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How do I represent a chemical structure in a matrix format in Matlab? Can I input a chemical structure into Matlab using the S.M.I.L.E.S notation?

I have to specify the connectivity of different atoms with others and type of bonds between them. I have to write the structure in matrix form, so that it can be utilized in some linear programming. For example, if one atom is connected to another atom I have to store 1 in matrix otherwise 0 (binary variables). I need to develop back end code for my purpose to design some molecules using this approach. As of now I am dealing with 2D structures.

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    $\begingroup$ what do you need it for? Depending on the need, different representations may be adequate, so, please, provide more info. $\endgroup$
    – permeakra
    Jul 15 '14 at 9:40
  • $\begingroup$ > utilize that in some linear programming | it still not enough. There are tens of ways to store molecular structure in matrix format. The problem arises from the fact that molecules are 3-d flexible objects, so you have to specify explicitly what molecular traits are critical for you. AFAIK Matlab does not have tools explicitly designed to read molecular data in any format (though it is not personal experience but second-hand knowledge). However openbabel allows conversions between tens of formats and some are either very simple plain text or xml-based, that's the only advice I can get now. $\endgroup$
    – permeakra
    Jul 15 '14 at 12:03
  • $\begingroup$ Ok, I got your case, here is the deal. There is no good solution for your problem (and people worked on it since start of computer era) The best approach I know is to develop library of 3d fragments and combine them using genetic algorithm approach, building molecular surface with desired electrostatic field piece by piece. The details may vary, for example the surface may be provided implicitly in form of target protein. 2d approach has shown .... inadequacy. In case of integral properties like melting points extrapolation from known structures still works better then computers.\ $\endgroup$
    – permeakra
    Jul 16 '14 at 7:19
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    $\begingroup$ @permeakra I would be delighted to upvote your comments, if you converted them into an answer (and then the comments can be removed). $\endgroup$ Jul 16 '14 at 11:21
  • $\begingroup$ @permeakra i would be doing the things suggested by you like GA approach and so later on..but the thing is even before to proceed to that step i need to input the structure into a databse(or an arrray ),which i am unable to do.. $\endgroup$
    – Kishore
    Jul 16 '14 at 11:58
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Are the use of MATLAB (or OCTAVE) and a self-designed molecular representation mandatory for you project?

Established 2D- and 3D representations for molecules beyond a connectivity matrix, i.e. with coordinates, (partial) charges, annotation of isotopes, etc. exist, such as in the form of the Chemical Markup Language (CML).

In addition, well-documented toolkits, frameworks and modules are available to operate on these data are available for C++, Java, Perl, Python, and Ruby.

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  • $\begingroup$ i have developed some part of code in MATLAB for my project...it would be better if i proceed with matlab itself.. $\endgroup$
    – Kishore
    Jul 17 '14 at 4:09
  • $\begingroup$ how can we proceed with coding in python?? i never used python before.. $\endgroup$
    – Kishore
    Jul 17 '14 at 4:11
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    $\begingroup$ @Kishore for specific programming questions I recommend StackOverflow, however make sure to read their Help Center so your question isn't closed $\endgroup$ Jul 17 '14 at 6:28

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