chemaxon.marvin.alignment
Class Pharmacophore3D

java.lang.Object
  chemaxon.marvin.alignment.Pharmacophore3D

public class Pharmacophore3D
extends java.lang.Object

3D Pharmacophore creation and representation for 3D alignments.

Author:

adrian

Field Summary

static int	ACCP
static int	ALIPHATIC_RINGCENTER
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
static int	SHAPE

Constructor Summary

Pharmacophore3D()

Pharmacophore3D(Molecule m)

Method Summary

int[]	getColors()
Molecule	getPharmacophore()
static boolean	isAcceptor(int t)
static boolean	isAliphaticRC(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 boolean	isShape(int t)
static int	labelWithShape(int t)
static java.lang.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, toString, wait, wait, wait

Field Detail

DONR

public static int DONR

ACCP

public static int ACCP

AROMATIC_ATOM

public static int AROMATIC_ATOM

HYDR

public static int HYDR

POS

public static int POS

NEG

public static int NEG

LP

public static int LP

H

public static int H

AROMATIC_RINGCENTER

public static int AROMATIC_RINGCENTER

ALIPHATIC_RINGCENTER

public static int ALIPHATIC_RINGCENTER

SHAPE

public static int SHAPE

Constructor Detail

Pharmacophore3D

public Pharmacophore3D()

Pharmacophore3D

public Pharmacophore3D(Molecule m)
                throws chemaxon.marvin.alignment.AlignmentException

Throws:

chemaxon.marvin.alignment.AlignmentException

Method Detail

typeLabel

public static java.lang.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)

labelWithShape

public static int labelWithShape(int t)

isShape

public static boolean isShape(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()