Merge pull request #4 from CurtisColwell/nix_jup

Nix jup

README.md

@@ -27,7 +27,7 @@ geometry/ directory.
 that will allow the molecule to release its strain and saving them as .xyz 
 files in the dummies/ directory.
 
-5. Run the dummy_input.py script to create input files that will optimize 
+5. Run the proton_opt.py script to create input files that will optimize 
 the proton added to the dummy molecules using Gaussian.
 
 6. Once the proton has been optimized, use Gaussian to calculate molecular 

atom_scripts.py

@@ -56,7 +56,7 @@ def vmd_vector_writer(script_name, vector_colors, geometry_filename, min, max):
 	script = open('output/' + script_name, "w")
 	script.write("# Minimum: %s\r# Maximum: %s\r\r" % (min,max))
 	script.write("# Load a molecule\rmol new %s\r\r" % (geometry_filename))
-	with open("vmd_vector_header.tcl") as script_header:
+	with open("headers/vmd_vector_header.tcl") as script_header:
 		for line in script_header:
 			script.write(line)
 	script.write("\r")

bond_scripts.py

@@ -35,9 +35,9 @@ def map_forces(geometry, force_output):
 	angle_forces_vmd, angle_min, angle_max = vmd_norm(compressed_angle_forces)
 	dihedral_forces_vmd, dihedral_min, dihedral_max = vmd_norm(compressed_dihedral_forces)
 
-	vmd_writer("vmd_bond_script_" + os.path.splitext(force_output)[0] + ".tcl", bond_forces_vmd, geometry, bond_min, bond_max, "vmd_bond_header.tcl")
-	vmd_writer("vmd_angle_script_" + os.path.splitext(force_output)[0] + ".tcl", angle_forces_vmd, geometry, angle_min, angle_max, "vmd_angle_and_dihedral_header.tcl")
-	vmd_writer("vmd_dihedral_script_" + os.path.splitext(force_output)[0] + ".tcl", dihedral_forces_vmd, geometry, dihedral_min, dihedral_max, "vmd_angle_and_dihedral_header.tcl")
+	vmd_writer("vmd_bond_script_" + os.path.splitext(force_output)[0] + ".tcl", bond_forces_vmd, geometry, bond_min, bond_max, "headers/vmd_bond_header.tcl")
+	vmd_writer("vmd_angle_script_" + os.path.splitext(force_output)[0] + ".tcl", angle_forces_vmd, geometry, angle_min, angle_max, "headers/vmd_angle_and_dihedral_header.tcl")
+	vmd_writer("vmd_dihedral_script_" + os.path.splitext(force_output)[0] + ".tcl", dihedral_forces_vmd, geometry, dihedral_min, dihedral_max, "headers/vmd_angle_and_dihedral_header.tcl")
 
 	return copy_bond_forces, copy_angle_forces, copy_dihedral_forces;
 
@@ -230,6 +230,6 @@ def combine_dummies(forces, geometry, force_type):
 	#Write the forces to a .tcl script
 	new_forces_vmd, scale_min, scale_max = vmd_norm(new_forces)
 	if force_type == "bond":
-		vmd_writer("vmd_" + force_type + "_script_total.tcl", new_forces_vmd, geometry, scale_min, scale_max, "vmd_bond_header.tcl")
+		vmd_writer("vmd_" + force_type + "_script_total.tcl", new_forces_vmd, geometry, scale_min, scale_max, "headers/vmd_bond_header.tcl")
 	else:
-		vmd_writer("vmd_" + force_type + "_script_total.tcl", new_forces_vmd, geometry, scale_min, scale_max, "vmd_angle_and_dihedral_header.tcl")
+		vmd_writer("vmd_" + force_type + "_script_total.tcl", new_forces_vmd, geometry, scale_min, scale_max, "headers/vmd_angle_and_dihedral_header.tcl")

dummies/.gitignore

@@ -0,0 +1,4 @@
+# Ignore everything in this directory
+*
+# Except this file
+!.gitignore

geometry/.gitignore

@@ -0,0 +1,4 @@
+# Ignore everything in this directory
+*
+# Except this file
+!.gitignore

output/.gitignore

@@ -0,0 +1,4 @@
+# Ignore everything in this directory
+*
+# Except this file
+!.gitignore

proton_opt.py

@@ -0,0 +1,14 @@
+import os
+from scripts import *
+
+for file in os.listdir('geometry'):
+    if file.endswith(".xyz"):
+        geometry_filename = 'geometry/' + file
+
+dummies = []
+for file in os.listdir('dummies'):
+    if file.endswith(".xyz"):
+        dummies.append('dummies/' + file)
+
+for file in dummies:
+    create_protonopts(geometry_filename, file)