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Revisions №58008

branch: master 「№58008」
Commited by: Vikram K. Mulligan
GitHub commit link: 「af389d856434f627」 「№654」
Difference from previous tested commit:  code diff
Commit date: 2015-07-24 01:34:14

Merge pull request #654 from RosettaCommons/vmullig/aa_composition_energy Add an energy term for penalizing deviations from a desired residue type composition This is a wholebody energy, which has the disadvantage of being ignored by the packer in its current implementation, but the advantage of permitting nonlinear penalties as the deviation from desired composition increases. Tasks: - Add AACompositionEnergy.cc - Add AACompositionEnergy.hh - Add AACompositionEnergy.fwd.hh - Add AACompositionEnergyCreator.hh - Register with init.cc, core.3.src.settings - Register scoretype in ScoreType.hh, ScoreTypeManager.cc. - Rename energy term from aa_composition_energy to aa_composition. - Write finalize_total_energy() function. - Write calculate_aa_composition_energy() function. - Permit penalties for deviation from desired composition by residue type. - Permit penalties for deviation from desired composition by residue properties (e.g. 40% hydrophobic, 10% aromatic). - Add PropertiesSet class to allow the above. - Create a helper class for storing data associated with this energy function. - Move the data access and data storage functions into this class. - Permit initialization (desired amino acid composition, penalty function) from a file. - Option for filename. - File read from database. - Parse properties setup, too. X Add default files to the database. --> Put off to a future pull request. Requires validation. (There are some sample files in the database now, mostly as user templates and for unit tests.) - Permit desired levels to be set by percentage (e.g. 7% valine) or by absolute number (e.g. I want exactly 1 tryptophan). - Unit test with initialization file that only penalizes a subset of properties, based on fraction (e.g. just AROMATIC). - Unit test with initialization file that only penalizes a subset of properties, based on absolute number of residues (e.g. just AROMATIC). - Unit test with initialization file that only penalizes a subset of residue types, based on absolute number of residues (e.g. just ALA and GLY). - Unit test with initialization file that only penalizes a subset of residue types, based on fraction (e.g. just ALA and GLY). - Unit test with noncanonicals. - Integration test for design. (This should currently do nothing during design, since it's a multibody energy. With Alex's changes, though, it should be very useful for controlling the packer's behaviour.) - Documentation

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