chemaxon.marvin.modules
Class MacroMolecule.Polymer

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

Direct Known Subclasses:

MacroMolecule.NucleicAcid, MacroMolecule.Protein

Enclosing class:

MacroMolecule

public class MacroMolecule.Polymer

extends MacroMolecule.Component

The Polymer class represents nucleic acid and amino acid chains. The sequence is stored along with atom coordinates. Missing residues as well as residues with the same residue number but different insertion code are represented.
The entire chain is not represented as one Molecule instance for the sake of speed and small storage space usage.

Nested Class Summary

class	MacroMolecule.Polymer.AtomIterator Enumerates all atoms of a polymer chain.
class	MacroMolecule.Polymer.AtomProperty Provides polymorphic access to atom properties of polymer atoms.
class	MacroMolecule.Polymer.BondIterator Iterates all bonds of the pylomer.
class	MacroMolecule.Polymer.Model

Field Summary

protected char	currentICode
protected int	currentModelSerial these are used in build-up phase
protected int	currentResidueIndex
protected int	currentResidueType
protected int	currentSeqNo
protected int	currentSequenceIndex
protected char[]	iCode insertion code of residues
protected MacroMolecule.Polymer.Model[]	models
protected int	molId
protected int[]	residueOffset index of the first atom of the residue in the atom coordinate arrays
protected int[]	residues residue type ids as defined by the ATOM/HETATOM records
protected int	seqBegin
protected int	seqEnd
protected int[]	seqNo sequence number of residues
protected int[]	sequence residue type ids as defined in the SEQRES records

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

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

Constructor Summary

MacroMolecule.Polymer(char chainId, int modelCount, int residueCount, int atomCount)
Creates an amino acid or nucleic acid polymer with the given name and chain identifier.

Method Summary

void	addAtom(int serial, int residueTypeId, int residueAtomIndex, int resSeqNo, char iCode, float x, float y, float z, float bFactor) Adds a residue atom to the chain.
void	addModelAtom(int modelSerial, int residueTypeId, int residueAtomIndex, int resSeqNo, char iCode, float x, float y, float z, float bFactor)
void	addModRes(int residueTypeId, int residueAtomCount, int resSeqNo)
void	addSeqRange(int seqBegin, int seqEnd) Specifies residue sequence number range within which residue sequence numbers in the ATOM records should fall.
void	addSequenceResidue(int residueTypeId) Adds a new residue to the current chain.
MoleculeIterators.AtomIteratorInterface	getAtomIterator(boolean enumerateHydrogens) Gets a new iterator that can enumerate all atoms of the Component.
MoleculeIterators.AtomIteratorInterface	getAtomIterator(int fromResidue, int toResidue)
java.lang.String	getAtomLabel(int atomIndex) Gets the label of the specified atom.
MoleculeIterators.AtomPropertyInterface	getAtomProperty() Gets a new AtomPropertyInterface that can retrieve various atom related properties.
MoleculeIterators.BondIteratorInterface	getBondIterator(boolean enumerateHydrogens) Gets a new iterator that can enumerate all bonds of the Component.
int	getResidueCount() Gets the nuber of residues defined by ATOM/HETATM records in the current chain.
int	getSequenceResidueCount() Gets the nuber of residues defined by SEQRES records in the current chain.
float	getX(int index) Gets the first coordinate of the spacified residue atom.
float	getY(int index) Gets the second coordinate of the spacified residue atom.
float	getZ(int index) Gets the third coordinate of the spacified residue atom.
boolean	hasChain(char chainId) Checks if this component represents the specified chain.
void	setSequenceResidueCount(int residueCount) Specifies the total number of residues in the given chain.

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

molId

protected int molId

seqBegin

protected int seqBegin

seqEnd

protected int seqEnd

sequence

protected int[] sequence

residue type ids as defined in the SEQRES records

residues

protected int[] residues

residue type ids as defined by the ATOM/HETATOM records

seqNo

protected int[] seqNo

sequence number of residues

iCode

protected char[] iCode

insertion code of residues

residueOffset

protected int[] residueOffset

index of the first atom of the residue in the atom coordinate arrays

models

protected MacroMolecule.Polymer.Model[] models

currentModelSerial

protected int currentModelSerial

these are used in build-up phase

currentSequenceIndex

protected int currentSequenceIndex

currentResidueIndex

protected int currentResidueIndex

currentResidueType

protected int currentResidueType

currentSeqNo

protected int currentSeqNo

currentICode

protected char currentICode

Constructor Detail

MacroMolecule.Polymer

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

Creates an amino acid or nucleic acid polymer with the given name and chain identifier.

Parameters:

chainId - chain identifier

residueCount - number of residues constituting the polymer chain

atomCount - number of atoms in the polymer

Method Detail

setSequenceResidueCount

public void setSequenceResidueCount(int residueCount)

Specifies the total number of residues in the given chain. Residues not represented in the PDB file by ATOM records are also considered.

Parameters:

residueCount - number of residues in the current component

addSeqRange

public void addSeqRange(int seqBegin,
                        int seqEnd)

Specifies residue sequence number range within which residue sequence numbers in the ATOM records should fall.

Parameters:

seqBegin - smallest sequence number on this chain

seqEnd - largest sequence number on this chain

addSequenceResidue

public void addSequenceResidue(int residueTypeId)

Adds a new residue to the current chain. This method is called when a residue type name is read from a SEQRES record processed.

Parameters:

residueTypeId - internal index of type of the residue (as determined by PDBResidues)

addModRes

public void addModRes(int residueTypeId,
                      int residueAtomCount,
                      int resSeqNo)

addAtom

public void addAtom(int serial,
                    int residueTypeId,
                    int residueAtomIndex,
                    int resSeqNo,
                    char iCode,
                    float x,
                    float y,
                    float z,
                    float bFactor)
             throws MacroMolecule.BadMoleculeException

Adds a residue atom to the chain.

Parameters:

serial - serial atom index in PDB

residueTypeId - internal index of type of the residue

residueAtomIndex - internal index of the atom in the residue

resSeqNo - sequence number as specified in the PDB file

iCode - insertion code as specified in the PDB file

x - atom coordinate x

y - atom coordinate y

z - atom coordinate z

Throws:

BadMoleculeException - not thrown, though it should be implemented later

MacroMolecule.BadMoleculeException

addModelAtom

public void addModelAtom(int modelSerial,
                         int residueTypeId,
                         int residueAtomIndex,
                         int resSeqNo,
                         char iCode,
                         float x,
                         float y,
                         float z,
                         float bFactor)
                  throws MacroMolecule.BadMoleculeException

Throws:

MacroMolecule.BadMoleculeException

hasChain

public boolean hasChain(char chainId)

Checks if this component represents the specified chain.

Parameters:

chainId - one letter chain identifier

Returns:

true if given chain is part of this Component

getSequenceResidueCount

public int getSequenceResidueCount()

Gets the nuber of residues defined by SEQRES records in the current chain.

Returns:

total number of residues, including missing residues

getResidueCount

public int getResidueCount()

Gets the nuber of residues defined by ATOM/HETATM records in the current chain.

Returns:

total number of residues, including missing residues

getAtomLabel

public java.lang.String getAtomLabel(int atomIndex)

Description copied from class: MacroMolecule.Component

Gets the label of the specified atom.

Overrides:

getAtomLabel in class MacroMolecule.Component

Parameters:

atomIndex - index of the atom quiried

Returns:

label of the specified atom

getX

public float getX(int index)

Gets the first coordinate of the spacified residue atom.

Parameters:

index - internal atom index as returned by an AtomIteratorInterface

Returns:

x coordinate

getY

public float getY(int index)

Gets the second coordinate of the spacified residue atom.

Parameters:

index - internal atom index as returned by an AtomIteratorInterface

Returns:

y coordinate

getZ

public float getZ(int index)

Gets the third coordinate of the spacified residue atom.

Parameters:

index - internal atom index as returned by an AtomIteratorInterface

Returns:

z coordinate

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.Component

Parameters:

enumerateHydrogens - indicates if hydrogen atoms are enumerated or not

Returns:

an initialized atom iterator

getAtomIterator

public MoleculeIterators.AtomIteratorInterface getAtomIterator(int fromResidue,
                                                               int toResidue)

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.Component

Parameters:

enumerateHydrogens - indicates if bonds to hydrogen atoms are enumerated or not

Returns:

an initialized bond iterator

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.Component

Returns:

an atom property interface