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CDK-R / cdkr

Integrating R and the CDK
https://cdk-r.github.io/cdkr/
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get.volume giving error #123

Open garimaloh opened 3 years ago

garimaloh commented 3 years ago

am trying to use get.volume to get the molecular volume. But i am getting error. Please would you help me to resolve the issue.

Here is my code:

mols <- parse.smiles(pep[4,SMILES])[[1]] convert.implicit.to.explicit(mols) get.tpsa(mols) [1] 624.96 get.volume(mols) Error in .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl, : org.openscience.cdk.exception.NoSuchAtomTypeException: The AtomType null could not be found

rajarshi commented 3 years ago

What is the SMILES string? And does this fail with the latest version from Github?

On Wed, Jun 30, 2021 at 11:07 PM Garima @.***> wrote:

am trying to use get.volume to get the molecular volume. But i am getting error. Please would you help me to resolve the issue.

Here is my code:

mols <- parse.smiles(pep[4,SMILES])[[1]] convert.implicit.to.explicit(mols) get.tpsa(mols) [1] 624.96 get.volume(mols) Error in .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl, : org.openscience.cdk.exception.NoSuchAtomTypeException: The AtomType null could not be found

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garimaloh commented 3 years ago

install_github("https://github.com/CDK-R/rcdklibs") install_github("https://github.com/CDK-R/cdkr", subdir="rcdk")

They dont work for me. How to install this tool from github

garimaloh commented 3 years ago

SMILES is a column name in a data table with value in 5th row

rajarshi commented 3 years ago

What is the error?

Sent from my iPhone

On Jul 2, 2021, at 7:58 PM, Garima @.***> wrote:

 SMILES is a column name in a data table with value in 5th row

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garimaloh commented 3 years ago

I was able to install from github. its= gives me same errors.

garimaloh commented 3 years ago

mols2 <- parse.smiles(pep[2,SMILES])[[1]] class(mols2) [1] "jobjRef" attr(,"package") [1] "rJava" kk=view.molecule.2d(mols2) Error in view.molecule.2d(mols2) : java.lang.NoSuchMethodError: get.volume(mols2) Error in .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl, : org.openscience.cdk.exception.NoSuchAtomTypeException: The AtomType null could not be found

rajarshi commented 3 years ago

What is the SMILES you're trying to parse?

On Fri, Jul 2, 2021 at 8:22 PM Garima @.***> wrote:

mols2 <- parse.smiles(pep[2,SMILES])[[1]] class(mols2) [1] "jobjRef" attr(,"package") [1] "rJava" kk=view.molecule.2d(mols2) Error in view.molecule.2d(mols2) : java.lang.NoSuchMethodError: get.volume(mols2) Error in .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl, : org.openscience.cdk.exception.NoSuchAtomTypeException: The AtomType null could not be found

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-- Rajarshi Guha | http://blog.rguha.net | @rguha https://twitter.com/rguha

rajarshi commented 3 years ago

The following works for me on OS X (10.15.7), R 4.0.2

m <- parse.smiles('CCC')[[1]]

view.molecule.2d(m)

set.atom.types(mol=m)

get.volume(m)

[1] 60.44441

On Fri, Jul 2, 2021 at 8:22 PM Garima @.***> wrote:

mols2 <- parse.smiles(pep[2,SMILES])[[1]] class(mols2) [1] "jobjRef" attr(,"package") [1] "rJava" kk=view.molecule.2d(mols2) Error in view.molecule.2d(mols2) : java.lang.NoSuchMethodError: get.volume(mols2) Error in .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl, : org.openscience.cdk.exception.NoSuchAtomTypeException: The AtomType null could not be found

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/CDK-R/cdkr/issues/123#issuecomment-873313735, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAAIMOOXFDDMWD7HQY7GXXTTVZJ4TANCNFSM47TSBS3Q .

-- Rajarshi Guha | http://blog.rguha.net | @rguha https://twitter.com/rguha