From b7842316b64e1cfcc5b13fa9351dc6332bd6ed63 Mon Sep 17 00:00:00 2001
From: Francois Gygi <fgygi@ucdavis.edu>
Date: Sat, 4 Jun 2016 18:25:04 +0000
Subject: [PATCH] add qbox_angle.py script

git-svn-id: http://qboxcode.org/svn/qb/trunk@1829 cba15fb0-1239-40c8-b417-11db7ca47a34
---
 util/qbox_angle.py | 104 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 104 insertions(+)
 create mode 100755 util/qbox_angle.py

diff --git a/util/qbox_angle.py b/util/qbox_angle.py
new file mode 100755
index 0000000..9642c7e
--- /dev/null
+++ b/util/qbox_angle.py
@@ -0,0 +1,104 @@
+#!/usr/bin/python
+# qbox_angle.py
+# extract angle defined by three atoms from Qbox output
+# use: qbox_angle.py name1 name2 name3 file.r
+import xml.sax
+import sys
+import math
+
+if len(sys.argv) != 5:
+  print "use: ",sys.argv[0]," name1 name2 name3 file.r"
+  sys.exit()
+
+name1 = ""
+name2 = ""
+name3 = ""
+
+# 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.buffer1 = ""
+    self.buffer2 = ""
+    self.buffer3 = ""
+
+  def startElement(self, name, attributes):
+    if name == "atomset":
+      self.buffer1 = ""
+      self.buffer2 = ""
+      self.buffer3 = ""
+      self.atom1done = 0
+      self.atom2done = 0
+      self.atom3done = 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 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
+
+  def endElement(self, name):
+    if name == "atomset":
+      self.pos1 = self.buffer1.split()
+      self.pos2 = self.buffer2.split()
+      self.pos3 = self.buffer3.split()
+      self.r1x = float(self.pos1[0])
+      self.r1y = float(self.pos1[1])
+      self.r1z = float(self.pos1[2])
+      self.r2x = float(self.pos2[0])
+      self.r2y = float(self.pos2[1])
+      self.r2z = float(self.pos2[2])
+      self.r3x = float(self.pos3[0])
+      self.r3y = float(self.pos3[1])
+      self.r3z = float(self.pos3[2])
+      #print "r1: ",self.r1x,self.r1y,self.r1z
+      #print "r2: ",self.r2x,self.r2y,self.r2z
+      #print "r3: ",self.r3x,self.r3y,self.r3z
+      # normalized r12
+      r12x = self.r1x - self.r2x
+      r12y = self.r1y - self.r2y
+      r12z = self.r1z - self.r2z
+      fac12 = 1.0/math.sqrt(r12x*r12x+r12y*r12y+r12z*r12z)
+      r12x = fac12 * r12x
+      r12y = fac12 * r12y
+      r12z = fac12 * r12z
+      # normalized r32
+      r32x = self.r3x - self.r2x
+      r32y = self.r3y - self.r2y
+      r32z = self.r3z - self.r2z
+      fac32 = 1.0/math.sqrt(r32x*r32x+r32y*r32y+r32z*r32z)
+      r32x = fac32 * r32x
+      r32y = fac32 * r32y
+      r32z = fac32 * r32z
+      sp = r12x*r32x + r12y*r32y + r12z*r32z
+      c = sp
+      c = max(-1.0,min(1.0,sp))
+      a = (180.0/math.pi)*math.acos(c)
+      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]
+filename = sys.argv[4]
+parser = xml.sax.make_parser()
+handler = QboxOutputHandler()
+parser.setContentHandler(handler)
+parser.parse(sys.argv[4])
--
libgit2 0.26.0