charite.christo.protein
Class HeteroCompound

java.lang.Object
  charite.christo.protein.HeteroCompound

All Implemented Interfaces:

HasPropertyMap, HasRenderer, HasRendererModiCount, HasWeakRef

public class HeteroCompound
extends java.lang.Object
implements HasRendererModiCount, HasPropertyMap, HasWeakRef

HELP The HeteroCompound class can hold two types of 3D-structures:

1. Ligands like NADH, FAD, FMN and metal ions encoded in PDB files in the form

   
   HETATM 1782  N1  FMN   250      48.214  29.647  32.784  1.00 17.44           N
   HETATM 1783  C2  FMN   250      49.266  29.076  32.156  1.00 18.90           C
   HETATM 1784  O2  FMN   250      49.813  28.099  32.542  1.00 19.30           O
   HETATM 1785  N3  FMN   250      49.770  29.656  30.913  1.00 18.58           N
   ...
   
   

2. and DNA/RNA-Chains

   ATOM      1  O5'  DA A  -7      30.070  92.468  -2.825  1.00 38.96           O
   ATOM      2  C5'  DA A  -7      30.552  92.351  -1.492  1.00 37.56           C
   ATOM      3  C4'  DA A  -7      29.981  93.462  -0.647  1.00 37.41           C
   ATOM      4  O4'  DA A  -7      28.542  93.348  -0.624  1.00 38.03           O
   ATOM      5  C3'  DA A  -7      30.417  93.452   0.816  1.00 36.92           C
   ATOM      6  O3'  DA A  -7      30.428  94.808   1.280  1.00 34.96           O
   ATOM      7  C2'  DA A  -7      29.316  92.653   1.489  1.00 37.67           C
   ...
   

Water, however, is skipped.

Two cases are treated differently:

1. A structure may be stored in one _file together with the peptide.
2. The structure is stored in a file on it's own. It is assigned to this peptide that has the smallest Euclidean distance. In the list of compounds a file context menu is opened by right-click

The compound inherits the 3D-transformation (rotation and translation) from the peptide structure it is assigned to. Protein structures are transformed in STRAP by 3D-superposition. Upon Drag-n-Drop the compound is written as a PDB-file. It might be exported in native coordinates or in transformed coordinates.

Field Summary

java.lang.Object	_wr
static HeteroCompound[]	NONE
static long	ONLY_PHOSPHATE

Fields inherited from interface charite.christo.HasRenderer

JLIST, STRIKE_THROUGH

Constructor Summary

HeteroCompound()

Method Summary

static javax.swing.AbstractButton	cbDndTransformHetero()
Protein	closestProtein(Protein[] pp, long options)
int	countAtoms()
boolean	equals(java.lang.Object o2)
int[]	getAtomName32()
int[]	getAtomNumber()
byte[]	getAtomType()
Protein	getBelongsToProtein()
char	getCompoundChain()
int	getCompoundName32()
int	getCompoundNumber()
float[]	getCoordinates()
java.io.File	getFile() Not null if it is defined in a PDB file on its own
byte[]	getLongName()
java.lang.String	getNameForPymol()
byte[]	getNucleotideBase()
int[]	getNucleotideNumber()
java.io.File	getPeptideFile() Not null if it is defined in the same file as a peptide chain
java.util.Map	getPropertyMap(boolean create)
java.lang.Object	getRenderer(long options, long[] rendOptions)
long	getRendererModiCount()
java.lang.Object	getWeakRef()
boolean	isDNA()
boolean	isNucleotideChain()
static HeteroCompound[]	parse(BA ba, boolean nuclBackbone)
java.lang.Object	run(java.lang.String id, java.lang.Object arg)
void	setCoordinates(float[] xyz)
void	setFile(java.io.File f)
void	setPeptideFile(java.io.File f)
float	squareDistanceToNucleotidechain(float[] xyz, int fromIdx, int toIdx, Matrix3D m3d, long options)
java.lang.String	toString()
BA	toText(long mode, Matrix3D m3d, BA sb0)

Methods inherited from class java.lang.Object

getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

NONE

public static final HeteroCompound[] NONE

ONLY_PHOSPHATE

public static final long ONLY_PHOSPHATE

See Also:

Constant Field Values

_wr

public final java.lang.Object _wr

Constructor Detail

HeteroCompound

public HeteroCompound()

Method Detail

isNucleotideChain

public boolean isNucleotideChain()

isDNA

public boolean isDNA()

setFile

public void setFile(java.io.File f)

getFile

public java.io.File getFile()

Not null if it is defined in a PDB file on its own

getPeptideFile

public java.io.File getPeptideFile()

Not null if it is defined in the same file as a peptide chain

setPeptideFile

public void setPeptideFile(java.io.File f)

getCompoundChain

public char getCompoundChain()

countAtoms

public int countAtoms()

getCompoundName32

public int getCompoundName32()

getCompoundNumber

public int getCompoundNumber()

getNucleotideBase

public byte[] getNucleotideBase()

getLongName

public byte[] getLongName()

getAtomType

public byte[] getAtomType()

getNucleotideNumber

public int[] getNucleotideNumber()

getAtomName32

public int[] getAtomName32()

getAtomNumber

public int[] getAtomNumber()

parse

public static HeteroCompound[] parse(BA ba,
                                     boolean nuclBackbone)

toText

public BA toText(long mode,
                 Matrix3D m3d,
                 BA sb0)

getNameForPymol

public java.lang.String getNameForPymol()

getBelongsToProtein

public Protein getBelongsToProtein()

closestProtein

public Protein closestProtein(Protein[] pp,
                              long options)

squareDistanceToNucleotidechain

public final float squareDistanceToNucleotidechain(float[] xyz,
                                                   int fromIdx,
                                                   int toIdx,
                                                   Matrix3D m3d,
                                                   long options)

setCoordinates

public void setCoordinates(float[] xyz)

getCoordinates

public float[] getCoordinates()

getRenderer

public java.lang.Object getRenderer(long options,
                                    long[] rendOptions)

Specified by:

getRenderer in interface HasRenderer

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

getRendererModiCount

public long getRendererModiCount()

Specified by:

getRendererModiCount in interface HasRendererModiCount

cbDndTransformHetero

public static javax.swing.AbstractButton cbDndTransformHetero()

run

public java.lang.Object run(java.lang.String id,
                            java.lang.Object arg)

getPropertyMap

public java.util.Map getPropertyMap(boolean create)

Specified by:

getPropertyMap in interface HasPropertyMap

getWeakRef

public java.lang.Object getWeakRef()

Specified by:

getWeakRef in interface HasWeakRef

equals

public boolean equals(java.lang.Object o2)

Overrides:

equals in class java.lang.Object