| Hi there, I'm converting some molecules to 2D format, and some of them are extremely small and/or uncommon in normal chemistry (e.g. nitrogen atoms). I'm running into an issue where sometimes it automatically adds hydrogen atoms. For example, I have a reaction where NH is split into N and H atoms, and I really just want it to display H-N on the left and N H on the right. Files are attached below. Thanks. :) - Lee-Ping Watch the right panel when I want to convert a separate nitrogen atom and hydrogen atom into PNG format: obabel reactants.cml products.cml -O ~/Dropbox/tmp.png --gen2d -xw 1200 -xh 600 |
<<inline: tmp.png>>
As you can see (above), it adds three "blue" hydrogen atoms to N which is not desired, plus it puts N and H on top of each other. If I use "--gen3d", it adds a hydrogen atom to H as well and makes them all gray. Adding "-h" does the same thing (below). It seems the stacking problem is gone, but having a balanced chemical equation is more important. |
<<inline: tmp.png>>
If I use "-d", now it deletes the hydrogen atom but adds three to the nitrogen atom. |
<<inline: tmp.png>>
products.cml
Description: Binary data
reactants.cml
Description: Binary data
------------------------------------------------------------------------------ Flow-based real-time traffic analytics software. Cisco certified tool. Monitor traffic, SLAs, QoS, Medianet, WAAS etc. with NetFlow Analyzer Customize your own dashboards, set traffic alerts and generate reports. Network behavioral analysis & security monitoring. All-in-one tool. http://pubads.g.doubleclick.net/gampad/clk?id=126839071&iu=/4140/ostg.clktrk
_______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
