Fix package lock violations

Some dead code, some internal stuff. I shadowed TYPE in the one
place because it was exported.

src/lisp/amber/amber-jobs.lisp

@@ -977,7 +977,7 @@ exec \"$@\"
 
 (defclass seen ()
   ((name :initarg :name :accessor name)
-   (stream :initarg :stream :accessor stream)))
+   (sstream :initarg :stream :accessor sstream)))
 
 (defun monitor (sim)
   (let ((seen (make-hash-table :test 'equal)))
@@ -1008,7 +1008,7 @@ exec \"$@\"
                                (format t "Saw: ~a~%" name)
                                (finish-output t)))
                             (saw
-                             (format t "Seen file ~a size: ~a~%" (name saw) (file-length (stream saw)))
+                             (format t "Seen file ~a size: ~a~%" (name saw) (file-length (sstream saw)))
                              (finish-output t)))))
                       seen)
           do (sleep 1))

src/lisp/cando/fortran.lisp

@@ -56,7 +56,7 @@
 (defun debug-off (&optional (ff *fortran-file*))
   (setf (fof-debug ff) nil))
 
-(defun debug (msg &optional (ff *fortran-file*))
+(defun debugprint (msg &optional (ff *fortran-file*))
   (when (fof-debug ff)
     (core:fmt (fof-stream ff) "{}{}%N" +fortran-debug-comment-char+ msg)))
 

src/lisp/cando/smirnoff/load.lisp

@@ -66,7 +66,7 @@
   ((terms :initform (make-array 16 :fill-pointer 0 :adjustable t) :initarg :terms :accessor terms)))
 
 (defclass nonbond-term (force-term)
-  ((type :initarg :type :accessor type)
+  ((ttype :initarg :type :accessor ttype)
    ;; in kj/mol
    (epsilon :initarg :epsilon :accessor epsilon)
    ;; in angstroms
@@ -83,12 +83,11 @@
    (switch-width :initarg :switch-width :accessor switch-width)
    ;; in radians
    (cutoff :initarg :cutoff :accessor cutoff)
-   (method :initarg :method :accessor method)
    (terms :initform (make-array 16 :fill-pointer 0 :adjustable t) :initarg :terms :accessor terms)))
 
 (defmethod print-object ((object nonbond-term) stream)
   (print-unreadable-object (object stream)
-    (format stream "~a ~s ~s" (class-name (class-of object)) :type (type object))
+    (format stream "~a ~s ~s" (class-name (class-of object)) :type (ttype object))
     (format stream " ~s ~s" :smirks (smirks object))
     (format stream " ~s ~s" :id (id object))))
 
@@ -274,8 +273,7 @@
                            :scale14 scale14
                            :scale15 scale15
                            :switch-width switch-width
-                           :cutoff cutoff
-                           :method method))
+                           :cutoff cutoff))
       (with-force-parser (node root "Atom")
         (let* ((attrs (plump:attributes node))
                (smirks (safe-gethash "smirks" attrs))

src/lisp/cando/smirnoff/smirnoff.lisp

@@ -73,7 +73,7 @@ The chem:force-field-type-rules-merged generic function was used to organize the
                       do (loop for index from (1- (length terms)) downto 0
                                for term = (aref terms index)
                                for compiled-smirks = (compiled-smirks term)
-                               for type = (type term)
+                               for type = (ttype term)
                                for match = (chem:matches compiled-smirks atom)
                                when match
                                  do (return-from assign-type type)))))
@@ -86,7 +86,7 @@ The chem:force-field-type-rules-merged generic function was used to organize the
   (loop with terms = (terms source)
         for index below (length terms)
         for term = (aref terms index)
-        for type = (type term)
+        for type = (ttype term)
         when (not (chem:has-type dest type))
           do (let* ((atomic-mass (smirks-head-atomic-mass (compiled-smirks term)))
                     (ffnonbond (chem:make-ffnonbond type

src/lisp/leap/leap.asd

@@ -20,7 +20,6 @@
                (:file "grammar")
                (:file "off")
                (:file "core")
-               (:file "sequence")
                (:file "solvate")
                (:file "add-ions")
                (:file "set-box")

src/lisp/leap/packages.lisp

@@ -60,13 +60,6 @@
    #:add-one-atom-type
    ))
 
-
-(defpackage #:leap.sequence
-  (:use #:common-lisp)
-  (:export
-   #:sequence
-   ))
-
 (defpackage #:leap.cmap
   (:use #:common-lisp)
   (:shadow #:count)
@@ -139,6 +132,7 @@
 
 (defpackage #:leap.off
   (:use #:common-lisp)
+  (:shadow #:type)
   (:export
    #:bug
    #:read-off-data-block

src/lisp/regression-tests/energy.lisp

@@ -105,10 +105,10 @@
 (test-true force-acos (< force-acos 0.01))
 
 
-(defparameter min (chem:make-minimizer ef))
+(defparameter minimizer (chem:make-minimizer ef))
 #+(or)(time (dotimes (i 10)
         (chem:save-coordinates-from-vector ef pos)
-        (chem:minimize min)))
+        (chem:minimize minimizer)))
 
 
 (defparameter spiro (cando:load-mol2 (merge-pathnames "data/struct-0000.mol2"

src/lisp/topology/define-topology.lisp

@@ -327,7 +327,7 @@ So if name is \"ALA\" and stereoisomer-index is 1 the name becomes ALA{CA/S}."
                                      (mapcar (lambda (info)
                                                (let* ((constitution-atom (constitution-atom info))
                                                       (name (atom-name constitution-atom))
-                                                      (type (type info)))
+                                                      (type (stype info)))
                                                  #+(or)(format t "fixed-chiral-info: ~s ~s~%" name type)
                                                  (when (eq type :undefined-configuration)
                                                    (error "Don't allow :undefined-configuration for ~a" name))
@@ -362,18 +362,18 @@ So if name is \"ALA\" and stereoisomer-index is 1 the name becomes ALA{CA/S}."
 
 (defclass stereocenter-info ()
   ((constitution-atom :initarg :constitution-atom :accessor constitution-atom)
-   (type :initarg :type :accessor type)))
+   (%type :initarg :type :accessor stype)))
 
 (defmethod print-object ((obj stereocenter-info) stream)
   (print-unreadable-object (obj stream :type t)
-    (format stream "~a ~a" (constitution-atom obj) (type obj))))
+    (format stream "~a ~a" (constitution-atom obj) (stype obj))))
 
 
 (defun build-stereo-information (name stereocenter-info stereoisomer-atoms)
   "Build stereoinformation from the stereocenter-info and return it."
   (multiple-value-bind (variable-chiral-atoms fixed-chiral-info)
       (loop for info in stereocenter-info
-            if (eq (type info) :both)
+            if (eq (stype info) :both)
               collect (atom-name (constitution-atom info)) into variable-chiral-atoms
             else
               collect info into fixed-chiral-info