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Fixes for nastruct, ZDNA and parallel DNA#1018

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drroe merged 29 commits intoAmber-MD:masterfrom
drroe:debug.nastruct.z
Mar 9, 2023
Merged

Fixes for nastruct, ZDNA and parallel DNA#1018
drroe merged 29 commits intoAmber-MD:masterfrom
drroe:debug.nastruct.z

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@drroe drroe commented Mar 9, 2023

Version 6.18.0.

  • ZDNA (left handed) is now properly detected and parameters have the correct sign.
  • Improved base pair detection, especially for parallel strands and/or Hoogsteen base pairing. Renders guessbp obsolete.
  • Parameters for parallel DNA can now be calculated using 3DNA-type conventions (new default) or Babcock et al. conventions (previous behavior). Can switch with new keyword, bpmode.
  • Improved Zp parameter calculation; fixed for parallel DNA.
  • Add new data set, <name>[nxyz] for printing the base pair axes normal (Z) vector.

drroe added 29 commits March 3, 2023 09:36
@drroe
Actually print rotated R2
789a2b2
@drroe
Debug print the original base 2 axis
6e30e71
@drroe
Add code to ensure that base axis Z vector points 5' to 3'
42b9feb
@drroe
Put base axes check in SetupBaseAxes()
0ca6ef6
@drroe
Add Y check
16a783e
@drroe
If a flip of Z axis has occurred, just check that Y is pointing in th…
b715ca5 
…e same direction. If so this was a chi flip and we also need to flip X. If not that is an error bc a flip around X should not be possible.
@drroe
Hide debug info
e79af44
@drroe
Hide more debug info
4c7c336
@drroe
Add res num to debug message
e429fcb
@drroe
Add base pair axes origin and normal data tracking
891b937
@drroe
Fix debug title
6dfe0c4
@drroe
Disable zdna X and Z axes flipping for now. When determining base pai…
6a33480 
…rs, ensure axes are properly flipped before looking at cutoffs etc
@drroe
Add bpmode keyword for using different axes flip conventions for para…
49d4734 
…llel base pairs
@drroe
Add missing break statements
a55d385
@drroe
Change bp origin cutoff to 5 ang to catch non wc basepairs. Deprecate…
18931bd 
… 'guessbp'; was always a hack to make up for the bad bp detection of non wc pairs which should now be fixed.
@drroe
Add routine for checking Z against strand direction
faf81c6
@drroe
Try to detect ZDNA
45ce3c1
@drroe
Make the ZDNA check solely depend on whether both Z axis are aligned …
8f71402 
…3' to 5'. Flipx XZ when ZDNA in base pair determination
@drroe
Save if basepair appears to be Z
dd6b88a
@drroe
Store position of glycosidic N
689f4e3
@drroe
Add glycosidic N-N distance calc; only for debugging currently.
a3a9426
@drroe
Protect some debug info
6017413
@drroe
Try to fix parallel zp calc. Still not working right
aa22ab8
@drroe
Remove guessbp code
4140d9e
@drroe
Rotate phosphate atoms, not the vector
a4c4235
@drroe
AT LONG LAST! Got the Zp calculation working properly for EVERYTHING.
9da6158 
That took a lonnnnng long time.
@drroe
Update nastruct
99b4947
@drroe
6.18.0. Minor version bump for fixed nastruct output for ZDNA and Zp
5a34c7d 
  calculation.
@drroe
Remove unneeded code
54b36b0
@drroe drroe added bugfix New keywords New keywords for existing commands. labels Mar 9, 2023
@drroe drroe self-assigned this Mar 9, 2023
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drroe commented Mar 9, 2023

@hainm I added a new data set to nastruct with aspect [nxyz] that is a DataSet_Vector (x y z, ox oy oz). How can I modify nucleic_acid_analysis.py in pytraj so it understands this? Right now the test is failing because everything else is a 1D array.

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drroe commented Mar 9, 2023

Since I have people waiting on this functionality I'm going to merge, but I'll open an issue over at pytraj so as not to forget.

@drroe drroe merged commit 8af5492 into Amber-MD:master Mar 9, 2023
@drroe drroe deleted the debug.nastruct.z branch March 9, 2023 21:19
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hainm commented Mar 9, 2023

but I'll open an issue over at pytraj so as not to forget.

yeah please open a case. Please post the error too.

@drroe drroe mentioned this pull request Mar 9, 2023
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