From 5725f42d24099a12dd01ff84636cd8eac9781fed Mon Sep 17 00:00:00 2001
From: Justin Lecher <jlec@gentoo.org>
Date: Fri, 2 Nov 2012 11:58:58 +0100
Subject: [PATCH] Added update script

(c) 2011-09-23 by Justin L Lorieau
(c) 2012-10-31 by Thomas Holder
---
 plot_noe.py | 78 +++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 78 insertions(+)
 create mode 100644 plot_noe.py

diff --git a/plot_noe.py b/plot_noe.py
new file mode 100644
index 00000000..4af4fc2a
--- /dev/null
+++ b/plot_noe.py
@@ -0,0 +1,78 @@
+'''
+plot_noe.py
+
+(c) 2011-09-23 by Justin L Lorieau
+(c) 2012-10-31 by Thomas Holder
+'''
+
+from pymol import cmd, CmdException
+
+def plot_noe(filename, selection='', line_color='gray20', line_width='1.0', single=0, quiet=1):
+    """
+DESCRIPTION
+
+    A function for plotting XPLOR NOE restraints on a structure
+
+ARGUMENTS
+
+    filename = string: The filename of the NOE retraint file in XPLOR NIH format.
+
+    selection = string: atom selection {default: all}
+
+    line_color = string: The color for the NOE lines. {default: black}
+
+    line_width = float: The thickness of the NOE lines. {default: 1.0}
+
+NOE Restraint Format Example
+
+    assign (residue 5 and name HB#) (residue 21 and name HA) 3.0 0.7 0.7
+
+EXAMPLE
+
+    PyMOL> plot_noe noe_short.tbl
+    """
+    from pymol.parsing import split
+
+    single, quiet = int(single), int(quiet)
+
+    count = 0
+
+    for line in open(filename):
+        line = line.replace('(', ' (').replace(')', ') ').replace('#', '*')
+
+        a = filter(None, split(line, ' \t'))
+        if len(a) < 4 or not a[0].startswith('assi'):
+            continue
+
+        try:
+            float(a[3])
+        except ValueError:
+            continue
+
+        sele1, sele2 = a[1:3]
+
+        if selection:
+            sele1 = '(%s) and (%s)' % (selection, sele1)
+            sele2 = '(%s) and (%s)' % (selection, sele2)
+
+        label = single and "NOE" or ("NOE_%d" % (count + 1))
+
+        try:
+            cmd.distance(label, sele1, sele2, quiet=quiet)
+        except CmdException:
+            print 'FAILED: %s - %s' % (sele1, sele2)
+            continue
+
+        cmd.set("dash_color", line_color, label)
+        cmd.set("dash_gap", 0, label)
+        cmd.set("dash_width", line_width, label)
+
+        count += 1
+
+    if not quiet:
+        print ' Info: Created distance objects for %d restraints' % (count)
+
+    cmd.hide("labels", "NOE*")
+
+cmd.extend("plot_noe", plot_noe)
+