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mdscriptlibrary

mechasvg

Python application for creating energy profile diagrams as '.svg' files. Extra analysis for catalytic cycle diagrams.

mobiotools

A simple yet versatile toolkit to setup quantum mechanical/molecular mechanical (QM/MM) calculations from molecular dynamics trajectories.

molden2aim

Molden2AIM is a utility program which can be used to create AIM-WFN, AIM-WFX, and NBO-47 files from a Molden file.

molden2vmd

python script format any MOLDEN to VMD

molden_orbital_movies

Molden Orbital Movies takes a set of molden files from a QM/MM MD simulation, checks the phases of each orbital compared to the previous step, and produces a VMD input file that can be used to generate a movie of the MD trajectory with a selected orbital shown.

molecular-dynamics-interaction-plot

Two scripts for MD interaction analysis (similar to interaction fraction on desmond).

molecular-entropies

Data and analysis scripts for understanding molecular entropies, including conformer flexibility

molscore

An automated scoring function to facilitate and standardize the evaluation of goal-directed generative models for de novo molecular design

mopac

Molecular Orbital PACkage

mopy

Some script to work with MOPAC output files

mpi-vina

An MPI based parallel implementation of Autodock Vina

nabladft

nablaDFT: Large-Scale Conformational Energy and Hamiltonian Prediction benchmark and dataset

nrgsuite

NRGsuite is a PyMOL plugin (GUI) for FlexAID

opendft

Open source graphical interface to various DFT/Quantum chemistry codes

openrbc

A lipid-resolution molecular dynamics simulator of human red blood cells

overreact

⚛️📈 Create and analyze chemical microkinetic models built from computational chemistry data

packmol

Packmol - Initial configurations for molecular dynamics simulations

pdb-tools

A dependency-free cross-platform swiss army knife for PDB files.

pdbfixer

PDBFixer fixes problems in PDB files

pdbtools

A set of tools for manipulating and doing calculations on wwPDB macromolecule structure files

plip

Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Salentin et al. (2015), https://www.doi.org/10.1093/nar/gkv315

porems

Pore generator for molecular simulations.

psi4

Open-Source Quantum Chemistry – an electronic structure package in C++ driven by Python

ptable_trends

Python script to plot periodic trends as a heat map over the periodic table of elements

pyadf-releases

PyADF - A scripting framework for multiscale quantum chemistry (public release versions)

pycontact

Analysis of non-covalent interactions in MD trajectories

pydescriptors

Python implementation of various 2D and 3D compactness measures.

pyentropy

Entropy for Python

pylat