Skip to content

Add dihedral RMS to reference action #736

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom
Merged
merged 26 commits into from
Jun 21, 2019
Merged

Add dihedral RMS to reference action #736

merged 26 commits into from
Jun 21, 2019

Conversation

drroe
Copy link
Contributor

@drroe drroe commented Jun 21, 2019 

  [help dihedralrms|dihrms]
	[<name>] <dihedral types> [out <file>]
	[ first | reference | ref <name> | refindex <#> | previous |
	  reftraj <name> [parm <name> | parmindex <#>] ]
	[dihtype <name>:<a0>:<a1>:<a2>:<a3>[:<offset>] ...]
  Calculate RMSD of selected dihedrals to dihedrals in a
  reference structure.

The dihedral selection syntax is similar to multidihedral. The minimum deviation is used. Addresses #734.

Also fixes another potential segfault when writing string data sets (related to #732).

Daniel R. Roe and others added 25 commits June 14, 2019 14:31
DRR - Cpptraj: Use forward declares. Add routine for using dihtype.
af332c7
DRR - Cpptraj: Use the new SearchForNewTypeArgs routine
4249341
DRR - Cpptraj: Enable command. Add reference keywords.
66c5d98
DRR - Cpptraj: Add the Action_DihedralRMS class
354f48f
DRR - Cpptraj: First incarnation of dihedral rms test.
d1f9b36
@drroe
DRR - Cpptraj: Make use of forward delcares. Make RefModeType public
55c56c7
@drroe
DRR - Cpptraj: Add some reference setup
aa4941e
DRR - Cpptraj: Do not print mask expression if no mask string is set.
2bcadf1
DRR - Cpptraj: Add reference setup when no mask string set. Make -1 p…
345bc87 
…assed into SetupRef() mean do not check number selected atoms.
DRR - Cpptraj: Add rms previous test
cd76b8b
DRR - Cpptraj: Test rms first with changing topology
6cebb1f
DRR - Cpptraj: Get rid of previous as a bool, add as a mode. Do not c…
a5a7a6d 
…hange modes during actions; this way classes using ReferenceAction always know how reference was selected.
DRR - Cpptraj: Use separate DihedralSearch for selecting reference di…
4e6346d 
…hedrals. Finish up dihedral rms calculation.
DRR - Cpptraj: Add to first and to reference tests.
64054d6
DRR - Cpptraj: Fix calc to previous ref
f823386
DRR - Cpptraj: Add to previous test
cbf99ee
DRR - Cpptraj: Only calculate reference values during setup if mode i…
ff4d0c4 
…s FRAME
DRR - Cpptraj: Add to reference traj test
5050ea8
DRR - Cpptraj: Hide some debug info
46fc7e2
DRR - Cpptraj: Remove obsolete test stuff, split into parallel/not pa…
3f28c32 
…rallel tests
DRR - Cpptraj: Add dihedral fluctuation (multidihedral plus avg) test
ee86b58
DRR - Cpptraj: Revision bump for new dihrms command
797fe07
DRR - Cpptraj: Take max of format specifier and actual data width whe…
6ec9bdb 
…n writing strings using Write
DRR - Cpptraj: Add missing test save
be9e017
@drroe
DRR - Cpptraj: Enabled dihedral rms test.
4e27f82
@drroe drroe self-assigned this Jun 21, 2019
@drroe drroe merged commit 837bb3f into Amber-MD:master Jun 21, 2019
@drroe drroe deleted the dihedralrms branch June 21, 2019 18:58
@drroe drroe mentioned this pull request Jun 22, 2019
Merged
@drroe drroe mentioned this pull request Jul 10, 2019
Closed
@hainm hainm mentioned this pull request Feb 10, 2022
Open
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers
No reviews
Assignees

@drroe drroe

Labels
new action
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
1 participant
@drroe