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Merge GSOC Implementations #49

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Merge GSOC Implementations #49

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6764a03
add visualize.py visualization for cubefile
Jul 14, 2021
803d227
added visualization and save to image and cxs
Jul 20, 2021
6a8731d
rdkit annotation 2D
Jul 22, 2021
de94a65
rdkit, label stereoisomers and cis/trans
Jul 22, 2021
488bbbc
removed unnecessary modules
Jul 22, 2021
b1dc0a1
currently nonfunctioning dihedral angle calculator
Jul 22, 2021
b59ab32
added flags option, atomic numbers, remove dihedral angle, ISSUE: SMI…
Jul 26, 2021
e088907
first push of jupyter
Jul 27, 2021
3cc93a2
backup.ipynb
Jul 28, 2021
ced71a0
1. removed extra imports 2. removed variables for functions 3. add in…
Jul 28, 2021
77ce8de
newest annotation notebook
Jul 29, 2021
2d070a7
special thanks Ali Tehrani; gradient viz scale set to 50 scatter plo…
Jul 29, 2021
1550969
add annotation
Jul 30, 2021
8d482ca
Special Thanks Ali Tehrani, annotations added
Jul 30, 2021
fc617d1
Special Thanks Ali Tehrani, annotations added
Jul 30, 2021
d45d66f
Create molecular-visualizer.ipynb
nwoodweb Jul 30, 2021
9f3887d
added material call, cannot visualize negatives, added installation link
Jul 30, 2021
0e24b82
Merge branch 'master' of https://github.com/nwoodweb/chemtools
Jul 30, 2021
98d0079
rdkit still throws errors
Jul 30, 2021
23cd7ac
2D Plotting, errors generating level curves for contour
Jul 30, 2021
60d72a2
error with iodata load_one
Jul 30, 2021
60068c9
conversion tool from IODATA to CHEMICAL JSON
Aug 4, 2021
5031fdd
Delete Annotate_RDKit.ipynb
nwoodweb Aug 6, 2021
098a597
Delete bkup.ipynb
nwoodweb Aug 6, 2021
c0dd11f
will no longer be updated
Aug 6, 2021
4c1218f
update
Aug 6, 2021
f448aea
Merge branch 'master' of https://github.com/nwoodweb/chemtools
Aug 6, 2021
3fee292
added contour plot, visualizes, but currently incorrect
Aug 6, 2021
6598e2c
added contour plot, visualizes, but currently incorrect
Aug 6, 2021
6c1ff2c
added contour plot, visualizes, but currently incorrect
Aug 6, 2021
443fcdf
added contour plot, visualizes, but currently incorrect
Aug 6, 2021
b4e4323
REWRITTEN;USE THIS; includes atomic indicies, will include the annota…
Aug 6, 2021
28885a7
rewrote, was able to annotate each atom with ESP charges, however, or…
Aug 7, 2021
8acea5f
rewrote, was able to annotate each atom with ESP charges, however, or…
Aug 7, 2021
cdffb68
rewrote, was able to annotate each atom with ESP charges, however, or…
Aug 7, 2021
98df7f6
disordered number:charge pair and location with index
Aug 8, 2021
69127ff
add 3d visualization ipynb; replaced method of obtaining esp
Aug 8, 2021
30e0c4a
still errors with ascribing correct values to atoms
Aug 9, 2021
045eb0f
no annotations
Aug 9, 2021
4ac2135
no annotations
Aug 9, 2021
ebfdd5b
generic molecule name annotation
Aug 9, 2021
6bbc40d
generic molecule name annotation, can visualize isosurfaces single co…
Aug 9, 2021
7ffd522
2Dannotate - errors with ascribing correct atomic number and esp char…
Aug 10, 2021
8c5f8ee
2Dannotate - errors with ascribing correct atomic number and esp char…
Aug 10, 2021
988a0c3
chimerax annotations, must now replace number wiht atomic symbol
Aug 11, 2021
bfe6b82
unable to obtain chemical symbols
Aug 11, 2021
c4ac1f2
erroneous suffix labeling for redundandNumberDict
Aug 11, 2021
6c50386
erroneous suffix labeling for redundandNumberDict
Aug 11, 2021
6dd1397
atomic numbers are ordered properly, however will have to reorganize …
Aug 11, 2021
a5cd671
revised function for coloring esp isosurfaces in chimerax
Aug 12, 2021
68d1923
cl and n match for example, however, Carbons are all incorrect
Aug 12, 2021
1ad1651
cl and n match for example, however, Carbons are all incorrect
Aug 12, 2021
ca36a8e
consolidated gradient vector field into independent function, however…
Aug 12, 2021
26c029a
consolidated gradient vector field into independent function, however…
Aug 12, 2021
c33d91f
redone scalar plot, errors with projection
Aug 12, 2021
a88fe57
increased number of shades for color gradient, produces more VMD-like…
Aug 13, 2021
4c96de5
add
Aug 13, 2021
0bc0173
iso = esp, color = rho, coloring is off, gaping hole at .003 = isosurf
Aug 13, 2021
68d7df0
incorrect shaping of scalarFuncPlotRefine`
Aug 13, 2021
467a08e
COMPLETE
Aug 14, 2021
8c655d0
modified scalemin to accept chimerax computation; added verbosity to …
Aug 15, 2021
bf36740
3D: followed suggestions about for loops, maintained workingBFactor; …
Aug 16, 2021
32640a7
Finalized
Aug 17, 2021
5355119
finalized in accordance with GA
Aug 17, 2021
384fb68
corrected 2d annotation
Aug 17, 2021
af0f121
finalization
Aug 19, 2021
76e411d
finalized, consolidated into functions
Aug 20, 2021
b4d72cb
main page
Aug 20, 2021
d5df616
revert readme
Aug 20, 2021
158ac19
consolidated documentation within function
Aug 20, 2021
e6e96fa
consolidated into function, tested in linux CLI
Aug 20, 2021
eb8e1ae
test main page edit
Aug 20, 2021
b25b7d5
test main page edit 2
Aug 20, 2021
99f6f42
test main page edit 2
Aug 20, 2021
e78b2af
Update README.md
nwoodweb Aug 20, 2021
aa6e3a4
Update README.md
nwoodweb Aug 20, 2021
887fba6
Update README.md
nwoodweb Aug 20, 2021
ef245f4
Update README.md
nwoodweb Aug 20, 2021
a37b0ab
Update README.md
nwoodweb Aug 20, 2021
fce31eb
Update README.md
nwoodweb Aug 20, 2021
6aac70a
Update README.md
nwoodweb Aug 20, 2021
fd254da
updated comments to all added
Aug 20, 2021
2ccd8e0
Merge branch 'master' of https://github.com/nwoodweb/chemtools
Aug 20, 2021
df02ab2
Update README.md
nwoodweb Aug 20, 2021
733ef2f
Update README.md
nwoodweb Aug 20, 2021
e367e51
Add files via upload
nwoodweb Aug 20, 2021
7d9d500
Add files via upload
nwoodweb Aug 20, 2021
e817aa6
Update README.md
nwoodweb Aug 20, 2021
98011bd
Update README.md
nwoodweb Aug 20, 2021
88e5ff8
Update README.md
nwoodweb Aug 20, 2021
0084be5
Update README.md
nwoodweb Aug 20, 2021
33540e5
separated into individual functions
Aug 20, 2021
c160a4d
Merge branch 'master' of https://github.com/nwoodweb/chemtools
Aug 20, 2021
6a9b876
Update README.md
nwoodweb Aug 20, 2021
f643156
Update README.md
nwoodweb Aug 20, 2021
3d3b864
Update README.md
nwoodweb Aug 20, 2021
6c01e67
Add files via upload
nwoodweb Aug 20, 2021
4784c80
Delete examples/annotate directory
nwoodweb Aug 20, 2021
845faa2
Delete visualize.py
nwoodweb Aug 20, 2021
c6ef951
Delete visualize_scl.py
nwoodweb Aug 20, 2021
11b0680
Delete Annotate_2D.ipynb
nwoodweb Aug 20, 2021
e7d3f1a
Delete Annotate_3D_Chimera_Stage2.py
nwoodweb Aug 20, 2021
86d9ecd
Delete Annotate_3D_Chimera_Stage1.ipynb
nwoodweb Aug 20, 2021
39af5dc
Delete 3DAnnotateExample.png
nwoodweb Aug 20, 2021
942501a
Update README.md
nwoodweb Aug 20, 2021
0c39a28
improved comments and formatting
Aug 20, 2021
1acbeee
Merge branch 'master' of https://github.com/nwoodweb/chemtools
Aug 20, 2021
6041bd4
improved annotations per Alis suggestion
Aug 20, 2021
a79ea8d
improved annotations per Alis suggestion
Aug 20, 2021
8e25ead
Update README.md
nwoodweb Aug 20, 2021
892bbb4
Update README.md
nwoodweb Aug 21, 2021
5b5e7db
added None as colorFile option
Aug 23, 2021
ea23074
can also render generic isosurfaces
Aug 23, 2021
129d8c4
revert readme
Aug 23, 2021
f2eb05f
removed incorrect comment
Aug 23, 2021
e3cea37
Update ex002_esp_plot.py
nwoodweb Aug 26, 2021
cc66a52
Update ex001_esp_plot.py
nwoodweb Aug 26, 2021
a270581
Delete README.md.bkup
nwoodweb Aug 26, 2021
55b3d69
Delete 3dannotate.png
nwoodweb Aug 26, 2021
d600784
Delete vmdfail.png
nwoodweb Aug 26, 2021
d42d022
Delete acroleinerror.png
nwoodweb Aug 26, 2021
329ea9d
Delete vmdcorrect.png
nwoodweb Aug 26, 2021
5edf309
Delete test11.png
nwoodweb Aug 26, 2021
fcb3987
Delete dichloropyridine26_q+0.png
nwoodweb Aug 26, 2021
09e8d1f
Delete dichlorgradient.png
nwoodweb Aug 26, 2021
b598f8c
Delete contour.png
nwoodweb Aug 26, 2021
a465f26
revamped colorfile if-then-else branching; implemented negatives by r…
Sep 2, 2021
faf7c3b
revamped colorfile if-then-else branching; implemented negatives by r…
Sep 2, 2021
8cb9117
Merge branch 'master' of https://github.com/nwoodweb/chemtools
Sep 2, 2021
45f68da
Update ex002_esp_plot.py
nwoodweb Sep 2, 2021
ce25dba
modified with file IO Parameters, can be executed without explicitly …
Oct 6, 2021
d70d48c
add comments explaining parameters
Oct 6, 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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Nathan Wood committed Aug 7, 2021
commit cdffb685ab6dfbd56f41ca6ac5655ca3b18c90bb
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