com.chemaxon.calculations.util

Class MU

java.lang.Object

com.chemaxon.calculations.util.MU

public final class MU
extends Object

Molecule related utilities.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	MU.BondList Represents a bond list.

Method Summary

Modifier and Type	Method and Description
static int[]	atnoArray(Molecule m) Extract atno array.
static double[][]	atomCoordinates3d(Molecule m) Extract 3D atom coordinates.
static MU.BondList	bondList(Molecule m) Extract a bondlist.
static int[][]	ctab(Molecule m) Extract a ctab.
static Molecule	ofMolSource(String src) Read a structure from source
static Molecule	ofSmiles(String smiles) Read a structure from SMILES.
static double[]	ringTorsionsDeg(Molecule m, int[] atoms) Calculate ring torsions of specified atoms in degrees.
static double[]	ringTorsionsRad(Molecule m, int[] atoms) Calculate ring torsions of specified atoms in radians.
static String	toSmiles(Molecule m) Convert molecule to SMILES.

Methods inherited from class java.lang.Object

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

Method Detail

ringTorsionsRad

public static double[] ringTorsionsRad(Molecule m,
                                       int[] atoms)

Calculate ring torsions of specified atoms in radians.

Parameters:

m - Molecule

atoms - Atom indices

Returns:

Ring torsions in radians

Throws:

IllegalArgumentException - when specified atoms are not part of a ring or less than 4 atoms specified

ringTorsionsDeg

public static double[] ringTorsionsDeg(Molecule m,
                                       int[] atoms)

Calculate ring torsions of specified atoms in degrees.

Parameters:

m - Molecule

atoms - Atom indices

Returns:

Ring torsions in radians

Throws:

IllegalArgumentException - when specified atoms are not part of a ring or less than 4 atoms specified

ofSmiles

public static Molecule ofSmiles(String smiles)

Read a structure from SMILES.

Parameters:

smiles - SMILES input

Returns:

Represented structure

Throws:

IllegalArgumentException - when parsing failed

ofMolSource

public static Molecule ofMolSource(String src)

Read a structure from source

Parameters:

src - Structure source

Returns:

Represented structure

Throws:

IllegalArgumentException - when parsing failed

toSmiles

public static String toSmiles(Molecule m)

Convert molecule to SMILES.

Parameters:

m - Molecule to convert

Returns:

SMILES representation

Throws:

IllegalArgumentException - in case of conversion error

atnoArray

public static int[] atnoArray(Molecule m)

Extract atno array.

Parameters:

m - Input structure

Returns:

Array of MolAtom.getAtno() values.

atomCoordinates3d

public static double[][] atomCoordinates3d(Molecule m)

Extract 3D atom coordinates.

Parameters:

m - Input molecule

Returns:

3D atom coordinates

ctab

public static int[][] ctab(Molecule m)

Extract a ctab.

Parameters:

m - Input structure

Returns:

Deep copy of the represented ctab

bondList

public static MU.BondList bondList(Molecule m)

Extract a bondlist.

Parameters:

m - Input structure

Returns:

Bond list