I'd suggest renaming CSharpDecompiler.DecompileWholeModuleAsSingleFile() to DecompileWholeModuleAsSingleSyntaxTree() as in my understanding it's not really doing anything with a single file. The documentation on the method reinforces this: "Decompiles the whole module into a single syntax tree.".

Am I missing something?

When inside the internal shell the cursor-up key just selects the lines in history with no (apparent) useful function.

It would be nice if it could instead access the history (as does ctrl-p/n).

A good example is ConfuserEx's anti tamper.
Just loading and saving the file with dnlib will remove the extra section injected by ConfuserEx and the assembly cannot be run or deobfuscated any further.

In the README it says that you can just put the relevant pdb.py file in a directory mentioned in the pythonpath in order to install pdbpp. This doesn't work because then fancycompleter isn't installed and you get an import error.

As the title says.

I took some notes, went to go save as, it only saved a portion of my notes.
Provided some screen shots of what I mean below.

This was using ReClassE

What's the intended meaning of PDBHeader.getDescription? It is populated in mmCIF with the _struct_keywords.pdbx_keywords field, the same as getClassification() (e.g. lyase, oxidase, etc). It seems to be unused in PDB files. It's also modified in a couple places for partial structures, e.g. "subset of 1ABC".

It looks like the documentation for mdtraj.rmsf() at http://mdtraj.org/1.9.3/api/generated/mdtraj.rmsf.html describes the mdtraj.rmsd() method instead.

I just tested both methods. It looks like rmsd() computes the RMSD of each frame over all selected atoms, with respect to a reference. This is what the docs say.

On the other hand, it looks like rmsf() computes the RMSF of each selected atom

I just started using biopandas and it seems nice. Toward promoting discussion related to its design, I have a general question regarding the column names, particularly for df['ATOM']. Note that I work with simulations of molecular structures so I care most about the df['ATOM'] field.

Coming from using VMD for several years, I noticed many differences to access the PDB fields. I have not

Currently, learning about the features of bioSyntax and what they translate to involves looking through the manual on our site. If we could package this together with the installation, I think users would be a lot more willing to learn it, especially if we could create custom help text within the editor. e.g. with vim we could possibly [incorporate the manual into the

This issue is a roadmap for Molly.jl development. Feel free to discuss things here or submit a PR. Bear in mind that significant refactoring will probably occur as the package develops.

Low hanging fruit

Want to get involved? These issues might be the place to start:

• Speedups to the code. Both on the level of individual functions and the overall algorithm. [Getting there]
• Look over