The Fortran90 source code associated with the paper by Li et al. [1] gives the following information about an amino acid glycine:
ConnectionTypes
================
atomConType =
{"CT1","CT2","CT3","C","CC","CPH1","CPH2","CPT","N",
"NH1","NH2","NH3","NC2","CY","NR2","NY","H","HA",
"HB","HC","HS","HR1","CA","HR3","HP","O","OC","OH1",
"S","CP1","CP2","CP3","NP"};
AcidInfo
================
name = "GLY";
heavyAtoms = 4;
totalAtoms = 7;
atomNames = {" N ", " CA ", " C ", " O ", " H ", "1HA ", "2HA "};
atomConnections = {10, 2, 4, 26, 17, 19, 19};
bdc = {{ 1, 4, 0, 0},
{ 4,-1, 1, 5},
{-1, 0, 1, 0},
{-1, 0, 0, 0},
{-4, 0, 0, 0},
{-4, 0, 0, 0},
{-5, 0, 0, 0},
{-3, 0, 0, 0}};
What do the values atomConType
, atomConnections
, and bdc
(bond distance count?) represent in the case of glycine?
Reference
- Li, Y.; Roy, A.; Zhang, Y. HAAD: A Quick Algorithm for Accurate Prediction of Hydrogen Atoms in Protein Structures. PLOS One 2009, 4 (8), e6701. DOI: 10.1371/journal.pone.0006701. (Open Access, PDF)