chemaxon.marvin.modules
Class MacroMolecule.Protein

java.lang.Object
  chemaxon.marvin.modules.MacroMolecule.Component
      chemaxon.marvin.modules.MacroMolecule.Polymer
          chemaxon.marvin.modules.MacroMolecule.Protein

Enclosing class:

MacroMolecule

public class MacroMolecule.Protein

extends MacroMolecule.Polymer

Represent a protein chain.

Nested Class Summary

class	MacroMolecule.Protein.AtomIterator
class	MacroMolecule.Protein.AtomProperty
class	MacroMolecule.Protein.BondIterator
class	MacroMolecule.Protein.CAlphaAtomIterator Enumerates alpha carbon atoms of the protein.
class	MacroMolecule.Protein.Helix
class	MacroMolecule.Protein.HelixIterator
class	MacroMolecule.Protein.SecondaryStructure
class	MacroMolecule.Protein.Sheet
class	MacroMolecule.Protein.SheetIterator
class	MacroMolecule.Protein.Turn
class	MacroMolecule.Protein.TurnIterator

Nested classes inherited from class chemaxon.marvin.modules.MacroMolecule.Polymer

MacroMolecule.Polymer.Model

Field Summary

protected java.util.Vector	helixes
protected java.util.Vector	sheets
protected java.util.Vector	turns

Fields inherited from class chemaxon.marvin.modules.MacroMolecule.Polymer

currentICode, currentModelSerial, currentResidueIndex, currentResidueType, currentSeqNo, currentSequenceIndex, iCode, models, molId, residueOffset, residues, seqBegin, seqEnd, seqNo, sequence

Fields inherited from class chemaxon.marvin.modules.MacroMolecule.Component

atomCount, bondCount, chainId, definedAtomCount, definedHCount, hCount, name

Constructor Summary

MacroMolecule.Protein(char chainId, int modelCount, int residueCount, int atomCount)
Creates an empty Protein with the given name and chain identifier.

Method Summary

void	addHelix(int serNum, java.lang.String helixId, char chainId, int initSeqNum, char initICode, int endSeqNum, char endICode, int helixClass, int length)
void	addSheet(int serNum, java.lang.String sheetId, char chainId, int initSeqNum, char initICode, int endSeqNum, char endICode, int sense, int numStrands)
void	addTurn(int seq, java.lang.String sheetId, char chainId, int initSeqNum, char initICode, int endSeqNum, char endICode)
MacroMolecule.Protein.AtomIterator	getAtomIterator()
MoleculeIterators.AtomIteratorInterface	getAtomIterator(boolean enumerateHydrogens) Gets a new iterator that can enumerate all atoms of the Component.
MoleculeIterators.AtomPropertyInterface	getAtomProperty() Gets a new AtomPropertyInterface that can retrieve various atom related properties.
MacroMolecule.Protein.BondIterator	getBondIterator()
MoleculeIterators.BondIteratorInterface	getBondIterator(boolean enumerateHydrogens) Gets a new iterator that can enumerate all bonds of the Component.
MoleculeIterators.AtomIteratorInterface	getCAlphaAtomIterator() Gets an initialized alpha carbon atom iterator.
MacroMolecule.Protein.HelixIterator	getHelixIterator()
MacroMolecule.Protein.SheetIterator	getSheetIterator()
MacroMolecule.Protein.TurnIterator	getTurnIterator()

Methods inherited from class chemaxon.marvin.modules.MacroMolecule.Polymer

addAtom, addModelAtom, addModRes, addSeqRange, addSequenceResidue, getAtomIterator, getAtomLabel, getResidueCount, getSequenceResidueCount, getX, getY, getZ, hasChain, setSequenceResidueCount

Methods inherited from class chemaxon.marvin.modules.MacroMolecule.Component

addToMolecule, containsAtom, getAtomCount, getChainId, getDefinedAtomCount, getHydrogenCount, getICode, getName, setName

Methods inherited from class java.lang.Object

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

Field Detail

helixes

protected java.util.Vector helixes

sheets

protected java.util.Vector sheets

turns

protected java.util.Vector turns

Constructor Detail

MacroMolecule.Protein

public MacroMolecule.Protein(char chainId,
                             int modelCount,
                             int residueCount,
                             int atomCount)

Creates an empty Protein with the given name and chain identifier.

Parameters:

chainId - one letter chain code

Method Detail

addHelix

public void addHelix(int serNum,
                     java.lang.String helixId,
                     char chainId,
                     int initSeqNum,
                     char initICode,
                     int endSeqNum,
                     char endICode,
                     int helixClass,
                     int length)

addSheet

public void addSheet(int serNum,
                     java.lang.String sheetId,
                     char chainId,
                     int initSeqNum,
                     char initICode,
                     int endSeqNum,
                     char endICode,
                     int sense,
                     int numStrands)

addTurn

public void addTurn(int seq,
                    java.lang.String sheetId,
                    char chainId,
                    int initSeqNum,
                    char initICode,
                    int endSeqNum,
                    char endICode)

getAtomIterator

public MacroMolecule.Protein.AtomIterator getAtomIterator()

getCAlphaAtomIterator

public MoleculeIterators.AtomIteratorInterface getCAlphaAtomIterator()

Gets an initialized alpha carbon atom iterator.

Returns:

alpha carbon atom iterator

getBondIterator

public MacroMolecule.Protein.BondIterator getBondIterator()

getAtomIterator

public MoleculeIterators.AtomIteratorInterface getAtomIterator(boolean enumerateHydrogens)

Description copied from class: MacroMolecule.Component

Gets a new iterator that can enumerate all atoms of the Component.

Overrides:

getAtomIterator in class MacroMolecule.Polymer

getBondIterator

public MoleculeIterators.BondIteratorInterface getBondIterator(boolean enumerateHydrogens)

Description copied from class: MacroMolecule.Component

Gets a new iterator that can enumerate all bonds of the Component.

Overrides:

getBondIterator in class MacroMolecule.Polymer

getAtomProperty

public MoleculeIterators.AtomPropertyInterface getAtomProperty()

Description copied from class: MacroMolecule.Component

Gets a new AtomPropertyInterface that can retrieve various atom related properties.

Overrides:

getAtomProperty in class MacroMolecule.Polymer

getHelixIterator

public MacroMolecule.Protein.HelixIterator getHelixIterator()

getSheetIterator

public MacroMolecule.Protein.SheetIterator getSheetIterator()

getTurnIterator

public MacroMolecule.Protein.TurnIterator getTurnIterator()