From fa2feeae555da086c10fdcd4e6879c505d756f24 Mon Sep 17 00:00:00 2001 From: Xavier Robin <xavier.robin@unibas.ch> Date: Fri, 5 Jan 2024 17:35:25 +0100 Subject: [PATCH] doc: new chemdict_tool flags --- modules/conop/doc/compoundlib.rst | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/modules/conop/doc/compoundlib.rst b/modules/conop/doc/compoundlib.rst index a83e59004..fcfa0fdbc 100644 --- a/modules/conop/doc/compoundlib.rst +++ b/modules/conop/doc/compoundlib.rst @@ -302,7 +302,11 @@ After downloading the file use :program:`chemdict_tool` to convert the MMCIF di Notes: - The :program:`chemdict_tool` only understands `.cif` and `.cif.gz` files. If you have would like to use other sources for the compound definitions, consider writing a script by using the :doc:`compound library <compoundlib>` API. -- This also loads compounds which are obsoleted by the PDB to maximize compatibility with older PDB files. +- This also loads compounds which are reserved or obsoleted by the PDB to maximize compatibility with older PDB files. You can change that and skip obsolete entries with the `-o` flag, and reserved entries with the `-i` flag. + +.. code-block:: bash + + chemdict_tool create <components.cif> <compounds.chemlib> -i -o If you are working with CHARMM trajectory files, you will also have to add the definitions for CHARMM. Assuming your are in the top-level source directory of -- GitLab