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]);!$(*(-a)-a)])] I would like a text version for that too :) Many thanks! Regards, Pascal ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ OpenBabel-discuss mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/openbabel-discuss |
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There is some discussion of this in the comments in my blog article:
http://baoilleach.blogspot.com/2007/07/pybel-hack-that-sd-file.html In particular, the links to the references are included. We will include this information in the openbabel website in future. Regarding your real question, I didn't check the references against the SMARTS strings, nor do I understand the SMARTS strings themeselves without going to the Daylight SMARTS documentation. Maybe someone here can comment further. If you are using these strings, you could do us all a big favour by checking the references and letting us know if everything is OK according to your own chemical knowledge. Noel On 11/09/2007, Pascal Muller <[hidden email]> wrote: > Dear all, > > I have a few questions about method used for descriptors calculations > in openbabel. > > What are the methods used for LogP, PSA and MR calculation? (a > reference could be enough, I didn't found this information on > openbabel website). > > Is amide bond considered as a rotatable bond? I think so after reading > the "bool IsRotor( )" description, but I prefer to be sure :) > > And can anybody decode the smarts strings posted by Noel (thanks!) > describing HBD and NHA? > > HBD: [!#6;!H0] > I understand the !#6 as "not carbon", but that's all... What does the > zero do? Does it mean a hydrogen attached to any atom excepted carbon? > > HBA: [$([$([#8,#16]);!$(*=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 > ------------------------------------------------------------------------- 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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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 > ------------------------------------------------------------------------- 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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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 > > > ------------------------------------------------------------------------- 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 |
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/ _______________________________________________ OpenBabel-discuss mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/openbabel-discuss |
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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/ > _______________________________________________ > OpenBabel-discuss mailing list > [hidden email] > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > ------------------------------------------------------------------------- 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 |
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] ------------------------------------------------------------------------- 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 |
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 ------------------------------------------------------------------------- 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 |
In reply to this post by Noel O'Boyle
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In reply to this post by Pascal Muller-3
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