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Merge GSOC Implementations #49

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Merge GSOC Implementations #49

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Commits on Jul 14, 2021

  1. add visualize.py visualization for cubefile

    nwcad2020 committed Jul 14, 2021
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Commits on Jul 20, 2021

  1. added visualization and save to image and cxs

    nwcad2020 committed Jul 20, 2021
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Commits on Jul 22, 2021

  1. rdkit annotation 2D

    nwcad2020 committed Jul 22, 2021
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  2. rdkit, label stereoisomers and cis/trans

    nwcad2020 committed Jul 22, 2021
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  3. removed unnecessary modules

    nwcad2020 committed Jul 22, 2021
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  4. currently nonfunctioning dihedral angle calculator

    nwcad2020 committed Jul 22, 2021
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Commits on Jul 26, 2021

  1. added flags option, atomic numbers, remove dihedral angle, ISSUE: SMI… 

    …LES FORMATTING
    Nathan Wood committed Jul 26, 2021
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Commits on Jul 27, 2021

  1. first push of jupyter

    Nathan Wood committed Jul 27, 2021
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Commits on Jul 28, 2021

  1. backup.ipynb

    Nathan Wood committed Jul 28, 2021
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  2. 1. removed extra imports 2. removed variables for functions 3. add in… 

    …structions to run in comments near beginning

"chimerax visualize.py"
    Nathan Wood committed Jul 28, 2021
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Commits on Jul 29, 2021

  1. newest annotation notebook

    Nathan Wood committed Jul 29, 2021
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  2. special thanks Ali Tehrani; gradient viz scale set to 50 scatter plo… 

    …t for visualization on affine plane set to 100, failed z plane assertion test
    Nathan Wood committed Jul 29, 2021
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Commits on Jul 30, 2021

  1. add annotation

    Nathan Wood committed Jul 30, 2021
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  2. Special Thanks Ali Tehrani, annotations added

    Nathan Wood committed Jul 30, 2021
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  3. Special Thanks Ali Tehrani, annotations added

    Nathan Wood committed Jul 30, 2021
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  4. Create molecular-visualizer.ipynb

    @nwoodweb
    nwoodweb committed Jul 30, 2021
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  5. added material call, cannot visualize negatives, added installation link

    Nathan Wood committed Jul 30, 2021
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  6. Merge branch 'master' of https://github.com/nwoodweb/chemtools

    Nathan Wood committed Jul 30, 2021
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  7. rdkit still throws errors

    Nathan Wood committed Jul 30, 2021
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  8. 2D Plotting, errors generating level curves for contour

    Nathan Wood committed Jul 30, 2021
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  9. error with iodata load_one

    Nathan Wood committed Jul 30, 2021
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Commits on Aug 4, 2021

  1. conversion tool from IODATA to CHEMICAL JSON

    Nathan Wood committed Aug 4, 2021
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Commits on Aug 6, 2021

  1. Delete Annotate_RDKit.ipynb 

    removed, no longer used, rewrite in progress
    @nwoodweb
    nwoodweb committed Aug 6, 2021
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  2. Delete bkup.ipynb 

    removed, no longer used, rewrite in progress
    @nwoodweb
    nwoodweb committed Aug 6, 2021
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  3. will no longer be updated

    Nathan Wood committed Aug 6, 2021
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  4. update

    Nathan Wood committed Aug 6, 2021
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  5. Merge branch 'master' of https://github.com/nwoodweb/chemtools

    Nathan Wood committed Aug 6, 2021
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  6. added contour plot, visualizes, but currently incorrect

    Nathan Wood committed Aug 6, 2021
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  7. added contour plot, visualizes, but currently incorrect

    Nathan Wood committed Aug 6, 2021
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  8. added contour plot, visualizes, but currently incorrect

    Nathan Wood committed Aug 6, 2021
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  9. added contour plot, visualizes, but currently incorrect

    Nathan Wood committed Aug 6, 2021
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  10. REWRITTEN;USE THIS; includes atomic indicies, will include the annota… 

    …tions in next update
    Nathan Wood committed Aug 6, 2021
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Commits on Aug 7, 2021

  1. rewrote, was able to annotate each atom with ESP charges, however, or… 

    …der of annotation is incorrect
    Nathan Wood committed Aug 7, 2021
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  2. rewrote, was able to annotate each atom with ESP charges, however, or… 

    …der of annotation is incorrect
    Nathan Wood committed Aug 7, 2021
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  3. rewrote, was able to annotate each atom with ESP charges, however, or… 

    …der of annotation is incorrect
    Nathan Wood committed Aug 7, 2021
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Commits on Aug 8, 2021

  1. disordered number:charge pair and location with index

    Nathan Wood committed Aug 8, 2021
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  2. add 3d visualization ipynb; replaced method of obtaining esp

    Nathan Wood committed Aug 8, 2021
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Commits on Aug 9, 2021

  1. still errors with ascribing correct values to atoms

    Nathan Wood committed Aug 9, 2021
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  2. no annotations

    Nathan Wood committed Aug 9, 2021
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  3. no annotations

    Nathan Wood committed Aug 9, 2021
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  4. generic molecule name annotation

    Nathan Wood committed Aug 9, 2021
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  5. generic molecule name annotation, can visualize isosurfaces single co… 

    …lor only
    Nathan Wood committed Aug 9, 2021
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Commits on Aug 10, 2021

  1. 2Dannotate - errors with ascribing correct atomic number and esp char… 

    …ge; 3d annotate - no change, added isosurface; plotting - WIP density contour plot
    Nathan Wood committed Aug 10, 2021
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  2. 2Dannotate - errors with ascribing correct atomic number and esp char… 

    …ge; 3d annotate - no change, added isosurface; plotting - WIP density contour plot
    Nathan Wood committed Aug 10, 2021
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Commits on Aug 11, 2021

  1. chimerax annotations, must now replace number wiht atomic symbol

    Nathan Wood committed Aug 11, 2021
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  2. unable to obtain chemical symbols

    Nathan Wood committed Aug 11, 2021
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  3. erroneous suffix labeling for redundandNumberDict

    Nathan Wood committed Aug 11, 2021
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  4. erroneous suffix labeling for redundandNumberDict

    Nathan Wood committed Aug 11, 2021
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  5. atomic numbers are ordered properly, however will have to reorganize … 

    …how to pair charge with correct atom
    Nathan Wood committed Aug 11, 2021
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Commits on Aug 12, 2021

  1. revised function for coloring esp isosurfaces in chimerax

    Nathan Wood committed Aug 12, 2021
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  2. cl and n match for example, however, Carbons are all incorrect

    Nathan Wood committed Aug 12, 2021
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  3. cl and n match for example, however, Carbons are all incorrect

    Nathan Wood committed Aug 12, 2021
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  4. consolidated gradient vector field into independent function, however… 

    … scalar counterplot unfinished
    Nathan Wood committed Aug 12, 2021
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  5. consolidated gradient vector field into independent function, however… 

    … scalar counterplot unfinished
    Nathan Wood committed Aug 12, 2021
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  6. redone scalar plot, errors with projection

    Nathan Wood committed Aug 12, 2021
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Commits on Aug 13, 2021

  1. increased number of shades for color gradient, produces more VMD-like… 

    … output surface visualization
    Nathan Wood committed Aug 13, 2021
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  2. add

    Nathan Wood committed Aug 13, 2021
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  3. iso = esp, color = rho, coloring is off, gaping hole at .003 = isosurf

    Nathan Wood committed Aug 13, 2021
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  4. incorrect shaping of scalarFuncPlotRefine` 

    `
    Nathan Wood committed Aug 13, 2021
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Commits on Aug 14, 2021

  1. COMPLETE

    Nathan Wood committed Aug 14, 2021
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Commits on Aug 15, 2021

  1. modified scalemin to accept chimerax computation; added verbosity to … 

    …3D annotation
    Nathan Wood committed Aug 15, 2021
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Commits on Aug 16, 2021

  1. 3D: followed suggestions about for loops, maintained workingBFactor; … 

    …2D Complete, will mend markdown text
    Nathan Wood committed Aug 16, 2021
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Commits on Aug 17, 2021

  1. Finalized

    Nathan Wood committed Aug 17, 2021
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  2. finalized in accordance with GA

    Nathan Wood committed Aug 17, 2021
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  3. corrected 2d annotation

    Nathan Wood committed Aug 17, 2021
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Commits on Aug 19, 2021

  1. finalization

    Nathan Wood committed Aug 19, 2021
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Commits on Aug 20, 2021

  1. finalized, consolidated into functions

    Nathan Wood committed Aug 20, 2021
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  2. main page

    Nathan Wood committed Aug 20, 2021
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  3. revert readme

    Nathan Wood committed Aug 20, 2021
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  4. consolidated documentation within function

    Nathan Wood committed Aug 20, 2021
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  5. consolidated into function, tested in linux CLI

    Nathan Wood committed Aug 20, 2021
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  6. test main page edit

    Nathan Wood committed Aug 20, 2021
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  7. test main page edit 2

    Nathan Wood committed Aug 20, 2021
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  8. test main page edit 2

    Nathan Wood committed Aug 20, 2021
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  9. Update README.md

    @nwoodweb
    nwoodweb committed Aug 20, 2021
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  10. Update README.md

    @nwoodweb
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  11. Update README.md

    @nwoodweb
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  12. Update README.md

    @nwoodweb
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  13. Update README.md

    @nwoodweb
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  14. Update README.md

    @nwoodweb
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  15. Update README.md

    @nwoodweb
    nwoodweb committed Aug 20, 2021
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  16. updated comments to all added

    Nathan Wood committed Aug 20, 2021
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  17. Merge branch 'master' of https://github.com/nwoodweb/chemtools

    Nathan Wood committed Aug 20, 2021
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  18. Update README.md

    @nwoodweb
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  19. Update README.md

    @nwoodweb
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  20. Add files via upload

    @nwoodweb
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  21. Add files via upload

    @nwoodweb
    nwoodweb committed Aug 20, 2021
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  22. Update README.md

    @nwoodweb
    nwoodweb committed Aug 20, 2021
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  23. Update README.md

    @nwoodweb
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  24. Update README.md

    @nwoodweb
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  25. Update README.md

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  26. separated into individual functions

    Nathan Wood committed Aug 20, 2021
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  27. Merge branch 'master' of https://github.com/nwoodweb/chemtools

    Nathan Wood committed Aug 20, 2021
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  28. Update README.md

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  29. Update README.md

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  30. Update README.md

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  31. Add files via upload

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  32. Delete examples/annotate directory

    @nwoodweb
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  33. Delete visualize.py

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  34. Delete visualize_scl.py

    @nwoodweb
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  35. Delete Annotate_2D.ipynb

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  36. Delete Annotate_3D_Chimera_Stage2.py

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  37. Delete Annotate_3D_Chimera_Stage1.ipynb

    @nwoodweb
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  38. Delete 3DAnnotateExample.png

    @nwoodweb
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  39. Update README.md

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  40. improved comments and formatting

    Nathan Wood committed Aug 20, 2021
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  41. Merge branch 'master' of https://github.com/nwoodweb/chemtools

    Nathan Wood committed Aug 20, 2021
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  42. improved annotations per Alis suggestion

    Nathan Wood committed Aug 20, 2021
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  43. improved annotations per Alis suggestion

    Nathan Wood committed Aug 20, 2021
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  44. Update README.md

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Commits on Aug 21, 2021

  1. Update README.md

    @nwoodweb
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Commits on Aug 23, 2021

  1. added None as colorFile option

    Nathan Wood committed Aug 23, 2021
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  2. can also render generic isosurfaces

    Nathan Wood committed Aug 23, 2021
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  3. revert readme

    Nathan Wood committed Aug 23, 2021
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  4. removed incorrect comment

    Nathan Wood committed Aug 23, 2021
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Commits on Aug 26, 2021

  1. Update ex002_esp_plot.py

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  2. Update ex001_esp_plot.py

    @nwoodweb
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  3. Delete README.md.bkup

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  4. Delete 3dannotate.png

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  5. Delete vmdfail.png

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  6. Delete acroleinerror.png

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  7. Delete vmdcorrect.png

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  9. Delete dichloropyridine26_q+0.png

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Commits on Sep 2, 2021

  1. revamped colorfile if-then-else branching; implemented negatives by r… 

    …eopening isoFile twice, and declaring isoSurfNegative from -isoSurf
    Nathan Wood committed Sep 2, 2021
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  2. revamped colorfile if-then-else branching; implemented negatives by r… 

    …eopening isoFile twice, and declaring isoSurfNegative from -isoSurf
    Nathan Wood committed Sep 2, 2021
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  3. Merge branch 'master' of https://github.com/nwoodweb/chemtools

    Nathan Wood committed Sep 2, 2021
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  4. Update ex002_esp_plot.py

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    nwoodweb committed Sep 2, 2021
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Commits on Oct 6, 2021

  1. modified with file IO Parameters, can be executed without explicitly … 

    …executing chimerax elf
    Nathan Wood committed Oct 6, 2021
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  2. add comments explaining parameters

    Nathan Wood committed Oct 6, 2021
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