masskit.apps.process.mols package

Subpackages

• masskit.apps.process.mols.conf package
  • Subpackages
    • masskit.apps.process.mols.conf.hydra package
      • Subpackages
      • Module contents
  • Module contents

Submodules

masskit.apps.process.mols.reactor module

masskit.apps.process.mols.reactor.reactor_app(config: omegaconf.DictConfig) → None

masskit.apps.process.mols.shortest_path module

class masskit.apps.process.mols.shortest_path.BatchWriter(output_file)

Bases: object

Doesn’t admit well to being a context manager as the file can’t be opened until write_table() is called as the file open functions require a table schema

close()

write_table(table)

masskit.apps.process.mols.shortest_path.batch_reader(input_file, row_batch_size=5000)

masskit.apps.process.mols.shortest_path.get_ring_paths(rd_mol)

masskit.apps.process.mols.shortest_path.get_shortest_paths(rd_mol, max_path_length=5)

Returns the shortest paths for the given rd_mol.

For every pair of atoms, if they are connected by a path <= max_path_length

the atoms on that path are enumerated. Otherwise, if there is a path, then the truncated path is given.

The returned object is a tuple of dictionaries. The first dictionary

contains the shortest paths for those with <= max_path_length. The second contains a pointer to the truncated path. The third contains the ring information for atoms inside rings.

masskit.apps.process.mols.shortest_path.mol2path(mol, max_path_length=5)

masskit.apps.process.mols.shortest_path.ordered_pair(a1, a2)

masskit.apps.process.mols.shortest_path.path_generator_app(config: omegaconf.DictConfig) → None

Module contents