The energy terms in InterfaceAnalyzer

[Anonymous]

Dear All,

There are many energy terms in the output of the InterfaceAnalyzer, but is there any articles or other forms of materials  which explain the basic principals or mathematical formats for calculating these energy terms in detail? And How rosetta codes for them? If I wished to add some energy terms in InterfaceAnalyzer, What is an effective way to learn the coding for this propose? 

I will appreciate any help. With many thanks.

 

[Anonymous]

> There are many energy terms in the output of the InterfaceAnalyzer

There are two similar concepts here,

• one is a command line application (main/source/bin/InterfaceAnalyzer.static.distro) described in https://www.rosettacommons.org/docs/latest/application_documentation/analysis/interface-analyzer
• and the other is a mover (InterfaceAnalyzerMover), described in https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/Movers/movers_pages/analysis/InterfaceAnalyzerMover

 

The latter is used in a XML script (or in PyRosetta) and can be customised… The former is more restricted but has a very long documentation.

> How rosetta codes for them?

To find out how a mover works in Rosetta at the code level you can look at the source code which is provided with most distribution, but also the tests (tests/integration) that use it.

The former should be in a folder in `main/source/src` (not bin). The find function in Mac Finder and Ubuntu Natilus look within C++ source files —no idea about the Windows one (or what it’s called), but maybe it does the same. C++ files can be split into header files (.hh), which define the functions/methods and contain top level (doxygen) comments, and source files (.cc) which define the function code proper. So the latter will tell you what happens, but the former may contain useful comments.

The online PyRosetta documentation may provide useful insigns into the mover as it’s easier to read than the source code.

> I wished to add some energy terms in InterfaceAnalyzer

The mover (i.e. InterfaceAnalyzerMover) in Rosetta scripts is the best option for customisation, but I do not believe it accepts additional mover etc. However, the simplest solution for a more out of the box analysis is to find the interface between the relevant chains, pull these apart and repack and do comparison with the split product. This is doable in PyRosetta and should be in scripts too… Which is a question that has definitely been asked here before

[Anonymous]

Hello Sun!

For the general details about the rosetta energy function and the terms composing it, I would suggest reading this publication:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5717763/#R5

As for coding new energy terms – 

This will require coding in C++ and extending the base energy term classes.

You can read more about it here:

https://new.rosettacommons.org/docs/latest/development_documentation/tutorials/new-energy-method

You can also see at the bottom of that page multiple resources for starting development on the Rosetta framework.

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