Molecule Features

Molecules are tagged with features. For example, just after mapping molecules from a spline, features will be like this:

layer = ui.mole_layers["Mole-0"]  # the molecules layer named "Mole-0"
layer.molecules.features

Output:

shape: (286, 3)
┌─────┬───────┬─────────────┐
│ nth ┆ pf-id ┆ position-nm │
│ --- ┆ ---   ┆ ---         │
│ i64 ┆ i64   ┆ f64         │
╞═════╪═══════╪═════════════╡
│ 0   ┆ 0     ┆ 6.1548      │
│ 0   ┆ 1     ┆ 5.2079      │
│ 0   ┆ 2     ┆ 4.261       │
│ 0   ┆ 3     ┆ 3.3141      │
│ …   ┆ …     ┆ …           │
│ 21  ┆ 9     ┆ 83.7184     │
│ 21  ┆ 10    ┆ 82.7715     │
│ 21  ┆ 11    ┆ 81.8246     │
│ 21  ┆ 12    ┆ 80.8777     │
└─────┴───────┴─────────────┘

The molecule features are stored as a polars.DataFrame object. You can get any of the columns by df["column-name"].

import matplotlib.pyplot as plt

df = layer.molecules.features
plt.scatter(df["pf-id"], df["score"])
plt.show()

Paint Molecules by Features

GUI: Molecules > View > Paint molecules or Ctrl+K → C

This method updates the color of each molecule according to the value of a feature column.

Calculate Features

API: calculate_molecule_features

GUI: Molecules > Features > Calculate molecule features

This method calculates features from the existing features. The input argument should follow the polars expression syntax.

calculate molecule features

Following function call will add a new feature named "pf-is-odd" to the molecules layer, which indicates whether the molecule id is odd or not.

ui.calculate_molecule_features(
    layer="Mole-0",
    column_name="pf-is-odd",
    expression="col('pf-id') % 2 == 1",
)
print(ui.mole_layers["Mole-0"].molecules.features["pf-is-odd"])  # print the feature

Calculate Lattice Structures

API: calculate_lattice_structure

GUI: Molecules > Features > Calculate lattice structure

Some of the structural parameters equivalent to CFT parameters can be calculated from the molecule coordinates and spline parameters.

calculate spacing and twist

ui.calculate_lattice_structure(
    layer="Mole-0",
    props=["spacing", "twist"],
)