public class MappingUtility extends TestUtility
BRENDA_RXN_DIR, BUG_RXN_DIR, INFORCHEM_RXN, KEGG_RXN_DIR, MACIE_RXN, METRXN_RXN, OTHER_RXN, RHEA_RXN_DIR
Constructor and Description |
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MappingUtility() |
Modifier and Type | Method and Description |
---|---|
ReactionMechanismTool |
getAnnotation(org.openscience.cdk.interfaces.IReaction cdkReaction) |
org.openscience.cdk.interfaces.IReaction |
map(org.openscience.cdk.interfaces.IReaction reaction) |
BondChangeCalculator |
map(java.lang.String reactionID,
java.lang.String directory) |
org.openscience.cdk.interfaces.IAtomContainer |
readMDLMolecule(java.lang.String name,
java.lang.String dir) |
org.openscience.cdk.interfaces.IReaction |
readReaction(java.lang.String name) |
org.openscience.cdk.interfaces.IReaction |
readReaction(java.lang.String name,
boolean reMap) |
org.openscience.cdk.interfaces.IReaction |
readReaction(java.lang.String name,
java.lang.String dir) |
org.openscience.cdk.interfaces.IReaction |
readReaction(java.lang.String name,
java.lang.String dir,
boolean reMap) |
BondChangeCalculator |
testRCReactions(java.lang.String reactionID,
java.lang.String directory) |
ReactionMechanismTool |
testReactions(java.lang.String reactionID,
java.lang.String directory) |
void |
writeToFile(java.awt.Image image,
java.lang.String outputDirPath,
java.lang.String name) |
addImplicitHydrogens, addImplicitHydrogens, addImplicitHydrogens, canonise, cleanReaction, detectAromaticity, detectAromaticity, draw, layout, makeBlankImage, mapReaction, mapReactions, readReactionFile, renumberMappingIDs, setLonePairs, setLonePairs, setMappingIDs, typeAtoms
public org.openscience.cdk.interfaces.IReaction readReaction(java.lang.String name) throws java.io.FileNotFoundException, org.openscience.cdk.exception.CDKException, java.lang.Exception
name
- java.io.FileNotFoundException
org.openscience.cdk.exception.CDKException
java.lang.Exception
public org.openscience.cdk.interfaces.IReaction readReaction(java.lang.String name, boolean reMap) throws java.io.FileNotFoundException, org.openscience.cdk.exception.CDKException, java.lang.Exception
name
- reMap
- java.io.FileNotFoundException
org.openscience.cdk.exception.CDKException
java.lang.Exception
public org.openscience.cdk.interfaces.IReaction readReaction(java.lang.String name, java.lang.String dir, boolean reMap) throws java.io.FileNotFoundException, org.openscience.cdk.exception.CDKException, java.lang.Exception
name
- dir
- reMap
- java.io.FileNotFoundException
org.openscience.cdk.exception.CDKException
java.lang.Exception
public org.openscience.cdk.interfaces.IReaction readReaction(java.lang.String name, java.lang.String dir) throws java.io.FileNotFoundException, org.openscience.cdk.exception.CDKException, java.lang.Exception
name
- dir
- java.io.FileNotFoundException
org.openscience.cdk.exception.CDKException
java.lang.Exception
public org.openscience.cdk.interfaces.IAtomContainer readMDLMolecule(java.lang.String name, java.lang.String dir) throws java.io.FileNotFoundException, org.openscience.cdk.exception.CDKException
name
- dir
- java.io.FileNotFoundException
org.openscience.cdk.exception.CDKException
public org.openscience.cdk.interfaces.IReaction map(org.openscience.cdk.interfaces.IReaction reaction)
reaction
- public void writeToFile(java.awt.Image image, java.lang.String outputDirPath, java.lang.String name) throws java.io.IOException
image
- outputDirPath
- name
- java.io.IOException
public ReactionMechanismTool testReactions(java.lang.String reactionID, java.lang.String directory) throws java.io.FileNotFoundException, java.lang.Exception
reactionID
- directory
- java.io.FileNotFoundException
java.lang.Exception
public ReactionMechanismTool getAnnotation(org.openscience.cdk.interfaces.IReaction cdkReaction) throws java.lang.AssertionError, java.lang.Exception
cdkReaction
- java.lang.AssertionError
java.lang.Exception
public BondChangeCalculator testRCReactions(java.lang.String reactionID, java.lang.String directory) throws java.io.FileNotFoundException, java.lang.Exception
reactionID
- directory
- java.io.FileNotFoundException
java.lang.Exception
public BondChangeCalculator map(java.lang.String reactionID, java.lang.String directory) throws java.io.FileNotFoundException, java.lang.Exception
reactionID
- directory
- java.io.FileNotFoundException
java.lang.Exception