MolExportModule (JChem Base API documentation (c) 1998-2020 ChemAxon Ltd.)

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

Direct Known Subclasses:: MolExport

@PublicAPI
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

Fields
Modifier and Type	Field and Description
`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, etc, 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

Constructors
Constructor and Description

MolExportModule()

Constructors
Constructor and Description
`MolExportModule()`

Method Summary

All Methods Static Methods Instance Methods Abstract Methods Concrete Methods Deprecated Methods
Modifier and Type	Method and Description
`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<OptionDescriptor> 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<OptionDescriptor> 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 atom)` 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)` Deprecated. Marvin 6.2 use `preconvert(chemaxon.struc.Molecule, boolean, int, boolean)` instead
`java.lang.String`	`setEncoding(java.lang.String opts, java.lang.String enc)` Sets the output encoding using the export options.
`void`	`setGlobalGUIProperties(MPropertyContainer ggp)` Pass and set the global GUI properties container.

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, etc, dearomatize if -1, do nothing if 0.
    
    See Also:
    
    MoleculeGraph.AROM_BASIC, MoleculeGraph.AROM_GENERAL, MoleculeGraph.AROM_LOOSE, MoleculeGraph.AROM_AMBIGUOUS
  - 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<OptionDescriptor> 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 atom)
```
    Checks whether the number of implicit hydrogens is important information for an atom or not. Implicit H count is exported: - if the atom has aromatic bond, has exactly one implicit hydrogen and can be ambiguous according to local aromatic valence check. Possible atoms are: B, C-, C+, N, P, As, S+, O+ - if the atom is an S atom and has 3 bonds and an implicit H.
    
    Parameters:
    
    atom - 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 optionsRe
    
    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
```
@Deprecated
protected final MoleculeGraph preconvert(MoleculeGraph molg,
                                                     boolean xg,
                                                     int xopts,
                                                     boolean ih)
```
    Deprecated. Marvin 6.2 use preconvert(chemaxon.struc.Molecule, boolean, int, boolean) instead
    
    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<OptionDescriptor> 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
  - setGlobalGUIProperties
```
public void setGlobalGUIProperties(MPropertyContainer ggp)
```
    Pass and set the global GUI properties container.
    
    Parameters:
    
    ggp -
    
    Since:
    
    Marvin 6.0, 2013.03.26.

Class MolExportModule

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

stringBuffer

aromatize

hydrogenize

addNumbering

Constructor Detail

MolExportModule

Method Detail

getOptionDescriptors

getOptionDescriptors

open

open

convert

close

getFormat

getOptions

isDocumentExport

isCleanable

isImplicitHcountImportant

isImplicitHcountImportant

setEncoding

getEncoding

parseOption

nextOpt

getOptionSign

parseCharIfOptionSign

preconvert

preconvert

preconvert

preconvert

addData

appendChars

appendLeft

appendRight

appendRight

getOptionDescriptors

setGlobalGUIProperties