add qbox_torsion.py script

git-svn-id: http://qboxcode.org/svn/qb/trunk@1830 cba15fb0-1239-40c8-b417-11db7ca47a34

util/qbox_torsion.py

+#!/usr/bin/python
+# qbox_torsion.py
+# extract torsion angle defined by four atoms from Qbox output
+# use: qbox_torsion.py name1 name2 name3 name4 file.r
+import xml.sax
+import sys
+import math
+
+if len(sys.argv) != 6:
+  print "use: ",sys.argv[0]," name1 name2 name3 name4 file.r"
+  sys.exit()
+
+name1 = ""
+name2 = ""
+name3 = ""
+name4 = ""
+
+def norm(x):
+  return math.sqrt(x[0]*x[0]+x[1]*x[1]+x[2]*x[2])
+
+def cross_product(a,b):
+# cross product c = a ^ b
+  cx = a[1] * b[2] - a[2] * b[1]
+  cy = a[2] * b[0] - a[0] * b[2]
+  cz = a[0] * b[1] - a[1] * b[0]
+  return (cx,cy,cz)
+
+# Qbox output handler to extract and process <atomset>
+class QboxOutputHandler(xml.sax.handler.ContentHandler):
+  def __init__(self):
+    self.readPos1 = 0
+    self.readPos2 = 0
+    self.readPos3 = 0
+    self.readPos4 = 0
+    self.buffer1 = ""
+    self.buffer2 = ""
+    self.buffer3 = ""
+    self.buffer4 = ""
+
+  def startElement(self, name, attributes):
+    if name == "atomset":
+      self.buffer1 = ""
+      self.buffer2 = ""
+      self.buffer3 = ""
+      self.buffer4 = ""
+      self.atom1done = 0
+      self.atom2done = 0
+      self.atom3done = 0
+      self.atom4done = 0
+    elif name == "atom":
+      self.atom_name = attributes["name"]
+      if self.atom_name == name1:
+        self.readPos1 = 1
+      elif self.atom_name == name2:
+        self.readPos2 = 1
+      elif self.atom_name == name3:
+        self.readPos3 = 1
+      elif self.atom_name == name4:
+        self.readPos4 = 1
+    elif name == "position":
+      self.buffer = ""
+
+  def characters(self, data):
+    if self.readPos1:
+      self.buffer1 += data
+    elif self.readPos2:
+      self.buffer2 += data
+    elif self.readPos3:
+      self.buffer3 += data
+    elif self.readPos4:
+      self.buffer4 += data
+
+  def endElement(self, name):
+    if name == "atomset":
+      pos1 = self.buffer1.split()
+      r1 = (float(pos1[0]),float(pos1[1]),float(pos1[2]))
+      pos2 = self.buffer2.split()
+      r2 = (float(pos2[0]),float(pos2[1]),float(pos2[2]))
+      pos3 = self.buffer3.split()
+      r3 = (float(pos3[0]),float(pos3[1]),float(pos3[2]))
+      pos4 = self.buffer4.split()
+      r4 = (float(pos4[0]),float(pos4[1]),float(pos4[2]))
+
+      #print "r1: ",r1
+      #print "r2: ",r2
+      #print "r3: ",r3
+      #print "r4: ",r4
+      # e12 = normalized r12
+      r12 = (r1[0]-r2[0],r1[1]-r2[1],r1[2]-r2[2])
+      fac12 = 1.0/norm(r12)
+      e12 = (fac12*r12[0],fac12*r12[1],fac12*r12[2])
+      # e32 = normalized r32
+      r32 = (r3[0]-r2[0],r3[1]-r2[1],r3[2]-r2[2])
+      fac32 = 1.0/norm(r32)
+      e32 = (fac32*r32[0],fac32*r32[1],fac32*r32[2])
+      # e43 = normalized r43
+      r43 = (r4[0]-r3[0],r4[1]-r3[1],r4[2]-r3[2])
+      fac43 = 1.0/norm(r43)
+      e43 = (fac43*r43[0],fac43*r43[1],fac43*r43[2])
+      # e23 = - e32
+      e23 = (-e32[0],-e32[1],-e32[2])
+
+      u = cross_product(e12,e32)
+      v = cross_product(e23,e43)
+
+      a = 0.0
+      unorm = norm(u)
+      vnorm = norm(v)
+      if (unorm!=0.0) and (vnorm!=0.0):
+        u = (u[0]/unorm,u[1]/unorm,u[2]/unorm)
+        v = (v[0]/vnorm,v[1]/vnorm,v[2]/vnorm)
+        uv = u[0]*v[0] + u[1]*v[1] + u[2]*v[2]
+        cc = max(min(uv,1.0),-1.0)
+
+        w = cross_product(u,v)
+        we32 = e32[0]*w[0] + e32[1]*w[1] + e32[2]*w[2]
+        ss = max(min(we32,1.0),-1.0)
+        a = (180.0/math.pi) * math.atan2(ss,cc)
+
+      print '%.4f' % a
+    elif name == "position":
+      self.readPos1 = 0
+      self.readPos2 = 0
+      self.readPos3 = 0
+
+name1 = sys.argv[1]
+name2 = sys.argv[2]
+name3 = sys.argv[3]
+name4 = sys.argv[4]
+filename = sys.argv[5]
+parser = xml.sax.make_parser()
+handler = QboxOutputHandler()
+parser.setContentHandler(handler)
+parser.parse(sys.argv[5])