Wfmesh

DESCRIPTION

This script will create an object for any Wavefront(.OBJ) mesh file. This is a way to extend the number of objects you can use. Also, you have more control over the coloring, transformations, etc than the CGOs. Although there are a number of these objs litered on the web, you can also easily created them with open source tools (OpenFX, Crossroads3D). It takes literally, 2 min to get an object created and then loaded into pymol. Simply open OpenFX Designer, click File->Insert->Model, then choose any of the models (or create your own of course!), then export it as .3ds file. Then open the .3ds file from Crossroads3D and export as Wavefront OBJ.

• createWFMesh

IMAGES

Star Wars Anyone?

A Torus, as an example shape you could do

SETUP

Simply "run WFMesh.py"

NOTES / STATUS

• Tested on Pymolv0.97, Windows platform, should work on linux as well.
• Post problems in the discussion page, on 'my talk' page or just email me : dwkulp@mail.med.upenn.edu

USAGE

createWFObj file, name [,translate=[0,0,0]] [,flip=0]

EXAMPLES

  createWFObj "torus.obj" "Torus" translate=[10,10,0] flip=1 # Flip = 1, if OBJ created by openFX, crossroads3D combination
  

SCRIPTS (WFMesh.py)

WFMesh.py

###############################################
#  File:          WFObj.py
#  Author:        Dan Kulp
#  Creation Date: 5/13/05
#
#  Notes:
#  Create openGL objects from a wavefront (obj) file
###############################################

import os
import string
import re
import math
from pymol.opengl.gl import *
from pymol.callback import Callback


# Wrapper Function, to create a given WFObj with a specific name (flip = 1 if OpenFX + Crossroads used)
def createWFObj(file, name,translate=[0,0,0],flip=0):
	obj = WFMesh(file,translate,flip)
	cmd.load_callback(obj,name)


# Class for Wavefront Mesh
class WFMesh(Callback):

    verts = []        # list of vertices
    polys = []        # list of poylgons
    pnorms = []       # list of polynomal normals
    vnorms = {}       # dict. of vertex normals
    vavenorms = []    # list of vertex normals, redundant -- I'm far froma python pro.
    sections = {}     # list of sections of mesh

    # Read mesh into memory
    def readOBJ(self,file):
        if os.path.exists(file):
	    input = open(file,'r')
	    for line in input:
		dat = re.split("\s+", line)

		# Find vertex line
		if line[0] == 'v' and line[1] != 't' and line[1] != 'n':    self.verts.append([dat[1],dat[2],dat[3]])

		# Find polygon line
       	        if line[0] == 'f':    self.polys.append([dat[1],dat[2],dat[3]])

		# Find section line
		if line[0] == 'g':    self.sections[len(self.polys)] = dat[1] 


    # Compute the normals for each polygon and each vertex   		
    def computeNorms(self):

	# Compute norms for each polygon
	for p in self.polys:
		v12 = [float(self.verts[int(p[1])-1][0]) - float(self.verts[int(p[0])-1][0]),\
		       float(self.verts[int(p[1])-1][1]) - float(self.verts[int(p[0])-1][1]),\
		       float(self.verts[int(p[1])-1][2]) - float(self.verts[int(p[0])-1][2]) \
		      ]
			
		v13 = [float(self.verts[int(p[2])-1][0]) - float(self.verts[int(p[0])-1][0]),\
		       float(self.verts[int(p[2])-1][1]) - float(self.verts[int(p[0])-1][1]),\
		       float(self.verts[int(p[2])-1][2]) - float(self.verts[int(p[0])-1][2]) \
		      ]	

		# Compute poly normal
		polynorm = self.cross(v12,v13) 
		norm = self.normalize(polynorm)


		# Files created by OpenFX, Crossroads combination need have their normals flipped	
		if self.flip:
			norm[0] = -norm[0]
			norm[1] = -norm[1]
			norm[2] = -norm[2]

		# Append poly norm to polygonal norm array
		self.pnorms.append(norm)

		# Add norm to each vertexes norm..
	        try:
		    self.vnorms[int(p[0])-1] = [float(self.vnorms[int(p[0])-1][0]) + norm[0],
					    float(self.vnorms[int(p[0])-1][1]) + norm[1],
					    float(self.vnorms[int(p[0])-1][2]) + norm[2]
					   ]
		except:
		    self.vnorms[int(p[0])-1] = [norm[0],norm[1],norm[2]]

	        try:					   
		    self.vnorms[int(p[1])-1]  = [float(self.vnorms[int(p[1])-1][0]) + norm[0],
					    float(self.vnorms[int(p[1])-1][1]) + norm[1],
					    float(self.vnorms[int(p[1])-1][2]) + norm[2]
					   ]
		except:
		    self.vnorms[int(p[1])-1] = [norm[0],norm[1],norm[2]]

		try:
		    self.vnorms[int(p[2])-1]  = [float(self.vnorms[int(p[1])-1][0]) + norm[0],
					    float(self.vnorms[int(p[1])-1][1]) + norm[1],
					    float(self.vnorms[int(p[1])-1][2]) + norm[2]
					   ]
		except:
		    self.vnorms[int(p[2])-1] = [norm[0],norm[1],norm[2]]

      
        # Average out each vnorm..
	index = 0
      	for v in self.vnorms.values():
		self.vavenorms.append([v[0]/4, v[1]/4, v[2]/4])		
		index += 1

    # Utility function to normalize a given vector
    def normalize(self,v):
	mag = v[0]*v[0]+v[1]*v[1]+v[2]*v[2]
	if mag <= 0:
  	    mag = 1
	else:
	    mag = math.sqrt(mag)
		
	return [v[0]/mag, v[1]/mag,v[2]/mag]

    # Utility cross product function
    def cross(self,v1,v2):
	x = 0
	y = 1
	z = 2

	return [v1[y]*v2[z] - v1[z]*v2[y],\
		v1[z]*v2[x] - v1[x]*v2[z],\
		v1[x]*v2[y] - v1[y]*v2[x]
		]
		          	
    # Constructor
    def __init__(self, file,translate=[0,0,0],flip=0):
        self.verts = []
        self.polys = [] 
        self.pnorms = []
        self.vnorms = {}
        self.vavenorms = []
	self.translate = translate
	self.flip      = flip 

        print "Read in file: "+str(file)
	self.readOBJ(file)
	print "Done reading in WFMesh, now compute norms"
	self.computeNorms()
	print "Done computing norms, now display WFMesh"

    # Draw Function
    def __call__(self):
	
	glColorMaterial(GL_FRONT, GL_DIFFUSE);	
        glEnable(GL_COLOR_MATERIAL);
	glShadeModel(GL_SMOOTH);

	# Color Everything grey
        glColor3f(0.5,0.5,0.5);

	index = 0
	glPushMatrix()
	glTranslated(self.translate[0],self.translate[1],self.translate[2])
	for p in self.polys:
		glBegin(GL_POLYGON)
		glNormal3f(float(self.pnorms[index][0]),float(self.pnorms[index][1]),float(self.pnorms[index][2]))
		
		for i in range(0,len(p)):
			glVertex3f(float(self.verts[int(p[i])-1][0]),float(self.verts[int(p[i])-1][1]),float(self.verts[int(p[i])-1][2]))

			# Vertex Normals - not computed correctly, so commented out for now
#			norm = self.vnorms[int(p[i])-1]
#			glNormal3f(float(norm[0]),float(norm[1]),float(norm[2]))
		glEnd()
		index += 1
	glPopMatrix()





cmd.extend("createWFObj", createWFObj)

ADDITIONAL RESOURCES

Torus.obj Once I figure out how to add files besides images I'll upload this file for demo purposes.