update

lib/e_2_xyz.py

@@ -47,7 +47,7 @@ def replicate(xyz_info, args):
                 b.step = i
                 toPdb(b, "output%05d.pdb"%i)
             # replicate the box using external code (genconf in Gromacs)
-            subprocess.Popen(["genconf", "-f", "output%05d.pdb"%i, 
+            subprocess.Popen(["gmx", "genconf", "-f", "output%05d.pdb"%i, 
                               "-o", "s_%05d.pdb"%i, "-nbox",
                                 "%d"%na, "%d"%nb, "%d"%nc],
                              stdout=subprocess.PIPE, stderr=subprocess.PIPE)

tools/Lammps/getInput.py

@@ -28,8 +28,8 @@
     LIB = "/net/hulk/home6/chengtao/soft/simpy/lib"
 elif socket.gethostname() == "zwicky":
     LIB = "/home/tcheng/Soft/simpy/lib"
-elif socket.gethostname() == "tao-Precision-Tower-3420":
-    LIB = "/home/tao/Soft/simpy/lib"
+elif socket.gethostname() == "tao-Precision-Tower-3420-ubuntu":
+    LIB = "/home/tao/soft/simpy/lib"
 elif "node" in socket.gethostname():
     LIB = "/net/hulk/home6/chengtao/soft/simpy/lib"
 elif socket.gethostname() == "tao-ThinkCentre-M79":

tools/linux/resize.sh

@@ -0,0 +1,10 @@
+convert slice-0.png -resize 800x400 -background 'rgb(255,255,255)' -compose Copy -gravity center -extent 300x300 re-00.png
+convert slice-1.png -resize 800x400 -background 'rgb(255,255,255)' -compose Copy -gravity center -extent 300x300 re-01.png
+convert slice-2.png -resize 800x400 -background 'rgb(255,255,255)' -compose Copy -gravity center -extent 300x300 re-02.png
+convert slice-3.png -resize 800x400 -background 'rgb(255,255,255)' -compose Copy -gravity center -extent 300x300 re-03.png
+convert slice-4.png -resize 800x400 -background 'rgb(255,255,255)' -compose Copy -gravity center -extent 300x300 re-04.png
+convert slice-5.png -resize 800x400 -background 'rgb(255,255,255)' -compose Copy -gravity center -extent 300x300 re-05.png
+convert slice-6.png -resize 800x400 -background 'rgb(255,255,255)' -compose Copy -gravity center -extent 300x300 re-06.png
+convert slice-7.png -resize 800x400 -background 'rgb(255,255,255)' -compose Copy -gravity center -extent 300x300 re-07.png
+convert slice-8.png -resize 800x400 -background 'rgb(255,255,255)' -compose Copy -gravity center -extent 300x300 re-08.png
+convert slice-9.png -resize 800x400 -background 'rgb(255,255,255)' -compose Copy -gravity center -extent 300x300 re-09.png

tools/sas/remove-low-coordinated.py

@@ -0,0 +1,21 @@
+f = open("cn.dat", "r")
+lines = f.readlines()
+f.close()
+
+f = open("out.xyz", "r")
+coords = f.readlines()
+f.close()
+
+new_coords = []
+
+for i in range(len(lines)):
+    nc = int(lines[i])
+    if nc > 5:
+        new_coords.append(coords[2+i])
+
+o = open("out.new.xyz", "w")
+o.write("%d\n\n"%len(new_coords))
+for i in new_coords:
+    o.write(i)
+o.close()
+