Changeset c03ca6

Timestamp:

Sep 28, 2009, 6:35:27 PM (16 years ago)

Author:

Frederik Heber <heber@…>

Children:

6f1551

Parents:

f2dfc5

Message:

ShiftPeriodic.py fixed for xyz files.

File:

• util/src/ShiftPeriodic.py.in (modified) (1 diff)

util/src/ShiftPeriodic.py.in

@@ -7 +7 @@
 wrout = sys.stdout.write
 
-if (len(sys.argv) < 9):
-  print "Usage: "+sys.argv[0]+" <file> <offset> <box x> <box y> <box z> <shift x> <shift y> <shift z>"
+if (len(sys.argv) < 10):
+  print "Usage: "+sys.argv[0]+" <xyzfile> <element offset> <xyzoffset> <box x> <box y> <box z> <shift x> <shift y> <shift z>"
   print "Output goes to STDOUT."
   sys.exit(1)
 
 # get parameters
-offset=int(sys.argv[2])
-box=[float(sys.argv[3]), float(sys.argv[4]),float(sys.argv[5])]
-shift=[float(sys.argv[6]),float(sys.argv[7]),float(sys.argv[8])]
+elementoffset=int(sys.argv[2])
+xyzoffset=int(sys.argv[3])
+box=[float(sys.argv[4]), float(sys.argv[5]),float(sys.argv[6])]
+shift=[float(sys.argv[7]),float(sys.argv[8]),float(sys.argv[9])]
 
 # parse the file and obtain maxid
-print "Parsing the PDB file "+sys.argv[1]+"."
+wrerr("Parsing the coordinate file "+sys.argv[1]+".\n")
 file = open(sys.argv[1], "r")
+#wrout(file.readline())
+#wrout(file.readline())
 atoms = {}
 maxid=-1
+nr=0
 for line in file:
   # simpy print everything else
-  if "END" in line or "CONECT" in line or "MASTER" in line or "#" in line:
-    print line
-  else:
+  if not ("END" in line or "CONECT" in line or "MASTER" in line or "#" in line):
+    nr+=1
+file.close()
+file = open(sys.argv[1], "r")
+wrout("%d\n\tShifted by $shift from PDB file.\n" % (nr))
+for line in file:
+  # simpy print everything else
+  if not ("END" in line or "CONECT" in line or "MASTER" in line or "#" in line):
     fields=line.split()
     for i in range(3):
-      value=float(fields[i+offset])+shift[i]
+      value=float(fields[i+xyzoffset])+shift[i]
       while value > box[i]:
         value = value - box[i]
       while value < 0:
         value = value + box[i]
-      fields[i+offset] = str(value)
-    for j in range(len(fields)):
-      wrout("%s " % (fields[j]))
+      fields[i+xyzoffset] = str(value)
+    wrout("%s\t%lg\t%lg\t%lg" % (fields[elementoffset], float(fields[0+xyzoffset]), float(fields[1+xyzoffset]), float(fields[2+xyzoffset])))
     wrout("\n")