chemaxon.marvin.alignment

Class Pharmacophore3D

java.lang.Object

chemaxon.marvin.alignment.Pharmacophore3D

public class Pharmacophore3D
extends Object

3D Pharmacophore representation for 3D alignments.

Author:

Adrian Kalaszi

Field Summary

Fields

Modifier and Type	Field and Description
static int	ACCP
static int	ALIPHATIC_RINGCENTER
static int	ANCHOR
static int	AROMATIC_ATOM
static int	AROMATIC_RINGCENTER
static int	DONR
static int	H
static int	HYDR
static int	LP
static int	NEG
static int	POS

Constructor Summary

Constructors

Constructor and Description
Pharmacophore3D()
Pharmacophore3D(Molecule m) Deprecated. Use Pharmacophore3DGenerator instead.
Pharmacophore3D(Molecule pharmacophore, int[] atomTypes)

Method Summary

Methods

Modifier and Type	Method and Description
static Molecule	create(Molecule m)
int[]	getColors()
Molecule	getPharmacophore()
static boolean	isAcceptor(int t)
static boolean	isAliphaticRC(int t)
static boolean	isAnchor(int t)
static boolean	isAromatic(int t)
static boolean	isAromaticRC(int t)
static boolean	isDonor(int t)
static boolean	isH(int t)
static boolean	isHydrophobic(int t)
static boolean	isLP(int t)
static boolean	isNegative(int t)
static boolean	isPositive(int t)
static int	labelAsAnchor(int t)
String	toString()
static String	typeLabel(int t)
static int	withoutType(int tOrig, int tRemove)

Methods inherited from class java.lang.Object

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

Field Detail

DONR

public static final int DONR

See Also:

Constant Field Values

ACCP

public static final int ACCP

See Also:

Constant Field Values

AROMATIC_ATOM

public static final int AROMATIC_ATOM

See Also:

Constant Field Values

HYDR

public static final int HYDR

See Also:

Constant Field Values

POS

public static final int POS

See Also:

Constant Field Values

NEG

public static final int NEG

See Also:

Constant Field Values

LP

public static final int LP

See Also:

Constant Field Values

H

public static final int H

See Also:

Constant Field Values

AROMATIC_RINGCENTER

public static final int AROMATIC_RINGCENTER

See Also:

Constant Field Values

ALIPHATIC_RINGCENTER

public static final int ALIPHATIC_RINGCENTER

See Also:

Constant Field Values

ANCHOR

public static final int ANCHOR

See Also:

Constant Field Values

Constructor Detail

Pharmacophore3D

public Pharmacophore3D(Molecule pharmacophore,
               int[] atomTypes)

Pharmacophore3D

public Pharmacophore3D()

Pharmacophore3D

@Deprecated
public Pharmacophore3D(Molecule m)

Deprecated. Use Pharmacophore3DGenerator instead.

Parameters:

m -

Method Detail

typeLabel

public static String typeLabel(int t)

getPharmacophore

public Molecule getPharmacophore()

isDonor

public static boolean isDonor(int t)

isAliphaticRC

public static boolean isAliphaticRC(int t)

isAromaticRC

public static boolean isAromaticRC(int t)

labelAsAnchor

public static int labelAsAnchor(int t)

isAnchor

public static boolean isAnchor(int t)

withoutType

public static int withoutType(int tOrig,
              int tRemove)

isAcceptor

public static boolean isAcceptor(int t)

isAromatic

public static boolean isAromatic(int t)

isHydrophobic

public static boolean isHydrophobic(int t)

isPositive

public static boolean isPositive(int t)

isNegative

public static boolean isNegative(int t)

isH

public static boolean isH(int t)

isLP

public static boolean isLP(int t)

getColors

public int[] getColors()

create

public static Molecule create(Molecule m)

toString

public String toString()

Overrides:

toString in class Object