Package chemaxon.formats

Class MolImporter

java.lang.Object
chemaxon.formats.MDocSource
chemaxon.formats.MolImporter
All Implemented Interfaces:
MolImporterInterface, Closeable, AutoCloseable, Iterable<Molecule>
@PublicApi public class MolImporter extends MDocSource implements MolImporterInterface
Molecule file importer.

The input file format is guessed automatically or specified as an import option to the constructor. Many different formats are supported like "mol", "rgf", "sdf", "rdf", "csmol", "csrgf", "cssdf", "csrdf", "mol2", "cml", "mrv", "smiles", "cxsmiles", "pdb", "xyz", "cube", "name". For more information on formats, please visit File Formats in Marvin. MolImporter can also import gzip compressed and base64 encoded structures.

The processing is single-threaded by default. Concurrent mode can be enabled using setThreadCount(int).

Serialized Molecule objects can also be imported using the "chemaxon.struc.Molecule" format. In this case, processing is always single-threaded, regardless of the configured thread count.

  • Constructor Details

    • MolImporter

      public MolImporter(InputStream is) throws IOException, MolFormatException
      Create a molecule importer for an input stream. Begins reading the input stream and determines the file format.
      Parameters:
      is - the input stream to read
      Throws:
      IOException - If I/O error occurred when determining the file format.
      MolFormatException - If the molecule file is in a format that cannot be read
      IllegalCharsetNameException - if illegal encoding is used
      UnsupportedCharsetException - if unsupported encoding is used

    • MolImporter

      public MolImporter(InputStream is, String opts) throws IOException, MolFormatException
      Create a molecule importer for an input stream. Begins reading the input stream and determines the file format. If the option string starts with the substring "MULTISET", then all the molecules in the stream are merged into one molecule object containing multiple atom sets. If it starts with "MOLMOVIE", then molecules are read taken to be frames of a molecule movie (default in XYZ format). If it starts with "NOMOLMOVIE", then multimolecule XYZ files are not interpreted as molecule movies. Other parts of the option string are passed to the import module. The input character encoding can also be set in "enc{encoding}" form.
      Parameters:
      is - the input stream to read
      opts - the file format and/or options separated by a colon; use null for automatic format recognition and default options
      Throws:
      IOException - If I/O error occurred when determining the file format.
      MolFormatException - If the molecule file is in a format that cannot be read
      IllegalCharsetNameException - if illegal encoding is used
      UnsupportedCharsetException - if unsupported encoding is used

    • MolImporter

      public MolImporter(InputStream is, String opts, String enc) throws IOException, MolFormatException
      Create a molecule importer for an input stream. Begins reading the input stream and determines the file format. If the option string starts with the substring "MULTISET", then all the molecules in the stream are merged into one molecule object containing multiple atom sets. If it starts with "MOLMOVIE", then molecules are read taken to be frames of a molecule movie (default in XYZ format). If it starts with "NOMOLMOVIE", then multimolecule XYZ files are not interpreted as molecule movies. Other parts of the option string are passed to the import module. The input character encoding can also be set in "enc{encoding}" form.
      Parameters:
      is - the input stream to read
      opts - the file format and/or options separated by a colon; use null for automatic format recognition and default options
      enc - charset name or null
      Throws:
      IOException - If I/O error occurred when determining the file format.
      MolFormatException - If the molecule file is in a format that cannot be read
      IllegalCharsetNameException - if illegal encoding is used
      UnsupportedCharsetException - if unsupported encoding is used
      Since:
      Marvin 3.5.5, 01/02/2006

    • MolImporter

      public MolImporter(InputStream is, String opts, String enc, String fileName) throws IOException, MolFormatException
      Create a molecule importer for an input stream. Begins reading the input stream and determines the file format. If the option string starts with the substring "MULTISET", then all the molecules in the stream are merged into one molecule object containing multiple atom sets. If it starts with "MOLMOVIE", then molecules are read taken to be frames of a molecule movie (default in XYZ format). If it starts with "NOMOLMOVIE", then multimolecule XYZ files are not interpreted as molecule movies. Other parts of the option string are passed to the import module. The input character encoding can also be set in "enc{encoding}" form.
      Parameters:
      is - the input stream to read
      opts - the file format and/or options separated by a colon; use null for automatic format recognition and default options
      enc - charset name or null
      fileName - the original filename the stream is reading from
      Throws:
      IOException - If I/O error occurred when determining the file format.
      MolFormatException - If the molecule file is in a format that cannot be read
      IllegalCharsetNameException - if illegal encoding is used
      UnsupportedCharsetException - if unsupported encoding is used
      Since:
      Marvin 5.8

    • MolImporter

      public MolImporter(File f, String opts) throws IOException
      Create a molecule importer for a file. Begins reading the input stream and determines the file format. If the option string starts with the substring "MULTISET", then all the molecules in the stream are merged into one molecule object containing multiple atom sets. If it starts with "MOLMOVIE", then molecules are read taken to be frames of a molecule movie (default in XYZ format). If it starts with "NOMOLMOVIE", then multimolecule XYZ files are not interpreted as molecule movies. The input character encoding can also be set in "enc{encoding}" form. Other parts of the option string are passed to the import module.
      Parameters:
      f - the file to read
      opts - the file format and/or options separated by a colon; use null for automatic format recognition and default options
      Throws:
      IOException - If I/O error occurred when determining the file format.
      MolFormatException - If the molecule file is in a format that cannot be read
      IllegalCharsetNameException - if illegal encoding is used
      UnsupportedCharsetException - if unsupported encoding is used
      See Also:

    • MolImporter

      public MolImporter(File f) throws IOException
      Create a molecule importer for a file. Begins reading the input stream and determines the file format. If the option string starts with the substring "MULTISET", then all the molecules in the stream are merged into one molecule object containing multiple atom sets. If it starts with "MOLMOVIE", then molecules are read taken to be frames of a molecule movie (default in XYZ format). If it starts with "NOMOLMOVIE", then multimolecule XYZ files are not interpreted as molecule movies. The input character encoding can also be set in "enc{encoding}" form. Other parts of the option string are passed to the import module.
      Parameters:
      f - the file to read
      Throws:
      IOException - If I/O error occurred when determining the file format.
      MolFormatException - If the molecule file is in a format that cannot be read
      IllegalCharsetNameException - if illegal encoding is used
      UnsupportedCharsetException - if unsupported encoding is used
      Since:
      Marinv 6.3
      See Also:

    • MolImporter

      public MolImporter(String fname) throws IOException, MolFormatException
      Create a molecule importer for a file. Begins reading the input stream and determines the file format. The filename string can contain options in the "file{options}" form. If the option string starts with the substring "MULTISET", then all the molecules in the stream are merged into one molecule object containing multiple atom sets. If it starts with "MOLMOVIE", then molecules are read taken to be frames of a molecule movie (default in XYZ format). If it starts with "NOMOLMOVIE", then multimolecule XYZ files are not interpreted as molecule movies. Other parts of the option string are passed to the import module. The input character encoding can also be set in "enc{encoding}" form.
      Parameters:
      fname - name of the file to read
      Throws:
      IOException - If I/O error occurred when determining the file format.
      MolFormatException - If the molecule file is in a format that cannot be read
      IllegalCharsetNameException - if illegal encoding is used
      UnsupportedCharsetException - if unsupported encoding is used
      See Also:

    • MolImporter

      public MolImporter(String fname, Component component, String msg) throws IOException, MolFormatException
      Create a molecule importer with a progress monitor. Begins reading the input stream and determines the file format. The filename string can contain options in the "file{options}" form. If the option string starts with "MULTISET" or "MULTISET,", then all the molecules in the stream are merged into one molecule object containing multiple atom sets. The input character encoding can also be set in "enc{encoding}" form. Other parts of the option string are passed to the import module.
      Parameters:
      fname - name of the file to read
      component - the parent component
      msg - displayed message, where %p is replaced by the file path
      Throws:
      IOException - If I/O error occurred when determining the file format.
      MolFormatException - If the molecule file is in a format that cannot be read
      IllegalCharsetNameException - if illegal encoding is used
      UnsupportedCharsetException - if unsupported encoding is used
      See Also:

  • Method Details

    • getFileName

      public String getFileName()
      Gets the name of the input file
      Returns:
      the name of the input file

    • getFile

      public File getFile()
      Gets the file object for the input.
      Returns:
      the File or null (if the input is not a File)

    • getOptions

      public final String getOptions()
      Gets the import options.
      Returns:
      the options

    • getMolImportModule

      public MolImportModule getMolImportModule()

    • getGrabbedMoleculeString

      public String getGrabbedMoleculeString()
      Gets the last grabbed molecule string with LF style line endings by default. If the "noLF" import option was set for MolImporter, then original line endings are kept. E.g. new MolImporter(stream, "mrv:noLF");
      Returns:
      the molecule as a string
      Since:
      4.0, 01/05/2005

    • isMultiSet

      public boolean isMultiSet()
      Are the imported molecules merged into one multi-set molecule?
      Returns:
      true if the input is a multi-set molecule

    • isMolMovie

      public boolean isMolMovie()
      Are the imported molecules merged into one multi-set molecule?
      Returns:
      true if the input is a multi-set molecule
      Since:
      Marvin 5.2, 02/12/2009

    • getMolStream

      public Stream<Molecule> getMolStream()
      Creates a Molecule stream with the iterator of the importer. Only one iterator can exist at a time, so only one stream can exist at a time.
      Specified by:
      getMolStream in interface MolImporterInterface
      Overrides:
      getMolStream in class MDocSource

    • getMDocumentStream

      public Stream<MDocument> getMDocumentStream()
      Creates an MDocument stream with the iterator of the importer. Adds MDocument to molecules without document. Only one iterator can exist at a time, so only one stream can exist at a time.
      Specified by:
      getMDocumentStream in interface MolImporterInterface
      Overrides:
      getMDocumentStream in class MDocSource

    • setThreadCount

      public void setThreadCount(int threadCount) throws IllegalStateException
      Sets the number of threads for concurrent processing. The default value is 1 (single-threaded mode).

      In concurrent mode, multiple threads are started in the background, which adds a considerable overhead to the processing, so only use this mode if the number of molecules is huge. In single-threaded mode, no background thread is used, every action is done on the caller thread.

      Parameters:
      threadCount - the number of threads, set 0 for the number of CPUs, 1 for single-threaded mode
      Throws:
      IllegalStateException - if concurrent processing is already started or if object input stream is used instead of record importer
      Since:
      Marvin 5.3

    • getQueryMode

      public boolean getQueryMode()
      Gets query mode. SMILES strings are imported as SMARTS if query mode is set.
      Returns:
      query mode
      Since:
      Marvin 3.3, 11/14/2003

    • setQueryMode

      public void setQueryMode(boolean q)
      Sets query mode. SMILES strings are imported as SMARTS if query mode is set.
      Parameters:
      q - query mode
      Since:
      Marvin 3.3, 11/14/2003

    • read

      public Molecule read() throws IOException
      Reads the next molecule from the stream/file.
      Specified by:
      read in interface MolImporterInterface
      Returns:
      the next molecule, or null if no more molecules can be imported.
      Throws:
      IOException - if an error occurred during reading.

    • nextDoc

      public MDocument nextDoc() throws IOException
      Reads the next document.
      Specified by:
      nextDoc in class MDocSource
      Returns:
      the next document or null at end of file
      Throws:
      IOException - If I/O error occurred
      Since:
      Marvin 4.1, 04/14/2006

    • skipRecord

      public boolean skipRecord() throws IOException
      Skips the next molecule or document instead of reading it into memory.
      Specified by:
      skipRecord in class MDocSource
      Returns:
      true if the end of molecule is found, false if there is no chance to continue
      Throws:
      IOException - if read error occurred
      Since:
      Marvin 4.1, 04/20/2006

    • readRecordAsText

      public String readRecordAsText() throws MolExportException, IOException
      Reads the next molecule in text format without creating a Molecule object. Processing is single-threaded.
      Returns:
      the grabbed record in its original format or null at end of file
      Throws:
      MolExportException - if binary data cannot be exported to MRV format text
      IOException - if read error occurred
      Since:
      Marvin 5.0, 11/13/2006

    • isRewindable

      public boolean isRewindable()
      Tests whether rewinding (seeking backwards) is possible in the underlying input stream. In concurrent mode always returns false. Therefore this method should not be called before calling setThreadCount(int).
      Specified by:
      isRewindable in class MDocSource
      Returns:
      true if rewinding is possible, false otherwise
      Since:
      Marvin 4.1, 04/20/2006
      See Also:

    • seekRecord

      public void seekRecord(int k, ProgressMonitor pmon) throws EOFException, IOException
      Seek the specified record. This method should not be called before calling setThreadCount(int). Backward seeking (rewinding) in the stream is only possible if the underlying input stream is seekable. Note, that in concurrent mode this is not true, the import is not rewindable. Forward seeking is always possible. Seeking terminates before reaching the specified position if the user cancels the progress dialog.
      Specified by:
      seekRecord in class MDocSource
      Parameters:
      k - position
      pmon - progress monitor or null
      Throws:
      EOFException - if end of file reached while trying to seek
      IOException - if read error occurred
      Since:
      Marvin 4.1, 04/19/2006
      See Also:

    • seekVisitedRecord

      protected void seekVisitedRecord(int k) throws IOException
      Seeks an already visited position in case of rewindable input. This method should not be called before calling setThreadCount(int).
      Specified by:
      seekVisitedRecord in class MDocSource
      Parameters:
      k - the record index
      Throws:
      IOException - if read error occurred
      Since:
      Marvin 4.1, 06/28/2006
      See Also:

    • isEndReached

      public boolean isEndReached()
      Tests whether the end of input is already reached.
      Specified by:
      isEndReached in class MDocSource
      Returns:
      true if the end was reached, false otherwise
      Since:
      Marvin 4.1, 06/18/2006

    • estimateNumRecords

      public int estimateNumRecords()
      Estimates the total number of records. If the end of file is already reached, then it returns the exact value. Otherwise, in case of a file with known length, it extrapolates from the last read record index and the value of the file pointer at the last read position. If the input is a stream with unknown total length, then it returns two times the current highest record number.
      Specified by:
      estimateNumRecords in class MDocSource
      Returns:
      estimated number of records or -1 at the beginning of file
      Since:
      Marvin 4.1, 04/18/2006

    • tell

      public long tell() throws IOException
      Returns the current file offset.
      Returns:
      the file pointer
      Throws:
      IOException - if the position cannot be determined

    • getLineCount

      public int getLineCount()
      Gets the current line number. This method should not be called before calling setThreadCount(int).
      Returns:
      the line number
      See Also:

    • getRecordCount

      public int getRecordCount()
      Gets the current record number.
      Specified by:
      getRecordCount in class MDocSource
      Returns:
      the record number
      Since:
      Marvin 4.1, 04/18/2006

    • getRecordCountMax

      public int getRecordCountMax()
      Gets the total number of records read.
      Specified by:
      getRecordCountMax in class MDocSource
      Returns:
      the number of records
      Since:
      Marvin 4.1, 04/18/2006

    • close

      public void close() throws IOException
      Closes the underlying input stream.

      WARNING: call this after reading molecules to close concurrent processing properly.

      Specified by:
      close in interface AutoCloseable
      Specified by:
      close in interface Closeable
      Specified by:
      close in interface MolImporterInterface
      Overrides:
      close in class MDocSource
      Throws:
      IOException - if an error occurred.

    • getFormat

      public String getFormat()
      Get the file format.
      Returns:
      "mrv", "mol", "csmol", "sdf", "cssdf", "rdf", "csrdf", "smiles", "sybyl", "mol2", "pdb", "xyz", "cube", "inchi", "csv", "gzip:{inner file format}", etc. or "chemaxon.struc.Molecule" if imported from ObjectInputStream (serialized molecule)

    • importMol

      public static Molecule importMol(byte[] b) throws MolFormatException
      Reads a molecule from a byte array. If the array contains multiple molecules (e.g. in the case of an SDF or MRV file), reads only the first one. Processing is single-threaded.
      Parameters:
      b - the molecule file contents
      Returns:
      the molecule
      Throws:
      MolFormatException - If the molecule file is in a format that cannot be read

    • importMol

      public static Molecule importMol(byte[] b, String opts, String enc) throws MolFormatException
      Reads a molecule from a byte array. If the array contains multiple molecules (e.g. in the case of an SDF or MRV file), reads only the first one. Processing is single-threaded.
      Parameters:
      b - the molecule file contents
      opts - the file format and/or options separated by a colon; use null for automatic format recognition and default options
      enc - encoding or null
      Returns:
      the molecule
      Throws:
      MolFormatException - If the molecule file is in a format that cannot be read
      Since:
      Marvin 5.0, 12/27/2007

    • importMol

      public static Molecule importMol(InputStream is, String opts, String enc) throws MolFormatException
      Reads a molecule from an input stream. If the array contains multiple molecules (e.g. in the case of an SDF or MRV file), reads only the first one.
      Parameters:
      is - the molecule file contents
      opts - the file format and/or options separated by a colon; use null for automatic format recognition and default options
      enc - encoding or null
      Returns:
      the molecule
      Throws:
      MolFormatException - If the molecule file is in a format that cannot be read
      Since:
      Marvin 5.0, 12/27/2007

    • importDoc

      public static MDocument importDoc(byte[] b) throws MolFormatException
      Reads a document from a byte array. If the array contains multiple molecules (e.g. in the case of an SDF or MRV file), reads only the first one. Processing is single-threaded.
      Parameters:
      b - the file contents
      Returns:
      the document or null if no document found in input
      Throws:
      MolFormatException - If the molecule file is in a format that cannot be read
      Since:
      Marvin 4.1.8, 04/20/2007

    • importDoc

      public static MDocument importDoc(byte[] b, String opts, String enc) throws MolFormatException
      Reads a document from a byte array. If the array contains multiple molecules (e.g. in the case of an SDF or MRV file), reads only the first one. Processing is single-threaded.
      Parameters:
      b - the file contents
      opts - the file format and/or options separated by a colon; use null for automatic format recognition and default options
      enc - encoding or null
      Returns:
      the document or null if no document found in input
      Throws:
      MolFormatException - If the molecule file is in a format that cannot be read
      Since:
      Marvin 5.0, 12/27/2007

    • importMol

      public static Molecule importMol(String s) throws MolFormatException
      Reads a molecule from a string. If the string contains multiple molecules (e.g. in the case of an SDF or MRV file), reads only the first one. If the format is known, it is faster to use importMol(String, String) to avoid wasting time with format recognition. Processing is single-threaded.
      Parameters:
      s - the molecule file contents
      Returns:
      the molecule
      Throws:
      MolFormatException - If the molecule file is in a format that cannot be read

    • importMol

      public static Molecule importMol(String s, String opts) throws MolFormatException
      Reads a molecule from a string. If the string contains multiple molecules (e.g. in the case of an SDF or MRV file), reads only the first one. Processing is single-threaded.
      Parameters:
      s - the molecule file contents
      opts - the file format and/or options separated by a colon; use null for automatic format recognition and default options
      Returns:
      the molecule
      Throws:
      MolFormatException - If the molecule file is in a format that cannot be read

    • importMol

      @Deprecated @SubjectToRemoval(date=JUL_01_2027) public static Molecule importMol(String s, Object options) throws MolFormatException
      Deprecated.
      Use importMol(String, String) instead and pass the options as a string (call toString() on the object). This method will be removed in a future release.
      Read a molecule from a string with the given options. If the string contains multiple molecules (e.g. in the case of an SDF or MRV file), reads only the first one. Processing is single-threaded. If an encoding is specified in the option, its value will not be used since the input is a string which can not be encoded.
      Parameters:
      s - the molecule file contents
      options - options defined by an options object
      Returns:
      the molecule
      Throws:
      MolFormatException - If the molecule file is in a format that cannot be read

    • getGlobalProperties

      public MPropertyContainer getGlobalProperties()
      Gets the global properties in a container that was retrieved from the input stream, earlier. Only MRV import supports global properties. Reads them by the initalization of the record importer.
      Returns:
      global properties in a container or null.
      Since:
      Marvin 5.0 06/05/2007