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authorCoprDistGit <infra@openeuler.org>2023-05-15 05:44:36 +0000
committerCoprDistGit <infra@openeuler.org>2023-05-15 05:44:36 +0000
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+%global _empty_manifest_terminate_build 0
+Name: python-BFEE2
+Version: 2.3.2
+Release: 1
+Summary: Binding Free Energy Estimator 2
+License: GPLv3
+URL: https://github.com/fhh2626/BFEE2
+Source0: https://mirrors.nju.edu.cn/pypi/web/packages/56/20/56865c30d1267bec081702a1f65b6f5ef0e864dcb6dc88ee7a0ae7108b07/BFEE2-2.3.2.tar.gz
+BuildArch: noarch
+
+Requires: python3-setuptools
+Requires: python3-pyside2
+Requires: python3-appdirs
+Requires: python3-MDAnalysis
+Requires: python3-matplotlib
+Requires: python3-numpy
+Requires: python3-scipy
+Requires: python3-parmed
+
+%description
+# Binding Free Energy Estimator 2
+[![DOI](https://zenodo.org/badge/322234705.svg)](https://zenodo.org/badge/latestdoi/322234705)
+
+Binding free energy estimator (BFEE) is a python-based software that automates absolute binding free energy calculations through either the alchemical or geometric route by molecular dynamics simulations.<br>
+
+## Theoretical backgrounds
+The degrees of freedom of the protein-ligand (or host-guest) system are described by a series of geometric variables (or collective variables), as firstly described by the [Karplus group](https://pubs.acs.org/doi/abs/10.1021/jp0217839). In BFEE, a generalized, best-fit-rotation-based geometric variables are used, making it in principle available to any protein-ligand complex. See [this paper](https://pubs.acs.org/doi/abs/10.1021/acs.jctc.7b00791) for introduction of these variables.<br>
+
+In the [geometric route](https://pubs.acs.org/doi/10.1021/ct3008099), the degrees of freedom is investigated one by one, through one-dimensional free-energy calculations. In BFEE, [WTM-eABF](https://pubs.acs.org/doi/abs/10.1021/acs.accounts.9b00473) is used, while other importance-sampling algorithms such as [plain eABF](https://pubs.acs.org/doi/abs/10.1021/acs.jctc.6b00447) are also acceptable.
+The [alchemical route](https://pubs.acs.org/doi/10.1021/ct3008099) is a variants of the [double decoupling method (DDM)](https://www.sciencedirect.com/science/article/pii/S0006349597787563). A thermodynamic cycle, in which the ligand and the geometric restraints are decoupled independently to guarantee the convergence of the simulations.<br>
+[这里](http://sioc-journal.cn/Jwk_hxxb/CN/10.6023/A20100489)是标准结合自由能计算方法的中文介绍.<br>
+
+## Features
+Generates all the input files for absolute binding free energy calculations;<br>
+Perform post-treatment automatedly;<br>
+Support NAMD (alchemical and geometric route) and Gromacs (geometric route) as molecular dynamics engines;<br>
+Support many file formats for the input complex structure (PSF/PDB/PRM, PRM7/RST7, TOP/PDB);<br>
+...<br>
+
+## Requirements
+Python 3.6+, PySide 2, numpy, scipy, matplotlib, parmed and MDAnalysis.<br>
+[NAMD 3.0 or later](https://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=NAMD) / [Colvars patched Gromacs](https://github.com/Colvars/colvars).<br>
+**Note: BFEE2 uses cutting-edge features of NAMD and Colvars. We highly suggest the end-user download the devel branch of NAMD from [here](https://gitlab.com/tcbgUIUC/namd/-/tree/devel) and patch it with [Colvars](https://github.com/Colvars/colvars) to prevent possible problems.**
+
+## Installation
+We suggest to install BFEE2 through conda. It will be safe if conda is install in a new environment<br>
+```
+conda create --name bfee (optional)
+conda activate bfee (optional)
+conda install -c conda-forge BFEE2
+```
+
+## Usage
+Simply run BFEE2Gui.py in terminal or PowerShell. One may need to use the absolute path on MS Windows.<br>
+A step-by-step tutorial is provided [here](https://www.nature.com/articles/s41596-021-00676-1).<br>
+
+## Citations
+When possible, please consider mentioning [Fu et al. Nat. Protoc. 2022, doi:10.1038/s41596-021-00676-1](https://www.nature.com/articles/s41596-021-00676-1#citeas) when BFEE2 is used in your project.
+
+
+Additional references:<br>
+BFEE2: [Fu et al. J. Chem. Inf. Model. 2021, 61, 2116–2123](https://pubs.acs.org/doi/abs/10.1021/acs.jcim.1c00269)<br>
+Alchemical and geometric routes [Gumbart et al. J. Chem. Theory Comput. 2013, 9, 794–802](https://pubs.acs.org/doi/abs/10.1021/ct3008099)<br>
+WTM-eABF: [Fu et al. Acc. Chem. Res. 2019, 52, 3254–3264](https://pubs.acs.org/doi/abs/10.1021/acs.accounts.9b00473) and [Fu et al. J. Phys. Chem. Lett. 2018, 9, 4738–4745](https://pubs.acs.org/doi/abs/10.1021/acs.jpclett.8b01994)<br>
+Collective variables: [Fu et al. J. Chem. Theory Comput. 2017, 13, 5173–5178](https://pubs.acs.org/doi/abs/10.1021/acs.jctc.7b00791)<br>
+Colvars module: [Fiorin et al. Mol. Phys. 2013 111, 3345-3362](https://www.tandfonline.com/doi/full/10.1080/00268976.2013.813594)<br>
+"Mother" of all restraint-based binding free-energy calculations: [Hermans et al. Isr. J. Chem. 1986, 27, 225–227](https://onlinelibrary.wiley.com/doi/abs/10.1002/ijch.198600032)<br>
+
+## Contact us
+Technique issues: Haohao Fu (fhh2626@mail.nankai.edu.cn) and Haochuan Chen (yjcoshc@mail.nankai.edu.cn)<br>
+
+This software is under the [GPLv3](https://www.gnu.org/licenses/gpl-3.0.en.html) license. For more information about the copyright of BFEE, contact the corresponding authors of the aforementioned papers (wscai@nankai.edu.cn, Christophe.Chipot@univ-lorraine.fr).
+
+
+%package -n python3-BFEE2
+Summary: Binding Free Energy Estimator 2
+Provides: python-BFEE2
+BuildRequires: python3-devel
+BuildRequires: python3-setuptools
+BuildRequires: python3-pip
+%description -n python3-BFEE2
+# Binding Free Energy Estimator 2
+[![DOI](https://zenodo.org/badge/322234705.svg)](https://zenodo.org/badge/latestdoi/322234705)
+
+Binding free energy estimator (BFEE) is a python-based software that automates absolute binding free energy calculations through either the alchemical or geometric route by molecular dynamics simulations.<br>
+
+## Theoretical backgrounds
+The degrees of freedom of the protein-ligand (or host-guest) system are described by a series of geometric variables (or collective variables), as firstly described by the [Karplus group](https://pubs.acs.org/doi/abs/10.1021/jp0217839). In BFEE, a generalized, best-fit-rotation-based geometric variables are used, making it in principle available to any protein-ligand complex. See [this paper](https://pubs.acs.org/doi/abs/10.1021/acs.jctc.7b00791) for introduction of these variables.<br>
+
+In the [geometric route](https://pubs.acs.org/doi/10.1021/ct3008099), the degrees of freedom is investigated one by one, through one-dimensional free-energy calculations. In BFEE, [WTM-eABF](https://pubs.acs.org/doi/abs/10.1021/acs.accounts.9b00473) is used, while other importance-sampling algorithms such as [plain eABF](https://pubs.acs.org/doi/abs/10.1021/acs.jctc.6b00447) are also acceptable.
+The [alchemical route](https://pubs.acs.org/doi/10.1021/ct3008099) is a variants of the [double decoupling method (DDM)](https://www.sciencedirect.com/science/article/pii/S0006349597787563). A thermodynamic cycle, in which the ligand and the geometric restraints are decoupled independently to guarantee the convergence of the simulations.<br>
+[这里](http://sioc-journal.cn/Jwk_hxxb/CN/10.6023/A20100489)是标准结合自由能计算方法的中文介绍.<br>
+
+## Features
+Generates all the input files for absolute binding free energy calculations;<br>
+Perform post-treatment automatedly;<br>
+Support NAMD (alchemical and geometric route) and Gromacs (geometric route) as molecular dynamics engines;<br>
+Support many file formats for the input complex structure (PSF/PDB/PRM, PRM7/RST7, TOP/PDB);<br>
+...<br>
+
+## Requirements
+Python 3.6+, PySide 2, numpy, scipy, matplotlib, parmed and MDAnalysis.<br>
+[NAMD 3.0 or later](https://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=NAMD) / [Colvars patched Gromacs](https://github.com/Colvars/colvars).<br>
+**Note: BFEE2 uses cutting-edge features of NAMD and Colvars. We highly suggest the end-user download the devel branch of NAMD from [here](https://gitlab.com/tcbgUIUC/namd/-/tree/devel) and patch it with [Colvars](https://github.com/Colvars/colvars) to prevent possible problems.**
+
+## Installation
+We suggest to install BFEE2 through conda. It will be safe if conda is install in a new environment<br>
+```
+conda create --name bfee (optional)
+conda activate bfee (optional)
+conda install -c conda-forge BFEE2
+```
+
+## Usage
+Simply run BFEE2Gui.py in terminal or PowerShell. One may need to use the absolute path on MS Windows.<br>
+A step-by-step tutorial is provided [here](https://www.nature.com/articles/s41596-021-00676-1).<br>
+
+## Citations
+When possible, please consider mentioning [Fu et al. Nat. Protoc. 2022, doi:10.1038/s41596-021-00676-1](https://www.nature.com/articles/s41596-021-00676-1#citeas) when BFEE2 is used in your project.
+
+
+Additional references:<br>
+BFEE2: [Fu et al. J. Chem. Inf. Model. 2021, 61, 2116–2123](https://pubs.acs.org/doi/abs/10.1021/acs.jcim.1c00269)<br>
+Alchemical and geometric routes [Gumbart et al. J. Chem. Theory Comput. 2013, 9, 794–802](https://pubs.acs.org/doi/abs/10.1021/ct3008099)<br>
+WTM-eABF: [Fu et al. Acc. Chem. Res. 2019, 52, 3254–3264](https://pubs.acs.org/doi/abs/10.1021/acs.accounts.9b00473) and [Fu et al. J. Phys. Chem. Lett. 2018, 9, 4738–4745](https://pubs.acs.org/doi/abs/10.1021/acs.jpclett.8b01994)<br>
+Collective variables: [Fu et al. J. Chem. Theory Comput. 2017, 13, 5173–5178](https://pubs.acs.org/doi/abs/10.1021/acs.jctc.7b00791)<br>
+Colvars module: [Fiorin et al. Mol. Phys. 2013 111, 3345-3362](https://www.tandfonline.com/doi/full/10.1080/00268976.2013.813594)<br>
+"Mother" of all restraint-based binding free-energy calculations: [Hermans et al. Isr. J. Chem. 1986, 27, 225–227](https://onlinelibrary.wiley.com/doi/abs/10.1002/ijch.198600032)<br>
+
+## Contact us
+Technique issues: Haohao Fu (fhh2626@mail.nankai.edu.cn) and Haochuan Chen (yjcoshc@mail.nankai.edu.cn)<br>
+
+This software is under the [GPLv3](https://www.gnu.org/licenses/gpl-3.0.en.html) license. For more information about the copyright of BFEE, contact the corresponding authors of the aforementioned papers (wscai@nankai.edu.cn, Christophe.Chipot@univ-lorraine.fr).
+
+
+%package help
+Summary: Development documents and examples for BFEE2
+Provides: python3-BFEE2-doc
+%description help
+# Binding Free Energy Estimator 2
+[![DOI](https://zenodo.org/badge/322234705.svg)](https://zenodo.org/badge/latestdoi/322234705)
+
+Binding free energy estimator (BFEE) is a python-based software that automates absolute binding free energy calculations through either the alchemical or geometric route by molecular dynamics simulations.<br>
+
+## Theoretical backgrounds
+The degrees of freedom of the protein-ligand (or host-guest) system are described by a series of geometric variables (or collective variables), as firstly described by the [Karplus group](https://pubs.acs.org/doi/abs/10.1021/jp0217839). In BFEE, a generalized, best-fit-rotation-based geometric variables are used, making it in principle available to any protein-ligand complex. See [this paper](https://pubs.acs.org/doi/abs/10.1021/acs.jctc.7b00791) for introduction of these variables.<br>
+
+In the [geometric route](https://pubs.acs.org/doi/10.1021/ct3008099), the degrees of freedom is investigated one by one, through one-dimensional free-energy calculations. In BFEE, [WTM-eABF](https://pubs.acs.org/doi/abs/10.1021/acs.accounts.9b00473) is used, while other importance-sampling algorithms such as [plain eABF](https://pubs.acs.org/doi/abs/10.1021/acs.jctc.6b00447) are also acceptable.
+The [alchemical route](https://pubs.acs.org/doi/10.1021/ct3008099) is a variants of the [double decoupling method (DDM)](https://www.sciencedirect.com/science/article/pii/S0006349597787563). A thermodynamic cycle, in which the ligand and the geometric restraints are decoupled independently to guarantee the convergence of the simulations.<br>
+[这里](http://sioc-journal.cn/Jwk_hxxb/CN/10.6023/A20100489)是标准结合自由能计算方法的中文介绍.<br>
+
+## Features
+Generates all the input files for absolute binding free energy calculations;<br>
+Perform post-treatment automatedly;<br>
+Support NAMD (alchemical and geometric route) and Gromacs (geometric route) as molecular dynamics engines;<br>
+Support many file formats for the input complex structure (PSF/PDB/PRM, PRM7/RST7, TOP/PDB);<br>
+...<br>
+
+## Requirements
+Python 3.6+, PySide 2, numpy, scipy, matplotlib, parmed and MDAnalysis.<br>
+[NAMD 3.0 or later](https://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=NAMD) / [Colvars patched Gromacs](https://github.com/Colvars/colvars).<br>
+**Note: BFEE2 uses cutting-edge features of NAMD and Colvars. We highly suggest the end-user download the devel branch of NAMD from [here](https://gitlab.com/tcbgUIUC/namd/-/tree/devel) and patch it with [Colvars](https://github.com/Colvars/colvars) to prevent possible problems.**
+
+## Installation
+We suggest to install BFEE2 through conda. It will be safe if conda is install in a new environment<br>
+```
+conda create --name bfee (optional)
+conda activate bfee (optional)
+conda install -c conda-forge BFEE2
+```
+
+## Usage
+Simply run BFEE2Gui.py in terminal or PowerShell. One may need to use the absolute path on MS Windows.<br>
+A step-by-step tutorial is provided [here](https://www.nature.com/articles/s41596-021-00676-1).<br>
+
+## Citations
+When possible, please consider mentioning [Fu et al. Nat. Protoc. 2022, doi:10.1038/s41596-021-00676-1](https://www.nature.com/articles/s41596-021-00676-1#citeas) when BFEE2 is used in your project.
+
+
+Additional references:<br>
+BFEE2: [Fu et al. J. Chem. Inf. Model. 2021, 61, 2116–2123](https://pubs.acs.org/doi/abs/10.1021/acs.jcim.1c00269)<br>
+Alchemical and geometric routes [Gumbart et al. J. Chem. Theory Comput. 2013, 9, 794–802](https://pubs.acs.org/doi/abs/10.1021/ct3008099)<br>
+WTM-eABF: [Fu et al. Acc. Chem. Res. 2019, 52, 3254–3264](https://pubs.acs.org/doi/abs/10.1021/acs.accounts.9b00473) and [Fu et al. J. Phys. Chem. Lett. 2018, 9, 4738–4745](https://pubs.acs.org/doi/abs/10.1021/acs.jpclett.8b01994)<br>
+Collective variables: [Fu et al. J. Chem. Theory Comput. 2017, 13, 5173–5178](https://pubs.acs.org/doi/abs/10.1021/acs.jctc.7b00791)<br>
+Colvars module: [Fiorin et al. Mol. Phys. 2013 111, 3345-3362](https://www.tandfonline.com/doi/full/10.1080/00268976.2013.813594)<br>
+"Mother" of all restraint-based binding free-energy calculations: [Hermans et al. Isr. J. Chem. 1986, 27, 225–227](https://onlinelibrary.wiley.com/doi/abs/10.1002/ijch.198600032)<br>
+
+## Contact us
+Technique issues: Haohao Fu (fhh2626@mail.nankai.edu.cn) and Haochuan Chen (yjcoshc@mail.nankai.edu.cn)<br>
+
+This software is under the [GPLv3](https://www.gnu.org/licenses/gpl-3.0.en.html) license. For more information about the copyright of BFEE, contact the corresponding authors of the aforementioned papers (wscai@nankai.edu.cn, Christophe.Chipot@univ-lorraine.fr).
+
+
+%prep
+%autosetup -n BFEE2-2.3.2
+
+%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-BFEE2 -f filelist.lst
+%dir %{python3_sitelib}/*
+
+%files help -f doclist.lst
+%{_docdir}/*
+
+%changelog
+* Mon May 15 2023 Python_Bot <Python_Bot@openeuler.org> - 2.3.2-1
+- Package Spec generated
generated by cgit v1.2.3 (git 2.25.1) at 2025-06-26 07:44:09 +0000