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Re: [OpenBabel-scripting] [openbabel-scripting] OBPairData problem

[Charlie Z. <zh....@gm...>]

I have the same problem when using obdotnet.
The error message is 
Attempted to read or write protected memory. This is often an indication
that other memory is corrupt.
   at OpenBabel.openbabelcsharpPINVOKE.delete_OBPairData(HandleRef jarg1)
   at OpenBabel.OBPairData.Dispose()
   at OpenBabel.OBPairData.Finalize()

Thanks for Noel's solution.

Charlie


baoilleach wrote:
> 
> Hello Loris,
> 
> This problem is due to the PairData object getting destroyed by
> Python, while the C++ OBMol still wants to keep it. The solution is to
> use CloneData instead of SetData. In other words, *never* use SetData
> from Python or any other scripting language. I will update the Python
> documentation to make this clear.
> 
> You might find it useful to look at the code of pybel.py to see how I
> do things there.
> 
> Noel
> 
> On 16/09/2008, Loris Moretti <lor...@ch...> wrote:
>> Hi all,
>>
>>  I am quite new to OpenBabel I am trying to develop a script in Python
>> with
>>  OpenBabel. The script reads a multiple sdf file, takes a molecule per
>> time and
>>  calculates some properties. It adds the property value and attribute to
>> the
>>  OBMol object with OBPairData and then, it writes out the molecules into
>> a
>>  multiple sdf file with the new field.
>>
>>  a very simple form of the script:
>>
>>  #########################################################
>>  #!/usr/bin/python
>>
>>  import openbabel
>>
>>  obConversion = openbabel.OBConversion()
>>  obConversion.SetInAndOutFormats("sdf", "sdf")
>>
>>  mol = openbabel.OBMol()
>>
>>  iteratorMol = obConversion.ReadFile(mol, "molecules.sdf")
>>
>>  while iteratorMol:
>>
>>     newData = openbabel.OBPairData()
>>     newData.SetAttribute("NEWDATA")
>>     newData.SetValue("blabla")
>>     mol.SetData(newData)
>>
>>     print obConversion.WriteString(mol)
>>
>>     iteratorMol = obConversion.Read(mol)
>>  #########################################################
>>
>>  The script works for the first molecule of the input file but fails for
>> the
>>  others with a "segmentation fault" error.
>>  I tested it line by line and I saw there is a problem to reuse the
>> OBPairData
>>  object.
>>
>>  It might be a trivial error of mine but I cannot see it!
>>  It might be an error of the system I use!
>>
>>  Can anyone help, please.
>>
>>  Thanks in advance,
>>  loris...
>>
>> 
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Re: [OpenBabel-scripting] openbabel 2.2.3 (windows) crashed while reading in large PDB formatted file

[Geoffrey H. <ge...@ge...>]

I have easily handled over 65,000 atoms in PDB files.

So here's my first question. Can you point me to a particular PDB file which is crashing for you?

Thanks very much,
-Geoff

On Dec 7, 2009, at 8:57 PM, qiancheng shen wrote:

> There are about 30,000 atoms in a 2M pdb file. You can try to read such a pdb file in openbabel 2.2.3, then the program will crash.
> 
> Best Regards.
> Qiancheng Shen

Re: [OpenBabel-scripting] openbabel 2.2.3 (windows) crashed while reading in large PDB formatted file

[Geoffrey H. <ge...@ge...>]

On Dec 7, 2009, at 4:18 AM, Noel O'Boyle wrote:

>> in a large pdb file (file size more than 2M).
...
> aromaticity detector hits a recursion limit when dealing with large
> files.

2MB should be nowhere near a "large file." Two GB might be a problem, but I haven't seen issues with 2MB files. How many atoms are in the PDB file?

Thanks very much,
-Geoff

Re: [OpenBabel-scripting] openbabel 2.2.3 (windows) crashed while reading in large PDB formatted file

[Noel O'B. <bao...@gm...>]

2009/12/6 qiancheng shen <qia...@gm...>:
> Dear All,
>     Openbabel 2.2.3 GUI crashes without giving any info when I want to read
> in a large pdb file (file size more than 2M).
>     When I want to read the pdb file by importing openbabel in Python:
>    #Code-------------------------
> -------------------------------
>    import openbabel as ob
>    obconv = ob.OBConversion()
>    obconv.SetInFormat("PDB")
>    mol = ob.OBMol()
>    obconv.ReadFile(mol,'test.pdb')
>    print mol
>    #---------------------------------------------------------------
>
>    The program just interrupted and a warning prompt "python.exe has stopped
> running" appeared.
>    Could anyone help me?

Could you file a bug report? I think that the problem is that our
aromaticity detector hits a recursion limit when dealing with large
files. In other words, the only workaround is to reduce the size of
your protein I'm afraid.

> Best Regards.
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[OpenBabel-scripting] openbabel 2.2.3 (windows) crashed while reading in large PDB formatted file

[qiancheng s. <qia...@gm...>]

Dear All,
    Openbabel 2.2.3 GUI crashes without giving any info when I want to read
in a large pdb file (file size more than 2M).
    When I want to read the pdb file by importing openbabel in Python:
   #Code-------------------------
-------------------------------
   import openbabel as ob
   obconv = ob.OBConversion()
   obconv.SetInFormat("PDB")
   mol = ob.OBMol()
   obconv.ReadFile(mol,'test.pdb')
   print mol
   #---------------------------------------------------------------

   The program just interrupted and a warning prompt "python.exe has stopped
running" appeared.
   Could anyone help me?

Best Regards.

[OpenBabel-scripting] openbabel 2.2.3 (windows) crashed while reading in large PDB formatted file

[qiancheng s. <qia...@gm...>]

Dear All,
    Openbabel 2.2.3 GUI crashes without giving any info when I want to read
in a large pdb file (file size more than 2M).
    When I want to read the pdb file by importing openbabel in Python:
   #Code--------------------------------------------------------
   import openbabel as ob
   obconv = ob.OBConversion()
   obconv.SetInFormat("PDB")
   mol = ob.OBMol()
   obconv.ReadFile(mol,'test.pdb')
   print mol
   #---------------------------------------------------------------

   The program just interrupted and a warning prompt "python.exe has stopped
running" appeared.
   Could anyone help me?

Best Regards.

Re: [OpenBabel-scripting] Access violation exception when reading/writing xml formats

[Noel O'B. <bao...@gm...>]

Seems to work fine from Python. Using OpenBabel on the trunk, I have:

>>> mol = pybel.readstring("smi", "CC(=O)Cl")
>>> print mol.write("cml")
<molecule>
 <atomArray>
  <atom id="a1" elementType="C"/>
  <atom id="a2" elementType="C"/>
  <atom id="a3" elementType="O"/>
  <atom id="a4" elementType="Cl"/>
 </atomArray>
 <bondArray>
  <bond atomRefs2="a1 a2" order="1"/>
  <bond atomRefs2="a2 a3" order="2"/>
  <bond atomRefs2="a2 a4" order="1"/>
 </bondArray>
</molecule>

>>>

I am using the libxml2.dll that comes with OpenBabel 2.2.3, which I
can test with Cygwin's "which" as follows:
C:\> which libxml2.dll
/cygdrive/c/Program Files/OpenBabel-2.2.3/libxml2.dll

I haven't done any work enabling other scripting languages on the
trunk, so I can't easily test whether it works from C# there...

- Noel

2009/12/1 Matt Sprague <mes...@gm...>:
> Nope, that didn't help. The program is crashing inside of the the call
> to xmlFreeTextReader. You can view the source here:
> http://svn.gnome.org/viewvc/libxml2/trunk/xmlreader.c?revision=3795&view=markup
> Whatever is happening occurs between the beginning of the function (line
> 2177)
> and the call to xmlFreeParserInputBuffer(input) (line 2245). I thought I was
> closing in on the problem, but the version of libxml2 I built with MinGW
> works just fine. So now I'm really puzzled.
>
> -Matt
>
>
>

Re: [OpenBabel-scripting] Access violation exception when reading/writing xml formats

[Matt S. <mes...@gm...>]

Nope, that didn't help. The program is crashing inside of the the call
to xmlFreeTextReader. You can view the source here:
http://svn.gnome.org/viewvc/libxml2/trunk/xmlreader.c?revision=3795&view=markup
<http://svn.gnome.org/viewvc/libxml2/trunk/xmlreader.c?revision=3795&view=markup>
Whatever is happening occurs between the beginning of the function (line
2177)
and the call to xmlFreeParserInputBuffer(input) (line 2245). I thought I was
closing in on the problem, but the version of libxml2 I built with MinGW
works just fine. So now I'm really puzzled.


-Matt

Re: [OpenBabel-scripting] Access violation exception when reading/writing xml formats

[Noel O'B. <bao...@gm...>]

No I didn't. I saw that Geoff had attempted to fix this issue so I was
waiting to hear from you:
http://openbabel.svn.sourceforge.net/viewvc/openbabel?view=rev&revision=3455

This is on the trunk, but presumably you could cut 'n' paste onto the branch.

If you can check this out, I'll follow up with python.

- Noel

2009/11/30 Matt Sprague <mes...@gm...>:
> Noel, did you ever get a chance to check whether or not this exception
> happens in the python bindings? I downloaded the libxml2 source and built
> the dll with MinGW using the posix threading library (pthreadgc2.dll) and
> that seems to work fine on my machine. Maybe be it's a bug in the VC
> runtime?
>
> -Matt
>
>
> On Thu, Nov 5, 2009 at 4:41 AM, Noel O'Boyle <bao...@gm...> wrote:
>>
>> 2009/11/4 Matt Sprague <mes...@gm...>:
>> > On Wed, Nov 4, 2009 at 7:11 AM, Noel O'Boyle <bao...@gm...>
>> > wrote:
>> > Are you working off the svn 22x branch?
>> >
>> > Yes, is there a another branch I should switch to?
>>
>> No - that's fine. Just checking.
>>
>> > Also, just to clarify,
>> > this is only a problem in with the bindings it works fine in C++.
>>
>> Ok - that's useful to know.
>>
>> That's pretty weird though. The XML formats are always problematic
>> though as everything goes through libxml and it seems to be a bit
>> messy. Could it be that it is picking up on the wrong libxml2 or
>> whatever? Or that there is some conflict there? Chris is the resident
>> expert on all things XML/Windows, but if it cannot be reproduced in
>> C++ it'll be next to impossible for him to debug.
>>
>> I have a mixture of different OBs on my computer so I can't easily
>> check whether XML read/writing works from Python, but I will do so as
>> soon as possible.
>>
>> - Noel
>
>

Re: [OpenBabel-scripting] Access violation exception when reading/writing xml formats

[Matt S. <mes...@gm...>]

Noel, did you ever get a chance to check whether or not this exception
happens in the python bindings? I downloaded the libxml2 source and built
the dll with MinGW using the posix threading library (pthreadgc2.dll) and
that seems to work fine on my machine. Maybe be it's a bug in the VC
runtime?

-Matt


On Thu, Nov 5, 2009 at 4:41 AM, Noel O'Boyle <bao...@gm...> wrote:

> 2009/11/4 Matt Sprague <mes...@gm...>:
> > On Wed, Nov 4, 2009 at 7:11 AM, Noel O'Boyle <bao...@gm...>
> wrote:
> > Are you working off the svn 22x branch?
> >
> > Yes, is there a another branch I should switch to?
>
> No - that's fine. Just checking.
>
> > Also, just to clarify,
> > this is only a problem in with the bindings it works fine in C++.
>
> Ok - that's useful to know.
>
> That's pretty weird though. The XML formats are always problematic
> though as everything goes through libxml and it seems to be a bit
> messy. Could it be that it is picking up on the wrong libxml2 or
> whatever? Or that there is some conflict there? Chris is the resident
> expert on all things XML/Windows, but if it cannot be reproduced in
> C++ it'll be next to impossible for him to debug.
>
> I have a mixture of different OBs on my computer so I can't easily
> check whether XML read/writing works from Python, but I will do so as
> soon as possible.
>
> - Noel
>

Re: [OpenBabel-scripting] python bindings: OBChemTsfm?

[Noel O'B. <bao...@gm...>]

I'm afraid you're right. It's just a simple matter of adding phmodel.h
to the SWIG interface file but it hasn't been done. I will do so now.

- Noel

2009/11/23 Andreas Kempe <a....@is...>:
> Hello,
>
> is there a way to access the class OBChemTsfm using python?
> Looks like it isn't implemented yet?
>
> Thanks in advance,
>
> Andreas
>
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[OpenBabel-scripting] python bindings: OBChemTsfm?

[Andreas K. <a....@is...>]

Hello,

is there a way to access the class OBChemTsfm using python?
Looks like it isn't implemented yet?

Thanks in advance,

Andreas

Re: [OpenBabel-scripting] ResidueIter for Perl??

[Geoffrey H. <ge...@ge...>]

> MAKE_ITER_CLASS(OBResidueIter, _OBResidueIter)
> Is this intentional or by mistake?

This is a mistake. We've generally enhanced the scripting interfaces as people have commented on problems. If you have SWIG, you can make the change yourself and rebuild the SWIG interface.

Cheers,
-Geoff

[OpenBabel-scripting] How to change serial numbers of atoms?

[InSuk J. <i....@gm...>]

Hi,
I try to open a pdb file and try to add an atom using Perl.

my $mol = Chemistry::OpenBabel::OBMol->new;
my $conv = Chemistry::OpenBabel::OBConversion->new;
$conv->SetInAndOutFormats( 'pdb', 'pdb' );
$conv->ReadFile( $mol, 'pdb' );

...

my $new_atom = $mol->NewAtom;
$new_atom->SetAtomicNum(8);

...

$conv->WriteFile( $mol, 'out.pdb' );

I want the new atom to be placed in the middle of the original molecule.  I
tried to change the serial number of the new atom
($residue->SetSerialNum($new_atom, XXX)) but no matter what serial number it
is , the new atom always were printed out at the bottom of 'out.pdb'.  How
can I fix this problem?

Best,
InSuk Joung

[OpenBabel-scripting] scripts/perl/Makefile.PL

[InSuk J. <i....@gm...>]

Hi,
I guess the ./scripts/perl/Makefile.PL has a small problem.
In the lines 6 and 7:
check_lib_or_exit( lib => 'openbabel' , libpath => @ENV{"LD_LIBRARY_PATH"}
);

@ENV{...} looks quite weird to me.  Also it doesn't seem to correctly parse
the environmental variable, "$LD_LIBRARY_PATH".

With the original code, I consistently get the message "Can't build and link
to 'openbabel'".

I changed the lines into
check_lib_or_exit( lib => 'openbabel' , libpath => [ split ':',
$ENV{"LD_LIBRARY_PATH"} ] );

The, it worked fine.

-- 
Best,
InSuk Joung

[OpenBabel-scripting] ResidueIter for Perl??

[InSuk J. <i....@gm...>]

Hi,
Thank you for the Iterators for Perl although this is very late response.
However, I found that OBResidueIter is still omitted.  Indeed, SWIG input
file does not have the line like:
MAKE_ITER_CLASS(OBResidueIter, _OBResidueIter)
Is this intentional or by mistake?

-- 
Best,
InSuk Joung

Re: [OpenBabel-scripting] problem with python bindings for openbabel

[Noel O'B. <bao...@gm...>]

Hello Carla,

Does import _openbabel work?

- Noel

2009/11/18 Carla Ng <c....@ma...>:
> Hello, I have just installed openbabel and the python bindings for
> windows.  I am running Python 2.6.4. (this is on parallels running on
> a macbook pro)
> When I try the import commands, I get the following error:
>
> Traceback (most recent call last):
>   File "C:/Python26/mol_weight.py", line 31, in <module>
>     import openbabel
>   File "C:\Python26\lib\site-packages\openbabel.py", line 25, in
> <module>
>     _openbabel = swig_import_helper()
>   File "C:\Python26\lib\site-packages\openbabel.py", line 24, in
> swig_import_helper
>     return _mod
> UnboundLocalError: local variable '_mod' referenced before assignment
>
> When I test the installation as described on the wiki page, the
> responses to the entered commands are as described up to the 'import
> pybel' command, which gives the above error.
>
> Any suggestions would be much appreciated.
>
> --Carla Ng
>
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[OpenBabel-scripting] problem with python bindings for openbabel

[Carla Ng <c....@ma...>]

Hello, I have just installed openbabel and the python bindings for  
windows.  I am running Python 2.6.4. (this is on parallels running on  
a macbook pro)
When I try the import commands, I get the following error:

Traceback (most recent call last):
   File "C:/Python26/mol_weight.py", line 31, in <module>
     import openbabel
   File "C:\Python26\lib\site-packages\openbabel.py", line 25, in  
<module>
     _openbabel = swig_import_helper()
   File "C:\Python26\lib\site-packages\openbabel.py", line 24, in  
swig_import_helper
     return _mod
UnboundLocalError: local variable '_mod' referenced before assignment

When I test the installation as described on the wiki page, the  
responses to the entered commands are as described up to the 'import  
pybel' command, which gives the above error.

Any suggestions would be much appreciated.

--Carla Ng

Re: [OpenBabel-scripting] Access violation exception when reading/writing xml formats

[Chris M. <c.m...@ga...>]

Matt Sprague wrote:
> I was working on  the next release of OBDotNet when I discovered that 
> read or writing any xml format triggers an access violation exception. 
> After debugging into the C++ code I was able to identify the call to 
> xmlFreeTextReader as the source of the exception. I've spent the last 3 
> days trying to figure out a work around but I'm stumped. Any thoughts?

I find libxml2 difficult and cumbersome to work with. Its interface is 
  C, not a C++, in style and sometimes, but not always, you have to 
delete the memory used by strings it has given you and other objects. 
I have to confess I never really sorted this out properly and the code 
was left working in C++ but possibly with memory leaks. I'm sorry if 
it has turned out to be more than this and has wasted your time.

I'll try to look at it again, but, in the meantime, it looks as if it 
could benefit addition of the second line here

xmlFreeTextReader(_reader);
_reader = NULL;

This would ensure it wasn't deleted twice, which might be the 
immediate cause of the error.

Chris

Re: [OpenBabel-scripting] Access violation exception when reading/writing xml formats

[Noel O'B. <bao...@gm...>]

2009/11/4 Matt Sprague <mes...@gm...>:
> On Wed, Nov 4, 2009 at 7:11 AM, Noel O'Boyle <bao...@gm...> wrote:
> Are you working off the svn 22x branch?
>
> Yes, is there a another branch I should switch to?

No - that's fine. Just checking.

> Also, just to clarify,
> this is only a problem in with the bindings it works fine in C++.

Ok - that's useful to know.

That's pretty weird though. The XML formats are always problematic
though as everything goes through libxml and it seems to be a bit
messy. Could it be that it is picking up on the wrong libxml2 or
whatever? Or that there is some conflict there? Chris is the resident
expert on all things XML/Windows, but if it cannot be reproduced in
C++ it'll be next to impossible for him to debug.

I have a mixture of different OBs on my computer so I can't easily
check whether XML read/writing works from Python, but I will do so as
soon as possible.

- Noel

Re: [OpenBabel-scripting] [openbabel-scripting] InChi generation options

[Charlie Z. <zh....@gm...>]

Hi Noel,

I am using the OBDotNet lib 2.0 and find the OBConversion don't add FixedH
layer to InChI output by default.
i.e. these 3 SMILES
c1([nH]c(nn1)N)CC(=O)O 115285.mol 
c1(nc(n[nH]1)N)CC(=O)O 154294.mol 
c1(nc([nH]n1)N)CC(=O)O 154307.mol 

Yield the same InChI (they have no Fixed H layer)
InChI=1S/C4H6N4O2/c5-4-6-2(7-8-4)1-3(9)10/h1H2,(H,9,10)(H3,5,6,7,8) 

And if I add below option to OBConversion object it will produce empty
string.

    public static SqlString conversion(SqlString molecule, SqlString intype,
SqlString outtype)
    {
        OBConversion obconv = new OBConversion();
        OBMol mol = new OBMol();

        obconv.AddOption("X", OBConversion.Option_type.OUTOPTIONS,
"FixedH");
        obconv.SetInAndOutFormats(intype.ToString(), outtype.ToString());
        obconv.ReadString(mol, molecule.ToString());
        String os = obconv.WriteString(mol);
        return obconv.WriteString(mol);
    }

So I replaced the "libstdinchi.dll" with the renamed "libinchi.dll" shipped
with Windows Open Babel GUI, the code accepts the option and outputs the
right InChI.

InChI=1/C4H6N4O2/c5-4-6-2(7-8-4)1-3(9)10/h1H2,(H,9,10)(H3,5,6,7,8)/f/h6,9H,5H2
InChI=1/C4H6N4O2/c5-4-6-2(7-8-4)1-3(9)10/h1H2,(H,9,10)(H3,5,6,7,8)/f/h7,9H,5H2
InChI=1/C4H6N4O2/c5-4-6-2(7-8-4)1-3(9)10/h1H2,(H,9,10)(H3,5,6,7,8)/f/h8-9H,5H2

Could you point out this is some defect or miss using? Thanks.

Charlie


Chris Morley-2 wrote:
> 
> Noel O'Boyle wrote:
>> pybel just uses the default options of each format. But even OpenBabel
>> currently doesn't seem to have the option you are looking for:
>>    "InChI format\n"
>>     "IUPAC/NIST molecular identifier\n"
>>     "Write options, e.g. -xat\n"
>>     " X <Option string> List of InChI options:\n"
> 
> On 27/03/2008, yez...@tp... <yez...@tp...> wrote:
>  > > I am trying to generate InChi codes using pybel like this:
>  > >
>  > >  descriptor={}
>  > >  descriptor['INCHI']=mol.write('INCHI')
>  > >
>  > >  While running, the output window reports an InChi warning that 
> protons have been added or
>  > >  removed. When I examine the structures, the InChi generation has 
> produced a new tautomeric form
>  > >  for many molecules eg amides as imine-alcohols. The corresponding 
> smiles representation using
>  > >  mol.write('CAN') works as expected ie the same tautomer as the 
> input structure.
>  > >
>  > >  I am aware that InChi allows the generation of mobile H atom and 
> fixed H atom models - can I pass
>  > >  something to mol.write('INCHI') to generate a fixed-H atom 
> representation?
>  > >
> 
> On the babel commandline adding the option -xX "FixedH" would include a 
> fixed hydrogen layer in the InChI. This is a bit cumbersome so I have 
> added a couple of other options to the development code.
>    F include fixed hydrogen layer
>    M include bonds to metal
> 
> You can now call simple output options like these from C++ code like
> conv.AddOption("F");
> where conv is the OBConversion object.
> 
> I guess the syntax from Python is similar. Maybe Pybel could wrap option 
> calls for output formats somehow?
> 
> Chris
> 
> 
> 
> 
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Re: [OpenBabel-scripting] Access violation exception when reading/writing xml formats

[Noel O'B. <bao...@gm...>]

Are you working off the svn 22x branch?

2009/11/4 Matt Sprague <mes...@gm...>:
> I was working on  the next release of OBDotNet when I discovered that read
> or writing any xml format triggers an access violation exception. After
> debugging into the C++ code I was able to identify the call to
> xmlFreeTextReader as the source of the exception. I've spent the last 3 days
> trying to figure out a work around but I'm stumped. Any thoughts?
>
> -Matt
>
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[OpenBabel-scripting] Access violation exception when reading/writing xml formats

[Matt S. <mes...@gm...>]

I was working on  the next release of OBDotNet when I discovered that read
or writing any xml format triggers an access violation exception. After
debugging into the C++ code I was able to identify the call to
xmlFreeTextReader as the source of the exception. I've spent the last 3 days
trying to figure out a work around but I'm stumped. Any thoughts?

-Matt

Re: [OpenBabel-scripting] Counting rotors

[Geoffrey H. <ge...@ge...>]

On Oct 16, 2009, at 6:54 PM, Richard West wrote:

> (i.e. is there an open-babel function to count the number of
> rotors in a statistical mechanics sense?)

No, it counts the number of rotors in a cheminformatics (i.e., quick- 
and-dirty) way.

You can also try this, which finds rotatable bonds based on SMARTS  
patterns:
       OpenBabel::OBRotorList rl;
       OpenBabel::OBMol obmol = m_molecule->OBMol();
       rl.Setup(obmol);
       cout << "# of Rotors" << rl.Size();

Hope that helps,
-Geoff

[OpenBabel-scripting] Counting rotors

[Richard W. <rw...@MI...>]

My understanding now is that OBMol.NumRotors() counts the number of  
rotors that lead to different conformers. Rotating about either of the  
two C-C bonds in propane does not yield any different conformers, and  
thus I get
 >>> propane = pybel.readstring('smi','CCC')
 >>> propane.OBMol.NumRotors()
0

butane however gives 1
 >>> pybel.readstring('smi','CCCC').OBMol.NumRotors()
1


However, in terms of statistical mechanics, both C-C bonds in propane  
are internal rotors, and I would want a rotor count of 2. For straight- 
chain alkanes it's tempting to just add 2 to the NumRotors() answer.
However, this will not work in general. Neopentane should gave 4  
internal rotors.
 >>> neopentane = pybel.readstring('smi','CC(C)(C)C')
 >>> neopentane.OBMol.NumRotors()
0


I can find another way (count the number of non-terminal non-cyclic  
single bonds in non-linear molecules) but is this re-inventing the  
wheel? (i.e. is there an open-babel function to count the number of  
rotors in a statistical mechanics sense?)

Also, is there documentation for NumRotors that I overlooked? It took  
me a little while to realise that this is not what I wanted and why.


Thanks