"""
scaffoldgraph.io.sdf
"""
from rdkit.Chem import ForwardSDMolSupplier, SDWriter, MolFromSmiles
from .supplier import MolSupplier, EnumeratedMolSupplier
def read_sdf(sdf_file, requires_length=False):
"""Read an sdf file.
Parameters
----------
sdf_file: A file-like object
requires_length: If True returns an enumerated Mol
supplier, i.e. when monitoring progress
Returns
-------
either a MolSupplier or an EnumeratedSupplier
depending on whether a length is required
"""
supplier = ForwardSDMolSupplier(sdf_file)
if not requires_length:
return MolSupplier(supplier)
count = sdf_count(sdf_file)
sdf_file.seek(0)
return EnumeratedMolSupplier(supplier, count)
def write_sdf_file(scaffold_graph, output_file):
"""Write an SDF file from a scaffoldgraph
Parameters
----------
scaffold_graph (sg.ScaffoldGraph): graph to be converted
output_file (str): path to output file
"""
N = scaffold_graph.num_scaffold_nodes
sorted_scaffolds = sorted(scaffold_graph.get_scaffold_nodes(data=True), key=lambda x: x[1]['hierarchy'])
mapping = dict(zip([s[0] for s in sorted_scaffolds], range(0, N)))
writer = SDWriter(output_file)
for scaffold, data in sorted_scaffolds:
molecule = MolFromSmiles(scaffold)
if molecule is not None:
subscaffolds = list(scaffold_graph.predecessors(scaffold))
molecule.SetProp('_Name', mapping[scaffold])
molecule.SetIntProp('HIERARCHY', scaffold_graph.nodes[scaffold]['HIERARCHY'])
molecule.SetProp('SMILES', scaffold)
molecule.SetProp('SUBSCAFFOLDS', ', '.join([str(mapping[s]) for s in subscaffolds]))
writer.write(molecule)
writer.close()
def sdf_count(file_obj):
"""Count the number of molecules in an SDF file.
Counts the number of times '$$$$' occurs at the start of lines
in the file.
Parameters
----------
file_obj: A file-like object
Returns
-------
count: The number of molecules in the file (int)
"""
return sum(1 for line in file_obj if line[:4] == b'$$$$')
