class pdb.PdbResidue extends ResidueBase

Available on all platforms

Container of a residue in pdb file. Non-amino acid molecules such as waters, co-factors, lipids are considered as residues.

Instance Fields

var atoms:Map<String, PdbAtom>

atoms in this residue, where the map key is the name of the atom.

var rama:RamaAngles

phi and psi angle information

var secondary:Int

secondary structure type. See SecondaryType.hx for the meaning of the values.

function new(n:String, i:Int, isnt:Bool, isct:Bool, sec:Int):Void

Constructor.

  • n: residue name
  • i: residue index
  • isnt: is this residue the N-terminal?
  • isct: is this residue the C-terminal?
  • sec: seondary structure type (see SecondaryType.hx)

function addAtom(a:PdbAtom):Void

add an atom to this residue

function clearAtoms():Void

remove all atoms from this residue

function genH(r:PdbResidue):Void

generate "H" atom, which binds to backbone "N" atom. the parameter c corresponds to the position of "C" atom in the previous residue. thus, "H" atom never be created for first residue

function genHatom(a:PdbAtom):Void

add H atom which binds to backbone N using C atom of adjacent residue given by a

function genHpos(c:Point3D):Void

generate H atom; generated atom is automatically registered in this instance

function genPoint():String

write position of alpha-carbon, "CA" in POINT element of WMXML xml.

function getAtom(a:String):PdbAtom

get atom of name a from this residue

function get_atoms():Map<String, PdbAtom>

getter of atoms

function get_rama():RamaAngles

getter of rama

function get_secondary():Int

gettter of secondary

function isAmino():Bool

returns whether this residue is amino acids or not

function set_secondary(s:Int):Int

settter of secondary