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| (defpackage #:chemicl-smiles | |
| (:use #:cl #:chemicl #:parser-combinators)) | |
| (in-package #:chemicl-smiles) | |
| ;;; | |
| ;;; parser-combinator utilities | |
| (defun as-digit? () | |
| (hook? #'digit-char-p (digit?))) | |
| ;;; | |
| ;;; Aliphatic Organic Subset Atoms (Cl Br B C N O S P F I) | |
| (defun <aliphatic-organic-atom> () | |
| (hook? #'make-atom | |
| (apply #'choices1 | |
| (map 'list | |
| #'string? | |
| '("Cl" "Br" "B" "C" "N" "O" "S" "P" "F" "I"))))) | |
| ;;; | |
| ;;; Aromatic Organic Subset Atoms (b c n o s p) | |
| (defun <aromatic-atom-matcher> (str) | |
| (hook? #'string-upcase (string? str))) | |
| (defun <aromatic-organic-atom> () | |
| (hook? #'make-atom | |
| (apply #'choices1 | |
| (map 'list | |
| #'<aromatic-atom-matcher> | |
| '("b" "c" "n" "o" "s" "p"))))) | |
| ;;; | |
| ;;; Bracketed atoms e.g. [Na] | |
| (defun <isotope> () | |
| (nat?)) | |
| (defun <hydrogen-count> () | |
| (opt? | |
| (named-seq* | |
| #\H | |
| (<- num (nat?)) | |
| (or num 1)))) | |
| (defun <charge> () | |
| (choice1 (named-seq* | |
| (char? #\+) | |
| (<- charge (opt? (choices1 (named-seq* (char? #\+) 2) | |
| (nat*)))) | |
| (or charge 1)) | |
| (named-seq* | |
| (char? #\-) | |
| (<- charge (opt? (choices1 (named-seq* (char? #\-) 2) | |
| (nat*)))) | |
| (- (or charge 1))))) | |
| (defun <bracket-aliphatic-atom-symbol> () | |
| (named-seq? (<- pre (upper?)) | |
| (<- suff (atmost? (lower?) 2)) | |
| (format nil "~A~{~A~}" pre suff))) | |
| (defun <bracket-aromatic-atom-symbol> () | |
| (apply #'choices1 | |
| (named-seq? (string? "se") "Se") | |
| (named-seq? (string? "as") "As") | |
| (map 'list | |
| #'<aromatic-atom-matcher> | |
| '("c" "n" "o" "p" "s")))) | |
| (defun <bracket-atom> () | |
| (named-seq? #\[ | |
| (<- atm (choice1 | |
| (<bracket-aliphatic-atom-symbol>) | |
| (<bracket-aromatic-atom-symbol>))) | |
| (<- hydrogen-count (<hydrogen-count>)) | |
| (<- charge (opt? (<charge>))) | |
| #\] | |
| (let ((atom (apply #'make-atom atm | |
| (append | |
| (when charge `(:charge ,charge)))))) | |
| (when hydrogen-count | |
| (print (list 'hydrogens hydrogen-count))) | |
| atom))) | |
| ;;; | |
| ;;; Atoms | |
| (defun <atom> () | |
| (choices1 (<bracket-atom>) | |
| (<aliphatic-organic-atom>) | |
| (<aromatic-organic-atom>))) | |
| ;;; | |
| ;;; Bonds | |
| (defun <single-bond> () (char? #\-)) | |
| (defun <double-bond> () (char? #\=)) | |
| (defun <triple-bond> () (char? #\#)) | |
| (defun <quadruple-bond> () (char? #\$)) | |
| (defun <aromatic-bond> () (char? #\:)) | |
| (defun <up-bond> () (char? #\/)) | |
| (defun <down-bond> () (char? #\\)) | |
| (defun <bond> () | |
| (choices | |
| (named-seq? (<single-bond>) 1) | |
| (named-seq? (<double-bond>) 2) | |
| (named-seq? (<triple-bond>) 3) | |
| (named-seq? (<quadruple-bond>) 4) | |
| (named-seq? (<aromatic-bond>) :aromatic) | |
| (named-seq? (<up-bond>) :up) | |
| (named-seq? (<down-bond>) :down))) | |
| (defun <bond-or-dot> () | |
| (choice1 (<bond>) | |
| (<dot>))) | |
| ;;; | |
| ;;; Core atom rule | |
| ;;; | |
| ;;; This rule encompasses the atom itself, all connected branches, | |
| ;;; ring-bond symbols, and a bond or dot symbol indicating arity (or | |
| ;;; disconnectedness) of the next (non-chain) bond from this atom | |
| (defun <atom-expr> (mol) | |
| (mdo (<- atom (<atom>)) | |
| (<- branches1 (many? (<branch> mol atom))) | |
| (<- rings (many? (<ring-bond>))) | |
| (<- branches2 (many? (<branch> mol atom))) | |
| (opt? (<bond-or-dot>)) | |
| (result (list atom branches1 rings branches2)))) | |
| ;;; | |
| ;;; Branches | |
| (defun <ring-bond> () | |
| (choice | |
| (named-seq? (opt? (<bond>)) | |
| #\% | |
| (<- digit1 (as-digit?)) | |
| (<- digit2 (as-digit?)) | |
| (+ (* 10 digit1) digit2)) | |
| (named-seq? (opt? (<bond>)) | |
| (<- digit1 (as-digit?)) | |
| digit1))) | |
| (defun <branched-atom> (mol) | |
| (mdo | |
| (<- bond (opt? (<bond>))) | |
| (<- atom (<atom>)) | |
| (<- ring-bonds (many? (<ring-bond>))) | |
| (<- branches (many? (<branch> mol atom))) | |
| (result (list bond atom ring-bonds branches)))) | |
| (defun <branch> (mol atom) | |
| (bracket? #\( | |
| (choices | |
| (<chain> mol) | |
| (named-seq? | |
| (<- bond (<bond>)) | |
| (<- chain (curtail? (<chain> mol))) | |
| (list bond chain)) | |
| (named-seq? | |
| (<- dot (<dot>)) | |
| (<- chain (curtail? (<chain> mol))) | |
| (list dot chain))) | |
| #\))) | |
| ;;; use order 0 for disconnected atoms! | |
| (defun <dot> () (char? #\.) ) | |
| (defun unzip (l) | |
| (if (and (car l) (listp (car l))) | |
| (cons (cdr l) (unzip (car l))) | |
| (cons (cdr l) (list (car l))))) | |
| ;;; | |
| ;;; Core chain rule -- a (possibly branched) chain of atoms | |
| (defun <chain> (mol) | |
| (hook? #'unzip (chainl1? | |
| (<branched-atom> mol) | |
| (result #'cons)))) | |
| ;;; | |
| ;;; Main (only?) (useful) entry point to all of this code | |
| ;;; | |
| ;;; Parsess a SMILES string and returns a molecule (should this really | |
| ;;; return a set of molecules?) | |
| (defun parse-smiles-string (str) | |
| (let ((mol (make-molecule))) | |
| (parse-string* (<chain> mol) str :complete t))) |
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