Working on am1bcc charges to handle charged residues

cando-developers · Jul 25, 2024 · 60ecf88 · 60ecf88
1 parent d005b25
commit 60ecf88
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Showing 2 changed files with 8 additions and 6 deletions.
diff --git a/src/lisp/cando/charges/am1bcc.lisp b/src/lisp/cando/charges/am1bcc.lisp
@@ -414,12 +414,13 @@
 (defun sqm-executable ()
   (probe-file "amber:bin;sqm"))
 
-(defun calculate-am1-bcc-charges (aggregate &key (maxcyc 9999) verbose)
-  "Calculate Am1-Bcc charges and add the results to the aggregate."
+(defun calculate-am1-bcc-charges (aggregate &key (maxcyc 9999) verbose (tmpdir #P"/tmp/"))
+  "Calculate Am1-Bcc charges and add the results to the aggregate. Write sqm files into tmpdir"
   (let* ((bcc (calculate-bcc-corrections aggregate))
-         (input-filename (sys:mkstemp "/tmp/sqm-input-"))
-         (output-filename (sys:mkstemp "/tmp/sqm-output-"))
-         (order (charges:write-sqm-calculation (open input-filename :direction :output) aggregate
+         (input-filename (sys:mkstemp (format nil "~asqm-input-" (namestring tmpdir))))
+         (output-filename (sys:mkstemp (format nil "~asqm-output-" (namestring tmpdir))))
+         (order (charges:write-sqm-calculation (open input-filename :direction :output)
+                                               aggregate
                                                :maxcyc maxcyc))
          (sqm-executable (sqm-executable))
          (args (list "-O"

diff --git a/src/lisp/cando/charges/packages.lisp b/src/lisp/cando/charges/packages.lisp
@@ -37,4 +37,5 @@
    #:read-am1-charges
    #:read-mopac-am1-charges
    #:calculate-charge-trainers
-   #:dump-residue-charges))
+   #:dump-residue-charges
+   #:residue-charges))