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org.xmlcml.simplecml
Class SimpleAtom  

java.lang.Object
  org.xmlcml.simplecml.SimpleAtom

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public class SimpleAtom

extends java.lang.Object

SimpleAtom manages a subset of CML functionality for atoms. It lacks many of the more sophisticated setters and getters and exposes the atom children directly (e.g. hydrogenCount). It should only be used with SimpleMolecule and SimpleBond.

Typical code:

	SimpleAtom atom = new SimpleAtom();
	atom.id = "a123";
	atom.elementType="Na";
	atom.formalCharge=1;















Field Summary



 java.lang.String
elementType



          elementType (1- or 2- letter atom symbol, e.g.



 int
formalCharge



          number of attached hydrogens: default = 0



 int
hydrogenCount



          number of attached hydrogens: default = 0



 java.lang.String
id



          the atom id; mandatory and should be unique



 java.lang.String
namespace



          the namespace



 double
x2



          2D x-coordinate (arbitrary units); default=NaN



 double
x3



          3D x-coordinate (Angstrom); default=NaN



 double
y2



          2D y-coordinate (arbitrary units); default=NaN



 double
y3



          3D y-coordinate (Angstrom); default=NaN



 double
z3



          3D z-coordinate (Angstrom); default=NaN


 






Constructor Summary


SimpleAtom()



          constructs a SimpleAtom with default child values


SimpleAtom(java.lang.String namespace)



          constructs a SimpleAtom with default child values and namespace


 






Method Summary



 java.lang.String
toCML(java.lang.String prefix)



          well-formed CML for an atom; uninitialised children are not included



 java.lang.String
toString()



          diagnostic string for an atom


 


Methods inherited from class java.lang.Object


clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait


 








Field Detail




hydrogenCount
public int hydrogenCount

number of attached hydrogens: default = 0







formalCharge
public int formalCharge

number of attached hydrogens: default = 0







elementType
public java.lang.String elementType

elementType (1- or 2- letter atom symbol, e.g. "Na", "Cl"; mandatory







id
public java.lang.String id

the atom id; mandatory and should be unique







x2
public double x2

2D x-coordinate (arbitrary units); default=NaN







y2
public double y2

2D y-coordinate (arbitrary units); default=NaN







x3
public double x3

3D x-coordinate (Angstrom); default=NaN







y3
public double y3

3D y-coordinate (Angstrom); default=NaN







z3
public double z3

3D z-coordinate (Angstrom); default=NaN







namespace
public java.lang.String namespace

the namespace











Constructor Detail




SimpleAtom
public SimpleAtom()

constructs a SimpleAtom with default child values





SimpleAtom
public SimpleAtom(java.lang.String namespace)

constructs a SimpleAtom with default child values and namespace









Method Detail




toString
public java.lang.String toString()

diagnostic string for an atom








toCML
public java.lang.String toCML(java.lang.String prefix)

well-formed CML for an atom; uninitialised children are not included














  

  
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