BAT.py | Binding Affinity Tool is a fully automated tool | GPU library

by GHeinzelmann Python Version: Current License: MIT

X-Ray Key Features Code Snippets Community Discussions(2)Vulnerabilities Install Support

kandi X-RAY | BAT.py Summary

BAT.py is a Python library typically used in Hardware, GPU applications. BAT.py has no bugs, it has no vulnerabilities, it has a Permissive License and it has low support. However BAT.py build file is not available. You can download it from GitHub.

The Binding Affinity Tool (BAT.py) is a python tool for fully automated absolute binding free energy calculations. Its workflow encompasses the creation of the bound complex, generation of parameters using Antechamber, preparation of the simulation files, and post-processing to retrieve the binding free energy. By using the pmemd.cuda software from AMBER20, it is able to perform several calculations at a reduced computational cost using graphics processing units (GPUs). BAT.py can perform binding free energy calculations by two alchemical routes in the presence of restraints, either with double decoupling (DD) procedure or with the simultaneous decoupling recoupling (SDR) method. It can also apply a physical route, through the APR method, suitable for ligands that have free access to the solvent. The program is compatible with the simulation package AMBER20, also requiring a few installed programs to work properly, which are listed in the next section.

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Security

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Support

BAT.py has a low active ecosystem.

It has 21 star(s) with 7 fork(s). There are 3 watchers for this library.

It had no major release in the last 6 months.

There are 4 open issues and 10 have been closed. On average issues are closed in 63 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of BAT.py is current.

Quality

BAT.py has no bugs reported.

Security

BAT.py has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

License

BAT.py is licensed under the MIT License. This license is Permissive.

Permissive licenses have the least restrictions, and you can use them in most projects.

Reuse

BAT.py releases are not available. You will need to build from source code and install.

BAT.py has no build file. You will be need to create the build yourself to build the component from source.

Installation instructions are available. Examples and code snippets are not available.

Top functions reviewed by kandi - BETA

kandi has reviewed BAT.py and discovered the below as its top functions. This is intended to give you an instant insight into BAT.py implemented functionality, and help decide if they suit your requirements.

Calculate fe values
Compute the error of the covariance matrix
Compute free energy differences
Generate the fd
Compute expectations
Convert KxLxN_max array to KxN
Compute the log of the sum of exponents
Compute the expectations in the inner function
R Compute the Shannon - Darling similarity test
Solve the m_k_k
Estimate the integrated autocorrelation time
Compute the free energies using self - consistent iteration
Compute objective function
Compute the overlap matrix
Subsample uncorrelated snapshots
Compute the PMF for a reduced distribution
Estimate the femm using OpenMM
Compute the average energy and entropy for each state
Compute multiple expectations
Compute the adaptive free energies using Newton s method
Plots a Q - Q - Q plot
R Compute the free energies
Compute the Perturbed expectations
Compute the free energies for each bin
Calculate the equilibration using a binary search
Detect the equilibration of a timeseries

Get all kandi verified functions for this library.

BAT.py Key Features

No Key Features are available at this moment for BAT.py.

BAT.py Examples and Code Snippets

No Code Snippets are available at this moment for BAT.py.

Community Discussions

Trending Discussions on BAT.py

Executing other python scripts gives NameError exception

How to fix: NameError: name 'on_key_release' is not defined? (Python)

QUESTION

Executing other python scripts gives NameError exception

Asked 2020-Jul-23 at 20:38

I have two .py scripts on the same folder, and I have a function like this on one:

...

ANSWER

Answered 2020-Jul-23 at 20:38

The exec() function supports dynamic execution of Python code. It is not executing a shell command. To execute a shell command, in your case calling another python file. Instead you can use for example:

Source https://stackoverflow.com/questions/63062635

QUESTION

How to fix: NameError: name 'on_key_release' is not defined? (Python)

Asked 2018-Feb-10 at 11:03

I was typing in some code (as most of us do) from a book, but when I ran it, I got this error: NameError: name 'on_key_release' is not defined. I typed it in perfectly, but it still won't work, and I know that I have defined it. It may be because the book is for python3 and I have python2. The full error is:

...

ANSWER

Answered 2017-Nov-08 at 04:25

You did not define on_key_release.

Over here, I can see that you defined on_key_press twice. did you mean to define one of them as on_key_release?

Source https://stackoverflow.com/questions/47171562

Community Discussions, Code Snippets contain sources that include Stack Exchange Network

Vulnerabilities

No vulnerabilities reported

Install BAT.py

To use BAT.py, download the files from this repository, which already contain an example for ligand binding to the second bromodomain of the BRD4 protein - BRD4(2). In order to perform all the steps from BAT.py, the following programs must be installed and in your path:. VMD (Visual Molecular Dynamics) [1] - https://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD. Openbabel 2.4.1 [2] - https://github.com/openbabel/openbabel/releases/tag/openbabel-2-4-1 †. MUSTANG v3.2.3 (MUltiple (protein) STructural AligNment alGorithm) [3] - http://lcb.infotech.monash.edu.au/mustang/. AmberTools20 or later [4] - http://ambermd.org/AmberTools.php ‡. pmemd.cuda software from AMBER20 [4] - http://ambermd.org/GetAmber.php. † Had problems with wrong protonation using Openbabel 3, so keeping the 2.4.1 version for now, might change in the future. ‡ If pdb4amber from Ambertools does not work, add the following line to your amber.sh file: export PYTHONPATH=$PYTHONPATH:$AMBERHOME/lib/python3.8/site-packages/pdb4amber-1.7.dev0-py3.8.egg/. The folder ./BAT/all-poses contains an example of system input files, with a docked receptor from the 5uez crystal structure (LMCSS-5uf0_5uez_docked.pdb), as well as 9 docked poses for the ligand with the 5uf0 crystal structure (pose0.pdb to pose8.pdb). The docking files were generated and converted to .pdb using Autodock Vina and AutodockTools, following a protocol adapted from the CELPP challenge tutorial (https://docs.google.com/document/d/1iJcPUktbdrRftAA8cuVa32Ri1TPr2XvZVqTccDja2OM). Inside the ./all-poses folder there is also the original crystal structure file for 5uf0. Below we show an example of using these files to calculate the standard binding free energies of the top 5 docked poses and the crystal structure, with all the necessary steps in the calculation.

Support

For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .

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