chemaxon.marvin.io.formats.mdl

Class MolfileUtil

java.lang.Object

chemaxon.marvin.io.formats.mdl.MolfileUtil

@PublicAPI
public class MolfileUtil
extends java.lang.Object

MDL molfile related utility methods.

Since:

Marvin 5.1.6, 03/10/2009

Version:

5.2, 03/10/2009

Author:

Peter Csizmadia

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String[]	SGROUP_TYPENAMES Array of S-group type names.

Constructor Summary

Constructors

Constructor and Description
MolfileUtil()

Method Summary

Modifier and Type	Method and Description
static int	codeHIsotopeMass(int originalCode, int massNo) Add mass number information to the given code.
static int	decodeHIsotopeMass(int code) Extract H isotope information from the given Chemaxon compressed mol format code of the atom.
static java.lang.Integer	getSgroupType(java.lang.String name) Gets the S-group type.
static boolean	isSpecBeilsteinGeneric(java.lang.String s) Tests whether the specified symbol is a Beilstein Generic except A, Q and X.
static byte[]	MDLCT2MDL(byte[] data) Converts an MDLCT data to MDL.

Methods inherited from class java.lang.Object

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

Field Detail

SGROUP_TYPENAMES

public static final java.lang.String[] SGROUP_TYPENAMES

Array of S-group type names.

Constructor Detail

MolfileUtil

public MolfileUtil()

Method Detail

getSgroupType

public static java.lang.Integer getSgroupType(java.lang.String name)

Gets the S-group type.

Parameters:

name - the S-group type name

Returns:

the type or null for invalid type name

isSpecBeilsteinGeneric

public static boolean isSpecBeilsteinGeneric(java.lang.String s)

Tests whether the specified symbol is a Beilstein Generic except A, Q and X.

Parameters:

s - the S-group type name

Returns:

the type or null for invalid type name

decodeHIsotopeMass

public static int decodeHIsotopeMass(int code)

Extract H isotope information from the given Chemaxon compressed mol format code of the atom.

Parameters:

code - given code

Returns:

the mass number stored in the code

codeHIsotopeMass

public static int codeHIsotopeMass(int originalCode,
                                   int massNo)

Add mass number information to the given code. Utility for compressed mol format coding of H isotopes.

Parameters:

originalCode - the code to which mass number is added

massNo - the mass number

Returns:

the modified code

MDLCT2MDL

public static final byte[] MDLCT2MDL(byte[] data)
                              throws java.io.IOException

Converts an MDLCT data to MDL. MDLCT format: sequence of records where each record is a C like String. Each record stores a line of the molfile (without EOL character). The first byte describes how many bytes are allocated for the string. The MDLCT stream starts with a zero byte since Mol file starts with an empty line.

Parameters:

data - the clipboard transferable MDL bytes

Returns:

an MDL file as a byte array

Throws:

java.io.IOException