rmsd

There are 0 repository under rmsd topic.

mdtraj / mdtraj
An open library for the analysis of molecular dynamics trajectories
molecular-dynamics python mdtraj rmsd dihedral-angles pdb pdb-files molecular-dynamics-trajectories
Language:Python 556
charnley / rmsd
Calculate Root-mean-square deviation (RMSD) of two molecules, using rotation, in xyz or pdb format
rmsd xyz pdb alignment molecule structure reordering kabsch atoms assignment
Language:Python 474
RMeli / spyrmsd
📐 Symmetry-corrected RMSD in Python
rmsd symmetry cadd computational-biology computational-chemistry computer-aided-drug-design docking drug-discovery molecular-docking
Language:Python 75
sarisabban / RamaNet
Preforms De novo protein design using machine learning and PyRosetta to generate a novel protein structure
protein-structure machine-learning pdb dataset neural-network denovo-design denovo protein-design rmsd topology hpc ab-initio amino-acids
Language:Python 47
jewettaij / superpose3d
register 3D point clouds using rotation, translation, and scale transformations.
registration 3d structure-comparison point-cloud rmsd point-cloud-registration scale-transformations cryo-em cryoem
Language:Python 39
jewettaij / superpose3d_cpp
header-only C++ library for registering 3D point clouds using rotation, translation, and scale transformations
registration 3d header-only point-cloud rmsd point-cloud-registration scale-transformations
Language:C++ 22
luisico / clustering
VMD plugin to calculate and visualize clusters of conformations for a trajectory
vmd rmsd clustering molecular-dynamics
Language:Tcl 20
hmcezar / clusttraj
Python script that receives a molecular dynamics or Monte Carlo trajectory and performs agglomerative clustering to classify similar structures.
clustering rmsd openbabel python-script molecular-dynamics monte-carlo-trajectory trajectory distance-matrix
Language:Python 18
RUBi-ZA / MODE-TASK
PCA and normal mode analysis of proteins
principal-component-analysis normal-modes tsne mds protein molecular-dynamics molecular-dynamics-simulation python rmsd trajectory-analysis pdb
Language:C++ 15
grimme-lab / rmsd-tool
Tool to calculate the root mean square deviation between molecular structures
rmsd structure-comparison
Language:Fortran 11
manny405 / mcse
Molecular Crystal Simulation Library (mcse) is an open-source Python package for manipulating and analyzing molecular crystal structures
polymorph polymorphism molecular crystals rmsd crystallography dft machine-learning molecular-crystals analysis generation python
Language:Python 11
berhane / arbalign
aligns arbitrarily ordered isomers
rmsd alignment hungarian-method isomer chemistry similarity-measures linear-assignment-problem
Language:Python 8
QDcvd / Gromacs-xvg2csv-Printer
利用xvg生成的csv文件进行画图的脚本
xvg rmsd gromacs python python-script
Language:Python 8
UnixJunkie / chemoinfo_recipes
Command line recipes for the working chemoinformatician
chemoinformatics howto openbabel rdkit ligand rmsd chemaxon
7
UnixJunkie / fragger
A protein fragments picker
rmsd protein-fragments-picker database protein-fragments ocaml protein-design
Language:OCaml 7
ardcore / fit_transform
Calculate and apply the optimal transformation matrix that minimizes the RMSD (root mean squared deviation) between two paired sets of points.
kabsch rmsd cheminformatics molecular-modeling
Language:JavaScript 4
nbehrnd / aRMSD
Pairwise structural comparison of .xyz, a fork of aRMSD to work without PyInstaller in Linux. Note the project «aRMSD-minimalWindowsSupport», too.
python structure model alignment crystallography kabsch kabsch-algorithm rmsd cif pdb xyz
Language:Python 4
RUBi-ZA / pyMODE-TASK
MODE-TASK plugin for PyMOL
pca nma molecular-dynamics normal-modes mds tsne-algorithm pymol pymol-plugin pymode-task tkinter principal-component-analysis protein-structure protein md pdb rmsd trajectory-analysis molecular-dynamics-simulation python
Language:C++ 4
GeoRouv / RMSD
📐 Implementation of the c-RMSD and d-RMSD algorithms
rmsd rmsd-algorithms conformation crmsd-distances distances
Language:Jupyter Notebook 3
luisico / rmsdtt
VMD plugin for rmsd calculation and fitting of molecular structures
vmd rmsd
Language:Tcl 3
Maximato / PDBan
Project for analysis of protein structures in .pdb file format. It calculates some structure parameters and can compare two structures by calculating the RMSD.
gyration-radius pdb-structure rmsd pdb
Language:Python 2
rsrchen / ecs129-project
A program that compares a protein structure prediction to a solved structure and evaluates the prediction's accuracy using RMSD.
alphafold2 protein protein-structure python rmsd
Language:Python 2
amaurypm / rmsdmat
Superimpose a set of protein structures and report a RSMD matrix, in CSV and Mega-compatible formats.
protein protein-structure rmsd structure bioinformatics bioinformatics-tool csv-export meg dendogram
Language:Julia 1
chanioxaris / molecular-configurations
Clustering for molecular configurations
clusters curves frechet-distance metric-distance-algorithm rmsd
Language:C 1
luisico / itrajcomp
interactive Trajectory Comparison
vmd rmsd molecular-dynamics
Language:Tcl 1
luisico / swap
VMD plugin to swap coordinates between atoms in a molecule
vmd rmsd
Language:Tcl 1
sorinlab / fahda-rmsd-rg
F@H Data Analysis: Root-mean-square Deviation & Radius of Gyration Calculations
rmsd rg radius-of-gyration root-mean-square-deviation atomic-distance
Language:Perl 1
stdlib-js / stats-incr-mrmse
Compute a moving root mean squared error (RMSE) incrementally.
nodejs javascript stdlib node node-js statistics stats mathematics math error err rmse rmsd mse msd residuals squares deviation difference diff
Language:Makefile 1
stdlib-js / stats-incr-rmse
Compute the root mean squared error (RMSE) incrementally.
nodejs javascript stdlib node node-js statistics stats mathematics math error err rmse rmsd mse msd residuals deviation difference diff delta
Language:Makefile 1
boneta / RMSD-Clustering
Clustering based on RMSD
chemistry clustering f2py kabsch rmsd
Language:Python 0
Jonas-Finkler / RMSD-finder
Program to determine the minimal RMSD between two atomic configurations
alignment atomistic-simulations hungarian-algorithm molecule rmsd root-mean-square-deviation
Language:Fortran 0
Joseph-Ellaway / per-residue-distance
Calculates the per-residue atomic distance between two proteins
bioinformatics bioinformatics-tool euclidean-distances gemmi matplotlib pdbe protein-structure rmsd structural-biology
Language:Python 0
m-rauen / Coordinates_Analyzer
Python web app that compare, calculate and plot the mathematical differences between 2 sets of atomic coordinates
bioinformatics chemistry computational-chemistry geometry-optimization kabsch-algorithm rmsd rmsd-algorithms xyz
Language:Python 0
saysayani11 / Structural-analysis-CK2A
RMSD and B Factor Analysis
b-factor biopython casein-kinase rmsd structural-biology
Language:Python 0
amaurypm / pyrmsdmat
Superimpose a set of protein structures and report a RSMD matrix, in CSV and Mega-compatible formats, using Pymol as a module
rmsd protein-structure bioinformatics bioinformatics-tool dendogram csv-export meg structure
Language:Python
nbehrnd / rmsdModerator
batchwise Kabsch test with Jimmy Charnley's calculate_rmsd (https://github.com/charnley/rmsd) on multiple CPUs
python crystallography kabsch similarity rmsd xyz
Language:Python

rmsd

mdtraj / mdtraj

charnley / rmsd

RMeli / spyrmsd

sarisabban / RamaNet

jewettaij / superpose3d

jewettaij / superpose3d_cpp

luisico / clustering

hmcezar / clusttraj

RUBi-ZA / MODE-TASK

grimme-lab / rmsd-tool

manny405 / mcse

berhane / arbalign

QDcvd / Gromacs-xvg2csv-Printer

UnixJunkie / chemoinfo_recipes

UnixJunkie / fragger

ardcore / fit_transform

nbehrnd / aRMSD

RUBi-ZA / pyMODE-TASK

GeoRouv / RMSD

luisico / rmsdtt

Maximato / PDBan

rsrchen / ecs129-project

amaurypm / rmsdmat

chanioxaris / molecular-configurations

luisico / itrajcomp

luisico / swap

sorinlab / fahda-rmsd-rg

stdlib-js / stats-incr-mrmse

stdlib-js / stats-incr-rmse

boneta / RMSD-Clustering

Jonas-Finkler / RMSD-finder

Joseph-Ellaway / per-residue-distance

m-rauen / Coordinates_Analyzer

saysayani11 / Structural-analysis-CK2A

amaurypm / pyrmsdmat

nbehrnd / rmsdModerator