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 : > 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: > • 3 signs your SCM is hindering your productivity > • Requirements for releasing software faster > • 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: • 3 signs your SCM is hindering your productivity • Requirements for releasing software faster • 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: • 3 signs your SCM is hindering your productivity • Requirements for releasing software faster • 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
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 : > > /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: > • 3 signs your SCM is hindering your productivity > • Requirements for releasing software faster > • 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: • 3 signs your SCM is hindering your productivity • Requirements for releasing software faster • 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 0xout 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# Output # mols with largest values minimizeForceField Energy Minimization (not displayed in GUI) partialcharge Calculate partial charges by specified method readconformerAdjacent conformers combined into a single molecule sIsomorphism filter(-s, -v options replacement)(not displayed in GUI) smallest# Output # mols with smallest values of descriptor(not displayed in GUI) sort 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: • 3 signs your SCM is hindering your productivity • Requirements for releasing software faster • 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
You should compile with Eigen. See the docs ( http://open-babel.readthedocs.org/en/latest/Installation/install.html#requirements ). - Noel On 7 May 2014 11:04, Douglas Houston wrote: > itiwks-> /usr/people/douglas/programs/openbabel-2.3.2/build/bin/obabel -L > ops > 0xout 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# Output # mols with largest values > minimizeForceField Energy Minimization (not displayed in GUI) > partialcharge Calculate partial charges by specified method > readconformerAdjacent conformers combined into a single molecule > sIsomorphism filter(-s, -v options replacement)(not displayed in GUI) > smallest# Output # mols with smallest values of descriptor(not > displayed in GUI) > sort 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: > • 3 signs your SCM is hindering your productivity > • Requirements for releasing software faster > • 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: • 3 signs your SCM is hindering your productivity • Requirements for releasing software faster • 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 : > 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 >: > > > > /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: > > • 3 signs your SCM is hindering your productivity > > • Requirements for releasing software faster > > • 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: > • 3 signs your SCM is hindering your productivity > • Requirements for releasing software faster > • 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: • 3 signs your SCM is hindering your productivity • Requirements for releasing software faster • 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: • 3 signs your SCM is hindering your productivity • Requirements for releasing software faster • 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
So I've recompiled obabel with eigen, but the output of obabel -L ops has not changed: 0xout 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# Output # mols with largest values minimizeForceField Energy Minimization (not displayed in GUI) partialcharge Calculate partial charges by specified method readconformerAdjacent conformers combined into a single molecule sIsomorphism filter(-s, -v options replacement)(not displayed in GUI) smallest# Output # mols with smallest values of descriptor(not displayed in GUI) sort Sort by descriptor(~desc for reverse) unique[param] remove duplicates by descriptor;default inchi vIsomorphism filter(-s, -v options replacement)(not displayed in GUI) obabel still writes only 1 conformer (with no error messages) no matter the options I use. -- View this message in context: http://forums.openbabel.org/Generating-a-diverse-set-of-conformers-tp4656011p4657403.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: • 3 signs your SCM is hindering your productivity • Requirements for releasing software faster • 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 -- 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: • 3 signs your SCM is hindering your productivity • Requirements for releasing software faster • 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: • 3 signs your SCM is hindering your productivity • Requirements for releasing software faster • 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
[Open Babel] Creating an OBMol by hand in C++
Dear all,
I am working with a program (in C++) which has its own way of dealing
with atoms and molecules. I would like to use the OpenBabel library to
assign types to atoms. For now, when I need to do it I write a .xyz
file and then read it in an OBMol object and assign the types.
This works, but I am not happy because it could be more efficient.
Thus, I would like to create the OBMol object by hand. I was thinking
of something such as:
struct Atom{
float x;
float y;
float z;
char Type[4];// Element name (H, C, N, O...).
char PotentialType[3]; // Atom type for the scoring function.
};
struct Molecule{
Atom atom[150];
int size;
};
/
OpenBabel::OBMol obMol;
OpenBabel::OBAtom *atom;
for (int i=0; iSetVector(molecule.atom[i].x, molecule.atom[i].y,
molecule.atom[i].z);
atom->SetType(molecule.atom[i].Type);
obMol.InsertAtom(*atom);
}
obMol.ConnectTheDots();
When I am doing this the code compiles but crashes (Segmentation
fault) and I have not been able to find what is going wrong. I have
also tried with SetVector(const vector3 & v ) but it is the same.
Does anyone have a clue of how I can create this object atom by atom?
Thank you
Nicolas
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Re: [Open Babel] Creating an OBMol by hand in C++
Never written something like this, but briefly looking at some code in
openbabel for reading molecules, you should do
atom = obMol.NewAtom();
At the beginning of each loop. Your code looks like it is just due referencing
an unset pointer, so no surprise it segfaults.
You maybe also have to do
obMol.ReserveAtoms(molecule.size);
-David
> On May 7, 2014, at 7:05 PM, Nicolas Cheron
> wrote:
>
> Dear all,
>
> I am working with a program (in C++) which has its own way of dealing
> with atoms and molecules. I would like to use the OpenBabel library to
> assign types to atoms. For now, when I need to do it I write a .xyz
> file and then read it in an OBMol object and assign the types.
>
> This works, but I am not happy because it could be more efficient.
> Thus, I would like to create the OBMol object by hand. I was thinking
> of something such as:
>
> struct Atom{
> float x;
> float y;
> float z;
> char Type[4];// Element name (H, C, N, O...).
> char PotentialType[3]; // Atom type for the scoring function.
> };
>
> struct Molecule{
> Atom atom[150];
> int size;
> };
>
> /
>
> OpenBabel::OBMol obMol;
> OpenBabel::OBAtom *atom;
> for (int i=0; i atom->SetVector(molecule.atom[i].x, molecule.atom[i].y,
> molecule.atom[i].z);
> atom->SetType(molecule.atom[i].Type);
> obMol.InsertAtom(*atom);
> }
> obMol.ConnectTheDots();
>
> When I am doing this the code compiles but crashes (Segmentation
> fault) and I have not been able to find what is going wrong. I have
> also tried with SetVector(const vector3 & v ) but it is the same.
>
>
> Does anyone have a clue of how I can create this object atom by atom?
>
> Thank you
>
> Nicolas
>
> --
> Is your legacy SCM system holding you back? Join Perforce May 7 to find out:
> • 3 signs your SCM is hindering your productivity
> • Requirements for releasing software faster
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