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org::openscience::cdk::io::cml::PDBConvention Class Reference

Inheritance diagram for org::openscience::cdk::io::cml::PDBConvention:

org::openscience::cdk::io::cml::CMLCoreModule org::openscience::cdk::io::cml::ICMLModule

List of all members.


Detailed Description

Implements the PDB convention used by PDB2CML.

This is a lousy implementation, though. Problems that will arise:

Definition at line 70 of file PDBConvention.java.


Public Member Functions

void characterData (CMLStack xpath, char ch[], int start, int length)
void characterData (CMLStack xpath, char[] ch, int start, int length)
void endDocument ()
void endElement (CMLStack xpath, String uri, String local, String raw)
void inherit (ICMLModule convention)
void newSequence ()
 PDBConvention (ICMLModule conv)
 PDBConvention (IChemFile chemFile)
IChemFile returnChemFile ()
void startDocument ()
void startElement (CMLStack xpath, String uri, String local, String raw, Attributes atts)

Protected Member Functions

int addArrayElementsTo (List toAddto, String array)
void newAtomData ()
void newBondData ()
void newCrystalData ()
void newMolecule ()
void newMoleculeData ()
void notify (String message, String systemId, int line, int column)
void storeAtomData ()
void storeBondData ()
void storeData ()

Protected Attributes

int atomCounter
List atomDictRefs
Map atomEnumeration
List atomParities
List bondARef1
List bondARef2
List bondAromaticity
int bondCounter
List bondDictRefs
List bondElid
List bondid
List bondStereo
String BUILTIN
int crystalScalar
int curRef
IAtom currentAtom
IBond currentBond
String currentChars
IChemFile currentChemFile
IChemModel currentChemModel
IChemSequence currentChemSequence
int CurrentElement
IAtomContainer currentMolecule
IMoleculeSet currentMoleculeSet
IMonomer currentMonomer
IReaction currentReaction
IReactionSet currentReactionSet
IStrand currentStrand
String DICTREF
String elementTitle
List elid
List elsym
List eltitles
List formalCharges
List hCounts
String inchi
List isotope
org.openscience.cdk.tools.LoggingTool logger
List occupancies
List order
List partialCharges
List spinMultiplicities
boolean stereoGiven
final String SYSTEMID = "CML-1999-05-15"
double[] unitcellparams
List x2
List x3
List xfract
List y2
List y3
List yfract
List z3
List zfract

Package Attributes

boolean cartesianAxesSet = false

Private Attributes

ArrayList altLocV
ArrayList chainIDV
String connect_root
boolean connectionTable
boolean hasScalar
ArrayList hetAtomV
ArrayList iCodeV
String idValue = ""
boolean isBond
boolean isELSYM
ArrayList nameV
ArrayList oxtV
ArrayList recordV
ArrayList resNameV
ArrayList resSeqV
ArrayList segIDV
ArrayList serialV
ArrayList tempFactorV

The documentation for this class was generated from the following file:

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