iphasimulator.visualisation.visualiser

PHA visualisation utilities. This module contains helper functions for visualising available PHA monomer units and generated polymers.

It currently uses RDKit to render 2D molecular depictions from SMILES strings.

Functions

`load_available_PHA_monomers`(residue_codes_csv)	Load available PHA monomer units from residue_codes.csv.
`smiles_to_mol`(smiles[, name])	Convert a SMILES string into an RDKit molecule.
`plot_available_PHA_monomers`([residue_codes_csv, ...])	Plot all available PHA monomer units from residue_codes.csv.
`show_available_PHA_monomers`([residue_codes_csv, ...])	Display all available PHA monomer units.
`show_PHA_monomer`(PHA_type[, residue_codes_csv, image_size])	Display one PHA monomer structure from residue_codes.csv.
`load_polymer_smiles`(polymer_smiles_csv)	Load polymer SMILES from polymer_smiles.csv.
`plot_available_PHA_polymers`([polymer_smiles_csv, ...])	Plot all available PHA polymers from polymer_smiles.csv.
`show_available_PHA_polymers`([polymer_smiles_csv, ...])	Display all available PHA polymers from polymer_smiles.csv.
`show_PHA_polymer`(polymer_name[, polymer_smiles_csv, ...])	Display one PHA polymer structure from polymer_smiles.csv.

Module Contents

iphasimulator.visualisation.visualiser.load_available_PHA_monomers(residue_codes_csv)

Load available PHA monomer units from residue_codes.csv.

Parameters:: residue_codes_csv (str or pathlib.Path) – Path to the residue code CSV file.
Returns:: List of (PHA_type, smiles) tuples for each available mainchain monomer unit.
Return type:: list[tuple[str, str]]

iphasimulator.visualisation.visualiser.smiles_to_mol(smiles, name=None)

Convert a SMILES string into an RDKit molecule.

Parameters:

smiles (str) – SMILES string to convert.
name (str, optional) – Optional molecule name used only for clearer error messages.

Returns:

RDKit molecule object.

Return type:

rdkit.Chem.rdchem.Mol

iphasimulator.visualisation.visualiser.plot_available_PHA_monomers(residue_codes_csv='structure_database/residue_codes.csv', output_file='available_PHA_monomers.png', mols_per_row=4, image_size=(300, 220))

Plot all available PHA monomer units from residue_codes.csv. The function reads the mainchain monomer SMILES for each registered PHA type, converts each SMILES string to an RDKit molecule and writes a grid image to disk.

Parameters:

residue_codes_csv (str or pathlib.Path, optional) – Path to residue_codes.csv.
output_file (str or pathlib.Path, optional) – Path where the output image should be written.
mols_per_row (int, optional) – Number of structures shown per row.
image_size (tuple[int, int], optional) – Size of each molecule panel in pixels.

Returns:

Path to the generated image.

Return type:

pathlib.Path

iphasimulator.visualisation.visualiser.show_available_PHA_monomers(residue_codes_csv='structure_database/residue_codes.csv', mols_per_row=4): Display all available PHA monomer units.

iphasimulator.visualisation.visualiser.show_PHA_monomer(PHA_type, residue_codes_csv='structure_database/residue_codes.csv', image_size=(300, 220))

Display one PHA monomer structure from residue_codes.csv.

Parameters:

PHA_type (str) – PHA type to display, e.g. “3HB” or “4HB”.
residue_codes_csv (str or pathlib.Path, optional) – Path to residue_codes.csv.
image_size (tuple[int, int], optional) – Size of the rendered molecule image.

Returns:

Rendered RDKit molecule image.

Return type:

PIL.Image.Image

iphasimulator.visualisation.visualiser.load_polymer_smiles(polymer_smiles_csv)

Load polymer SMILES from polymer_smiles.csv.

Parameters:: polymer_smiles_csv (str or pathlib.Path) – Path to polymer_smiles.csv.
Returns:: List of (polymer_name, smiles) tuples.
Return type:: list[tuple[str, str]]

iphasimulator.visualisation.visualiser.plot_available_PHA_polymers(polymer_smiles_csv='structure_database/polymer_smiles.csv', output_file='available_PHA_polymers.png', mols_per_row=3, image_size=(500, 280)): Plot all available PHA polymers from polymer_smiles.csv.

iphasimulator.visualisation.visualiser.show_available_PHA_polymers(polymer_smiles_csv='structure_database/polymer_smiles.csv', mols_per_row=3, image_size=(500, 280)): Display all available PHA polymers from polymer_smiles.csv.

iphasimulator.visualisation.visualiser.show_PHA_polymer(polymer_name, polymer_smiles_csv='structure_database/polymer_smiles.csv', image_size=(900, 300)): Display one PHA polymer structure from polymer_smiles.csv.