xyz-files

There are 0 repository under xyz-files topic.

• zotko / xyz2graph

  Convert an xyz file into a molecular graph and create a 3D visualisation of the graph.

  molecular-graphchemistryadjacency-listadjacency-matrixmoleculechemoinformaticscovalent-radiixyz-filesxyz-readervisualizationatomic-coordinatesplotly3d-plotnetworkxjupyter-notebookpythonatommolecule-visualizationxyzmolecular-graphs
  Language:Python 70

• radi0sus / xyz2tab

  Convert XYZ data to bond lengths & angles, calculate contacts, planes and dihedral angles and print tables

  xyzxyz-readerxyz-filesdft-calculationsxmolorca-quantum-chemistryorcacoordinatesbondlengthangletabletablesviewerxyz-viewermolecule-visualizationvisualizationbest-fit-planedihedral-anglestorsion-angles
  Language:Python 27

• justinmeiners / molecule-viewer

  3D chemical molecule visualizer for XYZ files.

  cppopenglxyz-fileschemistry
  Language:C++ 15

• antonin-lfv / 3D-plot-Python-interpolation

  How to plot a 3D surface with python by interpolation

  3d-graphics3d-plotxyz-filessurface-modelingcolor-themegradientcolour-spacesmatplotlib-pyplotinterpolation-methodslinear-regression3d3d-modelssurface
  Language:Python 6

• radi0sus / xyzoverlay

  Python 3 script for overlaying or superimposing two or more molecules. The overlayed / superimposed molecules can be displayed and the modified coordinates can be saved as xyz files. Coloring by atom or molecule is possible.

  computational-chemistrydftkabschkabsch-algorithmmoleculemoleculesoverlaysuperpositionxyz-filesxyz-readercoordinatesmolecule-viewermolecule-visualizationcoordination-chemistryinorganic-chemistry
  Language:Python 6

• li012589 / xyzFile2Animation

  A small python script to create animation from multiply xyz files

  molecular-dynamicsxyzxyz-filesanimation
  Language:Python 5
• color_voronoi

  kramergroup / color_voronoi

  Color Voronoi diagram according to scalar property of points.

  voronoivoronoi-polygonsxyz-tilesxyz-filesxyzcolormap
  Language:Jupyter Notebook 4

• mukherjee07 / ORCA-project-Li-ion-battery-material-discovery

  These are important tools written for working with ORCA (a computational chemistry open source package) in a super-computing environment. They include multiple job submission scripts (BASH), multiple job cancellation (BASH), job setup with different geometries (in python), data extraction (BASH), final optimized geometry extraction (BASH) and

  computational-chemistrycluster-computingorca-quantum-chemistrydata-extractionxyz-files
  Language:Python 4

• funkymunkycool / smooth_trajectory

  Script to smooth xyz and cube file trajectories. Applies spline interpolation to the trajectory

  atomic-physicsatomistic-simulationscubesolid-state-physicstrajectoryxyzxyz-files
  Language:Python 2

• HumanOsv / GSCheckDuplicates

  The comparison between two structures is based on the cartesian coords.

  cheminformaticsduplicatesxyz-files
  Language:Perl 2

• radi0sus / xyzalign

  Align atomic coordinates in xyz files. Align one or more atoms to x-, y- and z-axes. Set origin to a selected atom or a centroid of selected atoms. Rotate atomic coordinates about arbitrary angles. Translate atomic coordinates.

  3d-coordinatealigncomputational-chemistrycoordinatesdftmoleculesorcaorca-quantum-chemistryrotatetranslatexyzxyz-filesinorganic-chemistrycoordination-chemistrymoleculeorientationrotationrotation-matrixtranslationxyz-reader
  Language:Python 2

• AkimovLab / Project_NBRA-BL-NA-MD_SiNCs

  This repository contains the working files used in the work "Hot Electron Cooling in Silicon Nanoclusters via Landau-Zener Non-Adiabatic Molecular Dynamics: Size Dependence and Role of Surface Termination"

  adiabatic-molecular-dynamicsdftblandau-zenertrajectoriesxyzxyz-files
  Language:Python 1

• CTM-ITODYS / mol2surface

  Fortran code that convert xyz-file to POSCAR file for VASP calculation

  file-converterfortranposcarvaspvasp-calculationsvasp-filesxyz-files
  Language:Fortran 1

• CTM-ITODYS / xyz2bas

  Fortran code that convert xyz file to bas file for Fireball

  bas-filesfortranxyz-files
  Language:Fortran 1

• CTM-ITODYS / bas2xyz

  Fortran code that convert bas file to xyz file for Fireball.

  bas-filesfortranxyz-files
  Language:Fortran 0

• FachengG / XYZ_to_POSCAR

  Transfer XYZ file into POSCAR/CONTCAR file with re-center feature. Useful for single molecule calculation in VASP.

  vaspvasp-processingvasp-poscarxyzxyz-filesvasp-files
  Language:Python 0

• nbehrnd / xyz2pov

  Converts .xyz coordinate files to povray scenes

  pov-raypovrayvisualizationxyz-files
  Language:Python 0

• rutujsg / computational-chemistry

  chemistrycomputational-chemistrymolecular-structureslinear-algebrajupyter-notebookpython3xyz-filesperiodic-table
  Language:Jupyter Notebook 0

• TahsinGormus / basicConcepts

  Some codes that I prepared for fundamental research interests.

  biascorrelation-coefficientfitpolynomialroot-mean-square-errorscatter-indexxyz-files
  Language:MATLAB 0

• caefleury / PIBITI-SIMULACOES

  Simulações do projeto de iniciação científica em simulações termodinâmicas em estruturas nanomoleculares

  graphenelammpspythonxyz-filesreaxffcharge
  Language:Python

• li012589 / npz2xyz

  A small tool for converting npz files to xyz files.

  npz-filesxyz-filesmolecular-dynamics
  Language:Python

• rani8vish / config-management

  xyz-files

• Warpv / allatom-polymere-system-in-VMD

  create allatom polymere system from .xyz file in VMD

  pdbpdb-filesvmdxyzxyz-filespolymeremolecular-dynamics-simulation