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Merge GSOC Implementations #49

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Merge GSOC Implementations #49

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add visualize.py visualization for cubefile

added visualization and save to image and cxs

rdkit annotation 2D

rdkit, label stereoisomers and cis/trans

removed unnecessary modules

currently nonfunctioning dihedral angle calculator

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

first push of jupyter

1. removed extra imports 2. removed variables for functions 3. add in…

newest annotation notebook

special thanks Ali Tehrani; gradient viz scale set to 50 scatter plo…

Special Thanks Ali Tehrani, annotations added

Special Thanks Ali Tehrani, annotations added

Create molecular-visualizer.ipynb

nwoodweb Jul 30, 2021

added material call, cannot visualize negatives, added installation link

Merge branch 'master' of https://github.com/nwoodweb/chemtools

rdkit still throws errors

2D Plotting, errors generating level curves for contour

error with iodata load_one

conversion tool from IODATA to CHEMICAL JSON

Delete Annotate_RDKit.ipynb

nwoodweb Aug 6, 2021

Delete bkup.ipynb

nwoodweb Aug 6, 2021

will no longer be updated

Merge branch 'master' of https://github.com/nwoodweb/chemtools

added contour plot, visualizes, but currently incorrect

added contour plot, visualizes, but currently incorrect

added contour plot, visualizes, but currently incorrect

added contour plot, visualizes, but currently incorrect

REWRITTEN;USE THIS; includes atomic indicies, will include the annota…

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

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

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

disordered number:charge pair and location with index

add 3d visualization ipynb; replaced method of obtaining esp

still errors with ascribing correct values to atoms

generic molecule name annotation

generic molecule name annotation, can visualize isosurfaces single co…

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

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

chimerax annotations, must now replace number wiht atomic symbol

unable to obtain chemical symbols

erroneous suffix labeling for redundandNumberDict

erroneous suffix labeling for redundandNumberDict

atomic numbers are ordered properly, however will have to reorganize …

revised function for coloring esp isosurfaces in chimerax

cl and n match for example, however, Carbons are all incorrect

cl and n match for example, however, Carbons are all incorrect

consolidated gradient vector field into independent function, however…

consolidated gradient vector field into independent function, however…

redone scalar plot, errors with projection

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

iso = esp, color = rho, coloring is off, gaping hole at .003 = isosurf

incorrect shaping of scalarFuncPlotRefine`

modified scalemin to accept chimerax computation; added verbosity to …

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

finalized in accordance with GA

corrected 2d annotation

finalized, consolidated into functions

consolidated documentation within function

consolidated into function, tested in linux CLI

test main page edit

test main page edit 2

test main page edit 2

Update README.md

nwoodweb Aug 20, 2021

Update README.md

nwoodweb Aug 20, 2021

Update README.md

nwoodweb Aug 20, 2021

Update README.md

nwoodweb Aug 20, 2021

Update README.md

nwoodweb Aug 20, 2021

Update README.md

nwoodweb Aug 20, 2021

Update README.md

nwoodweb Aug 20, 2021

updated comments to all added

Merge branch 'master' of https://github.com/nwoodweb/chemtools

Update README.md

nwoodweb Aug 20, 2021

Update README.md

nwoodweb Aug 20, 2021

Add files via upload

nwoodweb Aug 20, 2021

Add files via upload

nwoodweb Aug 20, 2021

Update README.md

nwoodweb Aug 20, 2021

Update README.md

nwoodweb Aug 20, 2021

Update README.md

nwoodweb Aug 20, 2021

Update README.md

nwoodweb Aug 20, 2021

separated into individual functions

Merge branch 'master' of https://github.com/nwoodweb/chemtools

Update README.md

nwoodweb Aug 20, 2021

Update README.md

nwoodweb Aug 20, 2021

Update README.md

nwoodweb Aug 20, 2021

Add files via upload

nwoodweb Aug 20, 2021

Delete examples/annotate directory

nwoodweb Aug 20, 2021

Delete visualize.py

nwoodweb Aug 20, 2021

Delete visualize_scl.py

nwoodweb Aug 20, 2021

Delete Annotate_2D.ipynb

nwoodweb Aug 20, 2021

Delete Annotate_3D_Chimera_Stage2.py

nwoodweb Aug 20, 2021

Delete Annotate_3D_Chimera_Stage1.ipynb

nwoodweb Aug 20, 2021

Delete 3DAnnotateExample.png

nwoodweb Aug 20, 2021

Update README.md

nwoodweb Aug 20, 2021

improved comments and formatting

Merge branch 'master' of https://github.com/nwoodweb/chemtools

improved annotations per Alis suggestion

improved annotations per Alis suggestion

Update README.md

nwoodweb Aug 20, 2021

Update README.md

nwoodweb Aug 21, 2021

added None as colorFile option

can also render generic isosurfaces

removed incorrect comment

Update ex002_esp_plot.py

nwoodweb Aug 26, 2021

Update ex001_esp_plot.py

nwoodweb Aug 26, 2021

Delete README.md.bkup

nwoodweb Aug 26, 2021

Delete 3dannotate.png

nwoodweb Aug 26, 2021

Delete vmdfail.png

nwoodweb Aug 26, 2021

Delete acroleinerror.png

nwoodweb Aug 26, 2021

Delete vmdcorrect.png

nwoodweb Aug 26, 2021

Delete test11.png

nwoodweb Aug 26, 2021

Delete dichloropyridine26_q+0.png

nwoodweb Aug 26, 2021

Delete dichlorgradient.png

nwoodweb Aug 26, 2021

Delete contour.png

nwoodweb Aug 26, 2021

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

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

Merge branch 'master' of https://github.com/nwoodweb/chemtools

Update ex002_esp_plot.py

nwoodweb Sep 2, 2021

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

add comments explaining parameters

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Delete Annotate_RDKit.ipynb

removed, no longer used, rewrite in progress

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