Hi Greg, yes that mostly makes sense and is a great help.
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?
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
<mailto: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
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