Package chemaxon.marvin.io

Class MolExportModule

java.lang.Object
chemaxon.marvin.io.MolExportModule
Direct Known Subclasses:
MolExport
@PublicApi public abstract class MolExportModule extends Object
Abstract base class of molecule export modules. An export module for format "XXX" must have the name chemaxon.marvin.modules.XxxExport.

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

  • Field Details

    • stringBuffer

      protected 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:

    • 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 Details

    • MolExportModule

      public MolExportModule()

  • Method Details

    • getOptionDescriptors

      public final OptionDescriptor[] getOptionDescriptors(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(String fmtname, String optnames, 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 Object open(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:

    • open

      public Object open(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 in CmlExport and CXON)
      Returns:
      null (file header or null in overriding methods)
      Throws:
      MolExportException - Invalid format string.
      Since:
      Marvin 4.1, 03/22/2006

    • convert

      public abstract 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 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 String getFormat()
      Returns the output format.

    • getOptions

      protected final 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:

    • setEncoding

      public String setEncoding(String opts, 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:
      IllegalCharsetNameException - if the encoding is illegal
      UnsupportedCharsetException - if the encoding is unsupported
      Since:
      Marvin 4.0.4, 01/03/2006

    • getEncoding

      public String getEncoding()
      Gets the output encoding.
      Returns:
      the value of the encoding field or null

    • parseOption

      protected int parseOption(String opts, int i) throws 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:
      IllegalArgumentException - in case of parsing error

    • nextOpt

      protected static int nextOpt(String opts, int i, 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(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:

    • preconvert

      @Deprecated(forRemoval=true) @SubjectToRemoval(date=JUL_01_2025) protected final MoleculeGraph preconvert(MoleculeGraph molg, boolean xg, int xopts, boolean ih)
      Deprecated, for removal: This API element is subject to removal in a future version.
      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:

    • addData

      protected void addData(Molecule mol, MolAtom ma, String fieldName, 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:

    • appendLeft

      protected final void appendLeft(String t, int n)
      Append a string to the buffer in %-ns format.
      See Also:

    • appendRight

      protected final void appendRight(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:

    • 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:

    • getOptionDescriptors

      protected static String getOptionDescriptors(ResourceBundle rc, String fmtname, String optnames, 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.
      Since:
      Marvin 6.0, 2013.03.26.