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Published November 9, 2016 | Version 1.9.0
Software Open

mdtraj/mdtraj: MDTraj 1.9

Authors/Creators

  • 1. D.E. Shaw Research
  • 2. Stanford University
  • 3. Vanderbilt University
  • 4. Lutron Electronics, Inc.
  • 5. @pandegroup
  • 6. CMB group - Free University Berlin
  • 7. DeepMile Networks
  • 8. SLAC National Accelerator Lab
  • 9. Schrödinger
  • 10. Memorial Sloan-Kettering Cancer Center
  • 11. California Institute of Technology
  • 12. Ghent University
  • 13. Rutgers University
  • 14. Free University Berlin
  • 15. Chodera Lab // MSKCC
  • 16. San Diego Supercomputer Center
  • 17. MIT

Description

  • PR #1202: mdtraj.html has been removed. We recommend using nglview for visualizing MDTraj trajectory objects.
  • PR #1204: Fix search functionality with docs
  • PR #1167: Fix corner case in distancekernel.h
  • PR #1190: Fix issue with rmsd precentered = True and atom_indices != None
  • PR #1106: Speed up image_molecules
  • PR #1182: Add 'sidechain' and 'sidechain-heavy' options to compute_contacts
  • PR #1180: Handle unexpected keyword arguments gracefully in psf and prmtop parsers
  • PR #1171: Remove unnecessary restriction on iterload
  • PR #1170: Load single-element path lists without a copy
  • PR #1165: There should never be zero bins in Voxels class
  • PR #1158: Update deprecated use of scipy.stats.nanmean
  • PR #1153: [formats/XTC] in case of an out of bounds seek, raise IOError
  • PR #1161: Fix typos in examples
  • PR #1130: Automatically test examples to make sure they work
  • PR #1155: Update wording for simulation-with-openmm.ipynb
  • PR #1146: Ensure box vectors have right dtype
  • PR #1145: Check that file exists before trying to open it
  • PR #1139: Optimize baker_hubbard and wernet_nilsson functions
  • PR #1137: Allow standard_names as a keyword argument to md.load()
  • PR #1132: Fix bug in hoomdxml reader
  • PR #1125: Support Gromacs TNG files
  • PR #1123: Add md.join(trajs)

Files

mdtraj/mdtraj-1.9.0.zip

Files (19.3 MB)

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md5:a6ca81130e449bd0bac4f7f1c58c91f6
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Additional details

Related works

Is supplement to
https://github.com/mdtraj/mdtraj/tree/1.9.0 (URL)