date:20121204

Re: [Open Babel] Smiles conversion problems with Ion and Zwitterion

2012-12-04 Thread Miguel Quirós Olozábal

Hello, I am using openbabel to convert the CIFs of the Crystallography
Open Database to SMILES and subsequently perform substructure searches.
I have pointed out several times in this forum the problems that I am
finding in such conversions and searches, many of them similar to that
your are hinting to. The only suggestion I can offer from my experience
is to use version 2.2.3 instead of current 2.3.1. The former is less
prune to add spurious hydrogens, remove aromaticity when it should not,
etc (it does in many times, however, when metal atoms are involved which
is the case in most COD files).

Best wishes
Miguel Quirós

El mar, 04-12-2012 a las 15:34 +, Scott McKechnie escribió:
> Thanks Chris for the helpful comments. Sorry to keep on but I'm still
> left with the problem on going from cif to smiles where the original
> number of elements is not conserved. What I want is to be able to
> reliably represent the original cif molecule as a smiles string and
> from there recreate the molecule with gen3d. The problem at the moment
> is that the number of H atoms is changing. Any work around for this?
> 
> On 4 December 2012 15:05, Chris Morley  wrote:
> Scott
> 
> Your "correct smiles" is not right. The sum of the bond orders
> to the
> charged nitrogen should be 4, and is only 3 (it has no H
> attached). The
> correct SMILES is in my post below. Even with it, the round
> trip via xyz:
> 
> obabel -:"C(=O)(O)C[C@@H](C(=O)[O-])n1c[nH+]cc1" -oxyz --gen3D
> | obabel -ixyz -osmi --append formula
> 1 molecule converted
> C(=O)(O)C[C@@H](C(=O)[O])N1CNC=C1   C7H8N2O4
> 1 molecule converted
> 
> gives a di-radical rather than a zwitterion because xyz does
> not
> represent charges (or even bonds) and so OpenBabel didn't get
> any hints.
> xyz format is poor choice of format for general use. The round
> trip
> works ok with formats like mol or cml.
> 
> Chris
> 
> On 04/12/2012 10:51, Scott McKechnie wrote:
> > Hi Chris,
> >
> > Thanks for your reply and apologies for the delayed
> response. Converting
> > the cif to xyz and viewing the molecule shows the correct
> structure but
> > converting the xyz file to smi and then generating
> coordinates and
> > viewing shows the addition of a H atom.
> >
> > The correct smiles is: C(=O)(O)C[C@@H](C(=O)[O-])[N]1C=C[N
> +]=C1
> > The other smiles is:C(=O)([C@@H](CC(=O)O)N1C=CNC1)O
> >
> > One strange feature is that there doesn't appear to be a
> double bond
> > between the N atom in the ring and the C atom, leaving the C
> atom with
> > only three bonds. The smiles conversion seems to want to add
> a H here to
> > get the correct bonding.
> >
> > Similarly for an ion, using smiles conversion results in the
> addition of
> > H's.
> >
> > I've attached the cif file.
> >
> > Many thanks,
> >
> > Scott
> >
> >
> > On 30 November 2012 14:53, Chris Morley
>  
> > > wrote:
> >
> > On 30/11/2012 12:03, scott_m wrote:
> >  > Dear all,
> >  >
> >  > The conversion of
> (S)-3-carboxy-2-(imidazol-3-ium-1-yl)propanoate
> > from a
> >  > .cif file to .smi and subsequent generation of
> coordinates from
> > the .smi
> >  > file results in the addition of an extra H to one of
> the ring C
> > atoms. The
> >  > original cif formula is C7H8N2O4 but this changes to
> C7H9N2O4,
> > which is no
> >  > longer a zwitterion.
> >  >
> >  > I also noticed that converting an ion to smi and then
> from smi to xyz
> >  > resulted in the addition of hydrogen atoms. Can this
> be avoided?
> >  >
> >  > Is the smi conversion of ions and zwitterions known
> to cause
> > problems?
> >
> > Getting added hydrogens right is a recurrent issue.
> However the
> > conversion from SMILES to xyz (and other formats) seems
> ok. Your problem
> > may be in the conversion of the cif file, but you will
> need to append it
> > for somebody (probably not me) to debug.
> >
> >obabel -:"C(=O)(O)C[C@@H](C(=O)[O-])n1c[nH+]cc1
> > (S)-3-carboxy-2-(imidazol-3-ium-1-yl)propanoate" -oxyz
>  --gen3D
> > --title ""
> >--append formula
> > 21
> > C7H8N2O

[Open Babel] database

2012-12-04 Thread Sarah Rodriguez

Hi,

I asked the earlier question:

On 11/11/2012 04:01, Sarah Rodriguez wrote:
> Hello,
> I am wondering if I have 2 large databases that I want to compare the
> structures in, would I be able to do this in babel?

Thanks for your reply. I was really helpful. As a followup, is there anyway
to put those duplicated (non-unique) structures into a separate file??
Thanks!

Sarah
--
LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial
Remotely access PCs and mobile devices and provide instant support
Improve your efficiency, and focus on delivering more value-add services
Discover what IT Professionals Know. Rescue delivers
http://p.sf.net/sfu/logmein_12329d2d___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] Smiles conversion problems with Ion and Zwitterion

2012-12-04 Thread Scott McKechnie

Apologies, it was attached in the e-mail before last but had an identifier
name (SOXGES.search2.cif) and so may have caused confusion. I've attached
it again in this e-mail.

As a general question, is it possible to convert coordinates to smiles that
will always preserve the elements present (but may not get the bonding
correct)?

Best wishes,

Scott

On 4 December 2012 16:54, Chris Morley  wrote:

> Your problem is the incorrect conversion of a cif file, but you haven't
> shown one yet. (Not that I know much about cif files, but others may.)
> Conversions in OB go through an internal data structure, OBMol. It sound
> like the problem is in the cif to OBMol part, not in the OBMol to SMILES.
>
> Chris
>
> On 04/12/2012 15:34, Scott McKechnie wrote:
> > Thanks Chris for the helpful comments. Sorry to keep on but I'm still
> > left with the problem on going from cif to smiles where the original
> > number of elements is not conserved. What I want is to be able to
> > reliably represent the original cif molecule as a smiles string and from
> > there recreate the molecule with gen3d. The problem at the moment is
> > that the number of H atoms is changing. Any work around for this?
> >
> > On 4 December 2012 15:05, Chris Morley  > > wrote:
> >
> > Scott
> >
> > Your "correct smiles" is not right. The sum of the bond orders to the
> > charged nitrogen should be 4, and is only 3 (it has no H attached).
> The
> > correct SMILES is in my post below. Even with it, the round trip via
> > xyz:
> >
> > obabel -:"C(=O)(O)C[C@@H](C(=O)[O-])n1c[nH+]cc1" -oxyz --gen3D
> > | obabel -ixyz -osmi --append formula
> > 1 molecule converted
> > C(=O)(O)C[C@@H](C(=O)[O])N1CNC=C1   C7H8N2O4
> > 1 molecule converted
> >
> > gives a di-radical rather than a zwitterion because xyz does not
> > represent charges (or even bonds) and so OpenBabel didn't get any
> hints.
> > xyz format is poor choice of format for general use. The round trip
> > works ok with formats like mol or cml.
> >
> > Chris
> >
> > On 04/12/2012 10:51, Scott McKechnie wrote:
> >  > Hi Chris,
> >  >
> >  > Thanks for your reply and apologies for the delayed response.
> > Converting
> >  > the cif to xyz and viewing the molecule shows the correct
> > structure but
> >  > converting the xyz file to smi and then generating coordinates and
> >  > viewing shows the addition of a H atom.
> >  >
> >  > The correct smiles is: C(=O)(O)C[C@@H](C(=O)[O-])[N]1C=C[N+]=C1
> >  > The other smiles is:C(=O)([C@@H](CC(=O)O)N1C=CNC1)O
> >  >
> >  > One strange feature is that there doesn't appear to be a double
> bond
> >  > between the N atom in the ring and the C atom, leaving the C atom
> > with
> >  > only three bonds. The smiles conversion seems to want to add a H
> > here to
> >  > get the correct bonding.
> >  >
> >  > Similarly for an ion, using smiles conversion results in the
> > addition of
> >  > H's.
> >  >
> >  > I've attached the cif file.
> >  >
> >  > Many thanks,
> >  >
> >  > Scott
> >  >
> >  >
> >  > On 30 November 2012 14:53, Chris Morley  > 
> >  > >>
> wrote:
> >  >
> >  > On 30/11/2012 12:03, scott_m wrote:
> >  >  > Dear all,
> >  >  >
> >  >  > The conversion of
> > (S)-3-carboxy-2-(imidazol-3-ium-1-yl)propanoate
> >  > from a
> >  >  > .cif file to .smi and subsequent generation of coordinates
> > from
> >  > the .smi
> >  >  > file results in the addition of an extra H to one of the
> > ring C
> >  > atoms. The
> >  >  > original cif formula is C7H8N2O4 but this changes to
> C7H9N2O4,
> >  > which is no
> >  >  > longer a zwitterion.
> >  >  >
> >  >  > I also noticed that converting an ion to smi and then from
> > smi to xyz
> >  >  > resulted in the addition of hydrogen atoms. Can this be
> > avoided?
> >  >  >
> >  >  > Is the smi conversion of ions and zwitterions known to
> cause
> >  > problems?
> >  >
> >  > Getting added hydrogens right is a recurrent issue. However
> the
> >  > conversion from SMILES to xyz (and other formats) seems ok.
> > Your problem
> >  > may be in the conversion of the cif file, but you will need
> > to append it
> >  > for somebody (probably not me) to debug.
> >  >
> >  >obabel -:"C(=O)(O)C[C@@H](C(=O)[O-])n1c[nH+]cc1
> >  > (S)-3-carboxy-2-(imidazol-3-ium-1-yl)propanoate" -oxyz
>  --gen3D
> >  > --title ""
> >  >--append formula
> >  > 21
> >  > C7H8N2O4
> >  > C  2.456020.705701.56344
> >  > O

Re: [Open Babel] Intro to using Open Babel

2012-12-04 Thread Craig James

Very nice ... thanks for doing this.  Things like this should be available
in the OB documentation as a resource for those starting new projects or
trying to make a presentation to their management.

Craig

On Tue, Dec 4, 2012 at 3:31 AM, Noel O'Boyle  wrote:

> Hi all,
>
> Here are some introductory slides to features and usage of Open Babel:
>http://baoilleach.blogspot.co.uk/2012/12/intro-to-open-babel.html
>
> Regards,
>Noel
>
>
> --
> LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial
> Remotely access PCs and mobile devices and provide instant support
> Improve your efficiency, and focus on delivering more value-add services
> Discover what IT Professionals Know. Rescue delivers
> http://p.sf.net/sfu/logmein_12329d2d
> ___
> OpenBabel-discuss mailing list
> OpenBabel-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
--
LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial
Remotely access PCs and mobile devices and provide instant support
Improve your efficiency, and focus on delivering more value-add services
Discover what IT Professionals Know. Rescue delivers
http://p.sf.net/sfu/logmein_12329d2d___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] Smiles conversion problems with Ion and Zwitterion

2012-12-04 Thread Chris Morley

Your problem is the incorrect conversion of a cif file, but you haven't 
shown one yet. (Not that I know much about cif files, but others may.)
Conversions in OB go through an internal data structure, OBMol. It sound 
like the problem is in the cif to OBMol part, not in the OBMol to SMILES.

Chris

On 04/12/2012 15:34, Scott McKechnie wrote:
> Thanks Chris for the helpful comments. Sorry to keep on but I'm still
> left with the problem on going from cif to smiles where the original
> number of elements is not conserved. What I want is to be able to
> reliably represent the original cif molecule as a smiles string and from
> there recreate the molecule with gen3d. The problem at the moment is
> that the number of H atoms is changing. Any work around for this?
>
> On 4 December 2012 15:05, Chris Morley  > wrote:
>
> Scott
>
> Your "correct smiles" is not right. The sum of the bond orders to the
> charged nitrogen should be 4, and is only 3 (it has no H attached). The
> correct SMILES is in my post below. Even with it, the round trip via
> xyz:
>
> obabel -:"C(=O)(O)C[C@@H](C(=O)[O-])n1c[nH+]cc1" -oxyz --gen3D
> | obabel -ixyz -osmi --append formula
> 1 molecule converted
> C(=O)(O)C[C@@H](C(=O)[O])N1CNC=C1   C7H8N2O4
> 1 molecule converted
>
> gives a di-radical rather than a zwitterion because xyz does not
> represent charges (or even bonds) and so OpenBabel didn't get any hints.
> xyz format is poor choice of format for general use. The round trip
> works ok with formats like mol or cml.
>
> Chris
>
> On 04/12/2012 10:51, Scott McKechnie wrote:
>  > Hi Chris,
>  >
>  > Thanks for your reply and apologies for the delayed response.
> Converting
>  > the cif to xyz and viewing the molecule shows the correct
> structure but
>  > converting the xyz file to smi and then generating coordinates and
>  > viewing shows the addition of a H atom.
>  >
>  > The correct smiles is: C(=O)(O)C[C@@H](C(=O)[O-])[N]1C=C[N+]=C1
>  > The other smiles is:C(=O)([C@@H](CC(=O)O)N1C=CNC1)O
>  >
>  > One strange feature is that there doesn't appear to be a double bond
>  > between the N atom in the ring and the C atom, leaving the C atom
> with
>  > only three bonds. The smiles conversion seems to want to add a H
> here to
>  > get the correct bonding.
>  >
>  > Similarly for an ion, using smiles conversion results in the
> addition of
>  > H's.
>  >
>  > I've attached the cif file.
>  >
>  > Many thanks,
>  >
>  > Scott
>  >
>  >
>  > On 30 November 2012 14:53, Chris Morley  
>  > >> wrote:
>  >
>  > On 30/11/2012 12:03, scott_m wrote:
>  >  > Dear all,
>  >  >
>  >  > The conversion of
> (S)-3-carboxy-2-(imidazol-3-ium-1-yl)propanoate
>  > from a
>  >  > .cif file to .smi and subsequent generation of coordinates
> from
>  > the .smi
>  >  > file results in the addition of an extra H to one of the
> ring C
>  > atoms. The
>  >  > original cif formula is C7H8N2O4 but this changes to C7H9N2O4,
>  > which is no
>  >  > longer a zwitterion.
>  >  >
>  >  > I also noticed that converting an ion to smi and then from
> smi to xyz
>  >  > resulted in the addition of hydrogen atoms. Can this be
> avoided?
>  >  >
>  >  > Is the smi conversion of ions and zwitterions known to cause
>  > problems?
>  >
>  > Getting added hydrogens right is a recurrent issue. However the
>  > conversion from SMILES to xyz (and other formats) seems ok.
> Your problem
>  > may be in the conversion of the cif file, but you will need
> to append it
>  > for somebody (probably not me) to debug.
>  >
>  >obabel -:"C(=O)(O)C[C@@H](C(=O)[O-])n1c[nH+]cc1
>  > (S)-3-carboxy-2-(imidazol-3-ium-1-yl)propanoate" -oxyz  --gen3D
>  > --title ""
>  >--append formula
>  > 21
>  > C7H8N2O4
>  > C  2.456020.705701.56344
>  > O  3.445920.485862.25208
>  > O  1.436561.466702.00415
>  > C  2.263560.114370.19030
>  > C  3.145460.74947   -0.88078
>  > H  2.848310.31396   -1.84634
>  > C  2.830382.27406   -0.99631
>  > O  1.670902.60592   -0.61087
>  > O  3.794412.97728   -1.40748
>  > N  4.601370.42805   -0.71225
>  > C  5.359000.947620.25841
>  > N  6.587890.

Re: [Open Babel] Smiles conversion problems with Ion and Zwitterion

2012-12-04 Thread Scott McKechnie

Thanks Chris for the helpful comments. Sorry to keep on but I'm still left
with the problem on going from cif to smiles where the original number of
elements is not conserved. What I want is to be able to reliably represent
the original cif molecule as a smiles string and from there recreate the
molecule with gen3d. The problem at the moment is that the number of H
atoms is changing. Any work around for this?

On 4 December 2012 15:05, Chris Morley  wrote:

> Scott
>
> Your "correct smiles" is not right. The sum of the bond orders to the
> charged nitrogen should be 4, and is only 3 (it has no H attached). The
> correct SMILES is in my post below. Even with it, the round trip via xyz:
>
> obabel -:"C(=O)(O)C[C@@H](C(=O)[O-])n1c[nH+]cc1" -oxyz --gen3D
> | obabel -ixyz -osmi --append formula
> 1 molecule converted
> C(=O)(O)C[C@@H](C(=O)[O])N1CNC=C1   C7H8N2O4
> 1 molecule converted
>
> gives a di-radical rather than a zwitterion because xyz does not
> represent charges (or even bonds) and so OpenBabel didn't get any hints.
> xyz format is poor choice of format for general use. The round trip
> works ok with formats like mol or cml.
>
> Chris
>
> On 04/12/2012 10:51, Scott McKechnie wrote:
> > Hi Chris,
> >
> > Thanks for your reply and apologies for the delayed response. Converting
> > the cif to xyz and viewing the molecule shows the correct structure but
> > converting the xyz file to smi and then generating coordinates and
> > viewing shows the addition of a H atom.
> >
> > The correct smiles is: C(=O)(O)C[C@@H](C(=O)[O-])[N]1C=C[N+]=C1
> > The other smiles is:C(=O)([C@@H](CC(=O)O)N1C=CNC1)O
> >
> > One strange feature is that there doesn't appear to be a double bond
> > between the N atom in the ring and the C atom, leaving the C atom with
> > only three bonds. The smiles conversion seems to want to add a H here to
> > get the correct bonding.
> >
> > Similarly for an ion, using smiles conversion results in the addition of
> > H's.
> >
> > I've attached the cif file.
> >
> > Many thanks,
> >
> > Scott
> >
> >
> > On 30 November 2012 14:53, Chris Morley  > > wrote:
> >
> > On 30/11/2012 12:03, scott_m wrote:
> >  > Dear all,
> >  >
> >  > The conversion of (S)-3-carboxy-2-(imidazol-3-ium-1-yl)propanoate
> > from a
> >  > .cif file to .smi and subsequent generation of coordinates from
> > the .smi
> >  > file results in the addition of an extra H to one of the ring C
> > atoms. The
> >  > original cif formula is C7H8N2O4 but this changes to C7H9N2O4,
> > which is no
> >  > longer a zwitterion.
> >  >
> >  > I also noticed that converting an ion to smi and then from smi to
> xyz
> >  > resulted in the addition of hydrogen atoms. Can this be avoided?
> >  >
> >  > Is the smi conversion of ions and zwitterions known to cause
> > problems?
> >
> > Getting added hydrogens right is a recurrent issue. However the
> > conversion from SMILES to xyz (and other formats) seems ok. Your
> problem
> > may be in the conversion of the cif file, but you will need to
> append it
> > for somebody (probably not me) to debug.
> >
> >obabel -:"C(=O)(O)C[C@@H](C(=O)[O-])n1c[nH+]cc1
> > (S)-3-carboxy-2-(imidazol-3-ium-1-yl)propanoate" -oxyz  --gen3D
> > --title ""
> >--append formula
> > 21
> > C7H8N2O4
> > C  2.456020.705701.56344
> > O  3.445920.485862.25208
> > O  1.436561.466702.00415
> > C  2.263560.114370.19030
> > C  3.145460.74947   -0.88078
> > H  2.848310.31396   -1.84634
> > C  2.830382.27406   -0.99631
> > O  1.670902.60592   -0.61087
> > O  3.794412.97728   -1.40748
> > N  4.601370.42805   -0.71225
> > C  5.359000.947620.25841
> > N  6.587890.461240.10334
> > H  7.339920.616600.75954
> > C  6.69161   -0.15933   -1.12882
> > C  5.43119   -0.14873   -1.66026
> > H  0.845361.765801.27272
> > H  1.204390.19509   -0.08254
> > H  2.46795   -0.957670.27113
> > H  5.047741.616431.05753
> > H  7.65241   -0.48371   -1.46628
> > H  5.01646   -0.45579   -2.60586
> > 1 molecule converted
> >
> > Chris
> >
> >
> --
> > Keep yourself connected to Go Parallel:
> > TUNE You got it built. Now make it sing. Tune shows you how.
> > http://goparallel.sourceforge.net
> > ___
> > OpenBabel-discuss mailing list
> > OpenBab

Re: [Open Babel] Smiles conversion problems with Ion and Zwitterion

2012-12-04 Thread Chris Morley

Scott

Your "correct smiles" is not right. The sum of the bond orders to the 
charged nitrogen should be 4, and is only 3 (it has no H attached). The 
correct SMILES is in my post below. Even with it, the round trip via xyz:

obabel -:"C(=O)(O)C[C@@H](C(=O)[O-])n1c[nH+]cc1" -oxyz --gen3D
| obabel -ixyz -osmi --append formula
1 molecule converted
C(=O)(O)C[C@@H](C(=O)[O])N1CNC=C1   C7H8N2O4
1 molecule converted

gives a di-radical rather than a zwitterion because xyz does not 
represent charges (or even bonds) and so OpenBabel didn't get any hints. 
xyz format is poor choice of format for general use. The round trip 
works ok with formats like mol or cml.

Chris

On 04/12/2012 10:51, Scott McKechnie wrote:
> Hi Chris,
>
> Thanks for your reply and apologies for the delayed response. Converting
> the cif to xyz and viewing the molecule shows the correct structure but
> converting the xyz file to smi and then generating coordinates and
> viewing shows the addition of a H atom.
>
> The correct smiles is: C(=O)(O)C[C@@H](C(=O)[O-])[N]1C=C[N+]=C1
> The other smiles is:C(=O)([C@@H](CC(=O)O)N1C=CNC1)O
>
> One strange feature is that there doesn't appear to be a double bond
> between the N atom in the ring and the C atom, leaving the C atom with
> only three bonds. The smiles conversion seems to want to add a H here to
> get the correct bonding.
>
> Similarly for an ion, using smiles conversion results in the addition of
> H's.
>
> I've attached the cif file.
>
> Many thanks,
>
> Scott
>
>
> On 30 November 2012 14:53, Chris Morley  > wrote:
>
> On 30/11/2012 12:03, scott_m wrote:
>  > Dear all,
>  >
>  > The conversion of (S)-3-carboxy-2-(imidazol-3-ium-1-yl)propanoate
> from a
>  > .cif file to .smi and subsequent generation of coordinates from
> the .smi
>  > file results in the addition of an extra H to one of the ring C
> atoms. The
>  > original cif formula is C7H8N2O4 but this changes to C7H9N2O4,
> which is no
>  > longer a zwitterion.
>  >
>  > I also noticed that converting an ion to smi and then from smi to xyz
>  > resulted in the addition of hydrogen atoms. Can this be avoided?
>  >
>  > Is the smi conversion of ions and zwitterions known to cause
> problems?
>
> Getting added hydrogens right is a recurrent issue. However the
> conversion from SMILES to xyz (and other formats) seems ok. Your problem
> may be in the conversion of the cif file, but you will need to append it
> for somebody (probably not me) to debug.
>
>obabel -:"C(=O)(O)C[C@@H](C(=O)[O-])n1c[nH+]cc1
> (S)-3-carboxy-2-(imidazol-3-ium-1-yl)propanoate" -oxyz  --gen3D
> --title ""
>--append formula
> 21
> C7H8N2O4
> C  2.456020.705701.56344
> O  3.445920.485862.25208
> O  1.436561.466702.00415
> C  2.263560.114370.19030
> C  3.145460.74947   -0.88078
> H  2.848310.31396   -1.84634
> C  2.830382.27406   -0.99631
> O  1.670902.60592   -0.61087
> O  3.794412.97728   -1.40748
> N  4.601370.42805   -0.71225
> C  5.359000.947620.25841
> N  6.587890.461240.10334
> H  7.339920.616600.75954
> C  6.69161   -0.15933   -1.12882
> C  5.43119   -0.14873   -1.66026
> H  0.845361.765801.27272
> H  1.204390.19509   -0.08254
> H  2.46795   -0.957670.27113
> H  5.047741.616431.05753
> H  7.65241   -0.48371   -1.46628
> H  5.01646   -0.45579   -2.60586
> 1 molecule converted
>
> Chris
>
> 
> --
> Keep yourself connected to Go Parallel:
> TUNE You got it built. Now make it sing. Tune shows you how.
> http://goparallel.sourceforge.net
> ___
> OpenBabel-discuss mailing list
> OpenBabel-discuss@lists.sourceforge.net
> 
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
>


--
LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial
Remotely access PCs and mobile devices and provide instant support
Improve your efficiency, and focus on delivering more value-add services
Discover what IT Professionals Know. Rescue delivers
http://p.sf.net/sfu/logmein_12329d2d
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.

[Open Babel] Intro to using Open Babel

2012-12-04 Thread Noel O'Boyle

Hi all,

Here are some introductory slides to features and usage of Open Babel:
   http://baoilleach.blogspot.co.uk/2012/12/intro-to-open-babel.html

Regards,
   Noel

--
LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial
Remotely access PCs and mobile devices and provide instant support
Improve your efficiency, and focus on delivering more value-add services
Discover what IT Professionals Know. Rescue delivers
http://p.sf.net/sfu/logmein_12329d2d
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] Smiles conversion problems with Ion and Zwitterion

2012-12-04 Thread Scott McKechnie

Hi Chris,

Thanks for your reply and apologies for the delayed response. Converting
the cif to xyz and viewing the molecule shows the correct structure but
converting the xyz file to smi and then generating coordinates and viewing
shows the addition of a H atom.

The correct smiles is: C(=O)(O)C[C@@H](C(=O)[O-])[N]1C=C[N+]=C1
The other smiles is:C(=O)([C@@H](CC(=O)O)N1C=CNC1)O

One strange feature is that there doesn't appear to be a double bond
between the N atom in the ring and the C atom, leaving the C atom with only
three bonds. The smiles conversion seems to want to add a H here to get the
correct bonding.

Similarly for an ion, using smiles conversion results in the addition of
H's.

I've attached the cif file.

Many thanks,

Scott


On 30 November 2012 14:53, Chris Morley  wrote:

> On 30/11/2012 12:03, scott_m wrote:
> > Dear all,
> >
> > The conversion of (S)-3-carboxy-2-(imidazol-3-ium-1-yl)propanoate from a
> > .cif file to .smi and subsequent generation of coordinates from the .smi
> > file results in the addition of an extra H to one of the ring C atoms.
> The
> > original cif formula is C7H8N2O4 but this changes to C7H9N2O4, which is
> no
> > longer a zwitterion.
> >
> > I also noticed that converting an ion to smi and then from smi to xyz
> > resulted in the addition of hydrogen atoms. Can this be avoided?
> >
> > Is the smi conversion of ions and zwitterions known to cause problems?
>
> Getting added hydrogens right is a recurrent issue. However the
> conversion from SMILES to xyz (and other formats) seems ok. Your problem
> may be in the conversion of the cif file, but you will need to append it
> for somebody (probably not me) to debug.
>
>   obabel -:"C(=O)(O)C[C@@H](C(=O)[O-])n1c[nH+]cc1
> (S)-3-carboxy-2-(imidazol-3-ium-1-yl)propanoate" -oxyz  --gen3D --title ""
>   --append formula
> 21
> C7H8N2O4
> C  2.456020.705701.56344
> O  3.445920.485862.25208
> O  1.436561.466702.00415
> C  2.263560.114370.19030
> C  3.145460.74947   -0.88078
> H  2.848310.31396   -1.84634
> C  2.830382.27406   -0.99631
> O  1.670902.60592   -0.61087
> O  3.794412.97728   -1.40748
> N  4.601370.42805   -0.71225
> C  5.359000.947620.25841
> N  6.587890.461240.10334
> H  7.339920.616600.75954
> C  6.69161   -0.15933   -1.12882
> C  5.43119   -0.14873   -1.66026
> H  0.845361.765801.27272
> H  1.204390.19509   -0.08254
> H  2.46795   -0.957670.27113
> H  5.047741.616431.05753
> H  7.65241   -0.48371   -1.46628
> H  5.01646   -0.45579   -2.60586
> 1 molecule converted
>
> Chris
>
>
> --
> Keep yourself connected to Go Parallel:
> TUNE You got it built. Now make it sing. Tune shows you how.
> http://goparallel.sourceforge.net
> ___
> OpenBabel-discuss mailing list
> OpenBabel-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
>


SOXGES.search2.cif
Description: Binary data
--
LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial
Remotely access PCs and mobile devices and provide instant support
Improve your efficiency, and focus on delivering more value-add services
Discover what IT Professionals Know. Rescue delivers
http://p.sf.net/sfu/logmein_12329d2d___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] Invalid memory access during OBConversion.WriteFile()

2012-12-04 Thread mpillong

Sure thing! Is the code sufficient, or would you need a runnable jar?


package TestClasses;

import org.openbabel.OBConversion;
import org.openbabel.OBMol;

public class TestOBWriteFile {

public static void main(String[] args) {


System.load("/Applications/OpenBabel/openbabel-2.2.3/scripts/java/libopenbabel.jnilib");

OBMol mol=new OBMol();
OBConversion obc=new OBConversion();
boolean SetSuccessful=obc.SetInAndOutFormats("pdb", "pdb");
if (SetSuccessful) {

obc.ReadFile(mol, "/Users/max/propane.pdb");
obc.WriteFile(mol, "/Users/max/propaneOut.pdb");

}   

}

}


Thank you so much for your help!

Best,

Max



--
View this message in context: 
http://forums.openbabel.org/Invalid-memory-access-during-OBConversion-WriteFile-tp4655729p4655739.html
Sent from the General discussion mailing list archive at Nabble.com.

--
LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial
Remotely access PCs and mobile devices and provide instant support
Improve your efficiency, and focus on delivering more value-add services
Discover what IT Professionals Know. Rescue delivers
http://p.sf.net/sfu/logmein_12329d2d
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] Invalid memory access during OBConversion.WriteFile()

2012-12-04 Thread Noel O'Boyle

Can you provide a complete program that exhibits the problem? Please
make it as small as possible.

On 4 December 2012 10:06, mpillong  wrote:
> Ah yes, my bad! Of course, I have also tried different output formats, but
> the error remains the same!
>
>
>
> --
> View this message in context: 
> http://forums.openbabel.org/Invalid-memory-access-during-OBConversion-WriteFile-tp4655729p4655737.html
> Sent from the General discussion mailing list archive at Nabble.com.
>
> --
> LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial
> Remotely access PCs and mobile devices and provide instant support
> Improve your efficiency, and focus on delivering more value-add services
> Discover what IT Professionals Know. Rescue delivers
> http://p.sf.net/sfu/logmein_12329d2d
> ___
> OpenBabel-discuss mailing list
> OpenBabel-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

--
LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial
Remotely access PCs and mobile devices and provide instant support
Improve your efficiency, and focus on delivering more value-add services
Discover what IT Professionals Know. Rescue delivers
http://p.sf.net/sfu/logmein_12329d2d
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] Invalid memory access during OBConversion.WriteFile()

2012-12-04 Thread mpillong

Ah yes, my bad! Of course, I have also tried different output formats, but
the error remains the same!



--
View this message in context: 
http://forums.openbabel.org/Invalid-memory-access-during-OBConversion-WriteFile-tp4655729p4655737.html
Sent from the General discussion mailing list archive at Nabble.com.

--
LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial
Remotely access PCs and mobile devices and provide instant support
Improve your efficiency, and focus on delivering more value-add services
Discover what IT Professionals Know. Rescue delivers
http://p.sf.net/sfu/logmein_12329d2d
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] Invalid memory access during OBConversion.WriteFile()

2012-12-04 Thread Fredrik Wallner

Hi,

I was more curious about the output format, not the format of the input files. 
If the problem is indeed in the writing, it would be interesting to know if it 
is a specific format or something more general.

/Fredrik

4 dec 2012 kl. 10:44 skrev Max Pillong :

> Hey Fredrik,
> 
> thanks for the input. The SetInAndOutFormat returns true, so I'm guessing 
> there's nothing worng here. I've experienced this error with several 
> inputfiles of varying format (pdb, sdf, mol2).
> 
> Best regards,
> 
> Max
> 
> Am 04/12/2012 10:41, schrieb Fredrik Wallner:
>> Hi,
>> 
>> You should probably test the result from SetInAndOutFormats, just to be 
>> sure. If that step failed, you're in trouble. Do you get the error 
>> regardless of what format you're using for output?
>> 
>> Kind regards,
>> Fredrik
>> 
>> 4 dec 2012 kl. 10:16 skrev mpillong :
>> 
>>> Hmmm, sorry about that, I was using the < raw > Tag here ... but here's the
>>> original text.
>>> 
>>> Hey everyone,
>>> 
>>> I am currently running OpenBabel on a MacOSX 10.6.8 in Eclipse with Java.
>>> Recently, I encountered the following exception during using the WriteFile()
>>> Method in OBConversion:
>>> 
>>> 'Invalid memory access of location 0xfffb25991558 rip=0x7fff888cb683'
>>> 
>>> 
>>> I have used the same method to write molecules before, the code looks like
>>> this:
>>> 
>>> public static void writeOBMolecule(OBMol mol, String output, String format){
>>> OBConversion obc=new OBConversion();
>>> obc.SetInAndOutFormats(format, format);
>>> obc.WriteFile(mol, output);
>>> }
>>> 
>>> 
>>> I have tried multiple *.pdb files, the same error occurs every time
>>> (although the location does change every time). Any thoughts on this?
>>> 
>>> Thanks in advance!
>>> 
>>> Max
>>> 
>>> 
>>> 
>>> --
>>> View this message in context: 
>>> http://forums.openbabel.org/Invalid-memory-access-during-OBConversion-WriteFile-tp4655729p4655731.html
>>> Sent from the General discussion mailing list archive at Nabble.com.
>>> 
>>> --
>>> LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial
>>> Remotely access PCs and mobile devices and provide instant support
>>> Improve your efficiency, and focus on delivering more value-add services
>>> Discover what IT Professionals Know. Rescue delivers
>>> http://p.sf.net/sfu/logmein_12329d2d
>>> ___
>>> OpenBabel-discuss mailing list
>>> OpenBabel-discuss@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
> 
> 
> -- 
> ETH Zurich
> Computer-assisted Drug Design
> Dipl.-Bioinf. Max Pillong
> Institute of Pharmaceutical Sciences
> HCI G 496
> Wolfgang-Pauli-Str. 10
> 8093 Zürich, SWITZERLAND
> 
> Phone: +41 44 633 91 56
> E-Mail: max.pill...@pharma.ethz.ch
> 


--
LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial
Remotely access PCs and mobile devices and provide instant support
Improve your efficiency, and focus on delivering more value-add services
Discover what IT Professionals Know. Rescue delivers
http://p.sf.net/sfu/logmein_12329d2d
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] Invalid memory access during OBConversion.WriteFile()

2012-12-04 Thread mpillong

Hey Fredrik,

thanks for the input. The SetInAndOutFormat returns true, so I'm guessing
there's nothing worng here. I've experienced this error with several
inputfiles of varying format (pdb, sdf, mol2).

Best regards,

Max 



--
View this message in context: 
http://forums.openbabel.org/Invalid-memory-access-during-OBConversion-WriteFile-tp4655729p4655735.html
Sent from the General discussion mailing list archive at Nabble.com.

--
LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial
Remotely access PCs and mobile devices and provide instant support
Improve your efficiency, and focus on delivering more value-add services
Discover what IT Professionals Know. Rescue delivers
http://p.sf.net/sfu/logmein_12329d2d
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] Invalid memory access during OBConversion.WriteFile()

2012-12-04 Thread Fredrik Wallner

Hi,

You should probably test the result from SetInAndOutFormats, just to be sure. 
If that step failed, you're in trouble. Do you get the error regardless of what 
format you're using for output?

Kind regards,
Fredrik

4 dec 2012 kl. 10:16 skrev mpillong :

> Hmmm, sorry about that, I was using the < raw > Tag here ... but here's the
> original text.
> 
> Hey everyone,
> 
> I am currently running OpenBabel on a MacOSX 10.6.8 in Eclipse with Java.
> Recently, I encountered the following exception during using the WriteFile()
> Method in OBConversion:
> 
> 'Invalid memory access of location 0xfffb25991558 rip=0x7fff888cb683'
> 
> 
> I have used the same method to write molecules before, the code looks like
> this:
> 
> public static void writeOBMolecule(OBMol mol, String output, String format){
>   OBConversion obc=new OBConversion();
>   obc.SetInAndOutFormats(format, format);
>   obc.WriteFile(mol, output);
> }
> 
> 
> I have tried multiple *.pdb files, the same error occurs every time
> (although the location does change every time). Any thoughts on this?
> 
> Thanks in advance!
> 
> Max 
> 
> 
> 
> --
> View this message in context: 
> http://forums.openbabel.org/Invalid-memory-access-during-OBConversion-WriteFile-tp4655729p4655731.html
> Sent from the General discussion mailing list archive at Nabble.com.
> 
> --
> LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial
> Remotely access PCs and mobile devices and provide instant support
> Improve your efficiency, and focus on delivering more value-add services
> Discover what IT Professionals Know. Rescue delivers
> http://p.sf.net/sfu/logmein_12329d2d
> ___
> OpenBabel-discuss mailing list
> OpenBabel-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss


--
LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial
Remotely access PCs and mobile devices and provide instant support
Improve your efficiency, and focus on delivering more value-add services
Discover what IT Professionals Know. Rescue delivers
http://p.sf.net/sfu/logmein_12329d2d
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] Invalid memory access during OBConversion.WriteFile()

2012-12-04 Thread mpillong

Hey Noel,

indeed I started with the SetOutFormat method. Unfortunately, both methods
(SetOut/SetInAndOut) return true, yet, the error during writing still
remains, so I'm guessing it's happening somewhere during the writing :/.

Thanks for your input!

Max 



--
View this message in context: 
http://forums.openbabel.org/Invalid-memory-access-during-OBConversion-WriteFile-tp4655729p4655733.html
Sent from the General discussion mailing list archive at Nabble.com.

--
LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial
Remotely access PCs and mobile devices and provide instant support
Improve your efficiency, and focus on delivering more value-add services
Discover what IT Professionals Know. Rescue delivers
http://p.sf.net/sfu/logmein_12329d2d
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] Invalid memory access during OBConversion.WriteFile()

2012-12-04 Thread Noel O'Boyle

On 4 December 2012 09:16, mpillong  wrote:
> Hmmm, sorry about that, I was using the < raw > Tag here ... but here's the
> original text.
>
> Hey everyone,
>
> I am currently running OpenBabel on a MacOSX 10.6.8 in Eclipse with Java.
> Recently, I encountered the following exception during using the WriteFile()
> Method in OBConversion:
>
> 'Invalid memory access of location 0xfffb25991558 rip=0x7fff888cb683'
>
>
> I have used the same method to write molecules before, the code looks like
> this:
>
> public static void writeOBMolecule(OBMol mol, String output, String format){
> OBConversion obc=new OBConversion();
> obc.SetInAndOutFormats(format, format);
> obc.WriteFile(mol, output);
> }

You have forgotten to check the return value of SetInAndOutFormats and
also to close the output file (not a problem unless you write to it a
second time). Actually here you should just use SetOutFormat as
follows:

bool success = obc.SetOutFormat(format);
if (success) {
   obc.WriteFile(mol, output)
   obc.CloseOutFile()
   }
else
   {//handle exception}

>
> I have tried multiple *.pdb files, the same error occurs every time
> (although the location does change every time). Any thoughts on this?
>
> Thanks in advance!
>
> Max
>
>
>
> --
> View this message in context: 
> http://forums.openbabel.org/Invalid-memory-access-during-OBConversion-WriteFile-tp4655729p4655731.html
> Sent from the General discussion mailing list archive at Nabble.com.
>
> --
> LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial
> Remotely access PCs and mobile devices and provide instant support
> Improve your efficiency, and focus on delivering more value-add services
> Discover what IT Professionals Know. Rescue delivers
> http://p.sf.net/sfu/logmein_12329d2d
> ___
> OpenBabel-discuss mailing list
> OpenBabel-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

--
LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial
Remotely access PCs and mobile devices and provide instant support
Improve your efficiency, and focus on delivering more value-add services
Discover what IT Professionals Know. Rescue delivers
http://p.sf.net/sfu/logmein_12329d2d
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] Invalid memory access during OBConversion.WriteFile()

2012-12-04 Thread mpillong

Hmmm, sorry about that, I was using the < raw > Tag here ... but here's the
original text.

Hey everyone,

I am currently running OpenBabel on a MacOSX 10.6.8 in Eclipse with Java.
Recently, I encountered the following exception during using the WriteFile()
Method in OBConversion:

'Invalid memory access of location 0xfffb25991558 rip=0x7fff888cb683'


I have used the same method to write molecules before, the code looks like
this:

public static void writeOBMolecule(OBMol mol, String output, String format){
OBConversion obc=new OBConversion();
obc.SetInAndOutFormats(format, format);
obc.WriteFile(mol, output);
}


I have tried multiple *.pdb files, the same error occurs every time
(although the location does change every time). Any thoughts on this?

Thanks in advance!

Max 



--
View this message in context: 
http://forums.openbabel.org/Invalid-memory-access-during-OBConversion-WriteFile-tp4655729p4655731.html
Sent from the General discussion mailing list archive at Nabble.com.

--
LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial
Remotely access PCs and mobile devices and provide instant support
Improve your efficiency, and focus on delivering more value-add services
Discover what IT Professionals Know. Rescue delivers
http://p.sf.net/sfu/logmein_12329d2d
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] Smiles conversion problems with Ion and Zwitterion

[Open Babel] database

Re: [Open Babel] Smiles conversion problems with Ion and Zwitterion

Re: [Open Babel] Intro to using Open Babel

Re: [Open Babel] Smiles conversion problems with Ion and Zwitterion

Re: [Open Babel] Smiles conversion problems with Ion and Zwitterion

Re: [Open Babel] Smiles conversion problems with Ion and Zwitterion

[Open Babel] Intro to using Open Babel

Re: [Open Babel] Smiles conversion problems with Ion and Zwitterion

Re: [Open Babel] Invalid memory access during OBConversion.WriteFile()

Re: [Open Babel] Invalid memory access during OBConversion.WriteFile()

Re: [Open Babel] Invalid memory access during OBConversion.WriteFile()

Re: [Open Babel] Invalid memory access during OBConversion.WriteFile()

Re: [Open Babel] Invalid memory access during OBConversion.WriteFile()

Re: [Open Babel] Invalid memory access during OBConversion.WriteFile()

Re: [Open Babel] Invalid memory access during OBConversion.WriteFile()

Re: [Open Babel] Invalid memory access during OBConversion.WriteFile()

Re: [Open Babel] Invalid memory access during OBConversion.WriteFile()

18 matches

Site Navigation

Mail list logo

Footer information