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Commits on Sep 23, 2017

• Merge pull request #900 from swails/bugfix/psf-case-sensitivity

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Commits on Sep 22, 2017

• Match parameters on uppercase types for CHARMM PSF

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• Merge pull request #896 from swails/bugfix/close-file-handle

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Commits on Sep 13, 2017

• Do not close a file handle I did not open :)

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Commits on Sep 9, 2017

• Merge pull request #892 from swails/feature/logging

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Commits on Sep 7, 2017

• Merge branch 'master' into feature/logging

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• Merge pull request #891 from jchodera/charmm-patches-2

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Commits on Sep 6, 2017

• Trivial change to get travis to re-run

  jchodera

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• Allow CHARMM residues and patches to exist in distinct namespaces

  jchodera

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• Raise a ValueError if CHARMM tries to redefine residues as patches or vice-versa

  jchodera

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• Separate patch and residue compatibility dictionaries in case CHARMM recycles residue and patch names

  jchodera

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Commits on Sep 5, 2017

• Debugging...

  jchodera

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• Refine test skipping logic

  jchodera

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• Fix typo in escaped element content use

  jchodera

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• Escape XML characters

  jchodera

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• Don't test reading partial forcefields into app.ForceField

  jchodera

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Commits on Sep 4, 2017

• ffxml writer tests should also try reading their output back into simtk.openmm.app.ForceField

  jchodera

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• Merge branch 'master' into charmm-patches-2

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• Remove str(...) for %s

  jchodera

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• Minor change to logger %s substitution syntax

  jchodera

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• Change warning and print to logger debug

  jchodera

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• print -> logging and other cleanups

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• Merge pull request #890 from swails/bugfix/charmmpsf

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• Charmm parameter writing tests now require networkx due to patch handling

  jchodera

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• Address review comments

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Commits on Sep 3, 2017

• Skip test_patch_residue() test if networkx not available

  jchodera

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• Clean up pyflakes issues

  jchodera

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• Refine exception messages.

  jchodera

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• PatchTemplate now stores bonds to be added as list of tuples of atom names and bond order.

  jchodera

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• Process patches for compatibility by patch first so we can better see why patch combinations are rejected.

  jchodera

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• Add bond graph connectivity check to ResidueTemplate.apply_patch()

  jchodera

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• Add ResidueTemplate.to_networkx() to generate NetworkX graph if NetworkX installed.

  jchodera

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• Migrate patch validity checking code to ResidueTemplate.apply_patch()

  jchodera

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• Use first compatible residue in list to determine which atoms are added/changed and bonds are deleted.

  jchodera

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• Add atoms specified by patch if they are not already present.

  jchodera

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