public class ReactionDecoder extends Annotator
GENERATE_AAMIMAGE, GENERATE_IMAGE, PREFIX, REMAP, REPORT_ALL_MAPPINGS, REPORT_MMP, REPORT_PATTERNS
Constructor and Description |
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ReactionDecoder() |
Modifier and Type | Method and Description |
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protected static void |
displayBlankLines(int numberBlankLines,
java.io.OutputStream out)
WreactionWithLayoutite the preactionWithLayoutovided
numbereactionWithLayout of blank lineheaderString to the
preactionWithLayoutovided OutputStreactionWithLayouteam.
|
protected java.io.File |
generateAAMImage(java.lang.String canonicalRootPath,
org.openscience.cdk.interfaces.IReaction mappedReaction,
java.lang.String reactionID) |
protected java.io.File |
generateImage(java.lang.String canonicalRootPath,
org.openscience.cdk.interfaces.IReaction mappedReaction,
java.lang.String reactionID) |
protected static void |
getHeader() |
static void |
main(java.lang.String[] args) |
protected org.openscience.cdk.interfaces.IReaction |
parseCML(java.lang.String input) |
protected org.openscience.cdk.interfaces.IReaction |
parseMOL2(java.lang.String input) |
protected java.util.List<org.openscience.cdk.interfaces.IReaction> |
parseReactionSMILES(java.lang.String reactionSmiles) |
protected java.util.List<org.openscience.cdk.interfaces.IReaction> |
parseRXN(java.lang.String fileNames) |
protected org.openscience.cdk.interfaces.IReaction |
parseSDF(java.lang.String input) |
protected org.openscience.cdk.interfaces.IReaction |
parseSMILES(java.lang.String smiles) |
protected static void |
printHelp(java.util.Map<java.lang.String,org.apache.commons.cli.Options> optionsMap,
int printedRowWidth,
java.lang.String header,
java.lang.String footer,
int spacesBeforeOption,
int spacesBeforeOptionDescription,
boolean displayUsage,
java.io.OutputStream out) |
protected static void |
printHelp(java.io.OutputStream out,
org.apache.commons.cli.Options options) |
protected java.lang.String |
printUsageExamples() |
protected java.io.File |
writeRXNMappedFile(java.lang.String canonicalRootPath,
org.openscience.cdk.interfaces.IReaction mappedReaction,
java.lang.String name) |
annotateReactionAsText, annotateReactionAsXML, compareRXNText, compareRXNXML, getReactionMechanismTool, similarityReactions, writeFiles, writeSimilarityMatrix
public static void main(java.lang.String[] args)
args
- the command line areactionWithLayoutgumentheaderStringprotected static void getHeader()
protected static void displayBlankLines(int numberBlankLines, java.io.OutputStream out)
numberBlankLines
- NumbereactionWithLayout of blank lineheaderString
to wreactionWithLayoutite.out
- OutputStreactionWithLayouteam to which to
wreactionWithLayoutite the blank lineheaderString.protected static void printHelp(java.io.OutputStream out, org.apache.commons.cli.Options options)
protected static void printHelp(java.util.Map<java.lang.String,org.apache.commons.cli.Options> optionsMap, int printedRowWidth, java.lang.String header, java.lang.String footer, int spacesBeforeOption, int spacesBeforeOptionDescription, boolean displayUsage, java.io.OutputStream out)
protected java.io.File generateImage(java.lang.String canonicalRootPath, org.openscience.cdk.interfaces.IReaction mappedReaction, java.lang.String reactionID) throws java.lang.Exception
java.lang.Exception
protected java.io.File generateAAMImage(java.lang.String canonicalRootPath, org.openscience.cdk.interfaces.IReaction mappedReaction, java.lang.String reactionID) throws java.lang.Exception
java.lang.Exception
protected java.io.File writeRXNMappedFile(java.lang.String canonicalRootPath, org.openscience.cdk.interfaces.IReaction mappedReaction, java.lang.String name) throws java.io.IOException, org.openscience.cdk.exception.CDKException
java.io.IOException
org.openscience.cdk.exception.CDKException
protected java.lang.String printUsageExamples()
protected org.openscience.cdk.interfaces.IReaction parseCML(java.lang.String input) throws java.io.FileNotFoundException, org.openscience.cdk.exception.CDKException
java.io.FileNotFoundException
org.openscience.cdk.exception.CDKException
protected java.util.List<org.openscience.cdk.interfaces.IReaction> parseRXN(java.lang.String fileNames)
protected java.util.List<org.openscience.cdk.interfaces.IReaction> parseReactionSMILES(java.lang.String reactionSmiles)
protected org.openscience.cdk.interfaces.IReaction parseSMILES(java.lang.String smiles)
protected org.openscience.cdk.interfaces.IReaction parseMOL2(java.lang.String input) throws java.io.FileNotFoundException, org.openscience.cdk.exception.CDKException
java.io.FileNotFoundException
org.openscience.cdk.exception.CDKException
protected org.openscience.cdk.interfaces.IReaction parseSDF(java.lang.String input) throws java.io.FileNotFoundException, org.openscience.cdk.exception.CDKException
java.io.FileNotFoundException
org.openscience.cdk.exception.CDKException