2.6 KiB
Non-Canonical Amino Acid Residue Mapping
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.
Modes
| Mode | Description | Mappings |
|---|---|---|
minimal |
Default, backward-compatible (MSE->MET, MEN->ASN only) | 2 |
pdbfixer |
Extended set from pdbfixer (source code) | 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.
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
# Default (minimal)
prank predict -f protein.pdb
# Extended pdbfixer mappings
prank predict -f protein.pdb -aa_mapping pdbfixer
# Custom mapping file
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.
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
and append your entries.
Format - two-column CSV:
# Custom mappings
MSE,MET
LLP,LYS
SEC,CYS
Format notes:
- Lines starting with
#and empty lines are ignored - Codes are case-insensitive
- Whitespace around codes and commas is trimmed
- Duplicate source codes: warned, first mapping wins
- File not found or not readable: P2Rank exits with an error