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Python API for Pharmer
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?
In the pymol script from pharmer arrows begins at the surface. Should we do the same? I think so...
We should check how to play with transparent spheres and arrows when nglview.shapes is used.
I was working in the pharmacophore and viewer files to include receptor, ligand, and pharmacophore visualization. But there are some issues.
Json files from pharmer can be readed by using our libraries as:
import PyPharmer as phr
query=phr.Query ('foo.json')
view=query.get_nglview
But, files from servers (pharmit and ZINC pharmed) cannot be readed by our libraries.
'load_query' script is able to show data from json files from pharmer and servers (in PyMol). I will continue working on this issue
i use Pharmacophore_modeling.ipynb
protein is 1fpu_A.pdb
ligand is PRC_1fpu_A
but result json is different from that in the benchmark
and it has Nan in result
'Set02/ZINCpharmer.json' has a couple of attributes of points not imported by the pharmer pymol script. Are they really necessary?
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