### Install FreeSASA Python Module

Source: https://github.com/freesasa/freesasa-python/blob/master/docs/source/index.md

Install the FreeSASA Python Module using pip. This is the recommended method for most users.

```default
pip install freesasa
```

--------------------------------

### Build FreeSASA Python Module from Source

Source: https://github.com/freesasa/freesasa-python/blob/master/README.md

Developers can build the FreeSASA Python module from source. This process involves updating git submodules and running the setup script with Cython enabled.

```sh
git submodule update --init
USE_CYTHON=1 python setup.py build
```

--------------------------------

### SASA Selection Output

Source: https://github.com/freesasa/freesasa-python/blob/master/docs/source/intro.md

Example output for SASA calculations on selected atoms.

```default
alanine : 120.08 A2
r1_10 : 634.31 A2
```

--------------------------------

### Run FreeSASA Python Module Tests

Source: https://github.com/freesasa/freesasa-python/blob/master/docs/source/index.md

Run the tests for the FreeSASA Python module after building from source. This ensures the installation and build were successful.

```default
python setup.py test
```

--------------------------------

### Install FreeSASA Python Module with Conda

Source: https://github.com/freesasa/freesasa-python/blob/master/README.md

Install the FreeSASA Python module using conda from the conda-forge channel. This is an alternative installation method, particularly useful for managing complex dependencies.

```sh
conda install -c conda-forge freesasa-python
```

--------------------------------

### Basic SASA Calculation Output

Source: https://github.com/freesasa/freesasa-python/blob/master/docs/source/intro.md

Example output for a basic SASA calculation, showing total, polar, and apolar surface areas.

```default
Total : 4804.06 A2
Polar : 2504.22 A2
Apolar : 2299.84 A2
```

--------------------------------

### Build FreeSASA Python Module from Source

Source: https://github.com/freesasa/freesasa-python/blob/master/docs/source/index.md

Clone the FreeSASA Python repository and build the module from source. This method is for developers or users who need to build from the latest code.

```default
git clone https://github.com/freesasa/freesasa-python.git
git submodule update --init
python setyp.py build
```

--------------------------------

### Basic SASA Calculation

Source: https://github.com/freesasa/freesasa-python/blob/master/docs/source/intro.md

Perform a basic SASA calculation using default parameters on a PDB file. Requires the PDB file to be available.

```python
import freesasa

structure = freesasa.Structure("1ubq.pdb")
result = freesasa.calc(structure)
area_classes = freesasa.classifyResults(result, structure)

print "Total : %.2f A2" % result.totalArea()
for key in area_classes:
    print key, ": %.2f A2" % area_classes[key]
```

--------------------------------

### SASA Calculation for Atom Selections

Source: https://github.com/freesasa/freesasa-python/blob/master/docs/source/intro.md

Calculate SASA for specific atom selections using Pymol selection syntax. Requires a structure and a previous calculation result.

```python
selections = freesasa.selectArea(('alanine, resn ala', 'r1_10, resi 1-10'),
                                 structure, result)
for key in selections:
    print key, ": %.2f A2" % selections[key]
```

--------------------------------

### SASA Calculation with Custom Classifier

Source: https://github.com/freesasa/freesasa-python/blob/master/docs/source/intro.md

Perform SASA calculation using a custom NACCESS configuration file for atom classification and radii.

```python
classifier = freesasa.Classifier("naccess.config")
structure = freesasa.Structure("1ubq.pdb", classifier)
result = freesasa.calc(structure)
area_classes = freesasa.classifyResults(result, structure, classifier)
```

--------------------------------

### Custom SASA Classifier with Nitrogen Focus

Source: https://github.com/freesasa/freesasa-python/blob/master/docs/source/intro.md

Illustrates extending the FreeSASA Classifier to classify nitrogen atoms separately and assign radii based on element type.

```python
import freesasa
import re

class DerivedClassifier(freesasa.Classifier):
    # this must be set explicitly in all derived classifiers
    purePython = True

    def classify(self, residueName, atomName):
        if re.match('\s*N', atomName):
            return 'Nitrogen'
        return 'Not-nitrogen'

    def radius(self, residueName, atomName):
        if re.match('\s*N',atomName): # Nitrogen
            return 1.6
        if re.match('\s*C',atomName): # Carbon
            return 1.7
        if re.match('\s*O',atomName): # Oxygen
            return 1.4
        if re.match('\s*S',atomName): # Sulfur
            return 1.8
        return 0;                     # everything else (Hydrogen, etc)

classifier = DerivedClassifier()

# use the DerivedClassifier to calculate atom radii
structure = freesasa.Structure("1ubq.pdb", classifier)
result = freesasa.calc(structure)

# use the DerivedClassifier to classify atoms
area_classes = freesasa.classifyResults(result,structure,classifier)
```

--------------------------------

### High Precision SASA Calculation

Source: https://github.com/freesasa/freesasa-python/blob/master/docs/source/intro.md

Perform a high precision SASA calculation using the LeeRichards algorithm with 100 slices.

```python
result = freesasa.calc(structure,
                       freesasa.Parameters({'algorithm' : freesasa.LeeRichards,
                                            'n-slices' : 100}))
```

--------------------------------

### SASA Calculation with Bio.PDB Structure

Source: https://github.com/freesasa/freesasa-python/blob/master/docs/source/intro.md

Calculate SASA directly from a Bio.PDB Structure object using freesasa.calcBioPDB.

```python
from Bio.PDB import PDBParser
parser = PDBParser()
structure = parser.get_structure("Ubiquitin", "1ubq.pdb")
result, sasa_classes = freesasa.calcBioPDB(structure)
```

--------------------------------

### SASA Selection for Nitrogen Atoms

Source: https://github.com/freesasa/freesasa-python/blob/master/docs/source/intro.md

A simpler method to select and calculate SASA for nitrogen atoms using their symbol.

```python
selection = freesasa.selectArea('nitrogen, symbol n', structure, result)
```

--------------------------------

### Write SASA Results to PDB

Source: https://github.com/freesasa/freesasa-python/blob/master/docs/source/intro.md

Write the calculated SASA results to a new PDB file. This requires the input structure to have been parsed by FreeSASA.

```python
import freesasa

structure = freesasa.Structure('2ubq.pdb')
result = freesasa.calc(structure)
result.write_pdb('2ubq.sasa.pdb')
```

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