Models

Point3D

A point in a three-dimensional space.

Fields:

Name	Type	Description	Example	Default
x	float		0.0
y	float		0.0
z	float		0.0

Atom

Atom in a protein residue.

Fields:

Name	Type	Description	Example	Default
name	str	Name of the atom	"C"
coordinates	Point3D	Coordinates of the atom	{ "x": 0.0, "y": 0.5, "z": 1.0 }

ProteinResidue

Protein residue.

Fields:

Name	Type	Description	Example	Default
residue_id	str	ID of the residue	"1279"
name	Literal['GLY', 'ALA', 'PRO', 'CYS', 'THR', 'SER', 'ASP', 'ASN', 'GLU', 'GLN', 'LYS', 'HIS', 'ARG', 'VAL', 'ILE', 'LEU', 'MET', 'PHE', 'TYR', 'TRP']	Name of the residue	"SER"
atoms	List[Atom]	Atoms of the residue

ProteinChain

Protein chain

Fields:

Name	Type	Description	Example	Default
chain_id	str	ID of the chain	"A"
residues	List[ProteinResidue]	Residues of the chain

ProteinStructure

Protein structure.

Uses hierarchical structure, dissimilar to *.pdb file.

Fields:

Name	Type	Description	Example	Default
name	str
chains	List[ProteinChain]

Example

PDB lines:

ATOM   2085  N   PRO A1269       3.521  -3.568  11.905  1.00 22.18           N
ATOM   2086  CA  PRO A1269       3.490  -3.954  10.489  1.00 23.66           C
...
ATOM   2092  N   SER A1270       3.240  -1.630   9.821  1.00 23.51           N
ATOM   2093  CA  SER A1270       3.380  -0.475   8.946  1.00 23.35           C
...

Will be interpreted as the following protein structure:

{
    name: "protein_structure",
    chains: [
        {
            "chain_id": "A",
            "residues": [
                {
                    "residue_id": "1269",
                    "name": "PRO",
                    "atoms": [
                        {
                            "name": "N",
                            "coordinates": {
                                "x": 3.521,
                                "y": -3.568,
                                "z": 11.905
                            }
                        },
                        {
                            "name": "CA",
                            "coordinates": {
                                "x": 3.490,
                                "y": -3.954,
                                "z": 10.489
                            }
                        },
                        ...
                    ]
                },
                {
                    "residue_id": "1270",
                    "name": "SER",
                    "atoms": [
                        {
                            "name": "N",
                            "coordinates": {
                                "x": 3.240,
                                "y": -1.630,
                                "z": 9.821
                            }
                        },
                        {
                            "name": "CA",
                            "coordinates": {
                                "x": 3.380,
                                "y": -0.475,
                                "z": 8.946
                            }
                        },
                        ...
                    ]
                },
            ]
        }
    ]
}

ProteinAlignment

Result of a protein alignment algorithm.

Fields:

Name	Type	Description	Example	Default
ref_chain	str	Sequence of the reference protein in the alignment
tgt_chain	str	Sequence of the target protein in the alignment
block_id	str	Annotation of block id in the alignment
p_value	Optional[float]	P-value of the alignment		null
align_len	Optional[int]	Lenght of the alignment including gaps		null
opt_len	Optional[int]	Lenght of the alignment excluding gaps		null
opt_rmsd	Optional[float]	Root mean square deviation of the aligned C atoms, applyting twists, if any detected		null
chain_rmsd	Optional[float]	Root mean square deviation of the aligned C atoms, without twists.		null