Discover jensengroup/atom_mapper Open Source project

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Language
Python
License
MIT License
Created over 6 years ago
Updated over 3 years ago

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Atom order in one molecule is made to match that in another

propka

PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.

Python

236

xyz2mol

Converts an xyz file to an RDKit mol object

Python

204

molcalc

MolCalc is a web interface that allows anyone to build molecules and calculate molecular properties online

HTML

GB_GA

Graph-based genetic algorithm

Python

GB-GM

Graph-based generative model

Python

protonator

Quick and dirty protonation

Jupyter Notebook

fragbuilder

fragbuilder is a tool to create, setup and analyze QM calculations on peptides.

Python

RegioSQM

See http://dx.doi.org/10.1039/C7SC04156J for more details

Python

compute_pka

Computes apparent pKa values from QM dat

FP_RF_XAI

molstat

take_elementary_step

propka-3.0

PROPKA predicts the pKa values of ionizable groups in proteins based in the 3D structure.

Python

mol_gen

Molecule generation and optimization

Python

String-GA

String-based genetic algorithm

Python

GA_ChemSpace_exploration

Jupyter Notebook

mbh_catalyst_ga

Catalyst design for the Morita−Baylis−Hillman Reaction using a graph-based genetic algorithm

Python

get_conformations

generate molecular conformations

Python

RegioML

RegioML predicts the regioselectivity of electrophilic aromatic substitution reactions using machine learning.

Python

AutomatedReactionsMetaMD

Python

RegioSQM20

RegioSQM20 predicts the regioselectivity of electrophilic aromatic substitution reactions in heteroaromatic systems.

Python

ReactionDiscovery

Python

dha_htvs

Jupyter Notebook

molget

Generates molecular coordinates from chemical name using Babel and Cactus

Shell

HeckQM

A QM-based workflow for determining the regioselectivity of palladium-catalyzed Heck reactions.

Jupyter Notebook

procs

A Protein Chemical Shift Predictor

Python

smiles2coord

bash script to get coordinates from SMILES and Cactus.

Shell

TS_conf_search

Conformer search for transition states

Python

molcalc-1.3

MolCalc version 1.3 (php)

JavaScript

fragreact

Molecular reaction fragmentation scheme towards improving the accuracy of enthalpy calculation

Python

db-enzymes

Database of reaction barriers in proteins with structures

Python

statsig

Determination of statistical significance using composite errors

Python

MBH_CatalystDiscovery

Jupyter Notebook

procs15

DFT-based chemical shift predictor

C++

SI_RegioSQM20

Jupyter Notebook

CHSQM

Prediction of labile carbon hydrogens using semiempirical methods

Python

protonate

Python

RMSD_PP_TS

Locate TS based on RMSD-PP method

Python

optimized-protein-structures

Collection of optimized protein structures

xtb_gaussian

Python

find_heteroaromatic_rings

Python/RDKit script that finds unique heteroaromatic rings in a list of SMILES strings

Python

GED

Computes the graph edit distance between 2 graphs using RDKit and Networkx

Python

rdkit_qm_utilities

Python

db-regioselectivity

A database of compounds and their regioselective products

TeX

prohxms

Simple Protein HXMS prediction frame work with BioPython.

Python

procs-phaistos

ProCS amide proton chemical shift predictor module for Phaistos

C++

xyz2sdf

Python

camshift-phaistos

PHAISTOS module containing an implementation of the CamShift chemical shift predictor

C++

hydrogen-bond-correction-f3

Third-Generation Hydrogen-Bonding Corrections for Semiempirical QM Methods and Force Fields

Fortran

GA_schrock

Genetic algorithm for evolution of the Schrock catalyst.

Python

jensengroup/atom_mapper

jensengroup

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