This is a read-only mirror of pymolwiki.org

Difference between revisions of "Wfmesh"

From PyMOL Wiki
Jump to navigation Jump to search
m
m (26 revisions)
 
(21 intermediate revisions by 4 users not shown)
Line 1: Line 1:
 +
{{Infobox script-repo
 +
|type      = script
 +
|filename  = wfmesh.py
 +
|author    = [[User:Tmwsiy|Dan Kulp]]
 +
|license  = -
 +
}}
 +
 
===DESCRIPTION===
 
===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 ([http://www.openfx.org OpenFX], [http://synapses.mcg.edu/tools/xroads/xroads.stm 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.   
+
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 obj files on the web, you can also easily created them with open source tools ([http://www.openfx.org OpenFX], [http://synapses.mcg.edu/tools/xroads/xroads.stm 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 - create a mesh object from Wavefront (*.obj) formated file
  
−
*createWFMesh
 
 
===IMAGES===
 
===IMAGES===
 +
 
[[Image:Starwars_pymol.png|thumb|left|Star Wars Anyone?]]
 
[[Image:Starwars_pymol.png|thumb|left|Star Wars Anyone?]]
−
[[Image:Torus_pymol.png|thumb|left|A Torus, as an example shape you could do]]
 
−
 
−
 
−
 
−
 
−
 
−
 
−
 
−
 
−
 
−
 
−
 
−
 
−
 
  
 +
[[Image:Torus_pymol.png|thumb|left|A Torus, as an example shape you could do. Notice polygon normals are being used...need smoothing!]]
  
 
===SETUP===
 
===SETUP===
−
Simply "run WFMesh.py"
+
Simply "import wfmesh.py"
  
 
===NOTES / STATUS===
 
===NOTES / STATUS===
 
*Tested on Pymolv0.97, Windows platform, should work on linux as well.
 
*Tested on Pymolv0.97, Windows platform, should work on linux as well.
 +
*Coloring is fixed for grey and sections of mesh are stored, but not used.
 +
*Simple opengl calls; not optimized (display lists, etc) or anything.
 +
*Vertex Normal code is broken, so normals are per polygon right now.
 
*Post problems in the discussion page, on 'my talk' page or just email me : dwkulp@mail.med.upenn.edu
 
*Post problems in the discussion page, on 'my talk' page or just email me : dwkulp@mail.med.upenn.edu
  
−
===USAGE===
+
===EXAMPLES===
−
createWFObj file, name [,translate=[0,0,0]] [,flip=0]
+
import wfmesh
 +
cd /home/tlinnet/Software/pymol/Pymol-script-repo/files_for_examples
 +
wfmesh.createWFObj('torus.obj','Torus',flip=1)    # Flip = 1, if OBJ created by openFX, crossroads3D combination
 +
  wfmesh.createWFObj("torus.obj","Torus2",translate=[5,5,0], flip=1)
 +
wfmesh.createWFObj("ship.obj","Ship")
  
−
===EXAMPLES===
 
−
  createWFObj "torus.obj" "Torus" translate=[10,10,0] flip=1 # Flip = 1, if OBJ created by openFX, crossroads3D combination
 
−
 
 
 
===REFERENCES===
 
===REFERENCES===
−
 
+
[http://www.openfx.org OpenFX]
−
 
+
[http://synapses.mcg.edu/tools/xroads/xroads.stm Crossroads3D]
−
===SCRIPTS (WFMesh.py)===
 
−
WFMesh.py
 
−
<source lang="python">
 
−
###############################################
 
−
#  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)
 
−
 
 
−
</source>
 
  
 
===ADDITIONAL RESOURCES===
 
===ADDITIONAL RESOURCES===
 
Torus.obj
 
Torus.obj
−
Once I figure out how to add files besides images I'll upload this file for demo purposes.
+
[http://pymolwiki.org/images/9/98/Torus.zip Torus.zip]
 +
 
  
 
[[Category:Script_Library|WFMesh]]
 
[[Category:Script_Library|WFMesh]]
 +
[[Category:ThirdParty_Scripts]]
 +
[[Category:Pymol-script-repo]]

Latest revision as of 04:26, 28 March 2014

Type Python Script
Download wfmesh.py
Author(s) Dan Kulp
License -
This code has been put under version control in the project Pymol-script-repo

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 obj files 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 - create a mesh object from Wavefront (*.obj) formated file

IMAGES

Star Wars Anyone?
A Torus, as an example shape you could do. Notice polygon normals are being used...need smoothing!

SETUP

Simply "import wfmesh.py"

NOTES / STATUS

  • Tested on Pymolv0.97, Windows platform, should work on linux as well.
  • Coloring is fixed for grey and sections of mesh are stored, but not used.
  • Simple opengl calls; not optimized (display lists, etc) or anything.
  • Vertex Normal code is broken, so normals are per polygon right now.
  • Post problems in the discussion page, on 'my talk' page or just email me : dwkulp@mail.med.upenn.edu

EXAMPLES

import wfmesh
cd /home/tlinnet/Software/pymol/Pymol-script-repo/files_for_examples
wfmesh.createWFObj('torus.obj','Torus',flip=1)    # Flip = 1, if OBJ created by openFX, crossroads3D combination
wfmesh.createWFObj("torus.obj","Torus2",translate=[5,5,0], flip=1)
wfmesh.createWFObj("ship.obj","Ship")

REFERENCES

OpenFX Crossroads3D

ADDITIONAL RESOURCES

Torus.obj Torus.zip

Retrieved from "http://wiki.pymol.org/index.php?title=Wfmesh&oldid=10844"