示例#1
0
def load():
   cmd.set("valence")
   r = 0
   list = glob("pdb/*/*")
   (x,y,z)=(0,0,0)
   start = time.time()
   count = 1
   scale = 100.0
   for file in list:
      cmd.load(file,str(count),quiet=1)
      cmd.translate([x*scale,y*scale,z*scale],object=str(count))
#      cmd.disable(str(count))
      atoms = cmd.count_atoms()
      passed = time.time()-start
      print "%3d structures/%5.1f sec = %8.1f atom/sec over %6d atoms"%(count,passed,atoms/passed,atoms)
      count = count + 1
      if count>100: break
      x = x + 1
      if x>7:
         x = 0
         y = y + 1
         if y>7:
            y = 0
            z = z + 1
            if z>9:
               y = 0
               z = z + 1
   cmd.zoom()
   cmd.set("sphere_mode",1)
   cmd.as("spheres")
   cmd.rebuild()
   cmd.set("hash_max",250)
示例#2
0
文件: B05.py 项目: jchodera/pymol
def load():
   try:
      r = 0
      list = glob(ent_dir)
      list.sort()
#      list = [ "pdb/vq" ]
      for dir in list:
         sys.__stdout__.write("\n"+dir)
         sys.__stdout__.flush()
         for file in glob(dir+"/pdb*"):
            name = os.path.split(file)[-1]
            name = string.split(name,'.')[0]
            cmd.disable()
            cmd.load(file,name)
            cmd.as("cartoon",name)
            cmd.refresh()
            cmd.dss(name)
            cmd.refresh()
            time.sleep(0.1)
            sys.__stdout__.write(".")
            sys.__stdout__.flush()
         sys.__stdout__.write("("+str(cmd.count_atoms())+")")
         sys.__stdout__.flush()         
         cmd.dss()
         cmd.delete('all')
   except:
      traceback.print_exc()
示例#3
0
文件: B03.py 项目: jchodera/pymol
def load():
   cmd.set("valence")
   r = 0
   list = glob("pdb/*/*")
#   while list[0]!="pdb/f8/pdb1f8u":
#      list.pop(0)
   for file in list:
      try:
         cmd.delete('pdb')
         cmd.load(file,'pdb')
         cmd.set_title('pdb',1,os.path.split(file)[-1])
         cmd.rewind()
         cmd.orient('pdb')
         cmd.refresh()
         cmd.as("ribbon")
         cmd.refresh()
         cmd.as("sticks")
         cmd.refresh()
         sys.__stderr__.write(".")
         sys.__stderr__.flush()
         n = cmd.count_states()
         if n>1:
            cmd.rewind()
            sys.__stderr__.write(file+"\n")
            sys.__stderr__.flush()
            for a in range(1,n+1):
               cmd.forward()
               cmd.refresh()
      except:
         traceback.print_exc()
示例#4
0
文件: particle01.py 项目: Almad/pymol
    particle.append([resi] + 
                     map(lambda x:(random()-0.5)*box_size/2,[0]*3) + # x,y,z
                    [random()+0.5] + # r
                    map(lambda x:(random()-0.5),[0]*3) # vx,vy,vz
                    )
        
# create cloud object

for part in particle:
    cmd.pseudoatom("cloud",
                   resi = part[0],
                   pos = part[1:4],
                   vdw = part[4])

# draw spheres efficiently
cmd.as("spheres")
cmd.unset("cull_spheres") 

# position the camera

cmd.zoom()
cmd.zoom("center",box_size)

# let there be color

cmd.spectrum()

# this is the main loop

def simulation():
    import traceback
示例#5
0
文件: link_demo.py 项目: Almad/pymol
cmd.load("$TUT/1hpv.pdb")

# color by chain (aesthetics)

util.cbc()

# store the links as atom text_types

cmd.alter("name ca",r"text_type='http://delsci.info/cgi-bin/click.cgi?residue=%s%s%s'%(resn,resi,chain)")

# put the mouse into single-atom selection mode

cmd.set('mouse_selection_mode',0)

# just show ribbon (means we can only select labelled C-alphas)

cmd.as("cartoon") 

# set up the labels

cmd.label("name ca","'Link'") 

# color the labels white

cmd.set("label_color", 'white')

# activate the wizard

cmd.set_wizard(Clickurl()) 

示例#6
0
from sys import argv
from pymol import cmd, util

if len(argv) < 2:
	print "usage: " + argv[0] + "pdbfile\n"
	quit()

pdbfile = argv[1]


cmd.set('antialias', 1)
cmd.set('depth_cue', 0)
cmd.set('ray_opaque_background', 0)
cmd.set('ray_trace_fog', 0)

cmd.load(pdbfile)

cmd.as('sticks', 'cross*')
cmd.as('surface', 'protein')
cmd.color('wheat', 'protein')

cmd.orient('protein')
cmd.png('mappedpdb', width=600, height=450, dpi=72, ray=1)
 
def centerOfMass(selection):
   ## assumes equal weights (best called with "and name ca" suffix)
   model = cmd.get_model(selection)
   x,y,z=0,0,0
   for a in model.atom:
       x+= a.coord[0]
       y+= a.coord[1]
       z+= a.coord[2]
   return (x/len(model.atom), y/len(model.atom), z/len(model.atom))
 
cmd.load("/group/bioinf/Data/PDBLinks/1c7c.pdb")
cmd.select("domain", "/1c7c//A/143-283/ and name ca") ## selecting a domain
 
domainCenter=centerOfMass("domain")
 
print "Center of mass: (%.1f,%.1f,%.1f)"% domainCenter
cmd.as("cartoon", "all")
cmd.show("spheres", "domain")
 
## Creating a sphere CGO
com = [COLOR, 1.0, 1.0, 1.0, SPHERE]+list(domainCenter) + [3.0] ## white sphere with 3A radius
cmd.load_cgo(com, "CoM")
 
cmd.zoom("1c7c", 1.0)
cmd.center("domain")
 
#ah@bioinfws19:~/Projects/PyMOL$ pymol -qc centerOfMass4.py
#Center of mass: (-1.0,24.5,48.2)
#ah@bioinfws19:~/Projects/PyMOL$