Commits · a11b141c74442ffdf36ba1381802f0b651e6eeeb · open / pdbfixer

27 Jan, 2016 1 commit
- Support for additional solvation boxes · a11b141c
  Jaime RGP committed Jan 27, 2016
  
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19 Jan, 2016 2 commits
- Force cubic geometry by default · 1e02b130
  Jaime RG committed Jan 19, 2016
  
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- Specify water box dimensions with JS enhanced padding field · 24e8991d
  Jaime RGP committed Jan 19, 2016
  
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01 Sep, 2015 4 commits
- Merge pull request #110 from jchodera/master · 7b94709a
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Fix issue with mutations when chain appears in multiple places in PDB file
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  peastman committed Sep 01, 2015
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- Cleaner building of mutation list. · b76228cb
  Chodera committed Sep 01, 2015
  
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- Python 3 compatibility; fix issue with chain_numbers · eed66441
  Chodera committed Sep 01, 2015
  
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- Major mutation code cleanup · 9d054482
  Chodera committed Sep 01, 2015
  
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28 Aug, 2015 1 commit
- Fix issue with mutations when chain appears in multiple places in PDB file… · 2436468b
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Fix issue with mutations when chain appears in multiple places in PDB file separated by other chains.
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  Chodera committed Aug 28, 2015
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08 Aug, 2015 1 commit
- Merge pull request #107 from peastman/pdbx · ccc80f18
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[WIP] Added support for loading PDBx/mmCIF files
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  peastman committed Aug 07, 2015
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07 Aug, 2015 3 commits
- Fixed incorrect docstring · eb82172f
  Peter Eastman committed Aug 07, 2015
  
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- Minor updates to manual · 6b0bc5a3
  Peter Eastman committed Aug 07, 2015
  
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- Improved logic for detecting file format · c66c661e
  Peter Eastman committed Aug 07, 2015
  
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06 Aug, 2015 1 commit
- Added support for loading PDBx/mmCIF files · 82ce81d0
  Peter Eastman committed Aug 06, 2015
  
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05 Aug, 2015 2 commits
- Merge pull request #106 from peastman/structure · bbb8cfa8
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Removed the remaining internal dependence on PdbStructure
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  peastman committed Aug 05, 2015
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- Removed the remaining internal dependence on PdbStructure · ecd9e8cb
  Peter Eastman committed Aug 05, 2015
  
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04 Aug, 2015 2 commits
- Merge pull request #103 from jchodera/fix-travis · b2f347b0
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Fix issues with travis-ci and binstar upload of dev package.
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  peastman committed Aug 04, 2015
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- Fix issues with travis-ci and binstar upload of dev package. · 11ad578b
  Chodera committed Aug 04, 2015
  
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03 Aug, 2015 2 commits
- Merge pull request #102 from peastman/addedbonds · e546d5a5
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Fixed error when _addAtomsToTopology() added bonds but not atoms
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  peastman committed Aug 03, 2015
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- Fixed error when _addAtomsToTopology() added bonds but not atoms · 75b20c6e
  peastman committed Aug 03, 2015
  
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21 Jul, 2015 2 commits
- Merge pull request #98 from swails/travis · e1f65bf5
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Migrate to the new container architecture.
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  peastman committed Jul 21, 2015
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- Migrate to the new container architecture. · 5423ff85
  Jason Swails committed Jul 20, 2015
  
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20 Jul, 2015 6 commits
- Merge pull request #97 from peastman/timeout · ff039a65
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Test case doesn't download PDB as many times
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  peastman committed Jul 20, 2015
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- Further reduced number of downloads · 313bc041
  Peter Eastman committed Jul 20, 2015
  
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- Removed an unneeded import · 99e6d5ee
  Peter Eastman committed Jul 20, 2015
  
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- Test case doesn't download PDB as many times · af2513df
  Peter Eastman committed Jul 20, 2015
  
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- Merge pull request #96 from jchodera/master · 66d31f0a
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Added --pdbid, --url, and --verbose flags.
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  peastman committed Jul 20, 2015
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- Fixed py3 issue with test_cli · 326babc5
  John Chodera (MSKCC) committed Jul 20, 2015
  
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19 Jul, 2015 8 commits
- Incremented delay in nosetests. · 071a849e
  John Chodera (MSKCC) committed Jul 18, 2015
  
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- Slowing down rapid URL retrievals for nosetests. · 6b4c5054
  John Chodera (MSKCC) committed Jul 18, 2015
  
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- Attempting to fix URL timeout issues with nosetests. · def30674
  John Chodera (MSKCC) committed Jul 18, 2015
  
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- Updated HTML docs. · b8dc41c2
  John Chodera (MSKCC) committed Jul 18, 2015
  
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- Another try to get CLI tests to work on linux. · 26d19268
  John Chodera (MSKCC) committed Jul 18, 2015
  
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- Fix CLI nosetests. · d2df9a4e
  John Chodera (MSKCC) committed Jul 18, 2015
  
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- Updated CLI nosetest to be python3 friendly · a88d8d7a
  John Chodera (MSKCC) committed Jul 18, 2015
  
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- Added entry_points to devtools/conda-recipe to fix nosetests. · aca6fc60
  John Chodera (MSKCC) committed Jul 18, 2015
  
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18 Jul, 2015 2 commits

Added nosetests. · bc11f29c
John Chodera (MSKCC) committed Jul 18, 2015

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Added --pdbid, --url, and --verbose flags. · 4b868972

* Users can now specify '--pdbid pdbid' flag in command-line to retrieve PDB file from RCSB
* Users can also specify '--url URL' to retrieve from custom URL.
* --vebose flag for command-line now prints out some information about what is going on; maybe we can convert this to logging later

committed Jul 18, 2015

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06 Jul, 2015 1 commit
- Merge pull request #94 from jchodera/update-setup · 97c882cd
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Cowardly refuse to install unless openmm >= 6.3 is installed
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  peastman committed Jul 06, 2015
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04 Jul, 2015 1 commit
- Cowardly refuse to install unless openmm>=6.3 is installed. Update version to 1.2. · 383d9917
  John Chodera (MSKCC) committed Jul 04, 2015
  
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04 Mar, 2015 1 commit
- Merge pull request #86 from peastman/ids · b61152f5
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Preserve residue and chain IDs
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  peastman committed Mar 03, 2015
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