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update aa-mapping documentation: add links to pdbfixer source

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PDB structures often contain modified amino acid residues (e.g., selenomethionine MSE,
phosphoserine SEP). P2Rank maps these to standard amino acids for feature calculation.
The `aa_mapping` parameter controls which mappings are used.
The `-aa_mapping` parameter controls which mappings are used.
## Modes
| Mode | Description | Mappings |
|------|-------------|----------|
| `minimal` | Default, backward-compatible (MSE→MET, MEN→ASN only) | 2 |
| `pdbfixer` | Extended set from [OpenMM pdbfixer](https://github.com/openmm/pdbfixer) | 87 |
| `/path/to/file.csv` | Custom user-provided mapping file | User-defined |
| Mode | Description | Mappings |
|------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|----------|
| `minimal` | Default, backward-compatible (MSE→MET, MEN→ASN only) | 2 |
| `pdbfixer` | Extended set from [pdbfixer](https://github.com/openmm/pdbfixer) ([source code](https://github.com/openmm/pdbfixer/blob/94cfa4c0ca551cdc5f13320f9a658efd59f2b881/pdbfixer/pdbfixer.py#L66)) | 87 |
| `/path/to/file.csv` | Custom user-provided mapping file | User-defined |
Residue codes not in the active mapping pass through unchanged.
**`minimal`** preserves original P2Rank behavior. Sufficient for most X-ray/cryo-EM structures.
**`minimal`** preserves original P2Rank behavior.
**`pdbfixer`** covers phosphorylated, methylated, and acetylated residues, selenocysteine,
histidine protonation variants, D-amino acids, and other modifications. Recommended when
structures contain many modified residues.
**`pdbfixer`** covers comprehensive set of phosphorylated, methylated, and acetylated residues, selenocysteine,
histidine protonation variants, D-amino acids, and other modifications.
Derived from pdbfixer 1.12 (2025-10-01) , with one mapping ommited.
## Usage
@@ -36,10 +36,9 @@ prank predict -f protein.pdb -aa_mapping /path/to/my-mappings.csv
## Custom Mapping Files
Any value other than `minimal` or `pdbfixer` is treated as a file path.
To load a file literally named "minimal" or "pdbfixer", use a path: `./minimal`.
A custom file **replaces** all built-in mappings (it does not extend them).
To add entries on top of the pdbfixer set, copy the bundled `aa-mapping-pdbfixer.csv`
To add entries on top of the pdbfixer set, copy the bundled [`aa-mapping-pdbfixer.csv`](src/main/resources/mappings/aa-mapping-pdbfixer.csv)
and append your entries.
Format — two-column CSV: