From 60ecf88499d02501c215468fcafcef5014d6d2a7 Mon Sep 17 00:00:00 2001 From: meister Date: Thu, 25 Jul 2024 08:26:52 -0400 Subject: [PATCH] Working on am1bcc charges to handle charged residues --- src/lisp/cando/charges/am1bcc.lisp | 11 ++++++----- src/lisp/cando/charges/packages.lisp | 3 ++- 2 files changed, 8 insertions(+), 6 deletions(-) diff --git a/src/lisp/cando/charges/am1bcc.lisp b/src/lisp/cando/charges/am1bcc.lisp index eb08d000..19468ee0 100644 --- 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 index 17fb0285..2644fa92 100644 --- 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))