Apply Normal Mode Analysis to a Protein Data Bank structure (PDB) using Gaussian Network Modelling
Last update: 2020-11-19
This repository is administered by @aarondomenzain, Departamento de Física, Área de Física de Líquidos, Universidad Autónoma Metropolitana Unidad Iztapalapa.
- Numpy
- Matplotlib
- Scipy
- Prody
- Clone
main
branch from here. - Open a terminal window and run the following commands:
pip install numpy scipy matplotlib prody
Open the file .py
with Spyder and run the program to load functions.
The available functions and their arguments and outputs are described below
PDBname
must be a string of four characters in ' ' or " " corresponding to a PDB structural set in Protein Data Bank.ModelNumber
must be the number of models contained within the same PDB structural set
Anybody is welcome to contribute to the development of this repository, but please abide by the following guidelines.
Each function should start with a commented section describing the function and explaining the parameters. Existing functions can clarify what style should be used. When making any changes to an existing function (*.m
-file), change the date and name of developer near the bottom of this commented section in the last modified line.
- For any development, whether bugfixes, introducing new functions or new/updated features for existing functions: make a separate branch from
devel
and name the branch for instance after the function/feature you are fixing/developing. If you work on a fix, start the branch name withfix/
, if you work on a feature, start the branch name withfeat/
. Examples:fix/format_reactions
orfeat/new_algorithms
. - Make commits to this branch while developing. Aim for backwards compatibility to accommodate users with older software versions.
- When you are happy with your new function/feature, make a pull request to the
devel
branch. Also, see Pull request below.
Use semantic commit messages to make it easier to show what you are aiming to do:
chore
: updating binaries (modelMATLAB
structures), UniProt databases, physiology and protemics data files, etc.doc
: updating documentation (indoc
folder) or explanatory comments in functions.feat
: new feature added, e.g. new function introduced / new parameters / new algorithm / etc.fix
: bugfix.refactor
: see code refactoring.style
: minor format changes of functions (spaces, semi-colons, etc., no code change).
Examples:
feat: exportModel additional export to YAML
chore: any routine task
fix: optimizeProb parsing results from Gurobi
More detailed explanation or comments can be left in the commit description.
- No changes should be directly commited to the
master
ordevel
branches. Commits are made to side-branches, after which pull requests are made for merging withmaster
ordevel
. - The person making the pull request and the one accepting the merge cannot be the same person.
- A merge with the main branch invokes a new release.