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sreekanth221998 merged 1 commit into from
Aug 6, 2025
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update guides for inserting terminal groups #65

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40 changes: 31 additions & 9 deletions docs/how_to_guides.md
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Expand Up @@ -184,21 +184,23 @@ difference = comparator.compare(polymer, molecule) # (4)

The `MultipleFeaturizer` class is used to combine multiple featurizers into a single featurizer object. The `PolymerMoleculeComparator` class is then used to compare the polymer and molecule using the combined featurizers. The `compare` method returns the difference between the polymer and the molecule in terms of the features extracted by the featurizers.

### Adding terminal groups to polymers (user has to specify the terminal groups)
### Adding terminal groups to polymers (sidechain, backbone and full polymer)

When working with polymers, you may want to add terminal groups to the polymer backbone or sidechains. This can be done by specifying the terminal groups in the `terminal_groups` attribute of the `Polymer` class.

@sourcery-ai sourcery-ai Bot Aug 6, 2025

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issue: Update reference to 'terminal_groups' attribute to match code example.

Update the sentence to reference 'backbone_terminal_groups' and 'sidechain_terminal_groups' instead of 'terminal_groups' to match the code.


```python
from polymetrix.featurizers.polymer import Polymer
from polymetrix.featurizers.sidechain_backbone_featurizer import NumBackBoneFeaturizer, BackBoneFeaturizer, MultipleFeaturizer
from polymetrix.featurizers.sidechain_backbone_featurizer import NumBackBoneFeaturizer, BackBoneFeaturizer, MultipleFeaturizer, FullPolymerFeaturizer
from polymetrix.featurizers.chemical_featurizer import NumRings, NumAtoms, TopologicalSurfaceArea

polymer = Polymer.from_psmiles("c1ccccc1[*]CCO[*]")

print(polymer.backbone_nodes)
print(polymer.sidechain_nodes)
print(polymer.get_connection_points())
polymer = Polymer.from_psmiles("[*]=C(C#N)NC(=O)c1ccc(C(=O)NC(=[*])C#N)cc1")

# Add terminal groups
polymer.terminal_groups = {6: "C", 10: "O"} # (1)
# Add terminal groups for the sidechain and backbone
polymer.backbone_terminal_groups = {"[*]": "*O"}
polymer.sidechain_terminal_groups = {"[*]": "*CCO"}

# Featurizers for the backbone and sidechain with terminal groups
backbone_featurizers = [
NumBackBoneFeaturizer(),
BackBoneFeaturizer(NumRings()),
Expand All @@ -208,9 +210,29 @@ backbone_featurizers = [

backbone_multi_featurizer = MultipleFeaturizer(backbone_featurizers)
features = backbone_multi_featurizer.featurize(polymer)

# Sidechain featurizers with terminal groups
sidechain_featurizers = [
NumSideChainFeaturizer(),
SideChainFeaturizer(NumAtoms()),
SideChainFeaturizer(NumHBondDonors()),
SideChainFeaturizer(TopologicalSurfaceArea()),
]

sidechain_multi_featurizer = MultipleFeaturizer(sidechain_featurizers)
features = sidechain_multi_featurizer.featurize(polymer)

# Full polymer featurizers with terminal groups
full_polymer_featurizers = [
FullPolymerFeaturizer(NumAtoms()),
FullPolymerFeaturizer(NumHBondDonors()),
FullPolymerFeaturizer(TopologicalSurfaceArea()),
]
full_multi_featurizer = MultipleFeaturizer(full_polymer_featurizers)
features = full_multi_featurizer.featurize(polymer)
```

The `terminal_groups` attribute is a dictionary where the keys are the node indices of the polymer backbone and the values are the terminal groups to be added. The `MultipleFeaturizer` class is then used to apply multiple featurizers to the polymer with the added terminal groups.
The above code demonstrates how to add terminal groups to the polymer backbone and sidechains, and how to apply featurizers to the polymer with these terminal groups. The `backbone_terminal_groups` and `sidechain_terminal_groups` attributes are used to specify the terminal groups for the backbone and sidechains, respectively. The featurizers are then applied to the polymer with the terminal groups included.

## Datasets

Expand Down