Re: [Rdkit-discuss] Atom Symbol Case in MolFile?

Correct message thread this time: The joys of the molfile - was curious whether it was accepted/correctly > interpreted: > > ISIS Draw 2.5 Yes (arguably the arbitrator of the format) > ChemDraw 15 Yes > ChemDoodle No (accepted but only as a text label 'CL' no conversion) > MarvinSketch Yes >

Re: [Rdkit-discuss] Atom Symbol Case in MolFile?

Hi Greg, Thanks for that. Why do I ask? Because the sdf files [1] distributed by the wwPDB, such as this one: http://www.rcsb.org/pdb/files/ligand/CQ8_ideal.sdf from this page: http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=CQ8 are upper-cased. I didn't know whether that was

Re: [Rdkit-discuss] Atom Symbol Case in MolFile?

Paul, On Tue, Jan 19, 2016 at 7:59 PM, Paul Emsley wrote: > > Thanks for that. > > Why do I ask? Because the sdf files [1] distributed by the wwPDB, such as > this one: > > http://www.rcsb.org/pdb/files/ligand/CQ8_ideal.sdf > > from this page: > >

[Rdkit-discuss] Atom Symbol Case in MolFile?

Dear RDKitters, Is is clear what the case of the second character of an atom symbol in the atom block of a MolFile should be? i.e. "CL", "Cl" or either? Thanks, Paul. -- Site24x7 APM Insight: Get Deep Visibility

Re: [Rdkit-discuss] Atom Symbol Case in MolFile?

Hi Paul, ctfile.pdf says: "entry in periodic table" I interpret this to mean "Cl", since that's what one finds in the typical periodic table. The RDKit, curiously, agrees with me. ;-) -greg On Mon, Jan 18, 2016 at 8:45 AM, Paul Emsley wrote: > > Dear RDKitters, >