Docjar: A Java Source and Docuemnt Enginecom.*    java.*    javax.*    org.*    all    new    plug-in

Quick Search    Search Deep
Overview  Package   Class  Use  Deprecated  Index 
Home >> All >> org >> xmlcml >> [ cml overview ]  PREV CLASS  NEXT CLASS
SUMMARY: JavaDoc of org.xmlcml.cml.CMLCrystal JAVADOC | Sourc code of org.xmlcml.cml.CMLCrystal SOURCE | Download org.xmlcml.cml.CMLCrystal DOWNLOAD | NESTED | FIELD | CONSTR | METHOD DETAIL: FIELD | CONSTR | METHOD

org.xmlcml.cml
Interface CMLCrystal  view CMLCrystal download CMLCrystal.java

All Superinterfaces:
AbstractBase, AbstractBuiltinContainer, AttributeConvention, AttributeDictRef, AttributeId, AttributeTitle, BuiltinContainer, org.w3c.dom.Element, org.w3c.dom.Node
public interface CMLCrystal
extends AbstractBuiltinContainer, BuiltinContainer

CORE Interface
DTD Class
Supports a crystallographic unit cell (parameters and spacegroup). Provision for symmetry is limited

Field Summary
static int ACELL
           
static java.lang.String ACELL_NAME
           
static int ALPHA
           
static java.lang.String ALPHA_NAME
           
static int BCELL
           
static java.lang.String BCELL_NAME
           
static int BETA
           
static java.lang.String BETA_NAME
           
static java.lang.String[] builtinFloatValNames
           
static java.lang.String[] builtinIntegerValNames
           
static java.lang.String[] builtinStringValNames
           
static int CCELL
           
static java.lang.String CCELL_NAME
           
static int CRYSTAL_BUILTIN_COUNT
           
static int CRYSTAL_FLOATVAL_COUNT
           
static int CRYSTAL_FLOATVAL_END
           
static int CRYSTAL_FLOATVAL_START
           
static int CRYSTAL_INTEGERVAL_COUNT
           
static int CRYSTAL_INTEGERVAL_END
           
static int CRYSTAL_INTEGERVAL_START
           
static int CRYSTAL_STRINGVAL_COUNT
           
static int CRYSTAL_STRINGVAL_END
           
static int CRYSTAL_STRINGVAL_START
           
static int GAMMA
           
static java.lang.String GAMMA_NAME
           
static int SPACEGROUP
           
static java.lang.String SPACEGROUP_NAME
           
static int Z_FLOAT
           
static int Z_INT
           
static java.lang.String Z_NAME
           
 
Fields inherited from interface org.xmlcml.cml.AbstractBuiltinContainer
NONUNIQUE, STEREO_2D, STEREO_3D, STEREO_ANY, UNIQUE
 
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, 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
 
Method Summary
 void addSymmetryOperator(RealMatrix m)
          adds symmetry operator as 4*3 matrix; No checks at present (apart from shape).
 double[] getCellAngles()
          CORE Method
get cell angles IN DEGREES or null if not present
 double[] getCellLengths()
          CORE Method
get cell lengths IN ANGSTROM or null if not present
 double getMoleculesPerCell()
          CORE Method
gets Z (molecules/cell) as number; No checks at present.
 RealSquareMatrix getOrthogonalisationMatrix()
           
 java.lang.String getSpacegroup()
          CORE Method
gets spacegroup as String; No checks at present, and no defined convention null string ("") if not set
 int getSpacegroupNumber(int nsp)
          CORE Method
gets spacegroup as number; No checks at present.
 RealMatrix[] getSymmetryOperators()
          gets symmetry operators as an array of RealMatrix'es (3 rows, 4 columns)
 void setCellAngles(double alpha, double beta, double gamma)
          CORE Method
add cell angles IN DEGREES
 void setCellLengths(double a, double b, double c)
          CORE Method
add cell lengths as a double[3] If cell already present, returns false without action.
 void setMoleculesPerCell(double z)
          CORE Method
adds Z (molecules/cell) as number; No checks at present.
 void setSpacegroup(java.lang.String spg)
          CORE Method
adds spacegroup as String; No checks at present, and no defined convention
 void setSpacegroupNumber(int nsp)
          CORE Method
adds spacegroup as number; No checks at present.
 
Methods inherited from interface org.xmlcml.cml.AbstractBuiltinContainer
addBuiltinChildWithFloatValue, addBuiltinChildWithIntegerValue, addBuiltinChildWithStringValue, checkBuiltins, deleteNonBuiltinVal, getBuiltinChild, getBuiltinChildElements, getBuiltinChildFloatValue, getBuiltinChildIntegerValue, getBuiltinChildStringValue, getBuiltinCount, getBuiltinVal, getNonBuiltinVal, removeBuiltinChild, setBuiltinFloatChild, setBuiltinIntegerChild, setBuiltinStringChild, setBuiltinVal, setNonBuiltinVal
 
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
 

Field Detail

CRYSTAL_FLOATVAL_START

public static final int CRYSTAL_FLOATVAL_START
See Also:
Constant Field Values

ACELL

public static final int ACELL
See Also:
Constant Field Values

BCELL

public static final int BCELL
See Also:
Constant Field Values

CCELL

public static final int CCELL
See Also:
Constant Field Values

ALPHA

public static final int ALPHA
See Also:
Constant Field Values

BETA

public static final int BETA
See Also:
Constant Field Values

GAMMA

public static final int GAMMA
See Also:
Constant Field Values

Z_FLOAT

public static final int Z_FLOAT
See Also:
Constant Field Values

CRYSTAL_FLOATVAL_END

public static final int CRYSTAL_FLOATVAL_END
See Also:
Constant Field Values

CRYSTAL_FLOATVAL_COUNT

public static final int CRYSTAL_FLOATVAL_COUNT
See Also:
Constant Field Values

CRYSTAL_INTEGERVAL_START

public static final int CRYSTAL_INTEGERVAL_START
See Also:
Constant Field Values

Z_INT

public static final int Z_INT
See Also:
Constant Field Values

CRYSTAL_INTEGERVAL_END

public static final int CRYSTAL_INTEGERVAL_END
See Also:
Constant Field Values

CRYSTAL_INTEGERVAL_COUNT

public static final int CRYSTAL_INTEGERVAL_COUNT
See Also:
Constant Field Values

CRYSTAL_STRINGVAL_START

public static final int CRYSTAL_STRINGVAL_START
See Also:
Constant Field Values

SPACEGROUP

public static final int SPACEGROUP
See Also:
Constant Field Values

CRYSTAL_STRINGVAL_END

public static final int CRYSTAL_STRINGVAL_END
See Also:
Constant Field Values

CRYSTAL_STRINGVAL_COUNT

public static final int CRYSTAL_STRINGVAL_COUNT
See Also:
Constant Field Values

CRYSTAL_BUILTIN_COUNT

public static final int CRYSTAL_BUILTIN_COUNT
See Also:
Constant Field Values

ACELL_NAME

public static final java.lang.String ACELL_NAME
See Also:
Constant Field Values

BCELL_NAME

public static final java.lang.String BCELL_NAME
See Also:
Constant Field Values

CCELL_NAME

public static final java.lang.String CCELL_NAME
See Also:
Constant Field Values

ALPHA_NAME

public static final java.lang.String ALPHA_NAME
See Also:
Constant Field Values

BETA_NAME

public static final java.lang.String BETA_NAME
See Also:
Constant Field Values

GAMMA_NAME

public static final java.lang.String GAMMA_NAME
See Also:
Constant Field Values

Z_NAME

public static final java.lang.String Z_NAME
See Also:
Constant Field Values

builtinFloatValNames

public static final java.lang.String[] builtinFloatValNames

builtinIntegerValNames

public static final java.lang.String[] builtinIntegerValNames

SPACEGROUP_NAME

public static final java.lang.String SPACEGROUP_NAME
See Also:
Constant Field Values

builtinStringValNames

public static final java.lang.String[] builtinStringValNames
Method Detail

setCellLengths

public void setCellLengths(double a,
                           double b,
                           double c)
CORE Method
add cell lengths as a double[3] If cell already present, returns false without action. Arguments MUST BE IN ANGSTROM.

getCellLengths

public double[] getCellLengths()
                        throws CMLException
CORE Method
get cell lengths IN ANGSTROM or null if not present

getCellAngles

public double[] getCellAngles()
                       throws CMLException
CORE Method
get cell angles IN DEGREES or null if not present

setCellAngles

public void setCellAngles(double alpha,
                          double beta,
                          double gamma)
CORE Method
add cell angles IN DEGREES

setSpacegroup

public void setSpacegroup(java.lang.String spg)
CORE Method
adds spacegroup as String; No checks at present, and no defined convention

getSpacegroup

public java.lang.String getSpacegroup()
CORE Method
gets spacegroup as String; No checks at present, and no defined convention null string ("") if not set

setSpacegroupNumber

public void setSpacegroupNumber(int nsp)
CORE Method
adds spacegroup as number; No checks at present.

getSpacegroupNumber

public int getSpacegroupNumber(int nsp)
CORE Method
gets spacegroup as number; No checks at present. 0 if not set;

setMoleculesPerCell

public void setMoleculesPerCell(double z)
CORE Method
adds Z (molecules/cell) as number; No checks at present.

getMoleculesPerCell

public double getMoleculesPerCell()
CORE Method
gets Z (molecules/cell) as number; No checks at present. 0 if not set.

addSymmetryOperator

public void addSymmetryOperator(RealMatrix m)
                         throws CMLException
adds symmetry operator as 4*3 matrix; No checks at present (apart from shape).

getSymmetryOperators

public RealMatrix[] getSymmetryOperators()
gets symmetry operators as an array of RealMatrix'es (3 rows, 4 columns)

getOrthogonalisationMatrix

public RealSquareMatrix getOrthogonalisationMatrix()
                                            throws CMLException
Overview  Package   Class  Use  Deprecated  Index 
Home >> All >> org >> xmlcml >> [ cml overview ]  PREV CLASS  NEXT CLASS
SUMMARY: JavaDoc of org.xmlcml.cml.CMLCrystal JAVADOC | Sourc code of org.xmlcml.cml.CMLCrystal SOURCE | Download org.xmlcml.cml.CMLCrystal DOWNLOAD | NESTED | FIELD | CONSTR | METHOD DETAIL: FIELD | CONSTR | METHOD