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CDK-R / cdkr

Integrating R and the CDK
https://cdk-r.github.io/cdkr/
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Dual display of aromaticity after do.typing() #15

Closed sneumann closed 10 years ago

sneumann commented 10 years ago

Hi,

library(rcdk)
m <- parse.smiles("c1ccccc1")[[1]]
view.molecule.2d(m)
do.typing(m)
view.molecule.2d(m)

The first display is kinda correct: screenshot from 2014-02-12 22 49 47

while after typing I get dual aromaticity depiction: screenshot from 2014-02-12 22 51 11

It would be great to have just one of them. (Or even a choice :-) And I love the github issue tracker. Very well done.

Yours, Steffen

rajarshi commented 10 years ago

This seems to be resolved in 3.5.2 which is in Github - can you compile from the sources and try it out?

sneumann commented 10 years ago

Hi, thanks for the quick reply. Unfortunately no change, I built from source at the current HEAD ed0b3122175d89f4c19df4266bd34114069e29f1, I am at rcdk_3.2.5, rcdklibs_1.5.4. The fix you mention should've been from 2013-12-04 664302f99c14051cbe3a3af2e5bedfa5bd8ee59c ? Can Java make a difference here ? I am on OpenJDK 1.7.0_51, on Ubuntu 12.04. Thx, Steffen

rajarshi commented 10 years ago

Should be fixed in the latest master - make sure to also build and install rcdklibs from github. Also there is no need to separately do aromaticity perception. Please close if you think this is resolved

sneumann commented 10 years ago

Fixed in rcdk_3.2.6 and rcdklibs_1.5.5 . Thanks for the quick response!