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show_UNRES.py - large loops speedup by using xrange
author
Dawid Jagiela
<lightnir@chem.univ.gda.pl>
Sun, 22 Sep 2013 13:26:40 +0000
(15:26 +0200)
committer
Dawid Jagiela
<lightnir@chem.univ.gda.pl>
Sun, 22 Sep 2013 13:26:40 +0000
(15:26 +0200)
source/pymol/show_UNRES.py
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diff --git
a/source/pymol/show_UNRES.py
b/source/pymol/show_UNRES.py
index
179e1af
..
e922779
100644
(file)
--- a/
source/pymol/show_UNRES.py
+++ b/
source/pymol/show_UNRES.py
@@
-54,17
+54,17
@@
def show_UNRES(sl='(all)'):
# Get pseudo-peptide group positions
atoms=cmd.get_model(sl+" & n. CA").atom
p=[]
# Get pseudo-peptide group positions
atoms=cmd.get_model(sl+" & n. CA").atom
p=[]
- for i in range(0,len(atoms)-1):
+ for i in xrange(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=[]
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)):
+ for i in xrange(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=[]
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)):
+ for i in xrange(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] ] )
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] ] )
@@
-73,7
+73,7
@@
def show_UNRES(sl='(all)'):
#
# [ 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.
#
# [ 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)):
+ for i in xrange(0,len(e)):
# vactor CB->CA
tmp0=[e[i][4], e[i][5], e[i][6]]
#l=cpv.length(tmp0)
# vactor CB->CA
tmp0=[e[i][4], e[i][5], e[i][6]]
#l=cpv.length(tmp0)
@@
-98,10
+98,10
@@
def show_UNRES(sl='(all)'):
# Get Glicynes positions
atoms=cmd.get_model(sl+' & n. CA & resn GLY').atom
g=[]
# Get Glicynes positions
atoms=cmd.get_model(sl+' & n. CA & resn GLY').atom
g=[]
- for i in range(0,len(atoms)):
+ for i in xrange(0,len(atoms)):
g.append( [ atoms[i].resn, atoms[i].coord[0], atoms[i].coord[1], atoms[i].coord[2] ])
# Draw the glicyne spheres
g.append( [ atoms[i].resn, atoms[i].coord[0], atoms[i].coord[1], atoms[i].coord[2] ])
# Draw the glicyne spheres
- for i in range(0, len(g)):
+ for i in xrange(0, len(g)):
obj.extend( [ COLOR, resdb[g[i][0]][0], resdb[g[i][0]][1], resdb[g[i][0]][2] ] )
obj.extend( [ SPHERE, g[i][1], g[i][2], g[i][3], resdb[g[i][0]][3]])
obj.extend( [ COLOR, resdb[g[i][0]][0], resdb[g[i][0]][1], resdb[g[i][0]][2] ] )
obj.extend( [ SPHERE, g[i][1], g[i][2], g[i][3], resdb[g[i][0]][3]])