def findSurfaceAtoms(selection="all", cutoff=2.5, quiet=1):
"""
DESCRIPTION
Finds those atoms on the surface of a protein
that have at least 'cutoff' exposed A**2 surface area.
USAGE
findSurfaceAtoms [ selection, [ cutoff ]]
SEE ALSO
findSurfaceResidues
"""
cutoff, quiet = float(cutoff), int(quiet)
tmpObj = cmd.get_unused_name("_tmp")
cmd.create(tmpObj, "(" + selection + ") and polymer", zoom=0)
cmd.set("dot_solvent", 1, tmpObj)
cmd.get_area(selection=tmpObj, load_b=1)
# threshold on what one considers an "exposed" atom (in A**2):
cmd.remove(tmpObj + " and b < " + str(cutoff))
selName = cmd.get_unused_name("exposed_atm_")
cmd.select(selName, "(" + selection + ") in " + tmpObj)
cmd.delete(tmpObj)
if not quiet:
print("Exposed atoms are selected in: " + selName)
return selName
def findSurfaceAtoms(selection="all", cutoff=2.5, quiet=1):
"""
DESCRIPTION
Finds those atoms on the surface of a protein
that have at least 'cutoff' exposed A**2 surface area.
USAGE
findSurfaceAtoms [ selection, [ cutoff ]]
SEE ALSO
findSurfaceResidues
"""
cutoff, quiet = float(cutoff), int(quiet)
tmpObj = cmd.get_unused_name("_tmp")
cmd.create(tmpObj, "(" + selection + ") and polymer", zoom=0)
cmd.set("dot_solvent", 1, tmpObj)
cmd.get_area(selection=tmpObj, load_b=1)
# threshold on what one considers an "exposed" atom (in A**2):
cmd.remove(tmpObj + " and b < " + str(cutoff))
selName = cmd.get_unused_name("exposed_atm_")
cmd.select(selName, "(" + selection + ") in " + tmpObj)
cmd.delete(tmpObj)
if not quiet:
print("Exposed atoms are selected in: " + selName)
return selName
def set_raw_alignment(name, aln, transform=0):
'''
DESCRIPTION
API only.
Load an alignment object from a list like the one obtained with
cmd.get_raw_alignment
'''
import itertools
if not isinstance(aln[0], dict):
aln = [dict(idx_pair) for idx_pair in aln]
models = set(model for idx_pdict in aln for model in idx_pdict)
sele1 = cmd.get_unused_name('_sele1')
sele2 = cmd.get_unused_name('_sele2')
fit = cmd.fit if transform else cmd.rms_cur
for model1, model2 in itertools.combinations(models, 2):
index_list1 = []
index_list2 = []
for idx_pdict in aln:
if model1 in idx_pdict and model2 in idx_pdict:
index_list1.append(idx_pdict[model1])
index_list2.append(idx_pdict[model2])
cmd.select_list(sele1, model1, index_list1, mode='index')
cmd.select_list(sele2, model2, index_list2, mode='index')
fit(sele1, sele2, cycles=0, matchmaker=4, object=name)
cmd.delete(sele1)
cmd.delete(sele2)
def set_raw_alignment(name, aln, transform=0):
'''
DESCRIPTION
API only.
Load an alignment object from a list like the one obtained with
cmd.get_raw_alignment
'''
import itertools
if not isinstance(aln[0], dict):
aln = [dict(idx_pair) for idx_pair in aln]
models = set(model for idx_pdict in aln for model in idx_pdict)
sele1 = cmd.get_unused_name('_sele1')
sele2 = cmd.get_unused_name('_sele2')
fit = cmd.fit if transform else cmd.rms_cur
for model1, model2 in itertools.combinations(models, 2):
index_list1 = []
index_list2 = []
for idx_pdict in aln:
if model1 in idx_pdict and model2 in idx_pdict:
index_list1.append(idx_pdict[model1])
index_list2.append(idx_pdict[model2])
cmd.select_list(sele1, model1, index_list1, mode='index')
cmd.select_list(sele2, model2, index_list2, mode='index')
fit(sele1, sele2, cycles=0, matchmaker=4, object=name)
cmd.delete(sele1)
cmd.delete(sele2)
def apbs_surface(selection='all',
maximum=None,
minimum=None,
map_name=None,
ramp_name=None,
grid=0.5,
quiet=1):
'''
DESCRIPTION
Show electrostatic potential on surface (calculated with APBS).
Important: surface_color is a object property, so when calculating
surface potential for different selections and visualize them all
together, you should first split them into separate objects.
USAGE
apbs_surface [ selection [, maximum [, minimum ]]]
EXAMPLE
fetch 2x19, bsync=0
split_chains
apbs_surface 2x19_A, 10
apbs_surface 2x19_B, 10
SEE ALSO
map_new_apbs, APBS Tools Plugin, isosurface, gradient,
util.protein_vacuum_esp
'''
quiet = int(quiet)
if ramp_name is None:
ramp_name = cmd.get_unused_name('ramp')
if map_name is None:
map_name = cmd.get_unused_name('map')
map_new_apbs(map_name, selection, float(grid), quiet=quiet)
if maximum is not None:
maximum = float(maximum)
minimum = -maximum if minimum is None else float(minimum)
kwargs = {'range': [minimum, (minimum + maximum) * 0.5, maximum]}
else:
kwargs = {'selection': selection}
cmd.ramp_new(ramp_name, map_name, **kwargs)
object_names = cmd.get_object_list('(' + selection + ')')
for name in object_names:
cmd.set('surface_color', ramp_name, name)
cmd.show('surface', selection)
cmd.set('surface_solvent', 0)
cmd.set('surface_ramp_above_mode', 1)
def draw_shell_sphere(radius,
polar_cone_angle=np.pi / 36.,
axis0=np.array([0., 1., 0.]),
axis1=np.array([0., 0., 1.]),
linewidth=1,
linespacing=0.15,
alpha=0.35,
name=None):
"""Draw sphere and stereo regions at specified radius in PyMOL."""
center = np.array([0., 0., 0.], dtype=np.double)
obj = []
# draw sphere
obj.extend(
get_cgo_sphere_obj(center, radius, color=[1., 1., 1.], alpha=alpha))
cmd.load_cgo(obj, cmd.get_unused_name('sphere_{:.4f}'.format(radius)))
# draw polar circles
obj = []
obj.extend([BEGIN, LINES, COLOR] + [0., 0., 0.])
v_to_cone_center = radius * np.cos(polar_cone_angle) * axis0
cone_radius = radius * np.sin(polar_cone_angle)
obj.extend(
get_cgo_circle_obj(center + v_to_cone_center,
axis0,
cone_radius,
linespacing=linespacing))
obj.extend(
get_cgo_circle_obj(center - v_to_cone_center,
-axis0,
cone_radius,
linespacing=linespacing))
# draw equator
obj.extend(
get_cgo_circle_obj(center, axis0, radius, linespacing=linespacing))
# draw quadrant arcs
for i in (1, 3, 5, 7):
if i in (5, 7):
color = [.8, .8, .8]
else:
color = [0., 0., 0.]
disk_norm = get_disk_norm(axis0, axis1, i * np.pi / 4.)
arc_start = (cone_radius * as_unit(np.cross(disk_norm, axis0)) +
center + v_to_cone_center)
obj.extend(
get_cgo_arc_obj(center,
disk_norm,
arc_start,
np.pi - 2 * polar_cone_angle,
linespacing=linespacing,
color=color))
# draw axes
obj.append(END)
lname = cmd.get_unused_name('contours_{:.4f}'.format(radius))
cmd.load_cgo(obj, lname)
cmd.set("cgo_line_width", linewidth, lname)
def from_alignment(self, mobile, target, aln_obj):
'''
Use alignment given by "aln_obj" (name of alignment object)
'''
from .selecting import wait_for
wait_for(aln_obj)
self.mobile = '(%s) and %s' % (mobile, aln_obj)
self.target = '(%s) and %s' % (target, aln_obj)
if self.check():
return
# difficult: if selections spans only part of the alignment or
# if alignment object covers more than the two objects, then we
# need to pick those columns that have no gap in any of the two
# given selections
mobileidx = set(cmd.index(mobile))
targetidx = set(cmd.index(target))
mobileidxsel = []
targetidxsel = []
for column in cmd.get_raw_alignment(aln_obj):
mobiles = mobileidx.intersection(column)
if len(mobiles) == 1:
targets = targetidx.intersection(column)
if len(targets) == 1:
mobileidxsel.extend(mobiles)
targetidxsel.extend(targets)
self.mobile = cmd.get_unused_name('_mobile')
self.target = cmd.get_unused_name('_target')
self.temporary.append(self.mobile)
self.temporary.append(self.target)
mobile_objects = set(idx[0] for idx in mobileidxsel)
target_objects = set(idx[0] for idx in targetidxsel)
if len(mobile_objects) == len(target_objects) == 1:
mobile_index_list = [idx[1] for idx in mobileidxsel]
target_index_list = [idx[1] for idx in targetidxsel]
cmd.select_list(self.mobile,
mobile_objects.pop(),
mobile_index_list,
mode='index')
cmd.select_list(self.target,
target_objects.pop(),
target_index_list,
mode='index')
else:
cmd.select(self.mobile,
' '.join('%s`%d' % idx for idx in mobileidxsel))
cmd.select(self.target,
' '.join('%s`%d' % idx for idx in targetidxsel))
def apbs_surface(selection='all', maximum=None, minimum=None, map_name=None,
ramp_name=None, grid=0.5, quiet=1):
'''
DESCRIPTION
Show electrostatic potential on surface (calculated with APBS).
Important: surface_color is a object property, so when calculating
surface potential for different selections and visualize them all
together, you should first split them into separate objects.
USAGE
apbs_surface [ selection [, maximum [, minimum ]]]
EXAMPLE
fetch 2x19, async=0
split_chains
apbs_surface 2x19_A, 10
apbs_surface 2x19_B, 10
SEE ALSO
map_new_apbs, APBS Tools Plugin, isosurface, gradient,
util.protein_vacuum_esp
'''
quiet = int(quiet)
if ramp_name is None:
ramp_name = cmd.get_unused_name('ramp')
if map_name is None:
map_name = cmd.get_unused_name('map')
map_new_apbs(map_name, selection, float(grid), quiet=quiet)
if maximum is not None:
maximum = float(maximum)
minimum = -maximum if minimum is None else float(minimum)
kwargs = {'range': [minimum, (minimum+maximum)*0.5, maximum]}
else:
kwargs = {'selection': selection}
cmd.ramp_new(ramp_name, map_name, **kwargs)
object_names = cmd.get_object_list('(' + selection + ')')
for name in object_names:
cmd.set('surface_color', ramp_name, name)
cmd.show('surface', selection)
cmd.set('surface_solvent', 0)
cmd.set('surface_ramp_above_mode', 1)
def testGetUnusedName(self):
n1 = cmd.get_unused_name()
self.assertEqual(n1, "tmp01")
n2 = cmd.get_unused_name("foo", 0)
self.assertEqual(n2, "foo")
cmd.pseudoatom("foo")
n3 = cmd.get_unused_name("foo", 0)
self.assertEqual(n3, "foo01")
cmd.pseudoatom("foo01")
cmd.pseudoatom("foo02")
n4 = cmd.get_unused_name("foo")
self.assertEqual(n4, "foo03")
cmd.delete('*')
n5 = cmd.get_unused_name("foo")
self.assertEqual(n5, "foo01")
def myalign(method):
newmobile = cmd.get_unused_name(mobile_obj + '_' + method)
cmd.create(newmobile, mobile_obj)
start = time.time()
cmd.do('%s mobile=%s in %s, target=%s' % (method, newmobile, mobile, target))
if not quiet:
print('Finished: %s (%.2f sec)' % (method, time.time() - start))
def com(selection,state=None,mass=None,object=None, quiet=1, **kwargs):
"""
DESCRIPTION
Places a pseudoatom at the center of mass
Author: Sean Law
Michigan State University
slaw (at) msu . edu
SEE ALSO
pseudoatom, get_com
"""
quiet = int(quiet)
if (object == None):
object = cmd.get_legal_name(selection)
object = cmd.get_unused_name(object + "_COM", 0)
cmd.delete(object)
if (state != None):
x, y, z=get_com(selection,mass=mass, quiet=quiet)
if not quiet:
print "%f %f %f" % (x, y, z)
cmd.pseudoatom(object,pos=[x, y, z], **kwargs)
cmd.show("spheres",object)
else:
for i in range(cmd.count_states()):
x, y, z=get_com(selection,mass=mass,state=i+1, quiet=quiet)
if not quiet:
print "State %d:%f %f %f" % (i+1, x, y, z)
cmd.pseudoatom(object,pos=[x, y, z],state=i+1, **kwargs)
cmd.show("spheres", 'last ' + object)
def normalmodes_prody(selection, cutoff=15, first=7, last=10, guide=1,
prefix='prody', states=7, factor=-1, quiet=1):
'''
DESCRIPTION
Anisotropic Network Model (ANM) analysis with ProDy.
Based on:
http://www.csb.pitt.edu/prody/examples/dynamics/enm/anm.html
'''
try:
import prody
except ImportError:
print('Failed to import prody, please add to PYTHONPATH')
raise CmdException
first, last, guide = int(first), int(last), int(guide)
states, factor, quiet = int(states), float(factor), int(quiet)
assert first > 6
if guide:
selection = '(%s) and guide and alt A+' % (selection)
tmpsele = cmd.get_unused_name('_')
cmd.select(tmpsele, selection)
f = StringIO(cmd.get_pdbstr(tmpsele))
conf = prody.parsePDBStream(f)
modes = prody.ANM()
modes.buildHessian(conf, float(cutoff))
modes.calcModes(last - first + 1)
if factor < 0:
from math import log
natoms = modes.numAtoms()
factor = log(natoms) * 10
if not quiet:
print(' set factor to %.2f' % (factor))
for mode in range(first, last + 1):
name = prefix + '%d' % mode
cmd.delete(name)
if not quiet:
print(' normalmodes: object "%s" for mode %d' % (name, mode))
for state in range(1, states+1):
xyz_it = iter(modes[mode-7].getArrayNx3() * (factor *
((state-1.0)/(states-1.0) - 0.5)))
cmd.create(name, tmpsele, 1, state, zoom=0)
cmd.alter_state(state, name, '(x,y,z) = xyz_it.next() + (x,y,z)',
space=locals())
cmd.delete(tmpsele)
if guide:
cmd.set('ribbon_trace_atoms', 1, prefix + '*')
cmd.show_as('ribbon', prefix + '*')
else:
cmd.show_as('lines', prefix + '*')
def do_select(self, name): # map selects into picks
from .selecting import select_sspick
if self.name not in cmd.get_names('selections', enabled_only=1):
self.name = cmd.get_unused_name('ss')
select_sspick(name, self.name, self.selection_mode)
cmd.enable(self.name)
cmd.refresh_wizard()
def CMVDialog(self):
import tkFileDialog
import tkMessageBox
try:
import pygame as pg
except ImportError:
tkMessageBox.showerror('Error', 'This plugin requires the "pygame" module')
return
myFormats = [('Portable Network Graphics', '*.png'), ('JPEG / JFIF', '*.jpg')]
try:
image_file = tkFileDialog.askopenfilename(parent=self.root,
filetypes=myFormats, title='Choose the contact map image file')
if not image_file:
raise
except:
tkMessageBox.showerror('Error', 'No Contact Map!')
return
myFormatsPDB = [('Protein Data Bank', '*.pdb'), ('MDL mol', '*.mol'), ('PyMol Session File', '*.pse')]
try:
pdb_file = tkFileDialog.askopenfilename(parent=self.root,
filetypes=myFormatsPDB, title='Choose the corresponding PDB file')
if not pdb_file:
raise
except:
tkMessageBox.showerror('Error', 'No PDB file!')
return
name = cmd.get_unused_name('protein')
cmd.load(pdb_file, name)
contact_map_visualizer(image_file, name, 1, 0)
def normalmodes_prody(selection, cutoff=15, first=7, last=10, guide=1,
prefix='prody', states=7, factor=-1, quiet=1):
'''
DESCRIPTION
Anisotropic Network Model (ANM) analysis with ProDy.
Based on:
http://www.csb.pitt.edu/prody/examples/dynamics/enm/anm.html
'''
try:
import prody
except ImportError:
print('Failed to import prody, please add to PYTHONPATH')
raise CmdException
first, last, guide = int(first), int(last), int(guide)
states, factor, quiet = int(states), float(factor), int(quiet)
assert first > 6
if guide:
selection = '(%s) and guide and alt A+' % (selection)
tmpsele = cmd.get_unused_name('_')
cmd.select(tmpsele, selection)
f = StringIO(cmd.get_pdbstr(tmpsele))
conf = prody.parsePDBStream(f)
modes = prody.ANM()
modes.buildHessian(conf, float(cutoff))
modes.calcModes(last - first + 1)
if factor < 0:
from math import log
natoms = modes.numAtoms()
factor = log(natoms) * 10
if not quiet:
print(' set factor to %.2f' % (factor))
for mode in range(first, last + 1):
name = prefix + '%d' % mode
cmd.delete(name)
if not quiet:
print(' normalmodes: object "%s" for mode %d' % (name, mode))
for state in range(1, states+1):
xyz_it = iter(modes[mode-7].getArrayNx3() * (factor *
((state-1.0)/(states-1.0) - 0.5)))
cmd.create(name, tmpsele, 1, state, zoom=0)
cmd.alter_state(state, name, '(x,y,z) = next(xyz_it) + (x,y,z)',
space={'xyz_it': xyz_it, 'next': next})
cmd.delete(tmpsele)
if guide:
cmd.set('ribbon_trace_atoms', 1, prefix + '*')
cmd.show_as('ribbon', prefix + '*')
else:
cmd.show_as('lines', prefix + '*')
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 do_select(self, name): # map selects into picks
from .selecting import select_sspick
if self.name not in cmd.get_names('selections', enabled_only=1):
self.name = cmd.get_unused_name('ss')
select_sspick(name, self.name, self.selection_mode)
cmd.enable(self.name)
cmd.refresh_wizard()
def load_msms_surface(filename, name='', _colors=None):
'''
DESCRIPTION
Load MSMS .vert and .face files as a CGO
'''
from pymol import cgo
from pymol.cgo import NORMAL, VERTEX, COLOR
if _colors:
_colors = [cmd.get_color_tuple(c) for c in _colors]
if filename.endswith('.vert') or filename.endswith('.face'):
filename = filename[:-5]
# vertex file
line_iter = iter(open(filename + '.vert'))
# skip header
for line in line_iter:
if not line.startswith('#'):
break
# read vertices
vertices = [None] # make 1-indexable
for line in line_iter:
data = line.split()
vertex = [float(x) for x in data[0:3]]
normal = [float(x) for x in data[3:6]]
sphere = int(data[7]) - 1
vertices.append((vertex, normal, sphere))
# faces file
line_iter = iter(open(filename + '.face'))
# skip header
for line in line_iter:
if not line.startswith('#'):
break
cgobuf = [cgo.BEGIN, cgo.TRIANGLES]
# read triangles
for line in line_iter:
for index in line.split()[:3]:
data = vertices[int(index)]
if _colors:
cgobuf.append(COLOR)
cgobuf.extend(_colors[data[2]])
cgobuf.append(NORMAL)
cgobuf.extend(data[1])
cgobuf.append(VERTEX)
cgobuf.extend(data[0])
cgobuf.append(cgo.END)
if not name:
name = cmd.get_unused_name('msmssurf')
cmd.load_cgo(cgobuf, name)
def myalign(method):
newmobile = cmd.get_unused_name(mobile_obj + '_' + method)
cmd.create(newmobile, mobile_obj)
start = time.time()
cmd.do('%s mobile=%s in %s, target=%s' % (method, newmobile, mobile, target))
if not quiet:
print 'Finished: %s (%.2f sec)' % (method, time.time() - start)
def load_msms_surface(filename, name="", _colors=None):
"""
DESCRIPTION
Load MSMS .vert and .face files as a CGO
"""
from pymol import cgo
from pymol.cgo import NORMAL, VERTEX, COLOR
if _colors:
_colors = [cmd.get_color_tuple(c) for c in _colors]
if filename.endswith(".vert") or filename.endswith(".face"):
filename = filename[:-5]
# vertex file
line_iter = iter(open(filename + ".vert"))
# skip header
for line in line_iter:
if not line.startswith("#"):
break
# read vertices
vertices = [None] # make 1-indexable
for line in line_iter:
data = line.split()
vertex = [float(x) for x in data[0:3]]
normal = [float(x) for x in data[3:6]]
sphere = int(data[7]) - 1
vertices.append((vertex, normal, sphere))
# faces file
line_iter = iter(open(filename + ".face"))
# skip header
for line in line_iter:
if not line.startswith("#"):
break
cgobuf = [cgo.BEGIN, cgo.TRIANGLES]
# read triangles
for line in line_iter:
for index in line.split()[:3]:
data = vertices[int(index)]
if _colors:
cgobuf.append(COLOR)
cgobuf.extend(_colors[data[2]])
cgobuf.append(NORMAL)
cgobuf.extend(data[1])
cgobuf.append(VERTEX)
cgobuf.extend(data[0])
cgobuf.append(cgo.END)
if not name:
name = cmd.get_unused_name("msmssurf")
cmd.load_cgo(cgobuf, name)
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 drow2Dlattice(gName="",Type="Hexagonal",UCp0=[0,0,0],UCa=310,UCb=100,UCaAng=0,UCbAng=60,UCc=[218/256,165/256,32/256],UCr=1,SE=1,SEl=15,SEr=1.2):
'''
Start input some documentation here
This fucnction generate a pymol set of CGOs to illustrate the p632 plane symmetry
inputs:
UCp0 - origin of unit cell list/array of dimension 3
UCa - first unit cell primitive vector length (unit cell spacing) in Agstrom
UCb - second unit cell primitive vector length (unit cell spacing) in Agstrom, for some unit cell types this value is predetermined as equal to the first primitive vector
UCaAng - direction of the first primitive vector , by default along the x axis
UCbAng - angle of the second primitive vector in x,y plane vs. the first primitive vector, this is a variables only for unit cells of type Oblique and Rhombic
UCc - cgo cylinders color (currently type of orange)
UCr - cgo cylinders radio=us.
SE = boolian, drow symmetry elements
SEl - diameter of rotation symmetry object to be printed
SEr - cgo cylinders radius belonging to the rotation symmetry objects
Output:
gName = name of group all the objects are clustered under
objList - list of objects geerated (this allows pther functions to modify or delete produced selections. )
np.array(UCp0),p1,p2,p3 - Unitcell corners position in x,y,z list format
'''
SEc1 = [1,0,0] ; SEc2 = [0,1,0] ; SEc3 = [0,1,1] ; SEc4 = [0,0,1] # colors of symmetry operations
UCp0 = np.array(UCp0)
V0 = np.array([1,0,0]) # Default orientation (facing the x direction) in the plane in XY plane
UCp0,p1,p2,p3,objList1 = drowUnitCell3(Type="Hexagonal", UCp0=UCp0,UCa=UCa,UCb=UCb,V0=V0,UCaAng=UCaAng,UCbAng=UCbAng,UCc=UCc,UCr=UCr)
if SE: # default to drow the sym elements
nfold = 6
objList11=drowRect(UCp0,SEl,nfold,SEr,SEc1) ; objList12=drowRect(p1,SEl,nfold,SEr,SEc1) ;objList13=drowRect(p2,SEl,nfold,SEr,SEc1) ;objList14=drowRect(p3,SEl,nfold,SEr,SEc1)
nfold = 3 ; P3_1 = 2/3*np.array(UCp0)+1/3*p3 ; P3_2 = 1/3*np.array(UCp0)+ 2/3*p3
objList21=drowRect(P3_1,SEl,nfold,SEr,SEc2) ; objList22=drowRect(P3_2,SEl,nfold,SEr,SEc2)
nfold = 2 ; SEr=3;SEl=10; P2_1 = (np.array(UCp0)+p1)/2 ; P2_2 = (np.array(UCp0)+p2)/2 ; P2_3 = (p1+p3)/2 ;P2_4 = (p2+p3)/2 ; P2_5 = (np.array(UCp0)+p3)/2
objList31=drowRect(P2_1,SEl,nfold,SEr,SEc4) ; objList32=drowRect(P2_2,SEl,nfold,SEr,SEc4) ; objList33=drowRect(P2_3,SEl,nfold,SEr,SEc4); objList34=drowRect(P2_4,SEl,nfold,SEr,SEc4) ; objList35=drowRect(P2_5,SEl,nfold,SEr,SEc4)
### preparing pumol CGO selection output groups
objList = objList11+objList12+objList13+objList14+objList21+objList22+objList31+objList32+objList33+objList34+objList35
### list of unique names not in use in the pymol session
gName = cmd.get_unused_name('p6')
frameName = cmd.get_unused_name('frame')
elementsName = cmd.get_unused_name('elements')
### creating two sub groups of the unit cell frame and the symmetry elements within
[ cmd.group(frameName, members=name , action='add', quiet=1) for name in objList1]
[ cmd.group(elementsName, members=name , action='add', quiet=1) for name in objList]
### group of the two above
[ cmd.group(gName, members=name , action='add', quiet=1) for name in [frameName,elementsName]]
print("Unit Cell ",gName," Corbers are in: ", np.array(UCp0),p1,p2,p3)
return np.array(UCp0),p1,p2,p3,objList,gName
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 from_alignment(self, mobile, target, aln_obj):
'''
Use alignment given by "aln_obj" (name of alignment object)
'''
from .selecting import wait_for
wait_for(aln_obj)
self.mobile = '(%s) and %s' % (mobile, aln_obj)
self.target = '(%s) and %s' % (target, aln_obj)
if self.check():
return
# difficult: if selections spans only part of the alignment or
# if alignment object covers more than the two objects, then we
# need to pick those columns that have no gap in any of the two
# given selections
mobileidx = set(cmd.index(mobile))
targetidx = set(cmd.index(target))
mobileidxsel = []
targetidxsel = []
for column in cmd.get_raw_alignment(aln_obj):
mobiles = mobileidx.intersection(column)
if len(mobiles) == 1:
targets = targetidx.intersection(column)
if len(targets) == 1:
mobileidxsel.extend(mobiles)
targetidxsel.extend(targets)
self.mobile = cmd.get_unused_name('_mobile')
self.target = cmd.get_unused_name('_target')
self.temporary.append(self.mobile)
self.temporary.append(self.target)
mobile_objects = set(idx[0] for idx in mobileidxsel)
target_objects = set(idx[0] for idx in targetidxsel)
if len(mobile_objects) == len(target_objects) == 1:
mobile_index_list = [idx[1] for idx in mobileidxsel]
target_index_list = [idx[1] for idx in targetidxsel]
cmd.select_list(self.mobile, mobile_objects.pop(), mobile_index_list, mode='index')
cmd.select_list(self.target, target_objects.pop(), target_index_list, mode='index')
else:
cmd.select(self.mobile, ' '.join('%s`%d' % idx for idx in mobileidxsel))
cmd.select(self.target, ' '.join('%s`%d' % idx for idx in targetidxsel))
def extra_fit(selection='(all)', reference=None, method='align', zoom=1,
quiet=0, _self=cmd, **kwargs):
'''
DESCRIPTION
Like "intra_fit", but for multiple objects instead of
multiple states.
ARGUMENTS
selection = string: atom selection of multiple objects {default: all}
reference = string: reference object name {default: first object in selection}
method = string: alignment method (command that takes "mobile" and "target"
arguments, like "align", "super", "cealign" {default: align}
... extra arguments are passed to "method"
SEE ALSO
alignto, cmd.util.mass_align, align_all.py from Robert Campbell
'''
zoom, quiet = int(zoom), int(quiet)
sele_name = cmd.get_unused_name('_')
cmd.select(sele_name, selection) # for speed
models = cmd.get_object_list(sele_name)
if reference is None:
reference = models[0]
models = models[1:]
elif reference in models:
models.remove(reference)
else:
cmd.select(sele_name, reference, merge=1)
if cmd.is_string(method):
if method in cmd.keyword:
method = cmd.keyword[method][0]
else:
print('Unknown method:', method)
raise CmdException
for model in models:
x = method(mobile='%s and model %s' % (sele_name, model),
target='%s and model %s' % (sele_name, reference), **kwargs)
if not quiet:
if cmd.is_sequence(x):
print('%-20s RMS = %8.3f (%d atoms)' % (model, x[0], x[1]))
elif isinstance(x, float):
print('%-20s RMS = %8.3f' % (model, x))
elif isinstance(x, dict) and 'RMSD' in x:
natoms = x.get('alignment_length', 0)
suffix = (' (%s atoms)' % natoms) if natoms else ''
print('%-20s RMS = %8.3f' % (model, x['RMSD']) + suffix)
else:
print('%-20s' % (model,))
if zoom:
cmd.zoom(sele_name)
cmd.delete(sele_name)
def extra_fit(selection='(all)', reference=None, method='align', zoom=1,
quiet=0, _self=cmd, **kwargs):
'''
DESCRIPTION
Like "intra_fit", but for multiple objects instead of
multiple states.
ARGUMENTS
selection = string: atom selection of multiple objects {default: all}
reference = string: reference object name {default: first object in selection}
method = string: alignment method (command that takes "mobile" and "target"
arguments, like "align", "super", "cealign" {default: align}
... extra arguments are passed to "method"
SEE ALSO
alignto, cmd.util.mass_align, align_all.py from Robert Campbell
'''
zoom, quiet = int(zoom), int(quiet)
sele_name = cmd.get_unused_name('_')
cmd.select(sele_name, selection) # for speed
models = cmd.get_object_list(sele_name)
if reference is None:
reference = models[0]
models = models[1:]
elif reference in models:
models.remove(reference)
else:
cmd.select(sele_name, reference, merge=1)
if cmd.is_string(method):
if method in cmd.keyword:
method = cmd.keyword[method][0]
else:
print('Unknown method:', method)
raise CmdException
for model in models:
x = method(mobile='%s and model %s' % (sele_name, model),
target='%s and model %s' % (sele_name, reference), **kwargs)
if not quiet:
if cmd.is_sequence(x):
print('%-20s RMS = %8.3f (%d atoms)' % (model, x[0], x[1]))
elif isinstance(x, float):
print('%-20s RMS = %8.3f' % (model, x))
elif isinstance(x, dict) and 'RMSD' in x:
natoms = x.get('alignment_length', 0)
suffix = (' (%s atoms)' % natoms) if natoms else ''
print('%-20s RMS = %8.3f' % (model, x['RMSD']) + suffix)
else:
print('%-20s' % (model,))
if zoom:
cmd.zoom(sele_name)
cmd.delete(sele_name)
def __init__(self, selection=None, name=None, symbols='', state=-1):
try:
from pymol.plugins import get_pmgapp
pmgapp = get_pmgapp()
except ImportError:
pmgapp = None
if pmgapp is not None:
rootframe = Tkinter.Toplevel(pmgapp.root)
parent = rootframe
else:
rootframe = Tkinter.Tk()
parent = rootframe
rootframe.title(' Dynamic Angle Plotting ')
rootframe.protocol("WM_DELETE_WINDOW", self.close_callback)
canvas = SimplePlot(parent, width=320, height=320)
canvas.bind("<Button-2>", canvas.pickWhich)
canvas.bind("<Button-3>", canvas.pickWhich)
canvas.pack(side=Tkinter.LEFT, fill="both", expand=1)
canvas.axis(xint=150,
xlabels=[-180, -120, -60, 0, 60, 120, 180],
ylabels=[
-180, -150, -120, -90, -60, -30, 0, 30, 60, 90, 120,
150, 180
])
if symbols == 'ss':
canvas.symbols = 1
if name is None:
try:
name = cmd.get_unused_name('DynoRama')
except AttributeError:
name = 'DynoRamaObject'
self.rootframe = rootframe
self.canvas = canvas
self.name = name
self.lock = 0
self.state = state
if name != 'none':
auto_zoom = cmd.get('auto_zoom')
cmd.set('auto_zoom', 0)
cmd.load_callback(self, name)
cmd.set('auto_zoom', auto_zoom)
canvas.bind("<ButtonPress-1>", canvas.down)
canvas.bind("<ButtonRelease-1>", canvas.up)
canvas.bind("<Motion>", canvas.drag)
if selection is not None:
self.start(selection)
if with_mainloop and pmgapp is None:
rootframe.mainloop()
def ellipsoid(sel='all'):
model = cmd.get_model(sel + ' and name ca')
obj = cmd.get_object_list()[0]
coord = []
for at in model.atom:
coord.append(at.coord)
cm = get_cm(coord)
abc, g, v = get_moi(coord, cm) # axis-length, eigenvalues, eigenvectors
arrow_obj = []
color = 'red red'
pos2 = [x + y * abc[0] for x, y in zip(cm, v[0])]
arrow_obj += cgo_arrow(cm, pos2, color=color, radius=0.15)
color = 'green green'
pos2 = [x + y * abc[1] for x, y in zip(cm, v[1])]
arrow_obj += cgo_arrow(cm, pos2, color=color, radius=0.15)
color = 'blue blue'
pos2 = [x + y * abc[2] for x, y in zip(cm, v[2])]
arrow_obj += cgo_arrow(cm, pos2, color=color, radius=0.15)
name = cmd.get_unused_name('axis')
cmd.load_cgo(arrow_obj, name)
cgo = makeEllipsoid(cm[0], cm[1], cm[2], abc[0], abc[1], abc[2], m=v)
obj_ellipsoid = cmd.get_unused_name('ellipsoid')
cmd.load_cgo(cgo, obj_ellipsoid)
# Do some cosmetic work
cmd.set('cgo_transparency', 0.4, obj_ellipsoid)
cmd.color('green', obj_ellipsoid)
cmd.show_as('cartoon', obj)
cmd.color('orange', obj)
cmd.zoom(obj, animate=1)
print('The volume of the ellipsoid (4/3 Pi*a*b*c): %6.1f A' % \
(4.0/3.0*math.pi*abc[0]*abc[1]*abc[2]))
print('The volume of the spheroid (4/3 Pi*r**3): %6.1f A' % \
(4.0/3.0*math.pi*((abc[0]**2+abc[1]**2+abc[2]**2))**1.5))
def symdiff(sele1, sele2, byres=1, name=None, operator='in', quiet=0):
'''
DESCRIPTION
Symmetric difference between two molecules
SEE ALSO
diff
'''
byres, quiet = int(byres), int(quiet)
if name is None:
name = cmd.get_unused_name('symdiff')
tmpname = cmd.get_unused_name('__tmp')
diff(sele1, sele2, byres, name, operator, quiet)
diff(sele2, sele1, byres, tmpname, operator, quiet)
cmd.select(name, tmpname, merge=1)
cmd.delete(tmpname)
return name
def split(operator, selection, prefix='entity'):
'''
DESCRIPTION
Create a single object for each entity in selection, defined by operator
(e.g. bymolecule, bysegment, ...). Returns the number of created objects.
'''
cmd.disable(' '.join(cmd.get_object_list('(' + selection + ')')))
tmp = cmd.get_unused_name('_')
cmd.create(tmp, selection)
r = 0
while cmd.count_atoms(tmp) > 0:
name = cmd.get_unused_name(prefix)
cmd.extract(name, operator + ' first model ' + tmp)
r += 1
cmd.delete(tmp)
return r
def symdiff(sele1, sele2, byres=1, name=None, operator='in', quiet=0):
'''
DESCRIPTION
Symmetric difference between two molecules
SEE ALSO
diff
'''
byres, quiet = int(byres), int(quiet)
if name is None:
name = cmd.get_unused_name('symdiff')
tmpname = cmd.get_unused_name('__tmp')
diff(sele1, sele2, byres, name, operator, quiet)
diff(sele2, sele1, byres, tmpname, operator, quiet)
cmd.select(name, tmpname, merge=1)
cmd.delete(tmpname)
return name
def split(operator, selection, prefix="entity"):
"""
DESCRIPTION
Create a single object for each entity in selection, defined by operator
(e.g. bymolecule, bysegment, ...). Returns the number of created objects.
"""
cmd.disable(" ".join(cmd.get_object_list("(" + selection + ")")))
tmp = cmd.get_unused_name("_")
cmd.create(tmp, selection)
r = 0
while cmd.count_atoms(tmp) > 0:
name = cmd.get_unused_name(prefix)
cmd.extract(name, operator + " first model " + tmp)
r += 1
cmd.delete(tmp)
return r
def split(operator, selection, prefix='entity'):
'''
DESCRIPTION
Create a single object for each entity in selection, defined by operator
(e.g. bymolecule, bysegment, ...). Returns the number of created objects.
'''
cmd.disable(' '.join(cmd.get_object_list('(' + selection + ')')))
tmp = cmd.get_unused_name('_')
cmd.create(tmp, selection)
r = 0
while cmd.count_atoms(tmp) > 0:
name = cmd.get_unused_name(prefix)
cmd.extract(name, operator + ' first model ' + tmp)
r += 1
cmd.delete(tmp)
return r
def cubes(selection='all',
name='',
state=0,
scale=0.5,
atomcolors=1,
_func=cgo_cube):
'''
DESCRIPTION
Create a cube representation CGO for all atoms in selection.
ARGUMENTS
selection = string: atom selection {default: all}
name = string: name of CGO object to create
state = int: object state {default: 0 = all states}
scale = float: scaling factor. If scale=1.0, the corners of the cube will
be on the VDW surface of the atom {default: 0.5}
atomcolors = 0/1: use atom colors (cannot be changed), otherwise
apply one color to the object (can be changed with color command)
{default: 1}
SEE ALSO
tetrahedra
'''
if not name:
name = cmd.get_unused_name('cubes')
state, scale, atomcolors = int(state), float(scale), int(atomcolors)
if state < 0:
state = cmd.get_setting_int('state')
states = [state] if state else list(
range(1,
cmd.count_states(selection) + 1))
def callback(x, y, z, vdw, color):
if atomcolors:
obj.append(cgo.COLOR)
obj.extend(cmd.get_color_tuple(color))
obj.extend(_func(x, y, z, vdw * scale))
space = {'xcb': callback}
for state in states:
obj = []
cmd.iterate_state(state,
selection,
'xcb(x, y, z, vdw, color)',
space=space)
cmd.load_cgo(obj, name, state)
if not atomcolors:
cmd.color('auto', name)
def diff(sele1, sele2, byres=1, name=None, operator='in', quiet=0):
'''
DESCRIPTION
Difference between two molecules
ARGUMENTS
sele1 = string: atom selection
sele2 = string: atom selection
byres = 0/1: report residues, not atoms (does not affect selection)
{default: 1}
operator = in/like/align: operator to match atoms {default: in}
SEE ALSO
symdiff
'''
byres, quiet = int(byres), int(quiet)
if name is None:
name = cmd.get_unused_name('diff')
if operator == 'align':
alnobj = cmd.get_unused_name('__aln')
cmd.align(sele1, sele2, cycles=0, transform=0, object=alnobj)
sele = '(%s) and not %s' % (sele1, alnobj)
cmd.select(name, sele)
cmd.delete(alnobj)
else:
sele = '(%s) and not ((%s) %s (%s))' % (sele1, sele1, operator, sele2)
cmd.select(name, sele)
if not quiet:
if byres:
seleiter = 'byca ' + name
expr = 'print "/%s/%s/%s/%s`%s" % (model,segi,chain,resn,resi)'
else:
seleiter = name
expr = 'print "/%s/%s/%s/%s`%s/%s" % (model,segi,chain,resn,resi,name)'
cmd.iterate(seleiter, expr)
return name
def diff(sele1, sele2, byres=1, name=None, operator='in', quiet=0):
'''
DESCRIPTION
Difference between two molecules
ARGUMENTS
sele1 = string: atom selection
sele2 = string: atom selection
byres = 0/1: report residues, not atoms (does not affect selection)
{default: 1}
operator = in/like/align: operator to match atoms {default: in}
SEE ALSO
symdiff
'''
byres, quiet = int(byres), int(quiet)
if name is None:
name = cmd.get_unused_name('diff')
if operator == 'align':
alnobj = cmd.get_unused_name('__aln')
cmd.align(sele1, sele2, cycles=0, transform=0, object=alnobj)
sele = '(%s) and not %s' % (sele1, alnobj)
cmd.select(name, sele)
cmd.delete(alnobj)
else:
sele = '(%s) and not ((%s) %s (%s))' % (sele1, sele1, operator, sele2)
cmd.select(name, sele)
if not quiet:
if byres:
seleiter = 'byca ' + name
expr = 'print "/%s/%s/%s/%s`%s" % (model,segi,chain,resn,resi)'
else:
seleiter = name
expr = 'print "/%s/%s/%s/%s`%s/%s" % (model,segi,chain,resn,resi,name)'
cmd.iterate(seleiter, expr)
return name
def load_apbs_in(form, filename, contents=''):
import shlex
from pymol import cmd, importing
wdir = os.path.dirname(filename)
if not contents:
contents = cmd.file_read(filename)
if not isinstance(contents, str):
contents = contents.decode()
sectionkeys = ('read', 'elec', 'apolar', 'print')
section = ''
insert_write_pot = True
lines = []
for line in contents.splitlines():
a = shlex.split(line)
key = a[0].lower() if a else ''
if not section:
if key in sectionkeys:
section = key
elif key == 'end':
if section == 'elec' and insert_write_pot:
lines.append('write pot dx "{mapfile}"')
section = ''
elif section == 'read':
if len(a) > 2 and key in ('charge', 'kappa', 'mol', 'parm', 'pot'):
filename = os.path.join(wdir, a[2])
if os.path.exists(filename):
format = a[1].lower()
if key == 'mol' and format in ('pqr', 'pdb'):
# load into PyMOL and update selection dropdown
oname = importing.filename_to_objectname(a[2])
oname = cmd.get_unused_name(oname, 0)
cmd.load(filename, oname, format=format)
form.input_sele.addItem(oname)
form.input_sele.setEditText(oname)
# absolute path in input file
a[2] = '"' + filename + '"'
line = ' '.join(a)
elif section == 'elec':
if key == 'write':
if a[1:4] == ['pot', 'dx', "{mapfile}"]:
insert_write_pot = False
lines.append(line)
return '\n'.join(lines)
def __init__(self, selection=None, name=None, symbols='', state=-1):
try:
from pymol.plugins import get_pmgapp
pmgapp = get_pmgapp()
except ImportError:
pmgapp = None
if pmgapp is not None:
rootframe = Tkinter.Toplevel(pmgapp.root)
parent = rootframe
else:
rootframe = Tkinter.Tk()
parent = rootframe
rootframe.title(' Dynamic Angle Plotting ')
rootframe.protocol("WM_DELETE_WINDOW", self.close_callback)
canvas = SimplePlot(parent, width=320, height=320)
canvas.bind("<Button-2>", canvas.pickWhich)
canvas.bind("<Button-3>", canvas.pickWhich)
canvas.pack(side=Tkinter.LEFT, fill="both", expand=1)
canvas.axis(xint=150,
xlabels=[-180, -120, -60, 0, 60, 120, 180],
ylabels=[-180, -150, -120, -90, -60, -30, 0, 30, 60, 90, 120, 150, 180])
if symbols == 'ss':
canvas.symbols = 1
if name is None:
try:
name = cmd.get_unused_name('DynoRama')
except AttributeError:
name = 'DynoRamaObject'
self.rootframe = rootframe
self.canvas = canvas
self.name = name
self.lock = 0
self.state = state
if name != 'none':
auto_zoom = cmd.get('auto_zoom')
cmd.set('auto_zoom', 0)
cmd.load_callback(self, name)
cmd.set('auto_zoom', auto_zoom)
canvas.bind("<ButtonPress-1>", canvas.down)
canvas.bind("<ButtonRelease-1>", canvas.up)
canvas.bind("<Motion>", canvas.drag)
if selection is not None:
self.start(selection)
if with_mainloop and pmgapp is None:
rootframe.mainloop()
def draw_xy_axes(scale=1.0):
"""Draw x and y axes in PyMOL."""
logging.debug("Drawing axes.")
obj = []
obj.extend(
get_cgo_arrow_obj(start=np.array([0, 0, 0.]),
stop=scale * np.array([0., 1., 0.])))
obj.extend(
get_cgo_arrow_obj(start=np.array([0, 0, -.1]),
stop=scale * np.array([0., 0., 1.])))
cmd.load_cgo(obj, cmd.get_unused_name('axes'))
def cgoCylinder3(p0=[0,0,0],v0=[1,0,0],inputAng=0, L=20, radius=0.5 ,color=[1,0,0] ,name=''):
p0 = np.array(p0)
V0 = np.array(v0)
r = R.from_euler('z', inputAng, degrees=True)
p1 = np.around(R.apply(r,V0), decimals=6)*L+p0
PP0 = list(p0) ; PP1=list(p1)
obj = [cgo.CYLINDER] + PP0 + PP1 + [radius] + color + color
if not name:
name = cmd.get_unused_name('cylinderObj')
cmd.load_cgo(obj, name)
return name,obj, p1
def __init__(self, map_name, level, radius, name, sym_source):
self.level = level
self.radius = radius
self.map_name = map_name
self.name = name
self.center_name = cmd.get_unused_name('_center')
self.callback_name = cmd.get_unused_name('_cb')
cmd.set("auto_zoom", 0)
cmd.pseudoatom(self.center_name)
cmd.hide("everything", self.center_name)
symmetry = cmd.get_symmetry(sym_source or map_name)
if symmetry:
cmd.set("map_auto_expand_sym", 1)
cmd.set_symmetry(self.center_name, *symmetry)
cmd.set_key("pgup", self.contour_plus)
cmd.set_key("pgdn", self.contour_minus)
self.update()
def select_distances(names='',
name='sele',
state=1,
selection='all',
cutoff=-1,
quiet=1):
'''
DESCRIPTION
Turns a distance object into a named atom selection.
ARGUMENTS
names = string: names of distance objects (no wildcards!) {default: all
measurement objects}
name = a unique name for the selection {default: sele}
state = int: object state (-1: current, 0: all states) {default: 1}
SEE ALSO
get_raw_distances
'''
from collections import defaultdict
_assert_package_import()
from .querying import get_raw_distances
state, cutoff, quiet = int(state), float(cutoff), int(quiet)
states = [state] if state else list(
range(1,
cmd.count_states(selection) + 1))
sele_dict = defaultdict(set)
for state in states:
distances = get_raw_distances(names, state, selection)
for idx1, idx2, dist in distances:
if cutoff <= 0.0 or dist <= cutoff:
sele_dict[idx1[0]].add(idx1[1])
sele_dict[idx2[0]].add(idx2[1])
cmd.select(name, 'none')
tmp_name = cmd.get_unused_name('_')
r = 0
for model in sele_dict:
cmd.select_list(tmp_name, model, list(sele_dict[model]), mode='index')
r = cmd.select(name, tmp_name, merge=1)
cmd.delete(tmp_name)
if not quiet:
print(' Selector: selection "%s" defined with %d atoms.' % (name, r))
return r
def align(self, mobile, target, match):
'''
Align mobile to target using the alignment method given by "match"
'''
aln_obj = cmd.get_unused_name('_')
self.temporary.append(aln_obj)
align = cmd.keyword[match][0]
align(mobile, target, cycles=0, transform=0, object=aln_obj)
cmd.disable(aln_obj)
self.from_alignment(mobile, target, aln_obj)
def align(self, mobile, target, match):
'''
Align mobile to target using the alignment method given by "match"
'''
aln_obj = cmd.get_unused_name('_')
self.temporary.append(aln_obj)
align = cmd.keyword[match][0]
align(mobile, target, cycles=0, transform=0, object=aln_obj)
cmd.disable(aln_obj)
self.from_alignment(mobile, target, aln_obj)
def morpheasy_linear(source,
target,
source_state=0,
target_state=0,
name=None,
steps=30,
match='align',
quiet=1):
'''
DESCRIPTION
Morph by linear interpolation in cartesian space (like LSQMAN).
This is the poor man's version of morphing, it's quick but will produce
distorted intermediate conformations. Does not require rigimol (incentive
PyMOL product). Requires numpy.
SEE ALSO
morpheasy
'''
from numpy import array
from .fitting import matchmaker
from .importing import load_coords
from .querying import get_selection_state
# arguments
source_state = int(source_state)
target_state = int(target_state)
steps, quiet = int(steps), int(quiet)
if source_state < 1: source_state = get_selection_state(source)
if target_state < 1: target_state = get_selection_state(target)
msource, mtarget, tmp_names = matchmaker(source, target, match)
csource = array(cmd.get_model(msource, source_state).get_coord_list())
ctarget = array(cmd.get_model(mtarget, target_state).get_coord_list())
cdiff = ctarget - csource
if name is None:
name = cmd.get_unused_name('morph')
cmd.create(name, msource, source_state, 1)
for state in range(2, steps + 1):
c = csource + cdiff * float(state - 1) / (steps - 1)
load_coords(c.tolist(), name, state)
# clean up
for obj in tmp_names:
cmd.delete(obj)
return name
def __init__(self, map_name, level, radius, name, sym_source):
self.level = level
self.radius = radius
self.map_name = map_name
self.name = name
self.center_name = cmd.get_unused_name('_center')
self.callback_name = cmd.get_unused_name('_cb')
cmd.set("auto_zoom", 0)
cmd.pseudoatom(self.center_name)
cmd.hide("everything", self.center_name)
symmetry = cmd.get_symmetry(sym_source or map_name)
if symmetry:
cmd.set("map_auto_expand_sym", 1)
cmd.set_symmetry(self.center_name, *symmetry)
cmd.set_key("pgup", self.contour_plus)
cmd.set_key("pgdn", self.contour_minus)
self.update()
def count_molecules(selection="all"):
"""
By Thomas Holder.
"""
tmpsele = pm.get_unused_name("_tmp")
count = 0
if pm.select(tmpsele, selection):
count += 1
while pm.select(tmpsele, f"{tmpsele} &! bm. first {tmpsele}"):
count += 1
pm.delete(tmpsele)
return count
def set_raw_alignment(name, aln, transform=0, guide=''):
'''
DESCRIPTION
API only.
Load an alignment object from a list like the one obtained with
cmd.get_raw_alignment
SEE ALSO
cmd.set_raw_alignment in PyMOL 2.3
'''
if hasattr(cmd, 'set_raw_alignment') and not int(transform):
return cmd.set_raw_alignment(name, aln, guide=guide)
if not isinstance(aln[0], dict):
aln = [dict(idx_pair) for idx_pair in aln]
models = set(model for idx_pdict in aln for model in idx_pdict)
sele1 = cmd.get_unused_name('_sele1')
sele2 = cmd.get_unused_name('_sele2')
fit = cmd.fit if transform else cmd.rms_cur
if guide:
models.remove(guide)
model2 = guide
else:
model2 = models.pop()
for model1 in models:
index_list1 = []
index_list2 = []
for idx_pdict in aln:
if model1 in idx_pdict and model2 in idx_pdict:
index_list1.append(idx_pdict[model1])
index_list2.append(idx_pdict[model2])
cmd.select_list(sele1, model1, index_list1, mode='index')
cmd.select_list(sele2, model2, index_list2, mode='index')
fit(sele1, sele2, cycles=0, matchmaker=4, object=name)
cmd.delete(sele1)
cmd.delete(sele2)
def set_raw_alignment(name, aln, transform=0, guide=''):
'''
DESCRIPTION
API only.
Load an alignment object from a list like the one obtained with
cmd.get_raw_alignment
SEE ALSO
cmd.set_raw_alignment in PyMOL 2.3
'''
if hasattr(cmd, 'set_raw_alignment') and not int(transform):
return cmd.set_raw_alignment(name, aln, guide=guide)
if not isinstance(aln[0], dict):
aln = [dict(idx_pair) for idx_pair in aln]
models = set(model for idx_pdict in aln for model in idx_pdict)
sele1 = cmd.get_unused_name('_sele1')
sele2 = cmd.get_unused_name('_sele2')
fit = cmd.fit if transform else cmd.rms_cur
if guide:
models.remove(guide)
model2 = guide
else:
model2 = models.pop()
for model1 in models:
index_list1 = []
index_list2 = []
for idx_pdict in aln:
if model1 in idx_pdict and model2 in idx_pdict:
index_list1.append(idx_pdict[model1])
index_list2.append(idx_pdict[model2])
cmd.select_list(sele1, model1, index_list1, mode='index')
cmd.select_list(sele2, model2, index_list2, mode='index')
fit(sele1, sele2, cycles=0, matchmaker=4, object=name)
cmd.delete(sele1)
cmd.delete(sele2)
def findSurfaceResidues(selection="all",
cutoff=2.5,
doShow=0,
quiet=1,
pdb_id="",
oxygen=True):
"""
DESCRIPTION
Finds those residues on the surface of a protein
that have at least 'cutoff' exposed A**2 surface area.
USAGE
findSurfaceResidues [ selection, [ cutoff, [ doShow ]]]
ARGUMENTS
selection = string: object or selection in which to find exposed
residues {default: all}
cutoff = float: cutoff of what is exposed or not {default: 2.5 Ang**2}
RETURNS
(list: (chain, resv ) )
A Python list of residue numbers corresponding
to those residues w/more exposure than the cutoff.
"""
cutoff, doShow, quiet = float(cutoff), int(doShow), int(quiet)
selName = findSurfaceAtoms(selection, cutoff, quiet, oxygen)
exposed = set()
cmd.iterate(selName, "exposed.add((chain,resv))", space=locals())
selNameRes = cmd.get_unused_name("exposed_res_")
cmd.select(selNameRes, "byres " + selName)
if not quiet:
print("Exposed residues are selected in: " + selNameRes)
if doShow:
cmd.show_as("spheres", "(" + selection + ") and polymer")
cmd.color("white", selection)
cmd.color("yellow", selNameRes)
cmd.color("red", selName)
print(sorted(exposed))
df = pd.DataFrame(list(sorted(exposed)), columns=['Chain', 'Residue'])
write_df(df, pdb_id + "_surfaceresidues.csv", dir="./surface_residues")
return sorted(exposed)
def tetrahedra(selection='all', name='', state=0, scale=0.5, atomcolors=1):
'''
DESCRIPTION
Create a tetrahedra representation CGO for all atoms in selection.
SEE ALSO
cubes
'''
if not name:
name = cmd.get_unused_name('tetrahedra')
return cubes(selection, name, state, scale, atomcolors, cgo_tetrahedron)
def tetrahedra(selection='all', name='', state=0, scale=0.5, atomcolors=1):
'''
DESCRIPTION
Create a tetrahedra representation CGO for all atoms in selection.
SEE ALSO
cubes
'''
if not name:
name = cmd.get_unused_name('tetrahedra')
return cubes(selection, name, state, scale, atomcolors, cgo_tetrahedron)
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 morpheasy_linear(source, target, source_state=0, target_state=0, name=None,
steps=30, match='align', quiet=1):
'''
DESCRIPTION
Morph by linear interpolation in cartesian space (like LSQMAN).
This is the poor man's version of morphing, it's quick but will produce
distorted intermediate conformations. Does not require rigimol (incentive
PyMOL product). Requires numpy.
SEE ALSO
morpheasy
'''
from numpy import array
from .fitting import matchmaker
from .importing import load_coords
from .querying import get_selection_state
# arguments
source_state = int(source_state)
target_state = int(target_state)
steps, quiet = int(steps), int(quiet)
if source_state < 1: source_state = get_selection_state(source)
if target_state < 1: target_state = get_selection_state(target)
msource, mtarget, tmp_names = matchmaker(source, target, match)
csource = array(cmd.get_model(msource, source_state).get_coord_list())
ctarget = array(cmd.get_model(mtarget, target_state).get_coord_list())
cdiff = ctarget - csource
if name is None:
name = cmd.get_unused_name('morph')
cmd.create(name, msource, source_state, 1)
for state in range(2, steps+1):
c = csource + cdiff * float(state-1) / (steps-1)
load_coords(c.tolist(), name, state)
# clean up
for obj in tmp_names:
cmd.delete(obj)
return name
def cubes(selection='all', name='', state=0, scale=0.5, atomcolors=1, _func=cgo_cube):
'''
DESCRIPTION
Create a cube representation CGO for all atoms in selection.
ARGUMENTS
selection = string: atom selection {default: all}
name = string: name of CGO object to create
state = int: object state {default: 0 = all states}
scale = float: scaling factor. If scale=1.0, the corners of the cube will
be on the VDW surface of the atom {default: 0.5}
atomcolors = 0/1: use atom colors (cannot be changed), otherwise
apply one color to the object (can be changed with color command)
{default: 1}
SEE ALSO
tetrahedra
'''
if not name:
name = cmd.get_unused_name('cubes')
state, scale, atomcolors = int(state), float(scale), int(atomcolors)
if state < 0:
state = cmd.get_setting_int('state')
states = [state] if state else range(1,
cmd.count_states(selection) + 1)
def callback(x, y, z, vdw, color):
if atomcolors:
obj.append(cgo.COLOR)
obj.extend(cmd.get_color_tuple(color))
obj.extend(_func(x, y, z, vdw * scale))
space = {'xcb': callback}
for state in states:
obj = []
cmd.iterate_state(state, selection,
'xcb(x, y, z, vdw, color)', space=space)
cmd.load_cgo(obj, name, state)
if not atomcolors:
cmd.color('auto', name)
def findSurfaceResidues(selection="all", cutoff=2.5, doShow=0, quiet=1):
"""
DESCRIPTION
Finds those residues on the surface of a protein
that have at least 'cutoff' exposed A**2 surface area.
USAGE
findSurfaceResidues [ selection, [ cutoff, [ doShow ]]]
ARGUMENTS
selection = string: object or selection in which to find exposed
residues {default: all}
cutoff = float: cutoff of what is exposed or not {default: 2.5 Ang**2}
RETURNS
(list: (chain, resv ) )
A Python list of residue numbers corresponding
to those residues w/more exposure than the cutoff.
"""
cutoff, doShow, quiet = float(cutoff), int(doShow), int(quiet)
selName = findSurfaceAtoms(selection, cutoff, quiet)
exposed = set()
cmd.iterate(selName, "exposed.add((chain,resv))", space=locals())
selNameRes = cmd.get_unused_name("exposed_res_")
cmd.select(selNameRes, "byres " + selName)
if not quiet:
print("Exposed residues are selected in: " + selNameRes)
if doShow:
cmd.show_as("spheres", "(" + selection + ") and polymer")
cmd.color("white", selection)
cmd.color("yellow", selNameRes)
cmd.color("red", selName)
return sorted(exposed)
def select_distances(names='', name='sele', state=1, selection='all', cutoff=-1, quiet=1):
'''
DESCRIPTION
Turns a distance object into a named atom selection.
ARGUMENTS
names = string: names of distance objects (no wildcards!) {default: all
measurement objects}
name = a unique name for the selection {default: sele}
state = int: object state (-1: current, 0: all states) {default: 1}
SEE ALSO
get_raw_distances
'''
from collections import defaultdict
from .querying import get_raw_distances
state, cutoff, quiet = int(state), float(cutoff), int(quiet)
states = [state] if state else list(range(1, cmd.count_states(selection)+1))
sele_dict = defaultdict(set)
for state in states:
distances = get_raw_distances(names, state, selection)
for idx1, idx2, dist in distances:
if cutoff <= 0.0 or dist <= cutoff:
sele_dict[idx1[0]].add(idx1[1])
sele_dict[idx2[0]].add(idx2[1])
cmd.select(name, 'none')
tmp_name = cmd.get_unused_name('_')
r = 0
for model in sele_dict:
cmd.select_list(tmp_name, model, list(sele_dict[model]), mode='index')
r = cmd.select(name, tmp_name, merge=1)
cmd.delete(tmp_name)
if not quiet:
print(' Selector: selection "%s" defined with %d atoms.' % (name, r))
return r
def sketch_pseudo_coc(selection, state=None, name=None,
prefix='', suffix='_coc', **kwargs):
"""Create a pseudo atom which indicate the center of coordinate of the
selection
USAGE
sketch_pseudo_coc selection, state=state, name=name,
prefix=prefix, suffix=suffix
ARGUMENTS
selection a selection-expression
state a state-index if positive number or 0 to all, -1 to current
name a name of the pseudoatom, it will
automatically specified if None is specified (Default)
prefix a prefix of the pseudoatom. it will used only when name is
not specified
suffix a suffix of the pseudoatom. it will used only when name is
not specified
EXAMPLE
sketch_pcoc (resn PHE), state=10
"""
if name is None:
try:
name = cmd.get_legal_name(selection)
name = cmd.get_unused_name(
'{}{}{}'.format(prefix, name, suffix), 0
)
except:
name = '%s%s' % (prefix, suffix)
if state is not None:
com = geometry.find_center_of_coordinates(selection)
cmd.pseudoatom(name, pos=com, **kwargs)
else:
for state in range(1, cmd.count_states()+1):
com = geometry.find_center_of_coordinates(selection, state=state)
cmd.pseudoatom(name, pos=com, state=state, **kwargs)
def join_states(name, selection="all", discrete=-1, zoom=0, quiet=1):
"""
DESCRIPTION
The reverse of split_states
ARGUMENTS
name = string: name of object to create or modify
selection = string: atoms to include in the new object
discrete = -2: match atoms by sequence alignment
discrete = -1: Assume identical input objects (matching all atom
identifiers) but also check for missing atoms and only include atoms
that are present in all input objects {default}
discrete = 0: Assume identical input objects
discrete = 1: Input object may be (totally) different
"""
discrete, quiet = int(discrete), int(quiet)
if discrete == -2:
from .selecting import wait_for
aln_obj = cmd.get_unused_name("_")
models = cmd.get_object_list("(" + selection + ")")
for i in range(len(models)):
if discrete == -1 and i > 0:
cmd.remove("(%s) and not (alt A+ and (%s) in (%s))" % (name, name, models[i]))
cmd.create(name, "(%s) in (%s)" % (models[i], name), 1, i + 1, 0, 0, quiet)
elif discrete == -2 and i > 0:
cmd.align(models[i], name, cycles=0, transform=0, object=aln_obj)
wait_for(aln_obj)
cmd.remove("(%s) and not (%s)" % (name, aln_obj))
cmd.create(name, name, 1, i + 1, 0, 0, quiet)
cmd.update(name, "(%s) and (%s)" % (models[i], aln_obj), i + 1, 1, 0, quiet)
cmd.delete(aln_obj)
else:
cmd.create(name, models[i], 1, i + 1, discrete == 1, 0, quiet)
if int(zoom):
cmd.zoom(name, state=0)
def get_sasa(selection, state=-1, dot_density=5, quiet=1):
'''
DESCRIPTION
Get solvent accesible surface area
SEE ALSO
get_area
pymol.util.get_sasa (considered broken!)
'''
state, dot_density, quiet = int(state), int(dot_density), int(quiet)
if state < 1:
state = cmd.get_state()
n = cmd.get_unused_name('_')
cmd.create(n, selection, state, 1, zoom=0, quiet=1)
cmd.set('dot_solvent', 1, n)
if dot_density > -1:
cmd.set('dot_density', dot_density, n)
r = cmd.get_area(n, quiet=int(quiet))
cmd.delete(n)
return r