Re: [OpenBabel-scripting] (no subject)

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

(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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>