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onbiojava-4.2.11

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Commits on Dec 8, 2017

• Back porting fix and test for #716

  josemduarte

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• Fix and unit test for #715

  josemduarte

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Commits on Nov 16, 2017

• Backporting bugfix from 5.0 branch

  josemduarte

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Commits on Oct 19, 2017

• Merge pull request #707 from edlunde-dnastar/linelength424

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  josemduarte

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• Fixing test issues related to v5 and changes in rcsb

  josemduarte

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Commits on Oct 18, 2017

• Changes for CONECT/LINK

  larsonmattr

  committed
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Commits on Jul 6, 2017

• Better http than https

  josemduarte

  committed
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• Updating ligand URLs to latest RCSB convention

  josemduarte

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Commits on Jul 5, 2017

• Updating dssp urls to latest RCSB convention

  josemduarte

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Commits on Feb 18, 2017

• Catching empty coordinates earlier in quat sym detection

  josemduarte

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Commits on Feb 15, 2017

• Fix Quaternary symmetry symmetry detection bug

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  sbliven

  committed
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Commits on Feb 10, 2017

• Better rules for Quaternary symm self-alignments

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  sbliven

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Commits on Jan 21, 2017

• Now catching empty arrays in getCentroid

  josemduarte

  committed
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• Less verbose logging in AsaCalculator

  josemduarte

  committed
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• Better logging in symmetry package

  josemduarte

  committed
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• Fix for #631

  josemduarte

  committed
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Commits on Nov 30, 2016

• Added exception handler for out-of-bounds errors when parsing lines, usually indicative of misformated lines.

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  Matt Larson

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Commits on Nov 23, 2016

• Adding non-standard sg check to pdb parser

  josemduarte

  committed
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• Fixed bug: NPE for CrystalBuilder on 4hhb. Moved TestCrystalBuilder to integrationtest.

  josemduarte

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• Now using the new fields from CrystalBuilder

  josemduarte

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Commits on Nov 22, 2016

• Some extra rare fields in atom_sites

  josemduarte

  committed
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• Fixing npe introduced in last commit

  josemduarte

  committed
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• Implementing new crystallographic metadata fields.

  josemduarte

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• Implementing parsing of atom_sites category in mmcif parser/consumer

  josemduarte

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Commits on Sep 21, 2016

• Inserts space when altLoc is null, so that the rest of fields are properly aligned.

  

  altaite

  authored and

  josemduarte

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• FileConvert fix - added empty space if altLoc is null.

  

  altaite

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  josemduarte

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Commits on Aug 1, 2016

• Fixing cath urls according to their final layout

  josemduarte

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Commits on Jul 29, 2016

• Complete new CATH file names #546 and #544

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  lafita

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  josemduarte

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Commits on Jul 28, 2016

• Fixing #544 and improving logging

  josemduarte

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• Some work towards fixing #544

  josemduarte

  committed
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• Back-porting cloning fix (see #541) into bugfixes-4.2

  josemduarte

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• #542 changing default SCOP download location to Berkeley- SCOP.

  

  andreasprlic

  authored and

  josemduarte

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Commits on Jul 13, 2016

• Fixing #533

  josemduarte

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Commits on Jul 1, 2016

• #505 switching to https for all NCBI utils traffic.

  andreasprlic

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Commits on Jun 22, 2016

• Adding some more ignore fields in beans

  josemduarte

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