def visualize_orientation(direction, center=[0, 0, 0], scale=1.0, symmetric=False, color="green", color2="red"):
"""
Draw an arrow. Helper function for "helix_orientation" etc.
"""
from pymol import cgo
color_list = cmd.get_color_tuple(color)
color2_list = cmd.get_color_tuple(color2)
if symmetric:
scale *= 0.5
end = cpv.add(center, cpv.scale(direction, scale))
radius = 0.3
obj = [cgo.SAUSAGE]
obj.extend(center)
obj.extend(end)
obj.extend([radius, 0.8, 0.8, 0.8])
obj.extend(color_list)
if symmetric:
start = cpv.sub(center, cpv.scale(direction, scale))
obj.append(cgo.SAUSAGE)
obj.extend(center)
obj.extend(start)
obj.extend([radius, 0.8, 0.8, 0.8])
obj.extend(color2_list)
coneend = cpv.add(end, cpv.scale(direction, 4.0 * radius))
if cmd.get_version()[1] >= 1.2:
obj.append(cgo.CONE)
obj.extend(end)
obj.extend(coneend)
obj.extend([radius * 1.75, 0.0])
obj.extend(color_list * 2)
obj.extend([1.0, 1.0]) # Caps
cmd.load_cgo(obj, get_unused_name("oriVec"), zoom=0)
def loop_orientation(selection, visualize=1, quiet=0):
'''
DESCRIPTION
Get the center and approximate direction of a peptide. Works for any
secondary structure.
Averages direction of N(i)->C(i) pseudo bonds.
USAGE
loop_orientation selection [, visualize]
SEE ALSO
helix_orientation
'''
visualize, quiet = int(visualize), int(quiet)
stored.x = dict()
cmd.iterate_state(STATE, '(%s) and name N+C' % (selection),
'stored.x.setdefault(chain + resi, dict())[name] = x,y,z')
vec = cpv.get_null()
count = 0
for x in stored.x.itervalues():
if 'C' in x and 'N' in x:
vec = cpv.add(vec, cpv.sub(x['C'], x['N']))
count += 1
if count == 0:
print 'warning: count == 0'
raise CmdException
vec = cpv.normalize(vec)
return _common_orientation(selection, vec, visualize, quiet)
def testPairFit(self):
cmd.fragment('trp')
cmd.fragment('his')
# 1 atom
sele = ('trp and guide', 'his and guide')
pos = list(map(cmd.get_atom_coords, sele))
vec = cpv.sub(*pos)
mat_ref = [
1.0, 0.0, 0.0, -vec[0],
0.0, 1.0, 0.0, -vec[1],
0.0, 0.0, 1.0, -vec[2],
0.0, 0.0, 0.0, 1.0]
rms = cmd.pair_fit(*sele)
self.assertEqual(rms, 0.0)
mat = cmd.get_object_matrix('trp')
self.assertArrayEqual(mat, mat_ref, 1e-4)
# 2 atoms
sele += ('trp & name CB', 'his & name CB')
rms = cmd.pair_fit(*sele)
self.assertAlmostEqual(rms, 0.0082, delta=1e-4)
# 4 atoms
sele += ('trp & name CG', 'his & name CG',
'trp & name CD1', 'his & name CD2')
rms = cmd.pair_fit(*sele)
self.assertAlmostEqual(rms, 0.0713, delta=1e-4)
def append_cyl(self):
if self.l_vert and self.c_colr and self.l_radi:
if self.tri_flag:
self.tri_flag=0
self.obj.append(END)
self.obj.append(SAUSAGE)
d = cpv.sub(self.l_vert[1],self.l_vert[0])
d = cpv.normalize_failsafe(d)
d0 = cpv.scale(d,self.l_radi/4.0)
self.obj.extend(cpv.add(self.l_vert[0],d0))
self.obj.extend(cpv.sub(self.l_vert[1],d0))
self.obj.append(self.l_radi)
self.obj.extend(self.c_colr[0])
self.obj.extend(self.c_colr[1])
self.l_vert=None
self.c_colr=None
self.l_radi=None
def _cgo_quad(pos, normal, radius):
'''Return a CGO list specifying a quad.'''
v1 = cpv.normalize(_perp_vec(normal))
v2 = cpv.cross_product(normal, v1)
v1 = cpv.scale(v1, radius)
v2 = cpv.scale(v2, radius)
obj = [ cgo.BEGIN,
cgo.TRIANGLE_STRIP,
cgo.NORMAL]
obj.extend(normal)
obj.append(cgo.VERTEX)
obj.extend(cpv.add(pos, v1))
obj.append(cgo.VERTEX)
obj.extend(cpv.add(pos, v2))
obj.append(cgo.VERTEX)
obj.extend(cpv.sub(pos, v2))
obj.append(cgo.VERTEX)
obj.extend(cpv.sub(pos, v1))
obj.append(cgo.END)
return obj
def append_tri(self):
if self.l_vert:
d0 = cpv.sub(self.l_vert[0],self.l_vert[1])
d1 = cpv.sub(self.l_vert[0],self.l_vert[2])
n0 = cpv.cross_product(d0,d1)
n0 = cpv.normalize_failsafe(n0)
if not self.tri_flag:
self.obj.append(BEGIN)
self.obj.append(TRIANGLES)
self.tri_flag = 1
indices = [0, 1, 2]
if not self.l_norm:
# TODO could simplify this if ray tracing would support
# object-level two_sided_lighting. Duplicating the
# face with an offset is a hack and produces visible
# lines on edges.
n1 = [-n0[0],-n0[1],-n0[2]]
ns = cpv.scale(n0,0.002)
indices = [0, 1, 2, 4, 3, 5]
l_vert_offsetted = [cpv.add(v, ns) for v in self.l_vert]
l_vert_offsetted.extend(cpv.sub(v, ns) for v in self.l_vert)
self.l_vert = l_vert_offsetted
self.l_norm = [n0, n0, n0, n1, n1, n1]
elif cpv.dot_product(self.l_norm[0], n0) < 0:
indices = [0, 2, 1]
for i in indices:
self.obj.append(COLOR) # assuming unicolor
self.obj.extend(self.t_colr[i % 3])
self.obj.append(NORMAL)
self.obj.extend(self.l_norm[i])
self.obj.append(VERTEX)
self.obj.extend(self.l_vert[i])
self.l_vert=None
self.t_colr=None
self.l_norm=None
def helix_orientation(selection, visualize=1, sigma_cutoff=1.5, quiet=0):
"""
DESCRIPTION
Get the center and direction of a helix as vectors. Will only work
for helices and gives slightly different results than loop_orientation.
Averages direction of C(i)->O(i) bonds.
USAGE
helix_orientation selection [, visualize [, sigma_cutoff]]
ARGUMENTS
selection = string: atom selection of helix
visualize = 0 or 1: show fitted vector as arrow {default: 1}
sigma_cutoff = float: drop outliers outside
(standard_deviation * sigma_cutoff) {default: 1.5}
SEE ALSO
angle_between_helices, helix_orientation_hbond, loop_orientation, cafit_orientation
"""
visualize, quiet, sigma_cutoff = int(visualize), int(quiet), float(sigma_cutoff)
stored.x = dict()
cmd.iterate_state(
STATE, "(%s) and name C+O" % (selection), "stored.x.setdefault(chain + resi, dict())[name] = x,y,z"
)
vec_list = []
count = 0
for x in stored.x.values():
if "C" in x and "O" in x:
vec_list.append(cpv.sub(x["O"], x["C"]))
count += 1
if count == 0:
print("warning: count == 0")
raise CmdException
vec = _vec_sum(vec_list)
if count > 2 and sigma_cutoff > 0:
angle_list = [cpv.get_angle(vec, x) for x in vec_list]
angle_mu, angle_sigma = _mean_and_std(angle_list)
vec_list = [
vec_list[i] for i in range(len(vec_list)) if abs(angle_list[i] - angle_mu) < angle_sigma * sigma_cutoff
]
if not quiet:
print("Dropping %d outlier(s)" % (len(angle_list) - len(vec_list)))
vec = _vec_sum(vec_list)
vec = cpv.normalize(vec)
return _common_orientation(selection, vec, visualize, quiet)
def compute_surface_normals():
'''
Compute average normals from all adjacent triangles
on each vertex
'''
from functools import reduce
# don't use cpv.normalize which has an RSMALL4 limit
normalize = lambda v: cpv.scale(v, 1. / cpv.length(v))
for face in table['face']:
if 'vertex_index' in face:
indices = face['vertex_index']
elif 'vertex_indices' in face:
indices = face['vertex_indices']
else:
return
f_vert = [vertices[i] for i in indices]
f_xyz = [(v['x'], v['y'], v['z']) for v in f_vert]
try:
normal = normalize(cpv.cross_product(
cpv.sub(f_xyz[1], f_xyz[0]),
cpv.sub(f_xyz[2], f_xyz[1])))
except ZeroDivisionError:
continue
for v in f_vert:
v.setdefault('normals', []).append(normal)
for v in vertices:
try:
v['nx'], v['ny'], v['nz'] = normalize(
reduce(cpv.add, v.pop('normals')))
except (KeyError, ZeroDivisionError):
continue
def visualize_orientation(direction, center=[0.0]*3, scale=1.0, symmetric=False, color='green', color2='red'):
'''
DESCRIPTION
Draw an arrow. Helper function for "helix_orientation" etc.
'''
from pymol import cgo
color_list = cmd.get_color_tuple(color)
color2_list = cmd.get_color_tuple(color2)
if symmetric:
scale *= 0.5
end = cpv.add(center, cpv.scale(direction, scale))
radius = 0.3
obj = [cgo.SAUSAGE]
obj.extend(center)
obj.extend(end)
obj.extend([
radius,
0.8, 0.8, 0.8,
])
obj.extend(color_list)
if symmetric:
start = cpv.sub(center, cpv.scale(direction, scale))
obj.append(cgo.SAUSAGE)
obj.extend(center)
obj.extend(start)
obj.extend([
radius,
0.8, 0.8, 0.8,
])
obj.extend(color2_list)
coneend = cpv.add(end, cpv.scale(direction, 4.0*radius/cpv.length(direction)))
obj.append(cgo.CONE)
obj.extend(end)
obj.extend(coneend)
obj.extend([
radius * 1.75,
0.0,
])
obj.extend(color_list * 2)
obj.extend([
1.0, 1.0, # Caps
])
cmd.load_cgo(obj, get_unused_name('oriVec'), zoom=0)
def __init__(self, p1, p2, radius, color1,
color2=None, color3=None,
hlength=None, hradius=None,
hlength_scale=3.0, hradius_scale=0.6):
if hlength is None:
hlength = radius * hlength_scale
if hradius is None:
hradius = hlength * hradius_scale
normal = cpv.normalize(cpv.sub(p1, p2))
pM = cpv.add(cpv.scale(normal, hlength), p2)
line = Cylinder(p1, pM, radius, color1, color2)
cone = Cone(
pM, p2, hradius, color2 or color1, radius2=0, color2=color3
)
self._primitive = (line + cone).primitive
def scramble(self,mode):
if self.cmd.count_atoms(self.sculpt_object):
sc_tmp = "_scramble_tmp"
if mode == 0:
self.cmd.select(sc_tmp,self.sculpt_object+
" and not (fixed or restrained)")
if mode == 1:
self.cmd.select(sc_tmp,self.sculpt_object+
" and not (fixed)")
extent = self.cmd.get_extent(sc_tmp)
center = self.cmd.get_position(sc_tmp)
radius = 1.25*cpv.length(cpv.sub(extent[0],extent[1]))
self.cmd.alter_state(self.cmd.get_state(), sc_tmp,
"(x,y,z)=rsp(pos,rds)",
space= { 'rsp' : cpv.random_displacement,
'pos' : center,
'rds' : radius })
self.cmd.delete(sc_tmp)
def planeFromPoints(point1, point2, point3, facetSize):
v1 = cpv.normalize(cpv.sub(point2, point1))
v2 = cpv.normalize(cpv.sub(point3, point1))
normal = cpv.cross_product(v1, v2)
v2 = cpv.cross_product(normal, v1)
x = cpv.scale(v1, facetSize)
y = cpv.scale(v2, facetSize)
center = point2
corner1 = cpv.add(cpv.add(center, x), y)
corner2 = cpv.sub(cpv.add(center, x), y)
corner3 = cpv.sub(cpv.sub(center, x), y)
corner4 = cpv.add(cpv.sub(center, x), y)
return plane(corner1, corner2, corner3, corner4, normal)
def get_cgo(self, dot_mode=0, dot_radius=0.03):
"""Generate a CGO list for a dot."""
cgolist = []
# COLOR
cgolist.extend(_cgo_color(self.color))
if dot_mode == 0: # spheres
logger.debug("Adding dot to cgolist...")
cgolist.extend(_cgo_sphere(self.coords, dot_radius))
logger.debug("Finished adding dot to cgolist.")
if dot_mode == 1: # quads
logger.debug("Adding quad to cgolist...")
normal = cpv.normalize(cpv.sub(self.coords, self.atom['coords']))
cgolist.extend(_cgo_quad(self.coords, normal, dot_radius * 1.5))
logger.debug("Finished adding quad to cgolist.")
return cgolist
def loop_orientation(selection, state=STATE, visualize=1, quiet=1):
'''
DESCRIPTION
Get the center and approximate direction of a peptide. Works for any
secondary structure.
Averages direction of N(i)->C(i) pseudo bonds.
USAGE
loop_orientation selection [, visualize ]
SEE ALSO
helix_orientation
'''
state, visualize, quiet = int(state), int(visualize), int(quiet)
coords = dict()
cmd.iterate_state(state, '(%s) and name N+C' % (selection),
'coords.setdefault(chain + resi, {})[name] = x,y,z', space=locals())
vec = cpv.get_null()
center = cpv.get_null()
count = 0
for x in coords.itervalues():
if 'C' in x and 'N' in x:
vec = cpv.add(vec, cpv.sub(x['C'], x['N']))
for coord in x.itervalues():
center = cpv.add(center, coord)
count += 1
if count == 0:
print 'warning: count == 0'
raise CmdException
vec = cpv.normalize(vec)
center = cpv.scale(center, 1./count)
_common_orientation(selection, center, vec, visualize, 2.0*len(coords), quiet)
return center, vec
def helix_orientation_hbond(selection, visualize=1, cutoff=3.5, quiet=0):
'''
DESCRIPTION
Get the center and direction of a helix as vectors. Will only work
for alpha helices and gives slightly different results than
helix_orientation. Averages direction of O(i)->N(i+4) hydrogen bonds.
USAGE
helix_orientation selection [, visualize [, cutoff]]
ARGUMENTS
cutoff = float: maximal hydrogen bond distance {default: 3.5}
SEE ALSO
helix_orientation
'''
visualize, quiet, cutoff = int(visualize), int(quiet), float(cutoff)
stored.x = dict()
cmd.iterate_state(STATE, '(%s) and name N+O' % (selection),
'stored.x.setdefault(resv, dict())[name] = x,y,z')
vec_list = []
for resi in stored.x:
resi_other = resi + 4
if 'O' in stored.x[resi] and resi_other in stored.x:
if 'N' in stored.x[resi_other]:
vec = cpv.sub(stored.x[resi_other]['N'], stored.x[resi]['O'])
if cpv.length(vec) < cutoff:
vec_list.append(vec)
if len(vec_list) == 0:
print 'warning: count == 0'
raise CmdException
vec = _vec_sum(vec_list)
vec = cpv.normalize(vec)
return _common_orientation(selection, vec, visualize, quiet)
def cgo_grid(
pos1=[0,0,0],
pos2=[1,0,0],
pos3=[0,0,1],
length_x=30,
length_z='',
npoints_x='',
npoints_z='',
nwaves_x=2,
nwaves_z='',
offset_x=0,
offset_z='',
gain_x=1,
gain_z='',
thickness=2.0,
color='',
nstates=60,
startframe=1,
endframe=1,
mode=0,
view=0,
name='',
quiet=1):
'''
DESCRIPTION
Generates an animated flowing mesh object using the points provided
or the current view. The shape is affected substantially by the arguments!
USEAGE
cgo_grid [ pos1 [, pos2 [, pos3 [, length_x [, length_z
[, npoints_x [, npoints_z [, nwaves_x [, nwaves_z
[, offset_x [, offset_z [, gain_x [, gain_z [, thickness
[, color [, nstates [, startframe [, endframe [, mode
[, view [, name [, quiet ]]]]]]]]]]]]]]]]]]]]]]
EXAMPLE
cgo_grid view=1
ARGUMENTS
pos1 = single atom selection (='pk1') or list of 3 floats {default: [0,0,0]}
pos2 = single atom selection (='pk2') or list of 3 floats {default: [1,0,0]}
pos3 = single atom selection (='pk3') or list of 3 floats {default: [0,0,1]}
--> the plane is defined by pos1 (origin) and vectors to pos2 and pos3, respectively
length_x = <float>: length of membrane {default: 30}
length_z = <float>: length of membrane {default: ''} # same as length_x
npoints_x = <int>: number of points(lines) along x-direction
{default: ''} #will be set to give a ~1 unit grid
npoints_z = <int>: number of points(lines) along z-direction
{default: ''} #will be set to give a ~1 unit grid
{minimum: 1 # automatic}
nwaves_x = <float>: number of complete sin waves along object x-axis
{default: 2}
nwaves_z = <float>: number of complete sin waves along object z-axis
{default: ''} # same as nwaves_x
define separately to adjust number of waves in each direction
offset_x = <float> phase delay (in degrees) of sin wave in x-axis
can be set to affect shape and starting amplitude {default: 0}
offset_z = <float> phase delay (in degrees) of sin wave in z-axis
can be set to affect shape and starting amplitude
{default: ''} # same as offset_x
offset_x and offset_z can be used together to phase
otherwise identical objects
gain_x = <float>: multiplication factor for y-amplitude for x-direction
{default: 1}
gain_z = <float>: multiplication factor for y-amplitude for z-direction
{default: ''} #=gain_x
thickness = <float>: line thickness {default: 2}
color = color name <string> (e.g. 'skyblue') OR
rgb-value list of 3 floats (e.g. [1.0,1.0,1.0]) OR
{default: ''} // opposite of background
input illegal values for random coloring
nstates = <int>: number of states; {default: 60}
this setting will define how many states
the object will have (per wave) and how fluent and fast the
animation will be.
Higher values will promote 'fluent' transitions,
but decrease flow speed.
Note: Frame animation cycles thought the states one at a time
and needs to be set accordingly. Can also be used to phase
otherwise identical objects.
Set to 1 for static object {automatic minimum}
startframe: specify starting frame <int> or set (='') to use current frame
set to 'append' to extend movie from the last frame {default: 1}
endframe: specify end frame <int> or set (='') to use last frame
if 'append' is used for startframe,
endframe becomes the number of frames to be appended instead
{default: 1}
Note: if start- and endframe are the same, movie animation will
be skipped, the object will be loaded and can be used afterwards
mode: defines positioning {default: 0}:
0: pos1 is center
1: pos1 is corner
view {default: 0}:
'0': off/ uses provided points to create CGO
'1': overrides atom selections and uses current orienatation for positioning
- pos1 = origin/center
- pos2 = origin +1 in camera y
- pos3 = origin +1 in camera z
name: <string> name of cgo object {default: ''} / automatic
quiet: <boolean> toggles output
'''
########## BEGIN OF FUNCTION CODE ##########
def get_coord(v):
if not isinstance(v, str):
try:
return v[:3]
except:
return False
if v.startswith('['):
return cmd.safe_list_eval(v)[:3]
try:
if cmd.count_atoms(v)==1:
# atom coordinates
return cmd.get_atom_coords(v)
else:
# more than one atom --> use "center"
# alt check!
if cmd.count_atoms('(alt *) and not (alt "")')!=0:
print("cgo_grid: warning! alternative coordinates found for origin, using center!")
view_temp=cmd.get_view()
cmd.zoom(v)
v=cmd.get_position()
cmd.set_view(view_temp)
return v
except:
return False
def eval_color(v):
try:
if not v:
v=eval(cmd.get('bg_rgb'))
v=list(map(sum, list(zip(v,[-1,-1,-1]))))
v=list(map(abs, v))
if v[0]==v[1]==v[2]==0.5: # grey
v=[0,0,0]
return v
if isinstance(v, list):
return v[0:3]
if not isinstance(v, str):
return v[0:3]
if v.startswith('['):
return cmd.safe_list_eval(v)[0:3]
return list(cmd.get_color_tuple(v))
except:
return [random.random(),random.random(),random.random()]
cmd.extend("eval_color", eval_color)
color=eval_color(color)
try:
mode=int(mode)
except:
raise Exception("Input error in Mode")
if mode<0 or mode>1:
raise Exception("Mode out of range!")
try:
nstates=int(nstates)
if nstates<1:
nstates=1
print("NB! nstates set to 1 (automatic minimum)")
length_x=float(length_x)
if length_z=='':
length_z=length_x
else:
length_z=float(length_z)
if npoints_x=='':
npoints_x=int(length_x)+1
else:
npoints_x=int(npoints_x)
if npoints_x<1:
npoints_x=1
print("NB! npoints_x set to 1 (automatic minimum)")
if npoints_z =='':
npoints_z=int(length_z)+1
else:
npoints_z=int(npoints_z)
if npoints_z<1:
npoints_z=1
print("NB! npoints_x set to 1 (automatic minimum)")
nwaves_x=abs(float(nwaves_x))
if nwaves_z=='':
nwaves_z=nwaves_x
else:
nwaves_z=abs(float(nwaves_z))
offset_x=float(offset_x)*math.pi/180
if offset_z=='':
offset_z=offset_x
else:
offset_z=float(offset_z)*math.pi/180
thickness=float(thickness)
gain_x=float(gain_x)
if gain_z=='':
gain_z=gain_x
else:
gain_z=float(gain_z)
if not name:
name = cmd.get_unused_name('membrane')
else:
name = str(name)
if int(quiet):
quiet=True
else:
quiet=False
if int(view):
view=True
else:
view=False
except:
raise Exception("Input error in parameters!")
#prevent auto zooming on object
temp_auto_zoom=cmd.get('auto_zoom')
cmd.set('auto_zoom', '0')
if int(view):
xyz1=cmd.get_position()
tempname = cmd.get_unused_name('temp')
ori_ax=[[0,0,0],[10,0,0],[0,0,10]]
for a in range (0,len(ori_ax)):
cmd.pseudoatom(tempname, resi=''+str(a+1)+'', pos=xyz1)
cmd.translate(ori_ax[a],
selection=''+tempname+' and resi '+str(a+1)+'', camera='1')
ori_ax[a]=cmd.get_atom_coords(''+tempname+' and resi '+str(a+1)+'')
cmd.delete(tempname)
xyz1=ori_ax[0]
xyz2=ori_ax[1]
xyz3=ori_ax[2]
else:
xyz1 = get_coord(pos1)
xyz2 = get_coord(pos2)
xyz3 = get_coord(pos3)
if (not startframe):
startframe=cmd.get('frame')
if (not endframe):
endframe=cmd.count_frames()
if endframe==0: endframe=1
if (startframe=='append'):
startframe=cmd.count_frames()+1
try:
endframe=int(endframe)
cmd.madd('1 x'+str(endframe))
endframe=cmd.count_frames()
except ValueError:
raise Exception("Input error: Value for 'endframe' is not integer!")
try:
startframe=int(startframe)
endframe=int(endframe)
endframe/startframe
startframe/endframe
except ValueError:
raise Exception("Input error: Failed to convert to integer!")
except ZeroDivisionError:
raise Exception("Error: unexpected zero value!")
except:
raise Exception("Unexpected error!")
if (nstates==1):
if not quiet: print("Creating one state object!")
if startframe > endframe:
startframe, endframe = endframe, startframe
if not quiet: print("Inverted start and end frames!")
########## BEGIN OF FUNCTIONAL SCRIPT ##########
#normalize and get orthogonal vector
# define vectors from points
xyz2 = cpv.sub(xyz2, xyz1)
xyz3 = cpv.sub(xyz3, xyz1)
#NB! cpv.get_system2 outputs normalized vectors [x,y,z]
xyz4 = cpv.get_system2(xyz2,xyz3)
xyz2 = xyz4[0]
xyz3 = xyz4[1]
for x in range(0,3):
for z in range(0,3):
if x==z:
continue
if xyz4[x]==xyz4[z]:
raise Exception("Illegal vector settings!")
xyz4 = cpv.negate(xyz4[2]) #overwrites original
# transform origin to corner
if mode==0:
if npoints_x>1:
xyz1 = cpv.sub(xyz1, cpv.scale(xyz2,length_x/2))
if npoints_z>1:
xyz1 = cpv.sub(xyz1, cpv.scale(xyz3,length_z/2))
#defines array lines
nlines=max([npoints_x, npoints_z])
# in case only one line max
# create an empty array for xyz entries
# this may contain more values than are actually drawn later,
# but they are needed to draw lines in each direction
grid_xyz = []
for x in range(0,nlines):
grid_xyz.append([0.0,0.0,0.0]*nlines)
# grid distance and steps
# prevent zero divisions (lines=1) and enable calculations if lines=0
if (not (npoints_x-1<2)):
gap_length_x = length_x/(npoints_x-1)
step_line_x = 2*math.pi/(npoints_x-1)
else:
gap_length_x=length_x
step_line_x=2*math.pi
if (not (npoints_z-1<2)):
gap_length_z = length_z/(npoints_z-1)
step_line_z = 2*math.pi/(npoints_z-1)
else:
gap_length_z=length_z
step_line_z=2*math.pi
# calculate steps
if nstates==1:
step_state=0
else:
step_state = 2*math.pi/(nstates-1)
########## BEGIN STATE ITERATION ##########
# create a n-state object in PyMol
for a in range(0,nstates):
# Reset object
obj = []
#assign color
obj.extend( [ COLOR, color[0], color[1], color[2] ] )
#set width
obj.extend( [ LINEWIDTH, thickness ] )
# Calculate xyz-coordinates for each line
for x in range(0,nlines):
for z in range(0,nlines):
# update grid position in x-direction
xyztemp=cpv.add(xyz1,cpv.scale(xyz2,gap_length_x*x))
# update grid position in z-direction
xyztemp=cpv.add(xyztemp,cpv.scale(xyz3,gap_length_z*z))
# calculate amplitude for y-direction and update grid position
y_amp=(\
gain_x*math.sin(offset_x+nwaves_x*((a*step_state)+(x*step_line_x)))/2+\
gain_z*math.sin(offset_z+nwaves_z*((a*step_state)+(z*step_line_z)))/2\
)
xyztemp=cpv.add(xyztemp,cpv.scale(xyz4,y_amp))
grid_xyz[x][z]=xyztemp
#Now the coordinates for this state are defined!
#Now the coordinates are read separately:
# allow to run the loops as often as required
#if npoints_x==0:npoints_x=npoints_z
#lines along z in x direction
for z in range(0,npoints_z):
obj.extend( [ BEGIN, LINE_STRIP ] )
for x in range(0,npoints_x):
obj.extend( [ VERTEX, grid_xyz[x][z][0], grid_xyz[x][z][1], grid_xyz[x][z][2] ] )
obj.append( END )
#lines along x in z direction
for x in range(0,npoints_x):
obj.extend( [ BEGIN, LINE_STRIP ] )
for z in range(0,npoints_z):
obj.extend( [ VERTEX, grid_xyz[x][z][0], grid_xyz[x][z][1], grid_xyz[x][z][2] ] )
obj.append( END )
# Load state into PyMOL object:
cmd.load_cgo(obj,name,a+1)
# All states of object loaded!
#reset auto zooming to previous value
cmd.set('auto_zoom', temp_auto_zoom)
# animate object using frames instead of states
if (not endframe==startframe):
framecount=0
countvar=1
for frame in range(startframe, endframe + 1):
#increase count
framecount=framecount+countvar
# set state in frame
cmd.mappend(frame,
"/cmd.set('state', %s, %s)" % (repr(framecount), repr(name)))
# Looping
if framecount==nstates:
if ((int(nwaves_x)!=nwaves_x) or (int(nwaves_z)!=nwaves_z)):
#if not complete sinus wave
#--> reverse wave in ongoing animation
countvar=-1
else:
#wave is complete --> repeat
framecount=0
# count up from first state
if framecount==1: countvar=1
if not quiet: print("object loaded and animated with frames!")
else:
if not quiet: print("object loaded!")
#OUTPUT
if not quiet:
print("Grid variables for:",name)
print("corner:", xyz1)
print("vector 1:", xyz2)
print("vector 2:", xyz3)
print("length_x:",length_x)
print("length_z:",length_z)
print("npoints_x:", npoints_x)
print("npoints_z:", npoints_z)
print("nwaves_x:", nwaves_x)
print("nwaves_z:", nwaves_z)
print("offset_x:",offset_x)
print("offset_z:",offset_z)
print("gain_x:",gain_x)
print("gain_z:",gain_z)
print("thickness:",thickness)
print("states", nstates)
if (not endframe==startframe):
print("frames: start:",startframe,"end:",endframe)
return grid_xyz
def planeFromPoints(p1, p2, p3, vm1=None, vm2=None, center=True, settings={}):
v1 = cpv.sub(p1, p2)
v2 = cpv.sub(p3, p2)
normal = cpv.cross_product(v1, v2)
if 'translate' in settings:
vtran = cpv.scale(cpv.normalize(normal), settings['translate'])
p1_t = cpv.sub(p1, vtran)
p2_t = cpv.sub(p2, vtran)
p3_t = cpv.sub(p3, vtran)
print("New coordinates are:")
print_info("New", p1_t, p2_t, p3_t)
print("New coordinates are for normalized plane:")
v1_t = cpv.normalize(cpv.sub(p1_t, p2_t))
v2_t = cpv.normalize(cpv.sub(p3_t, p2_t))
normal_t = cpv.normalize(cpv.cross_product(v1_t, v2_t))
v2_t = cpv.normalize(cpv.cross_product(normal_t, v1_t))
p1_t2 = cpv.add(v1_t, p2_t)
p3_t2 = cpv.add(v2_t, p2_t)
print_info("Newnormal", p1_t2, p2_t, p3_t2)
if vm1 != None:
v1 = cpv.scale(cpv.normalize(v1), vm1)
if vm2 != None:
v2 = cpv.scale(cpv.normalize(v2), vm2)
centrum = p2
if center:
corner1 = cpv.add(cpv.add(centrum, v1), v2)
corner2 = cpv.sub(cpv.add(centrum, v1), v2)
corner3 = cpv.sub(cpv.sub(centrum, v1), v2)
corner4 = cpv.add(cpv.sub(centrum, v1), v2)
else:
corner1 = cpv.add(cpv.add(centrum, v1), v2)
corner2 = cpv.add(centrum, v1)
corner3 = centrum
corner4 = cpv.add(centrum, v2)
return plane(corner1, corner2, corner3, corner4, normal, settings)
def append_tri(self):
if self.l_vert and not self.l_norm:
d0 = cpv.sub(self.l_vert[0], self.l_vert[1])
d1 = cpv.sub(self.l_vert[0], self.l_vert[2])
n0 = cpv.cross_product(d0, d1)
n0 = cpv.normalize_failsafe(n0)
n1 = [-n0[0], -n0[1], -n0[2]]
ns = cpv.scale(n0, 0.002)
if not self.tri_flag:
self.obj.append(BEGIN)
self.obj.append(TRIANGLES)
self.tri_flag = 1
self.obj.append(COLOR) # assuming unicolor
self.obj.extend(self.t_colr[0])
self.obj.append(NORMAL)
self.obj.extend(n0)
self.obj.append(VERTEX)
self.obj.extend(cpv.add(self.l_vert[0], ns))
self.obj.append(COLOR) # assuming unicolor
self.obj.extend(self.t_colr[1])
self.obj.append(NORMAL)
self.obj.extend(n0)
self.obj.append(VERTEX)
self.obj.extend(cpv.add(self.l_vert[1], ns))
self.obj.append(COLOR) # assuming unicolor
self.obj.extend(self.t_colr[2])
self.obj.append(NORMAL)
self.obj.extend(n0)
self.obj.append(VERTEX)
self.obj.extend(cpv.add(self.l_vert[2], ns))
self.obj.append(COLOR) # assuming unicolor
self.obj.extend(self.t_colr[0])
self.obj.append(NORMAL)
self.obj.extend(n1)
self.obj.append(VERTEX)
self.obj.extend(cpv.sub(self.l_vert[0], ns))
self.obj.append(COLOR) # assuming unicolor
self.obj.extend(self.t_colr[1])
self.obj.append(NORMAL)
self.obj.extend(n1)
self.obj.append(VERTEX)
self.obj.extend(cpv.sub(self.l_vert[1], ns))
self.obj.append(COLOR) # assuming unicolor
self.obj.extend(self.t_colr[2])
self.obj.append(NORMAL)
self.obj.extend(n1)
self.obj.append(VERTEX)
self.obj.extend(cpv.sub(self.l_vert[2], ns))
elif self.l_vert and self.t_colr and self.l_norm:
if not self.tri_flag:
self.obj.append(BEGIN)
self.obj.append(TRIANGLES)
self.tri_flag = 1
self.obj.append(COLOR) # assuming unicolor
self.obj.extend(self.t_colr[0])
self.obj.append(NORMAL)
self.obj.extend(self.l_norm[0])
self.obj.append(VERTEX)
self.obj.extend(self.l_vert[0])
self.obj.append(COLOR) # assuming unicolor
self.obj.extend(self.t_colr[1])
self.obj.append(NORMAL)
self.obj.extend(self.l_norm[1])
self.obj.append(VERTEX)
self.obj.extend(self.l_vert[1])
self.obj.append(COLOR) # assuming unicolor
self.obj.extend(self.t_colr[2])
self.obj.append(NORMAL)
self.obj.extend(self.l_norm[2])
self.obj.append(VERTEX)
self.obj.extend(self.l_vert[2])
self.l_vert = None
self.t_colr = None
self.l_norm = None
def bbPlane(selection='(all)', color='gray', transp=0.3, state=-1, name=None, quiet=1):
"""
DESCRIPTION
Draws a plane across the backbone for a selection
ARGUMENTS
selection = string: protein object or selection {default: (all)}
color = string: color name or number {default: white}
transp = float: transparency component (0.0--1.0) {default: 0.0}
state = integer: object state, 0 for all states {default: 1}
NOTES
You need to pass in an object or selection with at least two
amino acids. The plane spans CA_i, O_i, N-H_(i+1), and CA_(i+1)
"""
from pymol.cgo import BEGIN, TRIANGLES, COLOR, VERTEX, END
from pymol import cgo
from chempy import cpv
# format input
transp = float(transp)
state, quiet = int(state), int(quiet)
if name is None:
name = cmd.get_unused_name("backbonePlane")
if state < 0:
state = cmd.get_state()
elif state == 0:
for state in range(1, cmd.count_states(selection) + 1):
bbPlane(selection, color, transp, state, name, quiet)
return
AAs = []
coords = dict()
# need hydrogens on peptide nitrogen
cmd.h_add('(%s) and n. N' % selection)
# get the list of residue ids
for obj in cmd.get_object_list(selection):
sel = obj + " and (" + selection + ")"
for a in cmd.get_model(sel + " and n. CA", state).atom:
key = '/%s/%s/%s/%s' % (obj, a.segi, a.chain, a.resi)
AAs.append(key)
coords[key] = [a.coord, None, None]
for a in cmd.get_model(sel + " and n. O", state).atom:
key = '/%s/%s/%s/%s' % (obj, a.segi, a.chain, a.resi)
if key in coords:
coords[key][1] = a.coord
for a in cmd.get_model(sel + " and ((n. N extend 1 and e. H) or (r. PRO and n. CD))", state).atom:
key = '/%s/%s/%s/%s' % (obj, a.segi, a.chain, a.resi)
if key in coords:
coords[key][2] = a.coord
# need at least two amino acids
if len(AAs) <= 1:
print("ERROR: Please provide at least two amino acids, the alpha-carbon on the 2nd is needed.")
return
# prepare the cgo
obj = [
BEGIN, TRIANGLES,
COLOR,
]
obj.extend(cmd.get_color_tuple(color))
for res in range(0, len(AAs) - 1):
curIdx, nextIdx = str(AAs[res]), str(AAs[res + 1])
# populate the position array
pos = [coords[curIdx][0], coords[curIdx][1], coords[nextIdx][2], coords[nextIdx][0]]
# if the data are incomplete for any residues, ignore
if None in pos:
if not quiet:
print(' bbPlane: peptide bond %s -> %s incomplete' % (curIdx, nextIdx))
continue
if cpv.distance(pos[0], pos[3]) > 4.0:
if not quiet:
print(' bbPlane: %s and %s not adjacent' % (curIdx, nextIdx))
continue
normal = cpv.normalize(cpv.cross_product(
cpv.sub(pos[1], pos[0]),
cpv.sub(pos[2], pos[0])))
obj.append(cgo.NORMAL)
obj.extend(normal)
# need to order vertices to generate correct triangles for plane
if cpv.dot_product(cpv.sub(pos[0], pos[1]), cpv.sub(pos[2], pos[3])) < 0:
vorder = [0, 1, 2, 2, 3, 0]
else:
vorder = [0, 1, 2, 3, 2, 1]
# fill in the vertex data for the triangles;
for i in vorder:
obj.append(VERTEX)
obj.extend(pos[i])
# finish the CGO
obj.append(END)
# update the UI
cmd.load_cgo(obj, name, state, zoom=0)
cmd.set("cgo_transparency", transp, name)
def cgo_modevec(atom1='pk1', atom2='pk2', radius=0.05, gap=0.0, hlength=-1, hradius=-1,
color='green', name='',scalefactor=10.0, cutoff=0.6, transparency=1.0): #was 0.6cut 12 scale
## scalefactor was 10.0
'''
DESCRIPTION
Create a CGO mode vector starting at atom1 and pointint in atom2 displacement
ARGUMENTS
atom1 = string: single atom selection or list of 3 floats {default: pk1}
atom2 = string: displacement to atom1 for modevec
radius = float: arrow radius {default: 0.5}
gap = float: gap between arrow tips and the two atoms {default: 0.0}
hlength = float: length of head
hradius = float: radius of head
color = string: one or two color names {default: blue red}
name = string: name of CGO object
scalefactor = scale how big of an arrow to make. Default 5
transparency = 0.0 ~ 1.0, default=1.0 means being totally opaque
'''
from chempy import cpv
radius, gap = float(radius), float(gap)
hlength, hradius = float(hlength), float(hradius)
scalefactor, cutoff = float(scalefactor), float(cutoff)
transparency = float(transparency)
try:
color1, color2 = color.split()
except:
color1 = color2 = color
color1 = list(cmd.get_color_tuple(color1))
color2 = list(cmd.get_color_tuple(color2))
def get_coord(v):
if not isinstance(v, str):
return v
if v.startswith('['):
return cmd.safe_list_eval(v)
return cmd.get_atom_coords(v)
xyz1 = get_coord(atom1)
xyz2 = get_coord(atom2)
newxyz2 = cpv.scale(xyz2, scalefactor)
newxyz2 = cpv.add(newxyz2, xyz1)
xyz2 = newxyz2
# xyz2 = xyz2[0]*scalefactor, xyz2[1]*scalefactor, xyz2[2]*scalefactor
normal = cpv.normalize(cpv.sub(xyz1, xyz2))
if hlength < 0:
hlength = radius * 3.0
if hradius < 0:
hradius = hlength * 0.6
if gap:
diff = cpv.scale(normal, gap)
xyz1 = cpv.sub(xyz1, diff)
xyz2 = cpv.add(xyz2, diff)
xyz3 = cpv.add(cpv.scale(normal, hlength), xyz2)
# dont draw arrow if distance is too small
distance = cpv.distance(xyz1, xyz2)
if distance <= cutoff:
return
#### generate transparent arrows;
#### The original codes are the next block
#### --Ran
obj = [25.0, transparency, 9.0] + xyz1 + xyz3 + [radius] + color1 + color2 + \
[25.0, transparency, 27.0] + xyz3 + xyz2 + [hradius, 0.0] + color2 + color2 + \
[1.0, 0.0]
# obj = [cgo.CYLINDER] + xyz1 + xyz3 + [radius] + color1 + color2 + \
# [cgo.CONE] + xyz3 + xyz2 + [hradius, 0.0] + color2 + color2 + \
# [1.0, 0.0]
if not name:
name = cmd.get_unused_name('arrow')
cmd.load_cgo(obj, name)
def helix_orientation(selection, state=STATE, visualize=1, cutoff=3.5, quiet=1):
'''
DESCRIPTION
Get the center and direction of a helix as vectors. Will only work
for alpha helices and gives slightly different results than
cafit_orientation. Averages direction of C(i)->O(i)->N(i+4).
USAGE
helix_orientation selection [, visualize [, cutoff ]]
ARGUMENTS
selection = string: atom selection of helix
visualize = 0 or 1: show fitted vector as arrow {default: 1}
cutoff = float: maximal hydrogen bond distance {default: 3.5}
SEE ALSO
angle_between_helices, loop_orientation, cafit_orientation
'''
state, visualize, quiet = int(state), int(visualize), int(quiet)
cutoff = float(cutoff)
atoms = {'C': dict(), 'O': dict(), 'N': dict()}
cmd.iterate_state(state, '(%s) and name N+O+C' % (selection),
'atoms[name][resv] = x,y,z', space={'atoms': atoms})
vec_list = []
for resi in atoms['C']:
resi_other = resi + 4
try:
aC = atoms['C'][resi]
aO = atoms['O'][resi]
aN = atoms['N'][resi_other]
except KeyError:
continue
dist = cpv.distance(aN, aO)
dist_weight = 1. - (2.8 - dist)
angle = cpv.get_angle_formed_by(aC, aO, aN)
angle_weight = 1. - (3.1 - angle)
if dist_weight > 0.0 and angle_weight > 0.0:
if not quiet:
print ' weight:', angle_weight * dist_weight
vec = cpv.scale(cpv.sub(aN, aC), angle_weight * dist_weight)
vec_list.append(vec)
if len(vec_list) == 0:
print 'warning: count == 0'
raise CmdException
center = cpv.scale(_vec_sum(atoms['O'].itervalues()), 1./len(atoms['O']))
vec = _vec_sum(vec_list)
vec = cpv.normalize(vec)
_common_orientation(selection, center, vec, visualize, 1.5*len(vec_list), quiet)
return center, vec
def cgo_grid(pos1=[0, 0, 0],
pos2=[1, 0, 0],
pos3=[0, 0, 1],
length_x=30,
length_z='',
npoints_x='',
npoints_z='',
nwaves_x=2,
nwaves_z='',
offset_x=0,
offset_z='',
gain_x=1,
gain_z='',
thickness=2.0,
color='',
nstates=60,
startframe=1,
endframe=1,
mode=0,
view=0,
name='',
quiet=1):
'''
DESCRIPTION
Generates an animated flowing mesh object using the points provided
or the current view. The shape is affected substantially by the arguments!
USEAGE
cgo_grid [ pos1 [, pos2 [, pos3 [, length_x [, length_z
[, npoints_x [, npoints_z [, nwaves_x [, nwaves_z
[, offset_x [, offset_z [, gain_x [, gain_z [, thickness
[, color [, nstates [, startframe [, endframe [, mode
[, view [, name [, quiet ]]]]]]]]]]]]]]]]]]]]]]
EXAMPLE
cgo_grid view=1
ARGUMENTS
pos1 = single atom selection (='pk1') or list of 3 floats {default: [0,0,0]}
pos2 = single atom selection (='pk2') or list of 3 floats {default: [1,0,0]}
pos3 = single atom selection (='pk3') or list of 3 floats {default: [0,0,1]}
--> the plane is defined by pos1 (origin) and vectors to pos2 and pos3, respectively
length_x = <float>: length of membrane {default: 30}
length_z = <float>: length of membrane {default: ''} # same as length_x
npoints_x = <int>: number of points(lines) along x-direction
{default: ''} #will be set to give a ~1 unit grid
npoints_z = <int>: number of points(lines) along z-direction
{default: ''} #will be set to give a ~1 unit grid
{minimum: 1 # automatic}
nwaves_x = <float>: number of complete sin waves along object x-axis
{default: 2}
nwaves_z = <float>: number of complete sin waves along object z-axis
{default: ''} # same as nwaves_x
define separately to adjust number of waves in each direction
offset_x = <float> phase delay (in degrees) of sin wave in x-axis
can be set to affect shape and starting amplitude {default: 0}
offset_z = <float> phase delay (in degrees) of sin wave in z-axis
can be set to affect shape and starting amplitude
{default: ''} # same as offset_x
offset_x and offset_z can be used together to phase
otherwise identical objects
gain_x = <float>: multiplication factor for y-amplitude for x-direction
{default: 1}
gain_z = <float>: multiplication factor for y-amplitude for z-direction
{default: ''} #=gain_x
thickness = <float>: line thickness {default: 2}
color = color name <string> (e.g. 'skyblue') OR
rgb-value list of 3 floats (e.g. [1.0,1.0,1.0]) OR
{default: ''} // opposite of background
input illegal values for random coloring
nstates = <int>: number of states; {default: 60}
this setting will define how many states
the object will have (per wave) and how fluent and fast the
animation will be.
Higher values will promote 'fluent' transitions,
but decrease flow speed.
Note: Frame animation cycles thought the states one at a time
and needs to be set accordingly. Can also be used to phase
otherwise identical objects.
Set to 1 for static object {automatic minimum}
startframe: specify starting frame <int> or set (='') to use current frame
set to 'append' to extend movie from the last frame {default: 1}
endframe: specify end frame <int> or set (='') to use last frame
if 'append' is used for startframe,
endframe becomes the number of frames to be appended instead
{default: 1}
Note: if start- and endframe are the same, movie animation will
be skipped, the object will be loaded and can be used afterwards
mode: defines positioning {default: 0}:
0: pos1 is center
1: pos1 is corner
view {default: 0}:
'0': off/ uses provided points to create CGO
'1': overrides atom selections and uses current orienatation for positioning
- pos1 = origin/center
- pos2 = origin +1 in camera y
- pos3 = origin +1 in camera z
name: <string> name of cgo object {default: ''} / automatic
quiet: <boolean> toggles output
'''
########## BEGIN OF FUNCTION CODE ##########
def get_coord(v):
if not isinstance(v, str):
try:
return v[:3]
except:
return False
if v.startswith('['):
return cmd.safe_list_eval(v)[:3]
try:
if cmd.count_atoms(v) == 1:
# atom coordinates
return cmd.get_atom_coords(v)
else:
# more than one atom --> use "center"
# alt check!
if cmd.count_atoms('(alt *) and not (alt "")') != 0:
print "cgo_grid: warning! alternative coordinates found for origin, using center!"
view_temp = cmd.get_view()
cmd.zoom(v)
v = cmd.get_position()
cmd.set_view(view_temp)
return v
except:
return False
def eval_color(v):
try:
if not v:
v = eval(cmd.get('bg_rgb'))
v = map(sum, zip(v, [-1, -1, -1]))
v = map(abs, v)
if v[0] == v[1] == v[2] == 0.5: # grey
v = [0, 0, 0]
return v
if isinstance(v, list):
return v[0:3]
if not isinstance(v, str):
return v[0:3]
if v.startswith('['):
return cmd.safe_list_eval(v)[0:3]
return list(cmd.get_color_tuple(v))
except:
return [random.random(), random.random(), random.random()]
cmd.extend("eval_color", eval_color)
color = eval_color(color)
try:
mode = int(mode)
except:
raise Exception("Input error in Mode")
if mode < 0 or mode > 1:
raise Exception("Mode out of range!")
try:
nstates = int(nstates)
if nstates < 1:
nstates = 1
print "NB! nstates set to 1 (automatic minimum)"
length_x = float(length_x)
if length_z == '':
length_z = length_x
else:
length_z = float(length_z)
if npoints_x == '':
npoints_x = int(length_x) + 1
else:
npoints_x = int(npoints_x)
if npoints_x < 1:
npoints_x = 1
print "NB! npoints_x set to 1 (automatic minimum)"
if npoints_z == '':
npoints_z = int(length_z) + 1
else:
npoints_z = int(npoints_z)
if npoints_z < 1:
npoints_z = 1
print "NB! npoints_x set to 1 (automatic minimum)"
nwaves_x = abs(float(nwaves_x))
if nwaves_z == '':
nwaves_z = nwaves_x
else:
nwaves_z = abs(float(nwaves_z))
offset_x = float(offset_x) * math.pi / 180
if offset_z == '':
offset_z = offset_x
else:
offset_z = float(offset_z) * math.pi / 180
thickness = float(thickness)
gain_x = float(gain_x)
if gain_z == '':
gain_z = gain_x
else:
gain_z = float(gain_z)
if not name:
name = cmd.get_unused_name('membrane')
else:
name = str(name)
if int(quiet):
quiet = True
else:
quiet = False
if int(view):
view = True
else:
view = False
except:
raise Exception("Input error in parameters!")
#prevent auto zooming on object
temp_auto_zoom = cmd.get('auto_zoom')
cmd.set('auto_zoom', '0')
if int(view):
xyz1 = cmd.get_position()
tempname = cmd.get_unused_name('temp')
ori_ax = [[0, 0, 0], [10, 0, 0], [0, 0, 10]]
for a in range(0, len(ori_ax)):
cmd.pseudoatom(tempname, resi='' + str(a + 1) + '', pos=xyz1)
cmd.translate(ori_ax[a],
selection='' + tempname + ' and resi ' + str(a + 1) +
'',
camera='1')
ori_ax[a] = cmd.get_atom_coords('' + tempname + ' and resi ' +
str(a + 1) + '')
cmd.delete(tempname)
xyz1 = ori_ax[0]
xyz2 = ori_ax[1]
xyz3 = ori_ax[2]
else:
xyz1 = get_coord(pos1)
xyz2 = get_coord(pos2)
xyz3 = get_coord(pos3)
if (not startframe):
startframe = cmd.get('frame')
if (not endframe):
endframe = cmd.count_frames()
if endframe == 0: endframe = 1
if (startframe == 'append'):
startframe = cmd.count_frames() + 1
try:
endframe = int(endframe)
cmd.madd('1 x' + str(endframe))
endframe = cmd.count_frames()
except ValueError:
raise Exception(
"Input error: Value for 'endframe' is not integer!")
try:
startframe = int(startframe)
endframe = int(endframe)
endframe / startframe
startframe / endframe
except ValueError:
raise Exception("Input error: Failed to convert to integer!")
except ZeroDivisionError:
raise Exception("Error: unexpected zero value!")
except:
raise Exception("Unexpected error!")
if (nstates == 1):
if not quiet: print "Creating one state object!"
if startframe > endframe:
startframe, endframe = endframe, startframe
if not quiet: print "Inverted start and end frames!"
########## BEGIN OF FUNCTIONAL SCRIPT ##########
#normalize and get orthogonal vector
# define vectors from points
xyz2 = cpv.sub(xyz2, xyz1)
xyz3 = cpv.sub(xyz3, xyz1)
#NB! cpv.get_system2 outputs normalized vectors [x,y,z]
xyz4 = cpv.get_system2(xyz2, xyz3)
xyz2 = xyz4[0]
xyz3 = xyz4[1]
for x in range(0, 3):
for z in range(0, 3):
if x == z:
continue
if xyz4[x] == xyz4[z]:
raise Exception("Illegal vector settings!")
xyz4 = cpv.negate(xyz4[2]) #overwrites original
# transform origin to corner
if mode == 0:
if npoints_x > 1:
xyz1 = cpv.sub(xyz1, cpv.scale(xyz2, length_x / 2))
if npoints_z > 1:
xyz1 = cpv.sub(xyz1, cpv.scale(xyz3, length_z / 2))
#defines array lines
nlines = max([npoints_x, npoints_z])
# in case only one line max
# create an empty array for xyz entries
# this may contain more values than are actually drawn later,
# but they are needed to draw lines in each direction
grid_xyz = []
for x in range(0, nlines):
grid_xyz.append([0.0, 0.0, 0.0] * nlines)
# grid distance and steps
# prevent zero divisions (lines=1) and enable calculations if lines=0
if (not (npoints_x - 1 < 2)):
gap_length_x = length_x / (npoints_x - 1)
step_line_x = 2 * math.pi / (npoints_x - 1)
else:
gap_length_x = length_x
step_line_x = 2 * math.pi
if (not (npoints_z - 1 < 2)):
gap_length_z = length_z / (npoints_z - 1)
step_line_z = 2 * math.pi / (npoints_z - 1)
else:
gap_length_z = length_z
step_line_z = 2 * math.pi
# calculate steps
if nstates == 1:
step_state = 0
else:
step_state = 2 * math.pi / (nstates - 1)
########## BEGIN STATE ITERATION ##########
# create a n-state object in PyMol
for a in range(0, nstates):
# Reset object
obj = []
#assign color
obj.extend([COLOR, color[0], color[1], color[2]])
#set width
obj.extend([LINEWIDTH, thickness])
# Calculate xyz-coordinates for each line
for x in range(0, nlines):
for z in range(0, nlines):
# update grid position in x-direction
xyztemp = cpv.add(xyz1, cpv.scale(xyz2, gap_length_x * x))
# update grid position in z-direction
xyztemp = cpv.add(xyztemp, cpv.scale(xyz3, gap_length_z * z))
# calculate amplitude for y-direction and update grid position
y_amp=(\
gain_x*math.sin(offset_x+nwaves_x*((a*step_state)+(x*step_line_x)))/2+\
gain_z*math.sin(offset_z+nwaves_z*((a*step_state)+(z*step_line_z)))/2\
)
xyztemp = cpv.add(xyztemp, cpv.scale(xyz4, y_amp))
grid_xyz[x][z] = xyztemp
#Now the coordinates for this state are defined!
#Now the coordinates are read separately:
# allow to run the loops as often as required
#if npoints_x==0:npoints_x=npoints_z
#lines along z in x direction
for z in range(0, npoints_z):
obj.extend([BEGIN, LINE_STRIP])
for x in range(0, npoints_x):
obj.extend([
VERTEX, grid_xyz[x][z][0], grid_xyz[x][z][1],
grid_xyz[x][z][2]
])
obj.append(END)
#lines along x in z direction
for x in range(0, npoints_x):
obj.extend([BEGIN, LINE_STRIP])
for z in range(0, npoints_z):
obj.extend([
VERTEX, grid_xyz[x][z][0], grid_xyz[x][z][1],
grid_xyz[x][z][2]
])
obj.append(END)
# Load state into PyMOL object:
cmd.load_cgo(obj, name, a + 1)
# All states of object loaded!
#reset auto zooming to previous value
cmd.set('auto_zoom', temp_auto_zoom)
# animate object using frames instead of states
if (not endframe == startframe):
framecount = 0
countvar = 1
for frame in range(startframe, endframe + 1):
#increase count
framecount = framecount + countvar
# set state in frame
cmd.mappend(
frame,
"/cmd.set('state', %s, %s)" % (repr(framecount), repr(name)))
# Looping
if framecount == nstates:
if ((int(nwaves_x) != nwaves_x)
or (int(nwaves_z) != nwaves_z)):
#if not complete sinus wave
#--> reverse wave in ongoing animation
countvar = -1
else:
#wave is complete --> repeat
framecount = 0
# count up from first state
if framecount == 1: countvar = 1
if not quiet: print "object loaded and animated with frames!"
else:
if not quiet: print "object loaded!"
#OUTPUT
if not quiet:
print "Grid variables for:", name
print "corner:", xyz1
print "vector 1:", xyz2
print "vector 2:", xyz3
print "length_x:", length_x
print "length_z:", length_z
print "npoints_x:", npoints_x
print "npoints_z:", npoints_z
print "nwaves_x:", nwaves_x
print "nwaves_z:", nwaves_z
print "offset_x:", offset_x
print "offset_z:", offset_z
print "gain_x:", gain_x
print "gain_z:", gain_z
print "thickness:", thickness
print "states", nstates
if (not endframe == startframe):
print "frames: start:", startframe, "end:", endframe
return grid_xyz
def append_tri(self):
if self.l_vert and not self.l_norm:
d0 = cpv.sub(self.l_vert[0],self.l_vert[1])
d1 = cpv.sub(self.l_vert[0],self.l_vert[2])
n0 = cpv.cross_product(d0,d1)
n0 = cpv.normalize_failsafe(n0)
n1 = [-n0[0],-n0[1],-n0[2]]
ns = cpv.scale(n0,0.002)
if not self.tri_flag:
self.obj.append(BEGIN)
self.obj.append(TRIANGLES)
self.tri_flag = 1
self.obj.append(COLOR) # assuming unicolor
self.obj.extend(self.t_colr[0])
self.obj.append(NORMAL)
self.obj.extend(n0)
self.obj.append(VERTEX)
self.obj.extend(cpv.add(self.l_vert[0],ns))
self.obj.append(COLOR) # assuming unicolor
self.obj.extend(self.t_colr[1])
self.obj.append(NORMAL)
self.obj.extend(n0)
self.obj.append(VERTEX)
self.obj.extend(cpv.add(self.l_vert[1],ns))
self.obj.append(COLOR) # assuming unicolor
self.obj.extend(self.t_colr[2])
self.obj.append(NORMAL)
self.obj.extend(n0)
self.obj.append(VERTEX)
self.obj.extend(cpv.add(self.l_vert[2],ns))
self.obj.append(COLOR) # assuming unicolor
self.obj.extend(self.t_colr[0])
self.obj.append(NORMAL)
self.obj.extend(n1)
self.obj.append(VERTEX)
self.obj.extend(cpv.sub(self.l_vert[0],ns))
self.obj.append(COLOR) # assuming unicolor
self.obj.extend(self.t_colr[1])
self.obj.append(NORMAL)
self.obj.extend(n1)
self.obj.append(VERTEX)
self.obj.extend(cpv.sub(self.l_vert[1],ns))
self.obj.append(COLOR) # assuming unicolor
self.obj.extend(self.t_colr[2])
self.obj.append(NORMAL)
self.obj.extend(n1)
self.obj.append(VERTEX)
self.obj.extend(cpv.sub(self.l_vert[2],ns))
elif self.l_vert and self.t_colr and self.l_norm:
if not self.tri_flag:
self.obj.append(BEGIN)
self.obj.append(TRIANGLES)
self.tri_flag = 1
self.obj.append(COLOR) # assuming unicolor
self.obj.extend(self.t_colr[0])
self.obj.append(NORMAL)
self.obj.extend(self.l_norm[0])
self.obj.append(VERTEX)
self.obj.extend(self.l_vert[0])
self.obj.append(COLOR) # assuming unicolor
self.obj.extend(self.t_colr[1])
self.obj.append(NORMAL)
self.obj.extend(self.l_norm[1])
self.obj.append(VERTEX)
self.obj.extend(self.l_vert[1])
self.obj.append(COLOR) # assuming unicolor
self.obj.extend(self.t_colr[2])
self.obj.append(NORMAL)
self.obj.extend(self.l_norm[2])
self.obj.append(VERTEX)
self.obj.extend(self.l_vert[2])
self.l_vert=None
self.t_colr=None
self.l_norm=None
def update_box(self):
if self.points_name in self.cmd.get_names():
model = self.cmd.get_model(self.points_name)
self.coord = (
model.atom[0].coord,
model.atom[1].coord,
model.atom[2].coord,
model.atom[3].coord,
)
p = self.coord[0]
d10 = sub(self.coord[1], p)
d20 = sub(self.coord[2], p)
d30 = sub(self.coord[3], p)
x10_20 = cross_product(d10, d20)
if self.mode != 'quad':
if dot_product(d30, x10_20) < 0.0:
p = model.atom[1].coord
d10 = sub(self.coord[0], p)
d20 = sub(self.coord[2], p)
d30 = sub(self.coord[3], p)
n10_20 = normalize(x10_20)
n10 = normalize(d10)
d100 = d10
d010 = remove_component(d20, n10)
if self.mode != 'quad':
d001 = project(d30, n10_20)
else:
d001 = n10_20
n100 = normalize(d100)
n010 = normalize(d010)
n001 = normalize(d001)
f100 = reverse(n100)
f010 = reverse(n010)
f001 = reverse(n001)
if self.mode == 'quad':
p000 = p
p100 = add(p, remove_component(d10, n001))
p010 = add(p, remove_component(d20, n001))
p001 = add(p, remove_component(d30, n001))
else:
p000 = p
p100 = add(p, d100)
p010 = add(p, d010)
p001 = add(p, d001)
p110 = add(p100, d010)
p011 = add(p010, d001)
p101 = add(p100, d001)
p111 = add(p110, d001)
obj = []
if self.mode == 'box': # standard box
obj.extend([BEGIN, TRIANGLE_STRIP])
obj.append(NORMAL)
obj.extend(f001)
obj.append(VERTEX)
obj.extend(p000)
obj.append(VERTEX)
obj.extend(p010)
obj.append(VERTEX)
obj.extend(p100)
obj.append(VERTEX)
obj.extend(p110)
obj.append(END)
obj.extend([BEGIN, TRIANGLE_STRIP])
obj.append(NORMAL)
obj.extend(n001)
obj.append(VERTEX)
obj.extend(p001)
obj.append(VERTEX)
obj.extend(p101)
obj.append(VERTEX)
obj.extend(p011)
obj.append(VERTEX)
obj.extend(p111)
obj.append(END)
obj.extend([BEGIN, TRIANGLE_STRIP])
obj.append(NORMAL)
obj.extend(f010)
obj.append(VERTEX)
obj.extend(p000)
obj.append(VERTEX)
obj.extend(p100)
obj.append(VERTEX)
obj.extend(p001)
obj.append(VERTEX)
obj.extend(p101)
obj.append(END)
obj.extend([BEGIN, TRIANGLE_STRIP])
obj.append(NORMAL)
obj.extend(n010)
obj.append(VERTEX)
obj.extend(p010)
obj.append(VERTEX)
obj.extend(p011)
obj.append(VERTEX)
obj.extend(p110)
obj.append(VERTEX)
obj.extend(p111)
obj.append(END)
obj.extend([BEGIN, TRIANGLE_STRIP])
obj.append(NORMAL)
obj.extend(f100)
obj.append(VERTEX)
obj.extend(p000)
obj.append(VERTEX)
obj.extend(p001)
obj.append(VERTEX)
obj.extend(p010)
obj.append(VERTEX)
obj.extend(p011)
obj.append(END)
obj.extend([BEGIN, TRIANGLE_STRIP])
obj.append(NORMAL)
obj.extend(n100)
obj.append(VERTEX)
obj.extend(p100)
obj.append(VERTEX)
obj.extend(p110)
obj.append(VERTEX)
obj.extend(p101)
obj.append(VERTEX)
obj.extend(p111)
obj.append(END)
model.atom[0].coord = p000
model.atom[1].coord = p100
model.atom[2].coord = add(p010, scale(d100, 0.5))
model.atom[3].coord = add(add(p001, scale(d010, 0.5)), d100)
elif self.mode == 'walls':
obj.extend([BEGIN, TRIANGLE_STRIP])
obj.append(NORMAL)
obj.extend(n001)
obj.append(VERTEX)
obj.extend(p000)
obj.append(VERTEX)
obj.extend(p100)
obj.append(VERTEX)
obj.extend(p010)
obj.append(VERTEX)
obj.extend(p110)
obj.append(END)
obj.extend([BEGIN, TRIANGLE_STRIP])
obj.append(NORMAL)
obj.extend(n010)
obj.append(VERTEX)
obj.extend(p000)
obj.append(VERTEX)
obj.extend(p001)
obj.append(VERTEX)
obj.extend(p100)
obj.append(VERTEX)
obj.extend(p101)
obj.append(END)
obj.extend([BEGIN, TRIANGLE_STRIP])
obj.append(NORMAL)
obj.extend(n100)
obj.append(VERTEX)
obj.extend(p000)
obj.append(VERTEX)
obj.extend(p010)
obj.append(VERTEX)
obj.extend(p001)
obj.append(VERTEX)
obj.extend(p011)
obj.append(END)
model.atom[0].coord = p000
model.atom[1].coord = p100
model.atom[2].coord = p010
model.atom[3].coord = p001
elif self.mode == 'plane':
obj.extend([BEGIN, TRIANGLE_STRIP])
obj.append(NORMAL)
obj.extend(n001)
obj.append(VERTEX)
obj.extend(p000)
obj.append(VERTEX)
obj.extend(p100)
obj.append(VERTEX)
obj.extend(p010)
obj.append(VERTEX)
obj.extend(p110)
obj.append(END)
model.atom[0].coord = p000
model.atom[1].coord = p100
model.atom[2].coord = p010
model.atom[3].coord = add(add(p001, scale(d010, 0.5)),
scale(d100, 0.5))
elif self.mode == 'quad':
obj.extend([BEGIN, TRIANGLE_STRIP])
obj.append(NORMAL)
obj.extend(n001)
obj.append(VERTEX)
obj.extend(p000)
obj.append(VERTEX)
obj.extend(p100)
obj.append(VERTEX)
obj.extend(p010)
obj.append(VERTEX)
obj.extend(p001)
obj.append(END)
model.atom[0].coord = p000
model.atom[1].coord = p100
model.atom[2].coord = p010
model.atom[3].coord = p001
self.cmd.load_model(model, '_tmp', zoom=0)
self.cmd.update(self.points_name, "_tmp")
self.cmd.delete("_tmp")
# then we load it into PyMOL
self.cmd.delete(self.cgo_name)
self.cmd.load_cgo(obj, self.cgo_name, zoom=0)
self.cmd.order(self.cgo_name + " " + self.points_name,
sort=1,
location='bottom')
self.cmd.set("nonbonded_size",
math.sqrt(dot_product(d10, d10)) / 10,
self.points_name)
def calculateNewPoint(p1, p2, distance):
v1 = cpv.normalize(cpv.sub(p1, p2))
return cpv.add(p1, cpv.scale(v1, distance))
def cgo_arrow(atom1='pk1', atom2='pk2', radius=0.5, gap=0.0, hlength=-1, hradius=-1,
color='black black', name=''):
'''
#I modify the color the line just before
DESCRIPTION
Create a CGO arrow between two picked atoms.
ARGUMENTS
atom1 = string: single atom selection or list of 3 floats {default: pk1}
atom2 = string: single atom selection or list of 3 floats {default: pk2}
radius = float: arrow radius {default: 0.5}
gap = float: gap between arrow tips and the two atoms {default: 0.0}
hlength = float: length of head
hradius = float: radius of head
color = string: one or two color names {default: blue red}
name = string: name of CGO object
'''
from chempy import cpv
radius, gap = float(radius), float(gap)
hlength, hradius = float(hlength), float(hradius)
try:
color1, color2 = color.split()
except:
color1 = color2 = color
color1 = list(cmd.get_color_tuple(color1))
color2 = list(cmd.get_color_tuple(color2))
def get_coord(v):
if not isinstance(v, str):
return v
if v.startswith('['):
return cmd.safe_list_eval(v)
return cmd.get_atom_coords(v)
xyz1 = get_coord(atom1)
xyz2 = get_coord(atom2)
normal = cpv.normalize(cpv.sub(xyz1, xyz2))
if hlength < 0:
hlength = radius * 3.0
if hradius < 0:
hradius = hlength * 0.6
if gap:
diff = cpv.scale(normal, gap)
xyz1 = cpv.sub(xyz1, diff)
xyz2 = cpv.add(xyz2, diff)
xyz3 = cpv.add(cpv.scale(normal, hlength), xyz2)
obj = [cgo.CYLINDER] + xyz1 + xyz3 + [radius] + color1 + color2 + \
[cgo.CONE] + xyz3 + xyz2 + [hradius, 0.0] + color2 + color2 + \
[1.0, 0.0]
if not name:
name = cmd.get_unused_name('arrow')
cmd.load_cgo(obj, name)
def visualize_orientation(direction,
center=[0.0] * 3,
scale=1.0,
symmetric=False,
color='green',
color2='red',
*,
_self=cmd):
'''
DESCRIPTION
Draw an arrow. Helper function for "helix_orientation" etc.
'''
from pymol import cgo
color_list = _self.get_color_tuple(color)
color2_list = _self.get_color_tuple(color2)
if symmetric:
scale *= 0.5
end = cpv.add(center, cpv.scale(direction, scale))
radius = 0.3
obj = [cgo.SAUSAGE]
obj.extend(center)
obj.extend(end)
obj.extend([
radius,
0.8,
0.8,
0.8,
])
obj.extend(color_list)
if symmetric:
start = cpv.sub(center, cpv.scale(direction, scale))
obj.append(cgo.SAUSAGE)
obj.extend(center)
obj.extend(start)
obj.extend([
radius,
0.8,
0.8,
0.8,
])
obj.extend(color2_list)
coneend = cpv.add(
end, cpv.scale(direction, 4.0 * radius / cpv.length(direction)))
obj.append(cgo.CONE)
obj.extend(end)
obj.extend(coneend)
obj.extend([
radius * 1.75,
0.0,
])
obj.extend(color_list * 2)
obj.extend([
1.0,
1.0, # Caps
])
_self.load_cgo(obj, _self.get_unused_name('oriVec'), zoom=0)
def drawmol(self,model):
print 'drawmol'
self.sphere_list= glGenLists(1)
glNewList(self.sphere_list, GL_COMPILE)
print 'making sphere list of ', len(model.atom),' atoms'
for a in model.atom:
try:
z = a.get_number()
except Exception:
z = 0
r,g,b = colours[z]
glColor3f(r,g,b)
glPushMatrix()
x = a.coord[0]
y = a.coord[1]
zz = a.coord[2]
glTranslatef (x, y, zz)
fac = rcov[z] / 2.0
glScale(fac,fac,fac)
glutSolidSphere(0.4, 16, 16)
glPopMatrix()
glEndList()
self.line_list= glGenLists(1)
glNewList(self.line_list, GL_COMPILE)
glLineWidth(2.0)
glBegin(GL_LINES)
line_count = 0
for a in model.atom:
try:
c = a.conn
except AttributeError:
c = []
for t in c:
if t.get_index() > a.get_index():
line_count = line_count + 1
vec = cpv.sub(t.coord, a.coord)
mid = cpv.add(a.coord,cpv.scale(vec,0.5))
try:
z = a.get_number()
except Exception:
z = 0
r,g,b = colours[z]
glColor3f(r, g, b)
glVertex3f(a.coord[0],a.coord[1],a.coord[2])
glVertex3f(mid[0],mid[1],mid[2])
try:
z = t.get_number()
except Exception:
z = 0
r,g,b = colours[z]
glColor3f(r, g, b)
glVertex3f(mid[0],mid[1],mid[2])
glVertex3f(t.coord[0],t.coord[1],t.coord[2])
glEnd()
glEndList()
print 'made line list of ', line_count, ' lines'
def cgo_arrow(atom1='pk1',
atom2='pk2',
radius=0.5,
gap=0.0,
hlength=-1,
hradius=-1,
color='blue red',
name=''):
'''
DESCRIPTION
Create a CGO arrow between two picked atoms.
ARGUMENTS
atom1 = string: single atom selection or list of 3 floats {default: pk1}
atom2 = string: single atom selection or list of 3 floats {default: pk2}
radius = float: arrow radius {default: 0.5}
gap = float: gap between arrow tips and the two atoms {default: 0.0}
hlength = float: length of head
hradius = float: radius of head
color = string: one or two color names {default: blue red}
name = string: name of CGO object
'''
from chempy import cpv
radius, gap = float(radius), float(gap)
hlength, hradius = float(hlength), float(hradius)
try:
color1, color2 = color.split()
except:
color1 = color2 = color
color1 = list(cmd.get_color_tuple(color1))
color2 = list(cmd.get_color_tuple(color2))
def get_coord(v):
if not isinstance(v, str):
return v
if v.startswith('['):
return cmd.safe_list_eval(v)
return cmd.get_atom_coords(v)
xyz1 = get_coord(atom1)
xyz2 = get_coord(atom2)
normal = cpv.normalize(cpv.sub(xyz1, xyz2))
if hlength < 0:
hlength = radius * 3.0
if hradius < 0:
hradius = hlength * 0.6
if gap:
diff = cpv.scale(normal, gap)
xyz1 = cpv.sub(xyz1, diff)
xyz2 = cpv.add(xyz2, diff)
xyz3 = cpv.add(cpv.scale(normal, hlength), xyz2)
obj = [cgo.CYLINDER] + xyz1 + xyz3 + [radius] + color1 + color2 + \
[cgo.CONE] + xyz3 + xyz2 + [hradius, 0.0] + color2 + color2 + \
[1.0, 0.0]
if not name:
name = cmd.get_unused_name('arrow')
cmd.load_cgo(obj, name)
def set_view(view, center, trans, volume, persp):
'''
view is their 4x4
center is the centor of rotation in tranformed coordinates
'''
view = list(view)
# print view[0:4]
# print view[4:8]
# print view[8:12]
# print view[12:16]
# print "\nmaestro_center: %8.3f %8.3f %8.3f"%tuple(center)
# print "maestro_transl: %8.3f %8.3f %8.3f"%tuple(trans)
mat = [ view[0:3], view[4:7], view[8:11] ]
tmp = cpv.sub(center,view[12:15])
pymol_center = cpv.transform(mat,tmp)
# print "volumeX: %8.3f %8.3f"%(tuple(volume[0:2]))
# print "volumeY: %8.3f %8.3f"%(tuple(volume[2:4]))
# print "volumeZ: %8.3f %8.3f"%(tuple(volume[4:6]))
# print "pymol_center: %8.3f %8.3f %8.3f"%tuple(pymol_center)
# print persp
if persp<0.0:
pymol_ortho = 1.0
else:
pymol_ortho = 0.0
if pymol_ortho==0.0:
fov = 1 + 100*(persp - 1.0)/3.0
cmd.set('field_of_view',fov)
fov = (math.pi * float(cmd.get("field_of_view")) / 180.0)
# unclear why we have to multiple by 1.17 to get the correct look
camera_dist = 1.17 * (abs(volume[2] - volume[3])/2.0)/math.atan(fov/2.0)
vol_center = [ (volume[0]+volume[1])/2.0,
(volume[2]+volume[3])/2.0,
(volume[4]+volume[5])/2.0 ]
pymol_objective = [ trans[0] + center[0] - vol_center[0],
trans[1] + center[1] - vol_center[1],
-camera_dist ]
# print "pymol_objective: %8.3f %8.3f %8.3f"%tuple(pymol_objective)
pymol_front = center[2] + trans[2] - volume[4] - pymol_objective[2]
pymol_back = center[2] + trans[2] - volume[5] - pymol_objective[2]
pymol_view = cmd.get_view()
cur_view = ( view[0:3] + view[4:7] + view[8:11] +
pymol_objective + pymol_center +
[ pymol_front, pymol_back, pymol_ortho ] )
# print cur_view
cmd.set_view(tuple(cur_view))
def helix_orientation(selection,
state=STATE,
visualize=1,
cutoff=3.5,
quiet=1):
'''
DESCRIPTION
Get the center and direction of a helix as vectors. Will only work
for alpha helices and gives slightly different results than
cafit_orientation. Averages direction of C(i)->O(i)->N(i+4).
USAGE
helix_orientation selection [, visualize [, cutoff ]]
ARGUMENTS
selection = string: atom selection of helix
visualize = 0 or 1: show fitted vector as arrow {default: 1}
cutoff = float: maximal hydrogen bond distance {default: 3.5}
SEE ALSO
angle_between_helices, loop_orientation, cafit_orientation
'''
state, visualize, quiet = int(state), int(visualize), int(quiet)
cutoff = float(cutoff)
atoms = {'C': dict(), 'O': dict(), 'N': dict()}
cmd.iterate_state(state,
'(%s) and name N+O+C' % (selection),
'atoms[name][resv] = x,y,z',
space={'atoms': atoms})
vec_list = []
for resi in atoms['C']:
resi_other = resi + 4
try:
aC = atoms['C'][resi]
aO = atoms['O'][resi]
aN = atoms['N'][resi_other]
except KeyError:
continue
dist = cpv.distance(aN, aO)
dist_weight = 1. - (2.8 - dist)
angle = cpv.get_angle_formed_by(aC, aO, aN)
angle_weight = 1. - (3.1 - angle)
if dist_weight > 0.0 and angle_weight > 0.0:
if not quiet:
print(' weight:', angle_weight * dist_weight)
vec = cpv.scale(cpv.sub(aN, aC), angle_weight * dist_weight)
vec_list.append(vec)
if len(vec_list) == 0:
print('warning: count == 0')
raise CmdException
center = cpv.scale(_vec_sum(atoms['O'].values()), 1. / len(atoms['O']))
vec = _vec_sum(vec_list)
vec = cpv.normalize(vec)
_common_orientation(selection, center, vec, visualize, 1.5 * len(vec_list),
quiet)
return center, vec
def update_box(self):
if self.points_name in self.cmd.get_names():
model = self.cmd.get_model(self.points_name)
self.coord = (
model.atom[0].coord,
model.atom[1].coord,
model.atom[2].coord,
model.atom[3].coord,
)
p = self.coord[0]
d10 = sub(self.coord[1], p)
d20 = sub(self.coord[2], p)
d30 = sub(self.coord[3], p)
x10_20 = cross_product(d10,d20)
if self.mode != 'quad':
if dot_product(d30,x10_20)<0.0:
p = model.atom[1].coord
d10 = sub(self.coord[0], p)
d20 = sub(self.coord[2], p)
d30 = sub(self.coord[3], p)
n10_20 = normalize(x10_20)
n10 = normalize(d10)
d100 = d10
d010 = remove_component(d20, n10)
if self.mode != 'quad':
d001 = project(d30, n10_20)
else:
d001 = n10_20
n100 = normalize(d100)
n010 = normalize(d010)
n001 = normalize(d001)
f100 = reverse(n100)
f010 = reverse(n010)
f001 = reverse(n001)
if self.mode == 'quad':
p000 = p
p100 = add(p, remove_component(d10,n001))
p010 = add(p, remove_component(d20,n001))
p001 = add(p, remove_component(d30,n001))
else:
p000 = p
p100 = add(p,d100)
p010 = add(p,d010)
p001 = add(p,d001)
p110 = add(p100, d010)
p011 = add(p010, d001)
p101 = add(p100, d001)
p111 = add(p110, d001)
obj = []
if self.mode == 'box': # standard box
obj.extend([ BEGIN, TRIANGLE_STRIP ])
obj.append(NORMAL); obj.extend(f001)
obj.append(VERTEX); obj.extend(p000)
obj.append(VERTEX); obj.extend(p010)
obj.append(VERTEX); obj.extend(p100)
obj.append(VERTEX); obj.extend(p110)
obj.append(END)
obj.extend([ BEGIN, TRIANGLE_STRIP ])
obj.append(NORMAL); obj.extend(n001)
obj.append(VERTEX); obj.extend(p001)
obj.append(VERTEX); obj.extend(p101)
obj.append(VERTEX); obj.extend(p011)
obj.append(VERTEX); obj.extend(p111)
obj.append(END)
obj.extend([ BEGIN, TRIANGLE_STRIP ])
obj.append(NORMAL); obj.extend(f010)
obj.append(VERTEX); obj.extend(p000)
obj.append(VERTEX); obj.extend(p100)
obj.append(VERTEX); obj.extend(p001)
obj.append(VERTEX); obj.extend(p101)
obj.append(END)
obj.extend([ BEGIN, TRIANGLE_STRIP ])
obj.append(NORMAL); obj.extend(n010)
obj.append(VERTEX); obj.extend(p010)
obj.append(VERTEX); obj.extend(p011)
obj.append(VERTEX); obj.extend(p110)
obj.append(VERTEX); obj.extend(p111)
obj.append(END)
obj.extend([ BEGIN, TRIANGLE_STRIP ])
obj.append(NORMAL); obj.extend(f100)
obj.append(VERTEX); obj.extend(p000)
obj.append(VERTEX); obj.extend(p001)
obj.append(VERTEX); obj.extend(p010)
obj.append(VERTEX); obj.extend(p011)
obj.append(END)
obj.extend([ BEGIN, TRIANGLE_STRIP ])
obj.append(NORMAL); obj.extend(n100)
obj.append(VERTEX); obj.extend(p100)
obj.append(VERTEX); obj.extend(p110)
obj.append(VERTEX); obj.extend(p101)
obj.append(VERTEX); obj.extend(p111)
obj.append(END)
model.atom[0].coord = p000
model.atom[1].coord = p100
model.atom[2].coord = add(p010, scale(d100,0.5))
model.atom[3].coord = add(add(p001, scale(d010,0.5)),d100)
elif self.mode=='walls':
obj.extend([ BEGIN, TRIANGLE_STRIP ])
obj.append(NORMAL); obj.extend(n001)
obj.append(VERTEX); obj.extend(p000)
obj.append(VERTEX); obj.extend(p100)
obj.append(VERTEX); obj.extend(p010)
obj.append(VERTEX); obj.extend(p110)
obj.append(END)
obj.extend([ BEGIN, TRIANGLE_STRIP ])
obj.append(NORMAL); obj.extend(n010)
obj.append(VERTEX); obj.extend(p000)
obj.append(VERTEX); obj.extend(p001)
obj.append(VERTEX); obj.extend(p100)
obj.append(VERTEX); obj.extend(p101)
obj.append(END)
obj.extend([ BEGIN, TRIANGLE_STRIP ])
obj.append(NORMAL); obj.extend(n100)
obj.append(VERTEX); obj.extend(p000)
obj.append(VERTEX); obj.extend(p010)
obj.append(VERTEX); obj.extend(p001)
obj.append(VERTEX); obj.extend(p011)
obj.append(END)
model.atom[0].coord = p000
model.atom[1].coord = p100
model.atom[2].coord = p010
model.atom[3].coord = p001
elif self.mode=='plane':
obj.extend([ BEGIN, TRIANGLE_STRIP ])
obj.append(NORMAL); obj.extend(n001)
obj.append(VERTEX); obj.extend(p000)
obj.append(VERTEX); obj.extend(p100)
obj.append(VERTEX); obj.extend(p010)
obj.append(VERTEX); obj.extend(p110)
obj.append(END)
model.atom[0].coord = p000
model.atom[1].coord = p100
model.atom[2].coord = p010
model.atom[3].coord = add(add(p001, scale(d010,0.5)),scale(d100,0.5))
elif self.mode=='quad':
obj.extend([ BEGIN, TRIANGLE_STRIP ])
obj.append(NORMAL); obj.extend(n001)
obj.append(VERTEX); obj.extend(p000)
obj.append(VERTEX); obj.extend(p100)
obj.append(VERTEX); obj.extend(p010)
obj.append(VERTEX); obj.extend(p001)
obj.append(END)
model.atom[0].coord = p000
model.atom[1].coord = p100
model.atom[2].coord = p010
model.atom[3].coord = p001
self.cmd.load_model(model, '_tmp', zoom=0)
self.cmd.update(self.points_name,"_tmp")
self.cmd.delete("_tmp")
# then we load it into PyMOL
self.cmd.delete(self.cgo_name)
self.cmd.load_cgo(obj,self.cgo_name,zoom=0)
self.cmd.order(self.cgo_name+" "+self.points_name,sort=1,location='bottom')
self.cmd.set("nonbonded_size",math.sqrt(dot_product(d10,d10))/10,self.points_name)
def cgo_arrow(origin, endpoint, color='blue', radius=0.10, gap=0.0, hlength=-1, hradius=-1,
type='electric', name='', scaling = 7):
'''
:param origin: List representing origin point of vector to be drawn
:type origin: List of floats
:param endpoint: List representing endpoint of vector to be drawn
:type endpoint: List of floats
:param color: Color of arrow
:type color: String, optional - default blue
:param radius: Radius of cylinder portion of arrow
:type radius: Float, optional - default .1
:param gap: Specifies a gap between the head and body of the arrow, if desired
:type gap: Float, optional - default 0
:param hlength: Length of the head of the arrow
:type hlength: Float, optional - default -1
:param hradius: Radius of the head of the arrow
:type hradius: Float, optional - default -1
:param type: Type of vector being drawn, electric or magnetic
:type type: String, optional - default electric
:param name: Name to be shown in PyMol for the cgo object
:type name: String, optional - default blank
:param scaling: Scaling factor that is passed to scale_endpoint function
:type scaling: Int, optional - default 7
:return: None
'''
from chempy import cpv
#converting parameters to floats
radius, gap = float(radius), float(gap)
hlength, hradius = float(hlength), float(hradius)
if type == 'electric':
color = 'red'
name = 'electric'+name
if type == 'magnetic':
color = 'blue'
name = 'magnetic'+name
try:
color1, color2 = color.split()
except:
color1 = color2 = color
color1 = list(cmd.get_color_tuple(color1))
color2 = list(cmd.get_color_tuple(color2))
if origin == 'sele':
xyz1 = cmd.get_coords('sele', 1)
xyz1 = xyz1.flatten()
xyz1 = xyz1.tolist()
length=np.linalg.norm(np.array(endpoint))
xyz2 = scale_endpoint(endpoint,scaling)
xyz2 = shift_vectors(xyz2, xyz1)
else:
xyz1 = origin
length=np.linalg.norm(np.array(endpoint)-np.array(xyz1))
xyz2 = scale_endpoint(endpoint,scaling)
normal = cpv.normalize(cpv.sub(xyz1, xyz2))
if hlength < 0:
hlength = radius * 3.0
if hradius < 0:
hradius = hlength * 0.6
if gap:
diff = cpv.scale(normal, gap)
xyz1 = cpv.sub(xyz1, diff)
xyz2 = cpv.add(xyz2, diff)
##Location where cylinder switches to cone
xyz3 = cpv.add(cpv.scale(normal, hlength), xyz2)
obj = [cgo.CYLINDER] + xyz1 + xyz3 + [radius] + color1 + color1 + \
[cgo.CONE] + xyz3 + xyz2 + [hradius, 0.0] + color1 + color2 + \
[1.0, 0.0]
print(obj)
##Place pseudoatom with label at midpoint of vector
v0=np.array(xyz1)
v1=np.array(xyz2)
loc=(v0+v1)/2
if not name:
name = cmd.get_unused_name('arrow')
cmd.load_cgo(obj, f"vec_{name}")
##For some reason pos fails, but it just happens to put it where I want
cmd.pseudoatom(f"lab_{name}",name="lab_"+name,label=f"{length:.2f}")#,pos=loc
cmd.group(name,members=f"lab_{name} vec_{name}")
