[Rdkit-devel] I found Bug

[Akihiro Y. <aki...@ya...>]

Dear developers,

Nice to meet you. I am a japanese researcher for computational chemistry,
and I am newly studying programming of cheminformatics. Therefore I am
studying RDKit code. I am very impressed by your effective, exciting, and
beautiful programs. I hope you go to continue to develop RDKit in a long
time.

And what I would like to say is I found a bug in RDKit. please see around
203th-line of RDKit_Q22009_1/Code/GraphMol/Depictor/EmbeddedFrag.cpp. 

----------Orignal--------------
d_eatoms[aid].nbr1 = nb1;
d_eatoms[aid].nbr1 = nb2;
-------------------------------

----------Correct?-------------
d_eatoms[aid].nbr1 = nb1;
d_eatoms[aid].nbr2 = nb2;
-------------------------------

This code makes a bug in case of the following (rare) case. I found it when
I am reading RDKitQ1_2009, but I think it is not be fixed yet in
RDKitQ2_2009.

When 4 atoms(e.g. A, B, C and E below) are already assigned their
coordinates, and will add the coordinate of D, RDKit makes invalid results.
(This is because nb2 is not changed from nb2=0.)

(And I found that you changed the initial value of nb2=0 instead of nb2=-1
in RDKitQ1_2009. I think nb2=-1 is preferred rather than nb2=0)

   B
   |
   |
A--E---C
   |
   |
   D

Best regard.

Akihiro Yokota



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