Hello,
I am new in cdk. I search molecules since a molfile with method:
Pattern queryPattern = VentoFoggia.findIdentical(molQuery);
boolean matched = queryPattern.matches(molDB);
In this point ,with some big molecules, the search does not finalize and
consumes 100% cpu in machine. With jstack, i see
at java.util.HashMap$TreeNode.find(HashMap.java:1859)
at java.util.HashMap$TreeNode.find(HashMap.java:1869)
at java.util.HashMap$TreeNode.find(HashMap.java:1869)
at java.util.HashMap$TreeNode.find(HashMap.java:1869)
at java.util.HashMap$TreeNode.getTreeNode(HashMap.java:1881)
at java.util.HashMap.getNode(HashMap.java:575)
at java.util.HashMap.get(HashMap.java:556)
at org.openscience.cdk.graph.GraphUtil$EdgeToBondMap.get(GraphUtil.java:339)
at org.openscience.cdk.isomorphism.VFState.feasible(VFState.java:123)
at
org.openscience.cdk.isomorphism.AbstractVFState.add(AbstractVFState.java:129)
at org.openscience.cdk.isomorphism.StateStream.map(StateStream.java:108)
at org.openscience.cdk.isomorphism.StateStream.findNext(StateStream.java:90)
at org.openscience.cdk.isomorphism.StateStream.next(StateStream.java:74)
at org.openscience.cdk.isomorphism.StateStream.next(StateStream.java:39)
at com.google.common.collect.Iterators$7.computeNext(Iterators.java:646)
at
com.google.common.collect.AbstractIterator.tryToComputeNext(AbstractIterator.java:143)
at
com.google.common.collect.AbstractIterator.hasNext(AbstractIterator.java:138)
at com.google.common.collect.Iterators.getNext(Iterators.java:860)
at com.google.common.collect.Iterables.getFirst(Iterables.java:775)
at org.openscience.cdk.isomorphism.Mappings.first(Mappings.java:497)
at org.openscience.cdk.isomorphism.VentoFoggia.match(VentoFoggia.java:119)
at org.openscience.cdk.isomorphism.Pattern.matches(Pattern.java:77)
It is possible to avoid this?
It is possible to set a timeout in the search?
Thank you very match.
Mark
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