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Re: [OpenBabel-scripting] (no subject)
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From: Noel O'B. <bao...@gm...> - 2010-03-11 15:18:43
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On 11 March 2010 15:01, Jason Power <pow...@gm...> wrote:
> Sorry about that, didn't pay attention..
>
> With this:
> import openbabel
> ring3 = openbabel.OBMol()
> ra1=ring3.NewAtom()
> ra2=ring3.NewAtom()
> ra3=ring3.NewAtom()
> ra1.SetAtomicNum(6)
> ra2.SetAtomicNum(6)
> ra3.SetAtomicNum(6)
> ring3.AddBond(1, 2, 1)
> ring3.AddBond(2, 3, 1)
> ring3.AddBond(3, 1, 1)
> print len(ring3.GetSSSR())
> builder = openbabel.OBOp.FindType("Gen3D")
> builder.Do(ring3)
> print len(ring3.GetSSSR())
> ra1.SetVector(1,0,0)
> ra2.SetVector(0,-1,0)
> ra3.SetVector(0,1,0)
>
> I now get the proper behavior of GetSSSR(), but I still get a segfault when I
> try to move the atoms. I assume this is because the pointers are not valid
> anymore. Why is this?
I'm not sure. I have a feeling it would work fine from C++, because
although the builder adds new atoms (Hs), it adds them at the end of
the molecule and doesn't disturb the existing atoms. The way to find
out would be the write the same code in C++ and step through it. In
any case, it should work fine if you get the atom again with
ring3.GetAtom(1).SetVector(whatever)
> Also, why would it work when I add a bond as you described and not work when I
> did it the way I was doing it? Does AddBond make some connections that I
> wasn't doing?
No that's not it. It's a limitation of the SWIG bindings. There are no
pointers in Python, so what you have is only pretending to be a
pointer as well as it can. In C++ your code would work as expected.
I'll add some notes to the documentation pointing people in the
direction of AddBond(). Perhaps I should also remove NewBond() from
the bindings.
> Thanks, I think with this I can get my code to work!
> Jason
>
> On Thursday 11 March 2010 09:52:27 am Noel O'Boyle wrote:
>> (Please cc to list)
>>
>> How about commenting about:
>>
>> ##rb1=ring3.NewBond()
>> ##rb2=ring3.NewBond()
>> ##rb3=ring3.NewBond()
>> ##rb1.SetBegin(ra1)
>> ##rb1.SetEnd(ra2)
>> ##rb2.SetBegin(ra2)
>> ##rb2.SetEnd(ra3)
>> ##rb3.SetBegin(ra3)
>> ##rb3.SetEnd(ra1)
>> ##rb1.SetBO(1)
>> ##rb2.SetBO(1)
>> ##rb3.SetBO(1)
>>
>> and replacing it with:
>>
>> ring3.AddBond(1, 2, 1)
>> ring3.AddBond(2, 3, 1)
>> ring3.AddBond(3, 1, 1)
>>
>> - Noel
>>
>> On 11 March 2010 14:28, Jason Power <pow...@gm...> wrote:
>> > Here is something that causes a segfault every time:
>> >
>> > import openbabel
>> > ring3 = openbabel.OBMol()
>> > ra1=ring3.NewAtom()
>> > ra2=ring3.NewAtom()
>> > ra3=ring3.NewAtom()
>> > ra1.SetAtomicNum(6)
>> > ra2.SetAtomicNum(6)
>> > ra3.SetAtomicNum(6)
>> > rb1=ring3.NewBond()
>> > rb2=ring3.NewBond()
>> > rb3=ring3.NewBond()
>> > rb1.SetBegin(ra1)
>> > rb1.SetEnd(ra2)
>> > rb2.SetBegin(ra2)
>> > rb2.SetEnd(ra3)
>> > rb3.SetBegin(ra3)
>> > rb3.SetEnd(ra1)
>> > rb1.SetBO(1)
>> > rb2.SetBO(1)
>> > rb3.SetBO(1)
>> > print len(ring3.GetSSSR()) # OUTPUT: 0
>> > builder = openbabel.OBOp.FindType("Gen3D")
>> > builder.Do(ring3)
>> > print len(ring3.GetSSSR()) # OUTPUT: 1
>> > ra1.SetVector(1,0,0)
>> > ra2.SetVector(0,-1,0)
>> > ra3.SetVector(0,1,0)
>> >
>> > Sometimes is segfaults on ra2.SetVector(0,-1,0) and sometimes on
>> > ra3.SetVector(0,1,0). Also, I don't understand why the first call the
>> > GetSSSR() doesn't return the right number.
>> >
>> > Thanks again!
>> > Jason
>> >
>> > On Thursday 11 March 2010 04:48:45 am you wrote:
>> >> Where do beginAtom and endAtom come from in your code snippet.
>> >>
>> >> The best thing would be if you can you create a simple and short
>> >> self-contained script that exhibits the problem.
>> >>
>> >> - Noel
>> >>
>> >> On 11 March 2010 03:59, Jason Power <pow...@gm...> wrote:
>> >> > Hi all,
>> >> >
>> >> > I am currently developing a pure-python 2-D molecule editor for use
>> >> > within another project I am currently working on. To begin with I
>> >> > decided to use the OBMol object as a model, thinking it would save me
>> >> > time and effort. However, I have run into a variety of issues that I'm
>> >> > not sure are due to my own misunderstandings, limitations of the
>> >> > python bindings, or bugs.
>> >> >
>> >> > I am building the OBMol object slowly over time as the user adds atoms
>> >> > and bonds. So I have a numerous places where I basically call
>> >> >
>> >> > self.mol.BeginModify()
>> >> > bond = self.mol.NewBond()
>> >> > bond.SetBegin(beginAtom)
>> >> > bond.SetEnd(endAtom)
>> >> > self.mol.EndModify()
>> >> >
>> >> > and
>> >> >
>> >> > self.mol.BeginModify()
>> >> > newAtom = self.mol.NewAtom()
>> >> > newAtom.SetVector(self.translateToAtomCoords(pos))
>> >> > newAtom.SetAtomicNum(atomicNum)
>> >> > self.mol.EndModify()
>> >> >
>> >> > and similar to delete. I find that with these calls when I go on to do
>> >> > other interesting things it fails, often as a segfault. Also, if I try
>> >> > to make a call like self.mol.GetSSSR() even though there is a ring, (I
>> >> > can trace the indices of the ends of the bonds myself), it returns a
>> >> > zero length list.
>> >> >
>> >> > I have found that if I call self.builder.Do(self.mol) before I run
>> >> > GetSSSR() it will return the right numbers, but I do not want to build
>> >> > the full 3-D coords, and worse, self.builder.Do(self.mol) randomly
>> >> > segfaults.
>> >> >
>> >> > Am I doing something wrong? Is there something that I am missing while
>> >> > building the molecule?
>> >> >
>> >> > Thanks for you help!
>> >> > Jason
>> >> >
>> >> >
>> >> > ----------------------------------------------------------------------
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>> >> > http://p.sf.net/sfu/intel-sw-dev
>> >> > _______________________________________________
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>> >> > Ope...@li...
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>>
>
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