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81 lines
2.9 KiB
Plaintext
81 lines
2.9 KiB
Plaintext
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Requirements
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============================================================================================
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* Java 1.8 or newer for execution
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* PyMOL 1.7.x for viewing visualizations
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Example commands (can be executed here in the installation directory)
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============================================================================================
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#
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# Print help:
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#
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prank help
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#
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# Ligand binding site prediction (P2RANK algorithm):
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#
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prank predict test.ds # run on whole dataset (list of pdb files)
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prank predict -f test_data/liganated/1aaxa.pdb # run on individual pdb file
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prank predict test.ds -o output_here # explicitly specify output directory
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prank predict -threads 8 test.ds # specify no. of working threads for parallel processing
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prank predict -c predict2.groovy test.ds # specify configuration file (predict2.groovy uses different
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prediction model and combination of parameters)
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#
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# Evaluate model for pocket prediction:
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#
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prank eval-predict test.ds
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prank eval-predict -f test_data/liganated/1aaxa.pdb
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#
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# Prediction output notes:
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#
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# For each file in the dataset program produces a CSV file in the output directory named
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# <pdb_file_name>_predictions.csv, which contains an ordered list of predicted pockets, their scores, coordinates
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# of their centroids and list of PDBSerials of adjacent amino acids and solvent exposed atoms.
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#
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# If coordinates connolly points that belong to individual pockets are needed they can be found
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# in viualisations/data/<pdb_file_name>_points.pdb. There "Residue sequence number" (23-26) of HETATM record
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# cocrresponds to the rank of corresponding pocket (points with value 0 do not belong to any pocket).
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#
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#
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# Rescore pocket detected by other methods (PRANK algorithm):
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#
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prank rescore test_data/fpocket.ds
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prank rescore fpocket.ds # test_data/ is default 'dataset_base_dir'
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prank rescore fpocket.ds -o output_dir # test_output/ is default 'output_base_dir'
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#
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# Override default params with custom config file:
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#
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prank rescore -c config/example.groovy test_data/fpocket.ds
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prank rescore -c example.groovy fpocket.ds
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#
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# It is also possible to override default params on a command line with their full name:
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# (to see complete list of params look into config/default.groovy)
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#
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prank rescore -seed 151 -threads 8 test_data/fpocket.ds
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prank rescore -c example.groovy -seed 151 -threads 8 test_data/fpocket.ds
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#
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# Evaluate model for pocket rescoring:
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#
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prank eval-rescore fpocket-pairs.ds
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prank eval-rescore -m model/default.model fpocket-pairs.ds
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prank eval-rescore -m default.model fpocket-pairs.ds
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prank eval-rescore -m other.model fpocket-pairs.ds
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prank eval-rescore -m other.model fpocket-pairs.ds -o output_dir |