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|
%global _empty_manifest_terminate_build 0
Name: python-biobb-structure-checking
Version: 3.13.0
Release: 1
Summary: BioBB_structure_checking performs MDWeb structure checking tool set as a command line utility.
License: Apache Software License
URL: https://github.com/bioexcel/biobb_structure_checking
Source0: https://mirrors.aliyun.com/pypi/web/packages/af/6b/580b883d738e617b7c12ae6eb5b02fc638be22b6abf67dc263927d48be6c/biobb_structure_checking-3.13.0.tar.gz
BuildArch: noarch
Requires: python3-psutil
Requires: python3-numpy
Requires: python3-biopython
%description
# biobb_structure_checking
### Introduction
Biobb_structure_checking provides a series of functions to check the quality of a 3D structure intended to facilitate the setup of a molecular dynamics simulation of protein or nucleic acids systems.
Biobb_structure_checking package allows to configure the system (selection of model/chains,alternative location, addition of disulfide bonds and hydrogen atoms, side chain mutations), to detect and fix structure errors (missing side chain atoms, backbone breaks, amide assignments, incorrect chirality). It works with structures obtained from the Protein Data Bank or user provided.
The Biobb_structure_checking package provides a command line utility ([check_structure](https://biobb-structure-checking.readthedocs.io/en/latest/command_line_usage.html)) and a python [API](https://biobb-structure-checking.readthedocs.io/en/latest/biobb_structure_checking.html).
The latest documentation of this package can be found in our readthedocs site:
[latest package documentation](http://biobb_structure_checking.readthedocs.io/en/latest/).
### Version
v3.13.0 June 2023
### Requirements
* Biopython
### Optional requirements
* psutil (required for --debug, included in conda pkg.)
* Modeller (required for some functionalities, not included in conda pkg.)
* jupyter & nglview (required for demonstration notebooks, not included in conda pkg.)
### Installation
Using PIP:
> **Important:** PIP only installs the package. All the dependencies must be installed separately. To perform a complete installation, please use ANACONDA.
* Installation:
pip install "biobb_structure_checking>=3.12.1"
* Usage: [Python API documentation](https://biobb_structure_checking.readthedocs.io/en/latest/modules.html).
Using ANACONDA:
* Installation:
conda install -c bioconda "biobb_structure_checking>=3.12.1"
* Usage: With conda installation BioBBs can be used with the [Python API documentation](https://biobb_structure_checking.readthedocs.io/en/latest/modules.html) and the [Command Line documentation](https://biobb_structure_checking.readthedocs.io/en/latest/command_line.html)
### Copyright & Licensing
This software has been developed in the MMB group (http://mmb.irbbarcelona.org) at the
BSC (https://www.bsc.es/) & IRB (https://www.irbbarcelona.org/) for the European BioExcel (https://bioexcel.eu/), funded by the European Commission
(EU H2020 [675728](https://cordis.europa.eu/projects/675728)).
* (c) 2015-2022 [Barcelona Supercomputing Center](https://www.bsc.es/)
* (c) 2015-2022 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)
Licensed under the
[GNU Lesser General Public License v2.1](https://www.gnu.org/licenses/old-licenses/lgpl-2.1.html).
%package -n python3-biobb-structure-checking
Summary: BioBB_structure_checking performs MDWeb structure checking tool set as a command line utility.
Provides: python-biobb-structure-checking
BuildRequires: python3-devel
BuildRequires: python3-setuptools
BuildRequires: python3-pip
%description -n python3-biobb-structure-checking
# biobb_structure_checking
### Introduction
Biobb_structure_checking provides a series of functions to check the quality of a 3D structure intended to facilitate the setup of a molecular dynamics simulation of protein or nucleic acids systems.
Biobb_structure_checking package allows to configure the system (selection of model/chains,alternative location, addition of disulfide bonds and hydrogen atoms, side chain mutations), to detect and fix structure errors (missing side chain atoms, backbone breaks, amide assignments, incorrect chirality). It works with structures obtained from the Protein Data Bank or user provided.
The Biobb_structure_checking package provides a command line utility ([check_structure](https://biobb-structure-checking.readthedocs.io/en/latest/command_line_usage.html)) and a python [API](https://biobb-structure-checking.readthedocs.io/en/latest/biobb_structure_checking.html).
The latest documentation of this package can be found in our readthedocs site:
[latest package documentation](http://biobb_structure_checking.readthedocs.io/en/latest/).
### Version
v3.13.0 June 2023
### Requirements
* Biopython
### Optional requirements
* psutil (required for --debug, included in conda pkg.)
* Modeller (required for some functionalities, not included in conda pkg.)
* jupyter & nglview (required for demonstration notebooks, not included in conda pkg.)
### Installation
Using PIP:
> **Important:** PIP only installs the package. All the dependencies must be installed separately. To perform a complete installation, please use ANACONDA.
* Installation:
pip install "biobb_structure_checking>=3.12.1"
* Usage: [Python API documentation](https://biobb_structure_checking.readthedocs.io/en/latest/modules.html).
Using ANACONDA:
* Installation:
conda install -c bioconda "biobb_structure_checking>=3.12.1"
* Usage: With conda installation BioBBs can be used with the [Python API documentation](https://biobb_structure_checking.readthedocs.io/en/latest/modules.html) and the [Command Line documentation](https://biobb_structure_checking.readthedocs.io/en/latest/command_line.html)
### Copyright & Licensing
This software has been developed in the MMB group (http://mmb.irbbarcelona.org) at the
BSC (https://www.bsc.es/) & IRB (https://www.irbbarcelona.org/) for the European BioExcel (https://bioexcel.eu/), funded by the European Commission
(EU H2020 [675728](https://cordis.europa.eu/projects/675728)).
* (c) 2015-2022 [Barcelona Supercomputing Center](https://www.bsc.es/)
* (c) 2015-2022 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)
Licensed under the
[GNU Lesser General Public License v2.1](https://www.gnu.org/licenses/old-licenses/lgpl-2.1.html).
%package help
Summary: Development documents and examples for biobb-structure-checking
Provides: python3-biobb-structure-checking-doc
%description help
# biobb_structure_checking
### Introduction
Biobb_structure_checking provides a series of functions to check the quality of a 3D structure intended to facilitate the setup of a molecular dynamics simulation of protein or nucleic acids systems.
Biobb_structure_checking package allows to configure the system (selection of model/chains,alternative location, addition of disulfide bonds and hydrogen atoms, side chain mutations), to detect and fix structure errors (missing side chain atoms, backbone breaks, amide assignments, incorrect chirality). It works with structures obtained from the Protein Data Bank or user provided.
The Biobb_structure_checking package provides a command line utility ([check_structure](https://biobb-structure-checking.readthedocs.io/en/latest/command_line_usage.html)) and a python [API](https://biobb-structure-checking.readthedocs.io/en/latest/biobb_structure_checking.html).
The latest documentation of this package can be found in our readthedocs site:
[latest package documentation](http://biobb_structure_checking.readthedocs.io/en/latest/).
### Version
v3.13.0 June 2023
### Requirements
* Biopython
### Optional requirements
* psutil (required for --debug, included in conda pkg.)
* Modeller (required for some functionalities, not included in conda pkg.)
* jupyter & nglview (required for demonstration notebooks, not included in conda pkg.)
### Installation
Using PIP:
> **Important:** PIP only installs the package. All the dependencies must be installed separately. To perform a complete installation, please use ANACONDA.
* Installation:
pip install "biobb_structure_checking>=3.12.1"
* Usage: [Python API documentation](https://biobb_structure_checking.readthedocs.io/en/latest/modules.html).
Using ANACONDA:
* Installation:
conda install -c bioconda "biobb_structure_checking>=3.12.1"
* Usage: With conda installation BioBBs can be used with the [Python API documentation](https://biobb_structure_checking.readthedocs.io/en/latest/modules.html) and the [Command Line documentation](https://biobb_structure_checking.readthedocs.io/en/latest/command_line.html)
### Copyright & Licensing
This software has been developed in the MMB group (http://mmb.irbbarcelona.org) at the
BSC (https://www.bsc.es/) & IRB (https://www.irbbarcelona.org/) for the European BioExcel (https://bioexcel.eu/), funded by the European Commission
(EU H2020 [675728](https://cordis.europa.eu/projects/675728)).
* (c) 2015-2022 [Barcelona Supercomputing Center](https://www.bsc.es/)
* (c) 2015-2022 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)
Licensed under the
[GNU Lesser General Public License v2.1](https://www.gnu.org/licenses/old-licenses/lgpl-2.1.html).
%prep
%autosetup -n biobb_structure_checking-3.13.0
%build
%py3_build
%install
%py3_install
install -d -m755 %{buildroot}/%{_pkgdocdir}
if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi
if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi
if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi
if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi
pushd %{buildroot}
if [ -d usr/lib ]; then
find usr/lib -type f -printf "\"/%h/%f\"\n" >> filelist.lst
fi
if [ -d usr/lib64 ]; then
find usr/lib64 -type f -printf "\"/%h/%f\"\n" >> filelist.lst
fi
if [ -d usr/bin ]; then
find usr/bin -type f -printf "\"/%h/%f\"\n" >> filelist.lst
fi
if [ -d usr/sbin ]; then
find usr/sbin -type f -printf "\"/%h/%f\"\n" >> filelist.lst
fi
touch doclist.lst
if [ -d usr/share/man ]; then
find usr/share/man -type f -printf "\"/%h/%f.gz\"\n" >> doclist.lst
fi
popd
mv %{buildroot}/filelist.lst .
mv %{buildroot}/doclist.lst .
%files -n python3-biobb-structure-checking -f filelist.lst
%dir %{python3_sitelib}/*
%files help -f doclist.lst
%{_docdir}/*
%changelog
* Tue Jun 20 2023 Python_Bot <Python_Bot@openeuler.org> - 3.13.0-1
- Package Spec generated
|
