Class JC


  • public final class JC
    extends java.lang.Object
    • Constructor Detail

      • JC

        public JC()
    • Method Detail

      • getNBOTypeFromName

        public static int getNBOTypeFromName​(java.lang.String nboType)
      • getCIPChiralityName

        public static java.lang.String getCIPChiralityName​(int flags)
      • getCIPRuleName

        public static java.lang.String getCIPRuleName​(int i)
      • getCIPChiralityCode

        public static int getCIPChiralityCode​(char c)
      • resolveDataBase

        static java.lang.String resolveDataBase​(java.lang.String database,
                                                java.lang.String id,
                                                java.lang.String format)
      • fixProtocol

        static java.lang.String fixProtocol​(java.lang.String name)
        Check for databases that have changed from http:// to https:// over time. We substitute https here in case this is from an old reference.
        Parameters:
        name -
        Returns:
        https protocol if necessary
      • fixOptimadeCall

        static java.lang.String fixOptimadeCall​(java.lang.String url)
        Get all necessary response fields if an optimade call. Note that the only conditions we have here is that this is http and "optimade" is in the URL. Obviously not exactly correct.
        Parameters:
        url -
        Returns:
        call with added necessary response_fields
      • embedScript

        public static java.lang.String embedScript​(java.lang.String s)
      • getShapeVisibilityFlag

        public static final int getShapeVisibilityFlag​(int shapeID)
      • shapeTokenIndex

        public static final int shapeTokenIndex​(int tok)
      • getShapeClassName

        public static final java.lang.String getShapeClassName​(int shapeID,
                                                               boolean isRenderer)
      • getEchoName

        public static java.lang.String getEchoName​(int type)
      • setZPosition

        public static int setZPosition​(int offset,
                                       int pos)
      • setPointer

        public static int setPointer​(int offset,
                                     int pointer)
      • getPointer

        public static int getPointer​(int offset)
      • getPointerName

        public static java.lang.String getPointerName​(int pointer)
      • isOffsetAbsolute

        public static boolean isOffsetAbsolute​(int offset)
      • getOffset

        public static int getOffset​(int xOffset,
                                    int yOffset,
                                    boolean isAbsolute)
        Construct an 32-bit integer packed with 10-byte x and y offsets (-500 to 500) along with flags to indicate if exact and, if not, a flag to indicate that the 0 in x or y indicates "centered". The non-exact default offset of [4,4] is represented as 0 so that new array elements do not have to be initialized.
        Parameters:
        xOffset -
        yOffset -
        isAbsolute -
        Returns:
        packed offset x and y with positioning flags
      • getXOffset

        public static int getXOffset​(int offset)
        X offset in pixels. negative of this is the actual screen offset
        Parameters:
        offset - 0 for an offset indicates "not set" and delivers the default offset
        Returns:
        screen offset from left
      • getYOffset

        public static int getYOffset​(int offset)
        Y offset in pixels; negative of this is the actual screen offset
        Parameters:
        offset - 0 for an offset indicates "not set" and delivers the default offset
        Returns:
        screen offset from bottom
      • getAlignment

        public static int getAlignment​(int offset)
      • setHorizAlignment

        public static int setHorizAlignment​(int offset,
                                            int hAlign)
      • getHorizAlignmentName

        public static java.lang.String getHorizAlignmentName​(int align)
      • isSmilesCanonical

        public static boolean isSmilesCanonical​(java.lang.String options)
      • getServiceCommand

        public static int getServiceCommand​(java.lang.String script)
      • getUnitIDFlags

        public static int getUnitIDFlags​(java.lang.String type)
        Get a unitID type
        Parameters:
        type - -mra (model name, residue, atom, and ins code), -mr (model and residue; no atom) -ra default - or -r just residue -t right-trim
        Returns:
        coded type
      • getBoolName

        public static java.lang.String getBoolName​(int g)