Class Structure

A high-level representation of the contents of a PDB file

The components of a structure can be accessed in several ways ('s' is an instance of this class):

• 's.residues' is a list of all PDB residues, in the order in which they occurred in the file.
• 's.peptide_chains' is a list of PeptideChain objects, containing all peptide chains in the file in their original order.
• 's.nucleotide_chains' is a list of NucleotideChain objects, containing all nucleotide chains in the file in their original order.
• 's.molecules' is a list of all PDB residues that are neither amino acid residues nor nucleotide residues, in their original order.
• 's.objects' is a list of all high-level objects (peptide chains, nucleotide chains, and molecules) in their original order.
• 's.to_fractional' is the transformation from real-space coordinates to fractional coordinates, as read from the SCALEn records.
• 's.from_fractional' is the transformation from fractional coordinates to real-space coordinates, the inverse of s.to_fractional.
• 's.ncs_transformations' is a list of transformations that describe non-crystallographic symmetries, as read from the MTRIXn records.
• if a CRYST1 record exists, 's.a', 's.b', 's.c', 's.alpha', 's.beta', 's.gamma' are the parameters of the unit cell and 's.space_group' is a string indicating the space group. If no CRYST1 record exists, all those values are None. Furthermore, 's.cs_transformations' is a list of transformations that describe crystallographic symmetries. If no CRYST1 record exists, the list is empty.

An iteration over a Structure instance by a for-loop is equivalent to an iteration over the residue list.