Merge pull request #5421 from RosettaCommons/JWLabonte/sugars/bidirectional_linkages
Carbohydrates: Enabling Bidirectional Glycosidic Linkages
This merge introduces "bidirectional glycosidic linkages" into Rosetta.
Most sugar linkages connect an oxygen _not_ attached to the anomeric carbon of one sugar to the anomeric carbon of the "child" sugar. Such linkages are designated with notation such as β-D-Glcp-(1→4)-β-D-Glcp, where C1 is the anomeric carbon and the child residue comes before the parent residue, (since it is considered a substituent to the main group, the parent. Yes, sugar sequences run "backwards" relative to protein ones.)
However, some disaccharides do not have a free hemiacetal group. That is, they are attached from the anomeric hydroxy group of the parent to the anomeric carbon of the child. The notation for such a linkage uses a bidirectional arrow, like in sucrose: α-D-Glcp-(1↔2)-β-D-Fruf.
(One could also write β-D-Fruf-(2↔1)-α-D-Glcp, and, in fact, this is the preferred IUPAC name, because of reasons of arbitrary "group priorities". (See: https://www.qmul.ac.uk/sbcs/iupac/2carb/36.html.) However, this naming is dumb, I declare, because it ignores the biochemical fact that it is the fructose's hydroxyl that is the nucleophile in natural biosyntheses of this disaccharide, and IUPAC allows this so-called "sequential method" for oligo- and polysaccharides: https://www.qmul.ac.uk/sbcs/iupac/2carb/37.html.)
Besides this naming ambiguity, which already mucks up the abyssal nomenclature of sugars in the PDB, there is an issue with main-chain length. "Normal" sugars in Rosetta were designed such that the main chain of a residue always starts at the anomeric carbon and proceeds to the linkage oxygen. However, if the linkage oxygen is off the anomeric carbon, this gives a too-short main chain for Rosetta to be able to handle, _e.g.,_ C2-O2-UPPER for the furanose residue above.
A further problem involves patching. The fructose residue of sucrose can only be a lower terminus; since its anomeric hydoxyl was the nucleophile used to form the linkage, it cannot also have been the leaving group to accept attack from a previous residue.
My solution is to make saccharide residues for such linkages `LOWER_TERMINUS` variants in their `.params` files and to build their main chains from one atom previous to their anomeric carbon. For ketoses, this is would be no big deal, but it is more challenging/annoying for aldoses, which have an anomeric carbon of C1. Thus, I use the virtual ring atom as the first atom for both cases, which requires some minor tweaking of rules for `Pose` creation.
Labonte 3 years I have fixed the broken PyRosetta4.notebook test, but the change needs to be approved and merged into master.
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Merge pull request #5466 from RosettaCommons/roccomoretti/include_fixes_IWYU
Remove unneeded headers with Include What You Use.
This doesn't use IWYU directly, due to differences in how it thinks things should be versus how Rosetta handles things, but instead uses a script to use the IWYU results to try removals/additions with test compilation. (With the general philosophy of removing as much as possible and being judicious about which additional headers are added.) -- This approach needs some manual fixes, particularly for extras/platforms where the test compilation isn't run.
These header removals speed up compilation on my machine by ~15%.
Note that I likely missed some of the rare platform/extra combinations, particularly ones which aren't tests on the test server. Hopefully fixing those won't be too much effort for the people who use them.
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Merge pull request #4831 from RosettaCommons/jonpliu-patch-4
Carbohydates: adding glycolylated amino sugars to the database
This merge will add glycolylated amino sugars to the database.
A glycolyl group is an acetyl group with a hydroxyl group on its alpha carbon.
Sialic acids in other creatures besides humans sometimes have glycolyl groups instead of acetyl groups on the neuraminic acids.
Appropriate nomenclature will be added in PR #4793.
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Merge pull request #4820 from RosettaCommons/JWLabonte/sugars/database2
Carbohydates: adding methylated sugars to the database
This merge will add O-methylated sugars into the Rosetta database.
(This merge integrates work started by former student @qjia73 and was expanded by @jonpliu .)
Appropriate nomenclature will be added in PR #4793.
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Merge pull request #4764 from RosettaCommons/jonathanpines-patch-1
Carbohydrates: adding propargyl sugars to the database
This merge will add patches and code for propargyl sugars to the database.
These are synthetic sugar analogs that can be used in "click" chemistry.
Appropriate nomenclature will be added in PR #4793.
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Merge pull request #4819 from RosettaCommons/JWLabonte/sugars/database
Carbohydrates: adding thiolated sugars to the database
This merge will add thiolated sugars into the Rosetta database.
(This merge integrates work started by former student @qjia73 and was expanded by @jonpliu .)
Thiol nomenclature will be added in PR #4793.
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Merge pull request #4976 from RosettaCommons/yingyue0414_update_mur
This PR adds O3_LACTYL_SUGAR to the VARIANT field of Muramic acid (Mur) in the database.
Patch O3_LACTYL_SUGAR was added in PR #4756
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