Pinned Repositories
benchmarkff
Compare optimized geometries and energies from various force fields with respect to a QM reference.
quanformer
quanformer: quantum mechanical analysis of molecular conformers
advent2021
Advent of Code, https://adventofcode.com/
mismatch
Web app to find mismatched base pairs between hybridized DNA sequences.
patfam
Web app to determine whether patent applications from different jurisdictions (USPTO, EPO, WIPO, etc.) are of the same family.
permeability
Adaptive biasing force (ABF) & umbrella sampling (US) simulations to calculate membrane permeability
plot_potential
Plot individual potential functions that comprise force fields. Ideal for presentations. Includes energy terms for bonds (harmonic), angles (harmonic), proper torsion (periodic cosine), improper torsion (harmonic), van der Waals (Lennard-Jones), electrostatics (Coulomb), and the Morse potential.
textsmoosh
Web app to process and combine multi-line text into a single line
vtlim's Repositories
vtlim/permeability
Adaptive biasing force (ABF) & umbrella sampling (US) simulations to calculate membrane permeability
vtlim/patfam
Web app to determine whether patent applications from different jurisdictions (USPTO, EPO, WIPO, etc.) are of the same family.
vtlim/plot_potential
Plot individual potential functions that comprise force fields. Ideal for presentations. Includes energy terms for bonds (harmonic), angles (harmonic), proper torsion (periodic cosine), improper torsion (harmonic), van der Waals (Lennard-Jones), electrostatics (Coulomb), and the Morse potential.
vtlim/advent2021
Advent of Code, https://adventofcode.com/
vtlim/dihedral-scan
Compute dihedral scan in some molecule, such as to compare an MM force field to QM results.
vtlim/GLIC
Scripts for fitting GLIC receptor to cryo-EM densities
vtlim/textsmoosh
Web app to process and combine multi-line text into a single line
vtlim/vtlim.github.io
Website of Victoria Lim
vtlim/mismatch
Web app to find mismatched base pairs between hybridized DNA sequences.
vtlim/alchemlyb
the simple alchemistry library
vtlim/alchemtest
the simple alchemistry test set
vtlim/conversion_tofix
vtlim/d3-flask-blog-post
Blog post on using D3 with flask
vtlim/drug-computing
Educational materials for, and related to, UC Irvine's Drug Discovery Computing Techniques course (PharmSci 175/275), currently taught by David Mobley.
vtlim/druid
Apache Druid: a high performance real-time analytics database.
vtlim/druid-website-src
Apache Druid website src
vtlim/Hv1
Free energy perturbation calculations for Hv1 protein
vtlim/letterlift
Bootstrap website for LetterLift, as a GitHub project page.
vtlim/misc
Miscellaneous scripts for research and data analysis using Python, OpenEye Python Toolkit, VMD/Tcl, or Grace.
vtlim/off_psi4
Quanformer is a Python-based pipeline for generating conformers, preparing quantum mechanical (QM) calculations, and processing QM results for a set of molecules and their conformers. *** This repo has a new location here:
vtlim/open-forcefield-data
Datasets for open forcefield parameterization and development
vtlim/sdsc-summer-institute-2017
SDSC Summer Institute 2017 teaching material
vtlim/shapes
From Github workshop with Caitlin (2/15/18)
vtlim/stb_proteinart
vtlim/stock-market
Exploratory analysis of stock market data in R.
vtlim/tech-docs
vtlim/TurbomoleScripts
All scripts I've written for interacting with the quantum mechanical calculation package Turbomole
vtlim/uci-thesis-latex
LaTeX template for thesis and dissertation documents at UC Irvine
vtlim/vtlim