Good way to produce a table of R-groups

2009-11-26T09:06:45Z

Hi all!

I have a rather large SDfile with compounds containing the same scaffold and I'm looking for an easy way to get this data into an editable (in Word or something similar) table. I have looked at ChemAxon's rgdecomp and the new deco command from Indigo. However, none of them is working completely as I would like. rgdecomp produces very nice results in an SDfile that can be displayed nicely in mview. The problem is that I don't have a good way to convert this into a table in Word.

Any ideas are appreciated!

Kind regards, Fredrik

How do I change the stereochemistry of atoms in my 3D molecules?

2010-03-18T13:45:52Z

I have a large set of 3D molecules in SD-files. Some of them have incorrect stereochemistry. How can I change the stereochemistry of individual atoms? Obviously I am looking for an automated way.

Molecule modifications in Drug Design, why?

2010-03-18T16:01:45Z

Hi,

in drug design, given an interesting compound which comes from the screening, we want to get more potency, or activity, etc. Sometimes this is just modifications of a CH3 group to a CF3 groups, etc. I would like to get sources of information about the usual modificaitons performed and their reasons, with a detailed explanation. I tried to find reviews about it, but all the publications are rather specific, and I can not buy books, as have no money.

Any suggestions in form of links or publications would be really appreciated.

Thanks

What are semi colons in InChI strings ?

2010-03-18T19:52:32Z

Hello All,

I came across this InChI here below with semi colons in it.

InChI=1/2C7H9N5O4.2ClH.2Cu.2H2O/c2*1-12-6(15)4(11-16)5(8)10-7(12)9-2-3(13)14;;;;;;/h2*2,8H2,1H3,(H,9,10)(H,13,14);2*1H;;;2*1H2/p-4

I ran babel on it to get 3D co-ordinates and I was expecting that babel would throw out an error but it actually got 3D cordinates.

What do semi colons mean in InChI string ??

Thanks

Is it possible to use Bioclipse as a python IDE?

2010-03-18T13:39:15Z

I would like to use Bioclipse not only for analysis of SDF files but also as a Python IDE. Is that possible?

Where is the Blue Obelisk dinner at the ACS Spring 2010 meeting?

2010-03-16T06:27:44Z

Where is the Blue Obelisk dinner at the ACS meeting next week? Who should be contacted? Will there be other Blue Obelisk meetings during the week? (I will not be present myself, but ask this for potential new people).

Connection tables: is there any rule for atom ordering?

2010-03-18T12:50:10Z

From a recent reported bug on the "InChI Facilities and Applications" mailing list:

Depending on the order one defines atoms in the molecule description, different InChIs are produced for the identical molecule

I have started a discussion with my colleagues about this issue: is there any rule that defines how atoms should be ordered in the connection table? Personally I would not consider this hypothesis, but still I cannot exclude the existence of any rule.

What does the SMILES sp2 hybridization imply to electron contributions to pi systems?

2010-03-16T18:29:55Z

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 another bug report around atom type detection in the CDK, and all fails I was emailed has basically this substructure in common: 'c1c2cc[nH]cc2nc1'.

Now, the first nitrogen in the SMILES (right one in the image) was causing the atom type not recognized, and the problem was that the CDK was looking at the number ring atoms and if the ring could be aromatic. (Yes, aromaticity again.)

That problem was easily fixed, leading to the next atom typing issue. The actual CDK atom type for the first nitrogen is N.planar3: a nitrogen with three neighbors and contribution a lone pair to a pi-system.

This brings me to me question. SP2 hybridization in the CDK typically implies that the atom has one electron available for pi-systems; the second nitrogen is like that, and that has the atom type N.sp2.

Therefore, my question is what SP2 hybridization in the context of (Open)SMILES means? Or, is the above SMILES actually valid, or should it really be 'c1c2cc[NH]cc2nc1' instead?

Which formats fall into "Open Data, Open Source, and Open Standards "?

2009-12-05T05:35:28Z

The Blue Obelisk page about "Open Standards" says that MDL and SMILES are "proprietary format[s]" and "not Open as there is no community process for its development; it can, in principle be modified by the owner at any stage."

I have strong feelings about this topic. Why is SMILES (and I mean here the representation and not the canonicalization) a proprietary format? It was published in a journal paper, included in a book chapter, and the details are available online for many to read. There are many different implementations of the language, and some groups have added their own extensions to SMILES. Daylight and the authors of SMILES have no trademark to the term SMILES and have no patent claim. Even if Daylight were to make a new version which was not compatible to existing SMILES, almost no one would follow suit unless it proved useful.

By any definition I can come up with, SMILES is an open standard. If you count OpenSMILES as a relevant community (which is hard to justify, since nothing from OpenSMILES has made its way even into the existing open source projects) then even that objection is gone.

By comparison, several participants of Blue Obelisk say that CML is an Open Standard. (Since I can't find the license for it, I'm not sure what that means, but I've asked for that clarification as another topic.) CML is controlled by one or two people, and it seems that while the CML specification can be distributed to others, it cannot be changed without the permission of those authors.

Is that really a community process, and for that matter, what does a community process mean?

Yet another example is the MDL connection table formats. That is listed as a proprietary format, but it's also a format which is well documented by the primary maintainer, described in published papers and books, implemented in a number of code bases, including open source ones. What makes it not open, under the Blue Obelisk definition? By the way, the vendor supplied format definition should be an example of what a good specification looks like. CML's format-through-schema-dump is not.

One possibility is that the MDL specification cannot be redistributed, legally. I have a copy of it but the copyright statement prohibits sharing that spec. Is that what makes it not Open? But in that case, the ISO 8601 date format is also not an open specification, because it costs about 85 Euros to purchase and cannot be copied without permission.

If this is a problem then two ways to resolve it are 1) ask for redistribution rights, so long as there are no changes (putting it on par with CML) or 2) develop an equivalent but open documentation.

Another possibility for not calling the MDL format "open" is that they can change the format without consulting "the community." They have changed the format once, although I suspect that that involved feedback from their user community. They introduced the V2000 format, and carefully made it backwards compatible with the old file format. If they had not, others would not have followed their lead. Indeed, I haven't seen that many V2000 files in the wild. It doesn't seem like they have strong control over the format.

On the other hand, I see that the Blue Obelisk page[1] lists InChI as an open format, base solely I assume on the source code being accessible since it is a somewhat closed development process which has changed the output several times. I have looked at the source code and can say that it is not a simple specification. I am unaware of any other implementation which can parse InChI strings with near 100% success rates.

Because of the lack of a good stand-alone specification, any developer who reads the LGPL-based source code in order to reimplement it might legally be considered "dirty" in terms of clean-room coding practices, meaning that the new code will also have to be LGPL. For reference, I prefer BSD. I would have thought that a good Open Standard also means the freedom to pick a different license, including free ones which are not compatible with the GPL family of licenses.

What then are the exemplar "Open Standard" formats in this field, why are they "Open", and why are they more Open than both the MDL and SMILES formats?

ADDENDUM

I was hoping specially for feedback on which formats are open and which aren't, and why. Is SMILES open or not? Why does OpenSMILES make a difference? Are the MDL formats open? What would be needed for an OpenMDL? Is the PDB format open?

If the format is published in a journal which does not allow redistribution without paying a standard copying fee, is the format itself open or closed? For example, the SMD format published in JCICS the early 1990s was meant to be a community-driven format definition, using a context-free grammar. Is this format open or not?

Can the SDF format be used with 0D data and still preserve stereochemistry?

2010-02-26T15:51:28Z

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 version of OpenBabel stores stereochemistry in the SDF file if only 0D information is available, so that SMILES<->SDF conversions (for example) preserve stereochemistry.

If the format is used to do so, is it within the specification? What Open Source (or indeed otherwise) software supports this use?

Fingerprint False Positive Benchmark Tool?

2010-02-22T23:27:05Z

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 structure searchable database. Let's further say the thing I care most about is minimizing the number of false positives that my atom-by-atom search needs to check.

Two questions:

How should I define a scoring function to best achieve my goal?
What tools currently exist (open source or otherwise) for performing this analysis on arbitrary datasets and groups of query structures?

Compute similarity between two distance matrices

2010-03-09T16:48:11Z

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 my goal is to see which X-data that is most similar to the Y-data. I could do something like a PLS with multi-Y, but I don't want to influence the X-data matrixes.

What I have is cross-reactivity data for a set of proteins and ligands. One of the X-distance matrixes consists of sequence homologies between the proteins and the Y-matrix will contain the distances derived from a PCA describing the ligand activities. I want to test another way of calculating the protein similarities and see if that measure is more correlated to the ligand activities. In the end, my goal is to take a new protein sequence, run it through the model and get suggestions on likely ligands.

What StackExchange alternative should we move to?

2010-02-24T10:46:20Z

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 move into a 45 day free trial. The pricing model is, unfortunately, not within our reach, with $129 a month.

I am happy to learn that beta7 does add an export facility, so we do not have to write tools to do this manually, though I have yet no clue how to import this into a clone. Fact is, we'll have to move the Blue Obelisk Exchange sooner than later.

So, my questions are:

what clone should we use? and is there even a hosting service?
who has a free server to host a clone?
who wants to help set it up and maintain it?

Great about this StackExchange beta period was that is was easy to set up, and that obviously comes at a price. I do not have overly much time to maintain a server, and could very much use some help. Perhaps someone even wants to take the concept over instead?

Using Bioclipse to manipulate SDF files

2010-02-24T22:26:54Z

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 them to the table, so that I can copy them out to a spreadsheet. Further the reverse is true, I'm unable to add comment info into the file from the interface, is there a native way to do this?

Thanks.

How do I get the "Chemical Classification" information from PubChem?

2009-12-27T19:21:31Z

The PubChem page for a given compound shows the "Chemical Classification" and "Pharmacological Classification" fields. For example, in CID 4075 (Mesalamine) the Chemical Classifications are:

Organic Chemicals > Carboxylic Acids > Acids, Carbocylic > Benzoic Acids >
     Hydroxybenzoic Acids > Salicyclic Acids > Aminosalicylic Acids > Mesalamine

plus a few others ("Hydroxy Acids" and "Phenols" are other ways to get to "Hydroxybenzoic Acids").

These appear to be MeSH terms. I can't figure out how to get that data directly. It isn't present in the ASN.1, XML, or SD files. I haven't found a data set which maps MeSH terms to compound ids.

My working solution is to download MeSH, get all of the children of "Organic Chemicals" in the MeSH tree, and use EUtils:esearch to get the pccompound uilist containing all "$group"[MSHN] terms.

That's going to require a lot of queries. Is there a better, more direct way?

Cross-Platform OpenBabel Java interface?

2009-12-04T08:31:23Z

I have seen that OpenBabel has a Java interface nowadays, but I am wondering if someone has made a single openbabel.jar that provides this API and has prebuild binary libraries for the C++ bits, much like jni-inchi provides a single jar, which includes prebuild InChI libraries for windows, linux and mac (32 + 64 bit). Is something like that available for OpenBabel too?

PubChem structural keys: why "those" SMARTS patterns?

2010-03-02T08:21:08Z

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.

Does anybody know any public document where is described "why" exactly those patterns were included in the FP specifications? Probably there was some data mining beyond, but I'm not sure...

Thanks!

What can we not yet do in chemistry with Open Data, Open Source, and Open Standards?

2009-11-11T15:53:57Z

Open Data, Open Source, and Open Standards does not solve all problems in chemistry. The Blue Obelisk is trying to change that, but this is certainly not the case yet. What are in your opinion important tasks in chemistry that cannot be performed with Open Data, Open Source, and Open Standards?

Please feel free to bash ODOSOS as much as you like here. I'd be more than willing to listen and think about how I can contribute to filling this gap.

Best way to convert a muti-compound .smi file to a .mol (or .sdf) file?

2010-02-17T20:47:36Z

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 split the file into individual .smi files, then rejoin them via open babel after converting all to .mol? My background in regular expressions is a bit week so I've been avoiding doing this...

Can this be done via Bioclipse? Once again, is easy to do one at a time (via the GuI).

How best to summarise ROC score

2010-02-24T21:02:36Z

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, false positives on x)? I was thinking about the length of the vector from the top left corner (perfect prediction) to the point in question. This will lose information about sensitivity vs specificity though.

Open source software for DNA and RNA short sequence 3D structure "estimation"

2010-02-24T16:02:52Z

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 ranging from 10 to 50 nucleotides?

Thanks

Why do I get a NullPointerException while trying to generate InChI with CDK?

2009-11-11T15:06:01Z

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 wrong?

[...] Caused by: java.lang.NullPointerException at net.sf.jnati.deploy.NativeArtefactLocator.getArtefact(NativeArtefactLocator.java:129) at net.sf.jnati.deploy.NativeLibraryLoader.loadLibrary(NativeLibraryLoader.java:37) at net.sf.jniinchi.JniInchiWrapper.loadLibrary(JniInchiWrapper.java:92) at org.openscience.cdk.inchi.InChIGeneratorFactory.(InChIGeneratorFactory.java:78) at org.openscience.cdk.inchi.InChIGeneratorFactory.getInstance(InChIGeneratorFactory.java:96) at net.bioclipse.structuredb.domain.DBMolecule.calculateInchi(DBMolecule.java:421) ... 34 more

The actual code is here

IRC channels to discuss about open source software and science

2010-02-21T14:53:34Z

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

3D Co-ordinates OpenBabel, OpenEyeChem(OMEGA) differ

2010-02-03T17:07:02Z

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 3D co-ordinates using the same Force Fields(MMFF94) or do they use different force fields?

Is there like a best force field ??

Pubchem documentation says it uses OpenEyeChem's OMEGA (MMFF94).

Well if I take a CID and get their 3D coordinates from PubChem and compare those co-ordinates with 3D co-ordinates generated using open babel --gen3D option I find the co-ordinates values differ. Are they not supposed to be same ? Why/why not ?

I actually have to further run Gaussian or GAMESS on these, so would not my results differ? Would that matter at all or no ?

Thanks for ur time.

Using google-closure graphics for chemical drawing and similar problems

2010-02-18T17:35:49Z

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 on the instruments.

Is goog.graphics module strong enough for this?

If anything is missing - what things would I have to implement myself? I've bumped into the first problem when I could not use goog.fx.Dragger to move the shapes around.

Heck, I'll tell you why I want this - I maintain a community site for NMR/EPR/MRI people called NMR Wiki and I want to develop all sorts of tools and things for the MR community.

Thank you people.

What are the free tools for molecular descriptors calculation?

2010-02-09T14:56:03Z

I know CDK Descriptor Calculator GUI, and the rCDK library, both developed by R. Guha:

any other suggestion?

Get coordinates of beads covering the surface of a protein

2009-12-22T12:54:36Z

Hi,

given a protein structur from the PDB, I would like to generate NS spheres of radius Rs which cover totally the protein surface. Given RS there, NS is the maximum number of spheres so they do not overlap. I would need the coordinates of the center of each sphere.

Does anybody know if this has been implemented in some method / program? Or how to do it with scripting.

Thanks

What formats fall into "Open Specification"?

2010-02-15T22:50:33Z

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"?, I think it is time to get down to business, and line up specifications in cheminformatics, and summarize the details.

My proposal is that an Open Specfication, unlike what the Blue Obelisk talks about on Open Standards, consists of these freedoms: the specification is:

freely distributable
freely implementable
freely modifiable

Such a specification can be raised to a standard by pinpointing a particular version, and releasing that as Open Standard.

So, I here ask, which Open Specification are there (one specification per answer, please; feel free to leave multiple answers)?

Where can the specification be downloaded, and ...
... under which license?
Is the specification complete, or lacking crucial details?
Are there any restrictions on implementing the specification, like patents?
Can the specification be modified, and ...
... redistributed?
What mechanism does the specification allow, to be proposed as standard, or does it merely await community consensus and to become a de facto standard?
Is there a reference implementation of the specification?
Are there Open Source implementations of the specification?

What is the CML license?

2009-12-05T03:03:06Z

What's the license on CML? I went looking for it in the repository but failed to find mention of a copyright or license. The only thing I found was in the Jumbo source

All JUMBO code is distributed under the Open Source Artistic License (http://www.opensource.org). You are free to modify the code but if you do it may no longer be distributed under the name JUMBO (or a derivative) without permission of Peter Murray-Rust. Any distribution must acknowledge the origins and also include copies of the JUMBO source (see Artistic License for details). You may not claim that a modified version is a compliant CML system and may not assert that it reads or writes CML. CML Schema is distributed under a Creative Commons license, allowing redistribution but NOT derivative works. This is to ensure that the schema does not mutate.

Peter Murray-Rust Henry Rzepa

2006-04-07

The CML SourceForge page under "Project Details" says "Artistic License", but I assume that's for JUMBO and not for CML itself.

I've searched and searched but found nothing else about this.

UPDATE:

I've been talking about this with PMR, including discussion on the BO-discuss list. It appears that he's going to explicitly license it under the "Artistic License 2.0", which is less confusing than that Artistic License. I don't know if he's going to keep in the above listed restrictions on using the term "CML compliant" and if a modified version can claim to read CML. One problem is that CDK (or was that Bioclipse? Or both?) is distributing a modified version of the JUMBO code, and I'm certain they and PMR want to continue to say the package supports CML.

Stackoverflow not open source -- not a problem?

2010-01-03T10:27:58Z

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 source. It is true, the devs behind StackExchange have suggested they may consider opening the source sometime in the future. But still... is this not in conflict with the principles of BlueObelisk? A purist might say it is even hypocritical.

What's more, there are free and open alternatives budding on the internet, why not support their initiative and use them instead?

Two threads from meta on the topic:

Two clones (like I already said, they are budding :D):

Top Questions - Blue Obelisk Exchange

Good way to produce a table of R-groups

How do I change the stereochemistry of atoms in my 3D molecules?

Molecule modifications in Drug Design, why?

What are semi colons in InChI strings ?

Is it possible to use Bioclipse as a python IDE?

Where is the Blue Obelisk dinner at the ACS Spring 2010 meeting?

Connection tables: is there any rule for atom ordering?

What does the SMILES sp2 hybridization imply to electron contributions to pi systems?

Which formats fall into "Open Data, Open Source, and Open Standards "?

Can the SDF format be used with 0D data and still preserve stereochemistry?

Fingerprint False Positive Benchmark Tool?

Compute similarity between two distance matrices

What StackExchange alternative should we move to?

Using Bioclipse to manipulate SDF files

How do I get the "Chemical Classification" information from PubChem?

Cross-Platform OpenBabel Java interface?

PubChem structural keys: why "those" SMARTS patterns?

What can we not yet do in chemistry with Open Data, Open Source, and Open Standards?

Best way to convert a muti-compound .smi file to a .mol (or .sdf) file?

How best to summarise ROC score

Open source software for DNA and RNA short sequence 3D structure "estimation"

Why do I get a NullPointerException while trying to generate InChI with CDK?

IRC channels to discuss about open source software and science

3D Co-ordinates OpenBabel, OpenEyeChem(OMEGA) differ

Using google-closure graphics for chemical drawing and similar problems

What are the free tools for molecular descriptors calculation?

Get coordinates of beads covering the surface of a protein

What formats fall into "Open Specification"?

What is the CML license?

Stackoverflow not open source -- not a problem?