate the density within a cylinder or square shape from the specified axis as defined by a distance cutoff. Values: cylinder, square.
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* **cutoff** (*float*) - (None) The distance cutoff for 'restrict'. Required if 'restrict' is specified.
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* **binary_path** (*str*) - ("cpptraj") Path to the cpptraj executable binary.
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* **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
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* **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
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* **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
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Examples:
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This is a use example of how to use the building block from Python::
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from biobb_mem.ambertools.cpptraj_density import cpptraj_density
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prop = {
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'density_type': 'number'
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}
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cpptraj_density(input_top_path='/path/to/myTopology.top',
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input_traj_path='/path/to/myTrajectory.xtc',
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output_cpptraj_path='/path/to/newAnalysis.dat',
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properties=prop)
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Info:
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* wrapped_software:
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* name: Ambertools Cpptraj
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* version: >=22.0
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* license: GNU
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* ontology:
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* name: EDAM
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* schema: http://edamontology.org/EDAM.owl
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"""
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|
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def __init__(self, input_top_path, input_traj_path, output_cpptraj_path,
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output_traj_path=None, properties=None, **kwargs) -> None:
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properties = properties or {}
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# Call parent class constructor
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super().__init__(properties)
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self.locals_var_dict = locals().copy()
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# Input/Output files
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self.io_dict = {
|
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|
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"in": {"input_top_path": input_top_path, "input_traj_path": input_traj_path},
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"out": {"output_cpptraj_path": output_cpptraj_path, "output_traj_path": output_traj_path}
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|
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}
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|
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|
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# Properties specific for BB
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|
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self.instructions_file = 'instructions.in'
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|
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self.start = properties.get('start', 1)
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79
|
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self.end = properties.get('end', -1)
|
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self.steps = properties.get('steps', 1)
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|
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self.slice = f' {self.start} {self.end} {self.steps}'
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+
self.density_type = properties.get('density_type', 'number')
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+
self.mask = properties.get('mask', '*')
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84
|
+
self.delta = properties.get('delta', 0.25)
|
|
85
|
+
self.axis = properties.get('axis', 'z')
|
|
86
|
+
self.bintype = properties.get('bintype', 'bincenter')
|
|
87
|
+
self.restrict = properties.get('restrict', None)
|
|
88
|
+
self.cutoff = properties.get('cutoff', None)
|
|
89
|
+
self.binary_path = properties.get('binary_path', 'cpptraj')
|
|
90
|
+
self.properties = properties
|
|
91
|
+
|
|
92
|
+
# Check the properties
|
|
93
|
+
self.check_properties(properties)
|
|
94
|
+
self.check_arguments()
|
|
95
|
+
|
|
96
|
+
def create_instructions_file(self, stage_io_dict, out_log, err_log):
|
|
97
|
+
"""Creates an input file using the properties file settings"""
|
|
98
|
+
instructions_list = []
|
|
99
|
+
# different path if container execution or not
|
|
100
|
+
self.instructions_file = str(PurePath(fu.create_unique_dir()).joinpath(self.instructions_file))
|
|
101
|
+
# fu.create_name(prefix=self.prefix, step=self.step, name=self.instructions_file)
|
|
102
|
+
instructions_list.append('parm ' + stage_io_dict["in"]["input_top_path"])
|
|
103
|
+
instructions_list.append('trajin ' + stage_io_dict["in"]["input_traj_path"] + self.slice)
|
|
104
|
+
density_command = f'density {self.density_type} out {stage_io_dict["out"]["output_cpptraj_path"]} {self.mask} delta {self.delta} {self.axis} {self.bintype}'
|
|
105
|
+
if self.restrict:
|
|
106
|
+
density_command += f' restrict {self.restrict}'
|
|
107
|
+
if self.cutoff:
|
|
108
|
+
density_command += f' cutoff {self.cutoff}'
|
|
109
|
+
instructions_list.append(density_command)
|
|
110
|
+
|
|
111
|
+
# trajout
|
|
112
|
+
if ("output_traj_path" in stage_io_dict["out"]):
|
|
113
|
+
instructions_list.append('trajout ' + stage_io_dict["out"]["output_traj_path"])
|
|
114
|
+
|
|
115
|
+
# create .in file
|
|
116
|
+
with open(self.instructions_file, 'w') as mdp:
|
|
117
|
+
for line in instructions_list:
|
|
118
|
+
mdp.write(line.strip() + '\n')
|
|
119
|
+
|
|
120
|
+
return self.instructions_file
|
|
121
|
+
|
|
122
|
+
@launchlogger
|
|
123
|
+
def launch(self) -> int:
|
|
124
|
+
"""Execute the :class:`CpptrajDensity <ambertools.cpptraj_density.CpptrajDensity>` ambertools.cpptraj_density.CpptrajDensity object."""
|
|
125
|
+
|
|
126
|
+
# Setup Biobb
|
|
127
|
+
if self.check_restart():
|
|
128
|
+
return 0
|
|
129
|
+
self.stage_files()
|
|
130
|
+
|
|
131
|
+
# create instructions file
|
|
132
|
+
self.create_instructions_file(self.stage_io_dict, self.out_log, self.err_log)
|
|
133
|
+
# create cmd and launch execution
|
|
134
|
+
self.cmd = [self.binary_path, '-i', self.instructions_file]
|
|
135
|
+
|
|
136
|
+
# Run Biobb block
|
|
137
|
+
self.run_biobb()
|
|
138
|
+
# Copy files to host
|
|
139
|
+
self.copy_to_host()
|
|
140
|
+
# remove temporary folder(s)
|
|
141
|
+
self.tmp_files.extend([
|
|
142
|
+
self.stage_io_dict.get("unique_dir"),
|
|
143
|
+
PurePath(self.instructions_file).parent
|
|
144
|
+
])
|
|
145
|
+
self.remove_tmp_files()
|
|
146
|
+
|
|
147
|
+
self.check_arguments(output_files_created=True, raise_exception=False)
|
|
148
|
+
|
|
149
|
+
return self.return_code
|
|
150
|
+
|
|
151
|
+
|
|
152
|
+
def cpptraj_density(input_top_path: str, input_traj_path: str, output_cpptraj_path: str, output_traj_path: str = None, properties: dict = None, **kwargs) -> int:
|
|
153
|
+
"""Execute the :class:`CpptrajDensity <ambertools.cpptraj_density.CpptrajDensity>` class and
|
|
154
|
+
execute the :meth:`launch() <ambertools.cpptraj_density.CpptrajDensity.launch>` method."""
|
|
155
|
+
|
|
156
|
+
return CpptrajDensity(input_top_path=input_top_path,
|
|
157
|
+
input_traj_path=input_traj_path,
|
|
158
|
+
output_cpptraj_path=output_cpptraj_path,
|
|
159
|
+
output_traj_path=output_traj_path,
|
|
160
|
+
properties=properties, **kwargs).launch()
|
|
161
|
+
|
|
162
|
+
|
|
163
|
+
def main():
|
|
164
|
+
"""Command line execution of this building block. Please check the command line documentation."""
|
|
165
|
+
parser = argparse.ArgumentParser(description="Calculates the density along an axis of a given cpptraj compatible trajectory.", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
|
|
166
|
+
parser.add_argument('--config', required=False, help='Configuration file')
|
|
167
|
+
|
|
168
|
+
# Specific args of each building block
|
|
169
|
+
required_args = parser.add_argument_group('required arguments')
|
|
170
|
+
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.')
|
|
171
|
+
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.')
|
|
172
|
+
required_args.add_argument('--output_cpptraj_path', required=True, help='Path to the output processed analysis.')
|
|
173
|
+
parser.add_argument('--output_traj_path', required=False, help='Path to the output processed trajectory.')
|
|
174
|
+
|
|
175
|
+
args = parser.parse_args()
|
|
176
|
+
args.config = args.config or "{}"
|
|
177
|
+
properties = settings.ConfReader(config=args.config).get_prop_dic()
|
|
178
|
+
|
|
179
|
+
# Specific call of each building block
|
|
180
|
+
cpptraj_density(input_top_path=args.input_top_path,
|
|
181
|
+
input_traj_path=args.input_traj_path,
|
|
182
|
+
output_cpptraj_path=args.output_cpptraj_path,
|
|
183
|
+
output_traj_path=args.output_traj_path,
|
|
184
|
+
properties=properties)
|
|
185
|
+
|
|
186
|
+
|
|
187
|
+
if __name__ == '__main__':
|
|
188
|
+
main()
|