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Rewrite and improve DSSP #748

Merged
merged 63 commits into from
Sep 3, 2019
Merged

Rewrite and improve DSSP #748

merged 63 commits into from
Sep 3, 2019

Commits on Aug 21, 2019

  1. DRR - Cpptraj: Start new DSSP action that more closely follows the de… 

    …finitions of Kabsch and Sander
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    drroe committed Aug 21, 2019
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Commits on Aug 22, 2019

  1. DRR - Cpptraj: Start adding residue setup

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  2. DRR - Cpptraj: Continue residue setup

    @drroe
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  3. DRR - Cpptraj: Coordinate indices setup/check

    Daniel R. Roe committed Aug 22, 2019
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  4. DRR - Cpptraj: Per residue data set setup

    Daniel R. Roe committed Aug 22, 2019
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  5. DRR - Cpptraj: Add some debug printout

    Daniel R. Roe committed Aug 22, 2019
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  6. DRR - Cpptraj: Incorporate as test command dssp2

    Daniel R. Roe committed Aug 22, 2019
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  7. DRR - Cpptraj: Add dssp hbond calc

    Daniel R. Roe committed Aug 22, 2019
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  8. DRR - Cpptraj: Debug print of what hbonds are formed

    Daniel R. Roe committed Aug 22, 2019
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  9. Merge branch 'master' into fixdssp

    Daniel R. Roe committed Aug 22, 2019
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  10. DRR - Cpptraj: Fix the offset

    Daniel R. Roe committed Aug 22, 2019
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Commits on Aug 23, 2019

  1. DRR - Cpptraj: Store data that is more in line with the original dssp… 

    … definitions
    Daniel R. Roe committed Aug 23, 2019
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  2. DRR - Cpptraj: Put all the SS chars in a single array. Start turn ass… 

    …ignment
    Daniel R. Roe committed Aug 23, 2019
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  3. DRR - Cpptraj: Add offset

    Daniel R. Roe committed Aug 23, 2019
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  4. DRR - Cpptraj: Will use num to refer to things indexed in Topology an… 

    …d idx to refer to things indexed in Residues_
    Daniel R. Roe committed Aug 23, 2019
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  5. DRR - Cpptraj: Look for previous/next residues

    Daniel R. Roe committed Aug 23, 2019
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  6. DRR - Cpptraj: bridge identification with set. Not sure I like this w… 

    …ay...
    Daniel R. Roe committed Aug 23, 2019
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  7. DRR - Cpptraj: Original way of assigning beta

    Daniel R. Roe committed Aug 23, 2019
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  8. DRR - Cpptraj: Reenable the new bridge search but leave the old one a… 

    …ctive for comparison. Start doing strand assignment.
    Daniel R. Roe committed Aug 23, 2019
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  9. DRR - Cpptraj: Fix off by one issue in parallel type b assignment. Ch… 

    …aracter assignment still seems off
    Daniel R. Roe committed Aug 23, 2019
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Commits on Aug 26, 2019

  1. DRR - Cpptraj: Start new approach, loop over hbonds instead of residues

    Daniel R. Roe committed Aug 26, 2019
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  2. DRR - Cpptraj: Not useful to assign ladder/sheet chars until full bet… 

    …a hbond network known
    Daniel R. Roe committed Aug 26, 2019
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  3. DRR - Cpptraj: Finish up new assignment.

    Daniel R. Roe committed Aug 26, 2019
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  4. DRR - Cpptraj: Calc hbonds for adjacent residues since very tight tur… 

    …ns are possible. When looking for beta, do not attempt to assign if 3-residue stretches would overlap. Report bend as degrees in debug.
    Daniel R. Roe committed Aug 26, 2019
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  5. DRR - Cpptraj: In order to correctly detect when cooperative helices … 

    …end, only assign one segment at a time.
    Daniel R. Roe committed Aug 26, 2019
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  6. DRR - Cpptraj: only attempt to assign secondary structure if a higher… 

    … priority assignment not already present
    Daniel R. Roe committed Aug 26, 2019
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Commits on Aug 27, 2019

  1. DRR - Cpptraj: Remove over residues code, going with over hbonds

    Daniel R. Roe committed Aug 27, 2019
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  2. DRR - Cpptraj: Not storing hbonds in SSres anymore

    Daniel R. Roe committed Aug 27, 2019
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  3. DRR - Cpptraj: Improve comments

    Daniel R. Roe committed Aug 27, 2019
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  4. DRR - Cpptraj: Start beta bulge calculation

    Daniel R. Roe committed Aug 27, 2019
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  5. DRR - Cpptraj: Finish up initial beta bulge detection - make sure ext… 

    …ended is set for both strands. Do not check for priority in SetSS() - rely on calling algorithm to do the right thing.
    Daniel R. Roe committed Aug 27, 2019
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  6. DRR - Cpptraj: Update comments

    Daniel R. Roe committed Aug 27, 2019
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  7. DRR - Cpptraj: Finish up print stuff

    Daniel R. Roe committed Aug 27, 2019
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  8. DRR - Cpptraj: Make sure ALPHA is not overwritten during BETA assignm… 

    …ent. Count previous residue assigned EXTENDED via bulge when determining extended beta. Look for 3-10 and PI helices after ALPHA and BETA assignment to prevent too-short regions of these helices from being assigned.
    Daniel R. Roe committed Aug 27, 2019
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  9. DRR - Cpptraj: Fix output string char and gnuplot z label

    Daniel R. Roe committed Aug 27, 2019
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Commits on Aug 28, 2019

  1. DRR - Cpptraj: Add new test with dssp2 code. Actually does the same a… 

    …ssignment as old code because of parallel beta sheets.
    @drroe
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  2. DRR - Cpptraj: Split up turn and beta - no beta char for now since we… 

    … arent actually calculating it yet. Clean up a bit.
    @drroe
    drroe committed Aug 28, 2019
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  3. DRR - Cpptraj: Rename some functions

    @drroe
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  4. DRR - Cpptraj: Ensure residue is always unassigned at the beginning o… 

    …f frame. Ensure bridge type is unsassigned.
    @drroe
    drroe committed Aug 28, 2019
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  5. DRR - Cpptraj: Use ResChar()

    @drroe
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  6. DRR - Cpptraj: FabI traj is actually 10 frames

    @drroe
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  7. DRR - Cpptraj: Accumulate stats on parallel and antiparallel sheet

    @drroe
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  8. DRR - Cpptraj: When looking for beta bulge, make sure bridge types match

    @drroe
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  9. DRR - Cpptraj: Start adding 'betadetail' keyword which will track par… 

    …allel/anti-parallel beta in place of extended/bridge (backwards compat.)
    @drroe
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  10. DRR - Cpptraj: Fix zlabels for betaDetail

    @drroe
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  11. DRR - Cpptraj: Fix sum output for betaDetail

    @drroe
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  12. DRR - Cpptraj: Fix ptrajformat for betadetail

    @drroe
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  13. DRR - Cpptraj: Change full name labels based on betaDetail

    @drroe
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  14. DRR - Cpptraj: Fix assignout for betaDetail

    @drroe
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  15. DRR - Cpptraj: Do normalization over total number of frames for backw… 

    …ards compat.
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Commits on Aug 29, 2019

  1. DRR - Cpptraj: Hide some debug info

    @drroe
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  2. DRR - Cpptraj: Report timing at Print()

    @drroe
    drroe committed Aug 29, 2019
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  3. DRR - Cpptraj: Fix for openmp

    @drroe
    drroe committed Aug 29, 2019
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  4. DRR - Cpptraj: Add MPI sync

    @drroe
    drroe committed Aug 29, 2019
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  5. DRR - Cpptraj: Minor revision bump for new dssp code.

    @drroe
    drroe committed Aug 29, 2019
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  6. DRR - Cpptraj: Replace old DSSP command with new one.

    @drroe
    drroe committed Aug 29, 2019
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  7. DRR - Cpptraj: Add 'betadetail' keyword to tests for backwards compat.

    @drroe
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Commits on Aug 30, 2019

  1. DRR - Cpptraj: Update manual.

    @drroe
    drroe committed Aug 30, 2019
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  2. DRR - Cpptraj: Secstruct has been completely rewritten.

    @drroe
    drroe committed Aug 30, 2019
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  3. DRR - Cpptraj: I have no idea how this was actually compiling and run… 

    …ning before...
    @drroe
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Commits on Aug 31, 2019

  1. DRR - Cpptraj: Update for revamped dssp.

    @drroe
    drroe committed Aug 31, 2019
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Commits on Sep 3, 2019

  1. DRR - Cpptraj: Fix printf format string; Range.Size() is int, not uns… 

    …igned.
    Daniel R. Roe committed Sep 3, 2019
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  2. DRR - Cpptraj: Protect test when no netcdf

    Daniel R. Roe committed Sep 3, 2019
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