Index _ | A | C | D | E | F | G | H | I | M | P | Q | R | S | T | W _ __init__() (yammbs.analysis.DDE method) (yammbs.analysis.DDECollection method) (yammbs.analysis.ICRMSD method) (yammbs.analysis.ICRMSDCollection method) (yammbs.analysis.RMSD method) (yammbs.analysis.RMSDCollection method) (yammbs.analysis.TFD method) (yammbs.analysis.TFDCollection method) (yammbs.checkmol.ChemicalEnvironment method) (yammbs.inputs.QCArchiveDataset method) (yammbs.inputs.QCArchiveMolecule method) (yammbs.inputs.QMDataset method) (yammbs.inputs.QMMolecule method) (yammbs.models.MMConformerRecord method) (yammbs.models.MoleculeRecord method) (yammbs.models.QMConformerRecord method) (yammbs.models.Record method) (yammbs.outputs.Metric method) (yammbs.outputs.MetricCollection method) (yammbs.outputs.MinimizedMolecule method) (yammbs.outputs.MinimizedQCArchiveDataset method) (yammbs.outputs.MinimizedQCArchiveMolecule method) (yammbs.outputs.MinimizedQMDataset method) A add_note() (yammbs.exceptions.DatabaseExistsError method) analyze_functional_groups() (in module yammbs.checkmol) append() (yammbs.analysis.DDECollection method) (yammbs.analysis.ICRMSDCollection method) (yammbs.analysis.RMSDCollection method) (yammbs.analysis.TFDCollection method) C ChemicalEnvironment (class in yammbs.checkmol) clear() (yammbs.analysis.DDECollection method) (yammbs.analysis.ICRMSDCollection method) (yammbs.analysis.RMSDCollection method) (yammbs.analysis.TFDCollection method) copy() (yammbs.analysis.DDE method) (yammbs.analysis.DDECollection method) (yammbs.analysis.ICRMSD method) (yammbs.analysis.ICRMSDCollection method) (yammbs.analysis.RMSD method) (yammbs.analysis.RMSDCollection method) (yammbs.analysis.TFD method) (yammbs.analysis.TFDCollection method) (yammbs.inputs.QCArchiveDataset method) (yammbs.inputs.QCArchiveMolecule method) (yammbs.inputs.QMDataset method) (yammbs.inputs.QMMolecule method) (yammbs.models.MMConformerRecord method) (yammbs.models.MoleculeRecord method) (yammbs.models.QMConformerRecord method) (yammbs.models.Record method) (yammbs.outputs.Metric method) (yammbs.outputs.MetricCollection method) (yammbs.outputs.MinimizedMolecule method) (yammbs.outputs.MinimizedQCArchiveDataset method) (yammbs.outputs.MinimizedQCArchiveMolecule method) (yammbs.outputs.MinimizedQMDataset method) count() (yammbs.analysis.DDECollection method) (yammbs.analysis.ICRMSDCollection method) (yammbs.analysis.RMSDCollection method) (yammbs.analysis.TFDCollection method) D DatabaseExistsError DDE (class in yammbs.analysis) DDECollection (class in yammbs.analysis) dump_hashable() (yammbs.analysis.DDE method) (yammbs.analysis.ICRMSD method) (yammbs.analysis.RMSD method) (yammbs.analysis.TFD method) (yammbs.inputs.QCArchiveDataset method) (yammbs.inputs.QCArchiveMolecule method) (yammbs.inputs.QMDataset method) (yammbs.inputs.QMMolecule method) (yammbs.models.MMConformerRecord method) (yammbs.models.MoleculeRecord method) (yammbs.models.QMConformerRecord method) (yammbs.models.Record method) (yammbs.outputs.Metric method) (yammbs.outputs.MetricCollection method) (yammbs.outputs.MinimizedMolecule method) (yammbs.outputs.MinimizedQCArchiveDataset method) (yammbs.outputs.MinimizedQCArchiveMolecule method) (yammbs.outputs.MinimizedQMDataset method) E extend() (yammbs.analysis.DDECollection method) (yammbs.analysis.ICRMSDCollection method) (yammbs.analysis.RMSDCollection method) (yammbs.analysis.TFDCollection method) F from_molecule() (yammbs.models.MoleculeRecord class method) from_qcarchive_record() (yammbs.models.QMConformerRecord class method) from_qcsubmit_collection() (yammbs.inputs.QCArchiveDataset class method) G get_hash() (yammbs.analysis.DDE method) (yammbs.analysis.ICRMSD method) (yammbs.analysis.RMSD method) (yammbs.analysis.TFD method) (yammbs.inputs.QCArchiveDataset method) (yammbs.inputs.QCArchiveMolecule method) (yammbs.inputs.QMDataset method) (yammbs.inputs.QMMolecule method) (yammbs.models.MMConformerRecord method) (yammbs.models.MoleculeRecord method) (yammbs.models.QMConformerRecord method) (yammbs.models.Record method) (yammbs.outputs.Metric method) (yammbs.outputs.MetricCollection method) (yammbs.outputs.MinimizedMolecule method) (yammbs.outputs.MinimizedQCArchiveDataset method) (yammbs.outputs.MinimizedQCArchiveMolecule method) (yammbs.outputs.MinimizedQMDataset method) get_internal_coordinate_differences() (in module yammbs.analysis) get_internal_coordinate_rmsds() (in module yammbs.analysis) get_internal_coordinates() (in module yammbs.analysis) get_rmsd() (in module yammbs.analysis) get_tfd() (in module yammbs.analysis) H hash_dict() (yammbs.analysis.DDE method) (yammbs.analysis.ICRMSD method) (yammbs.analysis.RMSD method) (yammbs.analysis.TFD method) (yammbs.inputs.QCArchiveDataset method) (yammbs.inputs.QCArchiveMolecule method) (yammbs.inputs.QMDataset method) (yammbs.inputs.QMMolecule method) (yammbs.models.MMConformerRecord method) (yammbs.models.MoleculeRecord method) (yammbs.models.QMConformerRecord method) (yammbs.models.Record method) (yammbs.outputs.Metric method) (yammbs.outputs.MetricCollection method) (yammbs.outputs.MinimizedMolecule method) (yammbs.outputs.MinimizedQCArchiveDataset method) (yammbs.outputs.MinimizedQCArchiveMolecule method) (yammbs.outputs.MinimizedQMDataset method) I ICRMSD (class in yammbs.analysis) ICRMSDCollection (class in yammbs.analysis) index() (yammbs.analysis.DDECollection method) (yammbs.analysis.ICRMSDCollection method) (yammbs.analysis.RMSDCollection method) (yammbs.analysis.TFDCollection method) insert() (yammbs.analysis.DDECollection method) (yammbs.analysis.ICRMSDCollection method) (yammbs.analysis.RMSDCollection method) (yammbs.analysis.TFDCollection method) M Metric (class in yammbs.outputs) MetricCollection (class in yammbs.outputs) MinimizedMolecule (class in yammbs.outputs) MinimizedQCArchiveDataset (class in yammbs.outputs) MinimizedQCArchiveMolecule (class in yammbs.outputs) MinimizedQMDataset (class in yammbs.outputs) MMConformerRecord (class in yammbs.models) model_config (yammbs.analysis.DDE attribute) (yammbs.analysis.ICRMSD attribute) (yammbs.analysis.RMSD attribute) (yammbs.analysis.TFD attribute) (yammbs.inputs.QCArchiveDataset attribute) (yammbs.inputs.QCArchiveMolecule attribute) (yammbs.inputs.QMDataset attribute) (yammbs.inputs.QMMolecule attribute) (yammbs.models.MMConformerRecord attribute) (yammbs.models.MoleculeRecord attribute) (yammbs.models.QMConformerRecord attribute) (yammbs.models.Record attribute) (yammbs.outputs.Metric attribute) (yammbs.outputs.MetricCollection attribute) (yammbs.outputs.MinimizedMolecule attribute) (yammbs.outputs.MinimizedQCArchiveDataset attribute) (yammbs.outputs.MinimizedQCArchiveMolecule attribute) (yammbs.outputs.MinimizedQMDataset attribute) model_construct() (yammbs.analysis.DDE class method) (yammbs.analysis.ICRMSD class method) (yammbs.analysis.RMSD class method) (yammbs.analysis.TFD class method) (yammbs.inputs.QCArchiveDataset class method) (yammbs.inputs.QCArchiveMolecule class method) (yammbs.inputs.QMDataset class method) (yammbs.inputs.QMMolecule class method) (yammbs.models.MMConformerRecord class method) (yammbs.models.MoleculeRecord class method) (yammbs.models.QMConformerRecord class method) (yammbs.models.Record class method) (yammbs.outputs.Metric class method) (yammbs.outputs.MetricCollection class method) (yammbs.outputs.MinimizedMolecule class method) (yammbs.outputs.MinimizedQCArchiveDataset class method) (yammbs.outputs.MinimizedQCArchiveMolecule class method) (yammbs.outputs.MinimizedQMDataset class method) model_copy() (yammbs.analysis.DDE method) (yammbs.analysis.ICRMSD method) (yammbs.analysis.RMSD method) (yammbs.analysis.TFD method) (yammbs.inputs.QCArchiveDataset method) (yammbs.inputs.QCArchiveMolecule method) (yammbs.inputs.QMDataset method) (yammbs.inputs.QMMolecule method) (yammbs.models.MMConformerRecord method) (yammbs.models.MoleculeRecord method) (yammbs.models.QMConformerRecord method) (yammbs.models.Record method) (yammbs.outputs.Metric method) (yammbs.outputs.MetricCollection method) (yammbs.outputs.MinimizedMolecule method) (yammbs.outputs.MinimizedQCArchiveDataset method) (yammbs.outputs.MinimizedQCArchiveMolecule method) (yammbs.outputs.MinimizedQMDataset method) model_dump() (yammbs.analysis.DDE method) (yammbs.analysis.ICRMSD method) (yammbs.analysis.RMSD method) (yammbs.analysis.TFD method) (yammbs.inputs.QCArchiveDataset method) (yammbs.inputs.QCArchiveMolecule method) (yammbs.inputs.QMDataset method) (yammbs.inputs.QMMolecule method) (yammbs.models.MMConformerRecord method) (yammbs.models.MoleculeRecord method) (yammbs.models.QMConformerRecord method) (yammbs.models.Record method) (yammbs.outputs.Metric method) (yammbs.outputs.MetricCollection method) (yammbs.outputs.MinimizedMolecule method) (yammbs.outputs.MinimizedQCArchiveDataset method) (yammbs.outputs.MinimizedQCArchiveMolecule method) (yammbs.outputs.MinimizedQMDataset method) model_dump_json() (yammbs.analysis.DDE method) (yammbs.analysis.ICRMSD method) (yammbs.analysis.RMSD method) (yammbs.analysis.TFD method) (yammbs.inputs.QCArchiveDataset method) (yammbs.inputs.QCArchiveMolecule method) (yammbs.inputs.QMDataset method) (yammbs.inputs.QMMolecule method) (yammbs.models.MMConformerRecord method) (yammbs.models.MoleculeRecord method) (yammbs.models.QMConformerRecord method) (yammbs.models.Record method) (yammbs.outputs.Metric method) (yammbs.outputs.MetricCollection method) (yammbs.outputs.MinimizedMolecule method) (yammbs.outputs.MinimizedQCArchiveDataset method) (yammbs.outputs.MinimizedQCArchiveMolecule method) (yammbs.outputs.MinimizedQMDataset method) model_extra (yammbs.analysis.DDE property) (yammbs.analysis.ICRMSD property) (yammbs.analysis.RMSD property) (yammbs.analysis.TFD property) (yammbs.inputs.QCArchiveDataset property) (yammbs.inputs.QCArchiveMolecule property) (yammbs.inputs.QMDataset property) (yammbs.inputs.QMMolecule property) (yammbs.models.MMConformerRecord property) (yammbs.models.MoleculeRecord property) (yammbs.models.QMConformerRecord property) (yammbs.models.Record property) (yammbs.outputs.Metric property) (yammbs.outputs.MetricCollection property) (yammbs.outputs.MinimizedMolecule property) (yammbs.outputs.MinimizedQCArchiveDataset property) (yammbs.outputs.MinimizedQCArchiveMolecule property) (yammbs.outputs.MinimizedQMDataset property) model_fields_set (yammbs.analysis.DDE property) (yammbs.analysis.ICRMSD property) (yammbs.analysis.RMSD property) (yammbs.analysis.TFD property) (yammbs.inputs.QCArchiveDataset property) (yammbs.inputs.QCArchiveMolecule property) (yammbs.inputs.QMDataset property) (yammbs.inputs.QMMolecule property) (yammbs.models.MMConformerRecord property) (yammbs.models.MoleculeRecord property) (yammbs.models.QMConformerRecord property) (yammbs.models.Record property) (yammbs.outputs.Metric property) (yammbs.outputs.MetricCollection property) (yammbs.outputs.MinimizedMolecule property) (yammbs.outputs.MinimizedQCArchiveDataset property) (yammbs.outputs.MinimizedQCArchiveMolecule property) (yammbs.outputs.MinimizedQMDataset property) model_json_schema() (yammbs.analysis.DDE class method) (yammbs.analysis.ICRMSD class method) (yammbs.analysis.RMSD class method) (yammbs.analysis.TFD class method) (yammbs.inputs.QCArchiveDataset class method) (yammbs.inputs.QCArchiveMolecule class method) (yammbs.inputs.QMDataset class method) (yammbs.inputs.QMMolecule class method) (yammbs.models.MMConformerRecord class method) (yammbs.models.MoleculeRecord class method) (yammbs.models.QMConformerRecord class method) (yammbs.models.Record class method) (yammbs.outputs.Metric class method) (yammbs.outputs.MetricCollection class method) (yammbs.outputs.MinimizedMolecule class method) (yammbs.outputs.MinimizedQCArchiveDataset class method) (yammbs.outputs.MinimizedQCArchiveMolecule class method) (yammbs.outputs.MinimizedQMDataset class method) model_parametrized_name() (yammbs.analysis.DDE class method) (yammbs.analysis.ICRMSD class method) (yammbs.analysis.RMSD class method) (yammbs.analysis.TFD class method) (yammbs.inputs.QCArchiveDataset class method) (yammbs.inputs.QCArchiveMolecule class method) (yammbs.inputs.QMDataset class method) (yammbs.inputs.QMMolecule class method) (yammbs.models.MMConformerRecord class method) (yammbs.models.MoleculeRecord class method) (yammbs.models.QMConformerRecord class method) (yammbs.models.Record class method) (yammbs.outputs.Metric class method) (yammbs.outputs.MetricCollection class method) (yammbs.outputs.MinimizedMolecule class method) (yammbs.outputs.MinimizedQCArchiveDataset class method) (yammbs.outputs.MinimizedQCArchiveMolecule class method) (yammbs.outputs.MinimizedQMDataset class method) model_post_init() (yammbs.analysis.DDE method) (yammbs.analysis.ICRMSD method) (yammbs.analysis.RMSD method) (yammbs.analysis.TFD method) (yammbs.inputs.QCArchiveDataset method) (yammbs.inputs.QCArchiveMolecule method) (yammbs.inputs.QMDataset method) (yammbs.inputs.QMMolecule method) (yammbs.models.MMConformerRecord method) (yammbs.models.MoleculeRecord method) (yammbs.models.QMConformerRecord method) (yammbs.models.Record method) (yammbs.outputs.Metric method) (yammbs.outputs.MetricCollection method) (yammbs.outputs.MinimizedMolecule method) (yammbs.outputs.MinimizedQCArchiveDataset method) (yammbs.outputs.MinimizedQCArchiveMolecule method) (yammbs.outputs.MinimizedQMDataset method) model_rebuild() (yammbs.analysis.DDE class method) (yammbs.analysis.ICRMSD class method) (yammbs.analysis.RMSD class method) (yammbs.analysis.TFD class method) (yammbs.inputs.QCArchiveDataset class method) (yammbs.inputs.QCArchiveMolecule class method) (yammbs.inputs.QMDataset class method) (yammbs.inputs.QMMolecule class method) (yammbs.models.MMConformerRecord class method) (yammbs.models.MoleculeRecord class method) (yammbs.models.QMConformerRecord class method) (yammbs.models.Record class method) (yammbs.outputs.Metric class method) (yammbs.outputs.MetricCollection class method) (yammbs.outputs.MinimizedMolecule class method) (yammbs.outputs.MinimizedQCArchiveDataset class method) (yammbs.outputs.MinimizedQCArchiveMolecule class method) (yammbs.outputs.MinimizedQMDataset class method) model_validate() (yammbs.analysis.DDE class method) (yammbs.analysis.ICRMSD class method) (yammbs.analysis.RMSD class method) (yammbs.analysis.TFD class method) (yammbs.inputs.QCArchiveDataset class method) (yammbs.inputs.QCArchiveMolecule class method) (yammbs.inputs.QMDataset class method) (yammbs.inputs.QMMolecule class method) (yammbs.models.MMConformerRecord class method) (yammbs.models.MoleculeRecord class method) (yammbs.models.QMConformerRecord class method) (yammbs.models.Record class method) (yammbs.outputs.Metric class method) (yammbs.outputs.MetricCollection class method) (yammbs.outputs.MinimizedMolecule class method) (yammbs.outputs.MinimizedQCArchiveDataset class method) (yammbs.outputs.MinimizedQCArchiveMolecule class method) (yammbs.outputs.MinimizedQMDataset class method) model_validate_json() (yammbs.analysis.DDE class method) (yammbs.analysis.ICRMSD class method) (yammbs.analysis.RMSD class method) (yammbs.analysis.TFD class method) (yammbs.inputs.QCArchiveDataset class method) (yammbs.inputs.QCArchiveMolecule class method) (yammbs.inputs.QMDataset class method) (yammbs.inputs.QMMolecule class method) (yammbs.models.MMConformerRecord class method) (yammbs.models.MoleculeRecord class method) (yammbs.models.QMConformerRecord class method) (yammbs.models.Record class method) (yammbs.outputs.Metric class method) (yammbs.outputs.MetricCollection class method) (yammbs.outputs.MinimizedMolecule class method) (yammbs.outputs.MinimizedQCArchiveDataset class method) (yammbs.outputs.MinimizedQCArchiveMolecule class method) (yammbs.outputs.MinimizedQMDataset class method) model_validate_strings() (yammbs.analysis.DDE class method) (yammbs.analysis.ICRMSD class method) (yammbs.analysis.RMSD class method) (yammbs.analysis.TFD class method) (yammbs.inputs.QCArchiveDataset class method) (yammbs.inputs.QCArchiveMolecule class method) (yammbs.inputs.QMDataset class method) (yammbs.inputs.QMMolecule class method) (yammbs.models.MMConformerRecord class method) (yammbs.models.MoleculeRecord class method) (yammbs.models.QMConformerRecord class method) (yammbs.models.Record class method) (yammbs.outputs.Metric class method) (yammbs.outputs.MetricCollection class method) (yammbs.outputs.MinimizedMolecule class method) (yammbs.outputs.MinimizedQCArchiveDataset class method) (yammbs.outputs.MinimizedQCArchiveMolecule class method) (yammbs.outputs.MinimizedQMDataset class method) MoleculeRecord (class in yammbs.models) P pop() (yammbs.analysis.DDECollection method) (yammbs.analysis.ICRMSDCollection method) (yammbs.analysis.RMSDCollection method) (yammbs.analysis.TFDCollection method) Q QCArchiveDataset (class in yammbs.inputs) QCArchiveMolecule (class in yammbs.inputs) QMConformerRecord (class in yammbs.models) QMDataset (class in yammbs.inputs) QMMolecule (class in yammbs.inputs) R Record (class in yammbs.models) remove() (yammbs.analysis.DDECollection method) (yammbs.analysis.ICRMSDCollection method) (yammbs.analysis.RMSDCollection method) (yammbs.analysis.TFDCollection method) reverse() (yammbs.analysis.DDECollection method) (yammbs.analysis.ICRMSDCollection method) (yammbs.analysis.RMSDCollection method) (yammbs.analysis.TFDCollection method) RMSD (class in yammbs.analysis) RMSDCollection (class in yammbs.analysis) S smiles (yammbs.models.MoleculeRecord property) sort() (yammbs.analysis.DDECollection method) (yammbs.analysis.ICRMSDCollection method) (yammbs.analysis.RMSDCollection method) (yammbs.analysis.TFDCollection method) T TFD (class in yammbs.analysis) TFDCollection (class in yammbs.analysis) to_csv() (yammbs.analysis.DDECollection method) (yammbs.analysis.ICRMSDCollection method) (yammbs.analysis.RMSDCollection method) (yammbs.analysis.TFDCollection method) to_dataframe() (yammbs.analysis.DDECollection method) (yammbs.analysis.ICRMSDCollection method) (yammbs.analysis.RMSDCollection method) (yammbs.analysis.TFDCollection method) W with_traceback() (yammbs.exceptions.DatabaseExistsError method)