rdkit-sdf-for-ccd.md

@@ -3,10 +3,10 @@
 * previous work [RDKit molecule from PDB CCD definition](rdkit-from-ccd) now extend to write sdf files.
 * start with a stub implementation and unit tests [Commit 5773ff0e](https://gitlab.com/pdbe/ccd_utils/commit/5773ff0e2b3f560ad344777452a567a88e57cf45)
 * initial implementation [Commit 7eb159fe](https://gitlab.com/pdbe/ccd_utils/commit/7eb159fedf4cc0cea5b3c53b92ca24995433664b)
-  * writes sdf files with the "ideal" coordinates successfully
+  * writes sdf files with the "ideal" coordinates and hydrogen successfully
   * these sdf files can be read by Mogul and the atoms are labelled with their PDB atom name. For instance reading `tests_out/ATP.ideal_withH.sdf` and selecting atom labels on results in:
   * ![ATP_ideal_withH_sdf_into_Mogul](/uploads/8e7c6e82ee4b024a3742f45debc55780/ATP_ideal_withH_sdf_into_Mogul.png)
-  * note that atoms are labelled according to the atom order in sdf that reflects the order in the input ccd cif. I thought that Mogul read alias (running old version - need to check newer). But it does not really matter.
+  * note that atoms are labelled according to the atom order in sdf that reflects the order in the input ccd cif. I thought that Mogul read the alias information but not in this case. Test was running an old Mogul version need to check with the latest. But actually it does not really matter.
   * pymol can also load although it does not get atom order or alias
   * obabel is confused by the alias but never mind.
 * many things left to to do