uibcdf / bifree Goto Github PK
View Code? Open in Web Editor NEWFirst steps of an open library to estimate binding free energies with the MM/GBSA approach and OpenMM.
Home Page: https://www.uibcdf.org/BiFrEE
License: MIT License
First steps of an open library to estimate binding free energies with the MM/GBSA approach and OpenMM.
Home Page: https://www.uibcdf.org/BiFrEE
License: MIT License
Should we base the project on the MOLSSI cookie-cutter.
We should spend a while reading about how to set the names or numbers of the versions.
@cramg, Let's open this task for you to learn how projects work on GitHub.
Please, please define the views "Priority", "Status", "Bugs" and "Next release" as we have in the project MolSysMT
Let's start working with forks, branches, and pull requests. This is what we will do from now on:
1- Make your own fork of this repository. Do not push changes straight to the uibcdf/OpenENM if not necessary. Do not work with this repo, work with your fork.
2- Clone your forked repository in your machine.
3- Any change, modification, implementation... do it in a new branch (different from main
) in your fork.
4- Create and work with as many branches as you need. Once the implementation developed in your branch XXX
has been finished, make a PR (Pull Request) from XXX
(of your fork) to the branch main
of the uibcdf repository.
5- PRs will be reviewed always by one of the main developers different from the author (at this point I review your PRs, and you mine).
6- Once a PR has been reviewed, accepted, and merged, you have to fetch the new changes from the main
branch of uibcdf repo to your main
branch (fork repo). Keep always your main
branch of your fork updated with the main
branch of this repository.
I am sure that you will have many doubts about this process. This is the place to ask. Courage! ๐ช๐ป
sdfasdf saf sdaf sd
We should check the differences between using setuptools and numpy.distutils to configure the setup.py file. Which one should we use?
Although Poisson-Boltzmann is not our priority, we have to start thinking how this implementation should be. Let's use this issue to collect some ideas.
There is a widely used tool to solve the Poisson-Boltzmann equation of continuum electrostatics, its the APBS (Adaptive Poisson-Boltzmann Solver). Many tools depend on this APBS implementation (maybe amber does it as well). Although there is a registration process to use it, it is embedded in some other packages (how? who knows...). We should look for python libraries using this tool.
Here the paper of the last version.
APBS repo in GitHub
APBS documentation
PDB2PQR repo in GitHub # required to work with APBS
PDB2PQR documentation
A declarative, efficient, and flexible JavaScript library for building user interfaces.
๐ Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. ๐๐๐
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google โค๏ธ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.