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Generate conformation libraries from BCE output #135

Merged
merged 34 commits into from
Apr 19, 2021
Merged

Generate conformation libraries from BCE output #135

merged 34 commits into from
Apr 19, 2021

Commits on Oct 27, 2020

  1. Add helper methods to Dihedral object

    @cescgina
    cescgina committed Oct 27, 2020
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  2. Add options to main to run dihedral calculations

    @cescgina
    cescgina committed Oct 27, 2020
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  3. Add default path to dihedral library file

    @cescgina
    cescgina committed Oct 27, 2020
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  4. Add module to calculate dihedral angles

    @cescgina
    cescgina committed Oct 27, 2020
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Commits on Oct 28, 2020

  1. Move rdkit dependencies into its toolkit

    @cescgina
    cescgina committed Oct 28, 2020
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Commits on Oct 30, 2020

  1. Change units of dihedral calculation to rad

    @cescgina
    cescgina committed Oct 30, 2020
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Commits on Nov 3, 2020

  1. Merge branch 'devel' into calc_dihedrals

    @cescgina
    cescgina committed Nov 3, 2020
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Commits on Nov 27, 2020

  1. Merge branch 'devel' into calc_dihedrals

    @cescgina
    cescgina committed Nov 27, 2020
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  2. Remove duplicated method from merge

    @cescgina
    cescgina committed Nov 27, 2020
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  3. Fix discrepancy in name of OPLS charges option

    @cescgina
    cescgina committed Nov 27, 2020
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  4. Udpate format of Dihedral library due to new changes

    @cescgina
    cescgina committed Nov 27, 2020
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  5. Revert changes in dihedral library format 

    By using the topology instead of the molecule we can retain the same
format as before
    @cescgina
    cescgina committed Nov 27, 2020
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  6. Sort the output of glob to get consistent output 

    This will produce the exact same dihedral library in all machines
    @cescgina
    cescgina committed Nov 27, 2020
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Commits on Nov 28, 2020

  1. Merge branch 'devel' into calc_dihedrals

    @cescgina
    cescgina committed Nov 28, 2020
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  2. Expose charge calculator types to main for consitency

    @cescgina
    cescgina committed Nov 28, 2020
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Commits on Nov 30, 2020

  1. Merge branch 'devel' into calc_dihedrals

    @cescgina
    cescgina committed Nov 30, 2020
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Commits on Dec 2, 2020

  1. Merge branch 'devel' into calc_dihedrals

    @cescgina
    cescgina committed Dec 2, 2020
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Commits on Dec 7, 2020

  1. Add function to calculate RMSD in RDKIT toolkit

    @cescgina
    cescgina committed Dec 7, 2020
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  2. Modify logger level inside BCEDihedrals

    @cescgina
    cescgina committed Dec 7, 2020
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  3. Add new mode in BCEDihedrals 

    In this new mode, the different clusters are ordered so that the jump
between two subsequent clusters involves the minimum structural
difference. This is done heuristically, and it is not guaranteed to be
optimal
    @cescgina
    cescgina committed Dec 7, 2020
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Commits on Dec 23, 2020

  1. Raise more informative error for missing BCEDihedrals

    @cescgina
    cescgina committed Dec 23, 2020
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  2. Avoid calculating rotamer libraries with BCE

    @cescgina
    cescgina committed Dec 23, 2020
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Commits on Dec 24, 2020

  1. Avoid logging rotamer library if not calculated

    @cescgina
    cescgina committed Dec 24, 2020
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Commits on Jan 5, 2021

  1. Do not avoid reading dihedrals with hydrogens

    @cescgina
    cescgina committed Jan 5, 2021
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Commits on Feb 15, 2021

  1. Merge branch 'devel' into calc_dihedrals

    @cescgina
    cescgina committed Feb 15, 2021
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Commits on Feb 17, 2021

  1. Add tests for outputHandler in the dihedral library

    @cescgina
    cescgina committed Feb 17, 2021
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  2. Pass dihedrals_mode argument to main

    @cescgina
    cescgina committed Feb 17, 2021
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  3. Test parsing dihedral library parameters in main

    @cescgina
    cescgina committed Feb 17, 2021
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  4. Add tests for new functions in rdkit toolkit

    @cescgina
    cescgina committed Feb 17, 2021
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  5. Add tests for BCEDihedrals module

    @cescgina
    cescgina committed Feb 17, 2021
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Commits on Mar 11, 2021

  1. Switch from calculating dihedrals to translations 

    In this new mode, the tranlation from each atom to the root atom of the
template is calculated instead of the dihedral angle
    @cescgina
    cescgina committed Mar 11, 2021
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Commits on Mar 15, 2021

  1. Update test for BCEConformations

    @cescgina
    cescgina committed Mar 15, 2021
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Commits on Mar 30, 2021

  1. Merge branch 'devel' into calc_dihedrals

    @cescgina
    cescgina committed Mar 30, 2021
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Commits on Apr 7, 2021

  1. Use parameterize_opls2005 function to avoid errors

    @cescgina
    cescgina committed Apr 7, 2021
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