chemaxon.marvin.io.formats.mdl
Class MolExport

java.lang.Object
  chemaxon.marvin.io.MolExportModule
      chemaxon.marvin.io.formats.mdl.MolExport

All Implemented Interfaces:

StereoConstants

public class MolExport
extends MolExportModule
implements StereoConstants

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

Since:

Marvin 1.2.3

Version:

5.0.7, 07/24/2008

Author:

Peter Csizmadia, Szabolcs Csepregi, Erika Biro

Field Summary

Fields inherited from class chemaxon.marvin.io.MolExportModule

aromatize, stringBuffer

Fields inherited from interface chemaxon.struc.StereoConstants

ATOMSTEREO_EITHER, ATOMSTEREO_MASK, ATOMSTEREO_NONE, ATOMSTEREO_SPECIFIC, CHIRALITY_MASK, CHIRALITY_R, CHIRALITY_S, CHIRALITYSUPPORT_ALL, CHIRALITYSUPPORT_NONE, CHIRALITYSUPPORT_SELECTED, CIS, CTUMASK, CTUNKNOWN, CTUNSPEC, DBS_ALL, DBS_MARKED, DBS_NONE, PARITY_EITHER, PARITY_EVEN, PARITY_MASK, PARITY_ODD, PARITY_UNSPEC, STGRP_ABS, STGRP_AND, STGRP_NONE, STGRP_OR, TRANS

Constructor Summary

MolExport()
Constructor.

Method Summary

protected void	appendMEnd(Molecule mol) Appends the "M END" line to the string buffer.
java.lang.Object	convert(Molecule mol) Creates an MDL mol or compressed mol representation of the molecule.
protected void	convertCoordinateBondsToData(Molecule mol) Converts coordinate bonds to data sgroups (attached data) with field name MRV_COORDINATE_BOND.
protected void	convertMultiCenterSgroupsToData(Molecule mol) Converts the multicenter sgroups to data sgroups in the molecule.
protected void	convertPageSettingsToData(Molecule mol) Converts page setting of multipage molecular document to data sgroups (attached data) with field name MRV_PAGE_XXX.
protected int	getMolfileVersion() Gets the molfile version.
protected void	getOptionDescriptors(java.lang.String fmtname, java.lang.String optnames, java.util.List l) Gets the option descriptors.
java.lang.Object	open(java.lang.String fmtopts) Open the exporter stream.
protected int	parseOption(java.lang.String opts, int i) Parses the bond length (b###) option.

Methods inherited from class chemaxon.marvin.io.MolExportModule

addData, appendChars, appendLeft, appendRight, appendRight, close, getEncoding, getFormat, getOptionDescriptors, getOptionDescriptors, getOptions, getOptionSign, isCleanable, isDocumentExport, isImplicitHcountImportant, isImplicitHcountImportant, isSupportedEncoding, open, parseCharIfOptionSign, preconvert, preconvert, preconvert, preconvert, setEncoding

Methods inherited from class java.lang.Object

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

Constructor Detail

MolExport

public MolExport()

Constructor. Sets the current date.

Method Detail

getOptionDescriptors

protected void getOptionDescriptors(java.lang.String fmtname,
                                    java.lang.String optnames,
                                    java.util.List l)

Gets the option descriptors.

Overrides:

getOptionDescriptors in class MolExportModule

Parameters:

fmtname - the format name or null

optnames - option names or null for all

l - the output list

Since:

Marvin 5.0, 06/06/2007

open

public java.lang.Object open(java.lang.String fmtopts)
                      throws MolExportException

Open the exporter stream.

Overrides:

open in class MolExportModule

Parameters:

fmtopts - output file format and options

Returns:

the head of the file for RDF, null otherwise

Throws:

MolExportException - Invalid format string.

See Also:

MolExportModule.getFormat(), MolExportModule.getOptions()

parseOption

protected int parseOption(java.lang.String opts,
                          int i)
                   throws java.lang.IllegalArgumentException

Parses the bond length (b###) option.

Overrides:

parseOption in class MolExportModule

Parameters:

opts - the options string

i - the current index

Returns:

index of the next option, or i if the current option is unknown

Throws:

java.lang.IllegalArgumentException - in case of parsing error

convert

public java.lang.Object convert(Molecule mol)
                         throws MolExportException

Creates an MDL mol or compressed mol representation of the molecule.

Specified by:

convert in class MolExportModule

Parameters:

mol - the molecule

Returns:

a string containing the molfile

Throws:

MolExportException - cannot be converted to MDL molfile

getMolfileVersion

protected int getMolfileVersion()

Gets the molfile version.

Returns:

2 or 3

Since:

Marvin 3.4.1, 07/16/2004

appendMEnd

protected void appendMEnd(Molecule mol)

Appends the "M END" line to the string buffer.

Parameters:

mol - the molecule

convertMultiCenterSgroupsToData

protected void convertMultiCenterSgroupsToData(Molecule mol)

Converts the multicenter sgroups to data sgroups in the molecule.

Parameters:

mol - the molecule that contains the sgroups to convert

convertPageSettingsToData

protected void convertPageSettingsToData(Molecule mol)

Converts page setting of multipage molecular document to data sgroups (attached data) with field name MRV_PAGE_XXX. The data is attached to the first atom.

Parameters:

mol - molecule to convert

Since:

Marvin 4.1 02/14/2006

convertCoordinateBondsToData

protected void convertCoordinateBondsToData(Molecule mol)

Converts coordinate bonds to data sgroups (attached data) with field name MRV_COORDINATE_BOND. The data is attached to the first atom.

Parameters:

mol - molecule to convert

Since:

Marvin 5.0 15/07/2007