[Open Babel] Release Date Openbabel 2.3 (Once again) AND Obconformer vs confab
Hi there @OpenBabel, First of all well done for this brilliant piece of (free) software. Secondly I am trying to determine the release date for OpenBabel 2.3 (I have looked in previous posts and on the website, without much success, even if the indication is close to end of summer [2010]). I found http://openbabel.org/wiki/Version_2.3_Projects (which is not the easiest page to fall on) and there are some interesting new additions. Also, and this is mostly what I need the new version for, will confab be part of this release [2.3]? Also what are the differences between Obconformer and Confab - from what I can see they both generate conformers right? Many Thanks, JP -- Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today. http://p.sf.net/sfu/beautyoftheweb___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Release Date Openbabel 2.3 (Once again) AND Obconformer vs confab
On 7 October 2010 10:19, Jean-Paul Ebejer wrote: > > Hi there @OpenBabel, > First of all well done for this brilliant piece of (free) software. > Secondly I am trying to determine the release date for OpenBabel 2.3 (I have > looked in previous posts and on the website, without much success, even if > the indication is close to end of summer [2010]). I > found http://openbabel.org/wiki/Version_2.3_Projects (which is not the > easiest page to fall on) and there are some interesting new additions. I can't speak for Geoff (Geoff is the release manager and lead developer), but my understanding is that no fixed date has been set - instead, Open Babel may be released within the next month - the exact date is dependent upon the time to takes to fix the final bugs. > Also, and this is mostly what I need the new version for, will confab be > part of this release [2.3]? Also what are the differences between > Obconformer and Confab - from what I can see they both generate conformers > right? I can speak for Confab, though. Confab will not be included in 2.3. It has some additional dependencies, and a few new classes that didn't make it into 2.3, and so requires a separate release, at least for the forseeable future. I think obconformer generates just a single low energy conformer (though I'm not 100% sure). > Many Thanks, > JP > > > -- > Beautiful is writing same markup. Internet Explorer 9 supports > standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. > Spend less time writing and rewriting code and more time creating great > experiences on the web. Be a part of the beta today. > http://p.sf.net/sfu/beautyoftheweb > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > -- Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today. http://p.sf.net/sfu/beautyoftheweb ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Release Date Openbabel 2.3 (Once again) AND Obconformer vs confab
Noel, you are actually the right person to ask this (since I saw an announcement on your blog): What happened to the Frog code (a conformer generator) which was donated to OpenBabel - is it wrapped in obconformer? Also are there any plans to integrate Frog2? I'm interested in getting confab up and running... On 7 October 2010 10:57, Noel O'Boyle wrote: > On 7 October 2010 10:19, Jean-Paul Ebejer > wrote: > > > > Hi there @OpenBabel, > > First of all well done for this brilliant piece of (free) software. > > Secondly I am trying to determine the release date for OpenBabel 2.3 (I > have > > looked in previous posts and on the website, without much success, even > if > > the indication is close to end of summer [2010]). I > > found http://openbabel.org/wiki/Version_2.3_Projects (which is not the > > easiest page to fall on) and there are some interesting new additions. > > I can't speak for Geoff (Geoff is the release manager and lead > developer), but my understanding is that no fixed date has been set - > instead, Open Babel may be released within the next month - the exact > date is dependent upon the time to takes to fix the final bugs. > > > Also, and this is mostly what I need the new version for, will confab be > > part of this release [2.3]? Also what are the differences between > > Obconformer and Confab - from what I can see they both generate > conformers > > right? > > I can speak for Confab, though. Confab will not be included in 2.3. It > has some additional dependencies, and a few new classes that didn't > make it into 2.3, and so requires a separate release, at least for the > forseeable future. I think obconformer generates just a single low > energy conformer (though I'm not 100% sure). > > > Many Thanks, > > JP > > > > > > > -- > > Beautiful is writing same markup. Internet Explorer 9 supports > > standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. > > Spend less time writing and rewriting code and more time creating great > > experiences on the web. Be a part of the beta today. > > http://p.sf.net/sfu/beautyoftheweb > > ___ > > OpenBabel-discuss mailing list > > OpenBabel-discuss@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > > > > -- Jean-Paul Ebejer Early Stage Researcher InhibOx Ltd Pembroke House 36-37 Pembroke Street Oxford OX1 1BP UK (+44 / 0) 1865 262 034 This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. Any unauthorised dissemination or copying of this email or its attachments, and any use or disclosure of any information contained in them, is strictly prohibited and may be illegal. If you have received this email in error please notify the sender and delete all copies from your system. We and our group companies accept no liability or responsibility for personal emails or emails unconnected with our business. Internet communications including emails and access and use of web sites cannot be guaranteed to be secure or error free as information can be intercepted, corrupted, lost or arrive late. Furthermore, while we have taken steps to control the spread of viruses on our systems, we cannot guarantee that this email and any files transmitted with it are virus free. No liability is accepted for any errors, omissions, interceptions, corrupted mail, lost communications or late delivery arising as a result of receiving this message via the Internet or for any virus that may be contained in it. -- Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today. http://p.sf.net/sfu/beautyoftheweb___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Release Date Openbabel 2.3 (Once again) AND Obconformer vs confab
The Frog code never made it into Open Babel. It was donated very
generously but never used in the end. The reason was that around the
same time, Tim Vandermeersch was becoming a contributor to Open Babel
and independently started writing his own 3D structure builder, which
is now part of OpenBabel ("--gen3d" runs this).
Thanks for the encouragement on confab - I'll try to polish it up over
the next few weeks, and get out some sort of initial release.
- Noel
On 7 October 2010 11:01, Jean-Paul Ebejer wrote:
> Noel, you are actually the right person to ask this (since I saw an
> announcement on your blog): What happened to the Frog code (a conformer
> generator) which was donated to OpenBabel - is it wrapped in obconformer?
> Also are there any plans to integrate Frog2?
> I'm interested in getting confab up and running...
>
> On 7 October 2010 10:57, Noel O'Boyle wrote:
>>
>> On 7 October 2010 10:19, Jean-Paul Ebejer
>> wrote:
>> >
>> > Hi there @OpenBabel,
>> > First of all well done for this brilliant piece of (free) software.
>> > Secondly I am trying to determine the release date for OpenBabel 2.3 (I
>> > have
>> > looked in previous posts and on the website, without much success, even
>> > if
>> > the indication is close to end of summer [2010]). I
>> > found http://openbabel.org/wiki/Version_2.3_Projects (which is not the
>> > easiest page to fall on) and there are some interesting new additions.
>>
>> I can't speak for Geoff (Geoff is the release manager and lead
>> developer), but my understanding is that no fixed date has been set -
>> instead, Open Babel may be released within the next month - the exact
>> date is dependent upon the time to takes to fix the final bugs.
>>
>> > Also, and this is mostly what I need the new version for, will confab be
>> > part of this release [2.3]? Also what are the differences between
>> > Obconformer and Confab - from what I can see they both generate
>> > conformers
>> > right?
>>
>> I can speak for Confab, though. Confab will not be included in 2.3. It
>> has some additional dependencies, and a few new classes that didn't
>> make it into 2.3, and so requires a separate release, at least for the
>> forseeable future. I think obconformer generates just a single low
>> energy conformer (though I'm not 100% sure).
>>
>> > Many Thanks,
>> > JP
>> >
>> >
>> >
>> > --
>> > Beautiful is writing same markup. Internet Explorer 9 supports
>> > standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3.
>> > Spend less time writing and rewriting code and more time creating great
>> > experiences on the web. Be a part of the beta today.
>> > http://p.sf.net/sfu/beautyoftheweb
>> > ___
>> > OpenBabel-discuss mailing list
>> > OpenBabel-discuss@lists.sourceforge.net
>> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>> >
>> >
>
>
>
> --
>
> Jean-Paul Ebejer
> Early Stage Researcher
> InhibOx Ltd
> Pembroke House
> 36-37 Pembroke Street
> Oxford
> OX1 1BP
> UK
> (+44 / 0) 1865 262 034
>
>
> This email and any files transmitted with it are confidential and intended
> solely for the use of the individual or entity to whom they are addressed.
> Any unauthorised dissemination or copying of this email or its attachments,
> and any use or disclosure of any information contained in them, is strictly
> prohibited and may be illegal. If you have received this email in error
> please notify the sender and delete all copies from your system.
>
> We and our group companies accept no liability or responsibility for
> personal emails or emails unconnected with our business.
>
> Internet communications including emails and access and use of web sites
> cannot be guaranteed to be secure or error free as information can be
> intercepted, corrupted, lost or arrive late. Furthermore, while we have
> taken steps to control the spread of viruses on our systems, we cannot
> guarantee that this email and any files transmitted with it are virus free.
> No liability is accepted for any errors, omissions, interceptions, corrupted
> mail, lost communications or late delivery arising as a result of receiving
> this message via the Internet or for any virus that may be contained in it.
>
>
--
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Spend less time writing and rewriting code and more time creating great
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[Open Babel] Build conformers of a loop.
Dear all,
I try to find conformers of the loop of a 9-mer peptide, with the N-terminal
(the 3 first residues) and the C-terminal end (the last 2 residues) fixed.
I have customized, for this purpose, the obconformer program this way:
int i,j;
unsigned int n;
OBResidue *residue=NULL;
vector atoms;
OBAtom *atom;
std::string atmtype;
OBFFConstraints constraints;
int fixlist[5]={1,2,3,8,9};
mol.Clear();
conv.Read(&mol);
for(i=0;i<5;i++)
{
residue=mol.GetResidue(fixlist[i]-1);
cout << residue->GetName()<<" ";
atoms=residue->GetAtoms();
for(j=0;j<4;j++) // only backbone is freezed
{
atom=atoms[j];
n=atom->GetIdx();
constraints.AddAtomConstraint(n);
}
}
cout << "\n";
OBForceField *pFF = OBForceField::FindForceField("MMFF94");
pFF->SetLogFile(&cerr);
pFF->SetLogLevel(OBFF_LOGLVL_LOW);
pFF->Setup(mol,constraints);
pFF->WeightedRotorSearch(weightSteps, geomSteps
pFF->ConjugateGradients(geomSteps); // final cleanup
pFF->UpdateCoordinates(mol);
conv.Write(&mol);
But When I fit the Nterminal ends of both molecules (initial conformer and the
result of the program), the C-terminal end is not superimposed. It looks as if
minimization can't deal with geometrical constraints. What's wrong in my
program?
Thanks for your help. Regards
François--
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Re: [Open Babel] Reset stereochemistry
Hi, On Mon, Oct 4, 2010 at 4:59 PM, Geoffrey Hutchison wrote: >> For Murcko framework generation using pybel, I would like to reset the >> stereochemistry. Even after hydrogen deletion, the E/Z stereochemistry >> is conserved. Is there any way to reset the stereo? > > Well, if you're using Python, there's an easy way to reset the > stereochemistry of a SMILES. Just replace/delete '@' and '/' and '\' > characters. :-) > > You raise a good question. I don't know if the 2.3 beta code has a method to > strip stereochem information. Stereochemistry information is stored using OBGenericData. This information can be deleted using OBMol::DeleteData(unsigned int type). The type is OBGenericDataType::StereoData (27). In python this is openbabel.StereoData. Tim > Cheers, > -Geoff > -- > Virtualization is moving to the mainstream and overtaking non-virtualized > environment for deploying applications. Does it make network security > easier or more difficult to achieve? Read this whitepaper to separate the > two and get a better understanding. > http://p.sf.net/sfu/hp-phase2-d2d > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > -- Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today. http://p.sf.net/sfu/beautyoftheweb ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
