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Re: [OpenBabel-scripting] python bindings GetCellVectors() error

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

Hello Andreas,

Looks like you've found a bug in OpenBabel, rather than a Python
problem. First of all, here's a workaround - use the Get method
instead:

>>> import pybel
>>> mol = pybel.readfile("cif", "ABENAX.cif").next()
>>> cv = mol.unitcell.GetCellVectors()[0]
>>> a = pybel.ob.doubleArray(3)
>>> cv.Get(a)
>>> a[0]
8.4589996337890625
>>> a[1]
0.0
>>> a[2]
0.0

I'll file a bug.

Noel

2009/5/22 Andreas Kempe <a....@is...>:
> Hello list,
>
> this code
>
> [...]
> uc = openbabel.toUnitCell(mol.GetData(openbabel.UnitCell))
> temp = uc.GetCellVectors()
> print temp[0].x()
>
> is not working (on windows). Why? How can I access the cell vectors with
> the python bindings?
>
> Thanks in advance,
>
> Andreas
>
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[OpenBabel-scripting] [openbabel-scripting] cmake and bindings

[Fredrik W. <fr...@wa...>]

Hi!

I was trying to find information on how to install the bindings (especially
python) with cMake without luck. I'm using openbabel from the 2.2.x-branch.
I know how to install them with configure, but I was hoping I could use
cMake instead.

Kind regards,
Fredrik
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[OpenBabel-scripting] python bindings GetCellVectors() error

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

Hello list,

this code

[...]
uc = openbabel.toUnitCell(mol.GetData(openbabel.UnitCell))
temp = uc.GetCellVectors()
print temp[0].x()

is not working (on windows). Why? How can I access the cell vectors with
the python bindings?

Thanks in advance,

Andreas

Re: [OpenBabel-scripting] OBDotNet 0.2

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

> Does mcs work fine?

Not really:

openbabelcsharp.cs(56,51): error CS1644: Feature `generics' is not  
available in Mono mcs1 compiler. Consider using the `gmcs' compiler  
instead

That's why I switched to gmcs.

-Geoff

Re: [OpenBabel-scripting] Help-errors installation python bindings

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

Hello Helen,

It's actually a chlorine "Cl", rather than a C followed by a one. I've
updated the documentation to use "Br" instead to avoid confusion in
future.

- Noel

2009/4/28 Helen Medina Miranda <hel...@in...>:
> Hello:
>
>
>
> In the testing Test Installation of python bindings, there are problems
> from:
>
>
>
> http://openbabel.org/wiki/Install_Python_bindings,
>
>
>
> Test Instalation
>
>
>
>>>> import pybel
>
>>>> mol=pybel.readstring("smi", "CC(=O)C1")
>
> ==============================
>
> *** Open Babel Warning  in OpenBabel::OBSmilesParser::ParseSmiles
>
>   Invalid SMILES string: 1 unmatched ring bonds.
>
>
>
> Traceback (most recent call last):
>
>   File "<stdin>", line 1, in <module>
>
>   File "c:\python26\lib\site-packages\pybel.py", line 119, in readstring
>
>     string, format))
>
> IOError: Failed to convert 'CC(=O)C1' to format 'smi'
>
>>>> mol.make3D()
>
> Traceback (most recent call last):
>
>   File "<stdin>", line 1, in <module>
>
> NameError: name 'mol' is not defined
>
>>>> print mol.write("sdf")
>
> Traceback (most recent call last):
>
>   File "<stdin>", line 1, in <module>
>
> NameError: name 'mol' is not defined
>
>
>
> I would like to know that these errors are how these errors could be solved.
>
> Greetings
>
>
>
>
>
> ------------------------------------------------------------------------------
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>
>

Re: [OpenBabel-scripting] OBDotNet 0.2

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

Does mcs work fine?

- Noel

2009/4/23 Geoffrey Hutchison <ge...@ge...>:
> One problem... I just tried building:
>
> (cd csharp; /usr/bin/gmcs /optimize /target:library /out:OBDotNet.dll *.cs);
> OBAromaticTyper.cs(17,88): error CS0117: `OpenBabel.openbabelcsharpPINVOKE'
> does not contain a definition for `OBAromaticTyperUpcast'
> openbabelcsharpPINVOKE.cs(14,7): (Location of the symbol related to previous
> error)
> OBAromaticTyper.cs(41,58): error CS0117: `OpenBabel.openbabelcsharpPINVOKE'
> does not contain a definition for `new_OBAromaticTyper'
> openbabelcsharpPINVOKE.cs(14,7): (Location of the symbol related to previous
> error)
> double_array.cs(42,68): error CS0117: `OpenBabel.openbabelcsharpPINVOKE'
> does not contain a definition for `new_double_array'
> openbabelcsharpPINVOKE.cs(14,7): (Location of the symbol related to previous
> error)
> Compilation failed: 3 error(s), 0 warnings
>
> Any suggestions? This is with Mono 2.4, which is the latest stable version.
>
> -Geoff
>

Re: [OpenBabel-scripting] [openbabel-scripting] Using Fingerprinter with perl

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

You're almost there. The result is in $fp.

BTW, if you are interested in writing up some Perl recipes (e.g. the
code below) on the wiki, it would be greatly appreciated. It would
help other users avoid the same pitfalls.

-- Noel

2009/4/27 Matt Ketterer <mke...@iu...>:
>
> Hi Noel,
> Yes openbabel does work.  I got perl to stop barking at me by taking away
> the "new" in front of the fingerprint class as I see it is static.  I'm
> still unsure of how to return or print the value.  I was trying to follow
> the python implementation at
> http://www.nabble.com/Re%3A-fingerprints-from-Python-td22189375.html#a22189375
> but am not sure how to manipulate the vector that was used.
>
> [matt@localhost Desktop]$ echo "C(=O)CCl" | babel -ismi -ofpt -xfFP2
>>   7 bits set
> 00000000 00000000 00000000 00000000 00000000 00000300
> 00000000 00000000 00000000 08000000 00000000 40000000
> 00008004 00000000 00000000 00020000
> 1 molecule converted
> 19 audit log messages
>
> #!/usr/bin/perl
> use Chemistry::OpenBabel;
>
> my $smiles = "C(=O)CCl";
> my $obMol = new Chemistry::OpenBabel::OBMol;
> my $obConversion = new Chemistry::OpenBabel::OBConversion;
> $obConversion->SetInFormat("smi");
> $obConversion->ReadString($obMol,$smiles);
> my $fingerprinter =
> Chemistry::OpenBabel::OBFingerprint::FindFingerprint("FP2");
>
> my $fp = new Chemistry::OpenBabel::vectorUnsignedInt();
> my $thumb = $fingerprinter->GetFingerprint($obMol, $fp);
> print "$thumb\n";  #only returns 1
>
>
>
>
>
>
>
> baoilleach wrote:
>>
>> Hello Matt,
>>
>> Did you download OpenBabel 2.2.1, remove any previous OpenBabel
>> installation, and install globally or locally following the instructions
>> at
>> http://openbabel.org/wiki/Install_(source_code)?
>>
>> Does using babel work? E.g.
>> bash-3.2$ echo "C(=O)CCl" | babel -ismi -ofpt -xfFP2
>>>   7 bits set
>> 00000000 00000000 00000000 00000000 00000000 00000000
>> 00000000 00000000 00000000 00000000 00000000 40000000
>> 00008000 00000000 00000000 00000000 00000000 00000000
>> 00000000 00000000 00000000 00000300 00000000 00000000
>> 00000000 08000000 00000000 00000000 00000004 00000000
>> 00000000 00020000
>> 1 molecule converted
>> 12 audit log messages
>>
>> OBFingerprint::FindFingerprint("FP2") should work fine if babel can find
>> FP2. You should test your perl script in an empty directory.
>>
>> - Noel
>>
>>
>> 2009/4/27 Matt Ketterer <mke...@iu...>
>>
>>>
>>> I downloaded a fresh install and installed the wrappers and in the Perl
>>> script I do see that it includes the header file for fingerprints but I
>>> just
>>> wanted to know if anyone else has had trouble pulling up methods from
>>> this
>>> class.  when I do the OBFingerprint::GetDefault() or
>>> OBFingerprint::FindFingerprint("FP2") it states that it might not be
>>> loaded.
>>> Thx,
>>> Matt
>>>
>>>
>>>
>>> Matt Ketterer wrote:
>>> >
>>> > I am somewhat confused on how to obtain fingerprints using perl.  I
>>> tried
>>> > doing a simple SetInAndOutFormats("smi","fpt") and then write the
>>> molecule
>>> > out but got a segmentation fault, while it worked for other formats
>>> such
>>> > as smiles to molfile.  I am also unfamiliar with using the
>>> > OBConversion.convert() function, as it complained that input and output
>>> > was not set.
>>> >
>>> > I know that pybel is available and could use that although I am already
>>> > using perl to parse pubchem data into a flat file before it goes into
>>> my
>>> > postgresql database and would like to calculate fingerprints from the
>>> > smiles of each line on the fly before it goes in.
>>> > Thanks for any help.
>>> >
>>>
>>> --
>>> View this message in context:
>>> http://www.nabble.com/Using-Fingerprinter-with-perl-tp23238185p23251252.html
>>> Sent from the openbabel-scripting mailing list archive at Nabble.com.
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
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>>> Check out the new simplified licensign option that enables unlimited
>>> royalty&#45;free distribution of the report engine for externally facing
>>> server and web deployment.
>>> http://p.sf.net/sfu/businessobjects
>>> _______________________________________________
>>> OpenBabel-scripting mailing list
>>> Ope...@li...
>>> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>>>
>>
>> ------------------------------------------------------------------------------
>> Crystal Reports &#45; New Free Runtime and 30 Day Trial
>> Check out the new simplified licensign option that enables unlimited
>> royalty&#45;free distribution of the report engine for externally facing
>> server and web deployment.
>> http://p.sf.net/sfu/businessobjects
>> _______________________________________________
>> OpenBabel-scripting mailing list
>> Ope...@li...
>> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>>
>>
>
> --
> View this message in context: http://www.nabble.com/Using-Fingerprinter-with-perl-tp23238185p23256721.html
> Sent from the openbabel-scripting mailing list archive at Nabble.com.
>
>
> ------------------------------------------------------------------------------
> Crystal Reports &#45; New Free Runtime and 30 Day Trial
> Check out the new simplified licensign option that enables unlimited
> royalty&#45;free distribution of the report engine for externally facing
> server and web deployment.
> http://p.sf.net/sfu/businessobjects
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>

Re: [OpenBabel-scripting] [openbabel-scripting] Using Fingerprinter with perl

[Matt K. <mke...@iu...>]

Hi Noel,
Yes openbabel does work.  I got perl to stop barking at me by taking away
the "new" in front of the fingerprint class as I see it is static.  I'm
still unsure of how to return or print the value.  I was trying to follow
the python implementation at
http://www.nabble.com/Re%3A-fingerprints-from-Python-td22189375.html#a22189375  
but am not sure how to manipulate the vector that was used.

[matt@localhost Desktop]$ echo "C(=O)CCl" | babel -ismi -ofpt -xfFP2
>   7 bits set 
00000000 00000000 00000000 00000000 00000000 00000300 
00000000 00000000 00000000 08000000 00000000 40000000 
00008004 00000000 00000000 00020000 
1 molecule converted
19 audit log messages 

#!/usr/bin/perl
use Chemistry::OpenBabel;

my $smiles = "C(=O)CCl";
my $obMol = new Chemistry::OpenBabel::OBMol;
my $obConversion = new Chemistry::OpenBabel::OBConversion;
$obConversion->SetInFormat("smi");
$obConversion->ReadString($obMol,$smiles);
my $fingerprinter =
Chemistry::OpenBabel::OBFingerprint::FindFingerprint("FP2");

my $fp = new Chemistry::OpenBabel::vectorUnsignedInt();
my $thumb = $fingerprinter->GetFingerprint($obMol, $fp); 
print "$thumb\n";  #only returns 1






 
baoilleach wrote:
> 
> Hello Matt,
> 
> Did you download OpenBabel 2.2.1, remove any previous OpenBabel
> installation, and install globally or locally following the instructions
> at
> http://openbabel.org/wiki/Install_(source_code)?
> 
> Does using babel work? E.g.
> bash-3.2$ echo "C(=O)CCl" | babel -ismi -ofpt -xfFP2
>>   7 bits set
> 00000000 00000000 00000000 00000000 00000000 00000000
> 00000000 00000000 00000000 00000000 00000000 40000000
> 00008000 00000000 00000000 00000000 00000000 00000000
> 00000000 00000000 00000000 00000300 00000000 00000000
> 00000000 08000000 00000000 00000000 00000004 00000000
> 00000000 00020000
> 1 molecule converted
> 12 audit log messages
> 
> OBFingerprint::FindFingerprint("FP2") should work fine if babel can find
> FP2. You should test your perl script in an empty directory.
> 
> - Noel
> 
> 
> 2009/4/27 Matt Ketterer <mke...@iu...>
> 
>>
>> I downloaded a fresh install and installed the wrappers and in the Perl
>> script I do see that it includes the header file for fingerprints but I
>> just
>> wanted to know if anyone else has had trouble pulling up methods from
>> this
>> class.  when I do the OBFingerprint::GetDefault() or
>> OBFingerprint::FindFingerprint("FP2") it states that it might not be
>> loaded.
>> Thx,
>> Matt
>>
>>
>>
>> Matt Ketterer wrote:
>> >
>> > I am somewhat confused on how to obtain fingerprints using perl.  I
>> tried
>> > doing a simple SetInAndOutFormats("smi","fpt") and then write the
>> molecule
>> > out but got a segmentation fault, while it worked for other formats
>> such
>> > as smiles to molfile.  I am also unfamiliar with using the
>> > OBConversion.convert() function, as it complained that input and output
>> > was not set.
>> >
>> > I know that pybel is available and could use that although I am already
>> > using perl to parse pubchem data into a flat file before it goes into
>> my
>> > postgresql database and would like to calculate fingerprints from the
>> > smiles of each line on the fly before it goes in.
>> > Thanks for any help.
>> >
>>
>> --
>> View this message in context:
>> http://www.nabble.com/Using-Fingerprinter-with-perl-tp23238185p23251252.html
>> Sent from the openbabel-scripting mailing list archive at Nabble.com.
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Crystal Reports &#45; New Free Runtime and 30 Day Trial
>> Check out the new simplified licensign option that enables unlimited
>> royalty&#45;free distribution of the report engine for externally facing
>> server and web deployment.
>> http://p.sf.net/sfu/businessobjects
>> _______________________________________________
>> OpenBabel-scripting mailing list
>> Ope...@li...
>> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>>
> 
> ------------------------------------------------------------------------------
> Crystal Reports &#45; New Free Runtime and 30 Day Trial
> Check out the new simplified licensign option that enables unlimited
> royalty&#45;free distribution of the report engine for externally facing 
> server and web deployment.
> http://p.sf.net/sfu/businessobjects
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> 
> 

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Re: [OpenBabel-scripting] [openbabel-scripting] Using Fingerprinter with perl

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

Hello Matt,

Did you download OpenBabel 2.2.1, remove any previous OpenBabel
installation, and install globally or locally following the instructions at
http://openbabel.org/wiki/Install_(source_code)?

Does using babel work? E.g.
bash-3.2$ echo "C(=O)CCl" | babel -ismi -ofpt -xfFP2
>   7 bits set
00000000 00000000 00000000 00000000 00000000 00000000
00000000 00000000 00000000 00000000 00000000 40000000
00008000 00000000 00000000 00000000 00000000 00000000
00000000 00000000 00000000 00000300 00000000 00000000
00000000 08000000 00000000 00000000 00000004 00000000
00000000 00020000
1 molecule converted
12 audit log messages

OBFingerprint::FindFingerprint("FP2") should work fine if babel can find
FP2. You should test your perl script in an empty directory.

- Noel


2009/4/27 Matt Ketterer <mke...@iu...>

>
> I downloaded a fresh install and installed the wrappers and in the Perl
> script I do see that it includes the header file for fingerprints but I
> just
> wanted to know if anyone else has had trouble pulling up methods from this
> class.  when I do the OBFingerprint::GetDefault() or
> OBFingerprint::FindFingerprint("FP2") it states that it might not be
> loaded.
> Thx,
> Matt
>
>
>
> Matt Ketterer wrote:
> >
> > I am somewhat confused on how to obtain fingerprints using perl.  I tried
> > doing a simple SetInAndOutFormats("smi","fpt") and then write the
> molecule
> > out but got a segmentation fault, while it worked for other formats such
> > as smiles to molfile.  I am also unfamiliar with using the
> > OBConversion.convert() function, as it complained that input and output
> > was not set.
> >
> > I know that pybel is available and could use that although I am already
> > using perl to parse pubchem data into a flat file before it goes into my
> > postgresql database and would like to calculate fingerprints from the
> > smiles of each line on the fly before it goes in.
> > Thanks for any help.
> >
>
> --
> View this message in context:
> http://www.nabble.com/Using-Fingerprinter-with-perl-tp23238185p23251252.html
> Sent from the openbabel-scripting mailing list archive at Nabble.com.
>
>
>
> ------------------------------------------------------------------------------
> Crystal Reports &#45; New Free Runtime and 30 Day Trial
> Check out the new simplified licensign option that enables unlimited
> royalty&#45;free distribution of the report engine for externally facing
> server and web deployment.
> http://p.sf.net/sfu/businessobjects
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>

Re: [OpenBabel-scripting] [openbabel-scripting] Using Fingerprinter with perl

[Matt K. <mke...@iu...>]

I downloaded a fresh install and installed the wrappers and in the Perl
script I do see that it includes the header file for fingerprints but I just
wanted to know if anyone else has had trouble pulling up methods from this
class.  when I do the OBFingerprint::GetDefault() or
OBFingerprint::FindFingerprint("FP2") it states that it might not be loaded.
Thx,
Matt



Matt Ketterer wrote:
> 
> I am somewhat confused on how to obtain fingerprints using perl.  I tried
> doing a simple SetInAndOutFormats("smi","fpt") and then write the molecule
> out but got a segmentation fault, while it worked for other formats such
> as smiles to molfile.  I am also unfamiliar with using the
> OBConversion.convert() function, as it complained that input and output
> was not set.
> 
> I know that pybel is available and could use that although I am already
> using perl to parse pubchem data into a flat file before it goes into my
> postgresql database and would like to calculate fingerprints from the
> smiles of each line on the fly before it goes in.
> Thanks for any help.
> 

-- 
View this message in context: http://www.nabble.com/Using-Fingerprinter-with-perl-tp23238185p23251252.html
Sent from the openbabel-scripting mailing list archive at Nabble.com.

[OpenBabel-scripting] [openbabel-scripting] Using Fingerprinter with perl

[Matt K. <mke...@iu...>]

I am somewhat confused on how to obtain fingerprints using perl.  I tried
doing a simple SetInAndOutFormats("smi","fpt") and then write the molecule
out but got a segmentation fault, while it worked for other formats such as
smiles to molfile.  I am also unfamiliar with using the
OBConversion.convert() function, as it complained that input and output was
not set.

I know that pybel is available and could use that although I am already
using perl to parse pubchem data into a flat file before it goes into my
postgresql database and would like to calculate fingerprints from the smiles
of each line on the fly before it goes in.
Thanks for any help.
-- 
View this message in context: http://www.nabble.com/Using-Fingerprinter-with-perl-tp23238185p23238185.html
Sent from the openbabel-scripting mailing list archive at Nabble.com.

Re: [OpenBabel-scripting] OBDotNet 0.2

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

One problem... I just tried building:

(cd csharp; /usr/bin/gmcs /optimize /target:library /out:OBDotNet.dll  
*.cs);
OBAromaticTyper.cs(17,88): error CS0117:  
`OpenBabel.openbabelcsharpPINVOKE' does not contain a definition for  
`OBAromaticTyperUpcast'
openbabelcsharpPINVOKE.cs(14,7): (Location of the symbol related to  
previous error)
OBAromaticTyper.cs(41,58): error CS0117:  
`OpenBabel.openbabelcsharpPINVOKE' does not contain a definition for  
`new_OBAromaticTyper'
openbabelcsharpPINVOKE.cs(14,7): (Location of the symbol related to  
previous error)
double_array.cs(42,68): error CS0117:  
`OpenBabel.openbabelcsharpPINVOKE' does not contain a definition for  
`new_double_array'
openbabelcsharpPINVOKE.cs(14,7): (Location of the symbol related to  
previous error)
Compilation failed: 3 error(s), 0 warnings

Any suggestions? This is with Mono 2.4, which is the latest stable  
version.

-Geoff

Re: [OpenBabel-scripting] OBDotNet 0.2

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

2009/4/22 Matt Sprague <mes...@gm...>

> Hello Noel,
>
> I've cobbled this email together from several emails I've been meaning to
> respond to so I hope that isn't too disjointed. The current version of the
> interface I've uploaded fixed an extend directive that was not being added
> to OBRotor. It should be good to go. Attached is a text file with a list of
> the new types available in v0.2 and a list of goals for v0.3. .Babel still
> needs a little more work before we do a release.
>
> I'm also planning to try and work up a test suite for the bindings that
> will test some of the C# only features over the next few weeks.
>
>
> A few outstanding things from previous emails:
>
> "BTW, if you're interested in support for std::pair, you'll need to
> %include std_pair.i."
>
> The problem with std::pair is that the typemap is not complete in
> swig_csharp. If we want to use std::pair and std::triple in the C# bindings
> we'll have to implement them ourselves. That's the only reason I've been
> looking at creating substitute methods using vectors.
>
> Also, it appears that they went ahead and added the generic vector wrapper
> to swig 1.3.39 so there is no need to include it separately. I've removed
> the file from the repository and added my additional method to the interface
> file.
>
>
>> I must admit that I preferred being able to compile directly using
>> obdotnet.bat from the VC2005 build. It seems to me that using the C#
>> sln file only introduces maintainence problems. E.g. the OB API
>> changes, so I need to update the OBDotNet solution file. Is there some
>> reason to prefer the solution file approach? Also, we may have to move
>> things out of the scripts/csharp directory that are not relevant to
>> the Unix build - however, we don't need to think about this until the
>> next OB release.
>
>
> My reasoning is as follows:
>
> 1)The files in the solution directory are replaced each time SWIG runs.
> Checking for changes just requires selecting View All Files and adding any
> new ones then refreshing or building the project to find and remove any
> missing files. Doing this from the project makes it easier to monitor
> changes in the bindings.
>
> 2)Using the sln it is easier to inspect the generated code and deal with
> errors/warnings that arise from modifying the interface file. It will also
> make things easier for other .Net programmers who might want to contribute
> to the project.
>
> 3)Having the solution allows developers to manually modify the swig
> generated files when protoyping new functionality.
>
> 4)It makes it easier for to keep DotBabel in sych with OBDotNet
>
> 5)Monodevelop has some support for importing VS projects. I haven't tested
> this (no current linux install) but it shouldn't be too difficult to create
> a parallel Monodevelop project for Linux/OSX users.
>
> If you still want to build with the bat file in addition to having a
> project I'm cool with that.
>

Understood. I think we will go with both if possible, or just with yours. I
will move your code into windows-vc2005 as it will confuse Unix users
otherwise. BTW, remember to edit the Changelog for each commit.


>
> Anyway, it's long past due time for OBDotNet 0.2. I think we should
>> base OBDotNet 0.2 on the same SVN revision that OB 2.2.1 is based on.
>> If you can check in AtomExtensions.cs, I will create a beta release of
>> 0.2. Then we can test it and write up some instructions for use and
>> get out the final release.
>>
>> - Noel
>>
>
> To revisit an older issue:
> "
> I'm assuming that it's not possible to access the cPtr in the
> SWIG-generated code (which would solve the problem, right?).
>
> I can't remember if I mentioned this or not, but the problem is that many
> of the intermediate methods are returning pointers to pointers so just
> comparing pointers fails in many cases.
>
> this is really a question for openbabel-devel. I have a feeling that
> the best you can do is to provide an equals method that just works for
> OBAtoms in the same molecule (using GetIdx), and leave it to the user
> to ensure that this is the case. Without being able to access the
> object pointer, it's never going to be possible to figure out if
> they're in the same molecule."
>
> I think it might be better to implement a couple of Comparer<T> types that
> do this rather than trying to customize the Equals methods. I can do it
> pretty quickly but I would like to get a new release out. Do you think this
> should be included in v0.2 or should we wait and add it in v0.3 as part of a
> larger effort aimed at getting equality comparisons working?
>

I think we want to get this out as soon as possible at this stage.


>
> Creating an installer has proved a little harder than I expected. The
> problem I'm having is that while creating the msi is easy, having it set the
> environment variables seems to be more complicated. Is there someone else
> with more dll deployment experience who can do it?
>

OB has special requirements due to its use of run-time plugins loaded from
DLLs. Would it be possible to reuse the DLLs supplied by the OpenBabelGUI?
This sets the environment variables PATH and BABELDATADIR. My Python
installer now just installs the .dll for Python (actually its a pyd) and
some py files, and uses the DLLs from OpenBabelGUI. The other thing is that
it installs the MSVC++ runtime, which is required by all of the bindings
(including the .NET ones).

But don't get bogged down in this - we can make do with a simple .zip file
if necessary, so long as we have clear installation instructions.

Can you explain (off-list probably better) how you are creating the msi and
I'll see if I can help some?


> Regarding documentation: I'm ready to update the wiki. Should I do it now
> or wait until we know when the release is coming.
>

Now is always better. :-) Just put it all under a heading like "Instructions
for OBDot 0.2" and say it's coming soon. Create an a/c and send me the name
if you haven't already.


>
> One final thing I'd like to start sending proper diff files but I keep
> getting the error message
>
> "svn: This client is too old to work with working copy '.'; please get a
> newer Subversion client"
> I looked it up on the web and what I found seemed to indicate that either
> my version of the client is either too new or too old. I've tried installing
> both newer and older versions but nothing fixes it. Any thoughts?
>

I use a mixture of tortoise svn (1.5.7) and the command-line client from
collabnet (1.5.5). Probably you should check out the whole repository into a
new folder with one of these guys and take it from there. SourceForge moved
to subversion 1.5 some time back, but until you used one of the newer
clients it didn't convert your local repository to subversion 1.5. After
that, the older clients wouldn't work.

>
> Apologies for the long email.
>

No probs. I'm very happy to see this going forward now.


>
> -Matt
>

Re: [OpenBabel-scripting] OBDotNet 0.2

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

The names of some classes have been changed in V.2 to follow standard C# naming conventions. No further changes will be made to class names.

Renamed Classes:

atomreftype -> AtomRefType
errorQualifier -> ErrorQualifier
obMessageLevel -> OBMessageLevel
vectorBond -> VectorBond
vectorDouble -> VectorDouble
vectorInt -> VectorInt
vectorMol -> VectorMol
vectorOBVector3 -> VectorOBVector3
vectorpAtom -> VectorpAtom
vectorpBond -> VectorpBond
vectorpData -> VectorpData
vectorpInternalCoord -> VectorpInternalCoord
vectorpRing -> VectorpRing
vectorResidue -> VectorResidue
vectorRing -> VectorRing
vectorString -> VectorString


New Types:

CByteArray
CDoubleArray
CIntArray
CUIntArray
OBGenericDataType
OBNasaThermoData
OBRateData
OBRotamerList
OBRotor
OBRotorKeys
OBRotorList
OBRotorRule
OBRotorRules
openbabelcsharp
Rate_Type
Reaction_Type
SWIGTYPE_p_std__vectorT_double_t__iterator
SWIGTYPE_p_std__vectorT_unsigned_char_p_t__iterator
VectorOBExternalBond
VectorpRotor
VectorTorsion
VectorUInt
VectorUShort
VectorVecDouble
VectorVecInt
VectorVecOBVector3
VectorVecUInt



Version 0.3 Goals
-Implement reference equality comparison.
 
-Improve C style array proxies by implementing some type of support from enumeration.
 This will require customizing the wrapper defined in carrays.i.
 
-Determine whether or not to implement standard C#/PInvoke array marshaling.
	-Pros: Converting to C# arrays simplifies creating arrays
	-Cons: The arrays being marshaled to C# are copies
               rather than references to an unmanaged array.
 
-Streams: Either build a wrapper or add methods that redirect standard in/out.

-Get FastSearch working or implement equivalent functionality in DotBabel. Stream wrappers are the main barrier. 

-Develop workaround or complete the typemaps for std::map, std::pair, and std::triple.
 OBTorsion will not be fully functional until this is done.

-Get proxy for shared_ptr working so that reaction.h can added.
	-The macro define at line 29 of reaction.h "#define shared_ptr boost::shared_ptr"
         causes namespace problems in the generated C++ wrapper

-Resolve std::string wrapper issues. Some strings are not mapping correctly.

-Fix VectorpData GC bug.


DotBabel goals:
-XML serialization of OB objects	`

Re: [OpenBabel-scripting] Problems Installing pybel: "Failed to make an instance PatternFP"

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

2009/4/16 R.L. Marchese-Robinson <rl...@ca...>

> Hi,
> I am working with Windows XP (32 bit).
>
> Following the instructions provided
> at:http://openbabel.org/wiki/Install_Python_bindings, I installed
> OpenBabel-2.2.1 using the installer OpenBabel2.2.1-Windows_Installer.exe.
> Since I am using python 2.5.2, I downloaded and ran
> openbabel-python-1.4.py2.5.exe.
>


> The output for all commands detailed in the instructions was as per the
> example output, save for import pybel. This generated: "***OpenBabelError
> in OpenBabel::OBDefine Failed to make an instance PatternFP"

I just repeated the procedure on my machine, which has the same setup, and
there were no problems. The first thing I did was uninstall all previous
OpenBabel installations and Python modules and check that the environment
variables PATH and BABEL_DATADIR contained no references to either.

Do you have several versions of Python installed? If so, did you select the
correct version during the installation procedure for the python module? Are
your environment variables set correctly (test at the command-line as
described on the installation page for the python module)? BABEL_DATADIR
needs to point to the OpenBabel installation directory. Try "import pybel"
while in an empty folder- you may have a filename conflict with a file in
BABEL_DATADIR.

- Noel

Re: [OpenBabel-scripting] Problems Installing pybel: "Failed to make an instance PatternFP"

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

Hello RL,

The problem could simply be that there's a pattern file missing in the
installer. I'll look into it.

Say hi to John.

- Noel

2009/4/16 R.L. Marchese-Robinson <rl...@ca...>

> Hi,
> I am working with Windows XP (32 bit).
>
> Following the instructions provided
> at:http://openbabel.org/wiki/Install_Python_bindings, I installed
> OpenBabel-2.2.1 using the installer OpenBabel2.2.1-Windows_Installer.exe.
> Since I am using python 2.5.2, I downloaded and ran
> openbabel-python-1.4.py2.5.exe.
>
> The output for all commands detailed in the instructions was as per the
> example output, save for import pybel. This generated: "***OpenBabelError
> in OpenBabel::OBDefine Failed to make an instance PatternFP"
>
> No such error was generated using "import openbabel"
>
> I can't find any specific documentation for this problem, but I believe it
> may be due to an error in fingeprints3.cpp. The only discernable effect
> would appear to be that molecule.calcfp('FPX') (where X DOES NOT EQUAL FP2)
> returns an empty list.
>
> Is the only way to fix this to modify fingerprints3.cpp and recompile from
> source?
>
> Thanks in advance for any assistance.
>
> Richard Marchese
>
>
> ------------------------------------------------------------------------------
> Stay on top of everything new and different, both inside and
> around Java (TM) technology - register by April 22, and save
> $200 on the JavaOne (SM) conference, June 2-5, 2009, San Francisco.
> 300 plus technical and hands-on sessions. Register today.
> Use priority code J9JMT32. http://p.sf.net/sfu/p
> _______________________________________________
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> Ope...@li...
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>

[OpenBabel-scripting] Problems Installing pybel: "Failed to make an instance PatternFP"

[R.L. Marchese-R. <rl...@ca...>]

Hi,
I am working with Windows XP (32 bit).

Following the instructions provided 
at:http://openbabel.org/wiki/Install_Python_bindings, I installed 
OpenBabel-2.2.1 using the installer OpenBabel2.2.1-Windows_Installer.exe. 
Since I am using python 2.5.2, I downloaded and ran 
openbabel-python-1.4.py2.5.exe.

The output for all commands detailed in the instructions was as per the 
example output, save for import pybel. This generated: "***OpenBabelError 
in OpenBabel::OBDefine Failed to make an instance PatternFP"

No such error was generated using "import openbabel" 

I can't find any specific documentation for this problem, but I believe it 
may be due to an error in fingeprints3.cpp. The only discernable effect 
would appear to be that molecule.calcfp('FPX') (where X DOES NOT EQUAL FP2) 
returns an empty list.

Is the only way to fix this to modify fingerprints3.cpp and recompile from 
source?

Thanks in advance for any assistance.

Richard Marchese 

Re: [OpenBabel-scripting] [openbabel-scripting] Problems with OBDotNet

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

Try putting the openbabel.dll and other files into system32 folder, that
perhaps works.

You'd better use Dependency Walker to check problems for the
DLLs(OBDotNet.dll/ openbabel.dll) to work. Download the free tool at
http://www.dependencywalker.com/

I have found the VC 2005 Redistributable Package is required on a
non-development machine by this way.

Charlie


Bob Trucchi wrote:
> 
> I'm having some troubles with getting OBDotNet to work and am hoping for
> some help. I have OpenBable-2.2.0 installed and am using VS 2008 sp1. I
> made the simplest program
> 
> using System;
> using OpenBabel;
> 
> namespace OpenBabelTesting
> {
> class Program
> {
> static void Main(string[] args)
> {
> OBConversion obc = new OBConversion();
> }
> 
> }
> }
> and when I run it I get this exception:
> System.TypeInitializationException was unhandled
> Message="The type initializer for 'OpenBabel.openbabelPINVOKE' threw an
> exception."
> Source="OBDotNet"
> TypeName="OpenBabel.openbabelPINVOKE"
> StackTrace:
> at OpenBabel.openbabelPINVOKE.new_OBConversion__SWIG_2()
> at OpenBabel.OBConversion..ctor()
> at OpenBabelTesting.Program.Main(String[] args) in
> C:\Projects\Constellation.HTS\ChemRegistration\OpenBabelTesting\Program.cs:line
> 10
> at System.AppDomain._nExecuteAssembly(Assembly assembly, String[] args)
> at System.AppDomain.ExecuteAssembly(String assemblyFile, Evidence
> assemblySecurity, String[] args)
> at Microsoft.VisualStudio.HostingProcess.HostProc.RunUsersAssembly()
> at System.Threading.ThreadHelper.ThreadStart_Context(Object state)
> at System.Threading.ExecutionContext.Run(ExecutionContext
> executionContext, ContextCallback callback, Object state)
> at System.Threading.ThreadHelper.ThreadStart()
> InnerException: System.TypeInitializationException
> Message="The type initializer for 'SWIGExceptionHelper' threw an
> exception."
> Source="OBDotNet"
> TypeName="SWIGExceptionHelper"
> StackTrace:
> at OpenBabel.openbabelPINVOKE.SWIGExceptionHelper..ctor()
> at OpenBabel.openbabelPINVOKE..cctor()
> InnerException: System.DllNotFoundException
> Message="Unable to load DLL 'openbabel': The specified module could not be
> found. (Exception from HRESULT: 0x8007007E)"
> Source="OBDotNet"
> TypeName=""
> StackTrace:
> at
> OpenBabel.openbabelPINVOKE.SWIGExceptionHelper.SWIGRegisterExceptionCallbacks_openbabel(ExceptionDelegate
> applicationDelegate, ExceptionDelegate arithmeticDelegate,
> ExceptionDelegate divideByZeroDelegate, ExceptionDelegate
> indexOutOfRangeDelegate, ExceptionDelegate invalidCastDelegate,
> ExceptionDelegate invalidOperationDelegate, ExceptionDelegate ioDelegate,
> ExceptionDelegate nullReferenceDelegate, ExceptionDelegate
> outOfMemoryDelegate, ExceptionDelegate overflowDelegate, ExceptionDelegate
> systemExceptionDelegate)
> at OpenBabel.openbabelPINVOKE.SWIGExceptionHelper..cctor()
> InnerException:
> 
> I thought it had something to do with openbabel.dll but I could not add it
> as a reference to my project or the GAC. Any ideas?
> 
> Thanks in advance,
> Bob
> 
> 
> ------------------------------------------------------------------------------
> Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco,
> CA
> -OSBC tackles the biggest issue in open source: Open Sourcing the
> Enterprise
> -Strategies to boost innovation and cut costs with open source
> participation
> -Receive a $600 discount off the registration fee with the source code:
> SFAD
> http://p.sf.net/sfu/XcvMzF8H
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> 
> 

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Re: [OpenBabel-scripting] Reactions in OpenBabel

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

On Mar 25, 2009, at 10:06 AM, Hasnain Lakhani wrote:

> Is there any way to use SMIRKS to carry out reactions in OpenBabel?  
> my search of the API didn't reveal anything clear.

Some support for reaction SMILES are in OBChemTsfm -- which is used  
internally for pH adjustment:
http://openbabel.org/api/2.2.0/classOpenBabel_1_1OBChemTsfm.shtml

Hope that helps,
-Geoff

[OpenBabel-scripting] Reactions in OpenBabel

[Hasnain L. <m.h...@gm...>]

I've been looking to write some simple software to simulate organic chemical
reactions for my HS syllabus. I came across OpenBabel, and it seems well
suited to the purpose, However I'm not sure how to edit molecules.

Is there any way to use SMIRKS to carry out reactions in OpenBabel? my
search of the API didn't reveal anything clear.

If that's not possible, how would I go about editing molecules? For example,
changing CH3CHO into CH3COOH?

Re: [OpenBabel-scripting] Can OpenBabel calculate intermolecular hydrogen bonds?

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

Hello Steve,

First of all, the supplied 1hv6_trimer_001_model_.pdb does seem to
have some serious problems. OpenBabel generates several warnings
reading it in and I'm not sure that it's a 100% valid structure. I
also note that the GOLD's GUI has trouble, and in fact, leaves out
several atoms in the molecule. I recommend you look at the PDB
specification and fix any errors with this file. You should also
contact the authors of whatever software generated this file.

In any case, assuming that the input is valid, here's some code to get
you started. Note that it all relies on the validity of the SMARTS
strings, which may need some tweaking (see comments on the blog post
referred to in the script).

Here's a link: http://gist.github.com/81077

Regards,
   Noel

2009/3/13 Steven Platt <Ste...@hp...>:
> I'll take your generous offer Noel.
> Attached are a couple of examples (1hv6 & 2auy) of a protein & ligand,
> with each pair in the same coordinate frame. The proteins are in a
> slightly weird format due to necessary prior processing by a docking
> algorithm.
>
> Excuse the lack of familiarity, but does OB also allow measurement of
> atom angles? I'd like to include this criterion in the Hbond detection,
> although I'm happy to have a bash & modify your script.
>
> Thanks
>
> Steve
>
> -----Original Message-----
> From: Noel O'Boyle [mailto:bao...@gm...]
> Sent: 13 March 2009 12:27
> To: Steven Platt
> Cc: ope...@li...
> Subject: Re: [OpenBabel-scripting] Can OpenBabel calculate
> intermolecular hydrogen bonds?
>
> Assuming that you already have the coordinates of the ligand in
> relation to the protein, you can script this quite easily. You just
> need to write a loop over the atoms of the ligand, and another loop
> over the atoms of the protein, see if they have the right atom types
> for hydrogen bonding (atom types are available from OB), and see if
> the heavy atom distance is < 3.0 or 3.1 Ang distance.
>
> In fact, I'd like to have a script that does this too, so if you send
> me (off list) an example PDB and ligand file, I will throw a prototype
> script together and report back to the list.
>
> An alternative is PyMol, which I guess has automatic hydrogen bond
> detection or so (I have never used PyMol so I'm not sure).
>
> Regards,
>   Noel
>
> 2009/3/12 Steven Platt <Ste...@hp...>:
>> Hi,
>>
>> Given a small carbohydrate ligand and a relatively large protein, can
>> OpenBabel calculate the hydrogen bonds between these two molecules and
>> report them to a file?
>>
>> I realise that there are GUIs that will do this, but I've got dozens
> of
>> ligand/protein combinations and would like to script the process.
>>
>> It's worth saying that I've got no experience with OB, so simple
> answers
>> please.
>>
>> Thanks
>>
>> Steve
>>
>> Dr Steven Platt
>>
>> Bioinformatics Support Coordinator
>>
>> Statistics, Modelling and Bioinformatics
>>
>> Health Protection Agency
>>
>> Centre for Infections
>>
>> 61 Colindale Avenue
>>
>> London
>>
>> NW9 5EQ
>>
>> 0208 327 6618
>>
>> www.hpa.org.uk/bioinformatics
>>
>> ________________________________
>>
>>
> ************************************************************************
> **
>> The information contained in the EMail and any attachments is
> confidential
>> and intended solely and for the attention and use of the named
> addressee(s).
>> It may not be disclosed to any other person without the express
> authority of
>> the HPA, or the intended recipient, or both. If you are not the
> intended
>> recipient, you must not disclose, copy, distribute or retain this
> message or
>> any part of it. This footnote also confirms that this EMail has been
> swept
>> for computer viruses, but please re-sweep any attachments before
> opening or
>> saving. HTTP://www.HPA.org.uk
>>
> ************************************************************************
> **
>>
>>
> ------------------------------------------------------------------------
> ------
>> Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM)
> are
>> powering Web 2.0 with engaging, cross-platform capabilities. Quickly
> and
>> easily build your RIAs with Flex Builder, the Eclipse(TM)based
> development
>> software that enables intelligent coding and step-through debugging.
>> Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com
>> _______________________________________________
>> OpenBabel-scripting mailing list
>> Ope...@li...
>> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>>
>>
>
>
> -----------------------------------------
> **************************************************************************
> The information contained in the EMail and any attachments is
> confidential and intended solely and for the attention and use of
> the named addressee(s). It may not be disclosed to any other person
> without the express authority of the HPA, or the intended
> recipient, or both. If you are not the intended recipient, you must
> not disclose, copy, distribute or retain this message or any part
> of it. This footnote also confirms that this EMail has been swept
> for computer viruses, but please re-sweep any attachments before
> opening or saving. HTTP://www.HPA.org.uk
> **************************************************************************

Re: [OpenBabel-scripting] [openbabel-scripting] [OpenBabel & Pybel] Atomic Types Automatically Changed

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

2009/3/18 Geoffrey Hutchison <ge...@ge...>:
>
> On Mar 18, 2009, at 6:14 AM, Noel O'Boyle wrote:
>
>>> Can we read a molecule with pybel with an option "read only the mol2 file
>>> without changing anything" ?
>>
>> I'm afraid not.
>
> Does pybel support the "copy" format?

Interesting - I didn't know about this (but I don't think this would
help here). We should probably create a wiki page with a list of
convenience formats (that is, formats that are not related to
particular programs).

Anyway, Pybel supports it, but I get an OpenBabel error: "Not a valid
output format". I presume it's not compatible with the Read/Write
functions used by the scripting interfaces. Will I file a proper bug
and see what happens?

> Cheers,
> -Geoff
>

Re: [OpenBabel-scripting] [openbabel-scripting] [OpenBabel & Pybel] Atomic Types Automatically Changed

[laurent.personal <lau...@gm...>]

Hello,

I am using babel 2.2.0 and I will update it to the 2.2.1 version.
Ty for the fast answer :)
Cheers,

Laurent


baoilleach wrote:
> 
> 2009/3/18 laurent.personal <lau...@gm...>:
>>
>> Hello
>>
>> I am using openbabel for a project (convert molec in different formats
>> ...).
>> Besides, I have to do some scripts in order to modify some molecules of
>> my
>> DB. I use pybel to do this.
>>
>> My problem is that pybel automatically changes some atomic types in
>> molecule
>> of my DB ... and it shouldn't do it. It replaces some carbons (C2 or
>> others)
>> by the type C.cat. The last is for the guanidium group but I don't have a
>> such group in my DB.
> 
> This bug has been fixed in the latest version of OpenBabel.
> 
>> I did a basic script in order to verify this :
>>
>> [quote]
>> #!/usr/bin/python
>> import openbabel
>> import pybel
>> for mol in pybel.readfile("mol2", "molec_test.mol2"):
>>        outputfile = pybel.Outputfile("mol2", "molec_pybel.mol2",
>> overwrite=True)
>>        outputfile.write(mol)
>>        outputfile.close()
>> [/quote]
>>
>> The input/output structure files are uploaded here.
>> http://www.nabble.com/file/p22574797/molec_pybel.mol2 molec_pybel.mol2
>> http://www.nabble.com/file/p22574797/molec_test.mol2 molec_test.mol2
>>
>> Can we read a molecule with pybel with an option "read only the mol2 file
>> without changing anything" ?
> 
> I'm afraid not.
> 
>> TIA for your answer,
>>
>> Cheers,
>>
>> Laurent
>> --
>> View this message in context:
>> http://www.nabble.com/-OpenBabel---Pybel--Atomic-Types-Automatically-Changed-tp22574797p22574797.html
>> Sent from the openbabel-scripting mailing list archive at Nabble.com.
>>
>>
>> ------------------------------------------------------------------------------
>> Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are
>> powering Web 2.0 with engaging, cross-platform capabilities. Quickly and
>> easily build your RIAs with Flex Builder, the Eclipse(TM)based
>> development
>> software that enables intelligent coding and step-through debugging.
>> Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com
>> _______________________________________________
>> OpenBabel-scripting mailing list
>> Ope...@li...
>> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>>
> 
> ------------------------------------------------------------------------------
> Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are
> powering Web 2.0 with engaging, cross-platform capabilities. Quickly and
> easily build your RIAs with Flex Builder, the Eclipse(TM)based development
> software that enables intelligent coding and step-through debugging.
> Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> 
> 

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Re: [OpenBabel-scripting] [openbabel-scripting] [OpenBabel & Pybel] Atomic Types Automatically Changed

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

On Mar 18, 2009, at 6:14 AM, Noel O'Boyle wrote:

>> Can we read a molecule with pybel with an option "read only the  
>> mol2 file
>> without changing anything" ?
>
> I'm afraid not.

Does pybel support the "copy" format?

Cheers,
-Geoff

Re: [OpenBabel-scripting] [openbabel-scripting] [OpenBabel & Pybel] Atomic Types Automatically Changed

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

2009/3/18 laurent.personal <lau...@gm...>:
>
> Hello
>
> I am using openbabel for a project (convert molec in different formats ...).
> Besides, I have to do some scripts in order to modify some molecules of my
> DB. I use pybel to do this.
>
> My problem is that pybel automatically changes some atomic types in molecule
> of my DB ... and it shouldn't do it. It replaces some carbons (C2 or others)
> by the type C.cat. The last is for the guanidium group but I don't have a
> such group in my DB.

This bug has been fixed in the latest version of OpenBabel.

> I did a basic script in order to verify this :
>
> [quote]
> #!/usr/bin/python
> import openbabel
> import pybel
> for mol in pybel.readfile("mol2", "molec_test.mol2"):
>        outputfile = pybel.Outputfile("mol2", "molec_pybel.mol2", overwrite=True)
>        outputfile.write(mol)
>        outputfile.close()
> [/quote]
>
> The input/output structure files are uploaded here.
> http://www.nabble.com/file/p22574797/molec_pybel.mol2 molec_pybel.mol2
> http://www.nabble.com/file/p22574797/molec_test.mol2 molec_test.mol2
>
> Can we read a molecule with pybel with an option "read only the mol2 file
> without changing anything" ?

I'm afraid not.

> TIA for your answer,
>
> Cheers,
>
> Laurent
> --
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