[Kalzium] Molecular Viewer Bug

[Benoit Jacob]

OK, I admit I'm a bit lost.
Can you replace the body of Color::set(const OpenBabel::OBAtom *atom) as
follows:

void Color::set(const OpenBabel::OBAtom *atom)
{
   if (!atom)
     return;

         std::vector<double> rgb = etab.GetRGB( atom->GetAtomicNum() );
         m_red = rgb[0];
         m_green = rgb[1];
         m_blue = rgb[2];
         m_alpha = 1.0;

 	qDebug()<< "atomic num = " << atom->GetAtomicNum();
 	qDebug()<< "rgb = " << m_red <<","<<m_green<<","<<m_blue;
}

and paste the exact output?

Can you join #kalzium so we can have a chat?

Benoit

On Sat, 25 Aug 2007, Johannes Simon wrote:

>> Let's find out why. Edit the body of this method: void Color::set(const
>> OpenBabel::OBAtom *atom) add add qDebug()'s to see what's going on. Is the
>> if(!atom) exiting the method prematuredly? If not, can you check the
>> std::vector rgb returned by OpenBabel?
> Same colors there: m_red = 0, m_green = 0, m_blue = 0, m_alpha = 1.
> I also checked atom->GetAtomicNum() which it passes to etab.getRGB(),
> and I found that it is the correct atomic number. So I took a look into
> the openbabel source code, src/data.cpp in the openbabel tree, to be
> exactly, and there I found this in OBElementTable::GetRGB(int
> atomicnum):
>
> if (atomicnum < 0 || atomicnum > static_cast<int>(_element.size()))
>   {
>     colors.push_back(0.0);
>     colors.push_back(0.0);
>     colors.push_back(0.0);
>     return(colors);
>   }
> So I had openbabel output _element.size() which is 117, so this does not
> seem to be the problem. After all, I should have added more debug
> output, but it simply takes to long to compile to play with it to find
> out where it starts returning wrong numbers.
>
>>> Changing m_red (or m_gree,m_blue,m_alpha)
>>> at the beginning of applyAsMaterials() doesn't make any difference at all.
>>
>> Uh, now that's strange. setting m_red to 1 should make a visual
>> difference (everything should look more red, at least not black)! If it
>> doesn't, that's a separate bug. I prefer to believe that we
>> didn't understand each other.
> Ok, my bad. For some reason, the changes just didn't take into effect
> last time I recompiled Kalzium. Now it does show me some white sticks,
> but no actual atoms after all.
>
> Joh
>
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