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Revisions №58716

branch: master 「№58716」
Commited by: Vikram K. Mulligan
GitHub commit link: 「2901de5732899211」 「№1359」
Difference from previous tested commit:  code diff
Commit date: 2016-06-01 15:11:54

Merge pull request #1359 from RosettaCommons/vmullig/design_cycpep_app_2 Add design capability to the simple_cycpep_predict application This allows the simple_cycpep_predict application to design every conformation that it samples. Tasks: - Add option for design. - Add option to read in file allowing specification of allowed residues by position. - Add options for prohibiting D-amino acids in negative-phi region of Ramachandran space, and prohibiting L-amino acids in positive-phi region. - Have the above options actually set up the SimpleCycpepPredictApplication's settings. - Read per-residue options from a file. - Unit test for this. - Override file read by slave processes in MPI mode. - Have the above options actually DO something -- i.e. add design to the SimpleCycpepPredictApplication::genkic_close() function. - Set up design TaskOperations. - Unit test. - Debug problems revealed by unit test. - Eliminate/refactor anything in SimpleCycpepPredictApplication that would cause repeated reads from disk. - Check that this also results in no disk reads in beta_nov15 mode. - Double-check this at the end. - Integration test. - MPI-mode integration test. - Documentation. - Beauty. - Test on Jojo. - Test on Cetus (Blue Gene/Q test nodes). - Performance benchmarks on Mira (Blue Gene/Q production nodes). - Fix broken unit tests. Also: X Add option to exclude i - i+1 hydrogen bonds from hydrogen bond count. --> Separate pull request. - Add option to stop sending jobs after a certain amount of execution time has elapsed (and just collect whatever has completed). - Add timer, to facilitate benchmarking. - Add support for external constraints file. (Would need to handle circular permutations, though). --> Separate pull request. - Add support for separate .comp files for L-alpha, L-beta, D-alpha, and D-beta regions of Ramachandran space. - Add the options. - Have these files be read in. - Add them to the parsed protocol for design (with a SequenceConstraint and a suitable ResidueSelector). - In MPI mode, have the master process read these data from disk and transmit them to the slaves, to avoid repeated read-ins. (This means setting comp_file_contents_L_alpha_, comp_file_contents_D_alpha_, comp_file_contents_L_beta_, comp_file_contents_D_beta_, and abba_bins_). - Have global aa_composition setup files cache their data, rather than being re-read from disk whenever the score type is instantiated. - Test this.

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