Networkx not add all the descriptors as cliques

[AngelRuizMoreno]

When I assign the pharmacophoric descriptors as cliques using Networkx library GRAPH function. It just assign a part of them.

For example:

data=phr.Descriptors (input_file=benchmark,select='enabled')
print (len (data.points))

11

This means that data.points has informations for 11 descriptors. Then when I run:

G= nx.Graph (pharmacophore='descriptors')

for element in data.points:
    node=(element[1],element[2],element[3]) # extracts x,y, and z positions for each descriptor
    G.add_node (node_for_adding=node, name=element[0])
print ('Number of nodes:',G.number_of_nodes ())

8

So, for a model with 11 descriptors I just can save and graph 8 in G (Networkx Graph).

How can I solve it?
Could it be something related to the degrees of freedom for Networkx Graph?

[AngelRuizMoreno]

I found the problem.

Because of the nature of the phamacophores is possible to have 2 or also more descriptors with the same x,y and z coordinates. However, because of the algorithm which is implemented in PyPharmer for clique detection and analysis, descriptors with the same coordinates are recognized by Networkx as duplicates.

How can I solve it?

I can include more data to differentiate between descriptors, but.... This strategy will modify the clustering analysis?