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Internal coordinate darting#92

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sgill2 wants to merge 146 commits intomasterMobleyLab/blues:masterfrom internalMobleyLab/blues:internalCopy head branch name to clipboard

+49,391-1,226

Commits

Commits on Jul 27, 2017

• removed xyz file requirement

  

  sgill2

  committed
  f538699

Commits on Jul 29, 2017

• made modifications

  

  sgill2

  committed
  eab9faf

Commits on Aug 1, 2017

• change version number

  

  sgill2

  committed
  0b96502

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

  

  sgill2

  committed
  b0e3ab9

Commits on Aug 2, 2017

• removed extraneous code, added docstrings

  

  sgill2

  committed
  5a6be7a

Commits on Aug 3, 2017

• changed to always compare to reference, still wip

  

  sgill2

  committed
  d8a01b3

Commits on Aug 4, 2017

• debugging positions

  

  sgill2

  committed
  2951457

Commits on Aug 8, 2017

• tentative fix of inaccurate darting

  

  sgill2

  committed
  d9d9dc3

Commits on Aug 15, 2017

• added temp files

  

  sgill2

  committed
  9c1aa3e

• added other necessary files

  

  sgill2

  committed
  d4863c6

• added files for tests

  

  sgill2

  committed
  a63d332

Commits on Nov 8, 2017

• functional icdarting before cleanup

  

  sgill2

  committed
  0fe3b81

Commits on Nov 9, 2017

• removed most print statements

  

  sgill2

  committed
  2e52f46

Commits on Nov 10, 2017

• fixed bug with at vs loc selection and when making darts with initial overlap

  

  sgill2

  committed
  b35f973

Commits on Nov 30, 2017

• added line to keep bonds, angles the same when darting

  

  sgill2

  committed
  473d1fd

Commits on Dec 5, 2017

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

  

  sgill2

  committed
  775a4d7

Commits on Jan 8, 2018

• modified to work with before/after clauses

  

  Samuel Gill

  committed
  d42b2dd

• Merge branch 'before_after' of https://github.com/MobleyLab/blues into ic_before

  

  Samuel Gill

  committed
  c4c61f9

• changed to appropriately handle systems

  

  Samuel Gill

  committed
  d0248bd

• added restraint file

  

  Samuel Gill

  committed
  780327a

Commits on Jan 30, 2018

• debugging

  

  sgill2

  committed
  084c039

Commits on Feb 1, 2018

• fixed bug with the incorrect positions being used to calculate rotation values

  

  sgill2

  committed
  c351325

• changed another area where superposing wasn't accounted for **might want to recheck**

  

  sgill2

  committed
  b06985b

Commits on Feb 2, 2018

• changes before restraint overhaul

  

  sgill2

  committed
  d4a9aea

Commits on Feb 6, 2018

• changes to make restraints optional/add parameters for restraint atoms

  

  sgill2

  committed
  dddd9c0

Commits on Feb 8, 2018

• debugging new options

  

  sgill2

  committed
  28b3410

Commits on Feb 28, 2018

• fixed issue with set overlap in dartcheck and changed trans/rot dart cutoff

  

  sgill2

  committed
  31c9d87

• added experimental freezing scheme change

  

  sgill2

  committed
  359158b

Commits on Mar 1, 2018

• debugging water freezing

  

  sgill2

  committed
  3d8eeb8

• fixed error causing waters to not switch correctly

  

  sgill2

  committed
  943f5d0

Commits on Mar 2, 2018

• updated options (like freeze_protein)

  

  sgill2

  committed
  21209aa

Commits on Mar 13, 2018

• fixed pandas issue

  

  sgill2

  committed
  8b781aa

Commits on Mar 22, 2018

• fixes for darting regions / detailed balance

  

  sgill2

  committed
  2ddbda4

Commits on Mar 28, 2018

• added darting test

  

  sgill2

  committed
  0198ca5

• added files for darting test

  

  sgill2

  committed
  215be29

• fixed files for checking to refereence dart

  

  sgill2

  committed
  7eff20d

• changed to unittest framework

  

  sgill2

  committed
  e082012

• Removed methods that already exist elsewhere and aren't used

  

  sgill2

  committed
  94de54f

• removed unused import

  

  sgill2

  committed
  553806f

Commits on Apr 4, 2018

• code cleanup and behavior fixing

  

  sgill2

  committed
  791f10c

Commits on Apr 10, 2018

• commit before compatiblity with chemcoord update

  

  sgill2

  committed
  b51381f

• udated to work with py3 and newer chemcoord

  

  sgill2

  committed
  37e9627

Commits on Apr 12, 2018

• updated yam

  

  sgill2

  committed
  d00c93e

• updated yaml to take chemcoord

  

  sgill2

  committed
  a41f4f7

• allow specification of restraint strength

  

  sgill2

  committed
  ae06ad9

• Cleanup (unused) functions

  

  sgill2

  committed
  0460d1f

• added restraints test

  

  sgill2

  committed
  58b73d6

• removed code for changing restraints in base class

  

  sgill2

  committed
  a332645

• renamed MolDart to match Move naming convention

  

  sgill2

  committed
  9db6f0c

Commits on Apr 13, 2018

• restructured moldart module location

  

  sgill2

  committed
  af2ff16

• restructured module for moldart

  

  sgill2

  committed
  ffb6cd9

• removed old lambda_restraints variable

  

  sgill2

  committed
  86c52cc

• exposed setting lambda_restraints in move

  

  sgill2

  committed
  a803acb

• remove debugging code

  

  sgill2

  committed
  a10a40f

• Merge pull request #118 from MobleyLab/ic_test

  Show description for bc39af4
  sgill2

  authored
  bc39af4

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

  

  sgill2

  committed
  a9a4b67

• debugging travis

  

  sgill2

  committed
  a0074ca

• removed merge header

  

  sgill2

  committed
  e27d3e0

• added future requirement

  

  sgill2

  committed
  446efa7

• fix future requirements

  

  sgill2

  committed
  87e8b50

• fix moldart import statements

  

  sgill2

  committed
  fc7cf14

• add boresch restraint file that didn't carry over from merge

  

  sgill2

  committed
  96410ac

• added yank requirements for boresch restraints

  

  sgill2

  committed
  cb85eb9

• fix attribute not being set (due to code changes)

  

  sgill2

  committed
  ac1228f

Commits on Apr 14, 2018

• removed restraint force debugging

  

  sgill2

  committed
  32cec53

• fixes force type check for boresch restraints

  

  sgill2

  committed
  55b5502

Commits on Apr 17, 2018

• added experimental option to handle rings

  

  sgill2

  committed
  c10ff36

Commits on Apr 25, 2018

• fixed import statement

  

  sgill2

  committed
  d6761c7

• remove experimental option

  

  sgill2

  committed
  7339d07

Commits on Apr 30, 2018

• Added transition matrix option to specify transition probabilities

  

  sgill2

  committed
  3af566c

Commits on May 1, 2018

• fixed move acceptance ratio factor for mc simulations

  

  sgill2

  committed
  1673a15

• removed debug print statements

  

  sgill2

  committed
  6cf00ab

• added transition matrix checks/tests

  

  sgill2

  committed
  15f4a2d

Commits on May 22, 2018

• removes ncmc_move_output portion

  

  sgill2

  committed
  61a464e

• added rigid_ring option as default

  

  sgill2

  committed
  7bc1e20

Commits on Jun 1, 2018

• Update moldart example

  

  Nathan Lim

  committed
  190858e

Commits on Jun 12, 2018

• Fix errror with saving energies to txt file

  nathanmlim

  committed
  9db66e2

Commits on Jun 13, 2018

• Merge conflicts with master

  nathanmlim

  committed
  3e56b85

• Add .gitignore file

  nathanmlim

  committed
  cb000d5

• Resolve more conflicts with master

  nathanmlim

  committed
  e2592d9

• Skip dart tests and remove old code

  nathanmlim

  committed
  0484870

Commits on Jun 20, 2018

• Merge branch 'master' into internal

  

  Nathan Lim

  authored
  f3197c3

Commits on Sep 11, 2018

• updated compatibility with current BLUES

  

  sgill2

  committed
  5b544d8

Commits on Sep 14, 2018

• changes before further optimization

  

  sgill2

  committed
  a44019b

Commits on Sep 17, 2018

• updated with new chemcoord

  

  sgill2

  committed
  a59ca7e

Commits on Sep 18, 2018

• save changes before more testing

  

  sgill2

  committed
  9d5e05e

Commits on Sep 20, 2018

• fixed compatability issues/cleaned up code

  

  sgill2

  committed
  3b3d297

Commits on Sep 24, 2018

• updated moldarting tests for new blues version

  

  sgill2

  committed
  30d1f60

Commits on Sep 25, 2018

• added wip dart setup tests

  

  sgill2

  committed
  e029579

Commits on Sep 26, 2018

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

  

  sgill2

  committed
  9e63e26

• update compatibility with pulled code

  

  sgill2

  committed
  f220559

• updated conda package requirements

  

  sgill2

  committed
  93c261f

Commits on Sep 27, 2018

• added conda-forge channel

  

  sgill2

  committed
  4a1a4e8

• update channels to work with travis

  

  sgill2

  committed
  4aa7491

• updated MoveEngine import from proper script

  

  sgill2

  committed
  6157d98

• updated Logger spelling to match convention

  

  sgill2

  committed
  0f59c20

• fixed self reference for class

  

  sgill2

  committed
  7f2e879

• fixed inheritance and assertion for test

  

  sgill2

  committed
  8e7a2c5

Commits on Sep 28, 2018

• removed depreciated files

  

  sgill2

  committed
  8836d92

• removed depreciated smartdarting code

  

  sgill2

  committed
  115f8c4

Commits on Oct 3, 2018

• vectorized setting arrays

  

  sgill2

  committed
  b96c780

• added dart region creation tests

  

  sgill2

  committed
  dda9e37

• added tests for lin algebra functions for moldarting

  

  sgill2

  committed
  2298580

• updated positional argument for test

  

  sgill2

  committed
  0d54349

Commits on Nov 7, 2018

• fix acceptance ratio handling for moves

  

  sgill2

  committed
  2543fd8

• change moldarting defaults

  

  sgill2

  committed
  e9cb96d

Commits on Nov 13, 2018

• added molecular darting sphinx documentation

  

  sgill2

  committed
  60cd42c

Commits on Jan 11, 2019

• fixes for implicit solvent simulations

  

  sgill2

  committed
  e3c2144

• update darting to handle multipe modes

  

  sgill2

  committed
  434fb7e

• fix correction factor debugging

  

  sgill2

  committed
  fcef812

Commits on Jan 14, 2019

• updated tests

  

  hiddenthief

  authored and

  hiddenthief

  committed
  b551fff

• remove debug printing statement

  

  hiddenthief

  authored and

  hiddenthief

  committed
  4a62045

Commits on Jan 30, 2019

• fixed tabulated function behavior for alchemical_function option

  

  sgill2

  committed
  7868683

• handle situation when no crds are used

  

  sgill2

  committed
  f636962

Commits on Feb 22, 2019

• allows changes in the order of defining the darting region

  

  sgill2

  committed
  51e7b8e

Commits on Feb 28, 2019

• added making darting region class function

  

  sgill2

  committed
  df3053b

• updated docstrings for moldart functions

  

  sgill2

  committed
  9b04405

Commits on Mar 1, 2019

• adds ability to check darts from a trajectory

  

  sgill2

  committed
  acc5493

• fixed bug with topology loading in _createBuildlist

  

  sgill2

  committed
  92801fe

Commits on Mar 2, 2019

• fixed handlling of multiple trajectories

  

  sgill2

  committed
  6b43578

Commits on Mar 11, 2019

• fixed darting region definitions for rot/trans

  

  sgill2

  committed
  44ed7a9

Commits on Mar 27, 2019

• Improved translational dart handling

  

  sgill2

  committed
  77d4571

• fixed bug handling translational/dihedral darts

  

  sgill2

  committed
  4ab2e78

Commits on Apr 2, 2019

• fixed translational darting, error handling

  

  sgill2

  committed
  6b6d38c

• fixed translational darts / dart overlap reporting

  

  sgill2

  committed
  fe7fa97

Commits on Apr 4, 2019

• fix dart reversibility handling

  

  sgill2

  committed
  3c20f14

Commits on Apr 5, 2019

• fixed handling of other darts when using rotational darts

  

  sgill2

  committed
  72fe5bc

• more generalized parameters for making darts

  

  sgill2

  committed
  f6e0517

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

  

  sgill2

  committed
  73eb977

• fixed str handling for _checkTrajectoryDarts

  

  sgill2

  committed
  ac158f5

Commits on Apr 9, 2019

• additional parameters for MolDartMove dart specifications

  

  sgill2

  committed
  61722ac

Commits on Apr 23, 2019

• initial commit to clean up overfit darts

  

  sgill2

  committed
  7ff992c

• remove print statements

  

  sgill2

  committed
  3e27ac0

Commits on Apr 24, 2019

• generalized restrained atoms for rmsd restraints

  

  sgill2

  committed
  722aaee

Commits on Apr 30, 2019

• fixed single dihedral case handling in removeRedundancy()

  

  sgill2

  committed
  610523b

• inital attempt for rigid body simulation

  

  sgill2

  committed
  133fa09

Commits on May 1, 2019

• added return to rigid function

  

  sgill2

  committed
  260b861

Commits on May 10, 2019

• fixed error handling for when svd doesnt converge for rotation

  sgill2

  committed
  df07b4a

Commits on May 13, 2019

• inital rigid body handling

  sgill2

  committed
  4147dc1

• fixed case where pos not set

  sgill2

  committed
  adc3de1

• added before portion for rigid body handling

  sgill2

  committed
  b77652c

Commits on May 14, 2019

• added parameters for debugging moldarting

  

  sgill2

  committed
  35551b5

Commits on May 15, 2019

• added options for individual restraint specification

  

  sgill2

  committed
  cfe36c4

Commits on May 28, 2019

• WIP changes for individual pose restraints

  sgill2

  committed
  cc1fd62

Commits on May 31, 2019

• next fix for fitting multiple poses

  sgill2

  committed
  768040b

• fix restrained receptor atoms

  sgill2

  committed
  7e5cf97