/Cheminf101/search.html#what-is-indexing
Thanks,
Andi
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Thanks Noel, I'll take a look at that code.
-Andi
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g, 6 and 7 are double and triple bonds respectively in a ring
structures. Is this correct?
Thanks,
-Andi
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I see, I'm pretty close to getting it to work, but I'm having a little
trouble with the CompileMoleculeQuery as I'm still learning C++.
Instead of inserting code, i've inserted a screenshot, this way it's much
readable...
Thanks,
Andi
I'm not sure if the Compil
some reason I am getting
a duplicate symbol error, and not sure why since QueryAtom is the only class
this method is defined
-Andi
This is just a reference of the earlier code
http://pastebin.com/k6Gy0zY7 http://pastebin.com/k6Gy0zY7
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file simply takes const OBBitVec &mask type.
Passing an integer in this case, would that suffice?
Thanks again,
Andi
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idea what might be causing this?
-Andi
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.
Is it possible to add extra conditions to check their bonds first, then the
atoms?
-Andi
I've included the two molecules for visualization purposes
http://forums.openbabel.org/file/n3391174/1-0.png
http://forums.openbabel.org/file/n3391174/1-1.png
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yAtom and OBQueryBond for some reason it's still not
finding a match between the two molecules and I can't really see where the
problem may be.
The two molecules are located above this reply and i've included the code at
this link.
http://pastebin.com/y877Vivb
Thanks in advance,
Never mind everyone, figured it out. Sorry about the trouble.
Andi
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Hey Craig, the fragments that I need are indeed for similarity.
Any thoughts?
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---
:
OBIsomorphismMapper* mapper = OBIsomorphismMapper::GetInstance(query);
OBIsomorphismMapper::Mapping map;
mapper->MapFirst(ethane, map);
Thanks,
Andi
ethane
http://forums.openbabel.org/file/n3400206/1-0.png
pentane
http://forums.openbabel.org/file/n3400206/1-9.png
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Ahh I see. So to make sure I understand this correctly, the number of bits
masked, is the number of atoms for possible consideration for the matching.
Is this a correct interpretation?
Thanks a lot Tim.
Andi
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erent
combinations of that particular size. (i.e if i wanted to match just 3 atoms
out of 5, then there would be 3 choose 5 combination variations with only
three atomsso there would 8 possible combinations)
Thanks again for your clarification,
Andi
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int nodeIndex;
Node* node; //Node reference
Node
int nodeID;
NSString* nodeLabel;
int type;
BOOL marked;
NSMutableArray* AdjEdges;
Thanks,
Andi
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it not be considered aromatic any longer?
Thanks,
Andi
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i can make some sense to what
they represent, but no luck.
Thanks,
Andi
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>If you're adding atoms and bonds programmatically, you should wrap the
modifications with:
>mol.BeginModify();
>// make changes
>mol.EndModify();
>The EndModify() call will reset aromatic perception.
Hi Geoff,
I tried doing that, but still doesn't seem to work. The only thing I can
think of that
b->SetBondOrder(1);
else if( b->GetBondOrder() == 11)
b->SetBondOrder(2);
else if ( b->GetBondOrder() == 12 )
b->SetBondOrder(3);
}
mols[0]->EndModify();
Is this not a correct way to do the begin and end modify function call?
Thanks,
?
The way I'm handling the problem now is by using an atom type that is not
possible to be in my molecules. I know it's not the best solution but hope
some of you can shine some light into this.
Thanks,
Andi
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I'm
getting a match in the ring.
http://forums.openbabel.org/file/n4404825/molecule.png
http://forums.openbabel.org/file/n4404825/fragment.png
Is this correct?
Thanks,
Andi
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Sent fro
>Yes, you should get all unique matches there are. The query doesn't
specify that the bond should be in a ring or not.
Yup, you're absolutely correct. What I did is subclass the
OBQueryAtom/OBQueryBond to get custom behavior
-Andi
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that explains
the file format.
http://forums.openbabel.org/file/n4655246/manual.pdf manual.pdf
Thanks,
Andi
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already build in
functionality).
Thanks,
Andi
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Great, thanks everyone for all your insights.
-Andi
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mage you'll see two simple examples.
<http://forums.openbabel.org/file/n4655904/example.png>
Can anyone see if I am doing something wrong or why is able to find the one
method but not the other. Greatly appreciated!
-Andi
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t the wrong way?
Much appreciated,
-Andi
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this?
Thanks,
-Andi
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Everyone hates
sing the mol and atom classes and overriding the operator+() and
clone() methods respectively in each of the classes.
Thanks,
-Andi
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ed to if someone could point out a different route.
my solution:
<http://forums.openbabel.org/file/n4655930/mysolution.png>
Much appreciated,
-Andi
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.
}
/
I think this assumes the order of atoms in the vector corresponding with
their indices. Is this a safe assumption for future?
Much appreciated,
-Andi
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attached file), I
get a match, but looking at the two files, I don't see how it could be.
Am I missing something?
Thanks in advance.
-Andi
Images:
progenitor.pdf <http://forums.openbabel.org/file/n4656194/progenitor.pdf>
10633.pdf <http://forums.openbabel.org/file/n4656194/10633.pdf&
2.3.2?
Thanks,
Andi
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Hi all,
Did the forums address changed in the last couple of days?
This site looks like it's no longer valid:
forums.openbabel.org<http://forums.openbabel.org/>
Thanks,
Andi
<http://forums.openbabel.org/>
causes the linking error. If the compiler setting is
switched to the setting "Compiler Default or Gnu C++ standard library", both of
these options will build correctly. If one is build a project from the command
line, clang++ with -std=c++11 option is sufficient…it knows how to find
-s
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