Constants

HHBLITS Mapping to Amino Acid Type

Name	Type	Description	Value
HHBLITS_AA_TO_ID	dict	Use the hhblits convention to map amino acids to corresponding numbers. Map B to D. Map J and O to X. Map U to C. Map Z to E. other letters are numbered in sequence.	HHBLITS_AA_TO_ID
ID_TO_HHBLITS_AA	dict	Inverse mapping of HHBLITS_AA_TO_ID, mapping the number to the amino acid type.	ID_TO_HHBLITS_AA
MAP_HHBLITS_AATYPE_TO_OUR_AATYPE	tuple	Mapping table from hhblits convention number to standard amino acid number, where the standard number is the alphabetical order of amino acids with three characters.	(0, 4, 3, 6, 13, 7, 8, 9, 11, 10, 12, 2, 14, 5, 1, 15, 16, 19, 17, 18, 20, 21)

The obtained MSA is converted from a letter to a number through HHBLITS_AA_TO_ID , and then converted to a restype id through MAP_HHBLITS_AATYPE_TO_OUR_AATYPE when it is sent to the network, consistent with other amino acid numbers in the network.

Amino Acid Correlation Constants

Name	Type	Description	Value
residue_atom_renaming_swaps	dict	Four of the 20 amino acids have partial atoms that are symmetrical. This dict records the mapping information of atomic pairs with symmetric invariance in each amino acid.	residue_atom_renaming_swaps
residue_atoms	dict	20 types of amino acids correspond to their atom types.	residue_atoms
restype_name_to_atom14_names	dict	Atom types each amino acid contains. If there are fewer than 14, use empty type “’’” to make up for it. The actual atoms are of the same type as residue_atoms .	restype_name_to_atom14_names
restype_1to3	dict	The mapping information of amino acids represented by one characters with amino acids represented by three characters. Key is amino acids represented by one characters and value is amino acids represented by three characters.	restype_1to3
restype_3to1	dict	The mapping information of amino acids represented by three characters with amino acids represented by one characters. Key is amino acids represented by three characters and value is amino acids represented by one characters.	restype_3to1
restype_atom14_mask	array	Mask of densely encoding of 21 types of amino acid (20 amino acid types and 1 unknown amino acid UNK ).	restype_atom14_mask
restype_atom37_mask	array	Mask of sparse encoding of 21 types of amino acid (20 amino acid types and 1 unknown amino acid UNK ).	restype_atom37_mask
restype_num	scalar	Total number of amino acid type, excluding unknown amino acid UNK .	20
resnames	list	List of amino acid types represented by three characters, including 20 types of amino acid and one type of unknown amino acid represented by UNK .	resnames
resname_to_idx	dict	Index of the amino acid types represented by three characters. Order is the same as the order of amino acids in the list of resnames.	resname_to_idx
restypes	list	List of amino acids, including a total of 20 amino acids, excluding UNK.	restypes
restype_order	dict	The index of amino acid. Order is consistent with the order of amino acid in the list of restypes .	restype_order
restypes_with_x	list	List of amino acids including ‘UNK’. ‘UNK’ means unknown amino acid and is represented by ‘X’. Totally (20 + 1) types of amino acid are in the list.	restypes_with_x
restype_order_with_x	dict	Index of the amino acid types represented by one characters. Order is the same as the order of amino acids in the list of restypes_with_x.	restype_order_with_x
order_restype_with_x	dict	Index corresponds to the amino acid. Order is the same as the order of amino acids in restypes , where ‘20’ represents the unknown amino acid number.	order_restype_with_x
restypes_with_x_and_gap	list	List of amino acid including GAP and UNK . GAP is represented by - . UNK means unknown amino acid and is represented by X. Totally (20 + 1 + 1) types of amino acid are in the list.	restypes_with_x_and_gap

Constants Associated with Atoms in Amino Acids

Name	Type	Description	Value
atom_order	dict	The name of all atoms of the amino acid and their index. Key is the atom name and value is its index.	atom_order
atom_type_num	scalar	The total number of atoms in an amino acid.	37
atom_types	list	List of names of all atoms of amino acid, including 37 types of atom.	atom_types

Empirical Constants Related to Amino Acid Bond Length and Bond Angle

Name	Type	Description	Value
between_res_bond_length_c_n	list	Amino acid peptide bond length. Unit is Å. The first value indicates the peptide bond length of amino acids other than proline, and the second value indicates the peptide bond length of proline.	[1.329, 1.341]
between_res_bond_length_stddev_c_n	list	Standard deviation of amino acid peptide bond length. Unit is Å. The first value represents amino acids other than proline, and the second represents proline.	[0.014, 0.016]
between_res_cos_angles_c_n_ca	list	The cosine of the dihedral Angle formed between amino acids \(C-N-C\alpha-(C+1)\) , The first value is the mean of the cosine, and the second value is the standard deviation of the cosine.	[-0.5203, 0.0353]
between_res_cos_angles_ca_c_n	list	The cosine of the dihedral Angle formed between amino acids \(N-C\alpha-C-(N-1)\) , The first value is the mean of the cosine, and the second value is the standard deviation of the cosine.	[-0.4473, 0.0311]
ca_ca	scalar	The distance between adjacent amino acids \(C\alpha-C\alpha\). Unit is Å.	3.80209737096

Van der Waals Atomic Radius

Name	Type	Description	Value
van_der_waals_radius	dict	Van der Waals radius of atom C, atom N , atom O and atom S .	van_der_waals_radius

Constants Associated with torsion angle

Name	Type	Description	Value
chi_angles_atoms	dict	The name of the atomic group that determines the side chain torsion angle in amino acids. Each amino acid has a maximum of four side chain torsion angles, among which ALA and GLY have no side chain torsion angle. Each torsion angle is determined by the position of 4 atomic groups (Dihedral Angle).	chi_angles_atoms
chi_angles_mask	list	If there is a mask of corresponding torsion angle in the amino acid. A two-dimensional array, first dimension is 20, consistent with the order of ‘restype_order’. The second dimension has a length of 4, with a value of 1.0 indicating the existence of the torsion angle and 0.0 indicating the absence of the torsion angle.	chi_angles_mask
chi_groups_for_atom	dict	Indexes of all atoms in amino acids in the corresponding side chain torsion angle encoding, where the side chain torsion angle encodings are shown in ‘chi_angles_atoms’.	chi_groups_for_atom
chi_pi_periodic	list	Whether torsion angles in amino acids is symmetric invariant, that is, rotating the corresponding torsion angle 180 degrees does not affect the overall three-dimensional structure.	chi_pi_periodic

Constants Associated with Local Coordinate System in Amino Acids

Name	Type	Description	Value
restype_atom14_rigid_group_positions	array	Densely encoding 21 amino acid types. Each amino acid contains the coordinates of the atoms in the local coordinate system of the rigid group to which it belongs. Shape is \((21, 14, 3)\) .	restype_atom14_rigid_group_positions
restype_atom14_to_rigid_group	array	Densely encoding 21 types of amino acid. Each amino acid contains the rigid group the atoms belong to. Shape is \((21, 14)\) .	restype_atom14_to_rigid_group
restype_atom37_rigid_group_positions	array	Sparse encoding 21 amino acid types. Each amino acid contains the coordinates of the atoms in the local coordinate system of the rigid group to which it belongs. Shape is \((21, 37, 3)\) .	restype_atom37_rigid_group_positions
restype_atom37_to_rigid_group	array	Sparse encoding 21 types of amino acid. Each amino acid contains the rigid group the atoms belong to. Shape is \((21, 37)\) .	restype_atom37_to_rigid_group
restype_rigid_group_default_frame	array	Affine transformation matrix of each rigid group of 21 amino acids, that is, the coordinate transformation matrix from the local coordinate system of each rigid group to the local coordinate system of the previous adjacent rigid group. Shape is \((21, 8, 4, 4)\) .	restype_rigid_group_default_frame
rigid_group_atom_positions	dict	The coordinates of the atoms in each amino acid in the local coordinate system of rigid group to which the atom belongs.	rigid_group_atom_positions