Visualize

class Visualize(topology: Topology, junctions: Junctions = None, infer_bond_order=True)[source]

Bases: object

Enables conversion of a molecular system representation (Polymer, Monomer or Topology) to a rdKit Chem mol for 2D and 3D visualisation.

Parameters:

  • topology (Topology) – the molecular system Topology to visualise.

  • junctions (Junctions, optional) – the Junctions present with the Topology, to enable optional highlighting of the Junction locations, defaults to None

  • infer_bond_order (bool, optional) – if true, the bond order will be inferred based on the atom type and its number of bonds, defaults to True

draw2D(filename: str, size: Tuple[int, int] = (600, 300), highlight_junctions=False, show_atom_ID=False, show_legend=True, remove_explicit_H=True)[source]

Draw the Visualize object (molecule) in 2D with RDKit’s DrawMolecule function.

Args:

filename (str): size (tuple[int,int]): highlight_junctions (bool): show_atom_ID (bool): if True, show the atom ID in the molecule show_legend (bool): remove_explicit_H (bool): if True, remove the explicit hydrogens from the molecule

Parameters:

  • filename (str) – the filename to save the image to

  • size (Tuple[int,int], optional) – the size of the image to draw, defaults to (600,300)

  • highlight_junctions (bool, optional) – if True, render the Junction bonds in a different colour to highlight them, defaults to False

  • show_atom_ID (bool, optional) – if True, render the drawing with the Atom’s labelled with their atom_id, defaults to False

  • show_legend (bool, optional) – if True, show the legend (the ‘title’ of the underlying Topology) in the image, defaults to True

  • remove_explicit_H (bool, optional) – if True, removes explicit hydrogens. Valuable for rendering larger images by making them less crowded, defaults to True

Raises:

ValueError – if both ‘show_atom_ID’ and ‘remove_explicit_H’ are True

draw3D(view=None, highlight_junctions: bool = False, show_atom_ID: bool = False, remove_explicit_H: bool = True)[source]

Draw the Visualize object (molecule) in 3D with RDKit’s DrawMolecule function.

Parameters:

  • view (py3Dmol.view, optional) – a py3Dmol.view() of desired width and height, defaults to None

  • highlight_junctions (bool, optional) – if True, render the Junction bonds in a different colour to highlight them, defaults to False

  • show_atom_ID (bool, optional) – if True, render the drawing with the Atom’s labelled with their atom_id, defaults to False

  • remove_explicit_H (bool, optional) – if True, removes explicit hydrogens. Valuable for rendering larger images by making them less crowded, defaults to True

infer_bond_order()[source]

Infer the bond order of all bonds in the Topology according to the valencies of the two Atoms that share the Bond and the number of other Bonds each of them have. The inferred bond order is saved to the ‘order’ property of each bond.

Double bonds will be added to the Topology using the known valencies of the Atoms and number of declared Bonds.

This function is called automatically by the Class initialiser if the parameter ‘infer_bond_order’ is True.

classmethod monomer(monomer: Monomer, infer_bond_order=True) → Visualize[source]

Class method to construct Visualize object from a Polymer.

Parameters:

  • monomer (Monomer) – the Monomer set to be converted to RDKit format and visualised.

  • infer_bond_order (bool, optional) – if true, the bond order will be inferred based on the atom type and its number of bonds, defaults to True.

Returns:

a Visualize object that can be drawn in 2D or 3D.

Return type:

Visualize

classmethod polymer(polymer: Polymer, infer_bond_order=True) → Visualize[source]

Class method to construct Visualize object from a Polymer.

Parameters:

  • polymer (Polymer) – the Polymer set to be converted to RDKit format and visualised.

  • infer_bond_order (bool, optional) – if true, the bond order will be inferred based on the atom type and its number of bonds, defaults to True.

Returns:

a Visualize object that can be drawn in 2D or 3D.

Return type:

Visualize

classmethod topology(topology: Topology, infer_bond_order=True) → Visualize[source]

Class method to construct Visualize object from a Topology.

Parameters:

  • topology (Topology) – the Topology set to be converted to RDKit format and visualised.

  • infer_bond_order (bool, optional) – if true, the bond order will be inferred based on the atom type and its number of bonds, defaults to True.

Returns:

a Visualize object that can be drawn in 2D or 3D.

Return type:

Visualize