If your ligand really came from the PDB, you can download the ligand
in SD format. (Just scroll down to "Ligand" and click the download
link.) SD files will have the bonding info and should solve your
problem.
Ling
- Forwarded Message -
>From: S.L. Chan
>To: radka ; "openbabel-discuss@
Radka,
PDB files simply don't have bonding information. There is just no
way to be absolutely sure whether a bond is single or double,
especially when there are no hydrogens around. While the bond in
question may be long, there are other factors, like the local
geometry, to be considered when bo
Please, can you help me with the following problem?:
I have this PDB file (sugar from Protein Data Bank):
HETATM 3781 C1 MAN C1129 35.524 5.379 57.298 1.00 26.66
C
HETATM 3782 C2 MAN C1129 34.930 6.750 56.924 1.00 26.33
C
HETATM 3783 C3 MAN C1129
$ grep append `/usr/bin/find . | grep .cpp`
./src/transform.cpp:itr = pOptions->find("append"); //Appends values of desc
riptors or properties to title
./src/transform.cpp:"--append Append properties or descriptors in list to
title:\n"
We're on github if you want to submit a patch for r
