adrien changed the topic of #ocaml to: Discussions about the OCaml programming language | http://www.ocaml.org | OCaml 4.09 release notes: https://caml.inria.fr/pub/distrib/ocaml-4.09/notes/Changes | Try OCaml in your browser: http://try.ocamlpro.com | Public channel logs at http://irclog.whitequark.org/ocaml
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<companion_cube> xvilka: so now you start flamewars on the coq issues, hmm? :)
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<cranix> hello
<cranix> i'm looking for a idiomatic way to implement cyclic non-directed graphs in ocaml
<cranix> tress are easy with recursive algebraic types
<cranix> but how i can implement cycle?
<cranix> in Ada or C i would use pointer
<dmbaturin> Adjacency matrix I guess.
<dmbaturin> Or you can use references for the vertices.
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<cranix> i would prefer not to use matrices because they are much less human readable
<cranix> dmbaturin: references sounds like a way to go (they are something pointer-like, right?)
<cranix> i'm intrested in more functional-style solution if it would be efficient
<companion_cube> or records with mutable fields
<companion_cube> functional way is probably map of adjacency list
<cranix> thanks
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<cranix> i'm afraid that adjacency list will be hard to input by hand or read by human
<cranix> or maybe put cycles as special nodes?
<cranix> but it can blow up easily...
<dmbaturin> cranix: I'm using it in https://baturin.org/code/ocaml-tsort/ Could be worse.
<cranix> thanks, i'm looking at this link
<cranix> btw. is there any good way to serialize cyclic graph?
<cranix> i have idea for hack for s-expressions (akin to SMILES approach to cycles) but not sure how elegant and good is this idea
<cranix> on stackoverflow i found idea with lazy or recursive functions
<cranix> but this graphs will be finite
<cranix> i prefer not to introducte possibility of inifite graphs
<companion_cube> I usually just go for a hashmap of records with mutable fields…
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<Armael> unlike trees, you cannot easily (efficiently) represent graphs using algebraic data types
<Armael> to my knowledge
<cranix> Armael: thanks for information
<cranix> so i will try records
<cranix> and not sure what to think about this approach
<Armael> it's probably too complicated for its own good and awkward to manipulate
<cranix> i need this data structure for representic organic chemical compunds
<dmbaturin> Representing adamantanes or propellanes is going to be fun. :)
<cranix> yes
<cranix> i will start with something simpler
<cranix> or cubane
<cranix> basicly i'm investigating possibilty of using formal grammars and parsers for finding route of synthesis of organic compounds
<cranix> and compiler theory
<cranix> there is risk that i will need context sensitive grammar and there is no information about parsing them
<dmbaturin> And then there's the issue of chirality.
<cranix> right
<cranix> i plan to work on it later
<cranix> but i can define another type of bond
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<dmbaturin> cranix: And then there are rotaxanes and molecular knots, but let's not think too hard about it...
<dmbaturin> The idea is interesting though. I don't know if it's viable or not, but it's in the "huge if true" category.
<cranix> the problem is that chemists do not know anything about computer science and computer sciencists about chemistry so i can not consult anybody
<dmbaturin> cranix: How do you plan to deal with routes that require adding protective groups to be selective?
<cranix> i'm thinking about this problem. i can define set of nonterminals that is 'safe' (no protection required) for given reaction
<cranix> or introduce context to grammar
<cranix> i'm afraid that protective groups will change length on right side of production rule less than left side -> turing completeness
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<cranix> i plan to encode reactions as production rules
<cranix> at first stage i plan some lexer that will convert just atoms into nodes composed of a few atoms that have more sematnics
<cranix> *semantics
<dmbaturin> Are things like LiAlH4 going to be outside of the normal encoding system?
<cranix> yes
<cranix> i'm going to focus on main molecule
<dmbaturin> I think Grignard can be a good smoke test for the system.
<cranix> like we have ester and convert it into alcohol (part from carboxylic acid, assuming that alcohol part is small and not intresting like ethyl group)
<cranix> i'm thinkig about this reaction at first too
<dmbaturin> If it can handle that, it's probably useful enough but that point.
<cranix> then some aldol condensations
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<cranix> i'm thinking about fexofenadine as first 'real world' target
<cranix> it is complex enough
<cranix> but realtively few corner cases
<cranix> i would love to have 1)algebraic structure made of set of organic compund and binary operation as reaction between them
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<cranix> 2)something like turing-compltenesess ie. set of simple substrates and reactions that will generate enough big set of intresting compounds
<dmbaturin> Macrolydes are living corner cases.
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<dmbaturin> * macrolides
<cranix> yes
<cranix> thats why i plan to start with fexofenadine
<cranix> i plan to treat cycle (cyclic parts of compund) as one entity
<cranix> becouse chemist think about cycle as one logical part with sematnics attached to it
<cranix> at first i hoped that parsers are reasearched very good and i will be able to easly find way to parse context sensitive grammar, but this is not true
<dmbaturin> Well... if you are to find a route to something explicitly polycyclic like anthracene, you have to deal with cycle closing.
<cranix> yes
<cranix> fused rings are another topic
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<cranix> if You are intrested i can later write You about progress of this topic
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<dmbaturin> cranix: Feel free to email me at daniil@baturin.org, or PM.
<cranix> i will
<cranix> it is very motivating that someone else is intrested in this topic
<cranix> my mail is cranix@hackerspace.pl
<dmbaturin> cranix: Sent you a test message.
<cranix> got it
<cranix> i will need to find a good way to input structure of compound to ocaml
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<dmbaturin> There are existing formats that you may want to parse. Those used by quantum chemistry tools.
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<cranix> i will have a look at them
<cranix> SMILES is simple
<cranix> and ASCII
<cranix> but not sure about converting it to graphs
<cranix> especially the way it handle cycles