Internal coordinate darting#92

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sgill2 wants to merge 146 commits intomasterfrom

Commits on Jul 27, 2017

removed xyz file requirement
sgill2
committed

Commits on Jul 29, 2017

made modifications
sgill2
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Commits on Aug 1, 2017

change version number
sgill2
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Merge branch 'master' of https://github.com/MobleyLab/blues into internal
sgill2
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Commits on Aug 2, 2017

removed extraneous code, added docstrings
sgill2
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Commits on Aug 3, 2017

changed to always compare to reference, still wip
sgill2
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Commits on Aug 4, 2017

debugging positions
sgill2
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Commits on Aug 8, 2017

tentative fix of inaccurate darting
sgill2
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Commits on Aug 15, 2017

added temp files
sgill2
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added other necessary files
sgill2
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added files for tests
sgill2
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Commits on Nov 8, 2017

functional icdarting before cleanup
sgill2
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Commits on Nov 9, 2017

removed most print statements
sgill2
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Commits on Nov 10, 2017

fixed bug with at vs loc selection and when making darts with initial overlap
sgill2
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Commits on Nov 30, 2017

added line to keep bonds, angles the same when darting
sgill2
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Commits on Dec 5, 2017

Merge branch 'internal' of https://github.com/MobleyLab/blues
sgill2
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Commits on Jan 8, 2018

modified to work with before/after clauses
Samuel Gill
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Merge branch 'before_after' of https://github.com/MobleyLab/blues into ic_before
Samuel Gill
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changed to appropriately handle systems
Samuel Gill
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added restraint file
Samuel Gill
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Commits on Jan 30, 2018

debugging
sgill2
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Commits on Feb 1, 2018

Commits on Feb 2, 2018

changes before restraint overhaul
sgill2
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Commits on Feb 6, 2018

changes to make restraints optional/add parameters for restraint atoms
sgill2
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Commits on Feb 8, 2018

debugging new options
sgill2
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Commits on Feb 28, 2018

Commits on Mar 1, 2018

debugging water freezing
sgill2
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fixed error causing waters to not switch correctly
sgill2
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Commits on Mar 2, 2018

updated options (like freeze_protein)
sgill2
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Commits on Mar 13, 2018

fixed pandas issue
sgill2
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Commits on Mar 22, 2018

fixes for darting regions / detailed balance
sgill2
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Commits on Mar 28, 2018

added darting test
sgill2
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added files for darting test
sgill2
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fixed files for checking to refereence dart
sgill2
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changed to unittest framework
sgill2
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Removed methods that already exist elsewhere and aren't used
sgill2
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removed unused import
sgill2
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Commits on Apr 4, 2018

code cleanup and behavior fixing
sgill2
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Commits on Apr 10, 2018

commit before compatiblity with chemcoord update
sgill2
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udated to work with py3 and newer chemcoord
sgill2
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Commits on Apr 12, 2018

updated yam
sgill2
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updated yaml to take chemcoord
sgill2
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allow specification of restraint strength
sgill2
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Cleanup (unused) functions
sgill2
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added restraints test
sgill2
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removed code for changing restraints in base class
sgill2
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renamed MolDart to match Move naming convention
sgill2
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Commits on Apr 13, 2018

restructured moldart module location
sgill2
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restructured module for moldart
sgill2
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removed old lambda_restraints variable
sgill2
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exposed setting lambda_restraints in move
sgill2
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remove debugging code
sgill2
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Merge pull request #118 from MobleyLab/ic_test
sgill2
authored
Merge branch 'internal' of https://github.com/MobleyLab/blues into internal
sgill2
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debugging travis
sgill2
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removed merge header
sgill2
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added future requirement
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fix future requirements
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fix moldart import statements
sgill2
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add boresch restraint file that didn't carry over from merge
sgill2
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added yank requirements for boresch restraints
sgill2
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fix attribute not being set (due to code changes)
sgill2
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Commits on Apr 14, 2018

removed restraint force debugging
sgill2
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fixes force type check for boresch restraints
sgill2
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Commits on Apr 17, 2018

added experimental option to handle rings
sgill2
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Commits on Apr 25, 2018

fixed import statement
sgill2
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remove experimental option
sgill2
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Commits on Apr 30, 2018

Added transition matrix option to specify transition probabilities
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Commits on May 1, 2018

fixed move acceptance ratio factor for mc simulations
sgill2
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removed debug print statements
sgill2
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added transition matrix checks/tests
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Commits on May 22, 2018

removes ncmc_move_output portion
sgill2
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added rigid_ring option as default
sgill2
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Commits on Jun 1, 2018

Update moldart example
Nathan Lim
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Commits on Jun 12, 2018

Fix errror with saving energies to txt file
nathanmlim
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Commits on Jun 20, 2018

Merge branch 'master' into internal
Nathan Lim
authored

Commits on Sep 11, 2018

updated compatibility with current BLUES
sgill2
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Commits on Sep 14, 2018

changes before further optimization
sgill2
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Commits on Sep 17, 2018

updated with new chemcoord
sgill2
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Commits on Sep 18, 2018

save changes before more testing
sgill2
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Commits on Sep 20, 2018

fixed compatability issues/cleaned up code
sgill2
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Commits on Sep 24, 2018

updated moldarting tests for new blues version
sgill2
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Commits on Sep 25, 2018

added wip dart setup tests
sgill2
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Commits on Sep 26, 2018

Merge branch 'master' of github.com:MobleyLab/blues into internal
sgill2
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update compatibility with pulled code
sgill2
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updated conda package requirements
sgill2
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Commits on Sep 27, 2018

added conda-forge channel
sgill2
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update channels to work with travis
sgill2
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updated MoveEngine import from proper script
sgill2
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updated Logger spelling to match convention
sgill2
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fixed self reference for class
sgill2
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fixed inheritance and assertion for test
sgill2
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Commits on Sep 28, 2018

removed depreciated files
sgill2
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removed depreciated smartdarting code
sgill2
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Commits on Oct 3, 2018

vectorized setting arrays
sgill2
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added dart region creation tests
sgill2
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added tests for lin algebra functions for moldarting
sgill2
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updated positional argument for test
sgill2
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Commits on Nov 7, 2018

fix acceptance ratio handling for moves
sgill2
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change moldarting defaults
sgill2
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Commits on Nov 13, 2018

added molecular darting sphinx documentation
sgill2
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Commits on Jan 11, 2019

fixes for implicit solvent simulations
sgill2
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update darting to handle multipe modes
sgill2
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fix correction factor debugging
sgill2
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Commits on Jan 14, 2019

updated tests

hiddenthief
authored and
hiddenthief
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remove debug printing statement

hiddenthief
authored and
hiddenthief
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Commits on Jan 30, 2019

fixed tabulated function behavior for alchemical_function option
sgill2
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handle situation when no crds are used
sgill2
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Commits on Feb 22, 2019

allows changes in the order of defining the darting region
sgill2
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Commits on Feb 28, 2019

added making darting region class function
sgill2
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updated docstrings for moldart functions
sgill2
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Commits on Mar 1, 2019

adds ability to check darts from a trajectory
sgill2
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fixed bug with topology loading in _createBuildlist
sgill2
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Commits on Mar 2, 2019

fixed handlling of multiple trajectories
sgill2
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Commits on Mar 11, 2019

fixed darting region definitions for rot/trans
sgill2
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Commits on Mar 27, 2019

Improved translational dart handling
sgill2
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fixed bug handling translational/dihedral darts
sgill2
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Commits on Apr 2, 2019

fixed translational darting, error handling
sgill2
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fixed translational darts / dart overlap reporting
sgill2
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Commits on Apr 4, 2019

fix dart reversibility handling
sgill2
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Commits on Apr 5, 2019

fixed handling of other darts when using rotational darts
sgill2
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more generalized parameters for making darts
sgill2
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Merge branch 'internal' of github.com:MobleyLab/blues into internal
sgill2
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fixed str handling for _checkTrajectoryDarts
sgill2
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Commits on Apr 9, 2019

additional parameters for MolDartMove dart specifications
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Commits on Apr 23, 2019

initial commit to clean up overfit darts
sgill2
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remove print statements
sgill2
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Commits on Apr 24, 2019

generalized restrained atoms for rmsd restraints
sgill2
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Commits on Apr 30, 2019

fixed single dihedral case handling in removeRedundancy()
sgill2
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inital attempt for rigid body simulation
sgill2
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Commits on May 1, 2019

added return to rigid function
sgill2
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Commits on May 10, 2019

fixed error handling for when svd doesnt converge for rotation
sgill2
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Commits on May 13, 2019

Commits on May 14, 2019

added parameters for debugging moldarting
sgill2
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Commits on May 15, 2019

added options for individual restraint specification
sgill2
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Commits on May 28, 2019

WIP changes for individual pose restraints
sgill2
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Commits on May 31, 2019