126a0653f0
Move misc/tutorials/ to documentation/ and add index readme. Update rescoring.md: add quick-start examples, paper links for all methods, add Pocketeer to supported methods list. Fix stale links in README.md (tutorials path, local-env.sh typo).
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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 OpenMM pdbfixer | 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.
pdbfixer covers phosphorylated, methylated, and acetylated residues, selenocysteine,
histidine protonation variants, D-amino acids, and other modifications. Recommended when
structures contain many modified residues.
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.
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
and append your entries.
Format — two-column CSV:
# Custom mappings
MSE,MET
LLP,LYS
SEC,CYS
- Lines starting with
#and empty lines are ignored - Codes are case-insensitive, 1-4 alphanumeric characters
- Whitespace around codes and commas is trimmed
- Duplicate source codes: warned, first mapping wins
- Self-mappings (e.g.,
ALA,ALA): skipped - Invalid lines: warned and skipped
- File not found or not readable: P2Rank exits with an error