internal-coordinates

Here are 4 public repositories matching this topic...

RMeli / irc

Transfrormation between Cartesian coordinates and redundant internal coordinates

chemistry computational-chemistry computational-physics coordinates chem coordinate-transformation electronic-structure phys internal-coordinates internal-redundant-coordinates geometry-optimization

Updated Jun 2, 2022
C++

falategan / motif-conformation-finder

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Python script to find all instances of an amino acid sequence motif in protein structures and parse their internal coordinates

bioinformatics structural-biology pdb protein-structure protein biopython peptides dihedral-angles internal-coordinates

Updated Sep 14, 2023
Python

An autoencoder designed for dimensionality reduction of a protein structure's feature space that describes the structural environment of an amino acid by looking at the relative relative positions, orientations and dihedral angles of neighbouring residues in Euclidean space.

bioinformatics deep-learning structural-biology pdb protein-structure protein biopython autoencoder dimensionality-reduction unsupervised-learning quaternions peptides dihedral-angles internal-coordinates

Updated Dec 1, 2024
Python

Tsumura-m / PySCIVR

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Python package for on-the-fly semiclassical (Herman–Kluk / SC-IVR) wavepacket dynamics and vibrational spectra in curvilinear coordinates

quantum-mechanics molecular-dynamics quaternion on-the-fly internal-coordinates vibrational-spectroscopy curvilinear-coordinates semiclassical-dynamics rotational-spectroscopy wave-packet

Updated Oct 27, 2026
Python

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