uibcdf / pypharmer

Python API for Pharmer

PyPharmer (in construction)

Python API for Pharmer

Conda environment

Those packages needed to run the library are reported in environment.yml. The conda environment can be created with the followind command:

conda env create -f environment.yml

If a new package is required and installed in a development environment, the next command updates 'environment.yml'.

conda env export > environment.yml

pypharmer's Issues

Networkx not add all the descriptors as cliques

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?

Is NGLview including transparency in shapes?

We should check how to play with transparent spheres and arrows when nglview.shapes is used.

running results are different from those in the benchmark

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

JSON files from servers

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

What are the pharmacophores attributes needed to make the class really universal?

'Set02/ZINCpharmer.json' has a couple of attributes of points not imported by the pharmer pymol script. Are they really necessary?

They are:

• 'maxsize': '',
• 'minsize': '',
• 'requirement': 'required',
• 'size': 1,
• 'vector_on': 1,

Arrows with the origin at the center of the sphere or at the surface?

In the pymol script from pharmer arrows begins at the surface. Should we do the same? I think so...