qbox_torsion.py 3.58 KB
Newer Older
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134
#!/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])