Calculate Root-mean-square deviation (RMSD) of two molecules, using rotation, in xyz or pdb format
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Mar 16, 2026 - Python
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atoms
Here are 18 public repositories matching this topic...
visualise atoms and molecules in 2D and 3D interactive..
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Mar 27, 2026 - Python
Standardized Gabor atom representations with minimal time-frequency uncertainty.
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Jul 10, 2024 - Python
Bioinformatics with Python and Blender 3D
python json bioinformatics chemistry blender dna collections atoms molecular globalvariables globalvariablesmanagement
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Dec 8, 2020 - Python
Contact Extractor from PDB/mmCIF coordinate files
atom parser geometry pdb contacts distance extractor structure atoms contact mmcif 3d 3d-structure 3d-coordinate bioinformatics-tool atom-atom macromolecules contact-extractor atom-atom-pairs clapnac
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May 9, 2025 - Python
Determine the frequency of different amino acid sequences in protein-protein interactions using a distributed memory parallelised computing environment with hyper-threading
python data-science bioinformatics algorithm hpc mpi container distributed-computing singularity protein high-performance-computing atoms interaction singularity-container amino-acids mpi4py hyper-threading distributed-memory
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Apr 7, 2021 - Python
Decoding atoms and molecules from trajectories.
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Aug 3, 2026 - Python
A tool for removing atoms in IMD config files, just like a cookie cutter in higher dimensions
atom simulation molecular-dynamics molecular-simulation molecular-dynamics-simulation atoms imd imd-cookie-cutter higher-dimensions
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Dec 9, 2020 - Python
Vpython Simulation of Moveing Air particles.
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Aug 19, 2018 - Python
What polarization of light does an atom "see"? Well, that depends...
quantum transitions atoms light-polarization rotations-operations electric-field amo-physics quantization-axis
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May 22, 2026 - Python
A project that I made for Physics class, a basic sim for simulating an excited electron in a hydrogen atom
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May 27, 2018 - Python
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