public class TestUtility
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
static java.lang.String |
BRENDA_RXN_DIR |
static java.lang.String |
BUG_RXN_DIR |
static java.lang.String |
INFORCHEM_RXN |
static java.lang.String |
KEGG_RXN_DIR |
static java.lang.String |
MACIE_RXN |
static java.lang.String |
METRXN_RXN |
static java.lang.String |
OTHER_RXN |
static java.lang.String |
RHEA_RXN_DIR |
Constructor and Description |
---|
TestUtility() |
Modifier and Type | Method and Description |
---|---|
protected static void |
addImplicitHydrogens(org.openscience.cdk.interfaces.IAtomContainer atomContainer) |
protected static void |
addImplicitHydrogens(org.openscience.cdk.interfaces.IAtomContainerSet molSet) |
protected static void |
addImplicitHydrogens(org.openscience.cdk.interfaces.IReaction reaction) |
protected static org.openscience.cdk.interfaces.IReaction |
canonise(org.openscience.cdk.interfaces.IReaction reaction) |
protected org.openscience.cdk.interfaces.IReaction |
cleanReaction(org.openscience.cdk.interfaces.IReaction reaction,
java.lang.String reactionName) |
protected static void |
detectAromaticity(org.openscience.cdk.interfaces.IAtomContainerSet molSet) |
protected static void |
detectAromaticity(org.openscience.cdk.interfaces.IReaction reaction) |
protected static void |
draw(DirectMoleculeDrawer molDrawer,
org.openscience.cdk.interfaces.IAtomContainer AtomContainer,
java.lang.String dirPath,
java.lang.String name) |
protected static org.openscience.cdk.interfaces.IAtomContainer |
layout(org.openscience.cdk.interfaces.IAtomContainer AtomContainer) |
protected static java.awt.image.BufferedImage |
makeBlankImage(int width,
int height) |
protected org.openscience.cdk.interfaces.IReaction |
mapReaction(org.openscience.cdk.interfaces.IReaction cdkReaction,
boolean remap) |
protected java.util.List<org.openscience.cdk.interfaces.IReaction> |
mapReactions(org.openscience.cdk.interfaces.IReactionSet reactionSet,
boolean remap) |
protected static org.openscience.cdk.interfaces.IReaction |
readReactionFile(java.lang.String name,
java.lang.String dir,
boolean reMap,
boolean removeHydrogens) |
protected static void |
renumberMappingIDs(org.openscience.cdk.interfaces.IReaction reaction) |
protected static void |
setLonePairs(org.openscience.cdk.interfaces.IAtomContainerSet AtomContainerSet,
org.openscience.cdk.tools.LonePairElectronChecker checker) |
protected static void |
setLonePairs(org.openscience.cdk.interfaces.IReaction reaction) |
protected static void |
setMappingIDs(org.openscience.cdk.interfaces.IReaction reaction) |
protected static void |
typeAtoms(org.openscience.cdk.interfaces.IAtomContainer atomContainer) |
public static final java.lang.String KEGG_RXN_DIR
public static final java.lang.String RHEA_RXN_DIR
public static final java.lang.String BRENDA_RXN_DIR
public static final java.lang.String BUG_RXN_DIR
public static final java.lang.String OTHER_RXN
public static final java.lang.String METRXN_RXN
public static final java.lang.String INFORCHEM_RXN
public static final java.lang.String MACIE_RXN
protected static void setLonePairs(org.openscience.cdk.interfaces.IReaction reaction)
reaction
- protected static void setLonePairs(org.openscience.cdk.interfaces.IAtomContainerSet AtomContainerSet, org.openscience.cdk.tools.LonePairElectronChecker checker)
AtomContainerSet
- checker
- protected static void detectAromaticity(org.openscience.cdk.interfaces.IReaction reaction)
reaction
- protected static void detectAromaticity(org.openscience.cdk.interfaces.IAtomContainerSet molSet)
molSet
- protected static void setMappingIDs(org.openscience.cdk.interfaces.IReaction reaction)
reaction
- protected static void renumberMappingIDs(org.openscience.cdk.interfaces.IReaction reaction)
reaction
- protected static void addImplicitHydrogens(org.openscience.cdk.interfaces.IReaction reaction)
reaction
- protected static void addImplicitHydrogens(org.openscience.cdk.interfaces.IAtomContainerSet molSet)
molSet
- protected static void addImplicitHydrogens(org.openscience.cdk.interfaces.IAtomContainer atomContainer)
atomContainer
- protected static void typeAtoms(org.openscience.cdk.interfaces.IAtomContainer atomContainer)
atomContainer
- protected static org.openscience.cdk.interfaces.IReaction canonise(org.openscience.cdk.interfaces.IReaction reaction)
reaction
- protected static org.openscience.cdk.interfaces.IAtomContainer layout(org.openscience.cdk.interfaces.IAtomContainer AtomContainer)
AtomContainer
- protected static java.awt.image.BufferedImage makeBlankImage(int width, int height)
width
- height
- protected static void draw(DirectMoleculeDrawer molDrawer, org.openscience.cdk.interfaces.IAtomContainer AtomContainer, java.lang.String dirPath, java.lang.String name) throws java.io.IOException
molDrawer
- AtomContainer
- dirPath
- name
- java.io.IOException
protected static org.openscience.cdk.interfaces.IReaction readReactionFile(java.lang.String name, java.lang.String dir, boolean reMap, boolean removeHydrogens) throws java.lang.Exception
name
- dir
- reMap
- removeHydrogens
- java.io.FileNotFoundException
org.openscience.cdk.exception.CDKException
java.lang.Exception
protected java.util.List<org.openscience.cdk.interfaces.IReaction> mapReactions(org.openscience.cdk.interfaces.IReactionSet reactionSet, boolean remap) throws java.io.FileNotFoundException, java.lang.Exception
reactionSet
- remap
- override existing mappingsjava.io.FileNotFoundException
java.lang.Exception
protected org.openscience.cdk.interfaces.IReaction mapReaction(org.openscience.cdk.interfaces.IReaction cdkReaction, boolean remap) throws java.io.FileNotFoundException, java.lang.Exception
cdkReaction
- reaction for be mappedremap
- override existing mappingsjava.io.FileNotFoundException
java.lang.Exception
protected org.openscience.cdk.interfaces.IReaction cleanReaction(org.openscience.cdk.interfaces.IReaction reaction, java.lang.String reactionName) throws java.lang.Exception
reaction
- reactionName
- java.io.FileNotFoundException
java.lang.Exception