Overview  Package   Class  Use  Deprecated  Index
Home >> All >> org >> xmlcml >> [ simplecml overview ]	PREV CLASS  NEXT CLASS
SUMMARY:  JAVADOC |  SOURCE |  DOWNLOAD | NESTED | FIELD | CONSTR | METHOD	DETAIL: FIELD | CONSTR | METHOD

---

org.xmlcml.simplecml
Class SimpleMolecule  

java.lang.Object
  org.xmlcml.simplecml.SimpleMolecule

---

public class SimpleMolecule

extends java.lang.Object

SimpleMolecule manages a subset of CML functionality for molecules. It lacks many of the more sophisticated methods and exposes the atoms and bonds as public vectors It should only be used with SimpleBond and SimpleAtom.

Typical code:

	SimpleMolecule mol = new SimpleMolecule();
	SimpleAtom atom1 = new SimpleAtom();
	atom1.elementType="C";
	atom1.id="c1";
	atomVector.addElement(atom1);
	SimpleAtom atom2 = new SimpleAtom();
	atom2.elementType="O";
	atom2.id="o2";
	atomVector.addElement(atom2);
	SimpleBond bond = new SimpleBond();
	bond.atomRef1 = atom1;
	bond.atomRef2 = atom2;
	bond.order = "T";
	bondVector.addElement(bond);
	

---

Field Summary
(package private)  java.util.Hashtable	atomTable
java.util.Vector	atomVector           Vector of atoms in molecules; initially set to new Vector()
java.util.Vector	bondVector           Vector of bonds in molecules; initially set to new Vector()
static java.lang.String	CML_DTD_NAMESPACE_URI           definitive namespace URI for CML V1.0
static java.lang.String	CML_SCHEMA_NAMESPACE_URI           definitive namespace URI for CML V2.0 (Schema)
java.lang.String	id           unique ID for molecule
java.util.Vector	moleculeVector           Vector of child molecules; initially set to new Vector()
java.lang.String	namespace           output namespace (default = CML1.0 DTD)
int	natoms           atom count in molecule; updated by addAtom()
int	nbonds           bond count in molecule; updated by addBond()
int	nmolecules           count of child molecules;

 

Constructor Summary

SimpleMolecule()           constructs a SimpleMolecule with new Vectors and zero counts

 

Method Summary
void	addAtom(SimpleAtom atom)           add atom; updates count
void	addBond(SimpleBond bond)           add bond; updates count
void	addMolecule(SimpleMolecule molecule)           add molecule; updates count
(package private) static java.lang.String	getPrefix(java.lang.String prefix)           return namespace prefix
void	setNamespace(java.lang.String namespace)           set flag to decide on CML-DTD (V1) or CML-Schema (V2)
java.lang.String	toCML()           default: no decl, no encoding, no dtd, useNamespace, no prefix, no arrays
java.lang.String	toCML(boolean useDecl, java.lang.String encoding, java.lang.String dtd, java.lang.String namespace, java.lang.String prefix, boolean arrayx)
java.lang.String	toString()           diagnostic string

 

Methods inherited from class java.lang.Object

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

 

Field Detail

CML_DTD_NAMESPACE_URI

public static final java.lang.String CML_DTD_NAMESPACE_URI

definitive namespace URI for CML V1.0

See Also:

Constant Field Values

---

CML_SCHEMA_NAMESPACE_URI

public static final java.lang.String CML_SCHEMA_NAMESPACE_URI

definitive namespace URI for CML V2.0 (Schema)

See Also:

Constant Field Values

---

atomVector

public java.util.Vector atomVector

Vector of atoms in molecules; initially set to new Vector()

---

bondVector

public java.util.Vector bondVector

Vector of bonds in molecules; initially set to new Vector()

---

moleculeVector

public java.util.Vector moleculeVector

Vector of child molecules; initially set to new Vector()

---

id

public java.lang.String id

unique ID for molecule

---

natoms

public int natoms

atom count in molecule; updated by addAtom()

---

nbonds

public int nbonds

bond count in molecule; updated by addBond()

---

nmolecules

public int nmolecules

count of child molecules;

---

namespace

public java.lang.String namespace

output namespace (default = CML1.0 DTD)

---

atomTable

java.util.Hashtable atomTable

Constructor Detail

SimpleMolecule

public SimpleMolecule()

constructs a SimpleMolecule with new Vectors and zero counts

Method Detail

toString

public java.lang.String toString()

diagnostic string

---

setNamespace

public void setNamespace(java.lang.String namespace)

set flag to decide on CML-DTD (V1) or CML-Schema (V2)

---

toCML

public java.lang.String toCML()

default: no decl, no encoding, no dtd, useNamespace, no prefix, no arrays

---

toCML

public java.lang.String toCML(boolean useDecl,
                              java.lang.String encoding,
                              java.lang.String dtd,
                              java.lang.String namespace,
                              java.lang.String prefix,
                              boolean arrayx)

---

getPrefix

static java.lang.String getPrefix(java.lang.String prefix)

return namespace prefix

---

addAtom

public void addAtom(SimpleAtom atom)

add atom; updates count

---

addBond

public void addBond(SimpleBond bond)

add bond; updates count

---

addMolecule

public void addMolecule(SimpleMolecule molecule)

add molecule; updates count

---

Overview  Package   Class  Use  Deprecated  Index
Home >> All >> org >> xmlcml >> [ simplecml overview ]	PREV CLASS  NEXT CLASS
SUMMARY:  JAVADOC |  SOURCE |  DOWNLOAD | NESTED | FIELD | CONSTR | METHOD	DETAIL: FIELD | CONSTR | METHOD

---