Hi all, using 2.3. w/ smiles string copied from http://chemlookup.com/CAS_Number/384835-54-5.html:
> CCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)([O-])OCCNC(=O)CCCC[C@H]1[C@@H]2[C@H](CS1)NC(=O)N2)OC(=O)CCCCCCCCCCCCCCC.[Na+] command line: > bin/obabel -d --gen2d --title "" -xb none -xP1200 -ismi -osvg scrambled.smi > -O scrambled_1.svg Compare the attached scrambled_1.svg with the image @ the URL above. The worst part is Na+ is nowhere near its O. However, what I really need is all atoms with labels, so > bin/obabel -h --gen2d --title "" -xb none -xi -xa -xP1200 -ismi -osvg > scrambled.smi -O scrambled_2.svg -- scrambled_2.svg is messed up, but not as bad as scrambled_3.svg that was generated without --gen2d > bin/obabel -h --title "" -xb none -xi -xa -xP1200 -ismi -osvg scrambled.smi > -O scrambled_3.svg So I guess my question is, is it possible to get a sane layout with all hydrogens added? And a wish list one: rather than generating a garbage picture, how about aborting when there are no 2D coordinates? (I've another one coming) -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
scrambled_1.svg.gz
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scrambled_2.svg.gz
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scrambled_3.svg.gz
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