Structure

The structure module represents atomic structures in accordance with the Protein Data Bank (PDB) specification, ensuring standardized handling of molecular data.

Constructor

Structure

Represents atomic structures per the Protein Data Bank (PDB) specification.

Attributes and underlying data

Structure.record_type	Array of record types, e.g.ATOM.
Structure.atom_serial_number	Array of serial numbers.
Structure.atom_name	Array of atom names.
Structure.atom_coordinate	Array of x,y,z atom coordinates.
Structure.alternate_location_indicator	Array of alternate location indices.
Structure.residue_name	Array of residue names.
Structure.chain_identifier	Array of chain identifiers.
Structure.residue_sequence_number	Array of residue ids.
Structure.code_for_residue_insertion	Array of insertion information.
Structure.occupancy	Array of occupancy factors.
Structure.temperature_factor	Array of B-factors.
Structure.segment_identifier	Array of segment identifiers.
Structure.element_symbol	Array of element symbols.
Structure.charge	Array of charges.
Structure.metadata	Metadata dictionary.

Serialization

Structure.to_file(filename)	Writes the Structure instance to disk.
Structure.from_file(filename[, ...])	Reads an atomic structure file and into a Structure instance.

Conversion

Structure.to_volume([shape, sampling_rate, ...])

Maps class instance to a volume.

Subsetting

Structure.copy()	Returns a copy of the Structure instance.
Structure.subset_by_chain([chain])	Return a subset of the structure that contains only atoms belonging to a specific chain.
Structure.subset_by_range(start, stop[, chain])	Return a subset of the structure within a specific range of residues.

Computations

Structure.rigid_transform(rotation_matrix, ...)	Performs a rigid transform of internal structure coordinates.
Structure.align_structures(structure1, ...)	Align structure2 to structure1 using the Kabsch Algorithm.
Structure.compare_structures(structure1, ...)	Compute root mean square deviation (RMSD) between two structures with the same number of atoms.
Structure.center_of_mass()	Calculate the center of mass of the structure.
Structure.centered()	Shifts the structure analogous to tme.density.Density.centered().