graph_from_chembl

tucan/io/graph_from_chembl.py

@@ -0,0 +1,78 @@
+
+import networkx as nx
+
+from chembl_webresource_client.new_client import new_client
+
+from tucan.element_properties import ELEMENT_PROPS
+
+def graph_from_chembl(id: int) -> nx.Graph:
+    """Instantiate a NetworkX graph from a ChEMBL entry.
+    Parameters
+    ----------
+    id: int
+        Non-zero integer number pointing to a ChEMBL entry [1].
+    Returns
+    -------
+    NetworkX Graph, error (is either True if correctly processed or False if problem was encountered)
+    References
+    ----------
+    [1] https://github.com/chembl/chembl_webresource_client
+    """
+
+    if(id < 1):
+        raise ChemblParserException(
+            f'Invalid Compound ID (ID) "{cid}"'
+        )
+
+    molecule = new_client.molecule
+
+    chembl_id = 'CHEMBL'+str(id)
+
+    error = False
+    try:
+        structure = molecule.filter(chembl_id = chembl_id).only(['molecule_structures'])[0]['molecule_structures']
+    except:
+        error = True
+        m = []
+
+    if(error == False):
+
+        try:
+            molfile2000 = structure['molfile']
+        except:
+            error = True
+            m = []
+
+        if(error == False):
+            lines = molfile2000.splitlines()
+
+            atoms = int(lines[3][0:3])
+            bonds = int(lines[3][4:6])
+
+            m = nx.Graph()
+
+            for a in range(0, atoms):
+                line = lines[4+a]
+                element = line[31:34]
+                element = element.replace(" ", "")
+                if(element == "D"):
+                    element = "H"
+                if(element == "T"):
+                    element = "H"
+                m.add_node(a+1)
+                atom_props = { a+1: {
+                                        "element_symbol": element,
+                                        "atomic_number": ELEMENT_PROPS[element]["atomic_number"]
+                                    }
+                             }
+                nx.set_node_attributes(m, atom_props)
+            for b in range(0, bonds):
+                line = lines[4+a+1+b]
+                atom1 = int(line[0:3])
+                atom2 = int(line[4:6])
+                m.add_edge(atom1, atom2)
+
+    return m, error
+
+class ChemblParserException(Exception):
+    pass