chemaxon.marvin.io.formats.mdl

Class MolImport

java.lang.Object

chemaxon.marvin.io.MolImportModule

chemaxon.marvin.io.formats.mdl.MolImport

All Implemented Interfaces:

StereoConstants

@PublicAPI
public class MolImport
extends MolImportModule
implements StereoConstants

Imports MDL Molfile, SDfile, RGfile, RDfile, Rxnfile and (ChemAxon) compressed molfile. In the Molfiles documentation, you can find details about import options.

Since:

Marvin 1.3

Version:

Marvin 6.1, 2013.04.11.

Author:

Peter Csizmadia, Szabolcs Csepregi, Erika Biro

Nested Class Summary

Nested classes/interfaces inherited from class chemaxon.marvin.io.MolImportModule

MolImportModule.PreferredView

Field Summary

Fields

Modifier and Type	Field and Description
protected boolean	fixSgroups
protected java.util.List<Sgroup>	sgroupList

Fields inherited from interface chemaxon.struc.StereoConstants

ANTI, ATOMSTEREO_EITHER, ATOMSTEREO_MASK, ATOMSTEREO_NONE, ATOMSTEREO_SPECIFIC, CHIRALITY_M, CHIRALITY_MASK, CHIRALITY_P, CHIRALITY_r, CHIRALITY_R, CHIRALITY_s, CHIRALITY_S, CHIRALITYSUPPORT_ALL, CHIRALITYSUPPORT_ALL_POSSIBLE, CHIRALITYSUPPORT_NONE, CHIRALITYSUPPORT_SELECTED, CIS, CIS_TRANS, CTUMASK, CTUNKNOWN, CTUNSPEC, DBS_ALL, DBS_MARKED, DBS_NONE, ENDO, EXO, PARITY_ALLENE, PARITY_EITHER, PARITY_EVEN, PARITY_MASK, PARITY_NONE, PARITY_ODD, PARITY_TETRAHEDRAL, PARITY_UNSPEC, STGRP_ABS, STGRP_AND, STGRP_NONE, STGRP_OR, SYN, TRANS

Constructor Summary

Constructors

Constructor and Description
MolImport()

Method Summary

Modifier and Type	Method and Description
Molecule	createMol() Creates a new target molecule object.
protected int	getMolfileVersion() Gets the molfile version.
void	initMolImport(MolInputStream is) Initializes the import module.
boolean	readMol(Molecule mol) Reads a molecule from MDL mol/sdf/rxn file.
void	setOptions(java.lang.String opts) Sets the import options.

Methods inherited from class chemaxon.marvin.io.MolImportModule

getLineCount, getPreferredView, initMolImport, isDocumentImporter, readDocument

Methods inherited from class java.lang.Object

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

Field Detail

fixSgroups

protected boolean fixSgroups

sgroupList

protected java.util.List<Sgroup> sgroupList

Constructor Detail

MolImport

public MolImport()

Method Detail

setOptions

public void setOptions(java.lang.String opts)

Sets the import options.

Overrides:

setOptions in class MolImportModule

Parameters:

opts - import options

initMolImport

public void initMolImport(MolInputStream is)
                   throws MolFormatException,
                          java.io.IOException

Initializes the import module.

Overrides:

initMolImport in class MolImportModule

Parameters:

is - the molecule input stream

Throws:

MolFormatException - if the file cannot be read because of a molecule file format related error

java.io.IOException - an I/O error occured while reading the file

readMol

public boolean readMol(Molecule mol)
                throws MolFormatException,
                       java.io.IOException

Reads a molecule from MDL mol/sdf/rxn file. All the nodes, edges, and properties are removed from mol before reading.

Specified by:

readMol in class MolImportModule

Parameters:

mol - the molecule object to read into

Returns:

true after successfully reading the molecule, false if no more molecule found

Throws:

MolFormatException - if the file is in bad format

java.io.IOException - in case of I/O error

createMol

public Molecule createMol()

Creates a new target molecule object.

Specified by:

createMol in class MolImportModule

Returns:

new Molecule, RgMolecule or RxnMolecule

Since:

Marvin 3.4, 05/08/2004

getMolfileVersion

protected int getMolfileVersion()

Gets the molfile version.

Returns:

2 or 3

Since:

Marvin 3.4.1, 07/16/2004