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branch: benchmark 「№646」
Commited by: Sergey Lyskov
GitHub commit link: 「adb7fd03faa1902e」
Difference from previous tested commit:  code diff
Commit date: 2023-12-18 13:55:20

updating self.info

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branch: benchmark 「№645」
Commited by: Sergey Lyskov
GitHub commit link: 「255a3e0178939dde」
Difference from previous tested commit:  code diff
Commit date: 2023-12-16 16:11:54
nil.none.root.self.info nil.none.self.info

updating self.info test

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branch: benchmark 「№644」
Commited by: Sergey Lyskov
GitHub commit link: 「dcdb11bf9fb6ba7e」
Difference from previous tested commit:  code diff
Commit date: 2023-12-16 15:27:47
nil.none.root.self.info nil.none.self.info

adding self.info test

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branch: benchmark 「№643」
Commited by: Sergey Lyskov
GitHub commit link: 「c295d8ba33fafdfe」
Difference from previous tested commit:  code diff
Commit date: 2023-12-08 11:20:05

Test server updating documentation submodule

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branch: benchmark 「№642」
Commited by: Sergey Lyskov
GitHub commit link: 「3782092cbcb3963a」
Difference from previous tested commit:  code diff
Commit date: 2023-08-24 20:14:59
linux.gcc.python310.self.python linux.gcc.python36.self.python linux.gcc.python37.self.python linux.gcc.python38.self.python linux.gcc.python39.self.python mac.clang.python310.self.python mac.clang.python38.self.python mac.clang.python39.self.python

fixing issue with release-as-git-repository

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branch: benchmark 「№641」
Commited by: Sergey Lyskov
GitHub commit link: 「8dfffbb0f374872b」
Difference from previous tested commit:  code diff
Commit date: 2023-08-24 20:02:44
linux.gcc.python310.self.python linux.gcc.python36.self.python linux.gcc.python37.self.python linux.gcc.python38.self.python linux.gcc.python39.self.python mac.clang.python310.self.python mac.clang.python38.self.python mac.clang.python39.self.python

fixing maintenance.documentation test

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branch: benchmark 「№640」
Commited by: Sergey Lyskov
GitHub commit link: 「47fe53543d8c01b1」
Difference from previous tested commit:  code diff
Commit date: 2023-08-24 17:17:55
linux.gcc.python310.self.python linux.gcc.python36.self.python linux.gcc.python37.self.python linux.gcc.python38.self.python linux.gcc.python39.self.python mac.clang.python310.self.python mac.clang.python38.self.python mac.clang.python39.self.python

fixing issue with release-as-git-repository for platforms with latest Git installed and when upstream repo is missing

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branch: benchmark 「№639」
Commited by: Sergey Lyskov
GitHub commit link: 「a6db45fc47889223」
Difference from previous tested commit:  code diff
Commit date: 2023-08-24 16:52:01
linux.gcc.python310.self.python linux.gcc.python36.self.python linux.gcc.python37.self.python linux.gcc.python38.self.python linux.gcc.python39.self.python mac.clang.python310.self.python mac.clang.python38.self.python mac.clang.python39.self.python

refactoring PyRosetta Conda release procedure so building package and re-indexing channel packages is now done in separate steps

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branch: benchmark 「№638」
Commited by: Guangfeng Zhou
GitHub commit link: 「5c52065b086fffa6」 「№6425」
Difference from previous tested commit:  code diff
Commit date: 2023-08-22 13:18:13
linux.gcc.python310.self.python linux.gcc.python36.self.python linux.gcc.python37.self.python linux.gcc.python38.self.python linux.gcc.python39.self.python mac.clang.python310.self.python mac.clang.python38.self.python mac.clang.python39.self.python

Merge pull request #6425 from RosettaCommons/guangfeng/galiganddock_vsx_update Added options to report the number of hydrogen bonds between the ligand and selected residues.

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branch: benchmark 「№637」
Commited by: Rocco Moretti
GitHub commit link: 「be92069389921d63」 「№6352」
Difference from previous tested commit:  code diff
Commit date: 2023-06-12 14:30:06
linux.gcc.python310.self.python linux.gcc.python36.self.python linux.gcc.python37.self.python linux.gcc.python38.self.python linux.gcc.python39.self.python mac.clang.python310.self.python mac.clang.python38.self.python mac.clang.python39.self.python

Merge pull request #6352 from RosettaCommons/roccomoretti/quick_restyping Speed PDB loading by adding a Quick-and-Dirty ResidueTyping option. One of the major contributors to the speed of PDB loading is figuring out the ResidueTypes to use. PR #5659 fixes this somewhat, but it still contributes non-trivially. For most PDBs (e.g. simple all-protein ones), figuring out the ResidueTypes is straightforward. As such, I've implemented an alternative ResidueTyping scheme which can be enabled with the new command line option -fast_restyping (and the corresponding option on StructFileReaderOptions. The way it works is to assume that the three letter code in the PDB is equivalent to the full type name. This should work for the canonical amino acids and -extra_res_fa ligands. To support more inputs, there's some epicycles added. The primary one is a fix-up for terminus patching. There's also some special casing for HIS/HIS_D calling, as well as D-aa/DNA/RNA/VRT. We also use the HETNAM specification if that's helpful, as well as falling back to the chemical components dictionaries for most everything else. -- The HETNAM records go part of the way towards round-tripping (that is, being able to read any Rosetta-outputted PDB properly with the flag on), but are insufficient. Adding full ResidueType name annotations in the output would be necessary for full support, and that's a potential future direction if this flag seems useful for people. This approach is far from complete. In particular, most patching which happens due to the presence of atom names is missed (deliberately so). This is particularly an issue with carbohydrate-containing residues. The option is definitely not recommended for general use, though if you have "simple" PDBs (non-modified proteins, mostly), it should hopefully work for you. Caveat emptor, though. In my test set, the time needed for ResidueType loading (which takes ~33% of the total runtime with current master) is reduced by a factor of 10, and most of the remaining portion of that is actually CCD residue type loading or ResidueTypeFinder time.

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branch: benchmark 「№636」
Commited by: Sergey Lyskov
GitHub commit link: 「ee829eef22125b89」
Difference from previous tested commit:  code diff
Commit date: 2023-04-05 22:12:21
linux.gcc.python310.self.python linux.gcc.python36.self.python linux.gcc.python37.self.python linux.gcc.python38.self.python linux.gcc.python39.self.python mac.clang.python310.self.python mac.clang.python38.self.python mac.clang.python39.self.python

fixing PyRosetta documentation build

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branch: benchmark 「№635」
Commited by: Sergey Lyskov
GitHub commit link: 「93c73929f0db45c7」
Difference from previous tested commit:  code diff
Commit date: 2023-04-03 16:42:17
linux.gcc.python310.self.python linux.gcc.python36.self.python linux.gcc.python37.self.python linux.gcc.python38.self.python linux.gcc.python39.self.python mac.clang.python310.self.python mac.clang.python38.self.python mac.clang.python39.self.python

setting NumPy version for Python-3.11

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branch: benchmark 「№634」
Commited by: Sergey Lyskov
GitHub commit link: 「214130e2175d69ae」
Difference from previous tested commit:  code diff
Commit date: 2023-03-31 17:41:19
linux.gcc.python310.self.python linux.gcc.python36.self.python linux.gcc.python37.self.python linux.gcc.python38.self.python linux.gcc.python39.self.python mac.clang.python310.self.python mac.clang.python38.self.python mac.clang.python39.self.python

updating Binder and pybind11

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branch: benchmark 「№633」
Commited by: Sergey Lyskov
GitHub commit link: 「9800e94ce3aceffa」
Difference from previous tested commit:  code diff
Commit date: 2023-03-30 17:43:04
linux.gcc.python310.self.python linux.gcc.python36.self.python linux.gcc.python37.self.python linux.gcc.python38.self.python linux.gcc.python39.self.python mac.clang.python310.self.python mac.clang.python38.self.python mac.clang.python39.self.python

updating pybind11 version

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branch: benchmark 「№632」
Commited by: Sergey Lyskov
GitHub commit link: 「f48622d3d901e4c4」
Difference from previous tested commit:  code diff
Commit date: 2023-03-30 14:26:21
linux.gcc.python310.self.python linux.gcc.python36.self.python linux.gcc.python37.self.python linux.gcc.python38.self.python linux.gcc.python39.self.python mac.clang.python310.self.python mac.clang.python38.self.python mac.clang.python39.self.python

Merge remote-tracking branch 'origin/master' into benchmark

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branch: benchmark 「№631」
Commited by: Sergey Lyskov
GitHub commit link: 「69b511ed70063deb」
Difference from previous tested commit:  code diff
Commit date: 2023-03-24 14:04:13
build.release linux.gcc.python310.self.python linux.gcc.python36.self.python linux.gcc.python37.self.python linux.gcc.python38.self.python linux.gcc.python39.self.python mac.clang.python310.self.python mac.clang.python38.self.python mac.clang.python39.self.python unit

Merge remote-tracking branch 'origin/benchmark' into benchmark

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