API Reference

Below is the API reference for yammbs. See the examples for details on how to use these objects.

Analysis

Tools for analyzing molecular mechanics results and comparing with QM data.

`DDE`	A model containing relative energy differences (DDEs) of a molecule.
`DDECollection`	A model containing DDEs of a dataset of molecules.
`ICRMSD`	A model containing the internal coordinate RMSDs of a molecule.
`ICRMSDCollection`	A model containing internal coordinate RMSDs of a dataset of molecules.
`RMSD`	A model containing the root-mean-square deviations of conformers a molecule.
`RMSDCollection`	A model containing RMSDs of a dataset of molecules.
`TFD`	A model containing the TFD of a molecule.
`TFDCollection`	A model containing TFDs of a collection of molecules.
`get_internal_coordinate_differences`	Get internal coordinate differences between two conformers of one molecule.
`get_internal_coordinate_rmsds`	Get internal coordinate RMSDs between two conformers of one molecule.
`get_internal_coordinates`	Get internal coordinates of two conformers of the same molecule using MDAnalysis.
`get_rmsd`	Compute the RMSD between two sets of coordinates.
`get_tfd`	Get the torsion fingerprint deviation between two conformers of one molecule.

Molecular structure analysis using the checkmol utility.

`analyze_functional_groups`	Employs checkmol to determine which chemical moieties are encoded by a given smiles pattern.
`ChemicalEnvironment`	Enum representing some chemical environments.

Custom exceptions for YAMMBS.

A database with this (file) name already exists.

Input data models for reading QCArchive and QM datasets.

`QCArchiveDataset`	A dataset of QCArchive molecules.
`QCArchiveMolecule`	A model for a QM molecule from QCArchive.
`QMDataset`	Base model for a dataset of QM molecules.
`QMMolecule`	A base model for a QM molecule.

Core data models for molecular mechanics calculations.

`MoleculeRecord`	A record which contains information for a labelled molecule.
`QMConformerRecord`	A record for storing coordinates computed from QC.
`MMConformerRecord`	A record for storing conformers originally from QM but optimized with MM.
`Record`	Base model class for a generic record.

Output data models for storing and analyzing results.

`Metric`	A model for small molecule metrics.
`MetricCollection`	A collection of metric models.
`MinimizedMolecule`	Base model for information about a minimized molecule.
`MinimizedQCArchiveDataset`	A model for a dataset of minimized molecules from QCArchive.
`MinimizedQCArchiveMolecule`	A model for a QCArchive molecule which was minimized.
`MinimizedQMDataset`	Base model for a dataset of minimized molecules.