On Wed, May 6, 2020 at 6:15 PM Tim Dudgeon <tdudgeon...@gmail.com> wrote:
> What's not clear is the usage of mergeMethod as this does not seem to be > specifiable in CombineFeatMaps(), but you say that that method uses it when > calling MergeFeatPoints(). Why isn't it in the signature of the former? > > Because CombineFeatMaps() is just a convenience function and we only ever ended up using the WeightedAverages in the end -greg > Tim > On 06/05/2020 16:55, Greg Landrum wrote: > > We're deep in the underdocumented space now. Sorry about that. > > Here's an attempt to provide some at least sense of what these things > mean. This is going from (old) memory and a quick skim of the code... > hopefully I don't make any egregious errors. > > mergeMetric is the metric used to determine whether or not two feature > points will be combined into a single point. These use the the mergeTol > - NoMerge means don't merge points at all > - Distance means combine points that are less than mergeTol apart > - Overlap means combine points that have an overlap more than > mergeTol (the feature map itself computes this with GetFeatFeatScore()) > > dirMergeMode is not used (thankfully) > > mergeMethod is a parameter to MergeFeatPoints, which CombineFeatMaps > calls. > The default value is to use the weighted average of the features to > determine the location and weight of the replacement feature. > The other two possibilities are Average (does a non-weighted average) and > UseLarger which just keeps the location and weight of the feature point > with the larger weight. > > does that help? > > -greg > > > > > On Wed, May 6, 2020 at 5:27 PM Tim Dudgeon <tdudgeon...@gmail.com> wrote: > >> I'm trying to use the FeatureMaps functionality in RDKit (described here >> http://rdkit.blogspot.com/2017/11/using-feature-maps.html) and have a >> question on the parameters for CombineFeatMaps. >> >> See here: >> >> http://rdkit.org/docs/source/rdkit.Chem.FeatMaps.FeatMapUtils.html?highlight=combinefeatmaps#rdkit.Chem.FeatMaps.FeatMapUtils.CombineFeatMaps >> >> In particular what is the meaning of the 'mergeMetric' param (Distance >> vs. Overlap) and the 'dirMergeMode' param (NoMerge vs. Sum). And there >> is a class for MergeMethod that seems relevant but that is not part of >> the parameters for CombineFeatMaps. >> >> Thanks >> Tim >> >> >> >> _______________________________________________ >> 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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