Index

A

a (molsystem.cell.Cell property) add_properties_from_file() (in module molsystem.properties) align() (molsystem.align.AlignMixin method) AlignMixin (class in molsystem.align)

alpha (molsystem.cell.Cell property) attach() (molsystem.system_db.SystemDB method) attached_as() (molsystem.system_db.SystemDB method) attributes() (molsystem.system_db.SystemDB method)

B

b (molsystem.cell.Cell property)

beta (molsystem.cell.Cell property) bonded_neighbors() (molsystem.topology.TopologyMixin method)

C

c (molsystem.cell.Cell property) canonical_smiles (molsystem.smiles.SMILESMixin property) Cell (class in molsystem.cell) check_openeye_license() (in module molsystem.openeye) (in module molsystem.smiles) CIFMixin (class in molsystem.cif) close() (molsystem.system_db.SystemDB method) CMSSchemaMixin (class in molsystem.cms_schema) configuration_ids (molsystem.system_db.SystemDB property)

configurations (molsystem.system_db.SystemDB property) coordinates_from_OBMol() (molsystem.openbabel.OpenBabelMixin method) coordinates_to_OBMol() (molsystem.openbabel.OpenBabelMixin method) cos() (in module molsystem.cell) create_molecule_subsets() (molsystem.topology.TopologyMixin method) create_molecule_templates() (molsystem.topology.TopologyMixin method) create_system() (molsystem.system_db.SystemDB method) create_table() (molsystem.system_db.SystemDB method) cursor (molsystem.system_db.SystemDB property)

D

db (molsystem.system_db.SystemDB property) db_version (molsystem.system_db.SystemDB property) debug_print() (molsystem.rdkit_.RDKitMixin method)

delete_system() (molsystem.system_db.SystemDB method) detach() (molsystem.system_db.SystemDB method) diff() (molsystem.system_db.SystemDB method) dot() (in module molsystem.cell)

E

equal() (molsystem.cell.Cell method)

F

filename (molsystem.system_db.SystemDB property) find_configurations() (molsystem.system_db.SystemDB method) find_molecules() (molsystem.topology.TopologyMixin method) find_substructures() (molsystem.openbabel.OpenBabelMixin method) from_cif_text() (molsystem.cif.CIFMixin method) from_inchi() (molsystem.inchi.InChIMixin method) from_inchikey() (molsystem.inchi.InChIMixin method) from_mmcif_text() (molsystem.cif.CIFMixin method) from_molfile_text() (molsystem.molfile.MolFileMixin method)

from_OBMol() (molsystem.openbabel.OpenBabelMixin method) from_OEMol() (molsystem.openeye.OpenEyeMixin method) from_pdb_text() (molsystem.pdb.PDBMixin method) from_qcschema_dict() (molsystem.qcschema.QCSchemaMixin method) from_qcschema_json() (molsystem.qcschema.QCSchemaMixin method) from_RDKMol() (molsystem.rdkit_.RDKitMixin method) from_sdf() (molsystem.openbabel.OpenBabelMixin method) from_sdf_text() (molsystem.openbabel.OpenBabelMixin method) from_smiles() (molsystem.smiles.SMILESMixin method) from_vectors() (molsystem.cell.Cell method)

G

gamma (molsystem.cell.Cell property) GenSMARTS (class in molsystem.smiles) get_configuration() (molsystem.system_db.SystemDB method) get_configuration_ids() (molsystem.system_db.SystemDB method) get_configurations() (molsystem.system_db.SystemDB method) get_molecule_smiles() (molsystem.topology.TopologyMixin method)

get_system() (molsystem.system_db.SystemDB method) get_system_ids() (molsystem.system_db.SystemDB method) get_systems() (molsystem.system_db.SystemDB method) grouped() (in module molsystem.atoms) (in module molsystem.bonds) (in module molsystem.subsets) (in module molsystem.table)

I

inchi (molsystem.inchi.InChIMixin property) inchikey (molsystem.inchi.InChIMixin property)

InChIMixin (class in molsystem.inchi) is_attached() (molsystem.system_db.SystemDB method)

L

list() (molsystem.system_db.SystemDB method)

M

masses() (in module molsystem.elements) module molsystem molsystem.align molsystem.atoms molsystem.bonds molsystem.cell molsystem.cif molsystem.cms_schema molsystem.column molsystem.configuration molsystem.configuration_properties molsystem.elements molsystem.frozencolumn molsystem.inchi molsystem.molfile molsystem.openbabel molsystem.openeye molsystem.pdb molsystem.properties molsystem.pubchem molsystem.qcschema molsystem.rdkit_ molsystem.smiles molsystem.subset molsystem.subsets molsystem.symmetry molsystem.system molsystem.system_db molsystem.system_properties molsystem.table molsystem.template molsystem.templates molsystem.topology mol_object (molsystem.smiles.GenSMARTS property) MolFileMixin (class in molsystem.molfile) molsystem module molsystem.align module molsystem.atoms module molsystem.bonds module molsystem.cell module molsystem.cif module molsystem.cms_schema module

molsystem.column module molsystem.configuration module molsystem.configuration_properties module molsystem.elements module molsystem.frozencolumn module molsystem.inchi module molsystem.molfile module molsystem.openbabel module molsystem.openeye module molsystem.pdb module molsystem.properties module molsystem.pubchem module molsystem.qcschema module molsystem.rdkit_ module molsystem.smiles module molsystem.subset module molsystem.subsets module molsystem.symmetry module molsystem.system module molsystem.system_db module molsystem.system_properties module molsystem.table module molsystem.template module molsystem.templates module molsystem.topology module

N

n_configurations (molsystem.system_db.SystemDB property) n_systems (molsystem.system_db.SystemDB property)

n_templates (molsystem.system_db.SystemDB property) names (molsystem.system_db.SystemDB property)

O

openbabel_version() (in module molsystem.openbabel) OpenBabelMixin (class in molsystem.openbabel)

openeye_version() (in module molsystem.openeye) OpenEyeMixin (class in molsystem.openeye)

P

parameters (molsystem.cell.Cell property) parent (molsystem.system_db.SystemDB property) PC_cid (molsystem.pubchem.PubChemMixin property) PC_from_cid() (molsystem.pubchem.PubChemMixin method)

PC_from_identifier() (molsystem.pubchem.PubChemMixin method) PC_iupac_name() (molsystem.pubchem.PubChemMixin method) PDBMixin (class in molsystem.pdb) properties (molsystem.system_db.SystemDB property) PubChemMixin (class in molsystem.pubchem)

Q

QCSchemaMixin (class in molsystem.qcschema)

R

rdkit_version() (in module molsystem.rdkit_) RDKitMixin (class in molsystem.rdkit_) read_cif_file() (molsystem.cif.CIFMixin method) reciprocal_lengths() (molsystem.cell.Cell method)

reciprocal_vectors() (molsystem.cell.Cell method) reimage_bonded_atoms() (molsystem.topology.TopologyMixin method) reimage_molecules() (molsystem.topology.TopologyMixin method) RMSD() (molsystem.align.AlignMixin method)

S

sin() (in module molsystem.cell) smarts (molsystem.smiles.SMILESMixin property) smiles (molsystem.smiles.SMILESMixin property) SMILESMixin (class in molsystem.smiles) strain() (molsystem.cell.Cell method)

system (molsystem.system_db.SystemDB property) system_exists() (molsystem.system_db.SystemDB method) system_ids (molsystem.system_db.SystemDB property) SystemDB (class in molsystem.system_db) systems (molsystem.system_db.SystemDB property)

T

templates (molsystem.system_db.SystemDB property) to_atnos() (in module molsystem.elements) to_cartesians() (molsystem.cell.Cell method) to_cartesians_transform() (molsystem.cell.Cell method) to_cif_text() (molsystem.cif.CIFMixin method) to_cms_schema() (molsystem.cms_schema.CMSSchemaMixin method) to_fractionals() (molsystem.cell.Cell method) to_fractionals_transform() (molsystem.cell.Cell method) to_inchi() (molsystem.inchi.InChIMixin method) to_mmcif_text() (molsystem.cif.CIFMixin method) to_molfile_text() (molsystem.molfile.MolFileMixin method)

to_OBMol() (molsystem.openbabel.OpenBabelMixin method) to_OEGraphMol() (molsystem.openeye.OpenEyeMixin method) to_pdb_text() (molsystem.pdb.PDBMixin method) to_qcschema_dict() (molsystem.qcschema.QCSchemaMixin method) to_qcschema_json() (molsystem.qcschema.QCSchemaMixin method) to_RDKMol() (molsystem.rdkit_.RDKitMixin method) to_sdf() (molsystem.openbabel.OpenBabelMixin method) to_sdf_text() (molsystem.openbabel.OpenBabelMixin method) to_smarts() (molsystem.smiles.SMILESMixin method) to_smiles() (molsystem.smiles.SMILESMixin method) to_symbols() (in module molsystem.elements) TopologyMixin (class in molsystem.topology)

V

vectors() (molsystem.cell.Cell method)

volume (molsystem.cell.Cell property)