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We need to add a CopyData() method in base.cpp:
There's a fundamental problem with using SWIG to wrap methods that
take and keep instances of objects created by the user. The only
example I know …
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- Given a dictionary of {annotation name: set of values}, return all edges from a graph matching all of the conditions (logical AND for annotation names, logical OR for the values in each)
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The Java OBConversion.ReadFile() method reads only one molecule from the supplied file and returns boolean (indicating success or failure), while the Python readfile() method returns an iterator over …
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Hi,
I have been working on a project which included a lot of malformed SMILES been fed to OpenBabel via Python bindings. I have found out a case when OpenBabel crashes with a segmentation fault. Af…
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OpenBabel 2.1.1 library, self-compiled with MinGW on Win32 (XP).
I found that GetMolWt() and GetFormula() never return when e.g. fed with the appended Molecule in MDL V2000 format.
It worked (an…
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When trying to convert a molecule from inchi to inchikey I get a segmentation fault. For example:
Python 2.7.2+ (default, Oct 4 2011, 20:06:09)
[GCC 4.6.1] on linux2
Type "help", "copyright", "…
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Loading a CML file and then attempting to save it as anything else, or the reverse operation (mol -> cml) results in python dying without any error.
Reported by: *anonymous
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Openbabel 2.2.3 (windows) GUI crashes without giving any info while reading in large pdb file. (file size larger than 1.5M). Python program stops with giving "The python.exe has stopped running."
Rep…
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Both from GUI and from command line, trying to search a database with the smarts pattern from Tutorial 4 ([#7D1,#7D2;!+]) fails with a SMARTS error in Open Babel:
```
(test-env) [asteeves @ ahsmbp…
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Following is a description of the bug in chain parsing I found using PyBel. The actual description is from an e-mail exchange with Noel O'Boyle, and I have modified it slightly to make more sense in …