molsystem

• molsystem package
  • Submodules
  • molsystem.align module
    • AlignMixin
      • AlignMixin.RMSD()
    • OB_RMSD()
    • RDK_RMSD()
    • RMSD()
  • molsystem.atoms module
    • grouped()
  • molsystem.bonds module
    • grouped()
  • molsystem.cell module
    • Cell
      • Cell.a
      • Cell.alpha
      • Cell.b
      • Cell.beta
      • Cell.c
      • Cell.equal()
      • Cell.from_vectors()
      • Cell.gamma
      • Cell.parameters
      • Cell.reciprocal_lengths()
      • Cell.reciprocal_vectors()
      • Cell.strain()
      • Cell.to_cartesians()
      • Cell.to_cartesians_transform()
      • Cell.to_fractionals()
      • Cell.to_fractionals_transform()
      • Cell.vectors()
      • Cell.volume
    • cos()
    • dot()
    • sin()
  • molsystem.cif module
    • Bond Orders
    • CIFMixin
      • CIFMixin.from_cif_text()
      • CIFMixin.from_mmcif_text()
      • CIFMixin.read_cif_file()
      • CIFMixin.to_cif_text()
      • CIFMixin.to_mmcif_text()
  • molsystem.cms_schema module
    • CMSSchemaMixin
      • CMSSchemaMixin.to_cms_schema()
  • molsystem.column module
  • molsystem.configuration module
  • molsystem.configuration_properties module
  • molsystem.elements module
    • masses()
    • to_atnos()
    • to_symbols()
  • molsystem.frozencolumn module
  • molsystem.inchi module
    • InChIMixin
      • InChIMixin.from_inchi()
      • InChIMixin.from_inchikey()
      • InChIMixin.inchi
      • InChIMixin.inchikey
      • InChIMixin.to_inchi()
  • molsystem.molfile module
    • MolFileMixin
      • MolFileMixin.from_molfile_text()
      • MolFileMixin.to_molfile_text()
  • molsystem.openbabel module
    • OpenBabelMixin
      • OpenBabelMixin.coordinates_from_OBMol()
      • OpenBabelMixin.coordinates_to_OBMol()
      • OpenBabelMixin.find_substructures()
      • OpenBabelMixin.from_OBMol()
      • OpenBabelMixin.from_sdf()
      • OpenBabelMixin.from_sdf_text()
      • OpenBabelMixin.to_OBMol()
      • OpenBabelMixin.to_sdf()
      • OpenBabelMixin.to_sdf_text()
    • openbabel_citations()
    • openbabel_version()
  • molsystem.openeye module
    • OpenEyeMixin
      • OpenEyeMixin.from_OEMol()
      • OpenEyeMixin.to_OEGraphMol()
    • check_openeye_license()
    • openeye_version()
  • molsystem.pdb module
    • To Do
    • File Format
    • PDBMixin
      • PDBMixin.from_pdb_text()
      • PDBMixin.to_pdb_text()
  • molsystem.properties module
    • add_properties_from_file()
  • molsystem.pubchem module
    • PC_standardize()
    • PubChemMixin
      • PubChemMixin.PC_cid
      • PubChemMixin.PC_from_cid()
      • PubChemMixin.PC_from_identifier()
      • PubChemMixin.PC_iupac_name()
  • molsystem.qcschema module
    • QCSchemaMixin
      • QCSchemaMixin.from_qcschema_dict()
      • QCSchemaMixin.from_qcschema_json()
      • QCSchemaMixin.to_qcschema_dict()
      • QCSchemaMixin.to_qcschema_json()
  • molsystem.rdkit_ module
    • RDKitMixin
      • RDKitMixin.coordinates_from_RDKMol()
      • RDKitMixin.coordinates_to_RDKMol()
      • RDKitMixin.from_RDKMol()
      • RDKitMixin.get_SSSR()
      • RDKitMixin.to_RDKMol()
    • rdkit_citations()
    • rdkit_version()
  • molsystem.smiles module
    • GenSMARTS
      • GenSMARTS.mol_object
    • SMILESMixin
      • SMILESMixin.canonical_smiles
      • SMILESMixin.from_smiles()
      • SMILESMixin.isomeric_smiles
      • SMILESMixin.smarts
      • SMILESMixin.smiles
      • SMILESMixin.to_smarts()
      • SMILESMixin.to_smiles()
    • check_openeye_license()
  • molsystem.subset module
  • molsystem.subsets module
    • grouped()
  • molsystem.symmetry module
  • molsystem.system module
  • molsystem.system_db module
    • SystemDB
      • SystemDB.attach()
      • SystemDB.attached_as()
      • SystemDB.attributes()
      • SystemDB.close()
      • SystemDB.configuration_ids
      • SystemDB.configurations
      • SystemDB.create_system()
      • SystemDB.create_table()
      • SystemDB.cursor
      • SystemDB.db
      • SystemDB.db_version
      • SystemDB.delete_system()
      • SystemDB.detach()
      • SystemDB.diff()
      • SystemDB.filename
      • SystemDB.find_configurations()
      • SystemDB.get_configuration()
      • SystemDB.get_configuration_ids()
      • SystemDB.get_configurations()
      • SystemDB.get_system()
      • SystemDB.get_system_ids()
      • SystemDB.get_systems()
      • SystemDB.is_attached()
      • SystemDB.list()
      • SystemDB.n_configurations
      • SystemDB.n_systems
      • SystemDB.n_templates
      • SystemDB.names
      • SystemDB.parent
      • SystemDB.properties
      • SystemDB.system
      • SystemDB.system_exists()
      • SystemDB.system_ids
      • SystemDB.systems
      • SystemDB.templates
  • molsystem.system_properties module
  • molsystem.table module
    • grouped()
  • molsystem.template module
  • molsystem.templates module
  • molsystem.topology module
    • TopologyMixin
      • TopologyMixin.bonded_neighbors()
      • TopologyMixin.create_molecule_subsets()
      • TopologyMixin.create_molecule_templates()
      • TopologyMixin.find_molecules()
      • TopologyMixin.get_molecule_smiles()
      • TopologyMixin.reimage_bonded_atoms()
      • TopologyMixin.reimage_molecules()
  • Module contents