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Merge GSOC Implementations #49
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Commits on Jul 14, 2021
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add visualize.py visualization for cubefile
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Commits on Jul 20, 2021
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added visualization and save to image and cxs
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Commits on Jul 22, 2021
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rdkit, label stereoisomers and cis/trans
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currently nonfunctioning dihedral angle calculator
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Commits on Jul 26, 2021
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added flags option, atomic numbers, remove dihedral angle, ISSUE: SMI…
…LES FORMATTING
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Commits on Jul 27, 2021
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1. removed extra imports 2. removed variables for functions 3. add in…
…structions to run in comments near beginning "chimerax visualize.py"
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Commits on Jul 29, 2021
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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
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Commits on Jul 30, 2021
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Special Thanks Ali Tehrani, annotations added
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Special Thanks Ali Tehrani, annotations added
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added material call, cannot visualize negatives, added installation link
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Merge branch 'master' of https://github.com/nwoodweb/chemtools
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2D Plotting, errors generating level curves for contour
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Commits on Aug 4, 2021
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conversion tool from IODATA to CHEMICAL JSON
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Commits on Aug 6, 2021
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removed, no longer used, rewrite in progress
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Merge branch 'master' of https://github.com/nwoodweb/chemtools
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added contour plot, visualizes, but currently incorrect
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added contour plot, visualizes, but currently incorrect
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added contour plot, visualizes, but currently incorrect
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added contour plot, visualizes, but currently incorrect
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REWRITTEN;USE THIS; includes atomic indicies, will include the annota…
…tions in next update
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Commits on Aug 7, 2021
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rewrote, was able to annotate each atom with ESP charges, however, or…
…der of annotation is incorrect
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rewrote, was able to annotate each atom with ESP charges, however, or…
…der of annotation is incorrect
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rewrote, was able to annotate each atom with ESP charges, however, or…
…der of annotation is incorrect
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Commits on Aug 8, 2021
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disordered number:charge pair and location with index
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add 3d visualization ipynb; replaced method of obtaining esp
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Commits on Aug 9, 2021
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still errors with ascribing correct values to atoms
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generic molecule name annotation
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generic molecule name annotation, can visualize isosurfaces single co…
…lor only
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Commits on Aug 10, 2021
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2Dannotate - errors with ascribing correct atomic number and esp char…
…ge; 3d annotate - no change, added isosurface; plotting - WIP density contour plot
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2Dannotate - errors with ascribing correct atomic number and esp char…
…ge; 3d annotate - no change, added isosurface; plotting - WIP density contour plot
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Commits on Aug 11, 2021
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chimerax annotations, must now replace number wiht atomic symbol
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unable to obtain chemical symbols
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erroneous suffix labeling for redundandNumberDict
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erroneous suffix labeling for redundandNumberDict
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atomic numbers are ordered properly, however will have to reorganize …
…how to pair charge with correct atom
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Commits on Aug 12, 2021
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revised function for coloring esp isosurfaces in chimerax
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cl and n match for example, however, Carbons are all incorrect
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cl and n match for example, however, Carbons are all incorrect
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consolidated gradient vector field into independent function, however…
… scalar counterplot unfinished
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consolidated gradient vector field into independent function, however…
… scalar counterplot unfinished
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redone scalar plot, errors with projection
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Commits on Aug 13, 2021
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increased number of shades for color gradient, produces more VMD-like…
… output surface visualization
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iso = esp, color = rho, coloring is off, gaping hole at .003 = isosurf
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Commits on Aug 14, 2021
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Commits on Aug 15, 2021
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modified scalemin to accept chimerax computation; added verbosity to …
…3D annotation
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Commits on Aug 16, 2021
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3D: followed suggestions about for loops, maintained workingBFactor; …
…2D Complete, will mend markdown text
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Commits on Aug 17, 2021
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finalized in accordance with GA
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Commits on Aug 20, 2021
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finalized, consolidated into functions
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consolidated documentation within function
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consolidated into function, tested in linux CLI
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Merge branch 'master' of https://github.com/nwoodweb/chemtools
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separated into individual functions
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Merge branch 'master' of https://github.com/nwoodweb/chemtools
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improved comments and formatting
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Merge branch 'master' of https://github.com/nwoodweb/chemtools
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improved annotations per Alis suggestion
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improved annotations per Alis suggestion
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Commits on Aug 21, 2021
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Commits on Aug 23, 2021
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added None as colorFile option
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can also render generic isosurfaces
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Commits on Sep 2, 2021
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revamped colorfile if-then-else branching; implemented negatives by r…
…eopening isoFile twice, and declaring isoSurfNegative from -isoSurf
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revamped colorfile if-then-else branching; implemented negatives by r…
…eopening isoFile twice, and declaring isoSurfNegative from -isoSurf
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Merge branch 'master' of https://github.com/nwoodweb/chemtools
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Commits on Oct 6, 2021
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modified with file IO Parameters, can be executed without explicitly …
…executing chimerax elf
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add comments explaining parameters
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