Hi Tim, Many thanks for your help! One further question: Is there any correlation between the maxAttempts and numConfs? For instance, do I need to set a higher maxAttempts value if I request a higher numConfs value?
Or to put it another way, what maxAttempts value can be considered as "enough"? Best, Leon On Tue, Dec 17, 2019 at 12:22 PM Tim Dudgeon <tdudgeon...@gmail.com> wrote: > This is in regard to the pruneRmsThresh option which removes very similar > conformers. > If let's say numConfs is set to 10 and maxAttempts is set to 20 then it > will use UP TO 20 attempts to generate 10 conformers. > If too many conformers get rejected due to pruneRmsThresh then you will > end up with less than 10 conformers. > > Or to put it another way, maxAttempts avoids you trying for ever to > generate conformers that are all the same and getting rejected! > > Tim > On 17/12/2019 16:24, topgunhaides . wrote: > > Hi guys, > > Can anyone tell me more about the "maxAttempts" option in > "EmbedMultipleConfs"? > > In the documentation, it says " maxAttempts: the maximum number of > attempts to try embedding". > Dose it mean the "maximum number of attempts" to generate each conformer > or to generate the total number of conformers specified by "numConfs"? Or > something else? > I need to generate a huge amount of conformers for each molecule, so I > want to know what is the proper "maxAttempts" to reach a balance between > accuracy and cost. > Thank you! > > Best, > Leon > > > > > _______________________________________________ > Rdkit-discuss mailing > listRdkit-discuss@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > _______________________________________________ > 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
