chemaxon.marvin.io
Class MolExportModule

java.lang.Object
  chemaxon.marvin.io.MolExportModule

Direct Known Subclasses:

MolExport, MolExportModule

public abstract class MolExportModule
extends java.lang.Object

Abstract base class of molecule export modules. An export module for format "XXX" must have the name chemaxon.marvin.modules.XxxExport. Converted structures are returned by molecule.toFormat("xxx") or toBinFormat("xxx") method calls, as Strings or byte[] arrays.

Example
The export module that can produce molecule files like the one in the MolImportModule example, is the following:

 package myio;

 import chemaxon.struc.*;

 public class MyFormatExport extends chemaxon.marvin.io.MolExportModule
 {
     public Object convert(Molecule mol) {
         StringBuffer s = stringBuffer;
         s.setLength(0);
         s.append(mol.getName());
         s.append('\n');
         // atoms
         s.append(String.valueOf(mol.getAtomCount()));
         s.append('\n');
         for(int i = 0; i < mol.getAtomCount(); ++i) {
             MolAtom a = mol.getAtom(i);
             s.append(a.getSymbol());
             s.append('\t');
             s.append(String.valueOf(a.getX()));
             s.append('\t');
             s.append(String.valueOf(a.getY()));
             s.append('\n');
         }
         // bonds
         s.append(String.valueOf(mol.getBondCount()));
         s.append('\n');
         for(int i = 0; i < mol.getBondCount(); ++i) {
             MolBond b = mol.getBond(i);
             s.append(String.valueOf(mol.indexOf(b.getAtom1()) + 1));
             s.append('\t');
             s.append(String.valueOf(mol.indexOf(b.getAtom2()) + 1));
             s.append('\t');
             s.append(String.valueOf(b.getType()));
             s.append('\n');
         }
         return s.toString();
     }
 }
 

After compiling and placing the class into Marvin's CLASSPATH, you can create "myformat" files with MolConverter,

 molconvert myformat pyrrole.mol -o pyrrole.myf
 

and the applets:

 s = msketch.getMol("myformat");
 

Since:

Marvin 2.7.9

Version:

5.2.1, 05/19/2009

Author:

Peter Csizmadia, Szabolcs Csepregi, Erika Biro

See Also:

Molecule.toFormat(java.lang.String), Molecule.toBinFormat(java.lang.String)

Field Summary

protected boolean	addNumbering Add numbers to atoms corresponding to the (IUPAC) naming of the molecule.
protected int	aromatize Aromatize molecule according to basic aromatization if MoleculeGraph.AROM_BASIC + 1, according to general aromatization if MoleculeGraph.AROM_GENERAL + 1, dearomatize if -1, do nothing if 0.
protected int	hydrogenize Add Hydrogen atoms if 1, remove if -1, do nothing if 0.
protected java.lang.StringBuffer	stringBuffer This buffer can contain the molecule file contents, in case of a text format.

Constructor Summary

MolExportModule()

Method Summary

protected void	addData(Molecule mol, MolAtom ma, java.lang.String fieldName, java.lang.String value) Adds a data sgroup to the given atom in the given molecule with fieldName and value.
protected void	appendChars(int n, char c) Append a character n times to the string buffer.
protected void	appendLeft(java.lang.String t, int n) Append a string to the buffer in %-ns format.
protected void	appendRight(int t, int n, char c) Append an integer to the buffer in the right hand side of an n-characters wide field.
protected void	appendRight(java.lang.String t, int n, char c) Append a string to the buffer in the right hand side of an n-characters wide field.
java.lang.Object	close() Close the stream.
abstract java.lang.Object	convert(Molecule mol) Convert a molecule to a string or byte array.
java.lang.String	getEncoding() Gets the output encoding.
java.lang.String	getFormat() Returns the output format.
protected static java.lang.String	getOptionDescriptors(java.util.ResourceBundle rc, java.lang.String fmtname, java.lang.String optnames, java.util.List l) Gets an array of option descriptors.
OptionDescriptor[]	getOptionDescriptors(java.lang.String fmtname) Gets an array of option descriptors for the specified format.
protected void	getOptionDescriptors(java.lang.String fmtname, java.lang.String optnames, java.util.List l) Gets an array of option descriptors.
protected java.lang.String	getOptions() Returns the output options.
protected int	getOptionSign() Gets the sign of the options.
boolean	isCleanable() Tests whether 2D or 3D cleaning is meaningful for this output format.
boolean	isDocumentExport() Tests if this export module is document export instead of a simple molecule export.
static boolean	isImplicitHcountImportant(MolAtom a) Checks whether the number of implicit hydrogens is important information for an atom or not.
boolean	isImplicitHcountImportant(MoleculeGraph mol) Checks whether the number of implicit hydrogens is important information for the atoms of mol or not.
protected static int	nextOpt(java.lang.String opts, int i, java.lang.String s) Tests whether the option string contains the specified substring at the specified position.
java.lang.Object	open(java.lang.String fmtopts) Opens the exporter stream.
java.lang.Object	open(java.lang.String fmtopts, MPropertyContainer props) Opens the exporter stream.
protected int	parseCharIfOptionSign(java.lang.String opts, int i) Parse the current character if it is an option sign.
protected int	parseOption(java.lang.String opts, int i) Parses the following option in the option string.
protected Molecule	preconvert(Molecule mol) Optionally performs aromatization or addition of explicit Hydrogens atoms.
protected Molecule	preconvert(Molecule mol, boolean xg) Optionally performs aromatization or addition of explicit Hydrogens atoms.
protected Molecule	preconvert(Molecule mol, boolean xg, int xopts, boolean ih) Optionally performs aromatization or addition of explicit Hydrogens atoms.
protected MoleculeGraph	preconvert(MoleculeGraph molg, boolean xg, int xopts, boolean ih) Optionally performs aromatization or addition of explicit Hydrogens atoms.
java.lang.String	setEncoding(java.lang.String opts, java.lang.String enc) Sets the output encoding using the export options.

Methods inherited from class java.lang.Object

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

Field Detail

stringBuffer

protected java.lang.StringBuffer stringBuffer

This buffer can contain the molecule file contents, in case of a text format.

aromatize

protected int aromatize

Aromatize molecule according to basic aromatization if MoleculeGraph.AROM_BASIC + 1, according to general aromatization if MoleculeGraph.AROM_GENERAL + 1, dearomatize if -1, do nothing if 0.

See Also:

MoleculeGraph.AROM_BASIC, MoleculeGraph.AROM_GENERAL

hydrogenize

protected int hydrogenize

Add Hydrogen atoms if 1, remove if -1, do nothing if 0.

addNumbering

protected boolean addNumbering

Add numbers to atoms corresponding to the (IUPAC) naming of the molecule.

Constructor Detail

MolExportModule

public MolExportModule()

Method Detail

getOptionDescriptors

public final OptionDescriptor[] getOptionDescriptors(java.lang.String fmtname)

Gets an array of option descriptors for the specified format.

Parameters:

fmtname - the format name or null

Since:

Marvin 5.0, 06/06/2007

getOptionDescriptors

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

Gets an array of option descriptors.

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

Opens the exporter stream. Overriding methods should call super.open(fmtopts) at the beginning. In case of some many-molecule formats such as RDfile, the files begin with a header. This header must be returned by open(), either as a String object or a byte[] array.

Parameters:

fmtopts - output file format and options

Returns:

null (file header or null in overriding methods)

Throws:

MolExportException - Invalid format string.

See Also:

getFormat(), getOptions()

open

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

Opens the exporter stream. Overriding methods should call super.open(fmtopts, props) at the beginning. In case of some many-molecule formats such as RDfile, the files begin with a header. This header must be returned by open(), either as a String object or a byte[] array.

Parameters:

fmtopts - output file format and options

props - global GUI properties (currently allowed for MRV only in CmlExport)

Returns:

null (file header or null in overriding methods)

Throws:

MolExportException - Invalid format string.

Since:

Marvin 4.1, 03/22/2006

convert

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

Convert a molecule to a string or byte array. When converted to a String, it should end with a '\n' character.

Parameters:

mol - the molecule

Returns:

a string or a byte array, null for failure

Throws:

MolExportException - molecule cannot be exported in this format

close

public java.lang.Object close()
                       throws MolExportException

Close the stream. This method is called after the last convert().

Returns:

last section of the file as a string or a byte array, or null

Throws:

MolExportException - molecule cannot be exported in this format

getFormat

public final java.lang.String getFormat()

Returns the output format.

getOptions

protected final java.lang.String getOptions()

Returns the output options.

isDocumentExport

public boolean isDocumentExport()

Tests if this export module is document export instead of a simple molecule export.

Returns:

false in the default implementation

Since:

Marvin 4.0, 07/01/2005

isCleanable

public boolean isCleanable()

Tests whether 2D or 3D cleaning is meaningful for this output format.

Returns:

true in the default implementation

Since:

Marvin 4.1, 02/12/2006

isImplicitHcountImportant

public static boolean isImplicitHcountImportant(MolAtom a)

Checks whether the number of implicit hydrogens is important information for an atom or not. Implicit H count is exported if possible for Nitrogen, Phosphorus and Arsenic atoms with two aromatic bonds.

Parameters:

a - the atom

Returns:

true if implicit H count is important on the atom.

Since:

Marvin 3.5, 10/08/2004

isImplicitHcountImportant

public boolean isImplicitHcountImportant(MoleculeGraph mol)

Checks whether the number of implicit hydrogens is important information for the atoms of mol or not.

Parameters:

mol - the molecule

Returns:

true if there is important implicit H in the molecule.

Since:

Marvin 4.0.2, 08/24/2005

See Also:

isImplicitHcountImportant(chemaxon.struc.MolAtom)

setEncoding

public java.lang.String setEncoding(java.lang.String opts,
                                    java.lang.String enc)

Sets the output encoding using the export options.

Parameters:

opts - the export options

enc - the default encoding

Returns:

the value of the encoding field or null

Throws:

java.nio.charset.IllegalCharsetNameException - if the encoding is illegal

java.nio.charset.UnsupportedCharsetException - if the encoding is unsupported

Since:

Marvin 4.0.4, 01/03/2006

getEncoding

public java.lang.String getEncoding()

Gets the output encoding.

Returns:

the value of the encoding field or null

parseOption

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

Parses the following option in the option string.

Parameters:

opts - the option string

i - 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

nextOpt

protected static int nextOpt(java.lang.String opts,
                             int i,
                             java.lang.String s)

Tests whether the option string contains the specified substring at the specified position.

Parameters:

opts - the option string

i - current index

s - the substring

Returns:

i + length of s if opts contains s at position i, i otherwise

Since:

Marvin 5.1.4, 11/09/2008

getOptionSign

protected final int getOptionSign()

Gets the sign of the options. The sign is a + or - character preceding the option(s) in the string.

Returns:

1, 0 or -1

parseCharIfOptionSign

protected int parseCharIfOptionSign(java.lang.String opts,
                                    int i)

Parse the current character if it is an option sign.

Parameters:

opts - the option string

i - current character index

Returns:

i + 1 if character at i is an option sign, i otherwise

Since:

Marvin 4.1.9, 06/06/2007

preconvert

protected Molecule preconvert(Molecule mol)

Optionally performs aromatization or addition of explicit Hydrogens atoms. Contracted S-groups are also expanded.

Parameters:

mol - the molecule

Returns:

the converted molecule or the argument (if conversion is not perfomed)

preconvert

protected final Molecule preconvert(Molecule mol,
                                    boolean xg)

Optionally performs aromatization or addition of explicit Hydrogens atoms. Contracted S-groups can also be expanded.

Parameters:

mol - the molecule

xg - expand S-groups (true) or not (false)

Returns:

the converted molecule or the argument (if conversion is not perfomed)

preconvert

protected final Molecule preconvert(Molecule mol,
                                    boolean xg,
                                    int xopts,
                                    boolean ih)

Optionally performs aromatization or addition of explicit Hydrogens atoms. Contracted S-groups can also be expanded.

Parameters:

mol - the molecule

xg - expand S-groups (true) or not (false)

xopts - expansion options

ih - if true, important implicit H-s are converted to attached data.

Returns:

the converted molecule or the argument (if conversion is not perfomed)

See Also:

Expandable.expand(int), Expandable.DEFAULT_OPTIONS, Expandable.MDL_EXPAND

preconvert

protected final MoleculeGraph preconvert(MoleculeGraph molg,
                                         boolean xg,
                                         int xopts,
                                         boolean ih)

Optionally performs aromatization or addition of explicit Hydrogens atoms. Contracted S-groups can also be expanded.

Parameters:

molg - the molecule

xg - expand S-groups (true) or not (false)

xopts - expansion options

ih - if true, important implicit H-s are converted to attached data.

Returns:

the converted molecule or the argument (if conversion is not perfomed)

Since:

Marvin 3.5.1, 11/16/2004

See Also:

Expandable.expand(int), Expandable.DEFAULT_OPTIONS, Expandable.MDL_EXPAND

addData

protected void addData(Molecule mol,
                       MolAtom ma,
                       java.lang.String fieldName,
                       java.lang.String value)

Adds a data sgroup to the given atom in the given molecule with fieldName and value.

Since:

Marvin 4.0.1 8/19/2005

appendChars

protected final void appendChars(int n,
                                 char c)

Append a character n times to the string buffer.

See Also:

stringBuffer

appendLeft

protected final void appendLeft(java.lang.String t,
                                int n)

Append a string to the buffer in %-ns format.

See Also:

stringBuffer

appendRight

protected final void appendRight(java.lang.String t,
                                 int n,
                                 char c)

Append a string to the buffer in the right hand side of an n-characters wide field. The left side is filled with the specified characters.

See Also:

stringBuffer

appendRight

protected final void appendRight(int t,
                                 int n,
                                 char c)

Append an integer to the buffer in the right hand side of an n-characters wide field. The left side is filled with the specified characters.

See Also:

stringBuffer

getOptionDescriptors

protected static java.lang.String getOptionDescriptors(java.util.ResourceBundle rc,
                                                       java.lang.String fmtname,
                                                       java.lang.String optnames,
                                                       java.util.List l)

Gets an array of option descriptors.

Parameters:

rc - the resource bundle containing the option info

fmtname - the format name or null

optnames - space separated list of option names

l - the output list

Returns:

the nonprocessed option names or null

Since:

Marvin 5.0, 06/06/2007