Dear OpenBabel discussion forum, I would like to raise two questions:
1) I would like to generate 3D structures from a smiles input - but when I try creating imidazole with "Generate 3D coordinates" ticked:
c1cnc[nH]1 I only get the attached awkward 3D sdf.The error is reproducable with OpenBabel versions 2.3.1 and 2.3.2 (I use Windows 7). I just installed the OpenBabel2.3.1_Windows_Installer.exe and there's really not many things one can do wrong it seems.
2) If task 1 is working I would like to be able to use a smiles list and a corresponding list of names as input for OpenBabel and get one 3D-sdf file for every smiles with the appropriate name (instead of 1.sdf, 2.sdf,...). So far I only found out how to get a name into the header of the respective sdf file - but I would like each and every sdf file to be named appropriately.
Does anyone have any suggestions? Many thanks in advance, Kai
imidazole_3D.sdf
Description: chemical/sdfile
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