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Types

Define the types of systems biology: the rules of Boolean networks and their candidates.

AtomProtocol

Bases: Protocol

Atom of a chain in Biopython, which the extra structures holds.

BiopythonStructureProtocol

Bases: Protocol

Structure in Biopython, which the extra structures holds.

get_chains()

Return the chains of the systems of the structure.

Source code in src/skcomplex/systems/biology/systems_biology/types.py 
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def get_chains(self) -> Iterator[ChainProtocol]:
    """Return the chains of the systems of the structure."""

ChainProtocol

Bases: Protocol

Chain of a structure in Biopython, which the extra structures holds.

atom_to_internal_coordinates()

Read the internal coordinates of the positions of the atoms.

Source code in src/skcomplex/systems/biology/systems_biology/types.py 
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def atom_to_internal_coordinates(self) -> None:
    """Read the internal coordinates of the positions of the atoms."""

get_atoms()

Return the atoms of the chain.

Source code in src/skcomplex/systems/biology/systems_biology/types.py 
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def get_atoms(self) -> Iterator[AtomProtocol]:
    """Return the atoms of the chain."""

get_residues()

Return the residues of the chain.

Source code in src/skcomplex/systems/biology/systems_biology/types.py 
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def get_residues(self) -> Iterator[ResidueProtocol]:
    """Return the residues of the chain."""

internal_to_atom_coordinates()

Write the positions of the atoms from the internal coordinates.

Source code in src/skcomplex/systems/biology/systems_biology/types.py 
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def internal_to_atom_coordinates(self) -> None:
    """Write the positions of the atoms from the internal coordinates."""

InternalCoordinatesProtocol

Bases: Protocol

Internal coordinates of a residue in Biopython, which the extra structures holds.

get_angle(name)

Return the angle of a name in degrees, or None when the residue has none.

Parameters:

Name Type Description Default
name str

The name of the angle.

 required

Returns:

Name Type Description
angle float | None

The angle in degrees, or None.
Source code in src/skcomplex/systems/biology/systems_biology/types.py 
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def get_angle(self, name: str) -> float | None:
    """Return the angle of a name in degrees, or `None` when the residue has none.

    Args:
        name:
            The name of the angle.

    Returns:
        angle:
            The angle in degrees, or `None`.
    """

set_angle(name, value)

Write the angle of a name in degrees.

Parameters:

Name Type Description Default
name str

The name of the angle.

 required
value float

The angle.

 required
Source code in src/skcomplex/systems/biology/systems_biology/types.py 
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def set_angle(self, name: str, value: float) -> None:
    """Write the angle of a name in degrees.

    Args:
        name:
            The name of the angle.

        value:
            The angle.
    """

ResidueProtocol

Bases: Protocol

Residue of a chain in Biopython, which the extra structures holds.