%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). ![](https://bioexcel.eu/wp-content/uploads/2015/12/Bioexcell_logo_1080px_transp.png "Bioexcel") %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). ![](https://bioexcel.eu/wp-content/uploads/2015/12/Bioexcell_logo_1080px_transp.png "Bioexcel") %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). ![](https://bioexcel.eu/wp-content/uploads/2015/12/Bioexcell_logo_1080px_transp.png "Bioexcel") %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 - 3.13.0-1 - Package Spec generated