Merge GSOC Implementations #49

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nwoodweb wants to merge 132 commits intotheochem:devfrom

nwoodweb:master

Commits on Jul 14, 2021

add visualize.py visualization for cubefile
nwcad2020
committed

Commits on Jul 20, 2021

added visualization and save to image and cxs
nwcad2020
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Commits on Jul 22, 2021

rdkit annotation 2D
nwcad2020
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rdkit, label stereoisomers and cis/trans
nwcad2020
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removed unnecessary modules
nwcad2020
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currently nonfunctioning dihedral angle calculator
nwcad2020
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Commits on Jul 26, 2021

added flags option, atomic numbers, remove dihedral angle, ISSUE: SMILES FORMATTING
Nathan Wood
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Commits on Jul 27, 2021

first push of jupyter
Nathan Wood
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Commits on Jul 28, 2021

backup.ipynb
Nathan Wood
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1. removed extra imports 2. removed variables for functions 3. add instructions to run in comments near beginning
Nathan Wood
committed

Commits on Jul 29, 2021

Commits on Jul 30, 2021

add annotation
Nathan Wood
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Special Thanks Ali Tehrani, annotations added
Nathan Wood
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Special Thanks Ali Tehrani, annotations added
Nathan Wood
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Create molecular-visualizer.ipynb
nwoodweb
authored
added material call, cannot visualize negatives, added installation link
Nathan Wood
committed
Merge branch 'master' of https://github.com/nwoodweb/chemtools
Nathan Wood
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rdkit still throws errors
Nathan Wood
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2D Plotting, errors generating level curves for contour
Nathan Wood
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error with iodata load_one
Nathan Wood
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Commits on Aug 4, 2021

conversion tool from IODATA to CHEMICAL JSON
Nathan Wood
committed

Commits on Aug 6, 2021

Delete Annotate_RDKit.ipynb
nwoodweb
authored
Delete bkup.ipynb
nwoodweb
authored
will no longer be updated
Nathan Wood
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update
Nathan Wood
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Merge branch 'master' of https://github.com/nwoodweb/chemtools
Nathan Wood
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added contour plot, visualizes, but currently incorrect
Nathan Wood
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added contour plot, visualizes, but currently incorrect
Nathan Wood
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added contour plot, visualizes, but currently incorrect
Nathan Wood
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added contour plot, visualizes, but currently incorrect
Nathan Wood
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REWRITTEN;USE THIS; includes atomic indicies, will include the annotations in next update
Nathan Wood
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Commits on Aug 7, 2021

Commits on Aug 8, 2021

disordered number:charge pair and location with index
Nathan Wood
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add 3d visualization ipynb; replaced method of obtaining esp
Nathan Wood
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Commits on Aug 9, 2021

still errors with ascribing correct values to atoms
Nathan Wood
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no annotations
Nathan Wood
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no annotations
Nathan Wood
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generic molecule name annotation
Nathan Wood
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generic molecule name annotation, can visualize isosurfaces single color only
Nathan Wood
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Commits on Aug 10, 2021

Commits on Aug 11, 2021

chimerax annotations, must now replace number wiht atomic symbol
Nathan Wood
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unable to obtain chemical symbols
Nathan Wood
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erroneous suffix labeling for redundandNumberDict
Nathan Wood
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erroneous suffix labeling for redundandNumberDict
Nathan Wood
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atomic numbers are ordered properly, however will have to reorganize how to pair charge with correct atom
Nathan Wood
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Commits on Aug 12, 2021

revised function for coloring esp isosurfaces in chimerax
Nathan Wood
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cl and n match for example, however, Carbons are all incorrect
Nathan Wood
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cl and n match for example, however, Carbons are all incorrect
Nathan Wood
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consolidated gradient vector field into independent function, however scalar counterplot unfinished
Nathan Wood
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consolidated gradient vector field into independent function, however scalar counterplot unfinished
Nathan Wood
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redone scalar plot, errors with projection
Nathan Wood
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Commits on Aug 13, 2021

increased number of shades for color gradient, produces more VMD-like output surface visualization
Nathan Wood
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add
Nathan Wood
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iso = esp, color = rho, coloring is off, gaping hole at .003 = isosurf
Nathan Wood
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incorrect shaping of scalarFuncPlotRefine`
Nathan Wood
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Commits on Aug 14, 2021

COMPLETE
Nathan Wood
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Commits on Aug 15, 2021

modified scalemin to accept chimerax computation; added verbosity to 3D annotation
Nathan Wood
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Commits on Aug 16, 2021

3D: followed suggestions about for loops, maintained workingBFactor; 2D Complete, will mend markdown text
Nathan Wood
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Commits on Aug 17, 2021

Finalized
Nathan Wood
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finalized in accordance with GA
Nathan Wood
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corrected 2d annotation
Nathan Wood
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Commits on Aug 19, 2021

finalization
Nathan Wood
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Commits on Aug 20, 2021

finalized, consolidated into functions
Nathan Wood
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main page
Nathan Wood
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revert readme
Nathan Wood
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consolidated documentation within function
Nathan Wood
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consolidated into function, tested in linux CLI
Nathan Wood
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test main page edit
Nathan Wood
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test main page edit 2
Nathan Wood
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test main page edit 2
Nathan Wood
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Update README.md
nwoodweb
authored
Update README.md
nwoodweb
authored
Update README.md
nwoodweb
authored
Update README.md
nwoodweb
authored
Update README.md
nwoodweb
authored
Update README.md
nwoodweb
authored
Update README.md
nwoodweb
authored
updated comments to all added
Nathan Wood
committed
Merge branch 'master' of https://github.com/nwoodweb/chemtools
Nathan Wood
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Update README.md
nwoodweb
authored
Update README.md
nwoodweb
authored
Add files via upload
nwoodweb
authored
Add files via upload
nwoodweb
authored
Update README.md
nwoodweb
authored
Update README.md
nwoodweb
authored
Update README.md
nwoodweb
authored
Update README.md
nwoodweb
authored
separated into individual functions
Nathan Wood
committed
Merge branch 'master' of https://github.com/nwoodweb/chemtools
Nathan Wood
committed
Update README.md
nwoodweb
authored
Update README.md
nwoodweb
authored
Update README.md
nwoodweb
authored
Add files via upload
nwoodweb
authored
Delete examples/annotate directory
nwoodweb
authored
Delete visualize.py
nwoodweb
authored
Delete visualize_scl.py
nwoodweb
authored
Delete Annotate_2D.ipynb
nwoodweb
authored
Delete Annotate_3D_Chimera_Stage2.py
nwoodweb
authored
Delete Annotate_3D_Chimera_Stage1.ipynb
nwoodweb
authored
Delete 3DAnnotateExample.png
nwoodweb
authored
Update README.md
nwoodweb
authored
improved comments and formatting
Nathan Wood
committed
Merge branch 'master' of https://github.com/nwoodweb/chemtools
Nathan Wood
committed
improved annotations per Alis suggestion
Nathan Wood
committed
improved annotations per Alis suggestion
Nathan Wood
committed
Update README.md
nwoodweb
authored

Commits on Aug 21, 2021

Update README.md
nwoodweb
authored

Commits on Aug 23, 2021

added None as colorFile option
Nathan Wood
committed
can also render generic isosurfaces
Nathan Wood
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revert readme
Nathan Wood
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removed incorrect comment
Nathan Wood
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Commits on Sep 2, 2021

Commits on Oct 6, 2021

modified with file IO Parameters, can be executed without explicitly executing chimerax elf
Nathan Wood
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add comments explaining parameters
Nathan Wood
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