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 write_scaffold(self, scaffold):
subscaffolds = ', '.join([str(s.id) for s in scaffold.subscaffolds])
if self.args.sdf:
molecule = MolFromSmiles(scaffold.smiles)
if molecule is not None:
molecule.SetProp('_Name', str(scaffold.id))
molecule.SetIntProp('HIERARCHY', scaffold.hierarchy)
molecule.SetProp('SMILES', scaffold.smiles)
molecule.SetProp('SUBSCAFFOLDS', subscaffolds)
self.output.write(molecule)
else:
logger.warning(f'Failed to parse scaffold: {scaffold.smiles}')
else:
self.output.write('{0}\t{1}\t{2}\t{3}\n'.format(
scaffold.id, scaffold.hierarchy, scaffold.smiles,
subscaffolds))
def write_sdf_file(scaffold_graph, output_file):
"""Write an SDF file from a ScaffoldGraph.
All scaffolds in the scaffoldgraph are written to the
SDF, while molecules are ignored. Scaffolds are sorted
in ascending order according to their hierarchy level.
The output follows the standard SDF specification with
the added property fields:
TITLE field: scaffold ID
SUBSCAFFOLDS field: list of sub-scaffold IDs
HIERARCHY field: hierarchy level of scaffold
SMILES field: scaffold canonical SMILES
Parameters
----------
scaffold_graph : scaffoldgraph.core.ScaffoldGraph
ScaffoldGraph to be written to an SDF.
output_file : str
Filepath to an 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()
