CPP back to basics: Designing classes Notes
Classes should be designed for change and extension. concise and focused on one prupose (SRP) developed iwth extensibility in mind (open-closed, OCP) split into smaller pieces to favor reuse (DRY), so...
View ArticleAdventures in Django to understand the pdbPreprocessor.
ipAddress//pdb/beta enter 1BUY It looks like you won’t need to change anything in the webpage, just make sure that the returned json from gems matches what it expected in the old one. Follow...
View ArticleBudget expense report grants funding
Project Status Report (PSR) Lite. Like a bank statement. Burn down rates and things we are attempting to do ourselves all seem to be available via their tools. I will need Robs login credentials to...
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GMML Design Issues
Here is the central data structure design with Node<T> shown: The big issue I’m facing is with Node<T> and Edge<T>. Note that the Edge class doesn’t know what Node is: Edge: private:...
View ArticleGlyspec grafting webtool inputs
Run information: Job ID -> b72ba407-eea9-4bfd-91c3-954766962caf Complex -> 2IHO.pdb Library -> v51 Email -> None provided ___________________________________________________________...
View ArticleERManI superimposition scripts
To create the separate snapshot folders, here is the script and cpptraj file. Keeping them all separate makes it easier. You need to edit the folder list and then run the...
View ArticleGmml design issue
When calling the copy ctor of PrepResidue you ran into trouble. Specifically because you have to call the base class: PrepResidue::PrepResidue(const PrepResidue& other) : cds::Residue(other) The...
View ArticleBetter Glycam Residue naming
Limitation of current nomenclature to express linkages e.g. 1,3 and residue e.g. DGlcpa. PDB file is limited to 3 spaces so 0-9 Aa – Zz is 62. 62C2 is 1891 permutations. 62 Choose 3 is 37820...
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Grant writing for research scientists lecture notes
Where to find grants: PIVOT: looking for grants to apply to. UGA has a subscription, you can have weekly alerts for what grants have certain keywords. Grants.gov Uga foundation relations e.g. bill...
View ArticleFigure out types from const ref pointer in C++
Graph(Node<T>* const& initialNode_t); initialNode_t is a reference to a const ptr of type Node<T>. https://c-faq.com/decl/spiral.anderson.html and https://cdecl.plus/ will help, but...
View ArticleDirectory structure for modeling projects on linux
Syncing Machines with rsync: Your folder structure on each machine (local, computing servers, backups etc) needs to be identical and synced using rsync. I have an exception in that I have a work folder...
View ArticlegRPC usage in gems and our webstack
Oliver is trying to understand our stack. When I read up on gRPC I get the idea of a “remote procedure call”; your program can run processes on remote machines (or the same machine) and those...
View ArticleCentral Data Structure Design GMML
Simplifying/Removing the inheritance structure. For now I’m not discussing: class Atom : public glygraph::Node<Atom> But rather, classes that inherit from cds::Atom. class PrepAtom : public...
View ArticleGlycosylation Enzymes: GnT-V
GnT-V transfers an N-acetylglucosamine (GlcNAc) residue from high-energy donor UDP-GlcNAc to the α1-6-linked mannose of N-glycans via a β1-6 linkage...
View ArticleGRASP mediated unconventional trafficking of Cystic fibrosis protein CFTR.
https://www.cell.com/cell/fulltext/S0092-8674(11)00819-1
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Bacterial extracytoplasm and SiaP
https://www.rcsb.org/structure/3b50 Characterization of the N-acetyl-5-neuraminic acid-binding site of the extracytoplasmic solute receptor (SiaP) of nontypeable Haemophilus influenzae strain 2019...
View ArticleGMML to GMML2 phases
Creating GMML2 from GMML1 rationale and approach. GMML1 was essentially two designs living together. The new and old “Central Data Structure” design. What became GMML2 was created in the...
View Articlevdw parameter modifcation glycam aggregation
So there is a known issue with vdW interactions: van der Waals Parameter Scanning with Amber Nucleic Acid Force Fields: Revisiting Means to Better Capture the RNA/DNA Structure through MD...
View ArticleCluster Slurm Jobs Submission scontrol hold release sinfo
Submitting to specific nodes: sbatch –exclude node[001-008] submit.GPU.thor.sh sbatch –nodelist node010 submit.GPU.thor.sh Holding jobs in the queue: This allows you to have jobs in the queue that...
View ArticleDev env series of issues
Issue 1: webdev@o-gw-grpc-delegator:/programs/gems/gmml$ git push The authenticity of host ‘github.com (140.82.121.3)’ can’t be established. ECDSA key fingerprint is...
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