11 packages found

numgrid

Numerical integration grid for molecules.
  1. dft
  2. grid
  3. integration
  4. molecular
  5. python-interface
4 Contributors
2.1.1published 9 months agoMPL-2.0

pdb2pqr

Automates many of the common tasks of preparing structures for continuum solvation calculations as well as many other types of biomolecular structure modeling, analysis, and simulation.
  1. chemistry
  2. molecular
  3. biology
  4. science
  5. bioinformatics
  6. biophysics
  7. hacktoberfest
  8. help-wanted
19 Contributors
3.7.1published 4 months agoOther

freud-analysis

Powerful, efficient trajectory analysis in scientific Python.
  1. simulation
  2. analysis
  3. molecular
  4. dynamics
  5. soft
  6. matter
  7. particle
  8. system
  9. computational
  10. physics
  11. computational-chemistry
  12. computational-physics
  13. data-analysis
  14. molecular-dynamics
  15. monte-carlo-simulation
  16. particle-system
  17. python
  18. science
  19. scientific-computing
  20. spatial-analysis
57 Contributors
3.2.0published 2 months agoOther

molecularnodes

Toolbox for molecular animations with Blender and Geometry Nodes.
  1. biochemistry
  2. blender
  3. blender-addon
  4. geometry-nodes
  5. molecular
  6. molecular-dynamics
  7. molecular-graphics
  8. molecular-modeling
  9. molecule
  10. pdb
  11. protein
  12. protein-data-bank
  13. protein-structure
  14. protein-visualization
  15. proteins
  16. sciart
  17. structural-biology
  18. visualisation
24 Contributors
4.2.12published 2 months agoGPL-3.0

metatensor-torch

TorchScript bindings for metatensor
  1. machine
  2. learning
  3. molecular
  4. modeling
  5. torch
0.7.5published 1 week agoBSD-3-Clause

alchemlyb

the simple alchemistry library
  1. free
  2. energy
  3. MBAR
  4. thermodynamic
  5. integration
  6. perturbation
  7. FEP
  8. alchemistry
  9. analysis
  10. GROMACS
  11. NAMD
  12. AMBER
  13. molecular
  14. dynamics
  15. free-energy
  16. library
  17. molecular-dynamics
  18. python
  19. science
20 Contributors
2.4.1published 7 months agoBSD-3-Clause

decoupler

Ensemble of methods to infer biological activities from omics data
  1. systems
  2. biology
  3. molecular
  4. signaling
  5. network
  6. transcriptomics
  7. modeling
  8. mechanistic
  9. activity
  10. inference
  11. omics
  12. biomedicine
  13. footprint
  14. signature
  15. bioinformatics
  16. data-science
  17. enrichment
  18. enrichment-analysis
  19. numba
  20. python
  21. single-cell
  22. spatial-transcriptomics
12 Contributors
1.9.2published 2 months agoGPL-3.0-only

GromacsWrapper

A Python wrapper around the GROMACS tools.
  1. science
  2. Gromacs
  3. analysis
  4. molecular
  5. dynamics
  6. gromacswrapper
  7. molecular-dynamics
  8. python
20 Contributors
0.9.1published 7 months agoCNRI-Python-GPL-Compatible

pypath-omnipath

Molecular signaling prior knowledge processing
  1. systems
  2. biology
  3. molecular
  4. omics
  5. network
  6. signaling
  7. database
  8. genetic-regulatory-network
  9. molecular-biology
  10. pathway
  11. python
  12. resource
21 Contributors
0.16.17published 6 months agoGPL-3.0-only

pymbar

Python implementation of the multistate Bennett acceptance ratio (MBAR) method
  1. molecular
  2. mechanics
  3. forcefield
  4. Bayesian
  5. parameterization
  6. bennett-acceptance-ratio
  7. equilibrium
  8. extended-bridge-sampling
  9. free-energies
  10. mbar
  11. molecular-dynamics-simulations
  12. multistate-bennett-acceptance-ratio
  13. pymbar
  14. python
  15. research
  16. single-molecule-pulling
  17. thermodynamic-states
19 Contributors
4.0.3published 1 year agoMIT
Showing 1 to 10 of 11 results