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 Component Dictionary of the wwPDB.

Residues and bonds

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

Component groups

amino_acid_names	Get a tuple of amino acid three-letter codes according to the PDB Chemical Component Dictionary.
nucleotide_names	Get a tuple of nucleotide three-letter codes according to the PDB Chemical Component Dictionary.
carbohydrate_names	Get a tuple of carbohydrate three-letter codes according to the PDB Chemical Component Dictionary.

Atom radii

vdw_radius_single	Get the Van-der-Waals radius of an atom from the given element.
vdw_radius_protor	Estimate the Van-der-Waals radius of an non-hydrogen atom, that includes the radius added by potential bonded hydrogen atoms.

Low-level CCD access

get_ccd	Get the internal subset of the PDB Chemical Component Dictionary (CCD).
get_from_ccd	Get the rows for the given residue in the given category from the internal subset of the PDB Chemical Component Dictionary (CCD).
set_ccd_path	Replace the internal Chemical Component Dictionary (CCD) with a custom one.

Miscellaneous

all_residues	Get a list of all residues/compound names in the PDB Chemical Component Dictionary (CCD).
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.
one_letter_code	Get the one-letter code of a residue/compound, based on the PDB chemical components dictionary.
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.