Interface Structure

bonds in structures given as [i, j, order], where i, j, and order are integers. i and j are the indices of the atoms bonded together, and order is the bond order, which can be 1 (for single bonds) or 2 (for double bonds) or 3 (for triple bonds)

Unit cell of the system, given as [ax ay az bx by bz cx cy cz], where a, b, and c are the unit cell vectors. All values should be expressed in Angströms.

Chain names of all atoms in the structure, if available. This is only used for secondary structure assignment.

Element names of all atoms in the structure, if available

Wether an atom is a heteroatom, i.e. not part of a biomolecule (protein, dna, …). If this is not provided, it is assumed to be true for all atoms.

This is only used for secondary structure assignment and cartoon representation.

Names of all atoms in the structure

Residue index for all atoms in the structure, if available. This is only used for secondary structure assignment.

Residue name for all atoms in the structure, if available. Atoms without a residue (e.g. water molecules, ions, etc.) should have their resname set to "UNK".

This is used for cartoon representation.

possible shapes to display, multiple groups of shapes with different names are allowed

Number of atoms in the structure

x position (cartesian coordinate) of all atoms in the structure

This array should have the same size as Structure.names, and contain values expressed in Angströms.

y position (cartesian coordinate) of all atoms in the structure

This array should have the same size as Structure.names, and contain values expressed in Angströms.

z position (cartesian coordinate) of all atoms in the structure

This array should have the same size as Structure.names, and contain values expressed in Angströms.