On 11/17/2015 10:34 AM, Alexandre Fassio wrote: > Indeed, we've tried the SDF and it is a good option. However, some small > ligands have covalent bonds with other small ligands and by using the SDF > format we won't able to detect it correctly. If you have any suggestion, > it'll be welcome.
If you mean in a macromolecule PDB structure, you can download the mmCIF file and take a look at _struct_conn table. I don't know of any software that would help much: both we and RCSB have a number of parser packages, but they'll just get you the table. You'll have to figure it out from there. -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
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