From f4ac8f477d3e2068af248ec1732294eaa5c3b6d5 Mon Sep 17 00:00:00 2001 From: CoprDistGit Date: Mon, 15 May 2023 05:44:36 +0000 Subject: automatic import of python-bfee2 --- .gitignore | 1 + python-bfee2.spec | 236 ++++++++++++++++++++++++++++++++++++++++++++++++++++++ sources | 1 + 3 files changed, 238 insertions(+) create mode 100644 python-bfee2.spec create mode 100644 sources diff --git a/.gitignore b/.gitignore index e69de29..2bdf1f9 100644 --- a/.gitignore +++ b/.gitignore @@ -0,0 +1 @@ +/BFEE2-2.3.2.tar.gz diff --git a/python-bfee2.spec b/python-bfee2.spec new file mode 100644 index 0000000..98aa25f --- /dev/null +++ b/python-bfee2.spec @@ -0,0 +1,236 @@ +%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.
+ +## 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.
+ +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.
+[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.
+ +## Features +Generates all the input files for absolute binding free energy calculations;
+Perform post-treatment automatedly;
+Support NAMD (alchemical and geometric route) and Gromacs (geometric route) as molecular dynamics engines;
+Support many file formats for the input complex structure (PSF/PDB/PRM, PRM7/RST7, TOP/PDB);
+...
+ +## Requirements +Python 3.6+, PySide 2, numpy, scipy, matplotlib, parmed and MDAnalysis.
+[NAMD 3.0 or later](https://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=NAMD) / [Colvars patched Gromacs](https://github.com/Colvars/colvars).
+**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
+``` +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.
+A step-by-step tutorial is provided [here](https://www.nature.com/articles/s41596-021-00676-1).
+ +## 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:
+BFEE2: [Fu et al. J. Chem. Inf. Model. 2021, 61, 2116–2123](https://pubs.acs.org/doi/abs/10.1021/acs.jcim.1c00269)
+Alchemical and geometric routes [Gumbart et al. J. Chem. Theory Comput. 2013, 9, 794–802](https://pubs.acs.org/doi/abs/10.1021/ct3008099)
+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)
+Collective variables: [Fu et al. J. Chem. Theory Comput. 2017, 13, 5173–5178](https://pubs.acs.org/doi/abs/10.1021/acs.jctc.7b00791)
+Colvars module: [Fiorin et al. Mol. Phys. 2013 111, 3345-3362](https://www.tandfonline.com/doi/full/10.1080/00268976.2013.813594)
+"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)
+ +## Contact us +Technique issues: Haohao Fu (fhh2626@mail.nankai.edu.cn) and Haochuan Chen (yjcoshc@mail.nankai.edu.cn)
+ +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.
+ +## 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.
+ +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.
+[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.
+ +## Features +Generates all the input files for absolute binding free energy calculations;
+Perform post-treatment automatedly;
+Support NAMD (alchemical and geometric route) and Gromacs (geometric route) as molecular dynamics engines;
+Support many file formats for the input complex structure (PSF/PDB/PRM, PRM7/RST7, TOP/PDB);
+...
+ +## Requirements +Python 3.6+, PySide 2, numpy, scipy, matplotlib, parmed and MDAnalysis.
+[NAMD 3.0 or later](https://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=NAMD) / [Colvars patched Gromacs](https://github.com/Colvars/colvars).
+**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
+``` +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.
+A step-by-step tutorial is provided [here](https://www.nature.com/articles/s41596-021-00676-1).
+ +## 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:
+BFEE2: [Fu et al. J. Chem. Inf. Model. 2021, 61, 2116–2123](https://pubs.acs.org/doi/abs/10.1021/acs.jcim.1c00269)
+Alchemical and geometric routes [Gumbart et al. J. Chem. Theory Comput. 2013, 9, 794–802](https://pubs.acs.org/doi/abs/10.1021/ct3008099)
+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)
+Collective variables: [Fu et al. J. Chem. Theory Comput. 2017, 13, 5173–5178](https://pubs.acs.org/doi/abs/10.1021/acs.jctc.7b00791)
+Colvars module: [Fiorin et al. Mol. Phys. 2013 111, 3345-3362](https://www.tandfonline.com/doi/full/10.1080/00268976.2013.813594)
+"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)
+ +## Contact us +Technique issues: Haohao Fu (fhh2626@mail.nankai.edu.cn) and Haochuan Chen (yjcoshc@mail.nankai.edu.cn)
+ +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.
+ +## 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.
+ +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.
+[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.
+ +## Features +Generates all the input files for absolute binding free energy calculations;
+Perform post-treatment automatedly;
+Support NAMD (alchemical and geometric route) and Gromacs (geometric route) as molecular dynamics engines;
+Support many file formats for the input complex structure (PSF/PDB/PRM, PRM7/RST7, TOP/PDB);
+...
+ +## Requirements +Python 3.6+, PySide 2, numpy, scipy, matplotlib, parmed and MDAnalysis.
+[NAMD 3.0 or later](https://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=NAMD) / [Colvars patched Gromacs](https://github.com/Colvars/colvars).
+**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
+``` +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.
+A step-by-step tutorial is provided [here](https://www.nature.com/articles/s41596-021-00676-1).
+ +## 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:
+BFEE2: [Fu et al. J. Chem. Inf. Model. 2021, 61, 2116–2123](https://pubs.acs.org/doi/abs/10.1021/acs.jcim.1c00269)
+Alchemical and geometric routes [Gumbart et al. J. Chem. Theory Comput. 2013, 9, 794–802](https://pubs.acs.org/doi/abs/10.1021/ct3008099)
+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)
+Collective variables: [Fu et al. J. Chem. Theory Comput. 2017, 13, 5173–5178](https://pubs.acs.org/doi/abs/10.1021/acs.jctc.7b00791)
+Colvars module: [Fiorin et al. Mol. Phys. 2013 111, 3345-3362](https://www.tandfonline.com/doi/full/10.1080/00268976.2013.813594)
+"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)
+ +## Contact us +Technique issues: Haohao Fu (fhh2626@mail.nankai.edu.cn) and Haochuan Chen (yjcoshc@mail.nankai.edu.cn)
+ +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 - 2.3.2-1 +- Package Spec generated diff --git a/sources b/sources new file mode 100644 index 0000000..3736e74 --- /dev/null +++ b/sources @@ -0,0 +1 @@ +7c6fa3bda68dcf5d4ac4e97cf291a64b BFEE2-2.3.2.tar.gz -- cgit v1.2.3