diff --git a/src/lisp/amber/amber-jobs.lisp b/src/lisp/amber/amber-jobs.lisp index 0b79bb6d..f4af86b0 100644 --- a/src/lisp/amber/amber-jobs.lisp +++ b/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)) diff --git a/src/lisp/cando/fortran.lisp b/src/lisp/cando/fortran.lisp index e1e6e137..051e702d 100644 --- a/src/lisp/cando/fortran.lisp +++ b/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))) diff --git a/src/lisp/cando/smirnoff/load.lisp b/src/lisp/cando/smirnoff/load.lisp index 6d9bd8f7..27c1358f 100644 --- a/src/lisp/cando/smirnoff/load.lisp +++ b/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)) diff --git a/src/lisp/cando/smirnoff/smirnoff.lisp b/src/lisp/cando/smirnoff/smirnoff.lisp index c92f1912..b8a6314b 100644 --- a/src/lisp/cando/smirnoff/smirnoff.lisp +++ b/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 diff --git a/src/lisp/leap/leap.asd b/src/lisp/leap/leap.asd index 6e4b0a36..2900c084 100644 --- a/src/lisp/leap/leap.asd +++ b/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") diff --git a/src/lisp/leap/packages.lisp b/src/lisp/leap/packages.lisp index 4397b146..3d603034 100644 --- a/src/lisp/leap/packages.lisp +++ b/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 diff --git a/src/lisp/leap/sequence.lisp b/src/lisp/leap/sequence.lisp deleted file mode 100644 index dde3f4ca..00000000 --- a/src/lisp/leap/sequence.lisp +++ /dev/null @@ -1,7 +0,0 @@ - -(in-package :leap.sequence) - - - -(defun sequence (args) - (format t "This is where the sequence magic happens args: ~a~%" args)) diff --git a/src/lisp/regression-tests/energy.lisp b/src/lisp/regression-tests/energy.lisp index 9e4da7fe..9bba58c6 100644 --- a/src/lisp/regression-tests/energy.lisp +++ b/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" diff --git a/src/lisp/topology/define-topology.lisp b/src/lisp/topology/define-topology.lisp index 6e72c581..6663dcb9 100644 --- a/src/lisp/topology/define-topology.lisp +++ b/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