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1. Commits on Jul 17, 2015

   • New parameter to control the threads used for Multiple Alignments

     lafita

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2. Commits on Jul 16, 2015

   • Fix bug in MultipleAlignmentEnsemble, now Atoms are not cloned

     lafita

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   • Implement a new MultipleAlignment superimposer using Core residues

     lafita

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   • Organize MultipleAlignment code in a util package

     lafita

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   • Test all String output Writer methods of MultipleAlignment

     lafita

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3. Commits on Jul 10, 2015

   • Merge remote-tracking branch 'upstream/master'

     josemduarte

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   • New method to get compounds, made getParentChains public

     josemduarte

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4. Commits on Jul 9, 2015

   • Review GUI code for MultipleAlignments

     lafita

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   • Show ligands in the MultipleAlignment display

     lafita

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5. Commits on Jul 8, 2015

   • Merge remote-tracking branch 'main/master' into minor

     lafita

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   • Create test for XML conversion and parsing of MultipleAlignments

     lafita

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   • Implement XML Converter and Parser for MultipleAlignments

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     lafita

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6. Commits on Jul 7, 2015

   • Merge pull request #295 from lafita/minor

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     andreasprlic

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   • Add more examples for the MultipleAlignment algorithm

     lafita

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   • Review MC Optimization code

     lafita

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7. Commits on Jul 6, 2015

   • Rename MC optimizer to a shorter name

     lafita

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8. Commits on Jul 1, 2015

   • Create Multiple Alignment GUI

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     lafita

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9. Commits on Jun 30, 2015

   • MultipleAlignment code revision

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     lafita

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   • Some fixes to error handling, logging and javadoc

     josemduarte

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10. Commits on Jun 26, 2015

    • Important bug fix in the insertGap() move of MC

      lafita

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    • Smooth probability function in MC optimization

      lafita

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    • Merge branch 'master' into minor

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    • Merge pull request #290 from lafita/multaln

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      sbliven

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    • Undo CLI changes for Multiple Structure Alignment

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11. Commits on Jun 25, 2015

    • Clean Demos for Multiple Alignments

      lafita

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    • Support flexible alignments in the MC optimization

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      lafita

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    • Fixing #289

      josemduarte

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    • Create templates for MultipleAlignment CLI #278

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      lafita

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    • Better exception handling, some more logging and removing warnings

      josemduarte

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    • fixing #287 as well as some performance improvements when parsing mmcif files.

      andreasprlic

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    • fixing #287 as well as some performance improvements when parsing mmcif files.

      andreasprlic

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12. Commits on Jun 23, 2015

    • Set AFPChain constructor algorithm name to unknown

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      lafita

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    • Fix updateSuperposition() bug with Transformation Matrices

      lafita

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13. Commits on Jun 22, 2015

    • Create Test templates for MultipleAlignment

      lafita

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    • Fix AFPChainConversionTest failure

      lafita

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