1
vote
1answer
27 views
What does the SMILES sp2 hybridization imply to electron contributions to pi systems?
SMILES and OpenSMILES have a sp2 concept related to the user of lower case element symbols for the organic subset; they are aimed at aromaticity annotation. Now, last week I had an …
1
vote
6answers
111 views
What are the free tools for molecular descriptors calculation?
I know CDK Descriptor Calculator GUI, and the rCDK library, both developed by R. Guha:
any other suggestion?
1
vote
4answers
87 views
3D coordinates best options: CDK, RDKit, OpenBabel… anything else?
Which cheminformatics library is the best to assign 3D coordinates to a structure file, RDKit or CDK? (best quality of the results) I'm looking for a free equivalent for CORINA.
h …
0
votes
2answers
53 views
Why do I get a NullPointerException while trying to generate InChI with CDK?
I am getting this NullpointerException deep in the internals when trying to generate InChI using the InChIGeneratorFactory in CDK. Can someone give me a hint to what could be going …
0
votes
1answer
18 views
How does your ODOSOS project deal with code review?
The CDK has a long standing tradition of code review... passive for a long while, using a Nightly build server that tests against certain quality standards, and since about a year …
0
votes
3answers
72 views
Who will go to SWAT4LS and wants to join a Blue Obelisk dinner?
Next week Friday the SWAT4LS meeting will take place, and I will be attending and present our work on Open Drug Data, featuring Bioclipse and the CDK.
Who is going too and wants t …
2
votes
1answer
78 views
How do I open an SDF file using the CDK?
I am writing a Java program to access the first molecule in an SDF file. How do I open an SDF file using the CDK?
0
votes
1answer
39 views
What docking tool can be easily integrated with the CDK?
I am looking for a script and/or code that calls a docking tool starting from a CDK data model. The parts I am most interested in, is how to set up the input for that docking tool …
1
vote
5answers
68 views
How can I access the CDK from Python?
I generally program in Python, but the CDK is a Java library. What is the easiest way to access the CDK from Python?
0
votes
1answer
18 views
How can a CDK data model be saved as Gromacs input for studies it supports?
Somewhat related to the docking question, I am looking for example code for integration of the CDK and Gromacs. Can Gromacs input be auto-generated from a CDK data model for, for e …
