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Add support for reading Desmond DTR (Anton) trajectories #796

Merged
merged 37 commits into from
Feb 7, 2020
Merged

Add support for reading Desmond DTR (Anton) trajectories #796

merged 37 commits into from
Feb 7, 2020

Commits on Feb 3, 2020

  1. DRR - Add the DTR plugin from VMD

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  2. DRR - Comment out vmd-specific includes

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  3. DRR - Rename since likely will want dms support as well

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  4. DRR - DMS plugin from vmd

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  5. DRR - Update README

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Commits on Feb 6, 2020

  1. DRR - Plugin is really from VMD

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  2. DRR - Add more files from VMD plugin framework to get dtr plugin to c… 

    …omple properly without too much modification
    @drroe
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  3. DRR - Restore original includes except for the byte swap routines; us… 

    …e the cpptraj versions for those
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  4. DRR - Update README

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  5. DRR - Initial version of TrajectoryIO class for DTR

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  6. DRR - Update dependencies

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  7. DRR - Function to determine file or directory

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  8. DRR - Try adding automatic ID

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  9. DRR - Add DTR to TrajectoryFile

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  10. DRR - Start adding memory allocation, deallocation. Use forward declare

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  11. DRR - Start trajectory setup

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  12. DRR - Try to return number of frames

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  13. DRR - Use version of FindDepend from clusterrevamp that can handle di… 

    …fferent directory levels
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  14. DRR - Follow cpptraj naming convention

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  15. DRR - Update dependencies

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  16. DRR - Fix init check, add some debug info

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  17. DRR - Make it easier to set box info from 6 floats. Finish coord and … 

    …box read.
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  18. DRR - Refactor reading of mol2 files for topologies since e.g. someti… 

    …mes VMD writes mol2s without type names
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  19. DRR - Hide debug info

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  20. DRR - Add Time

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Commits on Feb 7, 2020

  1. DRR - Put the VMD plugin interface behind ifdefs

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  2. DRR - Revision bump for addition of dtr

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  3. Merge branch 'master' into dtrplugin

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  4. DRR - Recognize file name clickme.dtr as desmond DTR for compat. with… 

    … vmd behavior
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  5. DRR - Add DTR to read traj array

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  6. DRR - Add DTR to trajectory table

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  7. DRR - Actually read the first frame to get box info instead of guessing

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  8. DRR - Add a sanity check

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  9. DRR - Add note about VMD dtr plugin to README

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  10. DRR - Try to fix the windows build by changing ifdef

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  11. DRR - Trouble compiling DTR plugin on windows, so disable for now.

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  12. DRR - Change from NO_DTR to ENABLE_DTR; disabled unless configure is … 

    …used on non-windows platform.
    @drroe
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