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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
[](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
[](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
[](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
|
