Re: [Rdkit-discuss] Usage of CombineFeatMaps

2020-05-06 Thread Greg Landrum 
On Wed, May 6, 2020 at 6:15 PM Tim Dudgeon  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  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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Re: [Rdkit-discuss] Usage of CombineFeatMaps

2020-05-06 Thread Tim Dudgeon 

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 > 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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Re: [Rdkit-discuss] Usage of CombineFeatMaps

2020-05-06 Thread Greg Landrum 
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  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
>
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[Rdkit-discuss] Usage of CombineFeatMaps

2020-05-06 Thread Tim Dudgeon 
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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