ProGAL.proteins
Class PDBFile.AtomRecord

java.lang.Object
  extended by ProGAL.proteins.PDBFile.AtomRecord
All Implemented Interfaces:
PDBFile.PDBRecord
Direct Known Subclasses:
PDBFile.HetatmRecord
Enclosing class:
PDBFile

public static class PDBFile.AtomRecord
extends java.lang.Object
implements PDBFile.PDBRecord


Field Summary
 java.lang.String aaType
          The type of amino acid in a three-letter code, for example: TYR, ALA or ARG
 java.util.LinkedList<Point> alternativeCoords
           
 int atomNumber
           
 java.lang.String atomType
          The type of atom.
 char chain
          A character identifying the chain
 Point coords
           
 java.lang.String element
          The atom element.
 double occupancy
           
 int residueNumber
           
 
Method Summary
 char getSingleCharAAType()
           
 boolean isHydrogen()
           
 boolean isHydrogenAcceptor()
          Returns true if the atom can act as a hydrogen acceptor in a hydrogen bond
 boolean isHydrogenDonor()
          Returns true if the atom can act as a hydrogen donor in a hydrogen bond
 boolean isOnBackbone()
           
 java.lang.String toString()
          Returns a string representation of this ATOM-record that follows the PDB-file format.
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

atomType

public java.lang.String atomType
The type of atom. Backbone types are N, CA, C and O. Side-chain types can be CB, CG1 etc.


aaType

public java.lang.String aaType
The type of amino acid in a three-letter code, for example: TYR, ALA or ARG


element

public java.lang.String element
The atom element. Typically either of C, N, O, S or H.


chain

public char chain
A character identifying the chain


atomNumber

public int atomNumber

residueNumber

public int residueNumber

coords

public Point coords

occupancy

public double occupancy

alternativeCoords

public java.util.LinkedList<Point> alternativeCoords
Method Detail

isOnBackbone

public boolean isOnBackbone()

isHydrogen

public boolean isHydrogen()

isHydrogenDonor

public boolean isHydrogenDonor()
Returns true if the atom can act as a hydrogen donor in a hydrogen bond


isHydrogenAcceptor

public boolean isHydrogenAcceptor()
Returns true if the atom can act as a hydrogen acceptor in a hydrogen bond


toString

public java.lang.String toString()
Returns a string representation of this ATOM-record that follows the PDB-file format. Following is from http://www.wwpdb.org/documentation/format32/sect9.html COLUMNS DATA TYPE FIELD DEFINITION ------------------------------------------------------------------------------------- 1 - 6 Record name "ATOM " 7 - 11 Integer serial Atom serial number. 13 - 16 Atom name Atom name. 17 Character altLoc Alternate location indicator. 18 - 20 Residue name resName Residue name. 22 Character chainID Chain identifier. 23 - 26 Integer resSeq Residue sequence number. 27 AChar iCode Code for insertion of residues. 31 - 38 Real(8.3) x Orthogonal coordinates for X in Angstroms. 39 - 46 Real(8.3) y Orthogonal coordinates for Y in Angstroms. 47 - 54 Real(8.3) z Orthogonal coordinates for Z in Angstroms. 55 - 60 Real(6.2) occupancy Occupancy. 61 - 66 Real(6.2) tempFactor Temperature factor. 77 - 78 LString(2) element Element symbol, right-justified. 79 - 80 LString(2) charge Charge on the atom.

Overrides:
toString in class java.lang.Object

getSingleCharAAType

public char getSingleCharAAType()