Re: [Open Babel] Structure is not tanimoto similar to itself
On 09/07/2012 20:59, Jeff Janes wrote: If I make a file foo.smi with just this in it: [N-]=[N+]=c1c(=O)ccc2=c1c(=O)c1c1c2=O And then make and use an index file: ~/openbabel/bin/obabel foo.smi -ofs ~/openbabel/bin/obabel foo.fs -ocan -sfoo.smi -at5 -aa --title I find that the structure is only 0.7 similar to itself. The problem is the [N-]=[N+]= structure, which could also be written [N]#[N]= . When indexing, dative bonds like these are converted into the second form. So when searching the target should also be in this form. obabel foo.smi -O foo1.smi -b 1 molecule converted obabel foo.fs -ocan -sfoo1.smi -at5 -aa --title [N-]=[N+]=c1c(=O)ccc2=c1c(=O)c1c1c2=O 1 1 molecule converted It has proved difficult to find a suitable user interface for this that does not interfere with other features, especially as the charged form is the more common one. Originally the target molecule was also automatically converted; this may be a better way. In the meantime I will add a note to the documentation. Chris -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] OBPointGroup in Python
I've recently been writing some code to automatically write GAMESS input files for me. As these files require a point group it would be advantageous to determine this automatically from a geometry. Unfortunately I'm having some difficulty accessing the OBPointGroup class with the python bindings. I'm not sure if this is a problem with how i'm trying to access the class or a bug in the python bindings. I would greatly appreciate any help or advise you can offer. It's simple enough to add the OBPointGroup to the python bindings, but it won't be enough. I'd also like to see GAMESS input files with automatic point groups. The problem is that GAMESS expects a particular frame of reference once you've specified, say C2V, and also expects only the symmetry-unique atoms. The OBPointGroup code is not yet at that level of sophistication. (Indeed, I think I may need to use a different implementation that was given to me -- I'm happy if someone wants to adapt it.) Sorry I can't be more help, -Geoff -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] OBPointGroup in Python
Hi Geoff, Thanks for the response. Is it not possible to rotate the molecule into the correct frame once you have determined its point group? Yours Ed On 12 Jul 2012, at 13:12, Geoff Hutchison wrote: I've recently been writing some code to automatically write GAMESS input files for me. As these files require a point group it would be advantageous to determine this automatically from a geometry. Unfortunately I'm having some difficulty accessing the OBPointGroup class with the python bindings. I'm not sure if this is a problem with how i'm trying to access the class or a bug in the python bindings. I would greatly appreciate any help or advise you can offer. It's simple enough to add the OBPointGroup to the python bindings, but it won't be enough. I'd also like to see GAMESS input files with automatic point groups. The problem is that GAMESS expects a particular frame of reference once you've specified, say C2V, and also expects only the symmetry-unique atoms. The OBPointGroup code is not yet at that level of sophistication. (Indeed, I think I may need to use a different implementation that was given to me -- I'm happy if someone wants to adapt it.) Sorry I can't be more help, -Geoff -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
[Open Babel] Weighted-rotor search
Is it possible to do a weighted rotor search in pybel? I have been using
openbabel and the WeightedRotorSearch function. I couldn't find any simple
example online and wanted to find out if the approach below is ok and if
anyone would advise changes. Am I right in saying that the mol is updated to
the best conformer and this is what will be written to the output file?
import openbabel
filename = 'test.mol2'
mol = openbabel.OBMol()
conversion = openbabel.OBConversion()
conversion.SetInAndOutFormats('mol2', 'mol2')
conversion.ReadFile(mol, filename)
ff = openbabel.OBForceField.FindForceField(MMFF94)
ff.SetLogLevel(openbabel.OBFF_LOGLVL_LOW)
ff.SetLogToStdErr()
ff.Setup(mol)
ff.WeightedRotorSearch(5, 500)
ff.GetConformers(mol)
conversion.WriteFile(mol, 'TEST1.mol2')
One thing I notice with a calculation, was that the lowest energy did not
match any of the conformer energies (see below). Is this an error?
CONFORMER ENERGY
1 192.047
2 212.909
3 234.580
4 216.623
5 211.296
LOWEST ENERGY: 191.771
Thanks in advance,
Scott
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Re: [Open Babel] OpenCL
Hi Chris, On 12.07.2012 13:16, Geoff Hutchison wrote: I've just seen a demo of the impact of running applications on the GPU and it does seem for some operations you can get striking performance gains. Would it be worth considering porting openbabel to OpenCL? Much like muti-threading, it's not clear how some operations in Open Babel would work in OpenCL. As Geoff points out they are couple of factors to consider in this regard. Sometimes making algorithmic changes can boost performance even more than going the GPU way. In my case however, I'm interested in optimization through parallel approaches. That's why I'm researching on GPU and I will be very glad to hear whatever ideas you might have. That said, there are certain types of code which make clear sense as multi-threaded and/or OpenCL, for example the force fields and conformer generation code, or the charge assignment. There's actually a student in Ireland sponsored by Noel who's investigating this as we speak. (You may have seen some posts from Omar already.) I have look at force fields and conformer generation codes since they are both related. When you are doing conformational search you also need to asses the energy of the conformer to decide if you are going to keep it. Improving forcefields calculation should also improve performance for conformer generation. Conformer generation also looks promising, Attached you can find a plot of the time spent generating conformers for several different drug like molecules using Confab [1]. I used the optimized Borodina set that you can get from Confab's article [2]. As you can appreciate from the plot as the number of conformers involved increases, execution times for conformational search increases noticeably. I will be happy if I can shave those numbers by a half factor offloading some operations to the GPU. Cheers, -- Omar [1] Confab - http://confab.googlecode.com/ [2] Confab Article (Borodina Optimized Set) - http://www.jcheminf.com/content/3/1/8 conformers_vs_generation_time.png Description: Binary data -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
