Christopher van den Berg's repositories
aizynthfinder-seq2seq-transformer
Research project and literature review focused on integrating SMILES-based retrosynthesis using attention-based encoder-decoder and transformer models into AstraZeneca’s AiZynthFinder retrosynthetic planning tool.
Caesar-and-Substitution-
Caesar and mixed alphabet substitution cipher.
gromacs-tutorials
Introductory GROMACS project that sets up the topology, energy minimisation, NVT and NPT equilibration and molecular dynamics simulation of the small protein 'Coagulation Factor Xa' in ionised water.
lammps-tutorials
Introductory LAMMPS project based on the tutorials authored by Simon Gravelle. The tutorial topics include the simple simulation of a Lennard-Jones fluid, deformation of a carbon nanotube, and the solvation of a simple PEG molecule in water.
machine-learning-in-drug-discovery
Literature review exploring the intersection of molecular representations, cheminformatics, and machine learning within the field of chemistry. Each section is supplemented with case studies presented as custom JupyterLab exercises, designed to facilitate hands-on learning and the practical application of the concepts discussed.
paper-qa-chemistry
Extends the Paper QA package for use with the author's Zotero database papers in organic chemistry, drug discovery & development, cheminformatics and the applications of machine learning to these areas.
Python-Programming-Exercises
A collection of Python exercises designed to cover basic to advanced topics. The exercises start with syntax reminders and commonly used modules, then progress to implementing search and sort algorithms, building neural networks, and more.
Plurality-
Simulates a plurality election with 9 candidates the user inputs along with their votes.
Readability
Readability test based on the Coleman-Liau index
Spell-checker-
A dictionary that uploads words from a file and stores them in either a hash table or trie data structure. This can then be used to spell check a given text. (Note, only the helper functions file has been uploaded as remaining files are the intellectual property of Harvard University).