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)
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()
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()
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
cmd.load("$TUT/1hpv.pdb")
# color by chain (aesthetics)
util.cbc()
# store the links as atom text_types
cmd.alter("name ca",r"text_type='http://delsci.info/cgi-bin/click.cgi?residue=%s%s%s'%(resn,resi,chain)")
# put the mouse into single-atom selection mode
cmd.set('mouse_selection_mode',0)
# just show ribbon (means we can only select labelled C-alphas)
cmd.as("cartoon")
# set up the labels
cmd.label("name ca","'Link'")
# color the labels white
cmd.set("label_color", 'white')
# activate the wizard
cmd.set_wizard(Clickurl())
from sys import argv
from pymol import cmd, util
if len(argv) < 2:
print "usage: " + argv[0] + "pdbfile\n"
quit()
pdbfile = argv[1]
cmd.set('antialias', 1)
cmd.set('depth_cue', 0)
cmd.set('ray_opaque_background', 0)
cmd.set('ray_trace_fog', 0)
cmd.load(pdbfile)
cmd.as('sticks', 'cross*')
cmd.as('surface', 'protein')
cmd.color('wheat', 'protein')
cmd.orient('protein')
cmd.png('mappedpdb', width=600, height=450, dpi=72, ray=1)
def centerOfMass(selection):
## assumes equal weights (best called with "and name ca" suffix)
model = cmd.get_model(selection)
x,y,z=0,0,0
for a in model.atom:
x+= a.coord[0]
y+= a.coord[1]
z+= a.coord[2]
return (x/len(model.atom), y/len(model.atom), z/len(model.atom))
cmd.load("/group/bioinf/Data/PDBLinks/1c7c.pdb")
cmd.select("domain", "/1c7c//A/143-283/ and name ca") ## selecting a domain
domainCenter=centerOfMass("domain")
print "Center of mass: (%.1f,%.1f,%.1f)"% domainCenter
cmd.as("cartoon", "all")
cmd.show("spheres", "domain")
## Creating a sphere CGO
com = [COLOR, 1.0, 1.0, 1.0, SPHERE]+list(domainCenter) + [3.0] ## white sphere with 3A radius
cmd.load_cgo(com, "CoM")
cmd.zoom("1c7c", 1.0)
cmd.center("domain")
#ah@bioinfws19:~/Projects/PyMOL$ pymol -qc centerOfMass4.py
#Center of mass: (-1.0,24.5,48.2)
#ah@bioinfws19:~/Projects/PyMOL$
