gitoliver

AbstractGraph

Inheritable Node and Edge classes

Carbohydrate_Builder

Takes an input file containing carbohydrate structures in glycam condensed format and builds their 3D structures with rotamers.

CHI_Energies

Anita Nivedha's CHI_energy Program. I need a place to store it.

CondensedSequence

Developing a standalone condensed sequence class to replace the one in GMML. It reads in a GLYCAM nomenclature condensed sequence (like generated at glycam.org/cb) and parses it into a graph structure. Ultimately goal is to generate a 3D structure. May adapt class to read in glyfinder queries.

cronGlycamWebAlive

Scripts designed to be run by cron that check if glycam.org is processing API requests for carbohydrates.

CYS-Bonds

Provide a pdb file, and this will write tleap bond commands for you.

gemsBranches

glibrary

glylib

TemplateGraph

Creating a Graph class that uses templates

gitoliver/TemplateGraph

Creating a Graph class that uses templates

gitoliver/Carbohydrate_Builder

Takes an input file containing carbohydrate structures in glycam condensed format and builds their 3D structures with rotamers.

gitoliver/AbstractGraph

Inheritable Node and Edge classes

gitoliver/CHI_Energies

Anita Nivedha's CHI_energy Program. I need a place to store it.

gitoliver/CondensedSequence

Developing a standalone condensed sequence class to replace the one in GMML. It reads in a GLYCAM nomenclature condensed sequence (like generated at glycam.org/cb) and parses it into a graph structure. Ultimately goal is to generate a 3D structure. May adapt class to read in glyfinder queries.

gitoliver/cronGlycamWebAlive

Scripts designed to be run by cron that check if glycam.org is processing API requests for carbohydrates.

gitoliver/CYS-Bonds

Provide a pdb file, and this will write tleap bond commands for you.

gitoliver/gemsBranches

gitoliver/glibrary

gitoliver/glylib

gitoliver/glylibScripts

Glylib programs and scripts I wrote for different science things.

gitoliver/gmmlBackupFeatureBranches

gitoliver/gmmlForkTest

Glycam Molecular Modeling Library

gitoliver/h-h_distances

Calculates h-h distances between a receptor.pdb file and a ligand.pdb file. Useful for comparing to STD-NMR data

gitoliver/pdb2glycam

Converts from pdb to glycam names in pdb files using gmml.

gitoliver/ReceptorOverlapGMML

Receptor overlap algorithm. Tried to make it general but needed to much personalization for the Erhard project. This is a good base to modify from in the future.

gitoliver/scienceScripts

Scripts I use for published work that I want to keep. LIkely not useful unless you've read the paper and want to do the same thing.

gitoliver/Superimpose_Enzyme_Calculate_Overlaps

gitoliver/wayland_monte_carlo

gitoliver/WiggleToSite

Adjusts glycosidic linkages to bring residues into a (second) binding site, to check if bidendate binding is possible.