2.3.2?
Thanks,
Andi
--
View this message in context:
http://forums.openbabel.org/Molecule-matching-via-OBIsomorphismMapper-tp4656194p4656195.html
Sent from the General discussion mailing list archive at Nabble.com
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&
.
}
/
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
--
View this message in context:
http://forums.openbabel.org/Accessing-newly-added-atoms-bonds-when-combining-two-molecules-tp4655937
ed to if someone could point out a different route.
my solution:
<http://forums.openbabel.org/file/n4655930/mysolution.png>
Much appreciated,
-Andi
--
View this message in context:
http://forums.openbabel.org/Bond-generic-data-tp4655930.html
Sent from the General discuss
sing the mol and atom classes and overriding the operator+() and
clone() methods respectively in each of the classes.
Thanks,
-Andi
--
View this message in context:
http://forums.openbabel.org/Find-Mol-atom-with-attribute-tp4655912p4655916.html
Sent from the General discussion mailing list arc
this?
Thanks,
-Andi
--
View this message in context:
http://forums.openbabel.org/Find-Mol-atom-with-attribute-tp4655912p4655914.html
Sent from the General discussion mailing list archive at Nabble.com.
--
Everyone hates
t the wrong way?
Much appreciated,
-Andi
--
View this message in context:
http://forums.openbabel.org/Find-Mol-atom-with-attribute-tp4655912.html
Sent from the General discussion mailing list archive at Nabble.com.
--
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
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
--
View this message in context:
http://forums.openbabel.org/At
Great, thanks everyone for all your insights.
-Andi
--
View this message in context:
http://forums.openbabel.org/File-format-tp4655246p4655256.html
Sent from the General discussion mailing list archive at Nabble.com
already build in
functionality).
Thanks,
Andi
--
View this message in context:
http://forums.openbabel.org/File-format-tp4655246p4655253.html
Sent from the General discussion mailing list archive at Nabble.com.
--
that explains
the file format.
http://forums.openbabel.org/file/n4655246/manual.pdf manual.pdf
Thanks,
Andi
--
View this message in context:
http://forums.openbabel.org/File-format-tp4655246.html
Sent from the General discussion mailing list archive at Nabbl
>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
--
View this message in context:
http://forums.
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
--
View this message in context:
http://forums.openbabel.org/Subgraph-isomorphism-tp4404825p4404825.html
Sent fro
?
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
--
View this message in context:
http://forums.openbabel.org/Custom
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,
>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
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/>
i can make some sense to what
they represent, but no luck.
Thanks,
Andi
--
View this message in context:
http://forums.openbabel.org/Atomic-Type-tp3419654p3419654.html
Sent from the General discussion mailing list archive at Nabble.com
it not be considered aromatic any longer?
Thanks,
Andi
--
View this message in context:
http://forums.openbabel.org/Setting-Aromaticity-tp3416960p3416960.html
Sent from the General discussion mailing list archive at
int nodeIndex;
Node* node; //Node reference
Node
int nodeID;
NSString* nodeLabel;
int type;
BOOL marked;
NSMutableArray* AdjEdges;
Thanks,
Andi
--
View this message in context:
http://forums.openbabel.org/Me
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
--
View this message in context:
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
--
View this message in context:
http://forums.openbabel.org/IsomorphismMapper
:
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
--
View this message
Hey Craig, the fragments that I need are indeed for similarity.
Any thoughts?
--
View this message in context:
http://forums.openbabel.org/Fragment-indexing-and-generation-tp3385311p3399439.html
Sent from the General discussion mailing list archive at Nabble.com.
---
Never mind everyone, figured it out. Sorry about the trouble.
Andi
--
View this message in context:
http://forums.openbabel.org/Isomorphism-between-cyclo-pentane-and-pentane-tp3389855p3392737.html
Sent from the General discussion mailing list archive at Nabble.com
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,
.
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
--
View this message in context:
idea what might be causing this?
-Andi
--
View this message in context:
http://forums.openbabel.org/Isomorphism-between-cyclo-pentane-and-pentane-tp3389855p3390410.html
Sent from the General discussion mailing list archiv
file simply takes const OBBitVec &mask type.
Passing an integer in this case, would that suffice?
Thanks again,
Andi
--
View this message in context:
http://forums.openbabel.org/Isomorphism-between-cyclo-pentane-and-pentane-tp3389855p3390391.html
Sent from the General discussion mai
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
--
View this message in context:
http://forums.openbabel.org
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
g, 6 and 7 are double and triple bonds respectively in a ring
structures. Is this correct?
Thanks,
-Andi
--
View this message in context:
http://forums.openbabel.org/Isomorphism-between-cyclo-pentane-and-pentane-tp3389855p3389855.html
Sent from the General discussion mailing list archive at
Thanks Noel, I'll take a look at that code.
-Andi
--
View this message in context:
http://forums.openbabel.org/Fragment-indexing-and-generation-tp3385311p3389824.html
Sent from the General discussion mailing list archive at Nabbl
/Cheminf101/search.html#what-is-indexing
Thanks,
Andi
--
View this message in context:
http://forums.openbabel.org/Fragment-indexing-and-generation-tp3385311p3385311.html
Sent from the General discussion mailing list archive at Nabble.com
35 matches
Mail list logo
