Merge pull request #1252 from RosettaCommons/jadolfbr/sugars/glycan_clash_check
Adding a pilot app specifically for glycan clashes which quantifies clashes between specified glycan branches and other chains and glycan branch - glycan branch clashes. Does not count clashes for intra glycan branch. Does not echo input files, adds info to output scorefile to allow for MPI runs.
Also adding description of Rosetta LJ in AtomType from a description by @aleaverfay in a dev list discussion some years ago (sigma1 vs sigma2) to help future travelers.
Clash Definition
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Atom is clashing if it clashes with ANY other atom
Count up clashes (hard and soft) per-residue
- Hard:
- distance <= LJ1 + LJ2
- Soft:
- distance <= (LJ1 + LJ2) * (1 - S). S is between 0 and 1. Here, we use .33 as default.
-> Intuitive definition, easily conceptualized, still quantitative
Relevant Options:
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-glycan_branches
- Required. Vector of glycan branches. Rosetta Residue numbering or PDB like RosettaScripts
-chech_chains
- Required. A list of chains to compute chain-based clashes. If not given, will only compute glycan-glycan clashes!
-ignore_hydrogens
- Should we calculate only heavy-heavy atom clashes?
-soft_clash
- When we calculate atom-atom distances using LJ distances, clash if distance < (atomI_LJ + atomJ_LJ)*(1 - soft_clash)