Nabble - Open Babel

Re: OBPairData problem

2009-12-09T16:09:21Z

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 <loris.moretti@chem.ox.ac.uk> 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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From forum: openbabel-scripting

formats plugin

2009-12-08T09:13:39Z

Hi,

I just installed ibabel and openbabel for Mac... I am trying to go
through the steps of the tutorial on fingerprints and tanimoto
similarity, but there seems to be something wrong with the formats
plugin. With -HAll I get the message that the formats is not a
recognized plugin type. Do I need to install this plugin separately?
Thanks,
Irene

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From forum: openbabel-discuss

Re: openbabel 2.2.3 (windows) crashed while reading in large PDB formatted file

2009-12-07T18:36:22Z

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

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Re: openbabel 2.2.3 (windows) crashed while reading in large PDB formatted file

2009-12-07T05:09:52Z

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
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Re: openbabel 2.2.3 (windows) crashed while reading in large PDB formatted file

2009-12-07T01:18:17Z

2009/12/6 qiancheng shen <qianchengshen@...>:

> 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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>

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From forum: openbabel-scripting

openbabel 2.2.3 (windows) crashed while reading in large PDB formatted file

2009-12-05T21:52:33Z

-------------------------------
   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.

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From forum: openbabel-discuss

openbabel 2.2.3 (windows) crashed while reading in large PDB formatted file

2009-12-05T19:28:42Z

From forum: openbabel-scripting

openbabel 2.2.3 (windows) crashed while reading in large PDB formatted file

2009-12-04T07:20:52Z

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.

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