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CDK-R / cdkr

Integrating R and the CDK
https://cdk-r.github.io/cdkr/
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get.mcs returns OutOfMemoryError #74

Open rickhelmus opened 5 years ago

rickhelmus commented 5 years ago

Hello,

For a specific set of molecules I cannot seem to calculate the mcs:

mol1 <- rcdk::parse.smiles("CC(=C)[C@@H]1CC[C@]2([C@H]1[C@H]3CC[C@H]4[C@]([C@@]3(CC2)C)(CC[C@H]([C@]4(C)CCOC(=O)C)C(C)(C)COC(=O)C)C)COC(=O)C")[[1]]
mol2 <- rcdk::parse.smiles("C[C@H]1[C@H](C2CC[C@@]3(C(=C2[C@]([C@@H]1C)(C)O)C=CC4[C@]3(CCC5[C@@]4(CCC(C5(C)C)O[C@H]6[C@@H]([C@H]([C@H](CO6)O)O)O)C)C)C)C")[[1]]
mcs <- rcdk::get.mcs(mol1, mol2)
Error in .jcall("org.guha.rcdk.util.Misc", "Lorg/openscience/cdk/interfaces/IAtomContainer;",  : 
  java.lang.OutOfMemoryError: Java heap space

The calculation takes a lot of time and usually fails with above error. Once in a while it may succeed though. Any thoughts? I am using the latest version of rcdk and rcdklibs from CRAN.

rajarshi commented 5 years ago

This may be an issue with the underlying CDK method