graph_from_chembl

[schatzsc]

The graph_from_chembl() routine generates a NetworkX graph by directly querying ChEMBL for a particular ID via a v2000 molfile which is returned from the server.

Requires network connection

So far tested on a couple of hundred ChEMBL entries

Needs more checks for input validity:

• Currently only checks if ID > 0 but not if ID is within upper limit
• Assumes that bonds and atoms read form a valid graph and all required node attributes are included
• Does not assign element_color according to Jmol definitions so far
• Quite a number of invalid entries returned, since ChEMBL ID numbers are also assigned to organisms, protein, and the like which do not have an associated molfile
• Molfile returned does not contain hydrogens by default

[schatzsc]

Here is a short tool which uses graph_from_chembl() to query a couple of hundred ChEMBL entries from the beginning of the database and displays different information, including graphics.

chembl_reader.zip