On 19/05/2023 10:28, Frank von Delft wrote:
Hello - as in the subject line, does anybody know of, or have, code
that will parse (1) a PDB (or mmCIF?) file with a ligand, and (2) the
restraints CIF file used in refinement, and generate a .mol (or .sdf)
file?
Isn't this a bit of strange request? .sdf files are for coordinates, it
is not clear to me how they would encode restraint information (other
than simply minimizing the ligand of course (and if you are using the
monomer library it is likely that Refmac has done this for you)).
Here's how you convert a residue/ligand to an sdf using coot:
import coot
imol = coot.get_monomer("AMP")
coot.residue_to_sdf_file(imol, "A", 1, "", "AMP.sdf")
Paul.
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