def cafit_orientation(selection, visualize=1, quiet=0):
'''
DESCRIPTION
Get the center and direction of a peptide by least squares
linear fit on CA atoms.
USAGE
cafit_orientation selection [, visualize]
NOTES
Requires python module "numpy".
SEE ALSO
helix_orientation
'''
visualize, quiet = int(visualize), int(quiet)
import numpy
stored.x = list()
cmd.iterate_state(STATE, '(%s) and name CA' % (selection),
'stored.x.append([x,y,z])')
x = numpy.array(stored.x)
U, s, Vh = numpy.linalg.svd(x - x.mean(0))
vec = cpv.normalize(Vh[0])
if cpv.dot_product(vec, x[-1] - x[0]) < 0:
vec = cpv.negate(vec)
return _common_orientation(selection, vec, visualize, quiet)
def cafit_orientation(selection, visualize=1, quiet=0):
'''
DESCRIPTION
Get the center and direction of a peptide by least squares
linear fit on CA atoms.
USAGE
cafit_orientation selection [, visualize]
NOTES
Requires python module "numpy".
SEE ALSO
helix_orientation
'''
visualize, quiet = int(visualize), int(quiet)
import numpy
stored.x = list()
cmd.iterate_state(STATE, '(%s) and name CA' % (selection),
'stored.x.append([x,y,z])')
x = numpy.array(stored.x)
U, s, Vh = numpy.linalg.svd(x - x.mean(0))
vec = cpv.normalize(Vh[0])
if cpv.dot_product(vec, x[-1] - x[0]) < 0:
vec = cpv.negate(vec)
return _common_orientation(selection, vec, visualize, quiet)
def plane_orientation(selection, state=-1, visualize=1, quiet=1):
'''
DESCRIPTION
Fit plane (for example beta-sheet). Can also be used with
angle_between_helices (even though this does not fit helices).
Returns center and normal vector of plane.
'''
try:
import numpy
except ImportError:
print ' Error: numpy not available'
raise CmdException
state, visualize, quiet = int(state), int(visualize), int(quiet)
coords = list()
cmd.iterate_state(state, '(%s) and guide' % (selection),
'coords.append([x,y,z])', space=locals())
if len(coords) < 3:
print 'not enough guide atoms in selection'
raise CmdException
x = numpy.array(coords)
U,s,Vh = numpy.linalg.svd(x - x.mean(0))
# normal vector of plane is 3rd principle component
vec = cpv.normalize(Vh[2])
if cpv.dot_product(vec, x[-1] - x[0]) < 0:
vec = cpv.negate(vec)
center = x.mean(0).tolist()
_common_orientation(selection, center, vec, visualize, 4.0, quiet)
# plane visualize
if visualize:
from pymol import cgo
dir1 = cpv.normalize(Vh[0])
dir2 = cpv.normalize(Vh[1])
sx = [max(i/4.0, 2.0) for i in s]
obj = [ cgo.BEGIN, cgo.TRIANGLES, cgo.COLOR, 0.5, 0.5, 0.5 ]
for vertex in [
cpv.scale(dir1, sx[0]),
cpv.scale(dir2, sx[1]),
cpv.scale(dir2, -sx[1]),
cpv.scale(dir1, -sx[0]),
cpv.scale(dir2, -sx[1]),
cpv.scale(dir2, sx[1]),
]:
obj.append(cgo.VERTEX)
obj.extend(cpv.add(center, vertex))
obj.append(cgo.END)
cmd.load_cgo(obj, cmd.get_unused_name('planeFit'))
return center, vec
def cafit_orientation(selection,
state=STATE,
visualize=1,
guide=1,
quiet=1,
*,
_self=cmd):
'''
DESCRIPTION
Get the center and direction of a peptide by least squares
linear fit on CA atoms.
USAGE
cafit_orientation selection [, visualize ]
NOTES
Requires python module "numpy".
SEE ALSO
helix_orientation
'''
import numpy
state, visualize, quiet = int(state), int(visualize), int(quiet)
if int(guide):
selection = '(%s) and guide' % (selection)
coords = []
_self.iterate_state(state,
selection,
'coords.append([x,y,z])',
space=locals())
x = numpy.array(coords)
center = x.mean(0).tolist()
U, s, Vh = numpy.linalg.svd(x - center)
vec = cpv.normalize(Vh[0])
if cpv.dot_product(vec, x[-1] - x[0]) < 0:
vec = cpv.negate(vec)
_common_orientation(selection,
center,
vec,
visualize,
s[0],
quiet,
_self=_self)
return center, vec
def cafit_orientation(selection, state=STATE, visualize=1, guide=1, quiet=1):
'''
DESCRIPTION
Get the center and direction of a peptide by least squares
linear fit on CA atoms.
USAGE
cafit_orientation selection [, visualize ]
NOTES
Requires python module "numpy".
SEE ALSO
helix_orientation
'''
try:
import numpy
except ImportError:
print ' Error: numpy not available'
raise CmdException
state, visualize, quiet = int(state), int(visualize), int(quiet)
if int(guide):
selection = '(%s) and guide' % (selection)
coords = []
cmd.iterate_state(state, selection,
'coords.append([x,y,z])', space=locals())
x = numpy.array(coords)
center = x.mean(0).tolist()
U,s,Vh = numpy.linalg.svd(x - center)
vec = cpv.normalize(Vh[0])
if cpv.dot_product(vec, x[-1] - x[0]) < 0:
vec = cpv.negate(vec)
_common_orientation(selection, center, vec, visualize, s[0], quiet)
return center, vec
def plane(corner1, corner2, corner3, corner4, normal, settings):
planeObj = []
planeObj.extend(point(corner1))
planeObj.extend(point(corner2))
planeObj.extend(point(corner3))
planeObj.extend(point(corner4))
planeObj.extend(line(corner1, corner2))
planeObj.extend(line(corner2, corner3))
planeObj.extend(line(corner3, corner4))
planeObj.extend(line(corner4, corner1))
# Make settings
if 'ALPHA' in settings:
planeObj.extend([ALPHA, settings['ALPHA']])
if 'COLOR' in settings:
planeObj.extend([
COLOR, settings['COLOR'][0], settings['COLOR'][1],
settings['COLOR'][2]
])
else:
planeObj.extend([COLOR, 0.8, 0.8, 0.8]) # greyish
planeObj.extend([BEGIN, TRIANGLE_STRIP])
planeObj.append(NORMAL)
if 'INVERT' in settings:
if settings['INVERT'] == True:
planeObj.extend(cpv.negate(normal))
else:
planeObj.extend(normal)
else:
planeObj.extend(normal)
for corner in [corner1, corner2, corner3, corner4, corner1]:
planeObj.append(VERTEX)
planeObj.extend(corner)
planeObj.append(END)
return planeObj
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 plane_orientation(selection, state=STATE, visualize=1, guide=0, quiet=1):
'''
DESCRIPTION
Fit plane (for example beta-sheet). Can also be used with
angle_between_helices (even though this does not fit helices).
Returns center and normal vector of plane.
'''
try:
import numpy
except ImportError:
print(' Error: numpy not available')
raise CmdException
state, visualize, quiet = int(state), int(visualize), int(quiet)
if int(guide):
selection = '(%s) and guide' % (selection)
coords = list()
cmd.iterate_state(state,
selection,
'coords.append([x,y,z])',
space=locals())
if len(coords) < 3:
print('not enough guide atoms in selection')
raise CmdException
x = numpy.array(coords)
U, s, Vh = numpy.linalg.svd(x - x.mean(0))
# normal vector of plane is 3rd principle component
vec = cpv.normalize(Vh[2])
if cpv.dot_product(vec, x[-1] - x[0]) < 0:
vec = cpv.negate(vec)
center = x.mean(0).tolist()
_common_orientation(selection, center, vec, visualize, 4.0, quiet)
# plane visualize
if visualize:
from pymol import cgo
dir1 = cpv.normalize(Vh[0])
dir2 = cpv.normalize(Vh[1])
sx = [max(i / 4.0, 2.0) for i in s]
obj = [cgo.BEGIN, cgo.TRIANGLES, cgo.COLOR, 0.5, 0.5, 0.5]
for vertex in [
cpv.scale(dir1, sx[0]),
cpv.scale(dir2, sx[1]),
cpv.scale(dir2, -sx[1]),
cpv.scale(dir1, -sx[0]),
cpv.scale(dir2, -sx[1]),
cpv.scale(dir2, sx[1]),
]:
obj.append(cgo.VERTEX)
obj.extend(cpv.add(center, vertex))
obj.append(cgo.END)
cmd.load_cgo(obj, get_unused_name('planeFit'))
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=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