Changeset 12171 in project

Timestamp:

10/16/08 01:57:48 (12 years ago)

Author:

Ivan Raikov

Message:

Version set to 1.1

Location:

release/3/nemo/trunk

Files:

• examples/AKP06/PotIhCa.scm (modified) (1 diff)
• nemo-nmodl.scm (modified) (5 diffs)
• nemo.setup (modified) (3 diffs)

release/3/nemo/trunk/examples/AKP06/PotIhCa.scm

@@ -14 +14 @@
                        (* 1e-6  (* 2 F) (- ci (* co (exp (neg zeta)))) (+ 1.0 (/ zeta 2)))
                        (/ (* 1e-6 (* 2 zeta F) (- ci (* co (exp (neg zeta))))) (- 1.0 (exp (neg zeta))))))))
-             
+
+             (decaying-pool (ca (depth 0.1) (beta 1)))
              
              (component (type ion-channel) (name Kv1)

release/3/nemo/trunk/nemo-nmodl.scm

@@ -701 +701 @@
                     (bkt-loop (cdr old-bkts) (cons (car old-bkts) new-bkts)))))))))
 
+(define (collect-epools sys)
+   (match-let ((($ nemo:quantity 'DISPATCH  dis) (environment-ref sys (nemo-intern 'dispatch))))
+      (let recur ((comp-name (nemo-intern 'toplevel)) (ax (list)))
+        (let* ((comp-symbols   ((dis 'component-symbols)   sys comp-name))
+               (subcomps       ((dis 'component-subcomps)  sys comp-name)))
+          (fold recur 
+                (fold (lambda (sym ax)
+                        (let ((en (environment-ref sys sym)))
+                          (match en
+                                 ((or (('decaying 'pool)  ('name (? symbol? ion)) . alst)
+                                      (('decaying-pool)   ('name (? symbol? ion)) . alst))
+                                  (cons (list ion alst) ax))
+                                 (else ax)))) ax comp-symbols)
+                (map third subcomps))))))
+
 
 (define (nemo:nmodl-translator sys . rest)
@@ -720 +735 @@
              (defuns      ((dis 'defuns) sys))
              (components  ((dis 'components) sys))
-             (ionchs      (filter-map (match-lambda ((name 'ion-channel id) (list name id)) (else #f)) components))) 
+             (ionchs      (filter-map (match-lambda ((name 'ion-channel id) (list name id)) (else #f)) components))
+             (epools      (collect-epools sys)))
+
         (match-let (((state-list asgn-list g) deps*))
          (let* ((poset          (vector->list ((dis 'depgraph->bfs-dist-poset) g)))
@@ -752 +769 @@
                                 (list) ionchs)
                            (lambda (x y) (eq? (car x) (car y)))))
+               (pool-ions (delete-duplicates
+                           (map (lambda (ep)
+                                  (let ((ion (car ep)))
+                                    `(,(nmodl-name ion) ,(nmodl-name (s+ 'i ion)) ,(nmodl-name (s+ ion 'i)))))
+                                epools)))
                )
+
+           (print "pool-ions = "  pool-ions)
+           (print "acc-ions = "   acc-ions)
+           (print "perm-ions = "  perm-ions)
+
+           (for-each 
+            (lambda (a p)
+              (let ((acc-ion   (car a))
+                    (pool-ion  (car p)))
+                (if (alist-ref acc-ion perm-ions)
+                    (nemo:error 'nemo:nmodl-translator 
+                                ": ion species " ion " cannot be declared as both accumulating and permeating"))
+                (if (alist-ref pool-ion perm-ions)
+                    (nemo:error 'nemo:nmodl-translator 
+                                ": ion species " ion " cannot be declared as both pool and permeating"))))
+            acc-ions)
 
            (pp indent ,nl (TITLE ,sysname))
@@ -771 +809 @@
                            (USEION ,(first x) READ ,(third x) ", " ,(fourth x) WRITE ,(second x))))
                      acc-ions)
+           (for-each (lambda (x)
+                       (pp indent+ (RANGE ,(first x))
+                           (USEION ,(first x) READ ,(second x)  WRITE ,(third x))))
+                     pool-ions)
            (let* ((const-names   (map first consts))
                   (is-const?     (lambda (x) (member x const-names)))
@@ -851 +893 @@
              (let* ((i-eqs (filter-map
                             (lambda (ionch) 
-                              (let* ((n     (second ionch))
-                                     (subcomps ((dis 'component-subcomps) sys n))
-                                     (acc   (lookup-def 'accumulating-substance subcomps))
-                                     (perm  (lookup-def 'permeating-substance subcomps))
-                                     (pore  (lookup-def 'pore subcomps))
-                                     (gate  (lookup-def 'gate subcomps))
-                                     (sts   (and gate ((dis 'component-exports) sys (cid gate)))))
+                              (let* ((n         (second ionch))
+                                     (subcomps  ((dis 'component-subcomps) sys n))
+                                     (acc       (lookup-def 'accumulating-substance subcomps))
+                                     (perm      (lookup-def 'permeating-substance subcomps))
+                                     (pore      (lookup-def 'pore subcomps))
+                                     (gate      (lookup-def 'gate subcomps))
+                                     (sts       (and gate ((dis 'component-exports) sys (cid gate)))))
                                 (cond ((and perm pore gate)
                                        (case (cn perm)

release/3/nemo/trunk/nemo.setup

@@ -49 +49 @@
 
   ; Assoc list with properties for your extension:
-  `((version 1.0)
+  `((version 1.1)
     ,@(if has-exports? `((exports "nemo-nmodl.exports")) (list)) ))
 
@@ -68 +68 @@
 
   ; Assoc list with properties for your extension:
-  `((version 1.0)
+  `((version 1.1)
     ,@(if has-exports? `((exports "nemo-hh.exports")) (list)) ))
 
@@ -82 +82 @@
 
   ; Assoc list with properties for the program:
-  '((version 1.0)
+  '((version 1.1)
     (documentation "nemo.html")))