def __call__(self):
# get view on screen
my_view = cmd.get_view()
delta_mv = 0.
for i in range(18):
delta_mv = max(delta_mv,abs(my_view[i] - self.my_view[i]))
self.my_view[i] = my_view[i]
#print my_view
# get orientation/position matrices for two molecules
# how does pymol define rotation center of molecule?
# apparnetly by geometric average
pdbmat1 = cmd.get_object_matrix(self.pdbobj1)
pdbmat2 = cmd.get_object_matrix(self.pdbobj2)
delta_mm = 0.
for i in range(12):
delta_mm = max(delta_mm,abs(pdbmat1[i] - self.objmat1[i]))
delta_mm = max(delta_mm,abs(pdbmat2[i] - self.objmat2[i]))
self.objmat1[i] = pdbmat1[i]
self.objmat2[i] = pdbmat2[i]
if(delta_mm > 0.01): # we only do expensive energy calc if pose changed
do_mm = True
else:
do_mm = False
if((delta_mv > 0.01) or do_mm): # we only update if pose or view changed
cgo_obj = pdb_interaction(pdbmat1,pdbmat2,self.pdb1,self.pdb2,self.gcen1,self.gcen2,
self.energy,do_mm,self.logscale,self.dielectric,self.eps,self.nbest,self.energy_min)
if(self.nbest[0] != self.nbest[1]):
# print('Switching models ',self.nbest)
self.nbest[1] = self.nbest[0]
#
# write new best pose to logfile
#
et = self.energy[0]
ee = self.energy[1]
ev = self.energy[2]
if(self.energy[0] < self.energy_min):
print(' NEW MIN ee: %12.3g ev: %12.3g et: %12.3g model %4d ' % (ee,ev,et,self.nbest[0]))
self.energy_min = et
self.dockeye_log.write('new min: %12.5g %12.5g %12.5g model %4d \n' % (ee,ev,et,self.nbest[0]))
for i in range(4):
for j in range(4):
indx = j + 4*i
self.dockeye_log.write('%12.5f ' % (pdbmat1[indx]))
self.dockeye_log.write('\n')
for i in range(4):
for j in range(4):
indx = j + 4*i
self.dockeye_log.write('%12.5f ' % (pdbmat2[indx]))
self.dockeye_log.write('\n')
#else:
# if(do_mm):
# #print('Current energy: ee: %12.3g ev: %12.3g et: %12.3g' % (ee,ev,et))
# continue
if(do_mm):
cmd.delete('dockeye_obj')
cmd.load_cgo(cgo_obj,'dockeye_obj')
draw_ligand(pdbmat2,self.pdb2,self.gcen2,self.nbest[0])
def test_matrix_copy(self):
cmd.fragment('ala')
cmd.fragment('gly')
cmd.rotate('x', 90, 'none', object='ala')
cmd.matrix_copy('ala', 'gly')
self.assertArrayEqual(cmd.get_object_matrix('gly'),
(1.0, 0.0, 0.0, 0.0, 0.0, 0.0, -1.0, 0.0, 0.0,
1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0), 1e-4)
cmd.matrix_reset('gly', mode=1)
self.assertArrayEqual(cmd.get_object_matrix('gly'),
(1.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0,
0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 1.0), 1e-4)
def testReset(self):
# view
v = cmd.get_view()
cmd.turn('x', 10)
cmd.move('y', 10)
self.assertNotEqual(v, cmd.get_view())
cmd.reset()
self.assertEqual(v, cmd.get_view())
# object
cmd.pseudoatom("m1")
x = cmd.get_object_matrix("m1")
cmd.translate([1,2,3], object="m1")
self.assertNotEqual(x, cmd.get_object_matrix("m1"))
cmd.reset("m1")
self.assertEqual(x, cmd.get_object_matrix("m1"))
def testReset(self):
# view
v = cmd.get_view()
cmd.turn('x', 10)
cmd.move('y', 10)
self.assertNotEqual(v, cmd.get_view())
cmd.reset()
self.assertEqual(v, cmd.get_view())
# object
cmd.pseudoatom("m1")
x = cmd.get_object_matrix("m1")
cmd.translate([1, 2, 3], object="m1")
self.assertNotEqual(x, cmd.get_object_matrix("m1"))
cmd.reset("m1")
self.assertEqual(x, cmd.get_object_matrix("m1"))
def calc_super_matrix(mobile, static):
'''
DESCRIPTION
Aligns two objects (or selections), returns the transformation matrix,
and resets the matrix of the mobile object.
Uses CEAlign PyMOL function for alignment.
ARGUMENTS
mobile = string: selection describing the mobile object whose rotation
matrix will be reported
static = string: selection describing the static object onto which the
mobile object will be aligned
REQUIRES: numpy
'''
cmd.cealign(static, mobile)
# cmd.super(mobile,static)
T = cmd.get_object_matrix(mobile)
R = numpy.identity(4)
k = 0
for i in range(0, 4):
for j in range(0, 4):
R[i][j] = T[k]
k += 1
return R
def calc_super_matrix(mobile, static):
'''
DESCRIPTION
Aligns two objects (or selections), returns the transformation matrix,
and resets the matrix of the mobile object.
Uses CEAlign PyMOL function for alignment.
ARGUMENTS
mobile = string: selection describing the mobile object whose rotation
matrix will be reported
static = string: selection describing the static object onto which the
mobile object will be aligned
REQUIRES: numpy
'''
cmd.cealign(static, mobile)
# cmd.super(mobile,static)
T = cmd.get_object_matrix(mobile)
R = numpy.identity(4)
k = 0
for i in range(0, 4):
for j in range(0, 4):
R[i][j] = T[k]
k += 1
return R
def test_matrix_copy(self):
cmd.fragment('ala')
cmd.fragment('gly')
cmd.rotate('x', 90, 'none', object='ala')
cmd.matrix_copy('ala', 'gly')
self.assertArrayEqual(cmd.get_object_matrix('gly'),
(1.0, 0.0, 0.0, 0.0,
0.0, 0.0,-1.0, 0.0,
0.0, 1.0, 0.0, 0.0,
0.0, 0.0, 0.0, 1.0), 1e-4)
cmd.matrix_reset('gly', mode=1)
self.assertArrayEqual(cmd.get_object_matrix('gly'),
(1.0, 0.0, 0.0, 0.0,
0.0, 1.0, 0.0, 0.0,
0.0, 0.0, 1.0, 0.0,
0.0, 0.0, 0.0, 1.0), 1e-4)
def testPairFit(self):
cmd.fragment('trp')
cmd.fragment('his')
# 1 atom
sele = ('trp and guide', 'his and guide')
pos = list(map(cmd.get_atom_coords, sele))
vec = cpv.sub(*pos)
mat_ref = [
1.0, 0.0, 0.0, -vec[0],
0.0, 1.0, 0.0, -vec[1],
0.0, 0.0, 1.0, -vec[2],
0.0, 0.0, 0.0, 1.0]
rms = cmd.pair_fit(*sele)
self.assertEqual(rms, 0.0)
mat = cmd.get_object_matrix('trp')
self.assertArrayEqual(mat, mat_ref, 1e-4)
# 2 atoms
sele += ('trp & name CB', 'his & name CB')
rms = cmd.pair_fit(*sele)
self.assertAlmostEqual(rms, 0.0082, delta=1e-4)
# 4 atoms
sele += ('trp & name CG', 'his & name CG',
'trp & name CD1', 'his & name CD2')
rms = cmd.pair_fit(*sele)
self.assertAlmostEqual(rms, 0.0713, delta=1e-4)
def testPairFit(self):
cmd.fragment('trp')
cmd.fragment('his')
# 1 atom
sele = ('trp and guide', 'his and guide')
pos = list(map(cmd.get_atom_coords, sele))
vec = cpv.sub(*pos)
mat_ref = [
1.0, 0.0, 0.0, -vec[0], 0.0, 1.0, 0.0, -vec[1], 0.0, 0.0, 1.0,
-vec[2], 0.0, 0.0, 0.0, 1.0
]
rms = cmd.pair_fit(*sele)
self.assertEqual(rms, 0.0)
mat = cmd.get_object_matrix('trp')
self.assertArrayEqual(mat, mat_ref, 1e-4)
# 2 atoms
sele += ('trp & name CB', 'his & name CB')
rms = cmd.pair_fit(*sele)
self.assertAlmostEqual(rms, 0.0082, delta=1e-4)
# 4 atoms
sele += ('trp & name CG', 'his & name CG', 'trp & name CD1',
'his & name CD2')
rms = cmd.pair_fit(*sele)
self.assertAlmostEqual(rms, 0.0713, delta=1e-4)
def test_set_object_ttt(self):
M = [
1.0, 0.0, 0.0, 0.0, 0.0, 0.0, -1.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0,
0.0, 0.0, 1.0
]
cmd.pseudoatom('m1')
cmd.set_object_ttt('m1', M)
self.assertArrayEqual(M, cmd.get_object_matrix('m1'), 1e-4)
def test_set_object_ttt(self):
M = [1.0, 0.0, 0.0, 0.0,
0.0, 0.0,-1.0, 0.0,
0.0, 1.0, 0.0, 0.0,
0.0, 0.0, 0.0, 1.0]
cmd.pseudoatom('m1')
cmd.set_object_ttt('m1', M)
self.assertArrayEqual(M, cmd.get_object_matrix('m1'), 1e-4)
def _update_transformation(self):
"""Checks if PyMOL object matrix has changed and updates self, if so."""
try:
if cmd.get_title(*Registry.get(self.attachment.main_object, "name", "state")) == "PD":
matrix = cmd.get_object_matrix(Registry.get(self.attachment.main_object, "name"))
self.reset()
self.add_rotation([matrix[:3], matrix[4:7], matrix[8:11]])
self.add_translation([matrix[3], matrix[7], matrix[11]])
self.add_prerotational_translation(list(matrix[12:15]))
except AttributeError:
return
def testGetObjectMatrix(self):
identity = (1.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0,
0.0, 0.0, 0.0, 1.0)
mat_x90 = (1.0, 0.0, 0.0, 0.0, 0.0, 0.0, -1.0, 0.0, 0.0, 1.0, 0.0, 0.0,
0.0, 0.0, 0.0, 1.0)
cmd.fragment('ala', 'm1')
cmd.fragment('gly', 'm2')
# default/identity
mat = cmd.get_object_matrix('m1', incl_ttt=1)
self.assertTrue(isinstance(mat, tuple))
self.assertArrayEqual(mat, identity, delta=1e-6)
mat = cmd.get_object_matrix('m1', incl_ttt=0)
self.assertArrayEqual(mat, identity, delta=1e-6)
# TTT
cmd.rotate('x', 90, object='m1', camera=0, object_mode=0)
mat = cmd.get_object_matrix('m1', incl_ttt=1)
self.assertArrayEqual(mat, mat_x90, delta=1e-6)
mat = cmd.get_object_matrix('m1', incl_ttt=0)
self.assertArrayEqual(mat, identity, delta=1e-6)
# state matrix
cmd.rotate('x', 90, object='m2', camera=0, object_mode=1)
mat = cmd.get_object_matrix('m2', incl_ttt=1)
self.assertArrayEqual(mat, mat_x90, delta=1e-6)
mat = cmd.get_object_matrix('m2', incl_ttt=0)
self.assertArrayEqual(mat, mat_x90, delta=1e-6)
def transf_matrix(chA, chB):
'''
DESCRIPTION
Align two selections/chains, and returns the transformation matrix. I used super to carry out the alignment, likely is possible to use cmd.align and
is going to be a bit faster, but I think is not going to work well with low-sequence-identity alignments.
'''
cmd.create('working', chA)
cmd.super('working', chB)
T = cmd.get_object_matrix('working')
global cmW
cmW = center_of_Mass('working')
cmd.delete('working')
return T
def transf_matrix(chA, chB):
'''
DESCRIPTION
Align two selections/chains, and returns the transformation matrix. I used super to carry out the alignment, likely is possible to use cmd.align and
is going to be a bit faster, but I think is not going to work well with low-sequence-identity alignments.
'''
cmd.create('working', chA)
cmd.super('working', chB)
T = cmd.get_object_matrix('working')
global cmW
cmW = center_of_Mass('working')
cmd.delete('working')
return T
def matrix_to_ttt(names, reverse=0, state=-1, quiet=1):
'''
DESCRIPTION
Objects can have state matrices and view (frames) matrices. This function
takes the total matrix and stores it either as view matrix or as state
matrix (reverse=1). For movie frames, movie_auto_store must be set.
'''
from . import querying
reverse, state, quiet = int(reverse), int(state), int(quiet)
ostate = state
for object in cmd.get_object_list('(' + names + ')'):
if ostate < 1:
state = querying.get_object_state(object)
matrix = cmd.get_object_matrix(object, state)
cmd.matrix_reset(object)
if reverse:
cmd.reset(object)
cmd.transform_object(object, matrix, homogenous=1)
else:
cmd.set_object_ttt(object, matrix)
def matrix_to_ttt(names, reverse=0, state=-1, quiet=1):
'''
DESCRIPTION
Objects can have state matrices and view (frames) matrices. This function
takes the total matrix and stores it either as view matrix or as state
matrix (reverse=1). For movie frames, movie_auto_store must be set.
'''
from . import querying
reverse, state, quiet = int(reverse), int(state), int(quiet)
ostate = state
for object in cmd.get_object_list('(' + names + ')'):
if ostate < 1:
state = querying.get_object_state(object)
matrix = cmd.get_object_matrix(object, state)
for i in range(cmd.count_states(object)):
cmd.matrix_reset(object, i + 1)
if reverse:
cmd.reset(object)
cmd.transform_object(object, matrix, homogenous=1)
else:
cmd.set_object_ttt(object, matrix)
def test(self):
cmd.pseudoatom('m1')
cmd.mset('1x1')
cmd.create('m2', 'm1')
cmd.ray()
v = cmd.get_object_matrix('m2')
self.assertArrayEqual(v, [
1.,
0.,
0.,
0.,
0.,
1.,
0.,
0.,
0.,
0.,
1.,
0.,
0.,
0.,
0.,
1.,
], 0.001, 'object matrix not identity')
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 alignlattice(
target,
mobile,
a,
b,
c,
color1="blue",
color2="red",
name1="supercell1",
name2="supercell2",
prefix1="m",
prefix2="n",
withmates=1,
cutoff=None,
):
"""
DESCRIPTION
Align two lattices. This facilitates the comparison of lattice contacts.
USAGE
alignlattice target, mobile, a, b, c, [color1/2, name1/2, prefix1/2, withmates, cutoff]
ARGUMENTS
target = string: name of object to generate the first lattice. This lattice
is generated aligned to the original coordinates.
mobile = string: name of the second object. The generated lattice will
align to the original object.
a, b, c = integer: repeat cell in x,y,z direction a,b,c times
{default: 1,1,1}
color1/2 = string: color of unit cell cgo objects {default: blue/red}
name1/2 = string: name of the cgo object to create {default: supercell1/2}
prefix1/2 = string: prefix for the symmetry mates {default: m/n}
withmates = bool: also create symmetry mates in displayed cells
{default: 1}
cutoff = int: restrict symmetry mates to within cutoff angstroms of the origin.
Use 0 to generate all symmetry mates. {default: 0}
SEE ALSO
show cell
cmd
"""
# Check that selections contain a single object each
mobileobj = "(byobj (%s))" % mobile
targetobj = "(byobj (%s))" % target
if len(cmd.get_object_list(mobileobj)) != 1:
print("Expected single object for %s" % mobile)
return
if len(cmd.get_object_list(targetobj)) != 1:
print("Expected single object for %s" % target)
return
mobilecopy = "mobile2823" # todo use unique name
# Copy the mobile unit and get its superposition with the target
cmd.create(mobilecopy, mobile)
initial_mat = cmd.get_object_matrix(mobilecopy)
cmd.super(mobilecopy, target)
final_mat = cmd.get_object_matrix(mobilecopy)
cmd.delete(mobilecopy)
# TODO handle non-identity initial matrix
orig_objects = set(cmd.get_object_list())
# Generate primary grid
supercell(
a,
b,
c,
targetobj,
color=color1,
name=name1,
withmates=withmates,
prefix=prefix1,
center=1,
transformation=None,
cutoff=cutoff,
)
# Generate rotated grid
supercell(
a,
b,
c,
mobileobj,
color=color2,
name=name2,
withmates=withmates,
prefix=prefix2,
center=1,
transformation=final_mat,
cutoff=cutoff,
)
colored_objects1 = set(cmd.get_object_list("(%s*)" % prefix1)) - orig_objects
colored_objects2 = set(cmd.get_object_list("(%s*)" % prefix2)) - orig_objects
for obj in colored_objects1:
cmd.color(color1, obj)
for obj in colored_objects2:
cmd.color(color2, obj)
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 biomolecule(name=None,
filename=None,
prefix=None,
number=1,
suffix=None,
quiet=0):
'''
DESCRIPTION
Create biological unit (quaternary structure) as annotated by the REMARK
350 BIOMOLECULE record.
USAGE
biomolecule name [, filename [, prefix [, number ]]]
ARGUMENTS
name = string: name of object and basename of PDB file, if
filename is not given {default: first loaded object}
filename = string: file to read remarks from {default: <name>.pdb}
prefix = string: prefix for new objects {default: <name>}
EXAMPLE
fetch 1rmv, async=0
biomolecule 1rmv
'''
import os
from .importing import local_mirror_pdb
try:
import numpy
except ImportError:
numpy = None
number, quiet = int(number), int(quiet)
if name is None:
name = cmd.get_object_list()[0]
if prefix is None:
prefix = name
if suffix is None:
suffix = str(number)
if filename is None:
candidates = [
'%s.pdb' % (name),
'%s/%s.pdb' % (cmd.get('fetch_path'), name),
local_mirror_pdb(name),
]
for filename in candidates:
if os.path.exists(filename):
break
else:
print('please provide filename')
raise CmdException
if not quiet:
print('loading from %s' % (filename))
remarks = pdbremarks(filename)
if 350 not in remarks:
print('There is no REMARK 350 in ' + filename)
raise CmdException
current = 1
biomt = {current: {}}
chains = tuple()
for line in remarks[350]:
if line.startswith('BIOMOLECULE:'):
current = int(line[12:])
biomt[current] = {}
elif line.startswith('APPLY THE FOLLOWING TO CHAINS:'):
chains = tuple(chain.strip() for chain in line[30:].split(','))
elif line.startswith(' AND CHAINS:'):
chains += tuple(chain.strip() for chain in line[30:].split(','))
elif line.startswith(' BIOMT'):
row = int(line[7])
num = int(line[8:12])
vec = line[12:].split()
vec = list(map(float, vec))
biomt[current].setdefault(chains,
dict()).setdefault(num, []).extend(vec)
if number not in biomt or len(biomt[number]) == 0:
print(' Error: no BIOMOLECULE number %d' % (number))
raise CmdException
if numpy is not None:
mat_source = numpy.reshape(cmd.get_object_matrix(name), (4, 4))
mat_source = numpy.matrix(mat_source)
for chains, matrices in biomt[number].items():
for num in matrices:
mat = matrices[num][0:12]
mat.extend([0, 0, 0, 1])
copy = '%s_%s_%d' % (prefix, suffix, num)
if not quiet:
print('creating %s' % (copy))
cmd.create(copy,
'model %s and chain %s' % (name, '+'.join(chains)))
cmd.alter(copy, 'segi="%d"' % (num))
if numpy is not None:
mat = mat_source * numpy.reshape(mat, (4, 4)) * mat_source.I
mat = list(mat.flat)
cmd.transform_object(copy, mat)
cmd.disable(name)
cmd.group('%s_%s' % (prefix, suffix), '%s_%s_*' % (prefix, suffix))
def biomolecule(name=None, filename=None, prefix=None, number=1, suffix=None,
quiet=0):
'''
DESCRIPTION
Create biological unit (quaternary structure) as annotated by the REMARK
350 BIOMOLECULE record.
USAGE
biomolecule name [, filename [, prefix [, number ]]]
ARGUMENTS
name = string: name of object and basename of PDB file, if
filename is not given {default: first loaded object}
filename = string: file to read remarks from {default: <name>.pdb}
prefix = string: prefix for new objects {default: <name>}
EXAMPLE
fetch 1rmv, async=0
biomolecule 1rmv
'''
import os
from .importing import local_mirror_pdb
try:
import numpy
except ImportError:
numpy = None
number, quiet = int(number), int(quiet)
if name is None:
name = cmd.get_object_list()[0]
if prefix is None:
prefix = name
if suffix is None:
suffix = str(number)
if filename is None:
candidates = [
'%s.pdb' % (name),
'%s/%s.pdb' % (cmd.get('fetch_path'), name),
local_mirror_pdb(name),
]
for filename in candidates:
if os.path.exists(filename):
break
else:
print('please provide filename')
raise CmdException
if not quiet:
print('loading from %s' % (filename))
remarks = pdbremarks(filename)
if 350 not in remarks:
print('There is no REMARK 350 in', filename)
raise CmdException
current = 1
biomt = {current: {}}
chains = tuple()
for line in remarks[350]:
if line.startswith('BIOMOLECULE:'):
current = int(line[12:])
biomt[current] = {}
elif line.startswith('APPLY THE FOLLOWING TO CHAINS:'):
chains = tuple(chain.strip() for chain in line[30:].split(','))
elif line.startswith(' AND CHAINS:'):
chains += tuple(chain.strip() for chain in line[30:].split(','))
elif line.startswith(' BIOMT'):
row = int(line[7])
num = int(line[8:12])
vec = line[12:].split()
vec = list(map(float, vec))
biomt[current].setdefault(chains, dict()).setdefault(num, []).extend(vec)
if number not in biomt or len(biomt[number]) == 0:
print(' Error: no BIOMOLECULE number %d' % (number))
raise CmdException
if numpy is not None:
mat_source = numpy.reshape(cmd.get_object_matrix(name), (4,4))
mat_source = numpy.matrix(mat_source)
for chains, matrices in biomt[number].items():
for num in matrices:
mat = matrices[num][0:12]
mat.extend([0,0,0,1])
copy = '%s_%s_%d' % (prefix, suffix, num)
if not quiet:
print('creating %s' % (copy))
cmd.create(copy, 'model %s and chain %s' % (name, '+'.join(chains)))
cmd.alter(copy, 'segi="%d"' % (num))
if numpy is not None:
mat = mat_source * numpy.reshape(mat, (4,4)) * mat_source.I
mat = list(mat.flat)
cmd.transform_object(copy, mat)
cmd.disable(name)
cmd.group('%s_%s' % (prefix, suffix), '%s_%s_*' % (prefix, suffix))
def __call__(self):
# 1st check for a dockeye action flag
de_action = 'none'
mark_number = 0
do_mm = True
try:
actionfile = open('dockeye_action', 'r')
line = actionfile.readline()
fields = line.split()
de_action = fields[0]
mark_number = int(fields[1])
actionfile.close()
os.system('/bin/rm -f dockeye_action')
#print(de_action,mark_number)
except:
#
de_action = 'none'
mark_number = 0
# get view on screen
my_view = cmd.get_view()
delta_mv = 0.
for i in range(18):
delta_mv = max(delta_mv, abs(my_view[i] - self.my_view[i]))
self.my_view[i] = my_view[i]
#print my_view
# get orientation/position matrices for two molecules
# how does pymol define rotation center of molecule?
# apparnetly by geometric average
pdbmat1 = cmd.get_object_matrix(self.pdbobj1)
pdbmat2 = cmd.get_object_matrix(self.pdbobj2)
#
if (de_action == 'mark'):
# write bookmark
print('bookmarking... ', mark_number)
et = self.energy[0]
ee = self.energy[1]
ev = self.energy[2]
print('current energies: %12.5g %12.5g %12.5g model %4d \n' %
(ee, ev, et, self.nbest[0]))
#mark_prt = 'dockeye_prt_mark_%d.pdb' % (mark_number)
mark_lig = 'dockeye_lig_mark_%d.pdb' % (mark_number)
ligfile = open(mark_lig, 'w')
ligfile.write('REMARK pdbfile 1: ' + self.pdbfile1 + '\n')
ligfile.write('REMARK pdbfile 2: ' + self.pdbfile2 + '\n')
ligfile.write('REMARK # of atoms 1: %6d 2: %6d\n' %
(self.pdb1.natom, self.pdb2.natom))
ligfile.write('REMARK geometric centers: \n')
ligfile.write('REMARK 1: %8.3f %8.3f %8.3f \n' %
(self.gcen1[0], self.gcen1[1], self.gcen1[2]))
ligfile.write('REMARK 2: %8.3f %8.3f %8.3f \n' %
(self.gcen2[0], self.gcen2[1], self.gcen2[2]))
ligfile.write('REMARK net charge 1: %8.3f 2: %8.3f \n' %
(self.qtot1, self.qtot2))
ligfile.write(
'REMARK energy parameters dielectric: blank VDW depth: blank\n'
)
ligfile.write('REMARK # of ligand conformers: %6d\n' %
(self.pdb2.nmodel))
ligfile.write(
'REMARK current energies: %12.5g %12.5g %12.5g model %4d \n' %
(ee, ev, et, self.nbest[0]))
for i in range(4):
for j in range(4):
indx = j + 4 * i
ligfile.write('REMARK %12.5f ' % (pdbmat1[indx]))
ligfile.write('\n')
for i in range(4):
for j in range(4):
indx = j + 4 * i
ligfile.write('REMARK %12.5f ' % (pdbmat2[indx]))
ligfile.write('\n')
#
# extract rot
rmtp = [[pdbmat1[0], pdbmat1[1], pdbmat1[2]],
[pdbmat1[4], pdbmat1[5], pdbmat1[6]],
[pdbmat1[8], pdbmat1[9], pdbmat1[10]]]
rmtl = [[pdbmat2[0], pdbmat2[1], pdbmat2[2]],
[pdbmat2[4], pdbmat2[5], pdbmat2[6]],
[pdbmat2[8], pdbmat2[9], pdbmat2[10]]]
#
# extract trans
trnp = [pdbmat1[3], pdbmat1[7], pdbmat1[11]]
trnl = [pdbmat2[3], pdbmat2[7], pdbmat2[11]]
#
# apply transrot to coords
# write out transrot to temporary pdb files
gcenp_rot = rot_vec(rmtp, self.gcen1)
gcenl_rot = rot_vec(rmtl, self.gcen2)
for k in range(3):
trnp[k] = trnp[k] - (self.gcen1[k] - gcenp_rot[k])
trnl[k] = trnl[k] - (self.gcen2[k] - gcenl_rot[k])
i1 = 0
#print(rmtp,trnp)
#print(rmtl,trnl)
xyz = [0., 0., 0.]
tmpfile = 'dockeye_lig_tmp.pdb'
for n in range(self.pdb2.nmodel):
ligfile.write('MODEL%4d \n' % (n + 1))
for i in range(self.pdb2.natom):
#
# apply rotations and translations
# and inverse of protein rot/trans to ligand
# in case user moved protein too- now ligand should be in
# coord frame of original protein pdb
for k in range(3):
xyz[k] = self.pdb2.coords[i1][k] - self.gcen2[k]
xyz1 = rot_vec(rmtl, xyz)
for k in range(3):
xyz[k] = xyz1[k] + self.gcen2[k] + trnl[
k] - self.gcen1[k] - trnp[k]
xyz2 = rot_vec(rmtp, xyz, inv=1)
for k in range(3):
xyz[k] = xyz2[k] + self.gcen1[k]
string = 'ATOM %6d%6s%4s%1s%4s %8.3f%8.3f%8.3f%6.2f%7.3f \n' \
% (i,self.pdb2.name[i],self.pdb2.res[i], \
self.pdb2.chain[i], self.pdb2.resnum[i], xyz[0],xyz[1],xyz[2], \
self.pdb2.radius[i],self.pdb2.bfact[i])
ligfile.write(string)
i1 += 1
ligfile.write('ENDMDL\n')
ligfile.close()
mark_pml = 'dockeye_mark_%d.pml' % (mark_number)
pmlfile = open(mark_pml, 'w')
pmlfile.write(
'#------------------------------------------------\n')
pmlfile.write('run $HOME/source/dockeye_multi/src/dockeyeM_c.py\n')
pmlfile.write('de("%s","%s")\n' % (self.pdbfile1, mark_lig))
pmlfile.write('#optional view settings\n')
pmlfile.write('hide lines\n')
pmlfile.write('spectrum b, red_white_blue\n')
pmlfile.write('show sticks, dockeye_lig\n')
pmlfile.write('show surface, dockeye_prt\n')
pmlfile.write('set transparency, 0.4\n')
pmlfile.write(
'#------------------------------------------------\n')
pmlfile.close()
# done with bookmarking
#
# check for new view or pose
#
delta_mm = 0.
for i in range(12):
delta_mm = max(delta_mm, abs(pdbmat1[i] - self.objmat1[i]))
delta_mm = max(delta_mm, abs(pdbmat2[i] - self.objmat2[i]))
self.objmat1[i] = pdbmat1[i]
self.objmat2[i] = pdbmat2[i]
if (delta_mm >
0.01): # we only do expensive energy calc if pose changed
do_mm = True
else:
do_mm = False
if ((delta_mv > 0.01)
or do_mm): # we only update if pose or view changed
cgo_obj = pdb_interaction(pdbmat1, pdbmat2, self.pdb1, self.pdb2,
self.gcen1, self.gcen2, self.energy,
do_mm, self.logscale, self.dielectric,
self.eps, self.nbest, self.energy_min)
if (self.nbest[0] != self.nbest[1]):
# print('Switching models ',self.nbest)
self.nbest[1] = self.nbest[0]
#
# write new best pose to logfile
#
et = self.energy[0]
ee = self.energy[1]
ev = self.energy[2]
if (self.energy[0] < self.energy_min):
print(
' NEW MIN ee: %12.3g ev: %12.3g et: %12.3g model %4d '
% (ee, ev, et, self.nbest[0]))
self.energy_min = et
self.dockeye_log.write(
'new min: %12.5g %12.5g %12.5g model %4d \n' %
(ee, ev, et, self.nbest[0]))
for i in range(4):
for j in range(4):
indx = j + 4 * i
self.dockeye_log.write('%12.5f ' % (pdbmat1[indx]))
self.dockeye_log.write('\n')
for i in range(4):
for j in range(4):
indx = j + 4 * i
self.dockeye_log.write('%12.5f ' % (pdbmat2[indx]))
self.dockeye_log.write('\n')
#else:
# if(do_mm):
# #print('Current energy: ee: %12.3g ev: %12.3g et: %12.3g' % (ee,ev,et))
# continue
if (do_mm):
cmd.delete('dockeye_obj')
cmd.load_cgo(cgo_obj, 'dockeye_obj')
draw_ligand(pdbmat2, self.pdb2, self.gcen2, self.nbest[0])