Updated Ligand Motifs Code (#59)
The code I am contributing here are updates to improve the functionality of the ligand motif code. This includes improvements to the following protocols:
motifs/LigandDiscoverySearch - Created a method for scoring placed ligands based on how much of a user-defined binding pocket is filled, improved use of score functions, collection and analysis of motifs collected off of placed ligands to confirm contacts against residues of interest
motifs/IdentifyLigandMotifs - Moved usage of process_for_motifs from private to public so that the function to collect motifs can be used on poses in runtime (and not exclusively from imported files). The process_for_motifs function is now used in LigandDiscoverySearch.
Added new options in options_rosetta.py under motifs for use in LigandDiscoverySearch.
Added public app remove_duplicate_motifs.cc, which removed motifs that are considered duplicates based on similar distance and angle of atoms involved. This helps improve runtimes of protocols that use lists of motifs by not considering the use of motifs that are effectively very similar/same. I have added an integration test as well.
Testing the TaskSelector
Author: Tom Linsky (tlinsky at uw dot edu)
LogFile log
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core.init.score_function_corrections: [ WARNING ] Flag -restore_talaris_behavior is set but -weights are also specified. Not changing input weights file!
core.init: Rosetta extras: []
core.init: command: ROSETTA/source/bin/rosetta_scripts.default.linuxgccaddsan -in:path:database_cache_dir ROSETTA/.database-binaries/ubuntugccaddsan @flags -database ROSETTA/database -testing:INTEGRATION_TEST
basic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111
basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937
protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter
protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs
protocols.jd2.PDBJobInputter: pushed inputs/trpcage.pdb nstruct index 1
protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ...
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from PDB inputs/trpcage.pdb
core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch LowerDNA as requested
core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch UpperDNA as requested
core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch VirtualDNAPhosphate as requested
core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch ShoveBB as requested
core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch VirtualBB as requested
core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch N_acetylated as requested
core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch C_methylamidated as requested
core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch SpecialRotamer as requested
core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch Cterm_amidation as requested
core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch pro_hydroxylated_case1 as requested
core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch pro_hydroxylated_case2 as requested
core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch ser_phosphorylated as requested
core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch thr_phosphorylated as requested
core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch tyr_phosphorylated as requested
core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch tyr_sulfated as requested
core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch lys_monomethylated as requested
core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch lys_dimethylated as requested
core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch lys_trimethylated as requested
core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch lys_acetylated as requested
core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch glu_carboxylated as requested
core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch cys_acetylated as requested
core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch tyr_diiodinated as requested
core.chemi