Merge pull request #5237 from RosettaCommons/roccomoretti/fix_boost_warnings
Fix Boost Deprecation Warnings
We're currently encountering a number of deprecation warnings from Boost. Infuriatingly, that's not because of anything we're doing in Rosetta, but instead it's due to Boost's own usage of Boost headers.
Since we initially updated to Boost 1.74 and ran into these issues, fixes for them have been posted to the upstream repos. This PR selectively updates the Boost submodules at issue to a version which has the fixes. (It's not a general update of Boost.)
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Merge pull request #5218 from RosettaCommons/vmullig/fix_glcyo_valgrind_issue
Fix an uninitialized variable issue in glycopeptide docking flagged by Valgrind
The options system read is done only if the user has specified the option, so a default value is needed for `interface_distance_` in the `GlycopeptideDockingFlags` class; otherwise this is uninitialized if the user doesn't provide a value with a commandline flag. I'm providing a default that matches the default in both the options system and in the `RestrictToInterface` task operation (which this variable is used to configure). Admittedly, better still would be having the default set in only one place.
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Merge pull request #4222 from RosettaCommons/jfell13/RosettaCM
RosettaCM scientific test: merging this to have it in master. Jason Fell needs to look at the cutoffs again. Seems like there are still discrepancies between the paper (Song 2013 Structure) and the data here, I am not sure where it's coming from.
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Merge pull request #5202 from RosettaCommons/vmullig/citation_script
Add a python script to automatically update the citations list in the database given a new PubMed ID
This adds a script to the `code_templates` directory called `add_citation_by_pubmed_id.py`. As the name suggests, it adds a new citation to `database/citations/rosetta_citations.txt` from an input PubMed ID. Example usage:
```
>~/rosetta_devcopy/Rosetta/main/source$ ./code_templates/add_citation_by_pubmed_id.py --pmid 31239046
Successfully imported pubmed-lookup package.
Successfully found article titled "Using Rosetta for RNA homology modeling.".
Adding PubMed ID 31239046 (DOI 10.1016/bs.mie.2019.05.026). to citations file.
Wrote sorted citations list to "../database/citations/rosetta_citations.txt". Please be sure to commit your changes with "git add ../database/citations/rosetta_citations.txt && git commit".
```
After running this, `git diff` gives you the following:
```
diff --git a/database/citations/rosetta_citations.txt b/database/citations/rosetta_citations.txt
index f8a24ebe767..855c5019c6f 100644
--- a/database/citations/rosetta_citations.txt
+++ b/database/citations/rosetta_citations.txt
@@ -504,6 +504,33 @@
[END_DOI]
[END_CITATION]
+[BEGIN_CITATION]
+ [BEGIN_PRIMARY_AUTHORS]
+ "" "Watkins" "AM"
+ [END_PRIMARY_AUTHORS]
+ [BEGIN_COAUTHORS]
+ "" "Rangan" "R"
+ [END_COAUTHORS]
+ [BEGIN_SENIOR_AUTHORS]
+ "" "Das" "R"
+ [END_SENIOR_AUTHORS]
+ [BEGIN_YEAR]
+ 2019
+ [END_YEAR]
+ [BEGIN_TITLE]
+ Using Rosetta for RNA homology modeling.
+ [END_TITLE]
+ [BEGIN_JOURNAL]
+ Methods Enzymol
+ [END_JOURNAL]
+ [BEGIN_VOLUME_ISSUE_PAGES]
+ 623:177-207
+ [END_VOLUME_ISSUE_PAGES]
+ [BEGIN_DOI]
+ 10.1016/bs.mie.2019.05.026
+ [END_DOI]
+[END_CITATION]
+
[BEGIN_CITATION]
[BEGIN_PRIMARY_AUTHORS]
"Vikram Khipple" "Mulligan" "VK"
@@ -539,3 +566,4 @@
10.1002/pro.3974
[END_DOI]
[END_CITATION]
```
It's not quite perfect since it doesn't fill in the first names, but it's close enough.
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