Merge pull request #2754 from RosettaCommons/jadolfbr/glycan_scanner3
Design Tools
A number of design tools are added in this PR, including some specifics for glycans.
New Resfile Commands
=================
First, we have 3 new resfile commands: `CHARGED`, `AROMATIC`, and `PROPERTY`.
The third is a general command that takes any ResidueProperty. Currently, it only works for Cannonicals, but perhaps that could be generalized int the future for NCs.
New General TaskOps/Movers
======================
- `ResfileCommandOperation` : This operation takes a residue selector and ANY resfile command operation line (without residue numbers) and applies it. It is incredibly powerful. For example, You can select all beginning of helices and design them as charged residues extremely easily. This works with NCs as well.
```
USAGE:
<ResfileCommandOperation name=(string) command=(string) residue_selector=(string)>
</ResfileCommandOperation>
```
- `SequenceMotifTaskOperation` : This is an operation that applies a given _design sequence motif_. This motif is kinda-sorta like regex syntax, but a bit different. It accepts a residue selector to design in this sequence motif starting at each position specified in the selector. Also takes resfile commands. The syntax for the operation is as follows:
```
<SequenceMotifTaskOperation name=(string) motif=(string) residue_selector=(string)>
</SequenceMotifTaskOperation>
EXAMPLE:
Glycosylation N-Linked glycosylation motif design: N[^P][ST]
motif (string): This is slightly similar to a regex, but not quite.
We are not matching a sequence,
we are designing in a motif regardless of the current sequence,
anywhere in a protein.
- Each letter corresponds to a position. Using [ ] indicates a more complicated expression
for that position.
- An X indicates it can be anything, and that we are designing here.
- An AA Letter, like V, indicates that that position will be designed to a V.
- A - charactor indicates that that position stays with whatever it is currently.
We essentially skip this position.
- An expression like: [^PAV] indicates that we will design anything except
Proline, Alanine, and Valine
- An expression like: [NTS] indicates that that position can be Asparigine,
Threonine, or Serine and
only of these will be enabled during the design.
- RESFILE commands are accepted as well.
These require a % charactor in from of the whole expression.
For example [%POLAR] would set that position to only polar design.
This is exactly the same as a resfile line, so you can even do NC like so:
[%EMPTY NC R2 NC T6 NC OP5]
```
- `CreateSequenceMotifMover` : Applies the operation, using the packer, packing neighbors by default. Has a few other options for common uses.
Glycans
======
- `CreateGlycanSequonMover` : This calls the SequenceMotifMover with pre-specified motifs, including using the enhanced motif that seems to result in higher glycosylation and less complex glycans ( references included in descriptions).
Other
========
New string_util functions
Updates to code templates
Integration tests for movers
Unit tests for operations, and each individual function including the string utility functions.