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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).
130 lines
5.3 KiB
Markdown
130 lines
5.3 KiB
Markdown
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# Hidden commands
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Apart from hidden commands for training and grid optimization (see `training-tutorial.md`) P2Rank contains some miscellaneous tools.
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## Analyze
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### residues
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List all residues with some details:
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* secondary structure
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* binding information
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See also "binding residues".
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~~~sh
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./prank.sh analyze residues <dataset.ds>
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~~~
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### binding residues
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List residues binding relevant ligands.
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Residue key format: `<chain_author_id>_<seq_number><ins_code>`
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~~~sh
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./prank.sh analyze binding-residues <dataset.ds>
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~~~
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Related parameters:
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- `-ligand_protein_contact_distance`: cutoff distance between ligand and protein atoms
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- params that determine which ligands are relevant:
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- `-min_ligand_atoms`: smaller ligands are ignored
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- `-ligc_prot_dist`: acceptable distance between ligand center and closest protein atom for relevant ligands
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- `-ignore_het_groups`: codes of ligands that are not considered relevant
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### labeled residues
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Analyze a dataset with an explicitly specified residue labeling.
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~~~sh
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./prank.sh analyze labeled-residues <dataset.ds>
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~~~
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## Export feature vectors for further analysis
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`-delete_vectors 0`
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`xyz` is a dummy feature that stores 3D coordinates of a given SAS point.
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~~~sh
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./prank.sh traineval -t test_data/basic.ds -e test_data/basic.ds \
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-loop 1 -delete_vectors 0 -sample_negatives_from_decoys 0 \
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-features '(chem,volsite,protrusion,bfactor,xyz)'
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~~~
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## Export chains to FASTA
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`fasta-raw` exports residue codes as P2Rank sees them.
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`fasta-mask` will transform any possible non-letter code (such as `_` or `?`) to `X`.
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~~~sh
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# run in P2Rank root directory (distro in repo)
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./prank analyze fasta-raw test_data/basic.ds # dataset
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./prank analyze fasta-raw -f test_data/2W83.pdb # single file
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./prank analyze fasta-raw test_data/basic.ds
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./prank analyze fasta-masked test_data/basic.ds # dataset
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./prank analyze fasta-masked -f test_data/2W83.pdb # single file
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./prank analyze fasta-masked test_data/basic.ds -o out_dir # specify output directory
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~~~
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## Reduce structure to chains
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~~~sh
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./prank.sh analyze reduce-to-chains -f <structure_file> -chains <chain_names> -out_format <format_file_extension> -out_file <file_name>
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~~~
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* `-f <>` required, structure fie in one of the formats `pdb|pdb.gz|cif|cif.gz`
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* `-chains` required, coma separated list of chain names, wildcards: `keep`, `all`
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* in the case of mmcif files, values refer to old PDB chain names (author id), not mmcif ids
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* `keep` keeps the structure as is, just saves with required format (may not work perfectly due to biojava), useful for debugging
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* `*` is not the same as keeping structure as is, but runs the reduction procedure with all the chains, useful for debugging
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* `-out_format` optional, default value is `keep` -- use the same format as the input
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* possible values: `keep|pdb|pdb.gz|cif|cif.gz`
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* `-out_file` optional, output structure file name, path relative to the shell working directory
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* if specified, reduced structure is saved under given name and no other output is produced
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* 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`
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Examples:
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~~~sh
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./prank.sh transform reduce-to-chains -f distro/test_data/2W83.cif -chains A # output: <out_dir>/2W83_A.cif
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./prank.sh transform reduce-to-chains -f distro/test_data/2W83.pdb -chains A # output: <out_dir>/2W83_A.pdb
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./prank.sh transform reduce-to-chains -f distro/test_data/2W83.cif.gz -chains A,B # output: <out_dir>/2W83_A,B.cif.gz
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./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
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./prank.sh transform reduce-to-chains -f distro/test_data/2W83.cif -chains keep # output: <out_dir>/2W83.cif
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./prank.sh transform reduce-to-chains -f distro/test_data/2W83.cif -chains keep -out_format pdb.gz # output: <out_dir>/2W83.pdb.gz
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./prank.sh transform reduce-to-chains -f distro/test_data/2W83.cif -chains all # output: <out_dir>/2W83_all.cif
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./prank.sh transform reduce-to-chains -f distro/test_data/2W83.cif -chains A -out_format keep # output: <out_dir>/2W83_A.cif
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./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
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./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
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~~~
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## Print
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### Print a list of features
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Check which features are enabled for a particular configuration.
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~~~sh
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./prank print features # for default config
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./prank print features -c other_config.groovy # for custom config
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~~~
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### Print model info
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Print information about trained model (`*.model` file).
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~~~
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./prank print model-info # for default model
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./prank print model-info -m model2.model # for custom model
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~~~
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