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Internal coordinate darting #92

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Internal coordinate darting #92

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Commits on Jul 27, 2017

  1. removed xyz file requirement

    sgill2 committed Jul 27, 2017
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Commits on Jul 29, 2017

  1. made modifications

    sgill2 committed Jul 29, 2017
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Commits on Aug 1, 2017

  1. change version number

    sgill2 committed Aug 1, 2017
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  2. Merge branch 'master' of https://github.com/MobleyLab/blues into inte… 

    …rnal
    sgill2 committed Aug 1, 2017
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Commits on Aug 2, 2017

  1. removed extraneous code, added docstrings

    sgill2 committed Aug 2, 2017
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Commits on Aug 3, 2017

  1. changed to always compare to reference, still wip

    sgill2 committed Aug 3, 2017
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Commits on Aug 4, 2017

  1. debugging positions

    sgill2 committed Aug 4, 2017
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Commits on Aug 8, 2017

  1. tentative fix of inaccurate darting

    sgill2 committed Aug 8, 2017
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Commits on Aug 15, 2017

  1. added temp files

    sgill2 committed Aug 15, 2017
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  2. added other necessary files

    sgill2 committed Aug 15, 2017
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  3. added files for tests

    sgill2 committed Aug 15, 2017
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Commits on Nov 8, 2017

  1. functional icdarting before cleanup

    sgill2 committed Nov 8, 2017
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Commits on Nov 9, 2017

  1. removed most print statements

    sgill2 committed Nov 9, 2017
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Commits on Nov 10, 2017

  1. fixed bug with at vs loc selection and when making darts with initial… 

    … overlap
    sgill2 committed Nov 10, 2017
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Commits on Nov 30, 2017

  1. added line to keep bonds, angles the same when darting

    sgill2 committed Nov 30, 2017
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Commits on Dec 5, 2017

  1. Merge branch 'internal' of https://github.com/MobleyLab/blues

    sgill2 committed Dec 5, 2017
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Commits on Jan 8, 2018

  1. modified to work with before/after clauses

    Samuel Gill committed Jan 8, 2018
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  2. Merge branch 'before_after' of https://github.com/MobleyLab/blues int… 

    …o ic_before
    Samuel Gill committed Jan 8, 2018
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  3. changed to appropriately handle systems

    Samuel Gill committed Jan 8, 2018
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  4. added restraint file

    Samuel Gill committed Jan 8, 2018
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Commits on Jan 30, 2018

  1. debugging

    sgill2 committed Jan 30, 2018
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Commits on Feb 1, 2018

  1. fixed bug with the incorrect positions being used to calculate rotati… 

    …on values
    sgill2 committed Feb 1, 2018
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  2. changed another area where superposing wasn't accounted for **might w… 

    …ant to recheck**
    sgill2 committed Feb 1, 2018
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Commits on Feb 2, 2018

  1. changes before restraint overhaul

    sgill2 committed Feb 2, 2018
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Commits on Feb 6, 2018

  1. changes to make restraints optional/add parameters for restraint atoms

    sgill2 committed Feb 6, 2018
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Commits on Feb 8, 2018

  1. debugging new options

    sgill2 committed Feb 8, 2018
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Commits on Feb 28, 2018

  1. fixed issue with set overlap in dartcheck and changed trans/rot dart … 

    …cutoff
    sgill2 committed Feb 28, 2018
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  2. added experimental freezing scheme change

    sgill2 committed Feb 28, 2018
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Commits on Mar 1, 2018

  1. debugging water freezing

    sgill2 committed Mar 1, 2018
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  2. fixed error causing waters to not switch correctly

    sgill2 committed Mar 1, 2018
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Commits on Mar 2, 2018

  1. updated options (like freeze_protein)

    sgill2 committed Mar 2, 2018
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Commits on Mar 13, 2018

  1. fixed pandas issue

    sgill2 committed Mar 13, 2018
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Commits on Mar 22, 2018

  1. fixes for darting regions / detailed balance

    sgill2 committed Mar 22, 2018
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Commits on Mar 28, 2018

  1. added darting test

    sgill2 committed Mar 28, 2018
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  2. added files for darting test

    sgill2 committed Mar 28, 2018
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  3. fixed files for checking to refereence dart

    sgill2 committed Mar 28, 2018
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  4. changed to unittest framework

    sgill2 committed Mar 28, 2018
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  5. Removed methods that already exist elsewhere and aren't used

    sgill2 committed Mar 28, 2018
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  6. removed unused import

    sgill2 committed Mar 28, 2018
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Commits on Apr 4, 2018

  1. code cleanup and behavior fixing

    sgill2 committed Apr 4, 2018
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Commits on Apr 10, 2018

  1. commit before compatiblity with chemcoord update

    sgill2 committed Apr 10, 2018
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  2. udated to work with py3 and newer chemcoord

    sgill2 committed Apr 10, 2018
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Commits on Apr 12, 2018

  1. updated yam

    sgill2 committed Apr 12, 2018
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  2. updated yaml to take chemcoord

    sgill2 committed Apr 12, 2018
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  3. allow specification of restraint strength

    sgill2 committed Apr 12, 2018
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  4. Cleanup (unused) functions

    sgill2 committed Apr 12, 2018
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  5. added restraints test

    sgill2 committed Apr 12, 2018
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  6. removed code for changing restraints in base class

    sgill2 committed Apr 12, 2018
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  7. renamed MolDart to match Move naming convention

    sgill2 committed Apr 12, 2018
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Commits on Apr 13, 2018

  1. restructured moldart module location

    sgill2 committed Apr 13, 2018
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  2. restructured module for moldart

    sgill2 committed Apr 13, 2018
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  3. removed old lambda_restraints variable

    sgill2 committed Apr 13, 2018
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  4. exposed setting lambda_restraints in move

    sgill2 committed Apr 13, 2018
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  5. remove debugging code

    sgill2 committed Apr 13, 2018
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  6. Merge pull request #118 from MobleyLab/ic_test 

    Merge working IC branch with PR IC branch
    @sgill2
    sgill2 authored Apr 13, 2018
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  7. Merge branch 'internal' of https://github.com/MobleyLab/blues into in… 

    …ternal
    sgill2 committed Apr 13, 2018
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  8. debugging travis

    sgill2 committed Apr 13, 2018
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  9. removed merge header

    sgill2 committed Apr 13, 2018
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  10. added future requirement

    sgill2 committed Apr 13, 2018
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  11. fix future requirements

    sgill2 committed Apr 13, 2018
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  12. fix moldart import statements

    sgill2 committed Apr 13, 2018
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  13. add boresch restraint file that didn't carry over from merge

    sgill2 committed Apr 13, 2018
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  14. added yank requirements for boresch restraints

    sgill2 committed Apr 13, 2018
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  15. fix attribute not being set (due to code changes)

    sgill2 committed Apr 13, 2018
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Commits on Apr 14, 2018

  1. removed restraint force debugging

    sgill2 committed Apr 14, 2018
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  2. fixes force type check for boresch restraints

    sgill2 committed Apr 14, 2018
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Commits on Apr 17, 2018

  1. added experimental option to handle rings

    sgill2 committed Apr 17, 2018
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Commits on Apr 25, 2018

  1. fixed import statement

    sgill2 committed Apr 25, 2018
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  2. remove experimental option

    sgill2 committed Apr 25, 2018
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Commits on Apr 30, 2018

  1. Added transition matrix option to specify transition probabilities

    sgill2 committed Apr 30, 2018
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Commits on May 1, 2018

  1. fixed move acceptance ratio factor for mc simulations

    sgill2 committed May 1, 2018
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  2. removed debug print statements

    sgill2 committed May 1, 2018
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  3. added transition matrix checks/tests

    sgill2 committed May 1, 2018
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Commits on May 22, 2018

  1. removes ncmc_move_output portion

    sgill2 committed May 22, 2018
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  2. added rigid_ring option as default

    sgill2 committed May 22, 2018
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Commits on Jun 1, 2018

  1. Update moldart example

    Nathan Lim committed Jun 1, 2018
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Commits on Jun 12, 2018

  1. Fix errror with saving energies to txt file

    @nathanmlim
    nathanmlim committed Jun 12, 2018
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Commits on Jun 13, 2018

  1. Merge conflicts with master

    @nathanmlim
    nathanmlim committed Jun 13, 2018
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  2. Add .gitignore file

    @nathanmlim
    nathanmlim committed Jun 13, 2018
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  3. Resolve more conflicts with master

    @nathanmlim
    nathanmlim committed Jun 13, 2018
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  4. Skip dart tests and remove old code

    @nathanmlim
    nathanmlim committed Jun 13, 2018
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Commits on Jun 20, 2018

  1. Merge branch 'master' into internal

    Nathan Lim authored Jun 20, 2018
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Commits on Sep 11, 2018

  1. updated compatibility with current BLUES

    sgill2 committed Sep 11, 2018
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Commits on Sep 14, 2018

  1. changes before further optimization

    sgill2 committed Sep 14, 2018
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Commits on Sep 17, 2018

  1. updated with new chemcoord

    sgill2 committed Sep 17, 2018
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Commits on Sep 18, 2018

  1. save changes before more testing

    sgill2 committed Sep 18, 2018
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Commits on Sep 20, 2018

  1. fixed compatability issues/cleaned up code

    sgill2 committed Sep 20, 2018
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Commits on Sep 24, 2018

  1. updated moldarting tests for new blues version

    sgill2 committed Sep 24, 2018
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Commits on Sep 25, 2018

  1. added wip dart setup tests

    sgill2 committed Sep 25, 2018
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Commits on Sep 26, 2018

  1. Merge branch 'master' of github.com:MobleyLab/blues into internal

    sgill2 committed Sep 26, 2018
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  2. update compatibility with pulled code

    sgill2 committed Sep 26, 2018
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  3. updated conda package requirements

    sgill2 committed Sep 26, 2018
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Commits on Sep 27, 2018

  1. added conda-forge channel

    sgill2 committed Sep 27, 2018
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  2. update channels to work with travis

    sgill2 committed Sep 27, 2018
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  3. updated MoveEngine import from proper script

    sgill2 committed Sep 27, 2018
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  4. updated Logger spelling to match convention

    sgill2 committed Sep 27, 2018
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  5. fixed self reference for class

    sgill2 committed Sep 27, 2018
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  6. fixed inheritance and assertion for test

    sgill2 committed Sep 27, 2018
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Commits on Sep 28, 2018

  1. removed depreciated files

    sgill2 committed Sep 28, 2018
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  2. removed depreciated smartdarting code

    sgill2 committed Sep 28, 2018
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Commits on Oct 3, 2018

  1. vectorized setting arrays

    sgill2 committed Oct 3, 2018
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  2. added dart region creation tests

    sgill2 committed Oct 3, 2018
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  3. added tests for lin algebra functions for moldarting

    sgill2 committed Oct 3, 2018
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  4. updated positional argument for test

    sgill2 committed Oct 3, 2018
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Commits on Nov 7, 2018

  1. fix acceptance ratio handling for moves

    sgill2 committed Nov 7, 2018
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  2. change moldarting defaults

    sgill2 committed Nov 7, 2018
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Commits on Nov 13, 2018

  1. added molecular darting sphinx documentation

    sgill2 committed Nov 13, 2018
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Commits on Jan 11, 2019

  1. fixes for implicit solvent simulations

    sgill2 committed Jan 11, 2019
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  2. update darting to handle multipe modes

    sgill2 committed Jan 11, 2019
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  3. fix correction factor debugging

    sgill2 committed Jan 11, 2019
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Commits on Jan 14, 2019

  1. updated tests

    hiddenthief authored and hiddenthief committed Jan 14, 2019
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  2. remove debug printing statement

    hiddenthief authored and hiddenthief committed Jan 14, 2019
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Commits on Jan 30, 2019

  1. fixed tabulated function behavior for alchemical_function option

    sgill2 committed Jan 30, 2019
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  2. handle situation when no crds are used

    sgill2 committed Jan 30, 2019
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Commits on Feb 22, 2019

  1. allows changes in the order of defining the darting region

    sgill2 committed Feb 22, 2019
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Commits on Feb 28, 2019

  1. added making darting region class function

    sgill2 committed Feb 28, 2019
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  2. updated docstrings for moldart functions

    sgill2 committed Feb 28, 2019
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Commits on Mar 1, 2019

  1. adds ability to check darts from a trajectory

    sgill2 committed Mar 1, 2019
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  2. fixed bug with topology loading in _createBuildlist

    sgill2 committed Mar 1, 2019
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Commits on Mar 2, 2019

  1. fixed handlling of multiple trajectories

    sgill2 committed Mar 2, 2019
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Commits on Mar 11, 2019

  1. fixed darting region definitions for rot/trans

    sgill2 committed Mar 11, 2019
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Commits on Mar 27, 2019

  1. Improved translational dart handling

    sgill2 committed Mar 27, 2019
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  2. fixed bug handling translational/dihedral darts

    sgill2 committed Mar 27, 2019
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Commits on Apr 2, 2019

  1. fixed translational darting, error handling

    sgill2 committed Apr 2, 2019
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  2. fixed translational darts / dart overlap reporting

    sgill2 committed Apr 2, 2019
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Commits on Apr 4, 2019

  1. fix dart reversibility handling

    sgill2 committed Apr 4, 2019
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Commits on Apr 5, 2019

  1. fixed handling of other darts when using rotational darts

    sgill2 committed Apr 5, 2019
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  2. more generalized parameters for making darts

    sgill2 committed Apr 5, 2019
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  3. Merge branch 'internal' of github.com:MobleyLab/blues into internal

    sgill2 committed Apr 5, 2019
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  4. fixed str handling for _checkTrajectoryDarts

    sgill2 committed Apr 5, 2019
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Commits on Apr 9, 2019

  1. additional parameters for MolDartMove dart specifications

    sgill2 committed Apr 9, 2019
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Commits on Apr 23, 2019

  1. initial commit to clean up overfit darts

    sgill2 committed Apr 23, 2019
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  2. remove print statements

    sgill2 committed Apr 23, 2019
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Commits on Apr 24, 2019

  1. generalized restrained atoms for rmsd restraints

    sgill2 committed Apr 24, 2019
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Commits on Apr 30, 2019

  1. fixed single dihedral case handling in removeRedundancy()

    sgill2 committed Apr 30, 2019
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  2. inital attempt for rigid body simulation

    sgill2 committed Apr 30, 2019
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Commits on May 1, 2019

  1. added return to rigid function

    sgill2 committed May 1, 2019
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Commits on May 10, 2019

  1. fixed error handling for when svd doesnt converge for rotation

    @sgill2
    sgill2 committed May 10, 2019
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Commits on May 13, 2019

  1. inital rigid body handling

    @sgill2
    sgill2 committed May 13, 2019
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  2. fixed case where pos not set

    @sgill2
    sgill2 committed May 13, 2019
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  3. added before portion for rigid body handling

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    sgill2 committed May 13, 2019
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Commits on May 14, 2019

  1. added parameters for debugging moldarting

    sgill2 committed May 14, 2019
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Commits on May 15, 2019

  1. added options for individual restraint specification

    sgill2 committed May 15, 2019
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Commits on May 28, 2019

  1. WIP changes for individual pose restraints

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    sgill2 committed May 28, 2019
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Commits on May 31, 2019

  1. next fix for fitting multiple poses

    @sgill2
    sgill2 committed May 31, 2019
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  2. fix restrained receptor atoms

    @sgill2
    sgill2 committed May 31, 2019
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