bfee2 2.5.0__py3-none-any.whl

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  1. BFEE2/__init__.py +0 -0
  2. BFEE2/commonTools/__init__.py +0 -0
  3. BFEE2/commonTools/commonSlots.py +48 -0
  4. BFEE2/commonTools/fileParser.py +327 -0
  5. BFEE2/commonTools/ploter.py +218 -0
  6. BFEE2/doc/Doc.pdf +0 -0
  7. BFEE2/doc/__init__.py +1 -0
  8. BFEE2/gui.py +2136 -0
  9. BFEE2/inputGenerator.py +2857 -0
  10. BFEE2/postTreatment.py +502 -0
  11. BFEE2/templates_gromacs/000.colvars.template +37 -0
  12. BFEE2/templates_gromacs/000.generate_tpr_sh.template +31 -0
  13. BFEE2/templates_gromacs/000.mdp.template +70 -0
  14. BFEE2/templates_gromacs/001.colvars.template +76 -0
  15. BFEE2/templates_gromacs/001.generate_tpr_sh.template +31 -0
  16. BFEE2/templates_gromacs/001.mdp.template +70 -0
  17. BFEE2/templates_gromacs/001.readme.template +1 -0
  18. BFEE2/templates_gromacs/002.colvars.template +101 -0
  19. BFEE2/templates_gromacs/002.generate_tpr_sh.template +31 -0
  20. BFEE2/templates_gromacs/002.mdp.template +70 -0
  21. BFEE2/templates_gromacs/003.colvars.template +125 -0
  22. BFEE2/templates_gromacs/003.generate_tpr_sh.template +36 -0
  23. BFEE2/templates_gromacs/003.mdp.template +70 -0
  24. BFEE2/templates_gromacs/004.colvars.template +148 -0
  25. BFEE2/templates_gromacs/004.generate_tpr_sh.template +37 -0
  26. BFEE2/templates_gromacs/004.mdp.template +70 -0
  27. BFEE2/templates_gromacs/005.colvars.template +170 -0
  28. BFEE2/templates_gromacs/005.generate_tpr_sh.template +38 -0
  29. BFEE2/templates_gromacs/005.mdp.template +70 -0
  30. BFEE2/templates_gromacs/006.colvars.template +192 -0
  31. BFEE2/templates_gromacs/006.generate_tpr_sh.template +39 -0
  32. BFEE2/templates_gromacs/006.mdp.template +70 -0
  33. BFEE2/templates_gromacs/007.colvars.template +210 -0
  34. BFEE2/templates_gromacs/007.generate_tpr_sh.template +40 -0
  35. BFEE2/templates_gromacs/007.mdp.template +69 -0
  36. BFEE2/templates_gromacs/007_eq.colvars.template +169 -0
  37. BFEE2/templates_gromacs/007_eq.generate_tpr_sh.template +64 -0
  38. BFEE2/templates_gromacs/007_min.mdp.template +58 -0
  39. BFEE2/templates_gromacs/008.colvars.template +42 -0
  40. BFEE2/templates_gromacs/008.generate_tpr_sh.template +31 -0
  41. BFEE2/templates_gromacs/008.mdp.template +70 -0
  42. BFEE2/templates_gromacs/008_eq.generate_tpr_sh.template +31 -0
  43. BFEE2/templates_gromacs/BFEEGromacs.py +1244 -0
  44. BFEE2/templates_gromacs/__init__.py +0 -0
  45. BFEE2/templates_gromacs/find_min_max.awk +27 -0
  46. BFEE2/templates_namd/__init__.py +0 -0
  47. BFEE2/templates_namd/configTemplate.py +1094 -0
  48. BFEE2/templates_namd/fep.tcl +299 -0
  49. BFEE2/templates_namd/scriptTemplate.py +149 -0
  50. BFEE2/templates_namd/solvate.tcl +9 -0
  51. BFEE2/templates_namd/solvate_mem.tcl +9 -0
  52. BFEE2/templates_namd/updateCenters.py +311 -0
  53. BFEE2/templates_readme/Readme_Gromacs_Geometrical.txt +25 -0
  54. BFEE2/templates_readme/Readme_NAMD_Alchemical.txt +20 -0
  55. BFEE2/templates_readme/Readme_NAMD_Geometrical.txt +34 -0
  56. BFEE2/templates_readme/__init__.py +1 -0
  57. BFEE2/third_party/__init__.py +0 -0
  58. BFEE2/third_party/py_bar.py +335 -0
  59. BFEE2/version.py +2 -0
  60. bfee2-2.5.0.data/scripts/BFEE2Gui.py +18 -0
  61. bfee2-2.5.0.dist-info/LICENSE +677 -0
  62. bfee2-2.5.0.dist-info/METADATA +76 -0
  63. bfee2-2.5.0.dist-info/RECORD +65 -0
  64. bfee2-2.5.0.dist-info/WHEEL +5 -0
  65. bfee2-2.5.0.dist-info/top_level.txt +1 -0
bfee2-2.5.0.dist-info/METADATA ADDED
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+ Metadata-Version: 2.1
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+ Name: bfee2
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+ Version: 2.5.0
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+ Summary: Binding Free Energy Estimator 2
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+ Home-page: https://github.com/fhh2626/BFEE2
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+ Author: Haohao Fu, Haochuan Chen, Wensheng Cai and Chris Chipot
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+ Author-email: wscai@nankai.edu.cn
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+ Maintainer: Haohao Fu
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+ Maintainer-email: fhh2626@mail.nankai.edu.cn
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+ License: GPLv3
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+ Requires-Python: >=3.6
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+ Description-Content-Type: text/markdown
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+ License-File: LICENSE
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+ Requires-Dist: setuptools
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+ Requires-Dist: pyside2
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+ Requires-Dist: appdirs
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+ Requires-Dist: MDAnalysis
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+ Requires-Dist: matplotlib
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+ Requires-Dist: numpy
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+ Requires-Dist: scipy
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+ Requires-Dist: parmed
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+
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+ # Binding Free Energy Estimator 2
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+ [![DOI](https://zenodo.org/badge/322234705.svg)](https://zenodo.org/badge/latestdoi/322234705)
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+
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+ 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>
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+
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+ ## Theoretical backgrounds
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+ 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>
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+
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+ 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.
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+ 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>
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+ [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>
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+
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+ ## Features
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+ Generates all the input files for absolute binding free energy calculations;<br>
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+ Perform post-treatment automatedly;<br>
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+ Support NAMD (alchemical and geometric route) and Gromacs (geometric route) as molecular dynamics engines;<br>
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+ Support many file formats for the input complex structure (PSF/PDB/PRM, PRM7/RST7, TOP/PDB);<br>
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+ Support both rigid (exclude RMSD CV) and flexible (include RMSD CV) ligands and protein-protein complexes (streamlined geometrical route);<br>
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+ ...<br>
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+
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+ ## Requirements
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+ Python 3.6+, PySide 2, numpy, scipy, matplotlib, parmed and MDAnalysis.<br>
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+ [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>
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+ **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.**
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+
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+ ## Installation
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+ We suggest to install BFEE2 through conda. It will be safe if conda is install in a new environment<br>
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+ ```
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+ conda create --name bfee (optional)
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+ conda activate bfee (optional)
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+ conda install -c conda-forge BFEE2
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+ ```
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+
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+ ## Usage
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+ Simply run BFEE2Gui.py in terminal or PowerShell. One may need to use the absolute path on MS Windows.<br>
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+ A step-by-step tutorial is provided [here](https://www.nature.com/articles/s41596-021-00676-1).<br>
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+ A tutorial about new streamlined geometrical route is provided in the SI of [this paper](https://pubs.acs.org/doi/full/10.1021/acs.jcim.3c00487).<br>
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+
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+ ## Citations
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+ 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.
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+
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+
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+ Additional references:<br>
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+ BFEE2: [Fu et al. J. Chem. Inf. Model. 2021, 61, 2116–2123](https://pubs.acs.org/doi/abs/10.1021/acs.jcim.1c00269)<br>
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+ 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>
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+ 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>
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+ 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>
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+ Colvars module: [Fiorin et al. Mol. Phys. 2013 111, 3345-3362](https://www.tandfonline.com/doi/full/10.1080/00268976.2013.813594)<br>
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+ "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>
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+
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+ ## Contact us
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+ Technique issues: Haohao Fu (fhh2626@mail.nankai.edu.cn) and Haochuan Chen (yjcoshc@mail.nankai.edu.cn)<br>
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+
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+ 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).
bfee2-2.5.0.dist-info/RECORD ADDED
@@ -0,0 +1,65 @@
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+ BFEE2/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ BFEE2/gui.py,sha256=RbWeGiuhljYb0CFTiamHrSgBcLEAh5FrjOFKkzfOZ14,101330
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+ BFEE2/inputGenerator.py,sha256=DjQPNvcB0hlToAxx27hVaLwMslEnx_gekLcEVASz1bE,139316
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+ BFEE2/postTreatment.py,sha256=lC8nB7xyLODxJcAqVNbmmMKNRGKW4VinXeN5HADFCe4,20408
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+ BFEE2/version.py,sha256=E7P4nPNcQO652COodOtIHFiQJcyAuN7QsQ2FSFOcGqs,49
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+ BFEE2/commonTools/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ BFEE2/commonTools/commonSlots.py,sha256=CQ8ISiF7JNmL0Bl9KujcprufjHz1lSmgHqDu0aVO2e8,1450
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+ BFEE2/commonTools/fileParser.py,sha256=0JwDcOx6bNnkl98yB279E0iJv3yHP0Yx9INSc7ZRBWQ,11005
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+ BFEE2/commonTools/ploter.py,sha256=9m0_sW_sQpuabWML1uHMlsGgRcRtu-dwlJ9vXUPK4SM,5677
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+ BFEE2/doc/Doc.pdf,sha256=zR_QAUa15IIjbpyyflx4N89NjUN5j2pHXozMaAW7QJE,143522
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+ BFEE2/doc/__init__.py,sha256=AbpHGcgLb-kRsJGnwFEktk7uzpZOCcBY74-YBdrKVGs,1
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+ BFEE2/templates_gromacs/000.colvars.template,sha256=Ir_0DQbJeWWLcNoNpiej79jQcXsAESBDVMpN5I2cJ7c,654
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+ BFEE2/templates_gromacs/000.generate_tpr_sh.template,sha256=tIv3wTLus4iGpRlbHt394mCdQnosEQ7lg36SVPwqRxI,1124
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+ BFEE2/templates_gromacs/000.mdp.template,sha256=JEZEA0-wjr7GLqIaJAUhK4_CYjNlwzBzabNE2DQv604,1516
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+ BFEE2/templates_gromacs/001.colvars.template,sha256=cs5NNbvurNI3RaTA4rzOYJhjr685g-OL9eh3hxlXus0,1595
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+ BFEE2/templates_gromacs/001.generate_tpr_sh.template,sha256=tIv3wTLus4iGpRlbHt394mCdQnosEQ7lg36SVPwqRxI,1124
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+ BFEE2/templates_gromacs/001.mdp.template,sha256=JEZEA0-wjr7GLqIaJAUhK4_CYjNlwzBzabNE2DQv604,1516
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+ BFEE2/templates_gromacs/001.readme.template,sha256=4W8VliAYUP1KY2gLJ_YDy2TmcXYVm-PY7XikQD_bFwA,2
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+ BFEE2/templates_gromacs/002.colvars.template,sha256=KlELDd_TkOA57gISL3wCxane9LLgGLePkpSTTXUdazs,2169
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+ BFEE2/templates_gromacs/002.generate_tpr_sh.template,sha256=tIv3wTLus4iGpRlbHt394mCdQnosEQ7lg36SVPwqRxI,1124
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+ BFEE2/templates_gromacs/002.mdp.template,sha256=JEZEA0-wjr7GLqIaJAUhK4_CYjNlwzBzabNE2DQv604,1516
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+ BFEE2/templates_gromacs/003.colvars.template,sha256=3LCO0s-dLghH8QafhVyfhjbzwqH_i0tAgDJz_9En9Jw,2708
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+ BFEE2/templates_gromacs/003.generate_tpr_sh.template,sha256=Tb2Qm6gJvu-uu8YklQYafFdhB1x08K-TS3d73YIKWdA,1397
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+ BFEE2/templates_gromacs/003.mdp.template,sha256=JEZEA0-wjr7GLqIaJAUhK4_CYjNlwzBzabNE2DQv604,1516
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+ BFEE2/templates_gromacs/004.colvars.template,sha256=_PvI1r8-sa6znoOOxl6kHZHomqw1b313MT7BYQtqs8I,3300
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+ BFEE2/templates_gromacs/004.generate_tpr_sh.template,sha256=DypdlGgq2lN8uufuKlGzaxtrazG79esVaeqSNnvgEfE,1525
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+ BFEE2/templates_gromacs/004.mdp.template,sha256=JEZEA0-wjr7GLqIaJAUhK4_CYjNlwzBzabNE2DQv604,1516
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+ BFEE2/templates_gromacs/005.colvars.template,sha256=TqhY8DnRINZMDI0V2R3YBDSC8Oxn1tOtfRFj0HqnSKg,3809
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+ BFEE2/templates_gromacs/005.generate_tpr_sh.template,sha256=NbW-wkB3ld614vKTWd3r8-CMlPBjEmIOisvZjscuaCo,1653
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+ BFEE2/templates_gromacs/005.mdp.template,sha256=JEZEA0-wjr7GLqIaJAUhK4_CYjNlwzBzabNE2DQv604,1516
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+ BFEE2/templates_gromacs/006.colvars.template,sha256=uJdDyl1jjQK1SR8SdWjgrrfBE8_Ry9wzbw_f9T8WimQ,4260
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+ BFEE2/templates_gromacs/006.generate_tpr_sh.template,sha256=JRsnmcghw0VE4zPYJ_ru-PNsNG6vLHhK_WzKohAAgvg,1781
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+ BFEE2/templates_gromacs/006.mdp.template,sha256=JEZEA0-wjr7GLqIaJAUhK4_CYjNlwzBzabNE2DQv604,1516
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+ BFEE2/templates_gromacs/007.colvars.template,sha256=_6XaT7qnoGdLy56OOYGZxJzIkQBQRUGwdM-Qdc3if2Q,4512
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+ BFEE2/templates_gromacs/007.generate_tpr_sh.template,sha256=EGv-6nyL3HqKyI6mSZFU2HEF_fCg1IQtpZNyWMZ01yY,1909
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+ BFEE2/templates_gromacs/007.mdp.template,sha256=HqGhzU-mIqQK0MH1VD7bgQqtYt-OyTWuInkShtvhmD4,1497
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+ BFEE2/templates_gromacs/007_eq.colvars.template,sha256=bBJR5W_atyF1RzNzTMz0eEgyTKtx6l-B-acf8ENtizA,3584
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+ BFEE2/templates_gromacs/007_eq.generate_tpr_sh.template,sha256=vNbFIYwTDvy6mep4t34LQCKtiXeF1uA19w5DAm4usMo,3118
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+ BFEE2/templates_gromacs/007_min.mdp.template,sha256=hQRmEcJyNXWBwU0CGS4ajdhACZjmX-5m_XmXnw5qSOY,1181
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+ BFEE2/templates_gromacs/008.colvars.template,sha256=NUTiSG3EcD0TRLhuWbvPBiPUKDQ3drFo5prfRdD63uk,1044
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+ BFEE2/templates_gromacs/008.generate_tpr_sh.template,sha256=tIv3wTLus4iGpRlbHt394mCdQnosEQ7lg36SVPwqRxI,1124
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+ BFEE2/templates_gromacs/008.mdp.template,sha256=JEZEA0-wjr7GLqIaJAUhK4_CYjNlwzBzabNE2DQv604,1516
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+ BFEE2/templates_gromacs/008_eq.generate_tpr_sh.template,sha256=EPCXFoSfhOoZVyuuUE3HC6jFIBzkjlHxNgwhA_E4eHQ,1079
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+ BFEE2/templates_gromacs/BFEEGromacs.py,sha256=74eTWo78JL-63uwDz9iV2JISD5YKM3_CUzabOJop_vo,74395
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+ BFEE2/templates_gromacs/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ BFEE2/templates_gromacs/find_min_max.awk,sha256=nCbymmZzIhMeEFJFmRD-FoQOASxPyMJDNuubAHBsoks,394
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+ BFEE2/templates_namd/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ BFEE2/templates_namd/configTemplate.py,sha256=I7A6TpUlYLQ-K1kOaVbiH_u79oAfgN2PolU9pIe70H8,45274
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+ BFEE2/templates_namd/scriptTemplate.py,sha256=IJnkdBPo0dfXt2dbW87nHZlbPJYHKgCCudmnEYqHrVU,4809
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+ BFEE2/templates_namd/solvate.tcl,sha256=zJj9x0mPGAa9itPWyZLPWtcoN8oVBoRz5lBH3qJEXX8,302
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+ BFEE2/templates_namd/solvate_mem.tcl,sha256=NcsE04VQV1avszP5KEJyzslkn4k3EqtgFbhXa_vSUK4,298
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+ BFEE2/templates_namd/updateCenters.py,sha256=oIVba4hkSE4ip1EcNBFDTP3bBSkMO0yq9klbA6q2Fxk,11661
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+ BFEE2/templates_readme/Readme_Gromacs_Geometrical.txt,sha256=bPsPZZy3-dB06uSSdchmiSlGmt7ivWE6amvyKnp30bs,1027
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+ BFEE2/templates_readme/Readme_NAMD_Alchemical.txt,sha256=ELWMpk7xNq_lVHfm9A5hKWEL9P5U6duQZP_d1jVYVUg,879
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+ BFEE2/templates_readme/__init__.py,sha256=AbpHGcgLb-kRsJGnwFEktk7uzpZOCcBY74-YBdrKVGs,1
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+ BFEE2/third_party/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ BFEE2/third_party/py_bar.py,sha256=BrlMgcG_LuvyNEk6Y0rUD3bQ-FwqdTuOr1M-EsaQ1ZE,15071
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+ bfee2-2.5.0.data/scripts/BFEE2Gui.py,sha256=fVwzX2dtqc0_Re3thZq-NRzJtIbA4p9jK8Umx_aXxG4,454
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+ bfee2-2.5.0.dist-info/LICENSE,sha256=D49NePXWPL2DWuRjzaaLEJCI-g7Td73f4Fn21ixqGQo,35349
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+ bfee2-2.5.0.dist-info/METADATA,sha256=ER_peJZNJDlIHBrZqrJ_nzP5jXag7wEJCdOmgSHUhho,5540
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+ bfee2-2.5.0.dist-info/WHEEL,sha256=pkctZYzUS4AYVn6dJ-7367OJZivF2e8RA9b_ZBjif18,92
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+ bfee2-2.5.0.dist-info/RECORD,,
bfee2-2.5.0.dist-info/WHEEL ADDED
@@ -0,0 +1,5 @@
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+ Wheel-Version: 1.0
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+ Generator: bdist_wheel (0.40.0)
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+ Root-Is-Purelib: true
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+ Tag: py3-none-any
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+
bfee2-2.5.0.dist-info/top_level.txt ADDED
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+ BFEE2