Re: [Open Babel] Generating a diverse set of conformers
Can I just check people received the input file? I used the Nabble forum to attach it ... -- View this message in context: http://forums.openbabel.org/Generating-a-diverse-set-of-conformers-tp4656011p4657429.html Sent from the General discussion mailing list archive at Nabble.com. -- Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE Instantly run your Selenium tests across 300+ browser/OS combos. Get unparalleled scalability from the best Selenium testing platform available Simple to use. Nothing to install. Get started now for free. http://p.sf.net/sfu/SauceLabs ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Generating a diverse set of conformers
I wrote this reply yesterday, but it didn’t make it to the babble list somehow. When I try obabel ~/Desktop/crystal_ligand_flex.sdf -O tst-res.sdf --confab --conf 5 (with your example file), I get a file with 2900 conformers written, so I believe there is a problem with your installation. Your list of ops indicate to me that the eigen support failed in your compile. I’m not an expert in compilation issues, but if you attach the output of cake and make we could try to see if there is a problem. To be sure to capture everything, I’d recommend that you do it with a clean build directory. Kind regards, Fredrik 12 maj 2014 kl. 11:36 skrev Douglas Houston dhous...@staffmail.ed.ac.uk: Actually that input file isn't the most flexible, here is a different one that is more flexible and also only generates one conformer. crystal_ligand_flex.sdf http://forums.openbabel.org/file/n4657427/crystal_ligand_flex.sdf -- View this message in context: http://forums.openbabel.org/Generating-a-diverse-set-of-conformers-tp4656011p4657427.html Sent from the General discussion mailing list archive at Nabble.com. -- Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE Instantly run your Selenium tests across 300+ browser/OS combos. Get unparalleled scalability from the best Selenium testing platform available Simple to use. Nothing to install. Get started now for free. http://p.sf.net/sfu/SauceLabs ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss signature.asc Description: Message signed with OpenPGP using GPGMail -- Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE Instantly run your Selenium tests across 300+ browser/OS combos. Get unparalleled scalability from the best Selenium testing platform available Simple to use. Nothing to install. Get started now for free. http://p.sf.net/sfu/SauceLabs___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Generating a diverse set of conformers
Actually that input file isn't the most flexible, here is a different one that is more flexible and also only generates one conformer. crystal_ligand_flex.sdf http://forums.openbabel.org/file/n4657427/crystal_ligand_flex.sdf -- View this message in context: http://forums.openbabel.org/Generating-a-diverse-set-of-conformers-tp4656011p4657427.html Sent from the General discussion mailing list archive at Nabble.com. -- Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE Instantly run your Selenium tests across 300+ browser/OS combos. Get unparalleled scalability from the best Selenium testing platform available Simple to use. Nothing to install. Get started now for free. http://p.sf.net/sfu/SauceLabs ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Generating a diverse set of conformers
It's gone worryingly quiet ... -- View this message in context: http://forums.openbabel.org/Generating-a-diverse-set-of-conformers-tp4656011p4657420.html Sent from the General discussion mailing list archive at Nabble.com. -- Is your legacy SCM system holding you back? Join Perforce May 7 to find out: #149; 3 signs your SCM is hindering your productivity #149; Requirements for releasing software faster #149; Expert tips and advice for migrating your SCM now http://p.sf.net/sfu/perforce ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Generating a diverse set of conformers
Well, you have been asked to provide your input file for easier debugging, one option could be to try that… Anyway, obconformer only outputs one conformer according to it’s documentation, that one is written on stdout, so it’s included in your output (which by the way didn’t appear when I read the message in my email, only on forums.openbabel.org). If you would like to have it in a file, the doc states that you need to pipe it like: /usr/local/bin/obconformer 10 10 crystal_ligand.sdf generatedconformer.sdf Have you made sure that when you call obabel, it’s your newly compiled version that’s compiled? If you run obabel -V, it will tell you the compilation date together with the version number. Did you get any messages during the recompilation? Kind regards, Fredrik 9 maj 2014 kl. 10:54 skrev Douglas Houston dhous...@staffmail.ed.ac.uk: It's gone worryingly quiet ... -- View this message in context: http://forums.openbabel.org/Generating-a-diverse-set-of-conformers-tp4656011p4657420.html Sent from the General discussion mailing list archive at Nabble.com. -- Is your legacy SCM system holding you back? Join Perforce May 7 to find out: #149; 3 signs your SCM is hindering your productivity #149; Requirements for releasing software faster #149; Expert tips and advice for migrating your SCM now http://p.sf.net/sfu/perforce ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss signature.asc Description: Message signed with OpenPGP using GPGMail -- Is your legacy SCM system holding you back? Join Perforce May 7 to find out: #149; 3 signs your SCM is hindering your productivity #149; Requirements for releasing software faster #149; Expert tips and advice for migrating your SCM now http://p.sf.net/sfu/perforce___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Generating a diverse set of conformers
Hi, Does the input file contain 3D-coordinates? As far as I have seen, neither confab nor conformer will generate an initial 3D structure if it’s not already present. Kind regards, Fredrik 6 maj 2014 kl. 19:39 skrev Douglas Houston dhous...@staffmail.ed.ac.uk: Anyone have any comment on this? I am observing the same problem as OP. I am using the following: /usr/people/douglas/programs/openbabel-2.3.2/build/bin/obabel crystal_ligand.sdf -O tmp.sdf --conformer --nconf 50 --writeconformers I only get 1 conformer in the 1 output file. I have also tried the following: /usr/people/douglas/programs/openbabel-2.3.2/build/bin/obabel crystal_ligand.sdf -O tmp.sdf --confab -rcutoff 0.1 -ecutoff 10 --original --verbose Still get 1 conformer in the 1 output file. The verbose option seems to have no effect, neither do the rcutoff and ecutoff options. I believe there may be something wrong with the way obabel is handling the options, it's like they aren't being used at all. Can anyone honestly state that they have observed this feature actually working? -- View this message in context: http://forums.openbabel.org/Generating-a-diverse-set-of-conformers-tp4656011p4657393.html Sent from the General discussion mailing list archive at Nabble.com. -- Is your legacy SCM system holding you back? Join Perforce May 7 to find out: #149; 3 signs your SCM is hindering your productivity #149; Requirements for releasing software faster #149; Expert tips and advice for migrating your SCM now http://p.sf.net/sfu/perforce ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss signature.asc Description: Message signed with OpenPGP using GPGMail -- Is your legacy SCM system holding you back? Join Perforce May 7 to find out: #149; 3 signs your SCM is hindering your productivity #149; Requirements for releasing software faster #149; Expert tips and advice for migrating your SCM now http://p.sf.net/sfu/perforce___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Generating a diverse set of conformers
/usr/people/douglas/programs/openbabel-2.3.2/build/bin/obabel -L outputs: charges descriptors fingerprints forcefields formats loaders ops How do I tell? -- View this message in context: http://forums.openbabel.org/Generating-a-diverse-set-of-conformers-tp4656011p4657397.html Sent from the General discussion mailing list archive at Nabble.com. -- Is your legacy SCM system holding you back? Join Perforce May 7 to find out: #149; 3 signs your SCM is hindering your productivity #149; Requirements for releasing software faster #149; Expert tips and advice for migrating your SCM now http://p.sf.net/sfu/perforce ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Generating a diverse set of conformers
itiwks- /usr/people/douglas/programs/openbabel-2.3.2/build/bin/obabel -L ops 0xoutfile.xxx Additional file output addfilenameAppend input filename to title AddInIndexAppend input index to title AddPolarHAdds hydrogen to polar atoms only canonicalCanonicalize the atom order energyForceField Energy Evaluation (not displayed in GUI) fillUC Fill the unit cell (strict or keepconnect) gen2DGenerate 2D coordinates gen3DGenerate 3D coordinates largest# descr Output # mols with largest values minimizeForceField Energy Minimization (not displayed in GUI) partialchargemethod Calculate partial charges by specified method readconformerAdjacent conformers combined into a single molecule sIsomorphism filter(-s, -v options replacement)(not displayed in GUI) smallest# descr Output # mols with smallest values of descriptor(not displayed in GUI) sortdesc Sort by descriptor(~desc for reverse) unique[param] remove duplicates by descriptor;default inchi vIsomorphism filter(-s, -v options replacement)(not displayed in GUI) I see no mention of conformers right enough ... However obabel -H output includes the line: --writeconformers Output multiple conformers separately -- View this message in context: http://forums.openbabel.org/Generating-a-diverse-set-of-conformers-tp4656011p4657399.html Sent from the General discussion mailing list archive at Nabble.com. -- Is your legacy SCM system holding you back? Join Perforce May 7 to find out: #149; 3 signs your SCM is hindering your productivity #149; Requirements for releasing software faster #149; Expert tips and advice for migrating your SCM now http://p.sf.net/sfu/perforce ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Generating a diverse set of conformers
Hi, Is the input molecule flexible? It would be much easier to test if you could sent it to the list. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2014-05-07 11:19 GMT+02:00 Fredrik Wallner fred...@wallner.nu: Continue by running obabel -L formats and obabel -L ops Kind regards, Fredrik Skickat från min iPhone 7 maj 2014 kl. 11:06 skrev Douglas Houston dhous...@staffmail.ed.ac.uk : /usr/people/douglas/programs/openbabel-2.3.2/build/bin/obabel -L outputs: charges descriptors fingerprints forcefields formats loaders ops How do I tell? -- View this message in context: http://forums.openbabel.org/Generating-a-diverse-set-of-conformers-tp4656011p4657397.html Sent from the General discussion mailing list archive at Nabble.com. -- Is your legacy SCM system holding you back? Join Perforce May 7 to find out: #149; 3 signs your SCM is hindering your productivity #149; Requirements for releasing software faster #149; Expert tips and advice for migrating your SCM now http://p.sf.net/sfu/perforce ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss -- Is your legacy SCM system holding you back? Join Perforce May 7 to find out: #149; 3 signs your SCM is hindering your productivity #149; Requirements for releasing software faster #149; Expert tips and advice for migrating your SCM now http://p.sf.net/sfu/perforce ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss -- Is your legacy SCM system holding you back? Join Perforce May 7 to find out: #149; 3 signs your SCM is hindering your productivity #149; Requirements for releasing software faster #149; Expert tips and advice for migrating your SCM now http://p.sf.net/sfu/perforce___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Generating a diverse set of conformers
OK will do. Just out of curiosity, what is my install of Babel doing when I specify those options? Just ignoring them, without informing the user? -- View this message in context: http://forums.openbabel.org/Generating-a-diverse-set-of-conformers-tp4656011p4657402.html Sent from the General discussion mailing list archive at Nabble.com. -- Is your legacy SCM system holding you back? Join Perforce May 7 to find out: #149; 3 signs your SCM is hindering your productivity #149; Requirements for releasing software faster #149; Expert tips and advice for migrating your SCM now http://p.sf.net/sfu/perforce ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Generating a diverse set of conformers
obconformer when run outputs: Usage: obconformer NSteps GeomSteps file -- View this message in context: http://forums.openbabel.org/Generating-a-diverse-set-of-conformers-tp4656011p4657404.html Sent from the General discussion mailing list archive at Nabble.com. -- Is your legacy SCM system holding you back? Join Perforce May 7 to find out: #149; 3 signs your SCM is hindering your productivity #149; Requirements for releasing software faster #149; Expert tips and advice for migrating your SCM now http://p.sf.net/sfu/perforce ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Generating a diverse set of conformers
obconformer with arguments: /usr/local/bin/obconformer 10 10 crystal_ligand.sdf outputs: The conformers appear to be generated - how do I get them written out? The input structure is in 3D by the way. -- View this message in context: http://forums.openbabel.org/Generating-a-diverse-set-of-conformers-tp4656011p4657405.html Sent from the General discussion mailing list archive at Nabble.com. -- Is your legacy SCM system holding you back? Join Perforce May 7 to find out: #149; 3 signs your SCM is hindering your productivity #149; Requirements for releasing software faster #149; Expert tips and advice for migrating your SCM now http://p.sf.net/sfu/perforce ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Generating a diverse set of conformers
This doesn't work either: /usr/people/douglas/programs/openbabel-2.3.2/build/bin/obabel crystal_ligand.sdf -oconfbareport -xf tmp.sdf -xr 1.0 I get: obabel: cannot write output format! Open Babel 2.3.2 -- Mar 20 2013 -- 08:59:03 Usage: obabel [-iinput-type] infilename [-ooutput-type] -Ooutfilename [Options] Try -H option for more information. -- View this message in context: http://forums.openbabel.org/Generating-a-diverse-set-of-conformers-tp4656011p4657394.html Sent from the General discussion mailing list archive at Nabble.com. -- Is your legacy SCM system holding you back? Join Perforce May 7 to find out: #149; 3 signs your SCM is hindering your productivity #149; Requirements for releasing software faster #149; Expert tips and advice for migrating your SCM now http://p.sf.net/sfu/perforce ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Generating a diverse set of conformers
Anyone have any comment on this? I am observing the same problem as OP. I am using the following: /usr/people/douglas/programs/openbabel-2.3.2/build/bin/obabel crystal_ligand.sdf -O tmp.sdf --conformer --nconf 50 --writeconformers I only get 1 conformer in the 1 output file. I have also tried the following: /usr/people/douglas/programs/openbabel-2.3.2/build/bin/obabel crystal_ligand.sdf -O tmp.sdf --confab -rcutoff 0.1 -ecutoff 10 --original --verbose Still get 1 conformer in the 1 output file. The verbose option seems to have no effect, neither do the rcutoff and ecutoff options. I believe there may be something wrong with the way obabel is handling the options, it's like they aren't being used at all. Can anyone honestly state that they have observed this feature actually working? -- View this message in context: http://forums.openbabel.org/Generating-a-diverse-set-of-conformers-tp4656011p4657393.html Sent from the General discussion mailing list archive at Nabble.com. -- Is your legacy SCM system holding you back? Join Perforce May 7 to find out: #149; 3 signs your SCM is hindering your productivity #149; Requirements for releasing software faster #149; Expert tips and advice for migrating your SCM now http://p.sf.net/sfu/perforce ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Generating a diverse set of conformers
Thanks for the comments. I am using Open Babel 2.3.1 on a mac. The command
still doesn't ouptut multiple conformers, only the one file with one
conformer in it.
obabel input.sdf -O out.sdf --conformer --nconf 50 --score rmsd
obabel input.sdf -O out.sdf --writeconformers --nconf 50 --score rmsd
Also for python code:
import openbabel as ob
input_file='test.sdf'
mol = ob.OBMol()
cv = ob.OBConversion()
cv.SetInAndOutFormats('sdf','sdf')
cv.ReadFile(mol, input_file)
cs=ob.OBConformerSearch()
cs.Setup(mol,30,5,5,25)
cs.GetConformers(mol)
cv.WriteFile(mol, conformers.sdf)
Is the conformer search meant to output multiple conformers or just the
lowest energy one? If it's meant to output multiple conformers, what is
missing above?
Thanks,
Scott
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