markush structures in openbabel

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markush structures in openbabel

Igor Filippov [Contr]-2
I've run into a problem with an SD file generated by OB with atomic
aliases. This file could not be opened by CambridgeSoft ChemBioDraw, or
displayed correctly by ChemAxxon MarvinSketch.
CamridgeSoft support tells me the atom numbers should be
right-justified, where they are left-justified in OB output. Akos Papp
from ChemAxxon says that there is not enough white space between "A" and
the atom number. Here is an example of OB output and what Akos
corrected:
OB output -

A  8
R5
A  10
R4
A  11
R3
A  14
R2
A  16
R1

Corrected -

A    8
R5
A   10
R4
A   11
R3
A   14
R2
A   16
R1

the corrected file can be opened by ChemDraw, MarvinSketch, as well as
Symyx Draw and CACTVS csbr. Could we correct the output of atomic
aliases in the next OB release?

Igor


On Mon, 2010-07-12 at 13:07 -0400, Geoffrey Hutchison wrote:
> On Jul 12, 2010, at 12:45 PM, Tim Vandermeersch wrote:
>
> >> So far I see only SetAtomicNum to specify atom type, but nothing to
set
> >> the atomic label to something like "R1".
> >
> > You can use AliasData for this.
>
> See src/formats/mdlformat.cpp for an exact example.
>
> Hope that helps,
> -Geoff



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Re: markush structures in openbabel

Chris Morley-3
Thanks. Corrected in r3897.
Chris

On 21/07/2010 15:46, Igor Filippov [Contr] wrote:

> I've run into a problem with an SD file generated by OB with atomic
> aliases. This file could not be opened by CambridgeSoft ChemBioDraw, or
> displayed correctly by ChemAxxon MarvinSketch.
> CamridgeSoft support tells me the atom numbers should be
> right-justified, where they are left-justified in OB output. Akos Papp
> from ChemAxxon says that there is not enough white space between "A" and
> the atom number. Here is an example of OB output and what Akos
> corrected:
> OB output -
>
> A  8
> R5
> A  10
> R4
> A  11
> R3
> A  14
> R2
> A  16
> R1
>
> Corrected -
>
> A    8
> R5
> A   10
> R4
> A   11
> R3
> A   14
> R2
> A   16
> R1
>
> the corrected file can be opened by ChemDraw, MarvinSketch, as well as
> Symyx Draw and CACTVS csbr. Could we correct the output of atomic
> aliases in the next OB release?
>
> Igor
>
>
> On Mon, 2010-07-12 at 13:07 -0400, Geoffrey Hutchison wrote:
>> On Jul 12, 2010, at 12:45 PM, Tim Vandermeersch wrote:
>>
>>>> So far I see only SetAtomicNum to specify atom type, but nothing to
> set
>>>> the atomic label to something like "R1".
>>>
>>> You can use AliasData for this.
>>
>> See src/formats/mdlformat.cpp for an exact example.
>>
>> Hope that helps,
>> -Geoff
>
>
>
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Re: markush structures in openbabel

Igor Filippov [Contr]-2
Chris,

Thank you. I'm trying to test it with the latest trunk (r3955) but even
though OB itself compiled fine I'm getting the following error when
trying to link libopenbabel to my program:

undefined reference to `OpenBabel::AliasData::GetAlias(bool) const'
collect2: ld returned 1 exit status

Was there some significant change in how libopenbabel should be linked?
It was working fine with 2.2.3 release.

Igor

On Thu, 2010-07-22 at 12:05 -0400, Chris Morley wrote:

> Thanks. Corrected in r3897.
> Chris
>
> On 21/07/2010 15:46, Igor Filippov [Contr] wrote:
> > I've run into a problem with an SD file generated by OB with atomic
> > aliases. This file could not be opened by CambridgeSoft ChemBioDraw, or
> > displayed correctly by ChemAxxon MarvinSketch.
> > CamridgeSoft support tells me the atom numbers should be
> > right-justified, where they are left-justified in OB output. Akos Papp
> > from ChemAxxon says that there is not enough white space between "A" and
> > the atom number. Here is an example of OB output and what Akos
> > corrected:
> > OB output -
> >
> > A  8
> > R5
> > A  10
> > R4
> > A  11
> > R3
> > A  14
> > R2
> > A  16
> > R1
> >
> > Corrected -
> >
> > A    8
> > R5
> > A   10
> > R4
> > A   11
> > R3
> > A   14
> > R2
> > A   16
> > R1
> >
> > the corrected file can be opened by ChemDraw, MarvinSketch, as well as
> > Symyx Draw and CACTVS csbr. Could we correct the output of atomic
> > aliases in the next OB release?
> >
> > Igor
> >
> >
> > On Mon, 2010-07-12 at 13:07 -0400, Geoffrey Hutchison wrote:
> >> On Jul 12, 2010, at 12:45 PM, Tim Vandermeersch wrote:
> >>
> >>>> So far I see only SetAtomicNum to specify atom type, but nothing to
> > set
> >>>> the atomic label to something like "R1".
> >>>
> >>> You can use AliasData for this.
> >>
> >> See src/formats/mdlformat.cpp for an exact example.
> >>
> >> Hope that helps,
> >> -Geoff
> >
> >
> >
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> >
> >
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>
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Re: markush structures in openbabel

Tim Vandermeersch
On Mon, Aug 9, 2010 at 5:50 PM, Igor Filippov [Contr]
<[hidden email]> wrote:

> Chris,
>
> Thank you. I'm trying to test it with the latest trunk (r3955) but even
> though OB itself compiled fine I'm getting the following error when
> trying to link libopenbabel to my program:
>
> undefined reference to `OpenBabel::AliasData::GetAlias(bool) const'
> collect2: ld returned 1 exit status
>
> Was there some significant change in how libopenbabel should be linked?
> It was working fine with 2.2.3 release.

No, the API and "linking method" is unchanged. However, the ABI will
be changed for the 2.3 release and the GetAlias function changed from:

std::string GetAlias() const;

to:

std::string GetAlias(bool rightAligned = false) const;

Since the linker complains about this symbol being undefined you are
probably using the new headers but link to the old library.

Tim

> Igor
>
> On Thu, 2010-07-22 at 12:05 -0400, Chris Morley wrote:
>> Thanks. Corrected in r3897.
>> Chris
>>
>> On 21/07/2010 15:46, Igor Filippov [Contr] wrote:
>> > I've run into a problem with an SD file generated by OB with atomic
>> > aliases. This file could not be opened by CambridgeSoft ChemBioDraw, or
>> > displayed correctly by ChemAxxon MarvinSketch.
>> > CamridgeSoft support tells me the atom numbers should be
>> > right-justified, where they are left-justified in OB output. Akos Papp
>> > from ChemAxxon says that there is not enough white space between "A" and
>> > the atom number. Here is an example of OB output and what Akos
>> > corrected:
>> > OB output -
>> >
>> > A  8
>> > R5
>> > A  10
>> > R4
>> > A  11
>> > R3
>> > A  14
>> > R2
>> > A  16
>> > R1
>> >
>> > Corrected -
>> >
>> > A    8
>> > R5
>> > A   10
>> > R4
>> > A   11
>> > R3
>> > A   14
>> > R2
>> > A   16
>> > R1
>> >
>> > the corrected file can be opened by ChemDraw, MarvinSketch, as well as
>> > Symyx Draw and CACTVS csbr. Could we correct the output of atomic
>> > aliases in the next OB release?
>> >
>> > Igor
>> >
>> >
>> > On Mon, 2010-07-12 at 13:07 -0400, Geoffrey Hutchison wrote:
>> >> On Jul 12, 2010, at 12:45 PM, Tim Vandermeersch wrote:
>> >>
>> >>>> So far I see only SetAtomicNum to specify atom type, but nothing to
>> > set
>> >>>> the atomic label to something like "R1".
>> >>>
>> >>> You can use AliasData for this.
>> >>
>> >> See src/formats/mdlformat.cpp for an exact example.
>> >>
>> >> Hope that helps,
>> >> -Geoff
>> >
>> >
>> >
>> > ------------------------------------------------------------------------------
>> > This SF.net email is sponsored by Sprint
>> > What will you do first with EVO, the first 4G phone?
>> > Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
>> > _______________________________________________
>> > OpenBabel-discuss mailing list
>> > [hidden email]
>> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>> >
>> >
>> >
>> >
>> > No virus found in this incoming message.
>> > Checked by AVG - www.avg.com
>> > Version: 9.0.851 / Virus Database: 271.1.1/3020 - Release Date: 07/21/10 19:36:00
>> >
>>
>>
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Re: markush structures in openbabel

Igor Filippov [Contr]-2
Tim,

You are absolutely right. As soon as I removed openbabel rpm which came
with my Fedora 12 installation I could compile and link things properly
with the svn snapshot libopenbabel.

Thank you,
Igor

P.S. Chris the fix for atomic aliases works like a charm, thanks once
again!


On Mon, 2010-08-09 at 12:11 -0400, Tim Vandermeersch wrote:

> On Mon, Aug 9, 2010 at 5:50 PM, Igor Filippov [Contr]
> <[hidden email]> wrote:
> > Chris,
> >
> > Thank you. I'm trying to test it with the latest trunk (r3955) but even
> > though OB itself compiled fine I'm getting the following error when
> > trying to link libopenbabel to my program:
> >
> > undefined reference to `OpenBabel::AliasData::GetAlias(bool) const'
> > collect2: ld returned 1 exit status
> >
> > Was there some significant change in how libopenbabel should be linked?
> > It was working fine with 2.2.3 release.
>
> No, the API and "linking method" is unchanged. However, the ABI will
> be changed for the 2.3 release and the GetAlias function changed from:
>
> std::string GetAlias() const;
>
> to:
>
> std::string GetAlias(bool rightAligned = false) const;
>
> Since the linker complains about this symbol being undefined you are
> probably using the new headers but link to the old library.
>
> Tim
>
> > Igor
> >
> > On Thu, 2010-07-22 at 12:05 -0400, Chris Morley wrote:
> >> Thanks. Corrected in r3897.
> >> Chris
> >>
> >> On 21/07/2010 15:46, Igor Filippov [Contr] wrote:
> >> > I've run into a problem with an SD file generated by OB with atomic
> >> > aliases. This file could not be opened by CambridgeSoft ChemBioDraw, or
> >> > displayed correctly by ChemAxxon MarvinSketch.
> >> > CamridgeSoft support tells me the atom numbers should be
> >> > right-justified, where they are left-justified in OB output. Akos Papp
> >> > from ChemAxxon says that there is not enough white space between "A" and
> >> > the atom number. Here is an example of OB output and what Akos
> >> > corrected:
> >> > OB output -
> >> >
> >> > A  8
> >> > R5
> >> > A  10
> >> > R4
> >> > A  11
> >> > R3
> >> > A  14
> >> > R2
> >> > A  16
> >> > R1
> >> >
> >> > Corrected -
> >> >
> >> > A    8
> >> > R5
> >> > A   10
> >> > R4
> >> > A   11
> >> > R3
> >> > A   14
> >> > R2
> >> > A   16
> >> > R1
> >> >
> >> > the corrected file can be opened by ChemDraw, MarvinSketch, as well as
> >> > Symyx Draw and CACTVS csbr. Could we correct the output of atomic
> >> > aliases in the next OB release?
> >> >
> >> > Igor
> >> >
> >> >
> >> > On Mon, 2010-07-12 at 13:07 -0400, Geoffrey Hutchison wrote:
> >> >> On Jul 12, 2010, at 12:45 PM, Tim Vandermeersch wrote:
> >> >>
> >> >>>> So far I see only SetAtomicNum to specify atom type, but nothing to
> >> > set
> >> >>>> the atomic label to something like "R1".
> >> >>>
> >> >>> You can use AliasData for this.
> >> >>
> >> >> See src/formats/mdlformat.cpp for an exact example.
> >> >>
> >> >> Hope that helps,
> >> >> -Geoff
> >> >
> >> >
> >> >
> >> > ------------------------------------------------------------------------------
> >> > This SF.net email is sponsored by Sprint
> >> > What will you do first with EVO, the first 4G phone?
> >> > Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
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> >> > [hidden email]
> >> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
> >> >
> >> >
> >> >
> >> >
> >> > No virus found in this incoming message.
> >> > Checked by AVG - www.avg.com
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> >>
> >>
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