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VariantType.cc File Reference

VariantTypes are used by Patches. More...

#include <core/chemical/VariantType.hh>

Namespaces

 core
 A class for defining atom parameters, known as atom_types.
 
 core::chemical
 

Constant Groups

 core
 A class for defining atom parameters, known as atom_types.
 
 core::chemical
 

Functions

VariantType const core::chemical::UPPER_TERMINUS ("UPPER_TERMINUS")
 C-terminus cap. More...
 
VariantType const core::chemical::LOWER_TERMINUS ("LOWER_TERMINUS")
 N-terminus cap. More...
 
VariantType const core::chemical::CUTPOINT_LOWER ("CUTPOINT_LOWER")
 for use during loop modeling, at positions before a cutpoint More...
 
VariantType const core::chemical::CUTPOINT_UPPER ("CUTPOINT_UPPER")
 for use during loop modeling, at positions after a cutpoint More...
 
VariantType const core::chemical::DISULFIDE ("DISULFIDE")
 
VariantType const core::chemical::BRANCH_POINT ("BRANCH_POINT")
 Variant type used for branched polymers and glycosylations. More...
 
VariantType const core::chemical::BRANCH_LOWER_TERMINUS ("BRANCH_LOWER_TERMINUS")
 Variant type used for branched polymers and glycosylations. More...
 
VariantType const core::chemical::ADDUCT ("ADDUCT")
 
VariantType const core::chemical::METHYLATION ("METHYLATION")
 
VariantType const core::chemical::CENTROID_HA ("CENTROID_WITH_HA")
 
VariantType const core::chemical::PROTONATED ("PROTONATED")
 
VariantType const core::chemical::DEPROTONATED ("DEPROTONATED")
 
VariantType const core::chemical::SPECIAL_ROT ("SPECIAL_ROT")
 Generic variant type that allows for differential scoring of a set of residues/rotamers. More...
 
VariantType const core::chemical::VIRTUAL_PHOSPHATE ("VIRTUAL_PHOSPHATE")
 
VariantType const core::chemical::VIRTUAL_RNA_RESIDUE ("VIRTUAL_RNA_RESIDUE")
 
VariantType const core::chemical::VIRTUAL_O2STAR_HYDROGEN ("VIRTUAL_O2STAR_HYDROGEN")
 
VariantType const core::chemical::PHOSPHORYLATION ("PHOSPHORYLATION")
 
VariantType const core::chemical::ACETYLATION ("ACETYLATION")
 
VariantType const core::chemical::SULFATION ("SULFATION")
 
VariantType const core::chemical::CARBOXYLATION ("CARBOXYLATION")
 
VariantType const core::chemical::HYDROXYLATION ("HYDROXYLATION")
 
VariantType const core::chemical::DIMETHYLATION ("DIMETHYLATION")
 
VariantType const core::chemical::TRIMETHYLATION ("TRIMETHYLATION")
 
VariantType const core::chemical::DIIODINATION ("DIIODINATION")
 
VariantType const core::chemical::ACETYLATED_NTERMINUS ("ACETYLATED_NTERMINUS")
 Acetylated N-terminus cap, written for creating amino acid dipeptides for NCAA rotamer libraries. More...
 
VariantType const core::chemical::METHYLATED_CTERMINUS ("METHYLATED_CTERMINUS")
 Methylated C-terminus cap, written for creating amino acid dipeptides for NCAA rotamer libraries. More...
 
VariantType const core::chemical::SC_ORBITALS ("SC_ORBITALS")
 
VariantType const core::chemical::N_ACETYLATION ("N_ACETYLATION")
 Cap extensions at termini to include peptide bonds, written for stepwise assembly (SWA) code. More...
 
VariantType const core::chemical::C_METHYLAMIDATION ("C_METHYLAMIDATION")
 
VariantType const core::chemical::REPLONLY ("REPLONLY")
 @ brief only the repulsive energy will be considered during structure calculations More...
 
VariantType const core::chemical::OOP_PRE ("OOP_PRE")
 @ brief oop_pre patch, used for oligooxopiperazines (OOPs) More...
 
VariantType const core::chemical::OOP_POST ("OOP_POST")
 @ brief oop_post patch, used for oligooxopiperazines (OOPs) More...
 
VariantType const core::chemical::HBS_PRE ("HBS_PRE")
 @ brief hbs_pre patch, used for hydrogen bond surrogates More...
 
VariantType const core::chemical::HBS_POST ("HBS_POST")
 @ brief hbs_post patch, used for hydrogen bond surrogates More...
 
VariantType const core::chemical::SIDECHAIN_CONJUGATION ("SIDECHAIN_CONJUGATION")
 This is used for chemically conjugable residues (LYX, CYX) used for sidechain conjugation (like ubiquitination) More...
 

Detailed Description

VariantTypes are used by Patches.

VariantTypes are utilized by Patches. All the type does is add a name that can be used later on in different protocols. It also helps the patch system keep track of what residues are patched with what type. The type has no magical meaning. It is a name handler.

Author
Phil Bradley Steven Combs - comments only
Last Modified: October 22 2010
Author
Phil Bradley