From bdcb3a1a0c8c27deb378dbd50070126582588f94 Mon Sep 17 00:00:00 2001
From: Dawid Jagiela <lightnir@chem.univ.gda.pl>
Date: Mon, 11 Feb 2013 00:44:52 +0100
Subject: [PATCH] added UNRES visualization plugin for PyMOL

---
 source/pymol/show_UNRES.py |  143 ++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 143 insertions(+)
 create mode 100644 source/pymol/show_UNRES.py

diff --git a/source/pymol/show_UNRES.py b/source/pymol/show_UNRES.py
new file mode 100644
index 0000000..a6097a4
--- /dev/null
+++ b/source/pymol/show_UNRES.py
@@ -0,0 +1,143 @@
+# -*- coding: utf-8 -*-
+'''
+-------------------------------------------------------------------------------
+  show_UNRES.py - UNRES model viewer v 1.0
+-------------------------------------------------------------------------------
+ 
+  Written by Dawid Jagieła (lightnir@chem.univ.gda.pl)  Feb 2013 
+ 
+'''
+
+from chempy import cpv
+from pymol import cmd
+import cmd
+from pymol.cgo import *
+
+from pymol.menu import *
+import pymol.menu
+
+def __init__(self):
+	# Add unres to known represtentations 
+	from pymol import constants
+	constants.repres_sc.append('unres')
+
+
+def show_UNRES(sl='(all)'):
+	# basic settings
+	p_radius = 0.6
+	e_size = 1.0
+	# residue dictionary
+	# resn = [color_Red, color_Green, color_Blue, elipsoid_side_width ]
+	resdb = {	'CYS': [1.000, 1.000, 0.000, 2.96868],
+				'MET': [0.000, 1.000, 0.000, 3.08863],
+				'PHE': [0.000, 0.392, 0.000, 3.04238],
+				'ILE': [0.000, 1.000, 0.000, 3.17389],
+				'LEU': [0.000, 1.000, 0.000, 2.52078],
+				'VAL': [0.000, 1.000, 0.000, 2.68924],
+				'TRP': [0.000, 0.392, 0.000, 3.47403],
+				'TYR': [0.596, 0.984, 0.596, 3.35434],
+				'ALA': [0.000, 1.000, 0.000, 1.72686],
+				'GLY': [1.000, 1.000, 1.000, 1.11383],
+				'THR': [1.000, 0.000, 1.000, 2.59210],
+				'SER': [1.000, 0.000, 1.000, 1.68800],
+				'GLN': [1.000, 0.000, 1.000, 2.22201],
+				'ASN': [1.000, 0.000, 1.000, 2.24946],
+				'GLU': [1.000, 0.000, 0.000, 2.05551],
+				'ASP': [1.000, 0.000, 0.000, 1.77556],
+				'HIS': [1.000, 0.000, 1.000, 3.02627],
+				'ARG': [0.000, 0.000, 1.000, 3.25143],
+				'LYS': [0.000, 0.000, 1.000, 4.50054],
+				'PRO': [0.000, 1.000, 1.000, 2.20525]
+			}
+
+
+	# Get pseudo-peptide group positions
+	atoms=cmd.get_model(sl+" & n. CA").atom
+	p=[]
+	for i in range(0,len(atoms)-1):
+		p.append( [atoms[i].coord[0]+(atoms[i+1].coord[0]-atoms[i].coord[0])/2, atoms[i].coord[1]+(atoms[i+1].coord[1]-atoms[i].coord[1])/2, atoms[i].coord[2]+(atoms[i+1].coord[2]-atoms[i].coord[2])/2 ] )
+	obj=[]
+	for i in range(0,len(p)):
+		obj.extend( [ COLOR, 0.643, 0.933, 0.960 ] )
+		obj.extend( [ SPHERE, p[i][0], p[i][1], p[i][2], p_radius ] )
+
+	# Get Sidechain elipsoids positions
+	atoms=cmd.get_model(sl+" & n. CB").atom
+	e=[]
+	for i in range(0,len(atoms)):
+		ca=cmd.get_model(sl+" & n. CA & resn "+atoms[i].resn+" & resi "+atoms[i].resi).atom
+		e.append( [ atoms[i].resn, atoms[i].coord[0], atoms[i].coord[1], atoms[i].coord[2], atoms[i].coord[0]-ca[0].coord[0], atoms[i].coord[1]-ca[0].coord[1], atoms[i].coord[2]-ca[0].coord[2] ] )
+
+	# This is from pymol devel example cgo07.py form http://pymol.sourcearchive.com/documentation/1.2r1/cgo07_8py-source.html
+    #
+	# [ ELLIPSOID, x_pos, y_pos, z_pos, size, x0, y0, z0, x1, y1, z2, x2, y2, z2 ]
+	# where the xyz vectors are orthogonal and of length 1.0 or less.
+	for i in range(0,len(e)):
+		# vactor CB->CA
+		tmp0=[e[i][4], e[i][5], e[i][6]]
+		l=cpv.length(tmp0)
+		# random vector
+		tmp1 = cpv.random_vector()
+		# orthogonal vector to tmp0 and tmp1 
+		tmp2 = cpv.cross_product(tmp1, tmp0)
+		tmp3 = cpv.cross_product(tmp0, tmp2)
+		tmp2 = cpv.normalize(tmp2)
+		tmp3 = cpv.normalize(tmp3)
+		tmp2 = cpv.scale(tmp2,0.9*resdb[e[i][0]][3])
+		tmp3 = cpv.scale(tmp3,0.9*resdb[e[i][0]][3])
+				
+		obj.extend( [ COLOR, resdb[e[i][0]][0], resdb[e[i][0]][1], resdb[e[i][0]][2] ] )
+		obj.extend( [ ELLIPSOID, e[i][1], e[i][2], e[i][3], e_size, ] + tmp0 + tmp2 + tmp3 )
+
+	cmd.set('cgo_ellipsoid_quality', 2)
+	cmd.load_cgo(obj,'UNRES_'+sl)
+
+
+# Hook up to PyMols show command
+
+def myshow(representation="",selection="",_self=cmd):
+	'''
+DESCRIPTION
+	 
+    "show" turns on representations for objects and selections.
+	 
+USAGE
+ 
+    show [ representation [, selection ]]
+ 
+ARGUMENTS
+ 
+    representation = lines, spheres, mesh, ribbon, cartoon, sticks,
+    dots, surface, labels, extent, nonbonded, nb_spheres, slice,
+    extent, slice, dashes, angles, dihedrals, cgo, cell, callback,
+    unres or everything
+ 
+    selection = string: a selection-expression or name-pattern
+ 
+NOTES
+ 
+    With no arguments, "show" alone turns on lines for all bonds and
+    nonbonded for all atoms in all molecular objects.
+ 
+EXAMPLES
+ 
+    show
+    show ribbon
+    show lines, (name ca or name c or name n)
+
+SEE ALSO
+ 
+    hide, enable, disable
+ 
+'''
+
+	if representation=='unres':
+		if selection=="":
+			show_UNRES('all')
+		else:
+			show_UNRES(selection)
+	else:
+		cmd.show(representation, selection,_self)
+
+
+cmd.extend('show',myshow)
-- 
1.7.9.5