Re: [Open Babel] Lucifox - chemistry in EPUB ebooks in Firefox?

Am 24.10.2012 16:57, schrieb Noel O'Boyle: This? http://web.chemdoodle.com/tutorial/2d-structure-canvases/viewer-canvas > Probably a javascript molecular viewer. > > On 22 October 2012 09:04, Haakon Meland Eriksen wrote: >> Lucifox is a free (as in freedom) EPUB reader addon for Firefox, >> cur

Re: [Open Babel] OpenCL

>AFAIK OB checks all >fingerprints in a list one by one so there is much room for >improvement. That is a killer for OpenCL on the GPU, because there is a considerable penalty for moving memory between Host and Device (GPU). Generally, you want to move large blocks of memory and do as much as po

Re: [Open Babel] Generating fs from sdf

speed limit will be set by how fast your box can deliver the datafiles to OpenBabel and how fast it can write the results back to disk. Best regards, Ernst-Georg Schmid -- Try before you buy = See our experts in action

Re: [Open Babel] Message-ID: <4f2ff94c.2070...@gaseq.co.uk>

For SVG: extern "C" char * ob_molfile_to_svg (char *molfile) { OBMol mol; OBConversion conv; string tmpStr (molfile); string outstring; istringstream molstream (tmpStr); ostringstream SVGstream; char *tmpSVG; conv.SetInAndOutFormats ("MDL", "SVG"); conv.Read (

Re: [Open Babel] Substructure search with .fs generated with FP3, FP4 and MACCS fingerprints

Hello, >i think with a .fs generated with FP3, FP4 or MACCS the -s parameter is a >SMARTS strings, instead a SMILES string, am i right? no. For FP3 and FP4 the SMARTS patterns in a pattern file generate the bits in the fingerprint. The input still has to be a SMILES. AFAIK OpenBabel cannot gene

Re: [Open Babel] Need complementary information on FP2

ld be able to write your own fingerprint based on the finger2.cpp source. Best regards, Ernst-Georg Schmid -- Learn Windows Azure Live! Tuesday, Dec 13, 2011 Microsoft is holding a special Learn Windows Azure train

Re: [Open Babel] Multiple Input File search

Dear Jochen, the CTFile formats specification can be obtained here http://accelrys.com/products/informatics/cheminformatics/ctfile-formats/no-fee.php for free. You may check your SDFile/Molfiles against the spec. The V2000 format uses fixed field/line sizes, so it is extremely picky when it co

Re: [Open Babel] Fastsearch format (fs) stored in a chemical structure database

Hello, >InChI-Key are exactly done for exact searching. exactly, unlike different SMILES canonicalization implementations the InChI algorithm is standardized. And despite the fact that the first InChI-Key collisions have been found, at least there is an estimate of their collision probability.

Re: [Open Babel] Fastsearch format (fs) stored in a chemical structure database

Hello, I'd say that the reason for choosing this storage method was a technical decision. Since an unfolded FP2 is 1024 bits long (1021 actually used) it doesn't fit into the largest integer datatype of MySQL, UNSIGNED BIGINT which is 2^64. So you either have to store it in a BLOB, but then you

Re: [Open Babel] Fastsearch format (fs) stored in a chemical structure database

~nhaider/cheminf/moldb5.html Yes, I know. ;-) http://merian.pch.univie.ac.at/~nhaider/cheminf/cmmm.html "Alternatively, you can use the Barsoi DLL, a library based on a C port of checkmol/matchmol which has been developed as a part of the pgchem::tigress project by Ernst-Georg Schmid (see belo

Re: [Open Babel] Fastsearch format (fs) stored in a chemical structure database

Hello, >Does anyone know what is the best way to store the fastsearch index (to >reuse it) in a chemical structures database? best field type to store it? >(i'm using MySQL). you could: - store it outside the database in a file with pointers to the records in the database as Craig A. James sugg

Re: [Open Babel] Need help in calculationg tanimoto coefficient

>Just a small comment... >Since Open Babel 2.3.0, it is possible to describe each of the set >bits using the "s" output option, e.g. Ah, nice feature. Then one can build a dictionary of fragment<->bit mappings for a given input set along FP2 generation, including detection of ambiguous mappings

Re: [Open Babel] Need help in calculationg tanimoto coefficient

Hi, FP2 is a Daylight type fingerprint. See 6.1.2 of http://www.daylight.com/dayhtml/doc/theory/theory.finger.html for an explanation. FP2 generates fragments up to 7 bonds length or shorter if a ring is encountered. The fragments are then hashed to the first 1021 bits of the 1024 bit space F

[Open Babel] C[C@@H](O)C(O)=O and C[C@H](O)C(O)=O match?

option (check R/S stereo) treats them as distinct structures. best regards, Ernst-Georg Schmid -- Increase Visibility of Your 3D Game App & Earn a Chance To Win $500! Tap into the largest installed PC base & get more

[Open Babel] C[C@@H](O)C(O)=O and C[C@H](O)C(O)=O match?

option (check R/S stereo) treats them as distinct structures. best regards, Ernst-Georg Schmid -- Increase Visibility of Your 3D Game App & Earn a Chance To Win $500! Tap into the largest installed PC base & get m

Re: [Open Babel] Run several instances in parallel

u run those instances as separate processes and not in threads, you should be safe in terms of unwanted interaction between the instances. best regards, Ernst-Georg Schmid -- Beautiful is writing same markup. Internet Explo

[Open Babel] Antwort: RE: Antwort: How to calcualate atom count and bond

I dont't know about the .NET wrappers but such basic functionality should be there also. Good luck Ernst-Georg Schmid -- Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed comp

[Open Babel] Antwort: How to calcualate atom count and bond

unsigned int ob_num_atoms (char *smiles) { OBMol mol; OBConversion conv; string tmpStr (smiles); istringstream molstream (tmpStr); unsigned int numatoms = 0; conv.SetInAndOutFormats ("SMI", "SMI"); conv.Read (&mol, &molstream); numatoms = mol.NumAtoms (); return (numatoms); }

[Open Babel] Antwort: Re: Somebody interested in a VF2 based structure matcher for OB?

By replacing the ordered list with a vector for the vertex lookup table I could reduce the overhead of converting an OBMol into an ARGraph. The match() function is now half as fast as SmartsPattern.match(). Combined with a fingerprint screen there is no noticeable difference for reasonably spec

[Open Babel] Antwort: Re: Somebody interested in a VF2 based structure matcher for OB?

w to use your vf2 implementation with RDKit molecules so I get an idea how it could be adapted to OMMol objects? Best Regards Ernst-Georg Schmid -- Return on Information: Google Enterprise Search pays you back Get the facts

[Open Babel] Antwort: Re: Somebody interested in a VF2 based structure matcher for OB?

Because I didn't knew gist.github.com... :-) http://gist.github.com/255970 Best Regards Ernst-Georg Schmid -- Return on Information: Google Enterprise Search pays you back Get the facts. http://p.sf.net/sfu/g

[Open Babel] Antwort: Re: Somebody interested in a VF2 based structure matcher for OB?

h - or maybe igraph_intersection and igraph_intersection_many can help. A open source MCSS finder is available in Java: http://github.com/asad/VFlib Best Regards Ernst-Georg Schmid -- Return on Information: Google Enterprise Sear

[Open Babel] Somebody interested in a VF2 based structure matcher for OB?

I have written an experimental substructure and exact matcher based on the VF2 algorithm and the libvf library (igraph seems posssible too but requires a rewrite). It currently is substantially (3x - 10x) slower than SmartsPattern.Match(), but can do exact matching on the graph level and allow

Re: [Open Babel] Why Openbabel output non-standard MDL Molfile (SDF) format?

Geoffrey Hutchison schrieb: > If you look at the specification, most of these are marked as "ignored when > read", query, reaction, or unused. I've definitely seen non-standard SD files > with fewer fields. Yes, but as far as I can see, Symyx Programs always set those fields to zero, which wor

Re: [Open Babel] Why Openbabel output non-standard MDL Molfile (SDF) format?

Hi, this is already a bug with ID 2897107. I didn't notice the short bond block though. regards, ergo -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design,