diff options
| -rw-r--r-- | .gitignore | 1 | ||||
| -rw-r--r-- | python-bfee2.spec | 330 | ||||
| -rw-r--r-- | sources | 2 |
3 files changed, 167 insertions, 166 deletions
@@ -1 +1,2 @@ /BFEE2-2.3.2.tar.gz +/BFEE2-2.4.0.tar.gz diff --git a/python-bfee2.spec b/python-bfee2.spec index 8f8b4a2..c673a01 100644 --- a/python-bfee2.spec +++ b/python-bfee2.spec @@ -1,11 +1,11 @@ %global _empty_manifest_terminate_build 0 Name: python-BFEE2 -Version: 2.3.2 +Version: 2.4.0 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 +Source0: https://mirrors.aliyun.com/pypi/web/packages/b9/ba/a6836935f50b0380412674e204320c27420a76d4979ca69a1e459d47127d/BFEE2-2.4.0.tar.gz BuildArch: noarch Requires: python3-setuptools @@ -18,58 +18,58 @@ 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).
+# 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 @@ -79,120 +79,120 @@ 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).
+# 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).
+# 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 +%autosetup -n BFEE2-2.4.0 %build %py3_build @@ -206,20 +206,20 @@ 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 + 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 + 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 + 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 + 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 + find usr/share/man -type f -printf "\"/%h/%f.gz\"\n" >> doclist.lst fi popd mv %{buildroot}/filelist.lst . @@ -232,5 +232,5 @@ mv %{buildroot}/doclist.lst . %{_docdir}/* %changelog -* Tue May 30 2023 Python_Bot <Python_Bot@openeuler.org> - 2.3.2-1 +* Thu Jun 08 2023 Python_Bot <Python_Bot@openeuler.org> - 2.4.0-1 - Package Spec generated @@ -1 +1 @@ -7c6fa3bda68dcf5d4ac4e97cf291a64b BFEE2-2.3.2.tar.gz +7ad79f8f9262185c6be1e7730ee4e0fb BFEE2-2.4.0.tar.gz |