1
vote
0answers
17 views
Open source software for DNA and RNA short sequence 3D structure “estimation”
Hi,
do you know some open source software (better if this is not a server) for RNA or DNA structure prediction even if this is not equilibrium optimized or so for sequences rangin …
1
vote
1answer
17 views
IRC channels to discuss about open source software and science
Hi,
can you recommend me interesting forums to chat about the subjects treated here? I had a look at the IRC servers freenode but found nothing relevant.
Thanks
WS
2
votes
4answers
175 views
Stackoverflow not open source — not a problem?
Awkward issue. This stackexchange is dedicated to question about open data and all things open source. It strikes me then that the very platform it has been created on is not open …
0
votes
3answers
28 views
Which Maven repositories are around providing which Blue Obelisk projects?
Packaging is an important part of dissemination of (scientific) Open Source software, and Maven bundles are one of the options. Maven repositories can be referred to, allowing deve …
2
votes
3answers
87 views
How do I validate if my MDL SD file is correct?
The CDK used to have a library to validate chemical graphs against common problems, including unknown atom types. Additionally, the file reader for the MDL SD format has a STRICT m …
4
votes
8answers
145 views
What Open Source cheminformatics libraries are available?
This question is a stub for a complete list of all Open Source cheminformatics software available. People are encouraged to reply tools they use, and under what Open Source license …
2
votes
3answers
64 views
Top Cited and ‘Highest Impact’ papers using current cheminformatics tools?
Yesterday, our group saw two thesis defenses; those of dr Spjuth and dr Eklund. The question was posed on how relevant Bioclipse is (part of both theses), and in particular what wa …
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 …
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?
2
votes
1answer
48 views
Is there an open source pKa or LogD tool available
Are you aware of any pKa prediction or LogD prediction tool, which is available as open source?
I know that several tools are calculating LogP, MR (molar refractivity), or TPSA (t …
1
vote
5answers
67 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?
