A B C D E F G H I J L M N P R S T U V W

S

saveOptionsSet() - Method in class de.modlab.smilib.gui.ControlPanel

Returns whether a target for library (GUI or file) is set.

Scaffold - Class in de.modlab.smilib.fragments

Stores SMILES and informations about a scaffold.

Scaffold(String, String) - Constructor for class de.modlab.smilib.fragments.Scaffold

Creates a new instance of Scaffold.

ScaffoldFactory - Class in de.modlab.smilib.fragments

Creates Scaffold fragments.

ScaffoldFactory() - Constructor for class de.modlab.smilib.fragments.ScaffoldFactory

Creates a new instance of ScaffoldFragmentFactory

setCWD(String) - Method in class de.modlab.smilib.gui.SmiLibFrame

Sets the current working directory.

setHelpFrame(HelpFrame) - Method in class de.modlab.smilib.gui.HelpAboutFrame

Sets the HelpFrame which is needed for license displaying.

setIterator(SmiLibIterator) - Method in class de.modlab.smilib.gui.SmiLibFrame

Sets Iterator used for enumeration.

setPopupMenuVisible(boolean) - Method in class de.modlab.smilib.gui.JButtonMenu

Method JMenu.setPopupMenuVisible is overwritten to prevent a visible popup menu when the menu is selected.

setStatistics(int, int, int) - Method in class de.modlab.smilib.gui.LibraryPanel

Shows some informations about the current job in GUI elements.

setStatistics(int, int, int) - Method in class de.modlab.smilib.gui.SmiLibFrame

Shows some statistics (number of scaffolds, linkers and building blocks in GUI.

setStop(boolean) - Method in class de.modlab.smilib.main.SmiLibRunner

Sets whether this thread shall be stopped or not.

setTime(long, long) - Method in class de.modlab.smilib.gui.LibraryPanel

Displays how long the current job was processed

setTime(long, long) - Method in class de.modlab.smilib.gui.SmiLibFrame

Shows time for enumeration in GUI.

setTitle(String) - Method in class de.modlab.smilib.gui.LibraryPanel

Changes title of the panel where library is shown.

showEndMessage(long, long) - Method in class de.modlab.smilib.gui.SmiLibFrame

Shows a message, that enumeration is completed or that it has been interrupted by the user.

showHelp(int) - Method in class de.modlab.smilib.gui.HelpFrame

Displays a specific help text.

showPreview(int) - Method in class de.modlab.smilib.io.SmilesFileWriter

Sets whether a preview shall be shown and how many molecules are shown in preview.

showPreview(int) - Method in class de.modlab.smilib.io.SmilesGuiWriter

Sets whether a preview shall be shown and how many molecules are shown in preview.

showPreview(int) - Method in class de.modlab.smilib.io.SmilesLineWriter

Sets whether a preview shall be shown and how many molecules are shown in preview.

showPreview(int) - Method in class de.modlab.smilib.io.SmilesListWriter

Sets whether a preview shall be shown and how many molecules are shown in preview.

showPreview(int) - Method in class de.modlab.smilib.io.SmilesToSDFWriter

Sets whether a preview shall be shown and how many molecules are shown in preview.

showPreview(int) - Method in interface de.modlab.smilib.io.SmilesWriter

Sets whether a preview shall be shown and how many molecules are shown in preview.

SmilesConcatenator - Class in de.modlab.smilib.main

Concatenates SMILES for SmiLib.

SmilesConcatenator() - Constructor for class de.modlab.smilib.main.SmilesConcatenator

Creates a new instance of SmilesConcatenator

SmilesFileReader<E extends Fragment> - Class in de.modlab.smilib.io

Reads SMILES from the input files.

SmilesFileReader(FragmentFactory, boolean, int) - Constructor for class de.modlab.smilib.io.SmilesFileReader

Creates a new instance of SmilesFileReader.

SmilesFileWriter - Class in de.modlab.smilib.io

Writes SMILES in a file.

SmilesFileWriter(String) - Constructor for class de.modlab.smilib.io.SmilesFileWriter

Creates a new instance of SmilesFileWriter.

SmilesGuiReader - Class in de.modlab.smilib.io

Parses SMILES to molecule fragments when SMILES are entered in the GUI mask.

SmilesGuiReader(boolean) - Constructor for class de.modlab.smilib.io.SmilesGuiReader

Creates a new instance of SmilesGuiReader

SmilesGuiWriter - Class in de.modlab.smilib.io

Writes SMILES to a JTextArea.

SmilesGuiWriter(JTextArea, boolean, boolean, boolean, boolean, String, SmiLibFrame) - Constructor for class de.modlab.smilib.io.SmilesGuiWriter

Creates a new instance of SmilesGuiWriter.

SmilesLineWriter - Class in de.modlab.smilib.io

Writes SMILES to the command line.

SmilesLineWriter() - Constructor for class de.modlab.smilib.io.SmilesLineWriter

Creates a new instance of SmilesLineWriter.

SmilesListWriter - Class in de.modlab.smilib.io

Writes output SMILES to a java.util.List

SmilesListWriter() - Constructor for class de.modlab.smilib.io.SmilesListWriter

Creates a new instance of SmilesLineWriter.

SmilesParser - Class in de.modlab.smilib.main

Parses a SMILES string and an AtomContainer.

SmilesParser() - Constructor for class de.modlab.smilib.main.SmilesParser

Constructor for the SmilesParser object

SmilesReader<E extends Fragment> - Interface in de.modlab.smilib.io

Interface used by all SmilesReaders.

SmilesToSDFWriter - Class in de.modlab.smilib.io

Writes the molecules created as SMILES in a SD file.

SmilesToSDFWriter(String, boolean) - Constructor for class de.modlab.smilib.io.SmilesToSDFWriter

Creates a new instance of SmilesToSDFWriter

SmilesWriter - Interface in de.modlab.smilib.io

Interface used by all SmiLib SmilesWriters.

SmiLib - Class in de.modlab.smilib.main

Main class of SmiLib.

SmiLib() - Constructor for class de.modlab.smilib.main.SmiLib

Creates a new instance of SmiLib.

SmiLibConformityException - Exception in de.modlab.smilib.exceptions

SmiLib specific Exception.

SmiLibConformityException() - Constructor for exception de.modlab.smilib.exceptions.SmiLibConformityException

Creates a new instance of SmiLibConformityException without detail message.

SmiLibConformityException(String) - Constructor for exception de.modlab.smilib.exceptions.SmiLibConformityException

Constructs an instance of SmiLibConformityException with the specified detail message.

SmiLibConformityException(Throwable) - Constructor for exception de.modlab.smilib.exceptions.SmiLibConformityException

Constructs an instance of SmiLibException with the specified cause.

SmiLibConformityException(String, Throwable) - Constructor for exception de.modlab.smilib.exceptions.SmiLibConformityException

Constructs an instance of SmiLibConformityException with the specified detail message and cause.

SmiLibException - Exception in de.modlab.smilib.exceptions

Superclass for SmiLib Exceptions.

SmiLibException() - Constructor for exception de.modlab.smilib.exceptions.SmiLibException

Creates a new instance of SmiLibException without detail message.

SmiLibException(String) - Constructor for exception de.modlab.smilib.exceptions.SmiLibException

Constructs an instance of SmiLibException with the specified detail message.

SmiLibException(Throwable) - Constructor for exception de.modlab.smilib.exceptions.SmiLibException

Constructs an instance of SmiLibException with the specified cause.

SmiLibException(String, Throwable) - Constructor for exception de.modlab.smilib.exceptions.SmiLibException

Constructs an instance of SmiLibException with the specified detail message and cause.

SmiLibFrame - Class in de.modlab.smilib.gui

Main frame of the GUI for SmiLib.

SmiLibFrame() - Constructor for class de.modlab.smilib.gui.SmiLibFrame

Creates new form SmiLibFrame

SmiLibIOException - Exception in de.modlab.smilib.exceptions

SmiLib specific Exception.

SmiLibIOException() - Constructor for exception de.modlab.smilib.exceptions.SmiLibIOException

Creates a new instance of SmiLibIOException without detail message.

SmiLibIOException(String) - Constructor for exception de.modlab.smilib.exceptions.SmiLibIOException

Constructs an instance of SmiLibIOException with the specified detail message.

SmiLibIOException(Throwable) - Constructor for exception de.modlab.smilib.exceptions.SmiLibIOException

Constructs an instance of SmiLibException with the specified cause.

SmiLibIOException(String, Throwable) - Constructor for exception de.modlab.smilib.exceptions.SmiLibIOException

Constructs an instance of SmiLibIOException with the specified cause.

SmiLibIterator - Interface in de.modlab.smilib.iterator

Interface to be implemented by all SMiLib iterators.

SmiLibRunner - Class in de.modlab.smilib.main

Enumerates the combinatorial libraray.

SmiLibRunner(String, String, String, boolean, String, boolean, boolean) - Constructor for class de.modlab.smilib.main.SmiLibRunner

Creates a new instance of SmiLibRunner using a FullCombinationIterator (without reaction scheme) for enumerating the virtual library.

SmiLibRunner(String, String, String, String, boolean, String, boolean, boolean) - Constructor for class de.modlab.smilib.main.SmiLibRunner

Creates a new instance of SmiLibRunner using a PartialCombinationIterator (with reaction scheme) for enumerating the virtual library.

SmiLibRunner(String[], String[], String[], boolean, String[], JTextArea, boolean, boolean, boolean, boolean, String, SmiLibFrame, boolean) - Constructor for class de.modlab.smilib.main.SmiLibRunner

Creates a new instance of SmiLibRunner, used when programm is started in GUI mode.

SmiLibRunner(String[], String[], String[], String[], boolean, SmilesWriter) - Constructor for class de.modlab.smilib.main.SmiLibRunner

Creates a new instance of SmiLibRunner that can be conveniently used in other Java projects when SmiLib is employed as a Java library.

Example to enumerate a complete SmiLib library:

SmiLibSdfException - Exception in de.modlab.smilib.exceptions

SmiLibSdfException is thrown when an error occurs during SMILES to SDF conversion with CDK.

SmiLibSdfException() - Constructor for exception de.modlab.smilib.exceptions.SmiLibSdfException

Creates a new instance of SmiLibSdfException without detail message.

SmiLibSdfException(String) - Constructor for exception de.modlab.smilib.exceptions.SmiLibSdfException

Constructs an instance of SmiLibSdfException with the specified detail message.

SmiLibSdfException(Throwable) - Constructor for exception de.modlab.smilib.exceptions.SmiLibSdfException

Constructs an instance of SmiLibSdfException with the specified cause.

SmiLibSdfException(String, Throwable) - Constructor for exception de.modlab.smilib.exceptions.SmiLibSdfException

Constructs an instance of SmiLibSdfException with the specified detail message and cause.

SourcePanel - Class in de.modlab.smilib.gui

GUI element for SmiLib GUI where source SMILES can be entered.

SourcePanel(SmiLibFrame) - Constructor for class de.modlab.smilib.gui.SourcePanel

Creates new form SourcePanel

stopEnumeration() - Method in class de.modlab.smilib.gui.SmiLibFrame

Enumeration of the combinatorial library is stopped by fullfilling a specific criterion in the thread that enumerates it.