a link to an object - usually from org.xmlcml.cml - but could be anything
uses XLink semantics where possible.
CMLList CMLList .
list is a generic container which has no predetermined children or attributes
and use the DOM emthods to access them
CMLMolecule CMLMolecule .CORE Interface CMLMoleculeFactory CMLMoleculeFactory .Creates Molecules of appropriate subclass CMLReaction CMLReaction . CMLSequence CMLSequence . CMLStringArray CMLStringArray . CMLStringVal CMLStringVal . CMLSymbol CMLSymbol .a placeholder for the need to hold symbolic values (e.g. CMLTorsion CMLTorsion .CORE Interface CML_DICTIONARY_FILENAME CMLDocument
CML_DICTIONARY_NAME CMLDocument
CML_DICTIONARY_NAMESPACE_URI CMLDocument
CML_DICTIONARY_PREFIX CMLDocument
CML_PREFIX AbstractBase
CONSTRAINT_COUNT ConventionCriteria
CONVENTION AttributeConvention
"convention" attribute name
COORD2 CMLMolecule
2-D coordinates
COORD3 CMLMolecule
3-D coordinates
COUNT AttributeCount
"count" attribute
CRITERIA_COUNT ConventionCriteria
CRYSTAL AbstractBase
CRYSTAL_BUILTIN_COUNT CMLCrystal
CRYSTAL_FLOATVAL_COUNT CMLCrystal
CRYSTAL_FLOATVAL_END CMLCrystal
CRYSTAL_FLOATVAL_START CMLCrystal
CRYSTAL_INTEGERVAL_COUNT CMLCrystal
CRYSTAL_INTEGERVAL_END CMLCrystal
CRYSTAL_INTEGERVAL_START CMLCrystal
CRYSTAL_STRINGVAL_COUNT CMLCrystal
CRYSTAL_STRINGVAL_END CMLCrystal
CRYSTAL_STRINGVAL_START CMLCrystal
Convention Convention . Convention() Convention
ConventionCriteria ConventionCriteria . checkBuiltins(String[], String[], String[]) AbstractBuiltinContainer
cloneAtom(CMLMolecule) CMLAtom
creates a new Atom - can use a Factory method internally if required.
cloneBond(HashMap) CMLBond
clone the bond.
combineSubMolecules() CMLMolecule
if molecule consists of submolecules combine them ("flatten") into a single
molecule (e.g.
constraintNames ConventionCriteria
contains(CMLAtom) CMLBond
true if bond contains this atom
convertFractionalToCartesian(CMLCrystal) CMLMolecule
convenience method; convert fractionals to cartesian
createArrayElement(Document) BuiltinArrayContainer
createArrayElement(Document) CMLAtomArray
createArrayElement(Document) CMLBondArray
createAtom(Document) CMLAtomFactory
create empty atom
createAtom(CMLMolecule, String) CMLAtomFactory
create atom in Molecule context and add to Molecule
createBond(Document) CMLBondFactory
createBond(CMLAtom, CMLAtom) CMLBondFactory
createBondToLigand(CMLAtom) CMLAtom
add ligand.
createDocument() CMLDocumentFactory
createFromString(String, String) CMLFormula
interpret string as a formula and replace contents.
createMolecule(Document) CMLMoleculeFactory
this should be the only way of creating Molecules
criteriaNames ConventionCriteria
D
DECREASE AbstractBond
DEFAULTXY2LENGTH AbstractBond
default screen bondlength
DEFAULTXYZ3LENGTH AbstractBond
default 3d bondlength
DELETE AbstractBond
DELIM CMLStringArray
DICTREF AttributeDictRef
"dictRef" attribute name
DOUBLE AbstractBond
double bond
deArrayify() CMLDocument
unpack stringArrays, etc.
debug(Writer) AbstractBase
output debug info to Writer and return String equivalent (e.g.
debug() AbstractBase
output debug info to System.out
debug(Writer) CMLDocument
output debug info to Writer and return String equivalent (e.g.
debug() CMLDocument
output debug to System.out
delete(CMLAtom) CMLAtomArray
delete(CMLBond) CMLBondArray
deleteAllAtoms() CMLMolecule
delete all Atoms.
deleteAllBonds() CMLMolecule
delete all Bonds.
deleteAllFormulas() CMLFormula
delete all Formulas.
deleteAngle(CMLAngle) CMLMolecule
CORE Method deleteAtom(CMLAtom) CMLMolecule
CORE Method deleteAtomRef(CMLAtom) AttributeAtomRefs
deleteBond(CMLBond) CMLMolecule
CORE Method deleteElectron(CMLElectron) CMLMolecule
Deletes a CMLElectron from the CMLMolecule content.
deleteElement(String) CMLStringArray
deleteFeature(CMLFeature) CMLMolecule
Deletes a CMLFeature from the CMLMolecule content.
deleteFormula(CMLFormula) CMLFormula
deleteFormula(CMLFormula) CMLMolecule
Deletes a CMLFormula from the CMLMolecule content.
deleteMolecule(CMLMolecule) CMLMolecule
CORE Method deleteNonBuiltinArray(String) BuiltinArrayContainer
deleteNonBuiltinArray(String) CMLAtomArray
deleteNonBuiltinArray(String) CMLBondArray
deleteNonBuiltinVal(String) AbstractBuiltinContainer
deleteNonBuiltinVal(String) BuiltinContainer
deleteProduct(CMLMolecule) CMLReaction
deleteReactant(CMLMolecule) CMLReaction
deleteSequence(CMLSequence) CMLMolecule
Deletes a CMLSequence from the CMLMolecule content.
deleteTorsion(CMLTorsion) CMLMolecule
CORE Method dereferenceLinks() CMLDocument
visit all
E
ELECTRON AbstractBase
ELEMENT_COUNT AbstractBase
ELEMENT_COUNT_WHITESPACE CMLFormula
Example "C2 H4 Cl2"
ELEMENT_NAMES AbstractBase
ELEMENT_TYPE AbstractAtom
ELEMENT_TYPE CMLFormula
ELEMENT_WHITESPACE_COUNT CMLFormula
Example "C 2 H 4 Cl 2"
ELTYPE_NAME AbstractAtom
EPSILON CMLAtomParity
minimum acceptable absolute value for parity, else assumed 0
EXECUTE AbstractBase
EXPLICIT_HYDROGENS ConventionCriteria
elementAt(int) AttributeSize
this will return an element of appropriate subclass
elementAt(int) CMLAtomArray
when an CMLAtom is extracted then it is combined from the various StringArrays
elementAt(int) CMLBondArray
when an CMLBond is extracted then it is combined from the various StringArrays
elementAt(int) CMLFloatArray
actually returns CMLFloatVal
elementAt(int) CMLIntegerArray
return value is actually CMLIntegerVal
elementAt(int) CMLStringArray
equals(Object) CMLAtomParity
are two parities equal? They must be zero or have identical signs
equals(Object) CMLBondStereo
are two stereos equal?
F
FCHARGE_NAME AbstractAtom
FEATURE AbstractBase
FLOAT AbstractBase
FLOAT CMLAtomParity
FLOATARRAY AbstractBase
FLOATMATRIX AbstractBase
FLOAT_TYPE AbstractBase
FORMAL_CHARGE CMLFormula
FORMAL_CHARGE_FLOAT AbstractAtom
FORMAL_CHARGE_INT AbstractAtom
FORMULA AbstractBase
FORMULA_BUILTIN_COUNT CMLFormula
FORMULA_FLOATVAL_COUNT CMLFormula
FORMULA_FLOATVAL_END CMLFormula
FORMULA_FLOATVAL_START CMLFormula
FORMULA_INTEGERVAL_COUNT CMLFormula
FORMULA_INTEGERVAL_END CMLFormula
FORMULA_INTEGERVAL_START CMLFormula
FORMULA_STRINGVAL_COUNT CMLFormula
FORMULA_STRINGVAL_END CMLFormula
FORMULA_STRINGVAL_START CMLFormula
G
GAMMA CMLCrystal
GAMMA_NAME CMLCrystal
generateId(int) CMLAtom
give each atom an ID.
getAngle() AbstractAngle
get value in degrees
getAngleList() CMLMolecule
CORE Method getAngleVector() CMLMolecule
CORE Method getAtom(int) CMLBond
CORE Method getAtom(int) CMLMolecule
convenience method for access i'th CMLAtom.
getAtomArray() CMLMolecule
packs current Atoms into an CMLAtomArray.
getAtomById(String) CMLMolecule
CORE Method getAtomCount() CMLMolecule
CORE Method getAtomFactory() CMLMoleculeFactory
this factory is required for creating Atoms;
it will be tied to the MoleculeFactory and cannot be reset
getAtomIdTable() CMLMolecule
getAtomList() CMLMolecule
CORE Method getAtomParity() CMLAtom
DOM Method CMLCore getAtomRef(int) AttributeAtomRefs
getAtomRefVector() AttributeAtomRefs
getAtomRefVector() CMLAtom
CORE Method getAtomVector() CMLMolecule
CORE Method getBond(CMLAtom, CMLAtom) CMLMolecule
CORE Method getBondArray() CMLMolecule
extracts ALL the bonds in a single CMLBondArray.
getBondCount() CMLMolecule
CORE Method getBondFactory() CMLMoleculeFactory
this factory is required for creating Bond
it will be tied to the MoleculeFactory and cannot be reset
getBondLength() CMLBond
CORE Method getBondList() CMLMolecule
CORE Method getBondVector() CMLMolecule
CORE Method getBuiltin() AbstractStringVal
getBuiltinArray(int) BuiltinArrayContainer
getBuiltinArray(int) CMLAtomArray
this is slightly tricky/ucky since CMLAtomArray is subclassed from CMLAtom and CMLStringArray
from CMLStringVal we can extract the array object as scalars and simply cast them
getBuiltinArray(int) CMLBondArray
this is rather trick since CMLBondArray is subclasses from CMLBond and CMLStringArray
from CMLStringVal we can extract the array object as scalars and simply cast them
getBuiltinChild(int, String[], int) AbstractBuiltinContainer
gets the SINGLE child with the given builtin
getBuiltinChildElements() AbstractBuiltinContainer
extracts all children with builtin attribute; if none empty Vector
getBuiltinChildFloatValue(int, String[]) AbstractBuiltinContainer
getBuiltinChildIntegerValue(int, String[]) AbstractBuiltinContainer
getBuiltinChildStringValue(int, String[]) AbstractBuiltinContainer
returns the value of a SINGLE child with given builtin
getBuiltinCount() AbstractBuiltinContainer
getBuiltinCount() BuiltinContainer
getBuiltinVal(int) AbstractBuiltinContainer
getBuiltinVal(int) BuiltinContainer
getCalculatedFormula() CMLMolecule
calculate a Formula from the Molecule.
getCalculatedMolecularMass() CMLFormula
NON-DOM convenience
getCellAngles() CMLCrystal
CORE Method IN DEGREES or null if not present
getCellLengths() CMLCrystal
CORE Method IN ANGSTROM or null if not present
getColumns() CMLFloatMatrix
getConventionName() AttributeConvention
getCount() AttributeCount
getCount() CMLMolecule
CORE Method getCrystal() CMLMolecule
CORE Method getData() CMLFloatMatrix
data in format [rows][cols].
getDataType() AbstractStringVal
String, Float, Integer all have dataType flag if required
getDelimiter() AttributeSize
getDelimiter() CMLFloatArray
getDelimiter() CMLIntegerArray
getDelimiter() CMLStringArray
getDictRef() AttributeDictRef
getDisplay() AbstractBase
a graphical display for this object
getElectronList() CMLMolecule
extracts ALL the Electrons as an array
getElectronVector() CMLMolecule
extracts ALL the Electrons as a Vector
getElementCounts() CMLFormula
count for corresponding element; no defaults
getElementType() CMLAtom
CORE Method
DOM Method getElementTypeList() CMLAtom
CORE Method
Query Method getElementTypes() CMLFormula
Element and count are ganged, so that element[i] corresponds to count[i].
getFeature() CMLMolecule
extracts the FIRST CMLFeature if any present
getFeatureList() CMLMolecule
extracts ALL the Features as an array
getFeatureVector() CMLMolecule
extracts ALL the Features as a Vector
getFloat() CMLAtomParity
CORE Method getFloat(int, CMLAtom) CMLAtomParity
get the actual parity as represented by the coordinates.
getFloat(int) CMLFloatArray
getFloatValue() CMLIsotope
CORE Method getFormalCharge() CMLAtom
CORE Method
DOM Method getFormalCharge() CMLFormula
get the charge on this formula moiety; defaults to zero
getFormalChargeList() CMLAtom
Query Method
get list of Formal charges
getFormattedString(String, String, boolean) CMLFormula
/** NON-DOM convenience get formatted formula
getFormula() CMLMolecule
extracts the CMLFormula if exactly one present.
getFormulaList() CMLMolecule
extracts ALL the Formulas as an array
getFormulaVector() CMLFormula
CORE Method getFormulaVector() CMLMolecule
extracts ALL the Formulas as a Vector
getHRef() CMLLink
getHydrogenCount() CMLAtom
Query Method
DOM Method getHydrogenCountList() CMLAtom
CORE Method
DOM Method getId() AttributeId
getIntValue() CMLIntegerVal
getInteger(int) CMLIntegerArray
getIntegerValue() CMLIsotope
CORE Method getIsotope() CMLAtom
CORE Method
DOM Method getLength(CMLAtom) CMLAtom
convenience method to get interatomic distance
getLigand(int) CMLAtom
convenience method to get element of ligand vector
getLigandCount() CMLAtom
get ligand count
getLigandList() CMLAtom
getLigandVector() CMLAtom
getMaximum() CMLFloatVal
maximum value, set by default to Double.MAX_VALUE
getMaximum() CMLIntegerVal
maximum value, set by default to Integer.MAX_VALUE (2147483647)
getMinimum() CMLFloatVal
minimum value, set by default to Double.MIN_VALUE
getMinimum() CMLIntegerVal
minimum value, set by default to Integer.MIN_VALUE (-2147483648)
getMolecule() AttributeAtomRefs
must have reference to a molecule
getMolecule() CMLAtom
CORE Method getMolecule() CMLBond
CORE Method getMolecule() CMLDocument
convenience method: returns the first CMLMolecule in the document or null if none
getMoleculeFactory() CMLDocument
get the MoleculeFactory - should be the only way of creating
molecules.
getMoleculeList() CMLDocument
convenience method: returns all top-level Molecules in the document
getMoleculeList() CMLMolecule
CORE Method getMoleculeVector() CMLDocument
convenience method: returns all top-level Molecules in the document
getMoleculeVector() CMLMolecule
CORE Method getMoleculesPerCell() CMLCrystal
CORE Method getNonBuiltinArray(String) BuiltinArrayContainer
getNonBuiltinArray(String) CMLAtomArray
getNonBuiltinArray(String) CMLBondArray
getNonBuiltinVal(String) AbstractBuiltinContainer
getNonBuiltinVal(String) BuiltinContainer
getNonHydrogenAtoms() CMLMolecule
convenience method: get Vector of all nonHydrogen atoms
getNonHydrogenCount() CMLAtom
DOM Method getNonHydrogenCountList() CMLAtom
DOM Method getNonHydrogenLigandList() CMLAtom
getNonHydrogenLigandVector() CMLAtom
get Vector of non-hydrogen ligands
getOccupancy() CMLAtom
CORE Method
DOM Method getOrder() CMLBond
CORE Method getOrthogonalisationMatrix() CMLCrystal
getOtherAtom(CMLAtom) CMLBond
returns other atom in a 2-atom bond else null
getRangeCentre() CMLMolecule
get centre of range (not centroid); null if no atoms
getRangeXY2() CMLMolecule
gets range of X and Y 2D coordinates.
getRangeXYZ3() CMLMolecule
gets range of X Y Z 3D coordinates.
getRealValue() CMLFloatVal
getResidueID() CMLAtom
getResidueType() CMLAtom
=======================================================
getRole() CMLLink
getRows() CMLFloatMatrix
getSMILES() CMLAtomParity
SMILES representation (deals with [...], etc)
getSequence() CMLMolecule
extracts the FIRST CMLSequence if any present
getSequence() CMLSequence
getSequenceVector() CMLMolecule
extracts ALL the Sequences as a Vector
getSize() AttributeSize
getSize() CMLFloatArray
getSize() CMLIntegerArray
getSize() CMLStringArray
getSpacegroup() CMLCrystal
CORE Method getSpacegroupNumber(int) CMLCrystal
CORE Method getStereo() CMLBond
CORE Method getString(int) CMLStringArray
getStringList() CMLFloatArray
getStringVal(int) CMLBond
getStringValue() AbstractStringVal
defaults to ""
getStringValue() CMLBondStereo
CORE Method getStringVector() AttributeSize
getStringVector() CMLFloatArray
getStringVector() CMLIntegerArray
getStringVector() CMLStringArray
getSymbol() CMLAtomParity
returns a floating point value; exception provides for symbolic values later
getSymbol() CMLBondStereo
returns a symbolic value
getSymmetryOperators() CMLCrystal
gets symmetry operators as an array of RealMatrix'es (3 rows, 4 columns)
getTitle() AttributeTitle
getTorsionList() CMLMolecule
CORE Method