Updated Ligand Motifs Code #59
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toadlover
added
90 standard tests
ready_for_review
…score function in high res dock need to beautify and add option for motifs::highresdock_with_whole_score_fxn
…that I do not remember why I had them,removed commented code for better presentation
…hen adjust score terms
…ange ddg scores otherwise)
…tps://github.com/RosettaCommons/rosetta into updated_ligand_discovery_search_code_ag_may_2024
…to allow customization of rounding error tolerance when calculating sin and cos
…for users to define tolerance Users can now use option run:sin_cos_range_tolerance to use tolerance values that are different from 0.001. Additionally, sin_cos_range can now allow any value pass with the use of run:keep_beyond_sin_cos_range being set to true.
…tps://github.com/RosettaCommons/rosetta into updated_ligand_discovery_search_code_ag_may_2024 yes
…https://github.com/RosettaCommons/rosetta into updated_ligand_discovery_search_code_ag_may_2024 yes
Reasoning is that library levels requirement makes it impossible for numeric code to call for basic (which is where options is).
…is() Increased tolerance to better account for rounding errors
…tps://github.com/RosettaCommons/rosetta into updated_ligand_discovery_search_code_ag_may_2024
…tps://github.com/RosettaCommons/rosetta into updated_ligand_discovery_search_code_ag_may_2024
…de of the native range A warning is thrown that the value is out of range, and the value is then set to the corresponding range bound, just like is done if using BOINC.
…tps://github.com/RosettaCommons/rosetta into updated_ligand_discovery_search_code_ag_may_2024
…breaks the function in benchmark tests for pyrosetta (works in other builds) I adjusted sin_cos_range anyway to always return -1 or 1 if the value is outside the range with tolerance
ll erge branch 'updated_ligand_discovery_search_code_ag_may_2024' of https://github.com/RosettaCommons/rosetta into updated_ligand_discovery_search_code_ag_may_2024
to be empty after running process_for_motifs
issue on why we are no longer recognizing any motifs
there are issues with passing motif_library_ all the way through. Instead, the motifs identified are added to motif_library instead for later potential use
real_match_found as false
not passing down right
…e enter the commit message for your changes. Lines starting
adding comment to working pose in LDS if a matrix is made of the placement so that the corresponding matrix can be found.
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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.