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From: Igor F. <igo...@gm...> - 2011-04-23 03:40:38
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Can anybody advise how to set up the level of MNA descriptors in Perl?
I tried
$obconversion->SetOptions('L3',
$Chemistry::OpenBabel::OBConversion::OUTOPTIONS);
It doesn't seem to do the trick.
Regards,
Igor
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From: Noel O'B. <bao...@gm...> - 2011-04-25 09:44:50
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The API docs say:
SetOptions: Set several single character options of specified type
from string like ab"btext"c"ctext".
Have you tried this?
- Noel
On 23 April 2011 04:40, Igor Filippov <igo...@gm...> wrote:
> Can anybody advise how to set up the level of MNA descriptors in Perl?
>
> I tried
> $obconversion->SetOptions('L3',
> $Chemistry::OpenBabel::OBConversion::OUTOPTIONS);
>
> It doesn't seem to do the trick.
>
> Regards,
> Igor
>
>
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From: Chris M. <c.m...@ga...> - 2011-04-25 12:37:43
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The function you need is AddOption
Chris
On 23/04/2011 04:40, Igor Filippov wrote:
> Can anybody advise how to set up the level of MNA descriptors in Perl?
>
> I tried
> $obconversion->SetOptions('L3',
> $Chemistry::OpenBabel::OBConversion::OUTOPTIONS);
>
> It doesn't seem to do the trick.
>
> Regards,
> Igor
>
>
> ------------------------------------------------------------------------------
> Fulfilling the Lean Software Promise
> Lean software platforms are now widely adopted and the benefits have been
> demonstrated beyond question. Learn why your peers are replacing JEE
> containers with lightweight application servers - and what you can gain
> from the move. http://p.sf.net/sfu/vmware-sfemails
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>
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From: Igor F. <igo...@gm...> - 2011-04-26 14:47:58
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Noel,
Hmmm, I'm not sure how to parse this into Perl.
Is it different from what I've tried (I put the line from my script in
the previous email)?
Igor
On Mon, 2011-04-25 at 10:44 +0100, Noel O'Boyle wrote:
> The API docs say:
> SetOptions: Set several single character options of specified type
> from string like ab"btext"c"ctext".
>
> Have you tried this?
>
> - Noel
>
> On 23 April 2011 04:40, Igor Filippov <igo...@gm...> wrote:
> > Can anybody advise how to set up the level of MNA descriptors in Perl?
> >
> > I tried
> > $obconversion->SetOptions('L3',
> > $Chemistry::OpenBabel::OBConversion::OUTOPTIONS);
> >
> > It doesn't seem to do the trick.
> >
> > Regards,
> > Igor
> >
> >
> > ------------------------------------------------------------------------------
> > Fulfilling the Lean Software Promise
> > Lean software platforms are now widely adopted and the benefits have been
> > demonstrated beyond question. Learn why your peers are replacing JEE
> > containers with lightweight application servers - and what you can gain
> > from the move. http://p.sf.net/sfu/vmware-sfemails
> > _______________________________________________
> > OpenBabel-scripting mailing list
> > Ope...@li...
> > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> >
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From: Noel O'B. <bao...@gm...> - 2011-04-26 14:56:05
|
In Python, I have either:
conv.SetOptions("L\"0\"", conv.OUTOPTIONS)
or
conv.SetOptions('L"1"', conv.OUTOPTIONS)
In other words, if you use double quotation marks, you need to escape
the inner double quotation marks.
- Noel
On 26 April 2011 15:43, Igor Filippov <igo...@gm...> wrote:
> Noel,
>
> Hmmm, I'm not sure how to parse this into Perl.
> Is it different from what I've tried (I put the line from my script in
> the previous email)?
>
> Igor
>
> On Mon, 2011-04-25 at 10:44 +0100, Noel O'Boyle wrote:
>> The API docs say:
>> SetOptions: Set several single character options of specified type
>> from string like ab"btext"c"ctext".
>>
>> Have you tried this?
>>
>> - Noel
>>
>> On 23 April 2011 04:40, Igor Filippov <igo...@gm...> wrote:
>> > Can anybody advise how to set up the level of MNA descriptors in Perl?
>> >
>> > I tried
>> > $obconversion->SetOptions('L3',
>> > $Chemistry::OpenBabel::OBConversion::OUTOPTIONS);
>> >
>> > It doesn't seem to do the trick.
>> >
>> > Regards,
>> > Igor
>> >
>> >
>> > ------------------------------------------------------------------------------
>> > Fulfilling the Lean Software Promise
>> > Lean software platforms are now widely adopted and the benefits have been
>> > demonstrated beyond question. Learn why your peers are replacing JEE
>> > containers with lightweight application servers - and what you can gain
>> > from the move. http://p.sf.net/sfu/vmware-sfemails
>> > _______________________________________________
>> > OpenBabel-scripting mailing list
>> > Ope...@li...
>> > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>> >
>
>
>
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From: Igor F. <igo...@gm...> - 2011-04-26 14:58:11
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Noel,
Good call, this works!
Thank you,
Igor
On Tue, 2011-04-26 at 15:55 +0100, Noel O'Boyle wrote:
> In Python, I have either:
>
> conv.SetOptions("L\"0\"", conv.OUTOPTIONS)
> or
> conv.SetOptions('L"1"', conv.OUTOPTIONS)
>
> In other words, if you use double quotation marks, you need to escape
> the inner double quotation marks.
>
> - Noel
>
> On 26 April 2011 15:43, Igor Filippov <igo...@gm...> wrote:
> > Noel,
> >
> > Hmmm, I'm not sure how to parse this into Perl.
> > Is it different from what I've tried (I put the line from my script in
> > the previous email)?
> >
> > Igor
> >
> > On Mon, 2011-04-25 at 10:44 +0100, Noel O'Boyle wrote:
> >> The API docs say:
> >> SetOptions: Set several single character options of specified type
> >> from string like ab"btext"c"ctext".
> >>
> >> Have you tried this?
> >>
> >> - Noel
> >>
> >> On 23 April 2011 04:40, Igor Filippov <igo...@gm...> wrote:
> >> > Can anybody advise how to set up the level of MNA descriptors in Perl?
> >> >
> >> > I tried
> >> > $obconversion->SetOptions('L3',
> >> > $Chemistry::OpenBabel::OBConversion::OUTOPTIONS);
> >> >
> >> > It doesn't seem to do the trick.
> >> >
> >> > Regards,
> >> > Igor
> >> >
> >> >
> >> > ------------------------------------------------------------------------------
> >> > Fulfilling the Lean Software Promise
> >> > Lean software platforms are now widely adopted and the benefits have been
> >> > demonstrated beyond question. Learn why your peers are replacing JEE
> >> > containers with lightweight application servers - and what you can gain
> >> > from the move. http://p.sf.net/sfu/vmware-sfemails
> >> > _______________________________________________
> >> > OpenBabel-scripting mailing list
> >> > Ope...@li...
> >> > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> >> >
> >
> >
> >
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From: dave.nunn <dav...@gm...> - 2011-05-06 22:22:09
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Did anyone get a Perl version that works? I've been attempting something
analogous using:
$OBConversion->SetOutFormat('sdf');
$OBConversion->AddOption('gen2d',
$Chemistry::OpenBabel::OBConversion::GENOPTIONS);
but $OBConversion->WriteString($OBMol) warns about missing coords and gives
me all 0.0000
--
View this message in context: http://forums.openbabel.org/level-of-MNA-descriptors-tp3472849p3504475.html
Sent from the openbabel-scripting mailing list archive at Nabble.com.
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From: Noel O'B. <bao...@gm...> - 2011-05-07 10:28:18
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Plugins are best called directly on a molecule with something like:
gen2d = OBOp.FindType("gen2d") # Looks up the plugin and returns it
gen2d.Do(mymol) # Calls the plugin on your molecule
- Noel
On 6 May 2011 23:22, dave.nunn <dav...@gm...> wrote:
> Did anyone get a Perl version that works? I've been attempting something
> analogous using:
>
> $OBConversion->SetOutFormat('sdf');
> $OBConversion->AddOption('gen2d',
> $Chemistry::OpenBabel::OBConversion::GENOPTIONS);
> but $OBConversion->WriteString($OBMol) warns about missing coords and gives
> me all 0.0000
>
> --
> View this message in context: http://forums.openbabel.org/level-of-MNA-descriptors-tp3472849p3504475.html
> Sent from the openbabel-scripting mailing list archive at Nabble.com.
>
> ------------------------------------------------------------------------------
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> OpenBabel-scripting mailing list
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> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>
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