p2rank/documentation/hidden-commands.md

Hidden commands

Apart from hidden commands for training and grid optimization (see training-tutorial.md) P2Rank contains some miscellaneous tools.

Analyze

residues

List all residues with some details:

• secondary structure
• binding information

See also "binding residues".

./prank.sh analyze residues <dataset.ds>

binding residues

List residues binding relevant ligands.

Residue key format: <chain_author_id>_<seq_number><ins_code>

./prank.sh analyze binding-residues <dataset.ds>

Related parameters:

• -ligand_protein_contact_distance: cutoff distance between ligand and protein atoms
• params that determine which ligands are relevant:
  • -min_ligand_atoms: smaller ligands are ignored
  • -ligc_prot_dist: acceptable distance between ligand center and closest protein atom for relevant ligands
  • -ignore_het_groups: codes of ligands that are not considered relevant

labeled residues

Analyze a dataset with an explicitly specified residue labeling.

./prank.sh analyze labeled-residues <dataset.ds>

Export feature vectors for further analysis

-delete_vectors 0
xyz is a dummy feature that stores 3D coordinates of a given SAS point.

./prank.sh traineval -t test_data/basic.ds -e test_data/basic.ds \
    -loop 1 -delete_vectors 0 -sample_negatives_from_decoys 0 \
    -features '(chem,volsite,protrusion,bfactor,xyz)'

Export chains to FASTA

fasta-raw exports residue codes as P2Rank sees them. fasta-mask will transform any possible non-letter code (such as _ or ?) to X.

# run in P2Rank root directory (distro in repo)

./prank analyze fasta-raw test_data/basic.ds         # dataset
./prank analyze fasta-raw -f test_data/2W83.pdb      # single file
./prank analyze fasta-raw test_data/basic.ds 

./prank analyze fasta-masked test_data/basic.ds      # dataset
./prank analyze fasta-masked -f test_data/2W83.pdb   # single file
./prank analyze fasta-masked test_data/basic.ds -o out_dir  # specify output directory

Reduce structure to chains

./prank.sh analyze reduce-to-chains -f <structure_file> -chains <chain_names> -out_format <format_file_extension> -out_file <file_name>

• -f <> required, structure fie in one of the formats pdb|pdb.gz|cif|cif.gz
• -chains required, coma separated list of chain names, wildcards: keep, all
  • in the case of mmcif files, values refer to old PDB chain names (author id), not mmcif ids
  • keep keeps the structure as is, just saves with required format (may not work perfectly due to biojava), useful for debugging
  • * is not the same as keeping structure as is, but runs the reduction procedure with all the chains, useful for debugging
• -out_format optional, default value is keep -- use the same format as the input
  • possible values: keep|pdb|pdb.gz|cif|cif.gz
• -out_file optional, output structure file name, path relative to the shell working directory
  • if specified, reduced structure is saved under given name and no other output is produced
  • if not specified, default name is generated (see examples) and file is saved in the output directory specified with parameters -o, -output_base_dir, -out_subdir

Examples:

./prank.sh transform reduce-to-chains -f distro/test_data/2W83.cif    -chains A                                                 # output: <out_dir>/2W83_A.cif
./prank.sh transform reduce-to-chains -f distro/test_data/2W83.pdb    -chains A                                                 # output: <out_dir>/2W83_A.pdb
./prank.sh transform reduce-to-chains -f distro/test_data/2W83.cif.gz -chains A,B                                               # output: <out_dir>/2W83_A,B.cif.gz
./prank.sh transform reduce-to-chains -f distro/test_data/2W83.cif.gz -chains A,B  -out_file distro/test_output/2W83_A,B.cif.gz # output: distro/test_output/2W83_A,B.cif.gz
./prank.sh transform reduce-to-chains -f distro/test_data/2W83.cif    -chains keep                                              # output: <out_dir>/2W83.cif
./prank.sh transform reduce-to-chains -f distro/test_data/2W83.cif    -chains keep -out_format pdb.gz                           # output: <out_dir>/2W83.pdb.gz
./prank.sh transform reduce-to-chains -f distro/test_data/2W83.cif    -chains all                                               # output: <out_dir>/2W83_all.cif
./prank.sh transform reduce-to-chains -f distro/test_data/2W83.cif    -chains A    -out_format keep                             # output: <out_dir>/2W83_A.cif
./prank.sh transform reduce-to-chains -f distro/test_data/2W83.cif.gz -chains A    -out_format pdb.gz                           # output: <out_dir>/2W83_A.pdb.gz
./prank.sh transform reduce-to-chains -f distro/test_data/2W83.pdb.gz -chains A,B  -out_format cif                              # output: <out_dir>/2W83_A,B.cif

Print

Print a list of features

Check which features are enabled for a particular configuration.

./prank print features                          # for default config
./prank print features -c other_config.groovy   # for custom config

Print model info

Print information about trained model (*.model file).

./prank print model-info                     # for default model
./prank print model-info -m model2.model     # for custom model