chemaxon.marvin.modules
Class MacroMolecule

java.lang.Object
  chemaxon.marvin.modules.MacroMolecule

public class MacroMolecule
extends java.lang.Object

The MacroMolecule class provides the internal representation of biochemical data stored in PDB files. One instance of this class is capable of storing an arbitrary number of protein chains, nucleic acid chains, small molecule compounds (e.g. ligands), and it also represents water molecules, ions.

Since:

Marvin 4.0.2

Version:

4.0.2, 28-Oct-2005

Author:

Miklos Vargyas

Nested Class Summary

class	MacroMolecule.BadMoleculeException The exception class thrown by methods of the MacroMolecule class.
static class	MacroMolecule.BondMaker
class	MacroMolecule.Component The Component class represents any kind of molecular structure connected by covalent bonds.
class	MacroMolecule.ComponentIterator Enumerates all components of the MacroMolecule.
class	MacroMolecule.Compound The Compound class partially represents the COMPND record in the PDB file.
class	MacroMolecule.HeteroComponent This class specializes the Component class to represent ligands, ions and water molecules.
class	MacroMolecule.NucleicAcid
class	MacroMolecule.Polymer The Polymer class represents nucleic acid and amino acid chains.
class	MacroMolecule.Protein Represent a protein chain.
class	MacroMolecule.Water

Constructor Summary

MacroMolecule(int modelCount, java.util.Hashtable chains, int[] residueCountPerChain, int[] atomCountPerChain, java.util.Hashtable heteroGroups, int[] atomCountPerHeteroGroup)
Creates an empty MacroMoleculeobject.

Method Summary

void	addAtom(int serial, java.lang.String name, char altLoc, java.lang.String resName, java.lang.String chainId, int resSeqNo, char iCode, float x, float y, float z, java.lang.String element, int charge, boolean hetero, float bFactor)
void	addAuthor(java.lang.String author)
void	addBond(int[] atomIndex)
void	addChain(java.lang.String chainId)
void	addCompound(java.lang.String molName)
void	addExpData(java.lang.String expData)
void	addHeader(java.lang.String classification, java.lang.String depDate, java.lang.String idCode)
void	addHelix(int serNum, java.lang.String helixId, java.lang.String chainId, int initSeqNum, char initICode, int endSeqNum, char endICode, int helixClass, int length)
void	addHet(java.lang.String hetId, java.lang.String chainId, int seqNum, char iCode, int numHetAtoms)
void	addHetNam(java.lang.String hetId, java.lang.String name)
void	addKeywords(java.lang.String keywords)
void	addMolId(int molId)
void	addMolName(java.lang.String molName)
void	addSeqNoRange(java.lang.String chainId, int seqBegin, int seqEnd)
void	addSeqres(int residueTypeId)
boolean	addSeqres(java.lang.String chainId, int residueCount, java.lang.String resName)
void	addSheet(int serNum, java.lang.String sheetId, java.lang.String chainId, int initSeqNum, char initICode, int endSeqNum, char endICode, int sense, int numStrands)
void	addSource(java.lang.String source)
void	addTer()
void	addTitle(java.lang.String title)
void	addTurn(int seq, java.lang.String sheetId, java.lang.String chainId, int initSeqNum, char initICode, int endSeqNum, char endICode)
void	addWater(java.lang.String hetId, int oCount, int hCount)
void	beginModel(int serialNumber)
void	end(int hydrogenizeMode, boolean fixBondTypes)
void	endModel()
protected int	findParentAtom(float x, float y, float z)
int	getAtomCount()
java.lang.String	getAuthor()
MacroMolecule.Polymer	getChain(java.lang.String chainId)
int	getDefinedAtomCount()
java.lang.String	getExpData()
java.lang.String	getHeader()
int	getHydrogenCount()
MacroMolecule.ComponentIterator	getIterator()
java.lang.String	getKeywords()
java.lang.String	getName()
java.lang.String	getSource()
java.lang.String	getTitle()
boolean	hasWater()
void	toMolecule(Molecule mol)

Methods inherited from class java.lang.Object

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

Constructor Detail

MacroMolecule

public MacroMolecule(int modelCount,
                     java.util.Hashtable chains,
                     int[] residueCountPerChain,
                     int[] atomCountPerChain,
                     java.util.Hashtable heteroGroups,
                     int[] atomCountPerHeteroGroup)

Creates an empty MacroMoleculeobject.

Method Detail

addHeader

public void addHeader(java.lang.String classification,
                      java.lang.String depDate,
                      java.lang.String idCode)

addTitle

public void addTitle(java.lang.String title)

addSource

public void addSource(java.lang.String source)

addKeywords

public void addKeywords(java.lang.String keywords)

addExpData

public void addExpData(java.lang.String expData)

addAuthor

public void addAuthor(java.lang.String author)

addMolId

public void addMolId(int molId)
              throws MacroMolecule.BadMoleculeException

Throws:

MacroMolecule.BadMoleculeException

addMolName

public void addMolName(java.lang.String molName)
                throws MacroMolecule.BadMoleculeException

Throws:

MacroMolecule.BadMoleculeException

addCompound

public void addCompound(java.lang.String molName)
                 throws MacroMolecule.BadMoleculeException

Throws:

MacroMolecule.BadMoleculeException

addChain

public void addChain(java.lang.String chainId)
              throws MacroMolecule.BadMoleculeException

Throws:

MacroMolecule.BadMoleculeException

addSeqNoRange

public void addSeqNoRange(java.lang.String chainId,
                          int seqBegin,
                          int seqEnd)
                   throws MacroMolecule.BadMoleculeException

Throws:

MacroMolecule.BadMoleculeException

addSeqres

public boolean addSeqres(java.lang.String chainId,
                         int residueCount,
                         java.lang.String resName)
                  throws MacroMolecule.BadMoleculeException

Throws:

MacroMolecule.BadMoleculeException

addSeqres

public void addSeqres(int residueTypeId)
               throws MacroMolecule.BadMoleculeException

Throws:

MacroMolecule.BadMoleculeException

addHet

public void addHet(java.lang.String hetId,
                   java.lang.String chainId,
                   int seqNum,
                   char iCode,
                   int numHetAtoms)

addHetNam

public void addHetNam(java.lang.String hetId,
                      java.lang.String name)

addHelix

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

addSheet

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

addTurn

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

beginModel

public void beginModel(int serialNumber)
                throws MacroMolecule.BadMoleculeException

Throws:

MacroMolecule.BadMoleculeException

endModel

public void endModel()
              throws MacroMolecule.BadMoleculeException

Throws:

MacroMolecule.BadMoleculeException

addAtom

public void addAtom(int serial,
                    java.lang.String name,
                    char altLoc,
                    java.lang.String resName,
                    java.lang.String chainId,
                    int resSeqNo,
                    char iCode,
                    float x,
                    float y,
                    float z,
                    java.lang.String element,
                    int charge,
                    boolean hetero,
                    float bFactor)
             throws MacroMolecule.BadMoleculeException

Throws:

MacroMolecule.BadMoleculeException

findParentAtom

protected int findParentAtom(float x,
                             float y,
                             float z)

addBond

public void addBond(int[] atomIndex)

addWater

public void addWater(java.lang.String hetId,
                     int oCount,
                     int hCount)

hasWater

public boolean hasWater()

addTer

public void addTer()

end

public void end(int hydrogenizeMode,
                boolean fixBondTypes)

getIterator

public MacroMolecule.ComponentIterator getIterator()

getName

public java.lang.String getName()

getHeader

public java.lang.String getHeader()

getTitle

public java.lang.String getTitle()

getSource

public java.lang.String getSource()

getKeywords

public java.lang.String getKeywords()

getExpData

public java.lang.String getExpData()

getAuthor

public java.lang.String getAuthor()

getChain

public MacroMolecule.Polymer getChain(java.lang.String chainId)

getAtomCount

public int getAtomCount()

getDefinedAtomCount

public int getDefinedAtomCount()

getHydrogenCount

public int getHydrogenCount()

toMolecule

public void toMolecule(Molecule mol)