class pdb.PdbModel

Available on all platforms

Container for a MODEL in pdb file. If there are no MODELs in pdb file, at least one MODEL exists and is used in this program.

Instance Fields

var chains:Map<String, PdbChain>

chains which belong to this MODEL

var index:Int

index of this MODEL

function new(i:Int):Void

Constructor. You can set MODEL number by i.

function addAtom(cid:String, resname:String, resid:Int, atom:PdbAtom):Void

add an PdbAtom atom to this MODEL.

  • cid: chain id
  • resname: residue name
  • resid: residue index
  • atom: a PdbAtom

function gatherHeteroes():Array<PdbAtom>

gather hetero atoms from all chains

function genSecondaryString():String

returns secondary structure information as a string. See the same name function in Pdb.hx for details.

function genXml():String

generate WMXML style xml data of this MODEL and return it as a string.

function genXmlHeteroes():String

return only NON-CHAIN, hetero atom part of XML data as a string.

function genXmlNotChains(atoms:Array<PdbAtom>):String

generate non-CHAIN xml data; ATOMs and BONDs

function generateXmlAtomsBonds(minx:Int, miny:Int, minz:Int, maxx:Int, maxy:Int, maxz:Int, atoms:Array<PdbAtom>, indexes:Array<Array<Array<Array<Int>>>>):String

generate ATOMs and BONDs for heteroes.

function get_chains():Map<String, PdbChain>

getter of chains

function get_index():Int

getter of index

function initializeSecondary():Void

initialize secondary structure type. COIL for amino acids and NONE for others.

function set_index(i:Int):Int

setter of index