Talk:Molecular graph

Definition

Very incorrect definition! Please, compare with “Molecular graph” article translated from Russian Wiki:

Molecular graph is connected undirected graph one-to-one corresponded to structural formula of chemical compound so that vertices of the graph correspond to atoms of the molecule and edges of the graph correspond to chemical bonds between these atoms. The concept of the molecular graph is basic concept for computer chemistry and chemical informatics. Like structural formula the molecular graph is a model, and as every model it is incomplete in some detail. In contrast with structural formula the vertices of molecular graph may be unlabeled, in this case molecular graph represents only structure (but not elemental composition) of the molecule. Also, the edges of the graph may be unlabeled, in this case distinctions for the multiple bonds are omitted. Very often the molecular graph represents carbon skeleton of molecule only. This level of abstraction is very useful for solving different chemical tasks by computer.

References.

Chemical Applications of Topology and Graph Theory, ed. by R. B. King, Elsevier, 1983.

For example, molecular graphs may be used to calculate topological index, but neither Wiener index, nor Hosoya index etc is defined for colored vertices and for colored edges.--Tim32 11:03, 15 November 2007 (UTC)[reply]

What exactly do you think is wrong with the definition? --Itub 11:23, 15 November 2007 (UTC)[reply]

"molecular graph or chemical graph": "chemical graph" - wrong name, what about name of graph for chemical reaction?
"A chemical graph is a colored graph" -wrong, usually it is not colored.
"For particular purposes any of the colorings may be ignored" -- usually ignored, and not "any", but "all".
"whose vertices correspond to the atoms of the compound" - incomplete, compare "correspond" (A->B) with "one-to-one correspond" (A<->B).
Also,Molecular graph is connected graph
Also,Molecular graph is undirected graph
etc,see my definition, hope it helps--Tim32 12:49, 15 November 2007 (UTC)[reply]

I think you may be misunderstanding the meaning of "colored". It is a technical term synonymous with labeling. A "colored graph" is one where the nodes have a type (whether it is literally a color, or in the case of chemistry typically an atomic number or atom type). Note that the term "colored" is used in the IUPAC definition. --Itub 13:00, 15 November 2007 (UTC)[reply]

The term chemical graph is used in many books, so it is not wrong. It's just a synonym for what you call molecular graph. Regarding the one-to-one correspondence and the non-directedness, you have a point that those properties should be specified in the article. However, not all chemical graphs are connected. You can perfectly well have a graph for an ion pair or nonbonded complex. --Itub 13:05, 15 November 2007 (UTC)[reply]

Molecular graph is defined for classical molecule only. The ion pair and nonbonded complex and free radical and topological bonded compounds etc. are not classical molecules. Of course, somebody can redefine standard definition to use it for purposes of his/her research. And you can find a lot of original definitions for original investigations. But to write a good article for Wiki you have to select standard definitions for standard tasks. Of course, you can add a few extended definitions also, but obviously you should mark these definitions as “extended” and you should not replace standard definition with extended. The standard task for computer chemistry may be following: “calculate Wiener index for standard classical molecules, for example, benzene, cyclohexane and pyridine.” To do it you can use following data structure for your computer program (in Pascal):

Var MolecularGraph : array [1..6,1..6] of Boolean; {Adjacency matrix: if atoms i,j are bonded, 
then MolecularGraph[i,j]=true, else ...=false}

And you will get the same values of Wiener index for these compounds. Standard topological indices do not recognize double bonds and atoms types (C,N), do not use hydrogen atoms and defined for connected undirected graphs only. Yes, at the same time IUPAC can use colored or labeled graphs for special purposes of chemical informatics, but note, please, these are special tasks, and original definitions.

About the term chemical graph: you did not answer my question “what about name of graph for chemical reaction?” Yes, every book’s author has a right to use original term, or redefine any term etc. If you want to make a puzzle from the Molecular graph article, then go on… --Tim32 10:33, 16 November 2007 (UTC)[reply]

You have an extremely limited vision of the concept of molecular graph. Computing the Wiener index is just one minor application. Molecular graphs are used in all chemical databases for storing structures and searching them, they are used by chemical drawing software, they are used in computer aided organic synthesis, they are used for canonicalization, for chemical file formats, line representations of molecules, isomer enumeration, and probably at least a couple of dozen other applications. All of the applications I mentioned require colored graphs, and most of them use disconnected graphs. I'll go with the definition given by IUPAC and every single textbook I've seen over your idea of what the "standard definition" is. --Itub 11:03, 16 November 2007 (UTC)[reply]

You wrote: "Molecular graphs are used in all chemical databases for storing structures and searching them" - never say "all". Ten years ago I myself used chemical database without molecular graphs. I think you have not info about ALL databases.:-) There is standard definition in the book "Chemical Applications of Topology and Graph Theory, ed. by R. B. King, Elsevier, 1983." IUPAC extends it. As I wrote before "you can add a few extended definitions also". But unfortunately this IUPAC definition is not enough strong to use it even for simple applications like Wiener index. As I wrote: "If you want to make a puzzle from the Molecular graph article, then go on…"---- Tim32 (talk) 18:40, 16 November 2007 (UTC)[reply]

And you did not answer my question “what about name of graph for chemical reaction?” ---- Tim32 (talk) 18:42, 16 November 2007 (UTC)[reply]

"chemical reaction graphs" `'Míkka >t 19:00, 16 November 2007 (UTC)[reply]

to Tim32

Here you again, engaging in endless discussions. Please find reliable sources and write some article text, for God's sake. I did not invent the definition. I provided my references. If you have other researchers who stick to other definitions, please add them. I see nothing unusual nor a big scientific disaster that different people use somewhat differing definitions.

BTW you wrote "Neither Wiener index, nor Hosoya index etc is defined for colored vertices and for colored edges" It is a misleading statement. The correct statement is "The definiton of Wiener index ignores colors of vertices". I've seen many more similar logical fallacies in your talks. I will not comment on them unless you try to put them into article text. `'Míkka >t 19:00, 16 November 2007 (UTC)[reply]

In 16:14, 13 November 2007, Míkka wrote in Talk:Mathematical chemistry#Computer chemistry: "Clearly both terms (and throw chemical graph theory in here) are neologisms, possibly adoped by certain schools, and to figure out what calls what requires real experts in the field who know the history and the inside movements." Dear Míkka, I see from that time you are becoming a real expert in computer chemistry. My congratulations! About the link. Yes, I have other researchers. For example, please, see my article: Trofimov M. I., An Optimization of Procedure for Calculation of Hosoya's Index, J. Math. Chem., 1991, 8, 327. ---- Tim32 (talk) 20:23, 16 November 2007 (UTC)(Michael Trofimov)[reply]

Chukcha not reader, chukcha writer. I don't want to read your chemical articles. I want you to write wikipedia articles. I wrote this one for the sole reason that you prefer bickering in talk pages rather than writing wikipedia articles. `'Míkka >t 23:17, 16 November 2007 (UTC)[reply]

Don't be a "chukcha" - read anything before writing;) You wrote the Hosoya index article just after I had inserted its definition to the matching aricle.--Tim32 (talk) 09:43, 17 November 2007 (UTC)[reply]