An open library for the analysis of molecular dynamics trajectories
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Dec 16, 2024 - Python
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rmsd
Here are 39 public repositories matching this topic...
Calculate Root-mean-square deviation (RMSD) of two molecules, using rotation, in xyz or pdb format
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Dec 17, 2024 - Python
📐 Symmetry-corrected RMSD in Python
computational-biology computational-chemistry drug-discovery docking symmetry rmsd cadd molecular-docking computer-aided-drug-design
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Nov 18, 2024 - Python
Preforms De novo protein design using machine learning and PyRosetta to generate a novel protein structure
machine-learning topology neural-network hpc pdb protein-structure dataset ab-initio amino-acids denovo protein-design rmsd denovo-design
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Jan 3, 2022 - Python
register 3D point clouds using rotation, translation, and scale transformations.
point-cloud registration cryo-em 3d rmsd cryoem point-cloud-registration structure-comparison scale-transformations
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Aug 12, 2024 - Python
header-only C++ library for registering 3D point clouds using rotation, translation, and scale transformations
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Jun 9, 2022 - C++
VMD plugin to calculate and visualize clusters of conformations for a trajectory
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Oct 24, 2018 - Tcl
Python script that receives a molecular dynamics or Monte Carlo trajectory and performs agglomerative clustering to classify similar structures.
clustering python-script molecular-dynamics openbabel trajectory rmsd distance-matrix monte-carlo-trajectory
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Sep 4, 2024 - Python
PCA and normal mode analysis of proteins
python pdb molecular-dynamics protein molecular-dynamics-simulation mds trajectory-analysis tsne principal-component-analysis rmsd normal-modes
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May 16, 2024 - C++
Molecular Crystal Simulation Library (mcse) is an open-source Python package for manipulating and analyzing molecular crystal structures
python machine-learning dft analysis crystallography generation polymorphism molecular rmsd polymorph molecular-crystals crystals
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May 30, 2022 - Python
Tool to calculate the root mean square deviation between molecular structures
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Jul 25, 2022 - Fortran
aligns arbitrarily ordered isomers
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Dec 28, 2019 - Python
A protein fragments picker
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Sep 26, 2019 - OCaml
Calculate and apply the optimal transformation matrix that minimizes the RMSD (root mean squared deviation) between two paired sets of points.
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Mar 13, 2019 - JavaScript
MODE-TASK plugin for PyMOL
python pdb pymol-plugin protein-structure molecular-dynamics protein pymol pca molecular-dynamics-simulation tkinter mds trajectory-analysis tsne-algorithm principal-component-analysis md rmsd nma normal-modes pymode-task
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Apr 28, 2023 - C++
📐 Implementation of the c-RMSD and d-RMSD algorithms
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Apr 23, 2021 - Jupyter Notebook
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