call_subprocess now accepts an array of arguments, so that arguments containing space...

[molby/Molby.git] / Scripts / md.rb

diff --git a/Scripts/md.rb b/Scripts/md.rb
index fa28cd3..ba80acc 100755 (executable)
--- a/Scripts/md.rb
+++ b/Scripts/md.rb
@@ -456,24 +456,24 @@ class Molecule
          ENV["AMBERHOME"] = amberhome
        end
        if calc_charge != 0
-         opt = "-nc #{nc} -c bcc"
+         opt = ["-nc", "#{nc}", "-c", "bcc"]
          if optimize_structure == 0
-           opt += " -ek 'maxcyc=0'"
+           opt.push(" -ek", "'maxcyc=0'")
          end
        else
-         opt = ""
+         opt = []
        end
        if guess_atom_types == 0
-         opt += " -j 0"
+         opt.push("-j", "0")
     end
-       n = call_subprocess("#{ante_dir}/antechamber -i mol.pdb -fi pdb -o mol.ac -fo ac #{opt}", "Antechamber")
+       n = call_subprocess(["#{ante_dir}/antechamber", "-i", "mol.pdb", "-fi", "pdb", "-o", "mol.ac", "-fo", "ac"] + opt, "Antechamber")
        if n != 0
          error_message_box("Antechamber failed: status = #{n}.")
          Dir.chdir(cwd)
          return n
        else
          if guess_atom_types != 0
-           n = call_subprocess("#{ante_dir}/parmchk -i mol.ac -f ac -o frcmod", "Parmchk")
+           n = call_subprocess(["#{ante_dir}/parmchk", "-i", "mol.ac", "-f", "ac", "-o", "frcmod"], "Parmchk")
            if n != 0
              error_message_box("Parmchk failed: status = #{n}.")
                  Dir.chdir(cwd)
@@ -1326,9 +1326,9 @@ class Molecule
          }
        
          #  Create resp input by respgen
-         status = call_subprocess("\"#{ante_dir}/respgen\" -i respgen_in.ac -o resp.input1 -f resp1", "respgen (stage 1)")
+      status = call_subprocess(["#{ante_dir}/respgen", "-i", "respgen_in.ac", "-o", "resp.input1", "-f", "resp1"], "respgen (stage 1)")
          if status == 0
-               status = call_subprocess("\"#{ante_dir}/respgen\" -i respgen_in.ac -o resp.input2 -f resp2", "respgen (stage 2)")
+               status = call_subprocess(["#{ante_dir}/respgen", "-i", "respgen_in.ac", "-o", "resp.input2", "-f", "resp2"], "respgen (stage 2)")
          end
          if status != 0
            error_message_box("Cannot run respgen: status = #{status}")
@@ -1353,9 +1353,9 @@ class Molecule
        }
 
     #  Run resp
-       status = call_subprocess("\"#{ante_dir}/resp\" -O -i resp.input1 -o resp.output1 -e resp.esp -t qout_stage1", "resp (stage 1)")
+       status = call_subprocess(["#{ante_dir}/resp", "-O", "-i", "resp.input1", "-o", "resp.output1", "-e", "resp.esp", "-t", "qout_stage1"], "resp (stage 1)")
        if status == 0
-         status = call_subprocess("\"#{ante_dir}/resp\" -O -i resp.input2 -o resp.output2 -e resp.esp -q qout_stage1 -t qout_stage2", "resp (stage 2)")
+         status = call_subprocess(["#{ante_dir}/resp", "-O", "-i", "resp.input2", "-o", "resp.output2", "-e", "resp.esp", "-q", "qout_stage1", "-t", "qout_stage2"], "resp (stage 2)")
          if status == 255 && File.exist?("punch")
                status = 0   #  Ignore error at the second stage
          end