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Fixes for nastruct, ZDNA and parallel DNA#1018

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

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

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@drroe

@drroe drroe commented Mar 9, 2023

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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
…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.
…rs, ensure axes are properly flipped before looking at cutoffs etc
… 'guessbp'; was always a hack to make up for the bad bp detection of non wc pairs which should now be fixed.
…3' to 5'. Flipx XZ when ZDNA in base pair determination
@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

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@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

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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
@hainm

hainm commented Mar 9, 2023

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

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

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