public class RuleHasOnlySaltSulphonateSulphate extends RuleOnlyAllowedSubstructures
cramer2.CramerRulesExtendedExtended)| Modifier and Type | Field and Description |
|---|---|
protected static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer |
aminoSulphate |
protected static ArrayList<String> |
elements |
protected static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer |
hClAmine |
protected static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer |
phosphate |
protected static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer |
salt |
protected static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer |
salt1 |
protected static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer |
salt2 |
protected static org.openscience.cdk.smiles.SmilesGenerator |
sg |
protected static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer |
sulphate |
protected static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer |
sulphonate |
ids, MSG_HASGROUPchanges, editable, ERR_STRUCTURENOTPREPROCESSED, examples, explanation, id, logger, MSG_NO, MSG_YES, no, residueIDHidden, titlexmltag_CATEGORIES, xmltag_CATEGORY, xmltag_CATEGORYTHRESHOLD, xmltag_CLASS, xmltag_EXPLANATION, xmltag_ID, xmltag_METHOD, xmltag_METHODPARAMETER, xmltag_METHODS, xmltag_NAME, xmltag_RULE, xmltag_RULEEXAMPLE, xmltag_RULES, xmltag_TREEROOT| Constructor and Description |
|---|
RuleHasOnlySaltSulphonateSulphate() |
| Modifier and Type | Method and Description |
|---|---|
protected String[] |
initMetals() |
protected String[] |
initMetals1() |
protected QueryAtomContainers |
initQuery() |
boolean |
verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol,
org.openscience.cdk.interfaces.IAtomContainer selected)
Calls the inherited
RuleOnlyAllowedSubstructures.verifyRule(IAtomContainer)
Removes sulphonate and sulphate groups if any by
FunctionalGroups.detachGroup(IAtomContainer, QueryAtomContainer)
and sets molflag property of a molecule to mf.setResidue(residue); This
makes subsequent rules to work with the residue rather than with the
original molecule If a rule needs the original structure instead, it can
get it by getProperty(MolFlags.PARENT) See for example Q24 and Q33 TODO
treat hydrochloride of amine as free amine |
isImplemented, verifyRuleaddSubstructure, clearSubstructures, equals, getIds, getQuery, getSubstructure, getSubstructures, getSubstructuresCount, removeSubstructure, setIds, setQuery, setSubstructuregetSelectoraddPropertyChangeListener, clearFlags, clone, createRule, fromXML, getEditor, getExampleMolecule, getExamples, getExplanation, getID, getNum, getTitle, hideResiduesID, isEditable, isResidueIDHidden, log, log, log, makeMolecule, removePropertyChangeListener, setEditable, setExampleMolecule, setExamples, setExplanation, setID, setNum, setTitle, toShallowXML, toString, toXMLaddObserver, clearChanged, countObservers, deleteObserver, deleteObservers, hasChanged, notifyObservers, notifyObservers, setChangedfinalize, getClass, hashCode, notify, notifyAll, wait, wait, waitaddPropertyChangeListener, clearFlags, clone, getEditor, getExampleMolecule, getExplanation, getID, getNum, getSelector, getTitle, hideResiduesID, isEditable, isResidueIDHidden, removePropertyChangeListener, setEditable, setExampleMolecule, setExplanation, setID, setNum, setTitle, toStringprotected static transient org.openscience.cdk.smiles.SmilesGenerator sg
protected static transient org.openscience.cdk.isomorphism.matchers.QueryAtomContainer phosphate
protected static transient org.openscience.cdk.isomorphism.matchers.QueryAtomContainer sulphonate
protected static transient org.openscience.cdk.isomorphism.matchers.QueryAtomContainer sulphate
protected static transient org.openscience.cdk.isomorphism.matchers.QueryAtomContainer aminoSulphate
protected static transient org.openscience.cdk.isomorphism.matchers.QueryAtomContainer salt
protected static transient org.openscience.cdk.isomorphism.matchers.QueryAtomContainer salt1
protected static transient org.openscience.cdk.isomorphism.matchers.QueryAtomContainer salt2
protected static transient org.openscience.cdk.isomorphism.matchers.QueryAtomContainer hClAmine
protected String[] initMetals()
protected String[] initMetals1()
protected QueryAtomContainers initQuery() throws Exception
initQuery in class RuleSubstructuresExceptionpublic boolean verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol,
org.openscience.cdk.interfaces.IAtomContainer selected)
throws DecisionMethodException
RuleOnlyAllowedSubstructures.verifyRule(IAtomContainer)
Removes sulphonate and sulphate groups if any by
FunctionalGroups.detachGroup(IAtomContainer, QueryAtomContainer)
and sets molflag property of a molecule to mf.setResidue(residue); This
makes subsequent rules to work with the residue rather than with the
original molecule If a rule needs the original structure instead, it can
get it by getProperty(MolFlags.PARENT) See for example Q24 and Q33 TODO
treat hydrochloride of amine as free amineverifyRule in class RuleOnlyAllowedSubstructuresDecisionMethodExceptionCopyright © 2004–2018 Ideaconsult Ltd. All rights reserved.