For stripping the counter ion of a salted ligand, I am basically using the
larger smiles string after splitting on "."
It's my understanding that for counter ions, they're pretty much not present in
an aqueous solution (inside cell). So for example, if sodium (+1) is the
counter ion for a
Before performing ligand energy minimization then docking with receptors, I am
adding hydrogens to ligands via the syntax:
Addhydrogens(False, False);
I am pretty sure this adds implicit H since polar-only is false. For docking,
should I only add polar H, or is ...(False, False) the
Hi,
I am trying to figure out the time complexity (Big O) of converting from OBMol
to canonical smiles. I tried to look at the code but it looks too complex. (I
am assuming "class OBMol2Cansmi" is the right place to look at.) Is there
relevant documentation/paper on this? Does anyone know the
