0
votes
1answer
30 views
Compute similarity between two distance matrices
I'm looking for a method to calculate the similarity between two distance matrices. I have two distance matrices that represents some X-data and another that represents Y-data and …
1
vote
1answer
70 views
Using Bioclipse to manipulate SDF files
Bioclipse is great at opening and displaying SDF files, however, I can't seem to figure out how to extract the calculated properties such as SMILES and Molecular Weight and add the …
1
vote
5answers
130 views
What StackExchange alternative should we move to?
Now that StackExchange announced beta7 and that there likely will only be one more beta, we are informed that after this the free beta trial will end, and that we'll automatically …
3
votes
3answers
114 views
Fingerprint False Positive Benchmark Tool?
Let's say I have two binary fingerprint implementations - for example, one from Open Babel and one from CDK. Let's also say I'm interested in picking one or the other for use in a …
1
vote
1answer
30 views
Can the SDF format be used with 0D data and still preserve stereochemistry?
The SDF format is typically used to store 3D and 2D data for molecules. However, this question relates to its use to store 0D (or connection table) information.
The development ve …
4
votes
1answer
51 views
PubChem structural keys: why “those” SMARTS patterns?
PubChem structural keys, that are implemented in the CDK (PubchemFingerprinter class)
are well described by this document.
A number of bits are simple and complex SMARTS patterns. …
2
votes
5answers
93 views
Best way to convert a muti-compound .smi file to a .mol (or .sdf) file?
What is th best way / program to convert a muti-compound .smi file to a .mol (or .sdf) file? Open babel fails on multiple compound smi to .mol conversion.
Is it best to just spli …
2
votes
10answers
104 views
What formats fall into “Open Specification”?
In reply to the lenghty, elaborate, confusing, contradicting, and passionate discussion between Andrew and me in Which formats fall into “Open Data, Open Source, and Open Standards …
1
vote
3answers
32 views
How best to summarise ROC score
Is there an accepted, preferably simple to calculate, number to best represent quality of a model by the position of the resulting point on a ROC diagram (true positives on y, fals …
2
votes
4answers
72 views
3D Co-ordinates OpenBabel, OpenEyeChem(OMEGA) differ
I am sorry there was already a question earlier on this, but I did not get what I wanted, hence I am asking as another question. Please answer.
Do OpenBabel, OpenEyeChem generate …
1
vote
6answers
108 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
2answers
56 views
Tanimoto(“raven”, “writing desk”)
(For background on the title, and use of the term 'bicycle' here, see http://www.straightdope.com/columns/read/1173/why-is-a-raven-like-a-writing-desk .)
Suppose fingerprint fp ha …
1
vote
0answers
16 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 …
2
votes
3answers
64 views
How do I get the “Chemical Classification” information from PubChem?
The PubChem page for a given compound shows the "Chemical Classification" and "Pharmacological Classification" fields. For example, in CID 4075 (Mesalamine) the Chemical Classifica …
1
vote
0answers
25 views
Using google-closure graphics for chemical drawing and similar problems
Hello, may I as for an advice about google closure graphics?
I intend to build a graphical tool to draw NMR pulse sequences and convert them into Varian and Bruker code that runs …
79
questions
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