diff options
| -rw-r--r-- | .gitignore | 1 | ||||
| -rw-r--r-- | python-vina.spec | 244 | ||||
| -rw-r--r-- | sources | 1 |
3 files changed, 246 insertions, 0 deletions
@@ -0,0 +1 @@ +/vina-1.2.3.tar.gz diff --git a/python-vina.spec b/python-vina.spec new file mode 100644 index 0000000..0983bd3 --- /dev/null +++ b/python-vina.spec @@ -0,0 +1,244 @@ +%global _empty_manifest_terminate_build 0 +Name: python-vina +Version: 1.2.3 +Release: 1 +Summary: Python interface to AutoDock Vina +License: Apache-2.0 +URL: https://ccsb.scripps.edu/ +Source0: https://mirrors.nju.edu.cn/pypi/web/packages/1f/14/fa0c505ddc96828a7164c5fa9946afd0f5019a0af135bc1bbd947149b010/vina-1.2.3.tar.gz +BuildArch: noarch + +Requires: python3-numpy + +%description +# AutoDock Vina - Python API + +### Requirements + +You need, at a minimum (requirements): +* Python (>=3.5) +* Numpy +* SWIG +* Boost-cpp +* Sphinx (documentation) +* Sphinx_rtd_theme (documentation) + +### Installation (from source) + +I highly recommand you to install the Anaconda distribution (https://www.continuum.io/downloads) if you want a clean python environnment with nearly all the prerequisites already installed. To install everything properly, you just have to do this: +```bash +$ conda create -n vina python=3 +$ conda activate vina +$ conda install -c conda-forge numpy swig boost-cpp sphinx sphinx_rtd_theme +``` + +Finally, we can install the `Vina` package +```bash +$ git clone https://github.com/ccsb-scripps/AutoDock-Vina +$ cd AutoDock-Vina +$ git checkout boost-python +$ cd build/python +$ python setup.py build install +``` + +### Quick tutorial +```python +#!/usr/bin/env python + +from vina import Vina + + +v = Vina() + +v.set_receptor(rigid_pdbqt_filename="protein.pdbqt") +v.set_ligand_from_file('ligand.pdbqt') + +v.compute_vina_maps(center=[0., 0., 0.], box_size=[30, 30, 30]) +print(v.score()) +print(v.optimize()) +v.dock(exhaustiveness=32) +v.write_poses(pdbqt_filename="docking_results.pdbqt") +``` + +### Full documentation + +The installation instructions, documentation and tutorials can be found on [readthedocs.org](https://autodock-vina.readthedocs.io/en/latest/). + +### Citations +* Trott, O., & Olson, A. J. (2010). AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of computational chemistry, 31(2), 455-461. + + + + +%package -n python3-vina +Summary: Python interface to AutoDock Vina +Provides: python-vina +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +%description -n python3-vina +# AutoDock Vina - Python API + +### Requirements + +You need, at a minimum (requirements): +* Python (>=3.5) +* Numpy +* SWIG +* Boost-cpp +* Sphinx (documentation) +* Sphinx_rtd_theme (documentation) + +### Installation (from source) + +I highly recommand you to install the Anaconda distribution (https://www.continuum.io/downloads) if you want a clean python environnment with nearly all the prerequisites already installed. To install everything properly, you just have to do this: +```bash +$ conda create -n vina python=3 +$ conda activate vina +$ conda install -c conda-forge numpy swig boost-cpp sphinx sphinx_rtd_theme +``` + +Finally, we can install the `Vina` package +```bash +$ git clone https://github.com/ccsb-scripps/AutoDock-Vina +$ cd AutoDock-Vina +$ git checkout boost-python +$ cd build/python +$ python setup.py build install +``` + +### Quick tutorial +```python +#!/usr/bin/env python + +from vina import Vina + + +v = Vina() + +v.set_receptor(rigid_pdbqt_filename="protein.pdbqt") +v.set_ligand_from_file('ligand.pdbqt') + +v.compute_vina_maps(center=[0., 0., 0.], box_size=[30, 30, 30]) +print(v.score()) +print(v.optimize()) +v.dock(exhaustiveness=32) +v.write_poses(pdbqt_filename="docking_results.pdbqt") +``` + +### Full documentation + +The installation instructions, documentation and tutorials can be found on [readthedocs.org](https://autodock-vina.readthedocs.io/en/latest/). + +### Citations +* Trott, O., & Olson, A. J. (2010). AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of computational chemistry, 31(2), 455-461. + + + + +%package help +Summary: Development documents and examples for vina +Provides: python3-vina-doc +%description help +# AutoDock Vina - Python API + +### Requirements + +You need, at a minimum (requirements): +* Python (>=3.5) +* Numpy +* SWIG +* Boost-cpp +* Sphinx (documentation) +* Sphinx_rtd_theme (documentation) + +### Installation (from source) + +I highly recommand you to install the Anaconda distribution (https://www.continuum.io/downloads) if you want a clean python environnment with nearly all the prerequisites already installed. To install everything properly, you just have to do this: +```bash +$ conda create -n vina python=3 +$ conda activate vina +$ conda install -c conda-forge numpy swig boost-cpp sphinx sphinx_rtd_theme +``` + +Finally, we can install the `Vina` package +```bash +$ git clone https://github.com/ccsb-scripps/AutoDock-Vina +$ cd AutoDock-Vina +$ git checkout boost-python +$ cd build/python +$ python setup.py build install +``` + +### Quick tutorial +```python +#!/usr/bin/env python + +from vina import Vina + + +v = Vina() + +v.set_receptor(rigid_pdbqt_filename="protein.pdbqt") +v.set_ligand_from_file('ligand.pdbqt') + +v.compute_vina_maps(center=[0., 0., 0.], box_size=[30, 30, 30]) +print(v.score()) +print(v.optimize()) +v.dock(exhaustiveness=32) +v.write_poses(pdbqt_filename="docking_results.pdbqt") +``` + +### Full documentation + +The installation instructions, documentation and tutorials can be found on [readthedocs.org](https://autodock-vina.readthedocs.io/en/latest/). + +### Citations +* Trott, O., & Olson, A. J. (2010). AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of computational chemistry, 31(2), 455-461. + + + + +%prep +%autosetup -n vina-1.2.3 + +%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-vina -f filelist.lst +%dir %{python3_sitelib}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Wed May 10 2023 Python_Bot <Python_Bot@openeuler.org> - 1.2.3-1 +- Package Spec generated @@ -0,0 +1 @@ +57e01e30ec4a95b96a45c2371706a514 vina-1.2.3.tar.gz |