chemaxon.marvin.io.formats.mdl

Class MolExport

java.lang.Object

chemaxon.marvin.io.MolExportModule

chemaxon.marvin.io.formats.mdl.MolExport

All Implemented Interfaces:

StereoConstants

@PublicAPI
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:

6.2

Author:

Peter Csizmadia, Szabolcs Csepregi, Erika Biro

Field Summary

Fields inherited from class chemaxon.marvin.io.MolExportModule

addNumbering, aromatize, hydrogenize, stringBuffer

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
MolExport() Constructor.

Method Summary

Modifier and Type	Method and Description
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 molecule) Converts coordinate bonds to data sgroups (attached data) with field name MRV_COORDINATE_BOND.
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<OptionDescriptor> l) Gets the option descriptors.
java.lang.Object	open(java.lang.String fmtopts, MPropertyContainer props) 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, nextOpt, open, parseCharIfOptionSign, preconvert, preconvert, preconvert, preconvert, setEncoding, setGlobalGUIProperties

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<OptionDescriptor> 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,
                             MPropertyContainer props)
                      throws MolExportException

Open the exporter stream.

Overrides:

open in class MolExportModule

Parameters:

fmtopts - output file format and options

props - the gui options or null (ignored parameter)

Returns:

the head of the file for RDF, null otherwise

Throws:

MolExportException - Invalid format string.

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. If the molecule source is in 0D, then cleans the moelcule in 2D before exporting it, since 0D olfiles cannot contains stereo information. This cleaning was introduced in Marvin 5.4, and can be omit by adding "omitClean0D" to the format options.

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

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 molecule)

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

Parameters:

molecule - molecule to convert

Since:

Marvin 5.0 15/07/2007