The ihm.dataset Python module

Classes for handling experimental datasets used by mmCIF models.

class ihm.dataset.Dataset(location, details=None)

A set of input data, for example, a crystal structure or EM map.

Parameters:

• location (ihm.location.Location) – a pointer to where the dataset is stored. This is usually a subclass of DatabaseLocation if the dataset is deposited in a database such as PDB or EMDB, or InputFileLocation if the dataset is stored in an external file.
• details (str) – Text giving more information about the dataset.

add_primary(dataset)

Add another Dataset from which this one was ultimately derived, i.e. it is added as a parent, unless a parent already exists, in which case it is added as a grandparent, and so on.

parents = None

A list of Dataset and/or TransformedDataset objects from which this one was derived. For example, a 3D EM map may be derived from a set of 2D images.

class ihm.dataset.TransformedDataset(dataset, transform)

A Dataset that should be rotated or translated before using. This is typically used for derived datasets (see Dataset.parents) where the derived dataset lies in a different dataset from the parent (for example, it was moved to better align with the model’s reference frame or other experimental data). The transformation that places the derived dataset on the parent is recorded here.

Parameters:

• dataset (Dataset) – The (parent) dataset.
• transform (ihm.geometry.Transformation) – The rotation and translation that places a derived dataset on this dataset.

class ihm.dataset.DatasetGroup(elements=(), name=None, application=None, details=None)

A set of Dataset objects that are handled together. This is implemented as a simple list.

Parameters:

• elements (sequence) – Initial set of datasets.
• name (str) – Short text name of this group.
• application (str) – Text that shows how this group is used.
• details (str) – Longer text that describes this group.

Normally a group is passed to one or more Protocol or Analysis objects, although unused groups can still be included in the file if desired by adding them to ihm.System.orphan_dataset_groups.

class ihm.dataset.CXMSDataset(location, details=None)

Processed cross-links from a CX-MS experiment

class ihm.dataset.MassSpecDataset(location, details=None)

Raw mass spectrometry files such as peaklists

class ihm.dataset.HDXDataset(location, details=None)

Data from a hydrogen/deuterium exchange experiment

class ihm.dataset.PDBDataset(location, details=None)

An experimentally-determined 3D structure as a set of a coordinates, usually in a PDB or mmCIF file

class ihm.dataset.ComparativeModelDataset(location, details=None)

A 3D structure determined by comparative modeling

class ihm.dataset.IntegrativeModelDataset(location, details=None)

A 3D structure determined by integrative modeling

class ihm.dataset.DeNovoModelDataset(location, details=None)

A 3D structure determined by de novo modeling

class ihm.dataset.NMRDataset(location, details=None)

A nuclear magnetic resonance (NMR) dataset

class ihm.dataset.MutagenesisDataset(location, details=None)

Mutagenesis data

class ihm.dataset.EMDensityDataset(location, details=None)

A 3D electron microscopy dataset

class ihm.dataset.EMMicrographsDataset(location, details=None)

Raw 2D electron micrographs

class ihm.dataset.EM2DClassDataset(location, details=None)

2DEM class average

class ihm.dataset.SASDataset(location, details=None)

SAS data

class ihm.dataset.FRETDataset(location, details=None)

Single molecule data from a Förster resonance energy transfer (FRET) experiment

class ihm.dataset.EnsembleFRETDataset(location, details=None)

Ensemble data from a Förster resonance energy transfer (FRET) experiment

class ihm.dataset.YeastTwoHybridDataset(location, details=None)

Yeast two-hybrid data

class ihm.dataset.GeneticInteractionsDataset(location, details=None)

Quantitative measurements of genetic interactions