Structure#

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

Constructor#

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`([weight_type])	Calculate the center of mass of the structure.
`Structure.centered`()	Shifts the structure analogous to `tme.density.Density.centered()`.