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

---

org.xmlcml.cml
Interface CMLAtomParity  

All Superinterfaces:

AbstractAtomRef, AbstractBase, AttributeAtomRefs, AttributeConvention, AttributeDictRef, AttributeId, AttributeTitle, org.w3c.dom.Element, org.w3c.dom.Node

---

public interface CMLAtomParity

extends AbstractAtomRef

CORE Interface
DTD Class
interface supporting atom-based parity . It requires 3 or 4 atomRefs to define the parity. At present the values are doubles and only the sign is important (the values could be computed as chiral volumes)

---

Field Summary
static double	EPSILON           minimum acceptable absolute value for parity, else assumed 0
static java.lang.String	FLOAT
static double	MINRAD           minimum improper torsion angle to be regarded as chiral
static double	PLANARITYLIMIT           maximum acceptable absolute value for planarity, else assumed 0 (Experimental)
static java.lang.String	SYMBOL
static int	THREEDIM
static int	TWODIM

 

Fields inherited from interface org.xmlcml.cml.AbstractBase

ANGLE, ATOM, ATOMARRAY, ATOMPARITY, BOND, BONDARRAY, BONDSTEREO, BUILTIN, CML, CML_PREFIX, CRYSTAL, ELECTRON, ELEMENT_COUNT, ELEMENT_NAMES, EXECUTE, FEATURE, FLOAT_TYPE, FLOATARRAY, FLOATMATRIX, FORMULA, INTEGER, INTEGER_TYPE, INTEGERARRAY, LINK, LIST, MOLECULE, NAMESPACE_URI, PACKAGE_NAME, REACTION, SEQUENCE, STRING, STRING_TYPE, STRINGARRAY, TORSION, UNK, UNK_ELEM, UNKNOWN

 

Fields inherited from interface org.w3c.dom.Node

ATTRIBUTE_NODE, CDATA_SECTION_NODE, COMMENT_NODE, DOCUMENT_FRAGMENT_NODE, DOCUMENT_NODE, DOCUMENT_POSITION_CONTAINED_BY, DOCUMENT_POSITION_CONTAINS, DOCUMENT_POSITION_DISCONNECTED, DOCUMENT_POSITION_FOLLOWING, DOCUMENT_POSITION_IMPLEMENTATION_SPECIFIC, DOCUMENT_POSITION_PRECEDING, DOCUMENT_TYPE_NODE, ELEMENT_NODE, ENTITY_NODE, ENTITY_REFERENCE_NODE, NOTATION_NODE, PROCESSING_INSTRUCTION_NODE, TEXT_NODE

 

Fields inherited from interface org.xmlcml.cml.AttributeTitle

TITLE

 

Fields inherited from interface org.xmlcml.cml.AttributeDictRef

DICTREF

 

Fields inherited from interface org.xmlcml.cml.AttributeId

ID

 

Fields inherited from interface org.xmlcml.cml.AttributeConvention

CONVENTION

 

Fields inherited from interface org.xmlcml.cml.AttributeAtomRefs

ATOM_REFS

 

Method Summary
boolean	equals(java.lang.Object obj)           are two parities equal? They must be zero or have identical signs
double	getFloat()           CORE Method Assumes that atom has a single parity - identical for 2D and 3D alike
double	getFloat(int Dimension, CMLAtom atomUp)           get the actual parity as represented by the coordinates.
java.lang.String	getSMILES()           SMILES representation (deals with [...], etc)
CMLSymbol	getSymbol()           returns a floating point value; exception provides for symbolic values later
java.lang.String	getType()           get the type of the parity
boolean	isZero()           true if parity is zero (i.e.
void	setFloat(int dimension, double value)           set the parity (independent of coordinates).
java.lang.String	toString()           String representation

 

Methods inherited from interface org.xmlcml.cml.AbstractBase

addTracer, debug, debug, getDisplay, processDOM, readXMLTest, removeTracer, setDOMNeedsProcessing, setDOMNeedsUpdating, updateDOM

 

Methods inherited from interface org.w3c.dom.Element

getAttribute, getAttributeNode, getAttributeNodeNS, getAttributeNS, getElementsByTagName, getElementsByTagNameNS, getSchemaTypeInfo, getTagName, hasAttribute, hasAttributeNS, removeAttribute, removeAttributeNode, removeAttributeNS, setAttribute, setAttributeNode, setAttributeNodeNS, setAttributeNS, setIdAttribute, setIdAttributeNode, setIdAttributeNS

 

Methods inherited from interface org.w3c.dom.Node

appendChild, cloneNode, compareDocumentPosition, getAttributes, getBaseURI, getChildNodes, getFeature, getFirstChild, getLastChild, getLocalName, getNamespaceURI, getNextSibling, getNodeName, getNodeType, getNodeValue, getOwnerDocument, getParentNode, getPrefix, getPreviousSibling, getTextContent, getUserData, hasAttributes, hasChildNodes, insertBefore, isDefaultNamespace, isEqualNode, isSameNode, isSupported, lookupNamespaceURI, lookupPrefix, normalize, removeChild, replaceChild, setNodeValue, setPrefix, setTextContent, setUserData

 

Methods inherited from interface org.xmlcml.cml.AttributeTitle

getTitle, processDOMHasTitle, setTitle, updateDOMHasTitle

 

Methods inherited from interface org.xmlcml.cml.AttributeDictRef

getDictRef, processDOMHasDictRef, setDictRef, updateDOMHasDictRef

 

Methods inherited from interface org.xmlcml.cml.AttributeId

getId, processDOMHasId, setId, updateDOMHasId

 

Methods inherited from interface org.xmlcml.cml.AttributeConvention

getConventionName, processDOMHasConvention, setConventionName, updateDOMHasConvention

 

Methods inherited from interface org.xmlcml.cml.AttributeAtomRefs

addAtomRef, deleteAtomRef, getAtomRef, getAtomRefVector, getMolecule, processDOMHasAtomRefs, updateDOMHasAtomRefs

 

Field Detail

FLOAT

public static final java.lang.String FLOAT

See Also:

Constant Field Values

---

SYMBOL

public static final java.lang.String SYMBOL

See Also:

Constant Field Values

---

TWODIM

public static final int TWODIM

See Also:

Constant Field Values

---

THREEDIM

public static final int THREEDIM

See Also:

Constant Field Values

---

MINRAD

public static final double MINRAD

minimum improper torsion angle to be regarded as chiral

See Also:

Constant Field Values

---

EPSILON

public static final double EPSILON

minimum acceptable absolute value for parity, else assumed 0

See Also:

Constant Field Values

---

PLANARITYLIMIT

public static final double PLANARITYLIMIT

maximum acceptable absolute value for planarity, else assumed 0 (Experimental)

See Also:

Constant Field Values

Method Detail

equals

public boolean equals(java.lang.Object obj)

are two parities equal? They must be zero or have identical signs

---

isZero

public boolean isZero()

true if parity is zero (i.e. not chiral

---

getType

public java.lang.String getType()

get the type of the parity

---

getFloat

public double getFloat()
                throws CMLException

CORE Method
Assumes that atom has a single parity - identical for 2D and 3D alike

---

getFloat

public double getFloat(int Dimension,
                       CMLAtom atomUp)
                throws CMLException

get the actual parity as represented by the coordinates. cannot be set.

---

setFloat

public void setFloat(int dimension,
                     double value)
              throws CMLException

set the parity (independent of coordinates). If dimension is zero, coordinates are not checked - this could lead to problems. If dimension is TWODIM, THREEDIM or TWODIM+THREEDIM, the coordinates are checked and if there is an inconsistency an exception is thrown

---

getSymbol

public CMLSymbol getSymbol()
                    throws CMLException

returns a floating point value; exception provides for symbolic values later

---

getSMILES

public java.lang.String getSMILES()

SMILES representation (deals with [...], etc)

---

toString

public java.lang.String toString()

String representation

---

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

---