biotite.structure.info

A subpackage for obtaining all kinds of chemical information about atoms and residues, including masses, radii, bonds, etc.

Most information is extracted from the chemical compound dictionary of the wwPDB via tools from the biotite-util repository.

Content

all_residues

Get a list of all residues/compound names in the PDB chemical components dictionary.

bond_dataset

Get a copy of the complete bond dataset extracted from the chemical components dictionary.

bond_order

Get the bond order for two atoms of the same residue, based on the PDB chemical components dictionary.

bond_type

Get the BondType for two atoms of the same residue, based on the PDB chemical components dictionary.

bonds_in_residue

Get a dictionary containing all atoms inside a given residue that form a bond.

full_name

Get the full name of a residue/compound from the up to 3-letter residue name, based on the PDB chemical components dictionary.

link_type

Get the linking type of a residue/compound, based on the PDB chemical components dictionary.

mass

Calculate the mass for the given object.

nucleotide_names

Get a list of nucleotide three-letter codes according to the PDB chemical compound dictionary.

residue

Get an atom array, representing the residue with the given name.

standardize_order

Get an index array for an input AtomArray or AtomArrayStack that reorders the atoms for each residue to obtain the standard RCSB PDB atom order.

vdw_radius_protor

Estimate the Van-der-Waals radius of an non-hydrogen atom, that includes the radius added by potential bonded hydrogen atoms.

vdw_radius_single

Get the Van-der-Waals radius of an atom from the given element.