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Internal coordinate darting #92

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@sgill2 sgill2 commented Aug 1, 2017 •
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This PR aims to incorporate internal coordinate darting moves with the existing set of moves in BLUES.

Things that still need to be done:

  1. Improve docstrings
  2. Clean up code
  3. Add tests

sgill2 and others added 30 commits July 27, 2017 14:25
removed xyz file requirement
f538699
made modifications
eab9faf
change version number
0b96502
Merge branch 'master' of https://github.com/MobleyLab/blues into inte…
b0e3ab9 
…rnal
removed extraneous code, added docstrings
5a6be7a
changed to always compare to reference, still wip
d8a01b3
debugging positions
2951457
tentative fix of inaccurate darting
d9d9dc3
added temp files
9c1aa3e
added other necessary files
d4863c6
added files for tests
a63d332
functional icdarting before cleanup
0fe3b81
removed most print statements
2e52f46
fixed bug with at vs loc selection and when making darts with initial…
b35f973 
… overlap
added line to keep bonds, angles the same when darting
473d1fd
Merge branch 'internal' of https://github.com/MobleyLab/blues
775a4d7
modified to work with before/after clauses
d42b2dd
Merge branch 'before_after' of https://github.com/MobleyLab/blues int…
c4c61f9 
…o ic_before
changed to appropriately handle systems
d0248bd
added restraint file
780327a
debugging
084c039
fixed bug with the incorrect positions being used to calculate rotati…
c351325 
…on values
changed another area where superposing wasn't accounted for **might w…
b06985b 
…ant to recheck**
changes before restraint overhaul
d4a9aea
changes to make restraints optional/add parameters for restraint atoms
dddd9c0
debugging new options
28b3410
fixed issue with set overlap in dartcheck and changed trans/rot dart …
31c9d87 
…cutoff
added experimental freezing scheme change
359158b
debugging water freezing
3d8eeb8
fixed error causing waters to not switch correctly
943f5d0
sgill2 and others added 30 commits February 28, 2019 15:43
updated docstrings for moldart functions
9b04405
adds ability to check darts from a trajectory
acc5493
fixed bug with topology loading in _createBuildlist
92801fe
fixed handlling of multiple trajectories
6b43578
fixed darting region definitions for rot/trans
44ed7a9
Improved translational dart handling
77d4571
fixed bug handling translational/dihedral darts
4ab2e78
fixed translational darting, error handling
6b6d38c
fixed translational darts / dart overlap reporting
fe7fa97
fix dart reversibility handling
3c20f14
fixed handling of other darts when using rotational darts
72fe5bc
more generalized parameters for making darts
f6e0517
Merge branch 'internal' of github.com:MobleyLab/blues into internal
73eb977
fixed str handling for _checkTrajectoryDarts
ac158f5
additional parameters for MolDartMove dart specifications
61722ac
initial commit to clean up overfit darts
7ff992c
remove print statements
3e27ac0
generalized restrained atoms for rmsd restraints
722aaee
fixed single dihedral case handling in removeRedundancy()
610523b
inital attempt for rigid body simulation
133fa09
added return to rigid function
260b861
@sgill2
fixed error handling for when svd doesnt converge for rotation
df07b4a
@sgill2
inital rigid body handling
4147dc1
@sgill2
fixed case where pos not set
adc3de1
@sgill2
added before portion for rigid body handling
b77652c
added parameters for debugging moldarting
35551b5
added options for individual restraint specification
cfe36c4
@sgill2
WIP changes for individual pose restraints
cc1fd62
@sgill2
next fix for fitting multiple poses
768040b
@sgill2
fix restrained receptor atoms
7e5cf97
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3 participants

@sgill2 @nathanmlim