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Reference LogP / PSA

Pascal Muller-3
Dear all,

I have a few questions about method used for descriptors calculations
in openbabel.

What are the methods used for LogP, PSA and MR calculation? (a
reference could be enough, I didn't found this information on
openbabel website).

Is amide bond considered as a rotatable bond? I think so after reading
the "bool IsRotor( )" description, but I prefer to be sure :)

And can anybody decode the smarts strings posted by Noel (thanks!)
describing HBD and NHA?

HBD: [!#6;!H0]
I understand the !#6 as "not carbon", but that's all... What does the
zero do? Does it mean a hydrogen attached to any atom excepted carbon?

HBA: [$([$([#8,#16]);!$(*=N~O);!$(*~N=O);X1,X2]),$([#7;v3;!$([nH]);!$(*(-a)-a)])]
I would like a text version for that too :)

Many thanks!
Regards,
Pascal

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Re: Reference LogP / PSA

Noel O'Boyle
Administrator
There is some discussion of this in the comments in my blog article:
http://baoilleach.blogspot.com/2007/07/pybel-hack-that-sd-file.html

In particular, the links to the references are included. We will
include this information in the openbabel website in future.

Regarding your real question, I didn't check the references against
the SMARTS strings, nor do I understand the SMARTS strings themeselves
without going to the Daylight SMARTS documentation.

Maybe someone here can comment further. If you are using these
strings, you could do us all a big favour by checking the references
and letting us know if everything is OK according to your own chemical
knowledge.

Noel

On 11/09/2007, Pascal Muller <[hidden email]> wrote:

> Dear all,
>
> I have a few questions about method used for descriptors calculations
> in openbabel.
>
> What are the methods used for LogP, PSA and MR calculation? (a
> reference could be enough, I didn't found this information on
> openbabel website).
>
> Is amide bond considered as a rotatable bond? I think so after reading
> the "bool IsRotor( )" description, but I prefer to be sure :)
>
> And can anybody decode the smarts strings posted by Noel (thanks!)
> describing HBD and NHA?
>
> HBD: [!#6;!H0]
> I understand the !#6 as "not carbon", but that's all... What does the
> zero do? Does it mean a hydrogen attached to any atom excepted carbon?
>
> HBA: [$([$([#8,#16]);!$(*=N~O);!$(*~N=O);X1,X2]),$([#7;v3;!$([nH]);!$(*(-a)-a)])]
> I would like a text version for that too :)
>
> Many thanks!
> Regards,
> Pascal
>
> -------------------------------------------------------------------------
> This SF.net email is sponsored by: Microsoft
> Defy all challenges. Microsoft(R) Visual Studio 2005.
> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> _______________________________________________
> OpenBabel-discuss mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>

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Re: Reference LogP / PSA

Noel O'Boyle
Administrator
In reply to this post by Pascal Muller-3
In relation to the other descriptors, see the following email on this list:
http://www.nabble.com/logP-calculation-tf4193856.html

(I find Nabble very useful for searching the mailing list - note to
self: add this to the documentation as well as these descriptor
references)

Regarding "Is amide bond considered as a rotatable bond?". Uh...this
requires looking at the code, which says:

  bool OBBond::IsRotor()
  {
    return(_bgn->GetHvyValence() > 1 && _end->GetHvyValence() > 1 &&
           _order == 1 && !IsInRing() && _bgn->GetHyb() != 1 &&
           _end->GetHyb() != 1);
  }

Hmmm....in an amide bond, I expect the hybridisation of the C and N to
be 2 (i.e. sp2), so it looks like the expression above evaluates to
True. I think this is a bug. Can some of the C++ guys comment?
Presumably adding a check for amide is possible, and also desirable?

Noel

On 11/09/2007, Pascal Muller <[hidden email]> wrote:

> Dear all,
>
> I have a few questions about method used for descriptors calculations
> in openbabel.
>
> What are the methods used for LogP, PSA and MR calculation? (a
> reference could be enough, I didn't found this information on
> openbabel website).
>
> Is amide bond considered as a rotatable bond? I think so after reading
> the "bool IsRotor( )" description, but I prefer to be sure :)
>
> And can anybody decode the smarts strings posted by Noel (thanks!)
> describing HBD and NHA?
>
> HBD: [!#6;!H0]
> I understand the !#6 as "not carbon", but that's all... What does the
> zero do? Does it mean a hydrogen attached to any atom excepted carbon?
>
> HBA: [$([$([#8,#16]);!$(*=N~O);!$(*~N=O);X1,X2]),$([#7;v3;!$([nH]);!$(*(-a)-a)])]
> I would like a text version for that too :)
>
> Many thanks!
> Regards,
> Pascal
>
> -------------------------------------------------------------------------
> This SF.net email is sponsored by: Microsoft
> Defy all challenges. Microsoft(R) Visual Studio 2005.
> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> _______________________________________________
> OpenBabel-discuss mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>

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Re: Reference LogP / PSA

Noel O'Boyle
Administrator
And one last comment (for now :-) )...

Since OpenBabel is not the only Open Source cheminformatics toolkit,
we can compare and contrast....

The CDK uses a SMARTS pattern for determining the number of rotatable
bonds as described here:
http://cheminfo.informatics.indiana.edu/~rguha/code/java/nightly/api/org/openscience/cdk/qsar/descriptors/molecular/RotatableBondsCountDescriptor.html

It would be interesting and useful to determine all those cases where
this value disagrees with OpenBabel...

Noel

On 11/09/2007, Noel O'Boyle <[hidden email]> wrote:

> In relation to the other descriptors, see the following email on this list:
> http://www.nabble.com/logP-calculation-tf4193856.html
>
> (I find Nabble very useful for searching the mailing list - note to
> self: add this to the documentation as well as these descriptor
> references)
>
> Regarding "Is amide bond considered as a rotatable bond?". Uh...this
> requires looking at the code, which says:
>
>   bool OBBond::IsRotor()
>   {
>     return(_bgn->GetHvyValence() > 1 && _end->GetHvyValence() > 1 &&
>            _order == 1 && !IsInRing() && _bgn->GetHyb() != 1 &&
>            _end->GetHyb() != 1);
>   }
>
> Hmmm....in an amide bond, I expect the hybridisation of the C and N to
> be 2 (i.e. sp2), so it looks like the expression above evaluates to
> True. I think this is a bug. Can some of the C++ guys comment?
> Presumably adding a check for amide is possible, and also desirable?
>
> Noel
>
> On 11/09/2007, Pascal Muller <[hidden email]> wrote:
> > Dear all,
> >
> > I have a few questions about method used for descriptors calculations
> > in openbabel.
> >
> > What are the methods used for LogP, PSA and MR calculation? (a
> > reference could be enough, I didn't found this information on
> > openbabel website).
> >
> > Is amide bond considered as a rotatable bond? I think so after reading
> > the "bool IsRotor( )" description, but I prefer to be sure :)
> >
> > And can anybody decode the smarts strings posted by Noel (thanks!)
> > describing HBD and NHA?
> >
> > HBD: [!#6;!H0]
> > I understand the !#6 as "not carbon", but that's all... What does the
> > zero do? Does it mean a hydrogen attached to any atom excepted carbon?
> >
> > HBA: [$([$([#8,#16]);!$(*=N~O);!$(*~N=O);X1,X2]),$([#7;v3;!$([nH]);!$(*(-a)-a)])]
> > I would like a text version for that too :)
> >
> > Many thanks!
> > Regards,
> > Pascal
> >
> > -------------------------------------------------------------------------
> > This SF.net email is sponsored by: Microsoft
> > Defy all challenges. Microsoft(R) Visual Studio 2005.
> > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> > _______________________________________________
> > OpenBabel-discuss mailing list
> > [hidden email]
> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
> >
>

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Re: Reference LogP / PSA

Pascal Muller-3
Hi,

Sorry, the mail is a bit long. 3 parts: LogP/PSA, HBD/HBA and RB. I
need help mainly on smarts reading.

[LogP]
> There is some discussion of this in the comments in my blog article:
> http://baoilleach.blogspot.com/2007/07/pybel-hack-that-sd-file.html

Right, thanks. I found the reference for LogP in
http://openbabel.svn.sourceforge.net/viewvc/openbabel/openbabel/trunk/data/logp.txt?view=markup

What for PSA?


[HBD/HBA]

> Maybe someone here can comment further. If you are using these
> strings,

I would like to, I must compute descriptors for my library.

> you could do us all a big favour by checking the references
> and letting us know if everything is OK according to your own chemical
> knowledge.

Like GMC2007 commented on your blog, I prefer to use Lipinski's
definition of donor/acceptor for library descriptors. However, if
Lipinski HBA definition include or exclude e.g. amide or aromatic
nitrogen, I don't know. I must check.

Here
http://openbabel.svn.sourceforge.net/viewvc/openbabel/openbabel/trunk/src/smartsdescriptors.cpp?view=markup#l_57
we have

HBD: "[!#6;!H0]","Number of Hydrogen Bond Donors (JoelLib)");
HBA1: "[$([!#6;+0]);!$([F,Cl,Br,I]);!$([o,s,nX3]);!$([Nv5,Pv5,Sv4,Sv6])]",
"Number of Hydrogen Bond Acceptors 1 (JoelLib)");
HBA2: "[$([$([#8,#16]);!$(*=N~O);!$(*~N=O);X1,X2]),$([#7;v3;!$([nH]);!$(*(-a)-a)])]",
"Number of Hydrogen Bond Acceptors 2 (JoelLib)");

Does the first part of HBA2 means "any oxygen (excepted in nitroso or
oxyme) or sulfur atom with one or 2 connections"? (It's the X1,X2 part
which is annoying me).

On Daylight website we can read:
Hydrogen-bond donor.
[!$([#6,H0,-,-2,-3])]
"A H-bond donor is a non-negatively charged heteroatom with at least one H"
[!H0;#7,#8,#9]
"Must have an N-H bond, an O-H bond, or a F-H bond"

I'll use HBD [#7,#8;!H0] (any nitrogen or oxygen with at least one
attached hydrogen) for my purpose.
(By the way, is P-H a HBD?)


Still from Daylight site:
 Hydrogen-bond acceptor
    [!$([#6,F,Cl,Br,I,o,s,nX3,#7v5,#15v5,#16v4,#16v6,*+1,*+2,*+3])]
    A H-bond acceptor is a heteroatom with no positive charge, note
that negatively charged oxygen or sulphur are included. Excluded are
halogens, including F, heteroaromatic oxygen, sulphur and pyrrole N.
Higher oxidation levels of N,P,S are excluded. Note P(III) is currentl
y included.

Well, amide nitrogen and e.g. Phe-NH2 are considered HBA with that
definition, and the same in JoelLib HBA1 and HBA2, isn't it?

Assuming all 3-connected nitrogen next to sp2 or sp carbon smarts is
[NX3][c,C&X3,C&X2] like written in the comment in Noel's blog post
(does this smarts means : a nitrogen atom, with 3 neighbours, bound to
an aromatic carbon, or to a carbon with 3 neighbours, or to a carbon
with 2 neighbours?)
the smarts for HBA should be (?):
[ !$([#6,F ... +3,]);  !$([NX3][c,C&X3,C&X2])  ]

OK, better to do some tests to see if I understood these unreadable smarts...


[Amide / rotatable bond]

> Regarding "Is amide bond considered as a rotatable bond?". Uh...this
> requires looking at the code, which says:

 bool OBBond::IsRotor()
 {
   return(_bgn->GetHvyValence() > 1 && _end->GetHvyValence() > 1 &&
          _order == 1 && !IsInRing() && _bgn->GetHyb() != 1 &&
          _end->GetHyb() != 1);
 }

I'm neither a C++ reader...
_bgn->GetHvyValence() > 1 && _end->GetHvyValence() > 1
Both atoms must not be hydrogen...

_order == 1
...and the bond must be simple...

!IsInRing()
... and is not included in a ring...

bgn->GetHyb() != 1 &&_end->GetHyb() != 1)
... and both atom must not... well, what are the values for hybridization?

> Hmmm....in an amide bond, I expect the hybridization of the C and N to
> be 2 (i.e. sp2), so it looks like the expression above evaluates to
> True. I think this is a bug. Can some of the C++ guys comment?
> Presumably adding a check for amide is possible, and also desirable?

In the "rule of 3" definition I found (and I'm interested in for the
moment), which include RB, the amide bond is not considered as
rotatable - I agree with that.
I would go either for considering amide bond as not rotatable, either
giving the choice (amide bond optionally rotatable / not rotatable by
default) to the user.
But of course that's would only corresponding to my personnal usage.

> Since OpenBabel is not the only Open Source cheminformatics toolkit,
> we can compare and contrast....
>
> The CDK uses a SMARTS pattern for determining the number of rotatable
> bonds as described here:
> http://cheminfo.informatics.indiana.edu/~rguha/code/java/nightly/api/org/openscience/cdk/qsar/descriptors/molecular/RotatableBondsCountDescriptor.html
>
> It would be interesting and useful to determine all those cases where
> this value disagrees with OpenBabel...

Following multiple links I got finally to
http://www.daylight.com/dayhtml_tutorials/languages/smarts/smarts_examples.html#ROTATE

Rotatable bond   [!$(*#*)&!D1]-!@[!$(*#*)&!D1]
"An atom which is not triply bonded and not one-connected i.e.terminal
connected by a single non-ring bond to and equivalent atom."

Consider amide bond as rotatable as far I understand the definition -
didn't even give a try for that smarts :)

Regards,
Pascal

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Re: Reference LogP / PSA

Noel O'Boyle
Administrator
Regarding the PSA ref...all the atomic contribution descriptors come
from JOELib: http://openbabel.svn.sourceforge.net/viewvc/*checkout*/openbabel/openbabel/trunk/data/psa.txt

Regarding RB,
hybridization (via GetHyb()) is 1 for sp, 2 for sp2 and 3 for sp3.

So I think there is an issue with amide bonds. Are there other bonds
where this is also a problem?

Regarding HBD, HBA...well, if you can argue strongly for a particular
SMARTS pattern, then it may be included. For example, we can have
HBA1, HBA2 and so on, as did JOELib.

Noel

On 11/09/2007, Pascal Muller <[hidden email]> wrote:

> Hi,
>
> Sorry, the mail is a bit long. 3 parts: LogP/PSA, HBD/HBA and RB. I
> need help mainly on smarts reading.
>
> [LogP]
> > There is some discussion of this in the comments in my blog article:
> > http://baoilleach.blogspot.com/2007/07/pybel-hack-that-sd-file.html
>
> Right, thanks. I found the reference for LogP in
> http://openbabel.svn.sourceforge.net/viewvc/openbabel/openbabel/trunk/data/logp.txt?view=markup
>
> What for PSA?
>
>
> [HBD/HBA]
>
> > Maybe someone here can comment further. If you are using these
> > strings,
>
> I would like to, I must compute descriptors for my library.
>
> > you could do us all a big favour by checking the references
> > and letting us know if everything is OK according to your own chemical
> > knowledge.
>
> Like GMC2007 commented on your blog, I prefer to use Lipinski's
> definition of donor/acceptor for library descriptors. However, if
> Lipinski HBA definition include or exclude e.g. amide or aromatic
> nitrogen, I don't know. I must check.
>
> Here
> http://openbabel.svn.sourceforge.net/viewvc/openbabel/openbabel/trunk/src/smartsdescriptors.cpp?view=markup#l_57
> we have
>
> HBD: "[!#6;!H0]","Number of Hydrogen Bond Donors (JoelLib)");
> HBA1: "[$([!#6;+0]);!$([F,Cl,Br,I]);!$([o,s,nX3]);!$([Nv5,Pv5,Sv4,Sv6])]",
> "Number of Hydrogen Bond Acceptors 1 (JoelLib)");
> HBA2: "[$([$([#8,#16]);!$(*=N~O);!$(*~N=O);X1,X2]),$([#7;v3;!$([nH]);!$(*(-a)-a)])]",
> "Number of Hydrogen Bond Acceptors 2 (JoelLib)");
>
> Does the first part of HBA2 means "any oxygen (excepted in nitroso or
> oxyme) or sulfur atom with one or 2 connections"? (It's the X1,X2 part
> which is annoying me).
>
> On Daylight website we can read:
> Hydrogen-bond donor.
> [!$([#6,H0,-,-2,-3])]
> "A H-bond donor is a non-negatively charged heteroatom with at least one H"
> [!H0;#7,#8,#9]
> "Must have an N-H bond, an O-H bond, or a F-H bond"
>
> I'll use HBD [#7,#8;!H0] (any nitrogen or oxygen with at least one
> attached hydrogen) for my purpose.
> (By the way, is P-H a HBD?)
>
>
> Still from Daylight site:
>  Hydrogen-bond acceptor
>     [!$([#6,F,Cl,Br,I,o,s,nX3,#7v5,#15v5,#16v4,#16v6,*+1,*+2,*+3])]
>     A H-bond acceptor is a heteroatom with no positive charge, note
> that negatively charged oxygen or sulphur are included. Excluded are
> halogens, including F, heteroaromatic oxygen, sulphur and pyrrole N.
> Higher oxidation levels of N,P,S are excluded. Note P(III) is currentl
> y included.
>
> Well, amide nitrogen and e.g. Phe-NH2 are considered HBA with that
> definition, and the same in JoelLib HBA1 and HBA2, isn't it?
>
> Assuming all 3-connected nitrogen next to sp2 or sp carbon smarts is
> [NX3][c,C&X3,C&X2] like written in the comment in Noel's blog post
> (does this smarts means : a nitrogen atom, with 3 neighbours, bound to
> an aromatic carbon, or to a carbon with 3 neighbours, or to a carbon
> with 2 neighbours?)
> the smarts for HBA should be (?):
> [ !$([#6,F ... +3,]);  !$([NX3][c,C&X3,C&X2])  ]
>
> OK, better to do some tests to see if I understood these unreadable smarts...
>
>
> [Amide / rotatable bond]
>
> > Regarding "Is amide bond considered as a rotatable bond?". Uh...this
> > requires looking at the code, which says:
>
>  bool OBBond::IsRotor()
>  {
>    return(_bgn->GetHvyValence() > 1 && _end->GetHvyValence() > 1 &&
>           _order == 1 && !IsInRing() && _bgn->GetHyb() != 1 &&
>           _end->GetHyb() != 1);
>  }
>
> I'm neither a C++ reader...
> _bgn->GetHvyValence() > 1 && _end->GetHvyValence() > 1
> Both atoms must not be hydrogen...
>
> _order == 1
> ...and the bond must be simple...
>
> !IsInRing()
> ... and is not included in a ring...
>
> bgn->GetHyb() != 1 &&_end->GetHyb() != 1)
> ... and both atom must not... well, what are the values for hybridization?
>
> > Hmmm....in an amide bond, I expect the hybridization of the C and N to
> > be 2 (i.e. sp2), so it looks like the expression above evaluates to
> > True. I think this is a bug. Can some of the C++ guys comment?
> > Presumably adding a check for amide is possible, and also desirable?
>
> In the "rule of 3" definition I found (and I'm interested in for the
> moment), which include RB, the amide bond is not considered as
> rotatable - I agree with that.
> I would go either for considering amide bond as not rotatable, either
> giving the choice (amide bond optionally rotatable / not rotatable by
> default) to the user.
> But of course that's would only corresponding to my personnal usage.
>
> > Since OpenBabel is not the only Open Source cheminformatics toolkit,
> > we can compare and contrast....
> >
> > The CDK uses a SMARTS pattern for determining the number of rotatable
> > bonds as described here:
> > http://cheminfo.informatics.indiana.edu/~rguha/code/java/nightly/api/org/openscience/cdk/qsar/descriptors/molecular/RotatableBondsCountDescriptor.html
> >
> > It would be interesting and useful to determine all those cases where
> > this value disagrees with OpenBabel...
>
> Following multiple links I got finally to
> http://www.daylight.com/dayhtml_tutorials/languages/smarts/smarts_examples.html#ROTATE
>
> Rotatable bond   [!$(*#*)&!D1]-!@[!$(*#*)&!D1]
> "An atom which is not triply bonded and not one-connected i.e.terminal
> connected by a single non-ring bond to and equivalent atom."
>
> Consider amide bond as rotatable as far I understand the definition -
> didn't even give a try for that smarts :)
>
> Regards,
> Pascal
>
> -------------------------------------------------------------------------
> This SF.net email is sponsored by: Microsoft
> Defy all challenges. Microsoft(R) Visual Studio 2005.
> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> _______________________________________________
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> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>

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Re: Reference LogP / PSA

Andrew Dalke
In reply to this post by Pascal Muller-3
On Sep 11, 2007, at 3:03 PM, Pascal Muller wrote:
> [HBD/HBA]

> Here
> http://openbabel.svn.sourceforge.net/viewvc/openbabel/openbabel/ 
> trunk/src/smartsdescriptors.cpp?view=markup#l_57
> we have
>
> HBD: "[!#6;!H0]","Number of Hydrogen Bond Donors (JoelLib)");
> HBA1: "[$([!#6;+0]);!$([F,Cl,Br,I]);!$([o,s,nX3]);!$
> ([Nv5,Pv5,Sv4,Sv6])]",
> "Number of Hydrogen Bond Acceptors 1 (JoelLib)");
> HBA2: "[$([$([#8,#16]);!$(*=N~O);!$(*~N=O);X1,X2]),$([#7;v3;!$
> ([nH]);!$(*(-a)-a)])]",
> "Number of Hydrogen Bond Acceptors 2 (JoelLib)");


In PyDaylight I used the same definition as HBA1, and I have a reference
for it:

# some SMARTS strings from:
#  Identification of Biological Activity Profiles Using Substructural
# Analysis and Genetic Algorithms -- Gillet, Willett and Bradshaw,
# U. of Sheffield and Glaxo Wellcome.
#  Presented at Random & Rational: Drug Discovery via Rational Design
# and Combinitorial Chemistry, Strategic Research Institute, Princeton
# NJ, Sept. 1995
hydrogen_bond_donor = "[!#6;!H0]"
hydrogen_bond_acceptor = \
        "[$([!#6;+0]);!$([F,Cl,Br,I]);!$([o,s,nX3]);!$
([Nv5,Pv5,Sv4,Sv6])]"



> [Amide / rotatable bond]
>
>> Regarding "Is amide bond considered as a rotatable bond?". Uh...this
>> requires looking at the code, which says:

> Following multiple links I got finally to
> http://www.daylight.com/dayhtml_tutorials/languages/smarts/ 
> smarts_examples.html#ROTATE
>
> Rotatable bond   [!$(*#*)&!D1]-!@[!$(*#*)&!D1]
> "An atom which is not triply bonded and not one-connected i.e.terminal
> connected by a single non-ring bond to and equivalent atom."
>
> Consider amide bond as rotatable as far I understand the definition -
> didn't even give a try for that smarts :)

I don't remember where I got this definition, but it came almost
certainly from somewhere on the Daylight web site, though that
includes presentations.

rotatable_bonds = \
        "[!$([NH]!@C(=O))&!D1&!$(*#*)]-&!@[!$([NH]!@C(=O))&!D1&!$(*#*)]"

I would have to sit down for a while to figure out what that looks
like.

                                Andrew
                                [hidden email]



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Re: NumRotors (was Reference LogP / PSA)

Geoffrey Hutchison
In reply to this post by Noel O'Boyle

On Sep 11, 2007, at 9:25 AM, Noel O'Boyle wrote:
>> [Amide / rotatable bond]
>>
>>> Regarding "Is amide bond considered as a rotatable bond?". Uh...this
>>> requires looking at the code, which says:
...
>> http://www.daylight.com/dayhtml_tutorials/languages/smarts/ 
>> smarts_examples.html#ROTATE
>>
>> Rotatable bond   [!$(*#*)&!D1]-!@[!$(*#*)&!D1]
>> "An atom which is not triply bonded and not one-connected  
>> i.e.terminal
>> connected by a single non-ring bond to and equivalent atom."


One "catch" about rotatable bonds in Open Babel is that there's  
essentially two methods for determining the number of rotatable  
bonds. What you describe is something like the "descriptor" method.  
In this case, the documentation clearly states what is a rotatable  
bond: (No need to read the code)

http://openbabel.SourceForge.net/api/2.1.0/
> Currently, this function classifies any bond with at least one  
> heavy atom, no sp-hybrid atoms (e.g., a triple bond somewhere) not  
> in a ring as a potential rotor. No other bond typing is attempted.
>
Now I don't know if the Open Babel definition matches "standard QSAR  
practice." If not, let's add a new function.

But the reason OBMol::NumRotors() and OBBond::IsRotor() overestimate  
whether a bond is rotatable is for rotamer/conformer searching (i.e.,  
using OBRotamerList, OBRotorList, and OBRotorRules). These classes  
can define a set of SMARTS patterns and likely dihedral angles. It's  
better to consider an amide as a bond to attempt to rotate, than to  
miss out on low-energy conformers.

Yes, this means that OBMol::NumRotors() serves double duty. If there  
needs to be a new "descriptor" version which returns the expected  
answer, that sounds like a good idea. But I'd also like to see the  
OBRotorRules database enhanced with some potential conformer  
searching rules too. This can be used to get a number of rotatable  
bonds too:

OBRotorList rl;
rl.Setup(mol);

cerr << " Number of rotors: " << rl.Size() << endl;

Cheers,
-Geoff

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browse around these guys

robertfcrocker
In reply to this post by Noel O'Boyle
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Re: browse around these guys

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