Pinned Repositories
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's Repositories
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.