class pdb.Pdb
Available on all platforms
data container for pdb file
- data hierarchy
Pdb - PdbModel - PdbChain(use chain id) - PdbResidue - PdbAtom
- PdbModel : MODELs which are often used for NMR structure
- PdbChain : A chain
- PdbResidue : A residue
- PdbAtom : An atom
keywords to be interpretted are: TER, END, ENDMDL, HELIX, SHEET, ATOM, HETATM
Class Fields
Instance Fields
function new(pdbText:String):Void
Constructor. If pdb text is given, input and secondary structure assign
will be performed. See also readAtOnce
.
function addAtom(mn:Int, cid:String, resname:String, resid:Int, atom:PdbAtom):Void
add an atom to this instance.
-mn: model number
-cid: chain id
-resname: residue name
-atom: PdbAtom; contains atom name, atom index, positions
see also PdbAtom
class.
function genSecondaryString():String
returns secondary structure assignements as a string. Each secondary structure element is written in one-character code as
- H: alpha helix
- 3: 3-10 helix
- P: pi-helix
- E: beta-strand
- C: coil
- T: turn
- B: bridge
function postProcess():Void
assign secondary structure. Note that this function does not return
the result of assignment. Use genSecondaryString
function to get
the result.
function readAtOnce(pdbText:String, doPostProcess:Bool):Void
read whole pdb file and store it data. If doPostProcess
is true,
secondary structure will be assigned.