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 testDihedralColor(self):
cmd.fragment('ala')
cmd.color('blue')
cmd.dihedral('dih01', 'index 8', 'index 5', 'index 2', 'index 1')
cmd.hide('label')
cmd.set('fog', '0')
cmd.set('ambient', '1')
cmd.set('dihedral_color', 'red')
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)
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 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 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)
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)
restraints = []
for filename in filenames:
with open(filename, 'r') as f:
lines = f.readlines()
lines = list(filter(filter_func , lines))
dih_pairs.extend(list(map(map_func, lines)))
restraints.extend(list(map(map_func2, lines)))
out_lines = []
for dih_pair,restraint in zip(dih_pairs, restraints):
group1 = "(id %d)" % dih_pair[0]
group2 = "(id %d)" % dih_pair[1]
group3 = "(id %d)" % dih_pair[2]
group4 = "(id %d)" % dih_pair[3]
cmd.dihedral("%d-%d-%d-%d" % dih_pair, group1, group2, group3, group4)
resns = []
resis = []
atoms = []
cmd.iterate("id %d+%d+%d+%d" % dih_pair, "resns.append(resn)")
cmd.iterate("id %d+%d+%d+%d" % dih_pair, "resis.append(resi)")
cmd.iterate("id %d+%d+%d+%d" % dih_pair, "atoms.append(name)")
dihedral = cmd.get_dihedral(group1, group2, group3, group4)
out_lines.append("[ %s%s(%s)-%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],resns[3], resis[3], atoms[3], dihedral) + restraint))
out_lines.append("%d %d %d %d\n" % dih_pair)
# write dis_pairs to distance_pairs.ndx for analysis
with open("dihedral_out.ndx", 'w') as f:
for line in out_lines:
f.write(line)
print(line)