Package com.actelion.research.chem.io

Class DWARFileParser

    • Field Detail

      • MODE_COORDINATES_PREFER_2D

        public static final int MODE_COORDINATES_PREFER_2D
        See Also:
        Constant Field Values

      • MODE_COORDINATES_PREFER_3D

        public static final int MODE_COORDINATES_PREFER_3D
        See Also:
        Constant Field Values

      • MODE_COORDINATES_REQUIRE_2D

        public static final int MODE_COORDINATES_REQUIRE_2D
        See Also:
        Constant Field Values

      • MODE_COORDINATES_REQUIRE_3D

        public static final int MODE_COORDINATES_REQUIRE_3D
        See Also:
        Constant Field Values

      • MODE_BUFFER_HEAD_AND_TAIL

        public static final int MODE_BUFFER_HEAD_AND_TAIL
        See Also:
        Constant Field Values

    • Constructor Detail

      • DWARFileParser

        public DWARFileParser​(java.lang.String fileName)
        Constructs a DWARFileParser from a file name with coordinate mode MODE_COORDINATES_PREFER_2D.
        Parameters:
        fileName -

      • DWARFileParser

        public DWARFileParser​(java.io.File file)
        Constructs a DWARFileParser from a File with coordinate mode MODE_COORDINATES_PREFER_2D.
        Parameters:
        file -

      • DWARFileParser

        public DWARFileParser​(java.io.Reader reader)
        Constructs a DWARFileParser from a Reader with coordinate mode MODE_COORDINATES_PREFER_2D.
        Parameters:
        reader -

      • DWARFileParser

        public DWARFileParser​(java.lang.String fileName,
                      int mode)
        Constructs a DWARFileParser from a file name with the specified coordinate mode.
        Parameters:
        fileName -
        mode - one of 4 MODE_COORDINATE... modes

      • DWARFileParser

        public DWARFileParser​(java.io.File file,
                      int mode)
        Constructs a DWARFileParser from a File with the specified coordinate mode.
        Parameters:
        file -
        mode - one of 4 MODE_COORDINATE... modes

      • DWARFileParser

        public DWARFileParser​(java.io.Reader reader,
                      int mode)
        Constructs a DWARFileParser from a Reader with the specified coordinate mode.
        Parameters:
        reader -
        mode - one of 4 MODE_COORDINATE... modes

    • Method Detail

      • hasStructures

        public boolean hasStructures()
        If you don't read any records after calling this method, don't forget to call close() to close the underlying file.
        Returns:
        whether the file contains chemical structures

      • hasStructureCoordinates

        public boolean hasStructureCoordinates()
        Returns:
        whether the file contains chemical structures with explicit atom coordinates

      • hasStructureCoordinates2D

        public boolean hasStructureCoordinates2D()
        Returns:
        whether the file contains chemical structures with explicit atom coordinates

      • hasStructureCoordinates3D

        public boolean hasStructureCoordinates3D()
        Returns:
        whether the file contains chemical structures with explicit atom coordinates

      • getStructureCoordinates3DColumnName

        public java.lang.String getStructureCoordinates3DColumnName()

      • getFieldNames

        public java.lang.String[] getFieldNames()
        Description copied from class: CompoundFileParser
        Compiles all column names that contain alpha-numerical information. Columns containing chemistry objects, coordinates or descriptors don't appear in the list.
        Specified by:
        getFieldNames in class CompoundFileParser
        Returns:
        columns name array in the order of appearance

      • getSpecialFieldIndex

        public int getSpecialFieldIndex​(java.lang.String columnName)
        Parameters:
        columnName -
        Returns:
        field index for special fields, e.g. to be used for getSpecialFieldData()

      • getChildFieldIndex

        public int getChildFieldIndex​(java.lang.String parentColumnName,
                              java.lang.String childType)
        Parameters:
        parentColumnName -
        childType -
        Returns:
        field index for special fields, e.g. to be used for getSpecialFieldData()

      • getRowCount

        public int getRowCount()
        Description copied from class: CompoundFileParser
        Depending on data source returns the total row count or -1 if unknown
        Specified by:
        getRowCount in class CompoundFileParser
        Returns:
        number of rows or -1

      • getHeadOrTail

        public java.util.ArrayList<java.lang.String> getHeadOrTail()
        Provided that the mode contains MODE_BUFFER_HEAD_AND_TAIL, then this method returns a list of all header/footer rows of the DWAR file. If this method is called before all rows have been read, then the header lines including column properties and the column title line are returned. If this method is called before all rows have been read, then all lines after the data table, i.e. the runtime properties, are returned.
        Returns:

      • getDetails

        public java.util.HashMap<java.lang.String,​byte[]> getDetails()
        Provided that the mode contains MODE_EXTRACT_DETAILS, then this method returns a map of all embedded detail objects of the DWAR file. This method must not be called before all rows have been read.
        Returns:

      • getRow

        public java.lang.String getRow()
        Returns the entire line containing all row data
        Returns:

      • advanceToNext

        protected boolean advanceToNext()
        Description copied from class: CompoundFileParser
        Dont't call this method directly. Use next() instead.
        Specified by:
        advanceToNext in class CompoundFileParser
        Returns:
        false if there is no next row

      • getIDCode

        public java.lang.String getIDCode()
        Description copied from class: CompoundFileParser
        Either this method and getCoordinates() or getMolecule() must be overwritten!!!
        Overrides:
        getIDCode in class CompoundFileParser
        Returns:
        the row content of the first column containing chemical structures

      • getCoordinates

        public java.lang.String getCoordinates()
        This returns encoded atom coordinates according to the defined mode. If the compound file does not contain atom coordinates, then null is returned. If mode is one of MODE_COORDINATES_REQUIRE... and the required coordinate dimensionality (2D or 3D) is not available then null is returned. If mode is one of MODE_COORDINATES_PREFER... and the preferred coordinate dimensionality (2D or 3D) is not available then coordinates in another dimensionality are returned.
        Overrides:
        getCoordinates in class CompoundFileParser
        Returns:
        idcoords of first chemical structure column of the current row

      • getCoordinates2D

        public java.lang.String getCoordinates2D()

      • getCoordinates3D

        public java.lang.String getCoordinates3D()

      • getMoleculeName

        public java.lang.String getMoleculeName()
        Specified by:
        getMoleculeName in class CompoundFileParser
        Returns:
        name/id of (primary) chemical structure of the current row

      • getDescriptor

        public java.lang.Object getDescriptor​(java.lang.String shortName)
        Description copied from class: CompoundFileParser
        If the file source contains encoded descriptors, then overwrite this method to save the calculation time.
        Overrides:
        getDescriptor in class CompoundFileParser
        Returns:
        descriptor as int[] or whatever is the descriptors binary format

      • getIndex

        public java.lang.String getIndex()
        Returns:
        the String encoded FragFp descriptor of the first column containing chemical structures

      • getFieldData

        public java.lang.String getFieldData​(int no)
        Description copied from class: CompoundFileParser
        Returns the cell content of the current row. Multi-line cell entries are separated by a '\n' character.
        Specified by:
        getFieldData in class CompoundFileParser
        Parameters:
        no - refers to alpha-numerical columns only, as getFieldNames()
        Returns:

      • getSpecialFieldMap

        public java.util.TreeMap<java.lang.String,​DWARFileParser.SpecialField> getSpecialFieldMap()
        Returns a columnName->SpecialField map of all non-alphanumerical columns. SpecialField.type is one of the types defined in CompoundTableConstants: cColumnTypeIDCode,cColumnTypeRXNCode,cColumnType2DCoordinates,cColumnType3DCoordinates, cColumnTypeAtomColorInfo, and descriptor shortNames;
        Returns:
        special fields

      • getSpecialFieldData

        public java.lang.String getSpecialFieldData​(int fieldIndex)
        Parameters:
        fieldIndex - is available from special-field-TreeMap by getSpecialFieldMap().get(columnName).fieldIndex
        Returns:
        String encoded data content of special field, e.g. idcode

      • getColumnProperties

        public java.util.Properties getColumnProperties​(java.lang.String columnName)
        Returns the original column properties of any source column by column name.
        Parameters:
        columnName -
        Returns: