abcount 0.2.10
Extended cheminformatics package to work with acidic and basic groups in molecules.
Requires Python: >=3.10

![ABCount logo](https://github.com/ghiander/abcount/blob/main/docs/static/logo.png?raw=true)

## Introduction
**ABCount** is an extended cheminformatics package to work with acidic and basic groups in molecules. The package includes the following functionalities:
- `ABCounter`: SMARTS-based matcher to determine the number of acidic and basic groups in molecules. Note that the method is not sensitive to tautomers.
- `ABClassBuilder`: Converter that accepts a dictionary of pKa numerical values and yields an `ABClassData` object with their corresponding classes such as `STRONG`, `WEAK`, and `NONE`.
- `IonMatcher`: Matcher that accepts an `ABClassData` object and yields an `IonDefinition` containing information about the major species at pH 7.4 and its corresponding ionic class and explanation.
- `pIPredictor`: Predictor based on the Henderson–Hasselbalch equation for calculating the pI of molecules. It accepts a dictionary of pKa values and calculates the pI using either the bisect method or value bounds. Note that the bisect method may yield results that are in disagreement with discrete charge methods: e.g., for a molecule with a weak acid [`pKa == 10`] and a weak base [`pKb == 2`], you would expect to find a zero charge as soon as pH moves from 2 towards basic values (`pI == pH == ~2.1`); however, this implementation calculates charges as fractional, hence for weak groups they leak shifting the pI towards the average [`pH ~= 6`].

## How to install the tool
ABCount can be installed from pypi (https://pypi.org/project/abcount).
```bash
pip install abcount
```

## Usage
### `ABCounter`
```python
from rdkit import Chem
from abcount import ABCounter

# Use the tool out of the box with default definitions.
mol = Chem.MolFromSmiles("[nH]1nnnc1-c3c2[nH]ncc2ccc3")
abc = ABCounter()
abc.count_acid_and_bases(mol)
```
```python
{'acid': 2, 'base': 2}
```

```python
from rdkit import Chem
from abcount import ABCounter

# Point the tool to using your own definitions.
# The format is JSON and attributes must be consistent to those in
# acid_definitions.json and base_definitions.json in abcount/data.
mol = Chem.MolFromSmiles("[nH]1nnnc1-c3c2[nH]ncc2ccc3")
abc = ABCounter(acid_defs_filepath="/my/path/acid_defs.json", base_defs_filepath="/my/path/base_defs.json")
abc.acid_matcher.definitions_fp
```
```python
PosixPath('/my/path/acid_defs.json')
```

### `ABClassBuilder` and `ABClassData`
```python
from abcount import ABClassBuilder

abcb = ABClassBuilder()
# The builder expects two acidic and two basic groups with these key names.
predictions = {"pka_acid1": 3.5, "pka_acid2": None, "pka_base1": 9.785, "pka_base2": None}
abcb.build(predictions)
```
```python
ABClassData(acid_1_class=<AcidType.STRONG: 'strong_acid'>, acid_2_class=<AcidType.NONE: 'no_acid'>, base_1_class=<BaseType.STRONG: 'strong_base'>, base_2_class=<BaseType.NONE: 'no_base'>)
```
```python
# to_dict() can be used to obtain a dictionary containing a mix of objects.
# Alternatively, the output can also be serialised using to_json()
abcb.build(predictions).to_json()
```
```python
'{"acid_1_class": "strong_acid", "acid_2_class": "no_acid", "base_1_class": "strong_base", "base_2_class": "no_base"}'
```

```python
from abcount import ABClassBuilder, PKaClassBuilder

abcb = ABClassBuilder()
# Custom names can be passed but these need to be
# configured in a `CustomPKaAttribute` class.
predictions = {"my_pka_acid1": 3.5, "my_pka_acid2": None, "my_pka_base1": 9.785, "my_pka_base2": None}
CustomPKaAttribute = PKaClassBuilder.build(ACID_1="my_pka_acid1", BASE_1="my_pka_base1", ACID_2="my_pka_acid2", BASE_2="my_pka_base2")

# The `CustomPKaAttribute` can then be passed to the builder
# which will map the new data to the rules.
abcb.build(predictions, CustomPKaAttribute)
```
```python
ABClassData(acid_1_class=<AcidType.STRONG: 'strong_acid'>, acid_2_class=<AcidType.NONE: 'no_acid'>, base_1_class=<BaseType.STRONG: 'strong_base'>, base_2_class=<BaseType.NONE: 'no_base'>)
```

```python
from abcount import ABClassBuilder

abcb = ABClassBuilder()
# It is possible to work with fewer acidic or basic groups
# These can be set as arguments in the builder
predictions = {"pka_acid1": 3.5, "pka_acid2": 7.5, "pka_base1": 9.785}
abcb.build(predictions, num_acids=2, num_bases=1)
```
```python
# Note that despite passing only one basic group, the builder still 
# returns `base_2_class` but associating that with a None instead of BaseType.NONE.
ABClassData(acid_1_class=<AcidType.STRONG: 'strong_acid'>, acid_2_class=<AcidType.NONE: 'no_acid'>, base_1_class=<BaseType.STRONG: 'strong_base'>, base_2_class=None)
```

### `IonMatcher`
```python
from abcount import ABClassBuilder, IonMatcher

abcb = ABClassBuilder()
predictions = {"pka_acid1": 3.5, "pka_acid2": 7.5, "pka_base1": 9.785}
abcd = abcb.build(predictions, num_acids=2, num_bases=1)

ion_matcher = IonMatcher()
ion_matcher.match_class_data(abcd)
```
```python
# Note that IonMatcher ignores AcidType.NONE and BaseType.NONE - treats them as None.
IonDefinition(class_data=ABClassData(acid_1_class=<AcidType.STRONG: 'strong_acid'>, acid_2_class=None, base_1_class=<BaseType.STRONG: 'strong_base'>, base_2_class=None), major_species_ph74_class='zwitterion', ion_class='zwitterion', explanation='acid_1_class: strong_acid, base_1_class: strong_base')
```
```python
# to_json() can also be applied to `IonDefinition`
# to yield a fully serialised representation.
# Alternatively, to_dict() can be used to obtain 
# a dictionary containing a mix of objects.
ion_matcher.match_class_data(abcd).to_dict()
```
```
{'class_data': {'acid_1_class': <AcidType.STRONG: 'strong_acid'>, 'acid_2_class': None, 'base_1_class': <BaseType.STRONG: 'strong_base'>, 'base_2_class': None}, 'major_species_ph74_class': 'zwitterion', 'ion_class': 'zwitterion', 'explanation': 'acid_1_class: strong_acid, base_1_class: strong_base'}
```

### `pIPredictor`
```python
from abcount import pIPredictor
predictions = {
        "pka_acid1": 3,
        "pka_acid2": None,
        "pka_base1": 12,
        "pka_base2": 8.5,
    }
pIPredictor.predict_input(predictions)
```
```
10.25
```

```python
from abcount import PKaClassBuilder
from abcount.components.isoelectric import pIPredictor

CustomPKaAttribute = PKaClassBuilder.build(ACID_1="my_pka_acid1", BASE_1="my_pka_base1", ACID_2="my_pka_acid2", BASE_2="my_pka_base2")
predictions = {
    "my_pka_acid1": 3,
    "my_pka_base1": 5.5,
    "my_pka_acid2": 12,
    "my_pka_base2": 8.5,
}
pIPredictor.predict_input(predictions, CustomPKaAttribute)
```
```
7.0
```

## SMARTS definitions source for `ABCounter`
The SMARTS patterns used in this project were obtained from the following sources. Note that definitions are not deduplicated, hence require curation to avoid redundant matching.

* Pan, X.; Wang, H.; Li, C.; Zhang, J. Z. H.; Ji, C., **MolGpka: A Web Server for Small Molecule pKa Prediction Using a Graph-Convolutional Neural Network**
*Journal of Chemical Information and Modeling* **2021**, *61* (7), 3159–3165. DOI: [10.1021/acs.jcim.1c00075](https://doi.org/10.1021/acs.jcim.1c00075)
* Wu, J.; Wan, Y.; Wu, Z.; Zhang, S.; Cao, D.; Hsieh, C.-Y.; Hou, T., **MF-SuP-pKa: Multi-fidelity modeling with subgraph pooling mechanism for pKa prediction** *Acta Pharmaceutica Sinica B* **2023**, *13* (6). DOI: [10.26434/chemrxiv-2022-t6q61](https://doi.org/10.26434/chemrxiv-2022-t6q61)
* Some manually curated definitions.

## Some useful commands
- Generate acidic and basic definitions from aggregated data: `python abcount/_definitions.py`. A follow up on how definitions can be curated will be provided.
- Run tests: `pytest -vss tests/test.py`
- Run validation: `cd tests && validation.py`. This will also generate four CSV files listing out false positives and negatives for the test data.

## For developers
- The package was created using `uv` (https://docs.astral.sh/uv/).
- The package can be installed from the wheel in the `dist/` folder. When a new version needs to be released, a new wheel must be built. That can be done by changing the version of the package inside `pyproject.toml` then calling `uv build` which will create a new build.
- The code can be automatically tested using `pytest -vss tests/test.py` which requires `pytest` to be installed.
- The `Makefile` can also be used for building (`make build`) or testing (`make test`).
- Before committing new code, please always check that the style and syntax are compliant using `pre-commit`.

### Setting up your development environment
The `pyproject.toml` already contains the optional dependencies needed for development. Follow these steps to set up the environment.
```bash
# Make sure you have got Python >= 3.10
python --version
> Python 3.12.7

# Installs `abcount` in editable mode and with dev dependencies
pip install -e .[dev]
> ...
> Successfully installed abcount ...

# Setup pre-commit hooks
pre-commit install
> pre-commit installed at .git/hooks/pre-commit
```