Changeset 13050 in project

Timestamp:

01/21/09 02:55:43 (11 years ago)

Author:

Ivan Raikov

Message:

Fixes to the matlab backend; better error messages in nmodl backend.

Location:

release/3/nemo/trunk

Files:

• examples/carelli05.nemo (modified) (4 diffs)
• nemo-matlab.scm (modified) (1 diff)
• nemo-nmodl.scm (modified) (1 diff)

release/3/nemo/trunk/examples/carelli05.nemo

@@ -113 +113 @@
    (component (type ion-channel) (name KCa)
 
-              (hh-ionic-conductance 
-               (KCa
-                (m-power 4) 
-                (h-power 0)
-                (initial-m ((Ca / (3 + Ca)) * (1 / (1 + (exp ((Vrest + 28.3) / -12.6))))))
-                (m-inf  ((Ca / (3 + Ca)) * (1 / (1 + (exp ((v + 28.3) / -12.6))))))
-                (m-tau  (180.6 - (150.2 / (1 + (exp ((v + 46) / -22.7))))))))
+              (component (type gate)
+
+                         (hh-ionic-conductance 
+                          (KCa
+                           (m-power 4) 
+                           (h-power 0)
+                           (initial-m ((Ca / (3 + Ca)) * (1 / (1 + (exp ((Vrest + 28.3) / -12.6))))))
+                           (m-inf  ((Ca / (3 + Ca)) * (1 / (1 + (exp ((v + 28.3) / -12.6))))))
+                           (m-tau  (180.6 - (150.2 / (1 + (exp ((v + 46) / -22.7))))))))
+                         )
      
               (component (type pore)
@@ -133 +136 @@
    (component (type ion-channel) (name Kd)
                        
-              (hh-ionic-conductance 
-                     (Kd
-                      (m-power 4) 
-                      (h-power 0)
-                      (initial-m (1 / (1 + (exp ((Vrest + 12.3) / -11.8)))))
-                      (m-inf  (1 / (1 + (exp ((v + 12.3) / -11.8)))))
-                      (m-tau  (14.4 - (12.8 / (exp ((v + 28.3) / -19.2)))))))
+              (component (type gate)
+
+                         (hh-ionic-conductance 
+                          (Kd
+                           (m-power 4) 
+                           (h-power 0)
+                           (initial-m (1 / (1 + (exp ((Vrest + 12.3) / -11.8)))))
+                           (m-inf  (1 / (1 + (exp ((v + 12.3) / -11.8)))))
+                           (m-tau  (14.4 - (12.8 / (exp ((v + 28.3) / -19.2)))))))
+                         )
 
               (component (type pore)
@@ -153 +159 @@
    (component (type ion-channel) (name A)
                        
-              (hh-ionic-conductance 
-               (A
-                (gbar 50)
-                (m-power 3) 
-                (h-power 1)
-                (initial-m (1 / (1 + (exp ((Vrest + 27.2) / -8.7)))))
-                (initial-h (1 / (1 + (exp ((Vrest + 56.9) / 4.9)))))
-                (m-inf  (1 / (1 + (exp ((v + 27.2) / -8.7)))))
-                (h-inf  (1 / (1 + (exp ((v + 56.9) / 4.9)))))
-                (m-tau  (23.2 - (20.8 / (1 + (exp ((v + 32.9) / -15.2))))))
-                (h-tau  (77.2 - (58.4 / (1 + (exp ((v + 38.9) / -26.5))))))))
+              (component (type gate)
+
+                         (hh-ionic-conductance 
+                          (A
+                           (gbar 50)
+                           (m-power 3) 
+                           (h-power 1)
+                           (initial-m (1 / (1 + (exp ((Vrest + 27.2) / -8.7)))))
+                           (initial-h (1 / (1 + (exp ((Vrest + 56.9) / 4.9)))))
+                           (m-inf  (1 / (1 + (exp ((v + 27.2) / -8.7)))))
+                           (h-inf  (1 / (1 + (exp ((v + 56.9) / 4.9)))))
+                           (m-tau  (23.2 - (20.8 / (1 + (exp ((v + 32.9) / -15.2))))))
+                           (h-tau  (77.2 - (58.4 / (1 + (exp ((v + 38.9) / -26.5))))))))
+                         )
 
               (component (type pore)
@@ -175 +184 @@
 
    (component (type ion-channel) (name H)
-                       
-              (hh-ionic-conductance 
-               (H
-                (m-power 1) 
-                (h-power 0)
-                (initial-m (1 / (1 + (exp ((Vrest + 75) / 5.5)))))
-                (m-inf  (1 / (1 + (exp ((v + 75) / 5.5)))))
-                (m-tau  (2.2 / ((exp ((v + 169.7) / -11.6)) + (exp ((v - 26.7) / 14.3)))))))
+
+              (component (type gate)
+
+                         (hh-ionic-conductance 
+                          (H
+                           (m-power 1) 
+                           (h-power 0)
+                           (initial-m (1 / (1 + (exp ((Vrest + 75) / 5.5)))))
+                           (m-inf  (1 / (1 + (exp ((v + 75) / 5.5)))))
+                           (m-tau  (2.2 / ((exp ((v + 169.7) / -11.6)) + (exp ((v - 26.7) / 14.3)))))))
+                         )
 
               (component (type pore)

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

@@ -204 +204 @@
                                                  (let ((fx (format-expr/MATLAB indent+ x))) fx)) rest)))))
                     
-                    (let ((op (case op ((neg) '-) (else op))))
+                    (let ((op (case op ((neg) '-) ((ln) 'log) (else op))))
                       (format-fncall/MATLAB indent op (map (lambda (x) (format-expr/MATLAB indent+ x)) rest))))))
            (if rv 

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

@@ -834 +834 @@
                                         (nemo:error 'nemo:nmodl-translator ": ion channel definition " label
                                                     (s+ "(" n ")")
-                                                    "lacks permeating-substance or accumulating-substance "
-                                                    "component"))))
+                                                    "lacks gate component"))))
 
                                       ((and acc pore gate)