Hi Stefan, The RDKit MMFF94 code assigns one of the 99 atom types, which is what is required to assign correct force field parameters to each atom. If you need the specific atom sub-type you will need to use SMARTS patterns or similar to identify the specific sub-environment of a certain MMFF94 atom type.
Alternatively, you may use a piece of software that I wrote ~10 years ago:that assigns numeric sub-types, that you may then relate to the respective symbolic atom type: http://sdf2xyz2sdf.sourceforge.net/ Hope this helps, cheers p. On Fri, Oct 22, 2021 at 7:22 PM Hiemer, Stefan <stefan.hie...@fau.de> wrote: > Dear Omar, > > I already know this thread. The problem is, that I do not know, how to > come from the GetMMFFAtomType returned unsigned integer to the string > representation. The unsigned integer code is not unique to a specific > symbolic atom type. Look for example at entry 2-4 of this file > https://github.com/openbabel/openbabel/blob/master/data/mmffdef.par: > > C=C 2 2 2 1 0 VINYLIC > * CSP2 2 2 2 1 0 GENERIC CSP2 > * CGD 2 2 2 1 0 GUANIDINE CARBON > > There you have the same numerical MMFF type (second column) for three > different symbolic atom types. So my question is: Since the numerical > MMFF is not unique to the symbolic atom type how can I get the symbolic > ones from rdkit? I need the symbolic types in order as the before > mentioned MC code takes them as input. > > Regards > Stefan > > > > Am 2021-10-22 06:40, schrieb Omar H94: > > Dear stefan, > > > > I had a similar issue, and based on answer by Paolo Tosco, you can find > > MMFF Symbols/Definitions here : > > https://github.com/openbabel/openbabel/blob/master/data/mmffdef.par > > The thread: https://sourceforge.net/p/rdkit/mailman/message/36949170/ > > > > I hope this helps, > > Omar. > > > > On Fri, Oct 22, 2021 at 7:12 AM Hiemer, Stefan <stefan.hie...@fau.de> > > wrote: > > > >> Hello everyone, > >> > >> I need to find the symbolic atom types of the Merck force field in > >> order > >> to create inputs for a Monte Carlo code > >> (http://towhee.sourceforge.net/) > >> as indicated in this example > >> ( > >> > https://sourceforge.net/p/towhee/code/HEAD/tree/Examples/Isobaric_Isothermal_Ensemble/MMFF94_Ethyleneoxide/towhee_input > ). > >> > >> As far as I can see, rdkit currently only provides the numerical MMFF > >> atom type via GetMMFFAtomType for each atom. Is there a convenient way > >> to get the symbolic ones (as the MC code requires them)? > >> > >> Thanks and Regards > >> Stefan > >> > >> > >> _______________________________________________ > >> Rdkit-discuss mailing list > >> Rdkit-discuss@lists.sourceforge.net > >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > >> > > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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