def testRepsExist(self):
cmd.viewport(200, 150)
cmd.load(self.datafile('1oky-frag.pdb'), 'm1')
# make some nonbonded
cmd.unbond('resi 115-', 'resi 115-')
# labels
cmd.label('all', 'name')
# measurements
cmd.distance('measure1', 'index 1', 'index 10')
cmd.angle('measure1', 'index 1', 'index 10', 'index 20')
cmd.dihedral('measure1', 'index 1', 'index 10', 'index 20', 'index 30')
# color test setup
cmd.color('white', '*')
cmd.set('ambient', 1)
cmd.set('depth_cue', 0)
cmd.set('antialias', 0)
cmd.set('line_smooth', 0)
cmd.orient()
# test most reps
for rep in REPS:
cmd.show_as(rep)
self.assertImageHasColor('white', msg='rep missing: ' + rep)
# test cartoon
cmd.show_as('cartoon')
for cart in CARTOONS:
cmd.cartoon(cart)
self.assertImageHasColor('white', msg='cartoon missing: ' + cart)
def testRepsExist(self):
cmd.viewport(200, 150)
cmd.load(self.datafile('1oky-frag.pdb'), 'm1')
# make some nonbonded
cmd.unbond('resi 115-', 'resi 115-')
# labels
cmd.label('all', 'name')
# measurements
cmd.distance('measure1', 'index 1', 'index 10')
cmd.angle('measure1', 'index 1', 'index 10', 'index 20')
cmd.dihedral('measure1', 'index 1', 'index 10', 'index 20', 'index 30')
# color test setup
cmd.color('white', '*')
cmd.set('ambient', 1)
cmd.set('depth_cue', 0)
cmd.set('antialias', 0)
cmd.set('line_smooth', 0)
cmd.orient()
# test most reps
for rep in REPS:
cmd.show_as(rep)
self.assertImageHasColor('white', msg='rep missing: ' + rep)
# test cartoon
cmd.show_as('cartoon')
for cart in CARTOONS:
cmd.cartoon(cart)
self.assertImageHasColor('white', msg='cartoon missing: ' + cart)
def draw_axis(chA, chB, scale_factor=20, w=0.6, r1=1, g1=1, b1=1, r2=1, g2=0, b2=0):
T = transf_matrix(chA, chB)
angle=angle_axis(chA, chB)
angle_degrees=(angle*180)/math.pi
axis1=[direction_cosines(chA, chB)[0], direction_cosines(chA, chB)[1], direction_cosines(chA, chB)[2]]
p = nearest_point_to_axis(chA, chB)
x1, y1, z1 = p[0] + (3*scale_factor*axis1[0]), p[1] + (3*scale_factor*axis1[1]), p[2] + (3*scale_factor*axis1[2])
x2, y2, z2 = p[0] - (3*scale_factor*axis1[0]), p[1] - (3*scale_factor*axis1[1]), p[2] - (3*scale_factor*axis1[2])
obj = [cgo.CYLINDER, x1, y1, z1, x2, y2, z2, w, r1, g1, b1, r2, g2, b2, 0.0]
cmd.load_cgo(obj, angle_degrees)
cmA=center_of_Mass(chA)
cmB=cmW
cmAver=(cmB+cmA)/2
vector=numpy.array([(cmB[0]-cmA[0]), (cmB[1]-cmA[1]), (cmB[2]-cmA[2])])
moduli_vector=numpy.linalg.norm(vector)
vector_director=numpy.array([(cmB[0]-cmA[0])/moduli_vector, (cmB[1]-cmA[1])/moduli_vector, (cmB[2]-cmA[2])/moduli_vector])
pC_A = proyeccion_centroide(chA, chA, chB)
pC_B = proyeccion_centroide_working(chA, chB)
trans_vector = numpy.array([(pC_B[0]-pC_A[0]), (pC_B[1]-pC_A[1]), (pC_B[2]-pC_A[2])])
modu_tr = numpy.linalg.norm(trans_vector)
rota_centroid_rad=numpy.dot(vector_director, axis1)
rota_centroid = (rota_centroid_rad*180)/math.pi
rota_centroid_absol_0= numpy.absolute(rota_centroid)
rota_centroid_absol=round(rota_centroid_absol_0,2)
if rota_centroid_absol == 0.00:
p1 = '_1'
p2 = '_2'
p3 = '_3'
cmd.pseudoatom (pos=[cmA[0], cmA[1], cmA[2]], object=p1)
cmd.pseudoatom (pos=[pC_A[0], pC_A[1], pC_A[2]], object=p2)
cmd.pseudoatom (pos=[cmB[0], cmB[1], cmB[2]], object=p3)
cmd.angle(None, p1, p2, p3)
print_information(T, axis1, angle_degrees, moduli_vector, obj, x1, y1, z1, x2, y2, z2, w, r1, g1, b1, r2, g2, b2)
if rota_centroid_absol != 0:
p1 = '_1'
p2 = '_2'
p3 = '_3'
p4 = '_4'
cmd.pseudoatom (pos=[cmA[0], cmA[1], cmA[2]], object=p1)
cmd.pseudoatom (pos=[pC_A[0], pC_A[1], pC_A[2]], object=p2)
cmd.pseudoatom (pos=[pC_B[0], pC_B[1], pC_B[2]], object=p3)
cmd.pseudoatom (pos=[cmB[0], cmB[1], cmB[2]], object=p4)
cmd.dihedral(None, p1, p2, p3, p4)
cmd.distance(None, p2, p3)
print_information(T, axis1, angle_degrees, moduli_vector, obj, x1, y1, z1, x2, y2, z2, w, r1, g1, b1, r2, g2, b2, modu_tr)
cmd.create('working', chA)
cmd.super('working', chB)
def testAngleColor(self):
cmd.fragment('ala')
cmd.color('blue')
cmd.angle('ang01', 'index 8', 'index 5', 'index 2')
cmd.hide('label')
cmd.set('fog', '0')
cmd.set('ambient', '1')
cmd.set('angle_color', 'red')
cmd.set('dash_gap', '0')
cmd.zoom()
#need to check to make sure screen image has red in it
img_array = self.get_imagearray(width=100, height=100, ray=0)
self.assertImageHasColor('red', img_array, delta=[10,0,0])
def doFinish(self):
r_aA = cmd.get_distance(atom1="pw2", atom2="pw3", state=0)
cmd.distance(self.params_str[0], "pw2", "pw3")
th_a = cmd.get_angle(atom1="pw1", atom2="pw2", atom3="pw3", state=0)
cmd.angle(self.params_str[1], "pw1", "pw2", "pw3")
th_A = cmd.get_angle(atom1="pw2", atom2="pw3", atom3="pw4", state=0)
cmd.angle(self.params_str[2], "pw2", "pw3", "pw4")
if not (r_aA and th_a and th_A):
showerror(self.parent, "Error!",
"Maybe you made a mistake when choosing atoms!")
self.reset()
phi_ba = cmd.get_dihedral(atom1="pw0",
atom2="pw1",
atom3="pw2",
atom4="pw3",
state=0)
cmd.dihedral(self.params_str[3], "pw0", "pw1", "pw2", "pw3")
phi_aA = cmd.get_dihedral(atom1="pw1",
atom2="pw2",
atom3="pw3",
atom4="pw4",
state=0)
cmd.dihedral(self.params_str[4], "pw1", "pw2", "pw3", "pw4")
phi_AB = cmd.get_dihedral(atom1="pw2",
atom2="pw3",
atom3="pw4",
atom4="pw5",
state=0)
cmd.dihedral(self.params_str[5], "pw2", "pw3", "pw4", "pw5")
index_c = cmd.id_atom("pw0")
index_c_name = getAtomString('pw0')
index_b = cmd.id_atom("pw1")
index_b_name = getAtomString('pw1')
index_a = cmd.id_atom("pw2")
index_a_name = getAtomString('pw2')
index_A = cmd.id_atom("pw3")
index_A_name = getAtomString('pw3')
index_B = cmd.id_atom("pw4")
index_B_name = getAtomString('pw4')
index_C = cmd.id_atom("pw5")
index_C_name = getAtomString('pw5')
self.setBondForceParam(r_aA, th_a, th_A, phi_ba, phi_aA, phi_AB,
index_c, index_b, index_a, index_A, index_B,
index_C)
self.setAtomsDef(index_c_name, index_b_name, index_a_name,
index_A_name, index_B_name, index_C_name)
top = Toplevel(
self.parent) # <- freeze when open gro file in pymol 1.X
Output(top, self.bondForceParams, self.atoms_def)
cmd.set_wizard()
def testMeasureBetweenStates(self):
cmd.load(self.datafile('1v5a-3models.cif'), 'm1')
# distance
d = cmd.distance('d1', '24/CZ', 'same', state1=2, state2=3)
self.assertAlmostEqual(d, 3.0, delta=1e-1)
# angle
a = cmd.angle('a1',
'24/CZ',
'same',
'same',
state1=2,
state2=3,
state3=1)
self.assertAlmostEqual(a, 73.5, delta=1e-1)
# visual test
cmd.viewport(100, 100)
cmd.set('dash_radius', 1.0)
self.ambientOnly()
for name in ['d1', 'a1']:
cmd.disable('*')
cmd.enable(name)
cmd.zoom(name)
self.assertImageHasColor('yellow')
def angle_between_helices(selection1, selection2, method='helix',
state1=STATE, state2=STATE, visualize=1, quiet=1):
'''
DESCRIPTION
Calculates the angle between two helices
USAGE
angle_between_helices selection1, selection2 [, method [, visualize]]
ARGUMENTS
selection1 = string: atom selection of first helix
selection2 = string: atom selection of second helix
method = string: function to calculate orientation {default: helix_orientation}
visualize = 0 or 1: show fitted vector as arrow {default: 1}
EXAMPLE
fetch 2x19, async=0
select hel1, /2x19//B/23-36/
select hel2, /2x19//B/40-54/
angle_between_helices hel1, hel2
angle_between_helices hel1, hel2, cafit
SEE ALSO
helix_orientation, loop_orientation, cafit_orientation, angle_between_domains
'''
import math
state1, state2 = int(state1), int(state2)
visualize, quiet = int(visualize), int(quiet)
try:
orientation = globals()[methods_sc[str(method)]]
except KeyError:
print 'no such method:', method
raise CmdException
if not int(quiet):
print ' Using method:', orientation.__name__
cen1, dir1 = orientation(selection1, state1, visualize, quiet=1)
cen2, dir2 = orientation(selection2, state2, visualize, quiet=1)
angle = cpv.get_angle(dir1, dir2)
angle = math.degrees(angle)
if not quiet:
print ' Angle: %.2f deg' % (angle)
if visualize:
# measurement object for angle
center = cpv.scale(cpv.add(cen1, cen2), 0.5)
tmp = get_unused_name('_')
for pos in [center,
cpv.add(center, cpv.scale(dir1, 5.0)),
cpv.add(center, cpv.scale(dir2, 5.0))]:
cmd.pseudoatom(tmp, pos=list(pos), state=1)
name = get_unused_name('angle')
cmd.angle(name, *[(tmp, i) for i in [2,1,3]])
cmd.delete(tmp)
cmd.zoom('(%s) or (%s)' % (selection1, selection2), 2,
state1 if state1 == state2 else 0)
return angle
def draw_axis(chA,
chB,
scale_factor=20,
w=0.6,
r1=1,
g1=1,
b1=1,
r2=1,
g2=0,
b2=0):
T = transf_matrix(chA, chB)
angle = angle_axis(chA, chB)
angle_degrees = (angle * 180) / math.pi
axis1 = [
direction_cosines(chA, chB)[0],
direction_cosines(chA, chB)[1],
direction_cosines(chA, chB)[2]
]
p = nearest_point_to_axis(chA, chB)
x1, y1, z1 = p[0] + (3 * scale_factor * axis1[0]), p[1] + (
3 * scale_factor * axis1[1]), p[2] + (3 * scale_factor * axis1[2])
x2, y2, z2 = p[0] - (3 * scale_factor * axis1[0]), p[1] - (
3 * scale_factor * axis1[1]), p[2] - (3 * scale_factor * axis1[2])
obj = [
cgo.CYLINDER, x1, y1, z1, x2, y2, z2, w, r1, g1, b1, r2, g2, b2, 0.0
]
cmd.load_cgo(obj, angle_degrees)
cmA = center_of_Mass(chA)
cmB = cmW
cmAver = (cmB + cmA) / 2
vector = numpy.array([(cmB[0] - cmA[0]), (cmB[1] - cmA[1]),
(cmB[2] - cmA[2])])
moduli_vector = numpy.linalg.norm(vector)
vector_director = numpy.array([(cmB[0] - cmA[0]) / moduli_vector,
(cmB[1] - cmA[1]) / moduli_vector,
(cmB[2] - cmA[2]) / moduli_vector])
pC_A = proyeccion_centroide(chA, chA, chB)
pC_B = proyeccion_centroide_working(chA, chB)
trans_vector = numpy.array([(pC_B[0] - pC_A[0]), (pC_B[1] - pC_A[1]),
(pC_B[2] - pC_A[2])])
modu_tr = numpy.linalg.norm(trans_vector)
rota_centroid_rad = numpy.dot(vector_director, axis1)
rota_centroid = (rota_centroid_rad * 180) / math.pi
rota_centroid_absol_0 = numpy.absolute(rota_centroid)
rota_centroid_absol = round(rota_centroid_absol_0, 2)
if rota_centroid_absol == 0.00:
p1 = '_1'
p2 = '_2'
p3 = '_3'
cmd.pseudoatom(pos=[cmA[0], cmA[1], cmA[2]], object=p1)
cmd.pseudoatom(pos=[pC_A[0], pC_A[1], pC_A[2]], object=p2)
cmd.pseudoatom(pos=[cmB[0], cmB[1], cmB[2]], object=p3)
cmd.angle(None, p1, p2, p3)
print_information(T, axis1, angle_degrees, moduli_vector, obj, x1, y1,
z1, x2, y2, z2, w, r1, g1, b1, r2, g2, b2)
if rota_centroid_absol != 0:
p1 = '_1'
p2 = '_2'
p3 = '_3'
p4 = '_4'
cmd.pseudoatom(pos=[cmA[0], cmA[1], cmA[2]], object=p1)
cmd.pseudoatom(pos=[pC_A[0], pC_A[1], pC_A[2]], object=p2)
cmd.pseudoatom(pos=[pC_B[0], pC_B[1], pC_B[2]], object=p3)
cmd.pseudoatom(pos=[cmB[0], cmB[1], cmB[2]], object=p4)
cmd.dihedral(None, p1, p2, p3, p4)
cmd.distance(None, p2, p3)
print_information(T, axis1, angle_degrees, moduli_vector, obj, x1, y1,
z1, x2, y2, z2, w, r1, g1, b1, r2, g2, b2, modu_tr)
cmd.create('working', chA)
cmd.super('working', chB)
def angle_between_domains(selection1,
selection2,
method='align',
state1=STATE,
state2=STATE,
visualize=1,
quiet=1):
'''
DESCRIPTION
Angle by which a molecular selection would be rotated when superposing
on a selection2.
Do not use for measuring angle between helices, since the alignment of
the helices might involve a rotation around the helix axis, which will
result in a larger angle compared to the angle between helix axes.
USAGE
angle_between_domains selection1, selection2 [, method ]
ARGUMENTS
selection1 = string: atom selection of first helix
selection2 = string: atom selection of second helix
method = string: alignment command like "align" or "super" {default: align}
EXAMPLE
fetch 3iplA 3iplB, bsync=0
select domain1, resi 1-391
select domain2, resi 392-475
align 3iplA and domain1, 3iplB and domain1
angle_between_domains 3iplA and domain2, 3iplB and domain2
SEE ALSO
align, super, angle_between_helices
'''
import math
try:
import numpy
except ImportError:
print(' Error: numpy not available')
raise CmdException
state1, state2 = int(state1), int(state2)
visualize, quiet = int(visualize), int(quiet)
if cmd.is_string(method):
try:
method = cmd.keyword[method][0]
except KeyError:
print('no such method:', method)
raise CmdException
mobile_tmp = get_unused_name('_')
cmd.create(mobile_tmp, selection1, state1, 1, zoom=0)
try:
method(mobile=mobile_tmp,
target=selection2,
mobile_state=1,
target_state=state2,
quiet=quiet)
mat = cmd.get_object_matrix(mobile_tmp)
except:
print(' Error: superposition with method "%s" failed' %
(method.__name__))
raise CmdException
finally:
cmd.delete(mobile_tmp)
try:
# Based on transformations.rotation_from_matrix
# Copyright (c) 2006-2012, Christoph Gohlke
R33 = [mat[i:i + 3] for i in [0, 4, 8]]
R33 = numpy.array(R33, float)
# direction: unit eigenvector of R33 corresponding to eigenvalue of 1
w, W = numpy.linalg.eig(R33.T)
i = w.real.argmax()
direction = W[:, i].real
# rotation angle depending on direction
m = direction.argmax()
i, j, k, l = [[2, 1, 1, 2], [0, 2, 0, 2], [1, 0, 0, 1]][m]
cosa = (R33.trace() - 1.0) / 2.0
sina = (R33[i, j] +
(cosa - 1.0) * direction[k] * direction[l]) / direction[m]
angle = math.atan2(sina, cosa)
angle = abs(math.degrees(angle))
except:
print(' Error: rotation from matrix failed')
raise CmdException
if not quiet:
try:
# make this import optional to support running this script standalone
from .querying import centerofmass, gyradius
except (ValueError, ImportError):
gyradius = None
try:
# PyMOL 1.7.1.6+
centerofmass = cmd.centerofmass
except AttributeError:
centerofmass = lambda s: cpv.scale(cpv.add(*cmd.get_extent(s)),
0.5)
center1 = centerofmass(selection1)
center2 = centerofmass(selection2)
print(' Angle: %.2f deg, Displacement: %.2f angstrom' %
(angle, cpv.distance(center1, center2)))
if visualize:
center1 = numpy.array(center1, float)
center2 = numpy.array(center2, float)
center = (center1 + center2) / 2.0
if gyradius is not None:
rg = numpy.array(gyradius(selection1), float)
else:
rg = 10.0
h1 = numpy.cross(center2 - center1, direction)
h2 = numpy.dot(R33, h1)
h1 *= rg / cpv.length(h1)
h2 *= rg / cpv.length(h2)
for pos in [center1, center2, center1 + h1, center1 + h2]:
cmd.pseudoatom(mobile_tmp, pos=list(pos), state=1)
# measurement object for angle and displacement
name = get_unused_name('measurement')
cmd.distance(name, *['%s`%d' % (mobile_tmp, i) for i in [1, 2]])
cmd.angle(name, *['%s`%d' % (mobile_tmp, i) for i in [3, 1, 4]])
# CGO arrow for axis of rotation
visualize_orientation(direction, center1, rg, color='blue')
cmd.delete(mobile_tmp)
return angle
def angle_between_helices(selection1,
selection2,
method='helix',
state1=STATE,
state2=STATE,
visualize=1,
quiet=1):
'''
DESCRIPTION
Calculates the angle between two helices
USAGE
angle_between_helices selection1, selection2 [, method [, visualize]]
ARGUMENTS
selection1 = string: atom selection of first helix
selection2 = string: atom selection of second helix
method = string: function to calculate orientation {default: helix_orientation}
visualize = 0 or 1: show fitted vector as arrow {default: 1}
EXAMPLE
fetch 2x19, bsync=0
select hel1, /2x19//B/23-36/
select hel2, /2x19//B/40-54/
angle_between_helices hel1, hel2
angle_between_helices hel1, hel2, cafit
SEE ALSO
helix_orientation, loop_orientation, cafit_orientation, angle_between_domains
'''
import math
state1, state2 = int(state1), int(state2)
visualize, quiet = int(visualize), int(quiet)
try:
orientation = globals()[methods_sc[str(method)]]
except KeyError:
print('no such method:', method)
raise CmdException
if not int(quiet):
print(' Using method:', orientation.__name__)
cen1, dir1 = orientation(selection1, state1, visualize, quiet=1)
cen2, dir2 = orientation(selection2, state2, visualize, quiet=1)
angle = cpv.get_angle(dir1, dir2)
angle = math.degrees(angle)
if not quiet:
print(' Angle: %.2f deg' % (angle))
if visualize:
# measurement object for angle
center = cpv.scale(cpv.add(cen1, cen2), 0.5)
tmp = get_unused_name('_')
for pos in [
center,
cpv.add(center, cpv.scale(dir1, 5.0)),
cpv.add(center, cpv.scale(dir2, 5.0))
]:
cmd.pseudoatom(tmp, pos=list(pos), state=1)
name = get_unused_name('angle')
cmd.angle(name, *[(tmp, i) for i in [2, 1, 3]])
cmd.delete(tmp)
cmd.zoom('(%s) or (%s)' % (selection1, selection2), 2,
state1 if state1 == state2 else 0)
return angle
cmd.select("current_surroundings",
"current_surroundings and bindingsite")
cmd.select("current_polar", "current_surroundings and polar_atoms")
polar_distance = cmd.dist("polar_contacts",
"ligand",
"polar_atoms",
mode=2)
print("Polar contact: ")
print polar_distance, halo.name, halo.resn, halo.resi
model_polar = cmd.get_model("current_polar")
for pol in model_polar.atom:
cmd.select("current_polar", "id %s" % (pol.id))
# check for halogen bonds, distances 5.0, angles: > 140
current_distance = cmd.distance("current_distance",
"current_halogen", "current_polar")
current_angle = cmd.angle("current_angle", "current_neighbor",
"current_halogen", "current_polar")
if (current_angle >= 140) and (current_distance <= 5.0):
print("Halogen bond: ")
print current_distance, current_angle, pol.name, pol.resn, pol.resi
cmd.delete("current_angle")
cmd.delete("current_distance")
# visualizations
cmd.hide("lines")
cmd.hide(
"nonbonded") # hide all nonbonded atoms, i.e. oxygen of water or ions
cmd.show("sticks", "ligand")
cmd.show("lines", "bindingsite")
cmd.show("nb_spheres", "water_bs") # nb_spheres = non bonded spheres
def create_selections(options):
# Hide everything
cmd.hide("lines")
cmd.hide("nonbonded")
# Protein structure
cmd.select("protein_structure", "all")
if options.has_key('no_ligand_selected'):
# Super basic option, call ligand and chain from organic
print("Attempting to automatically find ligand")
ligand_candidates_number = cmd.select("ligand_candidate", "organic")
candidate_resn = ""
candidate_chain = ""
if ligand_candidates_number:
ligand_candidates_model = cmd.get_model("ligand_candidate")
for cand_atom in ligand_candidates_model.atom:
candidate_resn, candidate_chain = cand_atom.resn, cand_atom.chain
break
if candidate_resn and candidate_chain:
print("Automatically detected ligand is '%s' in chain '%s'" %
(candidate_resn, candidate_chain))
options['ligand_name'] = candidate_resn
options['chain_name'] = candidate_chain
else:
raise argparse.ArgumentError(
"Could not automatically detect ligand. Please make sure a ligand is contained in the provided pdb-file or use the 'Basic Mode'."
)
# Ligand
cmd.select(
"sele_all_ligands", "organic and chain %s and resn %s" %
(options['chain_name'], options["ligand_name"]))
number_of_ligands_selected = cmd.select(
"sele_ligand", 'organic and chain %s and resn %s and alt a+""' %
(options['chain_name'], options["ligand_name"]))
# remove all duplicate conformations
cmd.remove("sele_all_ligands and not sele_ligand")
cmd.delete("sele_all_ligands")
#Feature: If we did not get a correct chain name from the user, we will try to guess through the whole alphabet to find it
# otherwise the ligand will not appear in the visualization
if not number_of_ligands_selected:
#list holding all ascii-letters
for letter in ascii_uppercase:
number_of_ligands_selected = cmd.select(
"sele_ligand",
'organic and chain %s and resn %s and alt a+""' %
(letter, options["ligand_name"]))
if number_of_ligands_selected:
options['chain_name'] = letter
break
cmd.create("ligand", "sele_ligand")
cmd.delete("sele_ligand")
cmd.show("sticks", "ligand")
cmd.color(options["colors"]['color_carbon'], "ligand and e. C")
cmd.color(options["colors"]['oxygen'], "ligand and e. O")
cmd.color(options["colors"]['nitrogen'], "ligand and e. N")
# Cofactor
if options["cofactor_in_binding_site"]:
cmd.select(
"sele_cofactor", "resn %s and chain %s" %
(options['cofactor_name'], options['chain_name']))
cmd.create("cofactor", "sele_cofactor")
cmd.show("sticks", "cofactor")
cmd.color(options['colors']['color_cofactor'], "cofactor and e. C")
cmd.delete("sele_cofactor")
# Surface
cmd.create("protein_surface", "all")
cmd.hide("lines", "protein_surface")
cmd.hide("sticks", "protein_surface")
cmd.hide("nonbonded", "protein_surface")
cmd.show("surface", "protein_surface")
cmd.color(options["colors"]['protein_surface'], "protein_surface")
# Cartoon
cmd.copy("protein_cartoon", "protein_surface")
cmd.hide("surface", "protein_cartoon")
cmd.show("cartoon", "protein_cartoon")
cmd.color(options["colors"]['protein_cartoon'], "protein_cartoon")
# Transparent Cartoon
cmd.copy("protein_cartoon_transparent", "protein_cartoon")
cmd.set("cartoon_transparency", options['cartoon_transparency'],
"protein_cartoon_transparent")
# 2nd Transparent Cartoon
cmd.copy("protein_cartoon_transparent_more", "protein_cartoon")
cmd.set("cartoon_transparency", 0.9, "protein_cartoon_transparent_more")
# Binding Site
cmd.select("sele_binding_site",
"ligand expand %s" % (options['binding_site_radius']))
cmd.select("sele_binding_site", "br. sele_binding_site")
cmd.select("sele_binding_site", "sele_binding_site and protein_structure")
cmd.select("sele_binding_site", "sele_binding_site and not ligand")
cmd.create("binding_site", "sele_binding_site")
cmd.delete("sele_binding_site")
cmd.delete("protein_structure")
cmd.hide("surface", "binding_site")
cmd.hide("nonbonded")
cmd.show("sticks", "binding_site")
cmd.show("nb_spheres", "binding_site and not resn HOH")
cmd.color(options["colors"]['binding_site'], "binding_site and e. C")
cmd.color(options["colors"]['nitrogen'], "binding_site and e. N")
cmd.color(options["colors"]['oxygen'], "binding_site and e. O")
# get polar interacting residues in binding site without water
cmd.select("sele_no_water_binding_site", "binding_site and not resn hoh")
cmd.select(
"sele_no_water_binding_site",
"sele_no_water_binding_site and not resn %s" % options['ligand_name'])
pairs = polarpairs("sele_no_water_binding_site",
"ligand",
cutoff=options['binding_site_radius'],
name="polar_int_d")
if pairs:
cmd.hide("labels", "polar_int_d")
cmd.color(options['colors']["interaction_polar"], "polar_int_d")
else:
print("No polar interaction pairs found")
options["no_polar_interactions_found"] = True
cmd.delete("sele_no_water_binding_site")
interacting_tuples = polartuples(pairs, selection_name="polar_interaction")
#create a list with selection names of polar_interacting residues
polar_selection_names = [
"resi %s and resn %s and chain %s" % tup for tup in interacting_tuples
]
# write the residues into a custom text file,
with open("%s" % (POLAR_INTERACTIONS_FILENAME, ), "w") as f:
f.write("#POLAR INTERACTION PARTNERS WITH %s\n" %
(options['ligand_name'], ))
f.write("RESI\tRESN\tCHAIN\n")
for tup in interacting_tuples:
f.write("%s\t%s\t%s\n" % tup)
#select all polar interacting residues at once for an overview
# cmd.select("polar_interacting_residues", "")
for i, selection_name in enumerate(polar_selection_names):
if i: # if i>0 and we already have sele_polar_interacting_residues
cmd.select(
"sele_polar_interacting_residues",
"sele_polar_interacting_residues or %s" % selection_name)
print(
"select sele_polar_interacting_residues, sele_polar_interacting_residues or %s"
% selection_name)
else:
cmd.select("sele_polar_interacting_residues", selection_name)
print("select sele_polar_interacting_residues, %s" %
selection_name)
if not options.has_key("no_polar_interactions_found"):
cmd.create("polar_interacting_residues",
"sele_polar_interacting_residues")
cmd.delete("sele_polar_interacting_residues")
cmd.show("sticks", "polar_interacting_residues")
cmd.color("grey50", "polar_interacting_residues and e. C")
cmd.color(options["colors"]['nitrogen'],
"polar_interacting_residues and e. N")
cmd.color(options["colors"]['oxygen'],
"polar_interacting_residues and e. O")
# create selection for HOH molecules in binding pocket and make nb_spheres
if options['water_in_binding_site']:
cmd.select("sele_water_binding_site", "binding_site and resn hoh")
water_pairs = polarpairs("sele_water_binding_site",
"ligand",
cutoff=options['binding_site_radius'])
# further filter polar interactions, discard water molecules that don't interact with binding site and ligand
# water molecules in interacting tuples are already forming a hbond to ligand
water_list = []
water_distance_list = []
water_polar_tuples_list = []
if water_pairs:
# print("water_bridge_candidates ", water_bridge_candidates)
print("water_bridge_candidates ", water_pairs)
# water_bridge_selection_names = ["resi %s and resn %s and chain %s and polar_interacting_residues" % tup for
water_bridge_selection_names = [
"(%s`%s)" % tup[0] for tup in water_pairs
]
for i, water_selection_name in enumerate(
water_bridge_selection_names):
print("Water bridge prediction \n")
print("select sele_water%s, %s" % (i, water_selection_name))
water_selection = cmd.select("sele_water%s" % i,
water_selection_name)
print("water selection has %s atoms" % water_selection)
cmd.select(
"sele_water_partner%s" % i, "sele_water%s expand %s" %
(i, options['binding_site_radius']))
cmd.select("sele_water_partner%s" % i,
"sele_water_partner%s and binding_site" % i)
cmd.select("sele_water_partner%s" % i,
"sele_water_partner%s and not ligand" % i)
possible_binding_site_partners = cmd.select(
"sele_water_partner%s" % i,
"sele_water_partner%s and (e. S or e. O or e. N)" % i)
print("Predicted %s possible_binding_site_partners for %s" %
(possible_binding_site_partners, water_selection_name))
if possible_binding_site_partners:
# check if angles allow hbond
possible_pairs = polarpairs(
"sele_water_partner%s" % i,
"sele_water%s" % i,
name="d_water_%s" % i,
cutoff=options['binding_site_radius'])
water_list.append("sele_water%s" %
i) # contains water molecule
water_distance_list.append(
"d_water_%s" %
i) # contains distance between water and binding site
# creates representation for residues interacting with water in binding site
water_polar_tuples_list.append(
polartuples(possible_pairs,
selection_name="h20_inter_%s" % i))
print("water_polar_tuples_list", water_polar_tuples_list)
cmd.delete("sele_water_partner%s" % i)
else:
cmd.delete("sele_water%s" % i)
# print("water_list", water_list)
# print("water_distance_list", water_distance_list)
# print("water_polar_tuples_list", water_polar_tuples_list)
# now only show water from water list
water_to_output_list = []
# list of water selections to enable in the movie
water_to_enable_list = []
for water_index, (water_name, water_distance_name) in enumerate(
zip(water_list, water_distance_list)):
# number_of_water = cmd.select("sele_water_binding_site", "binding_site and resn hoh")
number_of_water = cmd.select("sele_water_binding_site",
water_name)
if number_of_water:
cmd.create("water_%s" % water_index,
"sele_water_binding_site")
cmd.show("nb_spheres", "water_%s" % water_index)
#get identifier of water for polar_interactions written to file
w_model = cmd.get_model("water_%s" % water_index)
for water_mol in w_model.atom:
water_to_output_list.append(
(water_mol.resi, water_mol.resn, water_mol.chain))
water_to_enable_list.append("water_%s" % water_index)
water_to_enable_list.append(water_distance_name)
cmd.color(options['colors']["interaction_polar"],
water_distance_name)
cmd.hide("label", water_distance_name)
cmd.delete(water_name)
cmd.delete("sele_water_binding_site")
#append water molecules to polar interactions file
with open("%s" % (POLAR_INTERACTIONS_FILENAME, ), "a+") as f:
for tup in water_to_output_list:
# f.write("RESI\tRESN\tCHAIN\n")
f.write("%s\t%s\t%s\n" % tup)
# residues interacting with water and
options["water_to_enable_list"] = water_to_enable_list
# Halogen Bond
if options['check_halogen_interaction']:
halogen_bond_selections = []
halogen_interaction_partners = []
for halogen in ["Cl", "Br", "I"]:
number_of_halogen = cmd.select("sele_%s_interaction" % halogen,
"ligand and e. %s" % halogen)
print("We have %s %s atoms in our ligand" %
(number_of_halogen, halogen))
if number_of_halogen:
cmd.select("sele_candidates",
"sele_%s_interaction expand 4.5" % halogen)
cmd.select("sele_candidates",
"sele_candidates and (e. O or e. S)")
number_of_candidates = cmd.select(
"sele_candidates",
"sele_candidates and binding_site and not ligand")
print("We have %s potential candidates for %s bonds" %
(number_of_candidates, halogen))
if number_of_candidates:
# if angle ~160 and distance up to 4.5 A
# if angle 150-160 and distance up to 4.0 A
candidate_model = cmd.get_model("sele_candidates")
for atom in candidate_model.atom:
print("Candidate from model = %s %s" %
(atom.resn, atom.index))
cmd.select("sele_halo", "ligand and e. %s" % halogen)
model_br = cmd.get_model("sele_halo")
candidate_model = cmd.get_model("sele_candidates")
for i, atom in enumerate(model_br.atom):
# print("i= %s" % i)
sele_halo = cmd.select("sele_halo%s" % i,
"id %s and ligand" % atom.id)
# model_sele_halo = cmd.get_model("sele_halo%s" % i)
sele_halo_c = cmd.select("sele_halo%s_c" % i,
"neighbor sele_halo%s" % i)
# print("sele_halo %s" % sele_halo, "sele_halo_c %s" % sele_halo_c)
for j, oxygen_or_sulfur in enumerate(
candidate_model.atom):
cmd.select(
"ox_or_sulf_%s" % j,
"id %s and binding_site" % oxygen_or_sulfur.id)
distance = cmd.distance(
"halogen_bond_%s_%s_%s" % (halogen, i, j),
"sele_halo%s" % i, "ox_or_sulf_%s" % j)
angle = cmd.angle(
"halogen_bond_angle_%s_%s_%s" %
(halogen, i, j), "sele_halo%s_c" % i,
"sele_halo%s" % i, "ox_or_sulf_%s" % j)
print("Distance = %s, angle = %s" %
(distance, angle))
if (distance <= 4.5 and angle >= 160.0) or (
distance <= 4.0 and angle >= 150.0):
print(
"We have a halogen bond: halogen_bond_angle_%s_%s_%s"
% (halogen, i, j))
cmd.hide(
"label",
"halogen_bond_%s_%s_%s" % (halogen, i, j))
cmd.hide(
"label", "halogen_bond_angle_%s_%s_%s" %
(halogen, i, j))
cmd.color(
"cb_yellow",
"halogen_bond_%s_%s_%s" % (halogen, i, j))
cmd.color(
"cb_yellow",
"halogen_bond_angle_%s_%s_%s" %
(halogen, i, j))
#halogen_bond_selections.append("halogen_bond_%s_%s_%s" % (halogen, i, j))
halogen_bond_selections.append(
"halogen_bond_angle_%s_%s_%s" %
(halogen, i, j))
cmd.create("halogen_interaction_partner%s" % i,
"br. ox_or_sulf_%s" % j)
halogen_interaction_partners.append(
"halogen_interaction_partner%s" % i)
else:
print("No halogen bond, deleting selection!\n")
cmd.delete("halogen_bond_angle_%s_%s_%s" %
(halogen, i, j))
# always delete bond, angle is enough
cmd.delete("halogen_bond_%s_%s_%s" %
(halogen, i, j))
cmd.delete("ox_or_sulf_%s" % j)
#cleanup selections
cmd.delete("sele_halo%s" % i)
cmd.delete("sele_halo%s_c" % i)
cmd.delete("sele_halo%s_c" % i)
cmd.delete("sele_candidates")
cmd.delete("sele_halo")
cmd.delete("sele_%s_interaction" % halogen)
# check whether we found any halogen bond interactions
# if halogen_bond_selections has more than one element, it will
# evaluate as true, if empty it will be false
if halogen_bond_selections:
options['halogen_bond_selections'] = halogen_bond_selections
options[
'halogen_interaction_partners'] = halogen_interaction_partners
def ens_measure(pk1 = None,
pk2 = None,
pk3 = None,
pk4 = None,
name = None,
log = None,
verbose = True):
'''
DESCRIPTION
Statistics from ensemble structure measurements. If:
2 selections give = distance
3 selections give = angle
4 selections give = dihedral angle
USAGE
ens_measure pk1, pk2, pk3, pk4, name, log, verbose
ARGUMENTS
log = name of log file
verbose = prints individual measurements
EXAMPLE
ens_measure atom1, atom2, name = 'measure', log 'ens.log'
'''
print >> log, '\nEnsemble measurement'
if [pk1, pk2, pk3, pk4].count(None) > 2:
print '\nERROR: Please supply at least 2 seletions'
return
number_models = cmd.count_states(pk1)
measurements = []
# distance
if [pk1, pk2, pk3, pk4].count(None) == 2:
print >> log, 'Distance'
if name == None: name = 'ens_distance'
# display as object
cmd.distance(name = name,
selection1 = pk1,
selection2 = pk2)
# get individual values
for n in xrange(number_models):
measurements.append( cmd.get_distance(pk1, pk2, n+1) )
assert len(measurements) == number_models
# angle
if [pk1, pk2, pk3, pk4].count(None) == 1:
print >> log, 'Angle'
# display as object
if name == None: name = 'ens_angle'
cmd.angle(name = name,
selection1 = pk1,
selection2 = pk2,
selection3 = pk3)
# get individual values
for n in xrange(number_models):
measurements.append( cmd.get_angle(atom1 = pk1,
atom2 = pk2,
atom3 = pk3,
state = n+1) )
assert len(measurements) == number_models
# Dihedral angle
if [pk1, pk2, pk3, pk4].count(None) == 0:
print >> log, 'Dihedral angle'
# display as object
if name == None: name = 'ens_dihedral'
cmd.dihedral(name = name,
selection1 = pk1,
selection2 = pk2,
selection3 = pk3,
selection4 = pk4)
# get individual values
for n in xrange(number_models):
measurements.append( cmd.get_dihedral(atom1 = pk1,
atom2 = pk2,
atom3 = pk3,
atom4 = pk4,
state = n+1) )
assert len(measurements) == number_models
# print stats
if verbose:
print >> log, ' State Value'
for n, measurement in enumerate(measurements):
print >> log, ' %4d %3.3f '%(n+1, measurement)
print >> log, '\nMeasurement statistics'
print_array_stats(array = measurements,
log = log)
def find_halogen_bonds():
halogen_bonds = []
cmd.select("bindingsite1", "ligand_a expand 5.0"
) # expand selection by 5 angstrom, extend = extend along bonds
cmd.select(
"bindingsite1",
"br. bindingsite") # br extends the selection to the full residue
cmd.select("bindingsite1", "bindingsite and not ligand"
) # br extends the selection to the full residue
cmd.select(
"water",
"resn hoh") # resn = residues name, hoh = name of water molecules
cmd.select("water_bs", "water and bindingsite")
#select all relevant halogen atoms
number_of_halogens = cmd.select("hal", "hal and ligand_a")
cmd.select("polar_atoms", "e. O or e. N or e. S")
model_halogen = cmd.get_model("hal") # create model for halogen selection
for halo in model_halogen.atom:
print("A")
cmd.select("current_halogen",
"(e. I or e. Cl or e. Br) and id %s" % (halo.id))
cmd.select("current_neighbor", "current_halogen extend 1")
cmd.select("current_neighbor",
"current_neighbor and not current_halogen")
cmd.select("current_neighbor", "neighbor current_halogen")
cmd.select("current_surroundings", "current_halogen expand 5.0")
cmd.select("current_surroundings",
"current_surroundings and bindingsite1")
cmd.select("current_polar", "current_surroundings and polar_atoms")
model_polar = cmd.get_model("current_polar")
for pol in model_polar.atom:
cmd.select("current_polar",
"not water and polar_atoms and id %s" % (pol.id))
# check for halogen bonds, distances 5.0, angles: > 140
current_distance = cmd.distance("current_distance",
"current_halogen", "current_polar")
current_angle = cmd.angle("current_angle", "current_neighbor",
"current_halogen", "current_polar")
print(current_distance, current_angle)
if (current_angle >= 140) and (current_distance <= 5.0):
halogen_bonds.append((pol.resn, pol.resi, pol.id,
current_distance, current_angle))
#Append fitting halogen bonds to list
cmd.delete("current_angle")
cmd.delete("current_distance")
#Clear up selections
cmd.delete("current_halogen")
cmd.delete("current_neighbor")
cmd.delete("water")
cmd.delete("water_bs")
cmd.delete("current_polar")
cmd.delete("current_surroundings")
cmd.delete("bindingsite1")
#Sort the list by distance
halogen_bonds = sorted(halogen_bonds, key=lambda x: x[3])
return halogen_bonds
def angle_between_domains(selection1, selection2, method='align',
state1=STATE, state2=STATE, visualize=1, quiet=1):
'''
DESCRIPTION
Angle by which a molecular selection would be rotated when superposing
on a selection2.
Do not use for measuring angle between helices, since the alignment of
the helices might involve a rotation around the helix axis, which will
result in a larger angle compared to the angle between helix axes.
USAGE
angle_between_domains selection1, selection2 [, method ]
ARGUMENTS
selection1 = string: atom selection of first helix
selection2 = string: atom selection of second helix
method = string: alignment command like "align" or "super" {default: align}
EXAMPLE
fetch 3iplA 3iplB, async=0
select domain1, resi 1-391
select domain2, resi 392-475
align 3iplA and domain1, 3iplB and domain1
angle_between_domains 3iplA and domain2, 3iplB and domain2
SEE ALSO
align, super, angle_between_helices
'''
import math
try:
import numpy
except ImportError:
print ' Error: numpy not available'
raise CmdException
state1, state2 = int(state1), int(state2)
visualize, quiet = int(visualize), int(quiet)
if cmd.is_string(method):
try:
method = cmd.keyword[method][0]
except KeyError:
print 'no such method:', method
raise CmdException
mobile_tmp = get_unused_name('_')
cmd.create(mobile_tmp, selection1, state1, 1, zoom=0)
try:
method(mobile=mobile_tmp, target=selection2, mobile_state=1,
target_state=state2, quiet=quiet)
mat = cmd.get_object_matrix(mobile_tmp)
except:
print ' Error: superposition with method "%s" failed' % (method.__name__)
raise CmdException
finally:
cmd.delete(mobile_tmp)
try:
# Based on transformations.rotation_from_matrix
# Copyright (c) 2006-2012, Christoph Gohlke
R33 = [mat[i:i+3] for i in [0,4,8]]
R33 = numpy.array(R33, float)
# direction: unit eigenvector of R33 corresponding to eigenvalue of 1
w, W = numpy.linalg.eig(R33.T)
i = w.real.argmax()
direction = W[:, i].real
# rotation angle depending on direction
m = direction.argmax()
i,j,k,l = [
[2,1,1,2],
[0,2,0,2],
[1,0,0,1]][m]
cosa = (R33.trace() - 1.0) / 2.0
sina = (R33[i, j] + (cosa - 1.0) * direction[k] * direction[l]) / direction[m]
angle = math.atan2(sina, cosa)
angle = abs(math.degrees(angle))
except:
print ' Error: rotation from matrix failed'
raise CmdException
if not quiet:
try:
# make this import optional to support running this script standalone
from .querying import centerofmass, gyradius
except (ValueError, ImportError):
gyradius = None
try:
# PyMOL 1.7.1.6+
centerofmass = cmd.centerofmass
except AttributeError:
centerofmass = lambda s: cpv.scale(cpv.add(*cmd.get_extent(s)), 0.5)
center1 = centerofmass(selection1)
center2 = centerofmass(selection2)
print ' Angle: %.2f deg, Displacement: %.2f angstrom' % (angle, cpv.distance(center1, center2))
if visualize:
center1 = numpy.array(center1, float)
center2 = numpy.array(center2, float)
center = (center1 + center2) / 2.0
if gyradius is not None:
rg = numpy.array(gyradius(selection1), float)
else:
rg = 10.0
h1 = numpy.cross(center2 - center1, direction)
h2 = numpy.dot(R33, h1)
h1 *= rg / cpv.length(h1)
h2 *= rg / cpv.length(h2)
for pos in [center1, center2, center1 + h1, center1 + h2]:
cmd.pseudoatom(mobile_tmp, pos=list(pos), state=1)
# measurement object for angle and displacement
name = get_unused_name('measurement')
cmd.distance(name, *['%s`%d' % (mobile_tmp, i) for i in [1,2]])
cmd.angle(name, *['%s`%d' % (mobile_tmp, i) for i in [3,1,4]])
# CGO arrow for axis of rotation
visualize_orientation(direction, center1, rg, color='blue')
cmd.delete(mobile_tmp)
return angle
def ens_measure(pk1=None,
pk2=None,
pk3=None,
pk4=None,
name=None,
log=None,
verbose=True):
'''
DESCRIPTION
Statistics from ensemble structure measurements. If:
2 selections give = distance
3 selections give = angle
4 selections give = dihedral angle
USAGE
ens_measure pk1, pk2, pk3, pk4, name, log, verbose
ARGUMENTS
log = name of log file
verbose = prints individual measurements
EXAMPLE
ens_measure atom1, atom2, name = 'measure', log 'ens.log'
'''
print('\nEnsemble measurement', file=log)
if [pk1, pk2, pk3, pk4].count(None) > 2:
print('\nERROR: Please supply at least 2 seletions')
return
number_models = cmd.count_states(pk1)
measurements = []
# distance
if [pk1, pk2, pk3, pk4].count(None) == 2:
print('Distance', file=log)
if name == None: name = 'ens_distance'
# display as object
cmd.distance(name=name, selection1=pk1, selection2=pk2)
# get individual values
for n in range(number_models):
measurements.append(cmd.get_distance(pk1, pk2, n + 1))
assert len(measurements) == number_models
# angle
if [pk1, pk2, pk3, pk4].count(None) == 1:
print('Angle', file=log)
# display as object
if name == None: name = 'ens_angle'
cmd.angle(name=name, selection1=pk1, selection2=pk2, selection3=pk3)
# get individual values
for n in range(number_models):
measurements.append(
cmd.get_angle(atom1=pk1, atom2=pk2, atom3=pk3, state=n + 1))
assert len(measurements) == number_models
# Dihedral angle
if [pk1, pk2, pk3, pk4].count(None) == 0:
print('Dihedral angle', file=log)
# display as object
if name == None: name = 'ens_dihedral'
cmd.dihedral(name=name,
selection1=pk1,
selection2=pk2,
selection3=pk3,
selection4=pk4)
# get individual values
for n in range(number_models):
measurements.append(
cmd.get_dihedral(atom1=pk1,
atom2=pk2,
atom3=pk3,
atom4=pk4,
state=n + 1))
assert len(measurements) == number_models
# print stats
if verbose:
print(' State Value', file=log)
for n, measurement in enumerate(measurements):
print(' %4d %3.3f ' % (n + 1, measurement), file=log)
print('\nMeasurement statistics', file=log)
print_array_stats(array=measurements, log=log)
ang_pairs = []
restraints = []
for filename in filenames:
with open(filename, 'r') as f:
lines = f.readlines()
lines = list(filter(filter_func, lines))
ang_pairs.extend(list(map(map_func, lines)))
restraints.extend(list(map(map_func2, lines)))
out_lines = []
for ang_pair, restraint in zip(ang_pairs, restraints):
group1 = "(id %d)" % ang_pair[0]
group2 = "(id %d)" % ang_pair[1]
group3 = "(id %d)" % ang_pair[2]
cmd.angle("%d-%d-%d" % ang_pair, group1, group2, group3)
resns = []
resis = []
atoms = []
cmd.iterate("id %d+%d+%d" % ang_pair, "resns.append(resn)")
cmd.iterate("id %d+%d+%d" % ang_pair, "resis.append(resi)")
cmd.iterate("id %d+%d+%d" % ang_pair, "atoms.append(name)")
angle = cmd.get_angle(group1, group2, group3)
out_lines.append(
"[ %s%s(%s)-%s%s(%s)-%s%s(%s) ~ %.2f degree (%s, %s, %s) ]\n" %
((resns[0], resis[0], atoms[0], resns[1], resis[1], atoms[1], resns[2],
resis[2], atoms[2], angle) + restraint))
out_lines.append("%d %d %d\n" % ang_pair)
# write dis_pairs to distance_pairs.ndx for analysis
with open("angle_out.ndx", 'w') as f:
