Update sdf parser machinery This commit updates and modernizes the sdfparser facility in Rosetta. The previous sdf parser items were created by Sam Deluca in his early days in Rosetta, and never made it to usable status. At the recommendation of Sam, that attempt was gutted and replaced with a version which takes advantage of the current state of ResidueType. (The primary goal of this commit is actually to support within Rosetta all the ResidueType creation machinery which had previously been encapsulated only in molfile_to_params.py, a necessary step for the drug design efforts.) The SDF parser machinery is not quite ready for general use. Items still missing before it becomes usable: * Support for loading rotamers. * Ability to automatically match input PDB atom names with their SDF equivalents (Standard SDF does not have a concept of atom names.) On the wish list: * Input of *.mol2 files. * Support for NCAA generation. Additional unit tests added. Integration test changes observed: FAIL sdf_reader -- new integration test FAIL fold_and_dock nonempty diff ref/fold_and_dock/log new/fold_and_dock/log -- Cosmetic changes to tracer FAIL hts_io nonempty diff ref/hts_io/output_ligands/test.sdf.gz new/hts_io/output_ligands/test.sdf.gz -- Extra data added to output sdfs (Rosetta Name, Rosetta nbr_radius, etc. ) FAIL ligand_database_io nonempty diff ref/ligand_database_io/ligand_parameters.db3.dump new/ligand_database_io/ligand_parameters.db3.dump -- changes in (now) non-critical column Given that this commit touches ResidueType.hh extensively, the standard complement of sensitive integration test numerical noise is expected.

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update CrystalContactsOperation to calculate contact distance by nearest atom to nearest atom, nearest atom to CBeta (nbr_radius), or CBeta to CBeta. default is nearest atom to CBeta for symm unit to asymm unit so we can consider symm unit static while asymm unit samples rotamers during packing/rtmin. also set new default polar/apolar distances

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A few bugfixes for density code. Fixing failed assertion for annotated sequence with multichain input.

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Fix War of the WaRnINGs casualty Unused return value, but function modifies arguments. Integration test changes in make_rot_lib expected.

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merging RosettaTMH into master

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Fix recently introduced bug in ResidueCountFilter. Support for task_factory was added, but improperly initialized such that the task factory was always used, even if it wasn't specified. Also fixed a bug in ResidueCountFilter where disulfide cysteines ("CYD") would be counted twice because name3() is "CYS" and name() is "CYD"

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bugfix for crystal design

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make default constructor of Batch private, as this would yield an instance with badly initialized variables

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add missing initializer to 2nd constructor of jd2::archive::Batch

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Adding unit tests for utility::file FileName and PathName. Unit tests from Meiler Lab Powercoding. Team Amanda Duran and Alyssa Lokits.

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Unit tests for ContactMap Meiler Lab power coding with Joerg Schaarschmidt. New unit tests for ContactMap

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Corrected conformer substitution in UltraLightResidue, made sure new conformer is placed in same space as old conformer. Integration test differences expected in ligand_dock_grid

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Fixing Tacc.Stampede build

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another pilot app update

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Added a bond length creator for small molecules. Bond length sizes were determined from an averaging of the CSD. Works with gasteiger atom types. Added unit test.

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Switching Benchmark PyRosetta builds to monolith mode. Removing some undefined functions.

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