I am trying to create a scaffold tree of roughly 33k molecules. I have generated 2D canonicalised smiles for all these molecules using openbabel. However, when I import them, Scaffold hunter keeps complaining 'WARN edu.udo.scaffoldhunter.model.util.SVGGen - Warning: A Molecule does not contain valid 2D coordinates. New 2D coordinates will be calculated!'. All the molecules have the 'correct' format:
O=Cc1c(O)cc(c2c1Oc1c(OC2=O)c(C)c(c2c1(O)OC2=O)O)C,CID005379540
When being imported. I choose Column 1 to be smiles. When mapping, I set Column 2 to be Structure Name property.
Molecules are, however, still imported. Further, when I try to calculate the Scaffold tree for these molecules, my session eventually runs out of memory, throwing the error 'Exception in thread "Poller SunPKCS11-Darwin" java.lang.OutOfMemoryError: Java heap space'. I have tried to incease heap space (By setting the memory argument in run.sh) to 50GB (Yes, fifty gigabytes of RAM). While calculating the scaffold tree, it once again throws the warning about no valid 2D coordinates.
Any help would be appreciated.
Best,
David
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the warning can safely be ignored, it is most likely not related to the OutOfMemory error. Since SMILES come without 2D coordinates, which are required for depiction, Scaffold Hunter calculates them (using CDK). The warning should not appear when importing from different formats like SDF which contain coordinates.
I have used Scaffold Hunter with more than 100k molecules without memory problems, so 33k molecules should not cause any problems. However, it is recommended to use a MySQL server for large datasets. Are you using a MySQL database?
Best regards
Nils
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Hello,
I am trying to create a scaffold tree of roughly 33k molecules. I have generated 2D canonicalised smiles for all these molecules using openbabel. However, when I import them, Scaffold hunter keeps complaining 'WARN edu.udo.scaffoldhunter.model.util.SVGGen - Warning: A Molecule does not contain valid 2D coordinates. New 2D coordinates will be calculated!'. All the molecules have the 'correct' format:
O=Cc1c(O)cc(c2c1Oc1c(OC2=O)c(C)c(c2c1(O)OC2=O)O)C,CID005379540
When being imported. I choose Column 1 to be smiles. When mapping, I set Column 2 to be Structure Name property.
Molecules are, however, still imported. Further, when I try to calculate the Scaffold tree for these molecules, my session eventually runs out of memory, throwing the error 'Exception in thread "Poller SunPKCS11-Darwin" java.lang.OutOfMemoryError: Java heap space'. I have tried to incease heap space (By setting the memory argument in run.sh) to 50GB (Yes, fifty gigabytes of RAM). While calculating the scaffold tree, it once again throws the warning about no valid 2D coordinates.
Any help would be appreciated.
Best,
David
Hi David,
the warning can safely be ignored, it is most likely not related to the OutOfMemory error. Since SMILES come without 2D coordinates, which are required for depiction, Scaffold Hunter calculates them (using CDK). The warning should not appear when importing from different formats like SDF which contain coordinates.
I have used Scaffold Hunter with more than 100k molecules without memory problems, so 33k molecules should not cause any problems. However, it is recommended to use a MySQL server for large datasets. Are you using a MySQL database?
Best regards
Nils