Merge pull request #5136 from aleaverfay/fix_switch_chain_order_pdb_info_bug
Add nullptr check for pdb_info to SwitchChainOrderMover
SwitchChainOrderMover needs to check that the input pose's PDBInfo object is not null before trying to copy data out of it.
Thanks @rpark01
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Merge pull request #4987 from RosettaCommons/jadolfbr/custom_type_as_name
This PR is orthogonal to @roccomoretti 's awesome additions in PR #4986.
It adds two options to control the final naming of the metrics when used with RunSimpleMetrics.
-simple_metrics:use_name_as_custom_type
This option simply uses the tag name as the custom_type. If custom_type is given, it will override this option.
-simple_metrics:use_name_as_metric
This option uses the tag name as the core name. It ignores custom_type. Prefix/Suffix from RunSM is still added.
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Merge pull request #5164 from RosettaCommons/AmeyaHarmalkar/backrub_movemap
Allows Backrub to define pivot residues based on movemap and movemap_factory (#5163)
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Merge pull request #5176 from RosettaCommons/vmullig/fix_hyp_cutpoints
Fix a typo in the cutpoint patch affecting HYP and DHYP residue types. Virtual atom OVU1 was at some point mistranscribed as "OVR1", and this got copied a few times. This is a minor fix.
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Merge pull request #5155 from RosettaCommons/ninabozhanova/cro_reader
ChromophoreDataReader class and unit tests for the class.
The class reads information about correspondence between FP chromophore's and standard Rosetta residue's atom names from a provided text file.
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Merge pull request #5157 from RosettaCommons/vmullig/improve_d_aa_import
Improve import of D- and L-amino acids that cannot be distringuished by 3-letter code
D-amino acids that are mirror images of canonical L-amino acids have unique three-letter codes in Rosetta, and certain noncanonicals have also been given distinct three-letter codes. With only three letters to play with, though, it's not possible to ensure that omitting the third letter and prepending "D" would generate a unique three-letter code. (Even with the canonical amino acids, this would create name conflicts: "DAS" would be the code for both D-Asp and D-Asn, if we hadn't manually specified that the latter would be "DAN".) For this reason, Rosetta doesn't even try to assign unique three-letter codes when it auto-generates D-amino acid versions of canonical L-amino acids; it just keeps the same three-letter code for both. This creates problems on read-in.
This pull request ensures that if a structure is read in containing an alpha-, beta-, or gamma-amino acid for which the L- and D-amino acid three-letter codes are the same, the chirality is auto-determined by calling Andy's detect_ld_chirality_from_polymer_residue() function.
@everyday847 @dougrenfrew @JackMaguire
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Merge pull request #5156 from RosettaCommons/vmullig/fix_gcc_10_compilation
Fix gcc 10 build.
The gcc 10 compiler complains about a few minor things that the gcc 9 compiler is happy with. This PR aims to fix those.
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Merge pull request #5066 from RosettaCommons/TENeary/sequence_symmetry_update
SequenceSymmetricAnnealer update to allow use of any generic ResidueSelectors
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