def change_bfactors(bfactors):
"""Modify bfactors based on spatial location.
Due to inconsistencies in the indexing of atoms, residues and chains
between openbabel, plip and pymol, we must use coordinates to
identify atoms.
Arguments:
bfactors: dict of dict of dicts with the mapping:
x: y: z: value
where value is the number we wish to assign to the atom (as the
b-factor) for labelling. The x, y and z coordinates should be
in the format of strings, with 1 decimal place to avoid
problems with comparing floats (use '{:.1f}.format(<coord>).
"""
def modify_bfactor(x, y, z):
"""Return b factor given the x, y, z coordinates."""
x, y, z = ['{:.3f}'.format(coord) for coord in (x, y, z)]
bfactor = bfactors[x][y][z]
return bfactor
space = {'modify_bfactor': modify_bfactor}
cmd.alter_state(0,
'(all)',
'b=modify_bfactor(x, y, z)',
space=space,
quiet=True)
def testNumeric(self):
cmd.fragment('ala')
cmd.alter_state(1, 'all', 'p.x, p.y, p.index = x, y, index')
cmd.select('sele_p_x', 'p.x < 0')
cmd.select('sele_p_y', 'p.y > 0')
cmd.select('sele_p_i', 'p.index = 3')
cmd.select('sele_x', 'x < 0.0')
cmd.select('sele_y', 'y > 0.0')
cmd.select('sele_i', 'index 3')
counts = [
cmd.count_atoms('sele_p_x'),
cmd.count_atoms('sele_x'),
cmd.count_atoms('sele_x & sele_p_x'),
]
self.assertEqual(counts[0], 8)
self.assertEqual(counts[0], counts[1])
self.assertEqual(counts[0], counts[2])
counts = [
cmd.count_atoms('sele_p_y'),
cmd.count_atoms('sele_y'),
cmd.count_atoms('sele_y & sele_p_y'),
]
self.assertEqual(counts[0], 6)
self.assertEqual(counts[0], counts[1])
self.assertEqual(counts[0], counts[2])
counts = [
cmd.count_atoms('sele_i'),
cmd.count_atoms('sele_p_i'),
cmd.count_atoms('sele_i & sele_p_i'),
]
self.assertEqual(counts[0], 1)
self.assertEqual(counts[0], counts[1])
self.assertEqual(counts[0], counts[2])
def simulation():
import traceback
try:
while 1:
for part in particle:
# simplistic Euler intergration
# p = p + v
part[1] = (half_box + part[1] + part[5]) % box_size - half_box
part[2] = (half_box + part[2] + part[6]) % box_size - half_box
part[3] = (half_box + part[3] + part[7]) % box_size - half_box
# v = v + pseudo-gravitational acceleration
factor = max(0.1 * box_size,
0.1 * (part[1]**2 + part[2]**2 + part[3]**2)**1.5)
part[5] = part[5] - part[1] / factor
part[6] = part[6] - part[2] / factor
part[7] = part[7] - part[3] / factor
cmd.alter_state(1,
"cloud",
"(x,y,z) = particle[int(resi)][1:4]",
space=globals())
cmd.refresh()
except:
traceback.print_exc()
def testStereo(self):
cmd.fragment('ala')
cmd.remove('hydro')
# default: S configuration
labels = []
cmd.iterate('name CA', 'labels.append(stereo)', space=locals())
self.assertEqual(labels, ['S'])
# load R configuration (moves CB)
ala_conf_R = {
'N': (-0.67690, -1.23030, -0.49050),
'CA': (-0.00090, 0.06370, -0.49050),
'C': (1.49910, -0.11030, -0.49050),
'O': (2.03010, -1.22730, -0.50150),
# 'CB' : (-0.50890, 0.85570, 0.72650), # S configuration
'CB': (-0.33784, 0.82664, -1.78310), # R configuration
}
cmd.alter_state(1,
'ala',
'(x,y,z) = ala_conf_R.get(name)',
space=locals())
labels = []
cmd.iterate('name CA', 'labels.append(stereo)', space=locals())
self.assertEqual(labels, ['R'])
def superpose(self):
#get the position of the selected residue's O atom
stored.xyz = []
if self.currentLabel.modifiedAA:
cmd.iterate_state(1, "%s & name O" % self.residue1Name,
"stored.xyz.append([x,y,z])")
args = []
i = 0
while i < len(self.currentLabel.atomsForSuperposition):
args.append(
"%s & name %s" %
("currentLabel", self.currentLabel.atomsForSuperposition[i]))
args.append("%s & name %s" %
(self.residue1Name,
self.currentLabel.atomsForSuperposition[i]))
i += 1
#print args
if apply(cmd.pair_fit, args):
#set the label's O atom to the stored position
if self.currentLabel.modifiedAA:
cmd.alter_state(1, "%s & name O" % "currentLabel",
"(x,y,z)=stored.xyz.pop(0)")
return True
else:
return False
def simulation():
import traceback
try:
while 1:
for part in particle:
# simplistic Euler intergration
# p = p + v
part[1] = (half_box + part[1] + part[5]) % box_size - half_box
part[2] = (half_box + part[2] + part[6]) % box_size - half_box
part[3] = (half_box + part[3] + part[7]) % box_size - half_box
# v = v + pseudo-gravitational acceleration
factor = max(0.1 * box_size, 0.1 * (part[1] ** 2 + part[2] ** 2 + part[3] ** 2) ** 1.5)
part[5] = part[5] - part[1] / factor
part[6] = part[6] - part[2] / factor
part[7] = part[7] - part[3] / factor
cmd.alter_state(1, "cloud", "(x,y,z) = particle[int(resi)][1:4]", space=globals())
cmd.refresh()
except:
traceback.print_exc()
def sculpt(self,cleanup=0):
if not cleanup:
cmd.set("suspend_updates",1,quiet=1)
cmd.disable()
cmd.delete("sculpt")
cmd.set("sphere_scale","1.0")
cmd.set("sphere_mode",5)
cmd.load("$PYMOL_DATA/demo/pept.pdb","sculpt")
cmd.hide("lines","sculpt")
# cmd.show("sticks","sculpt")
cmd.show("spheres","sculpt")
# cmd.set("sphere_transparency","0.75","sculpt")
# cmd.set("sphere_color","grey","sculpt")
cmd.frame(1)
cmd.set("auto_sculpt",1)
cmd.set("sculpting",1)
cmd.sculpt_activate("sculpt")
cmd.set("sculpting_cycles","100")
cmd.do("edit_mode")
cmd.set("valence","0.05")
cmd.set("suspend_updates",0,quiet=0)
cmd.sculpt_iterate("sculpt")
cmd.alter_state(1,"sculpt","x=x*1.5;y=y*0.1;z=z*1.5")
cmd.zoom()
cmd.unpick()
else:
cmd.set("valence","0")
cmd.set("sculpting",0)
cmd.set("auto_sculpt",0)
cmd.delete("sculpt")
cmd.mouse()
def testAlterState(self):
cmd.fragment('ala')
cmd.create('ala', 'ala', 1, 2)
v_count = cmd.count_atoms('all')
v_mock = [
list(map(float, list(range(i * 3, (i + 1) * 3))))
for i in range(v_count)
]
v_xyz_1_pre = cmd.get_model('all', state=1).get_coord_list()
v_xyz_2_pre = cmd.get_model('all', state=2).get_coord_list()
cmd.alter_state(2,
'all',
'(x,y,z) = next(xyz_iter)',
space={
'xyz_iter': iter(v_mock),
'next': next
})
v_xyz_1_post = cmd.get_model('all', state=1).get_coord_list()
v_xyz_2_post = cmd.get_model('all', state=2).get_coord_list()
self.assertEqual(v_xyz_1_post, v_xyz_1_pre)
self.assertEqual(v_xyz_2_post, v_mock)
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 sculpt(self, cleanup=0):
if not cleanup:
cmd.set("suspend_updates", 1, quiet=1)
cmd.disable()
cmd.delete("sculpt")
cmd.set("sphere_scale", "1.0")
cmd.set("sphere_mode", 5)
cmd.load("$PYMOL_DATA/demo/pept.pdb", "sculpt")
cmd.hide("lines", "sculpt")
# cmd.show("sticks","sculpt")
cmd.show("spheres", "sculpt")
# cmd.set("sphere_transparency","0.75","sculpt")
# cmd.set("sphere_color","grey","sculpt")
cmd.frame(1)
cmd.set("auto_sculpt", 1)
cmd.set("sculpting", 1)
cmd.sculpt_activate("sculpt")
cmd.set("sculpting_cycles", "100")
cmd.do("edit_mode")
cmd.set("valence", "0.05")
cmd.set("suspend_updates", 0, quiet=0)
cmd.sculpt_iterate("sculpt")
cmd.alter_state(1, "sculpt", "x=x*1.5;y=y*0.1;z=z*1.5")
cmd.zoom()
cmd.unpick()
else:
cmd.set("valence", "0")
cmd.set("sculpting", 0)
cmd.set("auto_sculpt", 0)
cmd.delete("sculpt")
cmd.mouse()
def cell_shift(object, dX, dY, dZ, rename=1):
if rename:
oldName = object.split("_")
oldPre = oldName[0]
oldX = int(oldName[1])
oldY = int(oldName[2])
oldZ = int(oldName[3])
newX = "_" + str(int(dX) + oldX)
newY = "_" + str(int(dY) + oldY)
newZ = "_" + str(int(dZ) + oldZ)
newName = oldPre + newX + newY + newZ
#if cmd.get_names().find(newName) != -1:
# print "Symmetry partner already exists in destination position!"
# quit()
cmd.set_name(object, newName)
object = newName
stored.shift = [float(dX), float(dY), float(dZ)]
stored.sgInfo = cmd.get_symmetry(object)
a, b, c, alpha, beta, gamma = stored.sgInfo[0:6]
ca = math.cos(math.radians(alpha))
cb = math.cos(math.radians(beta))
cg = math.cos(math.radians(gamma))
sb = math.sin(math.radians(beta))
sg = math.sin(math.radians(gamma))
stored.fracToOrt = N.array(
[[a, b * cg, c * cb], [0.0, b * sg, c * (ca - cb * cg) / sg],
[0.0, 0.0,
c * sb * math.sqrt(1.0 - ((cb * cg - ca) / (sb * sg))**2)]])
stored.fracToOrt = stored.fracToOrt.transpose()
stored.ortToFrac = inv(stored.fracToOrt)
cmd.cell_shift_helper = cell_shift_helper
cmd.alter_state(1, object,
"x,y,z = cmd.cell_shift_helper([x,y,z],stored.shift)")
def cell_shift(object, dX, dY, dZ, rename = 1):
if rename:
oldName = object.split("_")
oldPre = oldName[0]
oldX = int(oldName[1])
oldY = int(oldName[2])
oldZ = int(oldName[3])
newX = "_" + str(int(dX) + oldX)
newY = "_" + str(int(dY) + oldY)
newZ = "_" + str(int(dZ) + oldZ)
newName = oldPre + newX + newY + newZ
#if cmd.get_names().find(newName) != -1:
# print "Symmetry partner already exists in destination position!"
# quit()
cmd.set_name(object, newName)
object = newName
stored.shift = [float(dX),float(dY),float(dZ)]
stored.sgInfo = cmd.get_symmetry(object)
a,b,c,alpha,beta,gamma = stored.sgInfo[0:6]
ca = math.cos(math.radians(alpha))
cb = math.cos(math.radians(beta))
cg = math.cos(math.radians(gamma))
sb = math.sin(math.radians(beta))
sg = math.sin(math.radians(gamma))
stored.fracToOrt = N.array([[a, b * cg, c * cb],
[0.0, b * sg, c * (ca - cb * cg) / sg],
[0.0, 0.0, c * sb * math.sqrt(1.0 - ((cb * cg - ca) / (sb * sg))**2)]])
stored.fracToOrt = stored.fracToOrt.transpose()
stored.ortToFrac = inv(stored.fracToOrt)
cmd.cell_shift_helper = cell_shift_helper
cmd.alter_state(1, object, "x,y,z = cmd.cell_shift_helper([x,y,z],stored.shift)")
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 test_atom_state_settings_3f(self, f, data):
m1 = "pseudo01"
lp1, lp2 = lp = map(f, data)
cmd.pseudoatom(m1)
cmd.pseudoatom(m1)
cmd.create(m1, m1, 1, 2)
stored.pos = {}
stored.lp1 = lp1
stored.lp2 = lp2
stored.origp = None
# get origp (should be 0.,0.,0.
cmd.alter("(index 1)", "stored.origp = s['label_placement_offset']")
# change atom-state setting to lp1 for atom in both states
cmd.alter_state(0, "(index 1)", "s['label_placement_offset']=stored.lp1")
# change atom-level setting for all atoms to something else
cmd.alter("all", "s['label_placement_offset']=stored.lp2")
# get atom-state settings
cmd.iterate_state(0, "all", "stored.pos['%s-%s-%s' % (model, state, index)]=s['label_placement_offset']")
# atom-state setting should be lp1 for atom 1
self.assertEqual(tuple(lp1), stored.pos['%s-%s-%s' % (m1, 1, 1)])
self.assertEqual(tuple(lp1), stored.pos['%s-%s-%s' % (m1, 2, 1)])
# atom setting should override to lp2 for atom 2 in both states
self.assertEqual(tuple(lp2), stored.pos['%s-%s-%s' % (m1, 1, 2)])
self.assertEqual(tuple(lp2), stored.pos['%s-%s-%s' % (m1, 2, 2)])
# unset all atom-level settings, atom-state settings should still exist
cmd.alter("all", "s['label_placement_offset']=None")
stored.pos = {}
cmd.iterate_state(0, "all", "stored.pos['%s-%s-%s' % (model, state, index)]=s['label_placement_offset']")
self.assertEqual(tuple(lp1), stored.pos['%s-%s-%s' % (m1, 1, 1)])
self.assertEqual(tuple(lp1), stored.pos['%s-%s-%s' % (m1, 2, 1)])
self.assertEqual(tuple(stored.origp), stored.pos['%s-%s-%s' % (m1, 1, 2)])
self.assertEqual(tuple(stored.origp), stored.pos['%s-%s-%s' % (m1, 2, 2)])
def update(self):
self.center = cmd.get_position()
cmd.alter_state(0,
self.center_name,
"(x, y, z) = p",
space={'p': self.center})
cmd.isomesh(self.name,
self.map_name,
self.level,
self.center_name,
carve=self.radius)
def update_structure(pose_name):
'''Update the structure of the pose.'''
pose = poses[pose_name]
for i in range(1, pose.size() + 1):
for j in range(1, pose.residue(i).natoms() + 1):
name = pose.residue(i).atom_name(j)
xyz = pose.residue(i).xyz(j)
cmd.alter_state(
1, '{0} and res {1} and n. {2}'.format(pose_name, i, name),
'(x, y, z)=({0}, {1}, {2})'.format(xyz.x, xyz.y, xyz.z))
def testAtomStateLevelSettingsOnRemove(self):
if cmd.get_setting_int('suspend_undo'):
self.skipTest("need suspend_undo=0")
cmd.load(self.datafile("1molecule.mae"))
cmd.load(self.datafile("1molecule.mae"))
cmd.label("index 10", "'Test Label'")
plv = [ 5., 0., 0.]
cmd.alter_state(1, "index 10", "s.label_placement_offset = %s" % plv)
cmd.remove("index 10")
cmd.undo()
stored.offset = None
cmd.iterate_state(1, "index 10", "stored.offset = list(s.label_placement_offset)")
self.assertEqual(stored.offset, plv)
def testAlterState(self):
self.load_big_example_multistate()
v_count = cmd.count_atoms() * cmd.count_states()
assert v_count > 10**5
xyz = []
with self.timing('i', 5.0):
cmd.iterate_state(0, 'all', 'xyz.append((x,y,z))', space=locals())
self.assertEqual(v_count, len(xyz))
with self.timing('a', 5.0):
cmd.alter_state(0, 'all', '(x,y,z) = next(xyz_rev)',
space={'xyz_rev': reversed(xyz), 'next': next})
cmd.iterate_state(0, 'last all', 'stored.xyz = (x,y,z)')
self.assertEqual(stored.xyz, xyz[0])
def createRotamerInPymol(self, rotamer, ensembleName):
atomNames = self.currentLabel.atomNames
for atomName in atomNames:
thisAtom = rotamer.atoms[atomName]
stored.xyz = []
stored.xyz = thisAtom.coordinate
try:
cmd.alter_state(1,
"%s & name %s " % ("currentLabel", atomName),
"(x,y,z)=stored.xyz")
except:
print "Could not alter coordinate"
cmd.alter("%s & name %s " % ("currentLabel", atomName),
"segi='%s'" % self.currentLabel.uid)
cmd.create(
"%s_%s_%s" %
(self.residue1Name, self.currentLabel.identifier, ensembleName),
"currentLabel", 1, rotamer.id + 1)
def testAlterState(self):
cmd.fragment('ala')
cmd.create('ala', 'ala', 1, 2)
v_count = cmd.count_atoms('all')
v_mock = [list(map(float, list(range(i*3, (i+1)*3)))) for i in range(v_count)]
v_xyz_1_pre = cmd.get_model('all', state=1).get_coord_list()
v_xyz_2_pre = cmd.get_model('all', state=2).get_coord_list()
cmd.alter_state(2, 'all', '(x,y,z) = next(xyz_iter)',
space={'xyz_iter': iter(v_mock), 'next': next})
v_xyz_1_post = cmd.get_model('all', state=1).get_coord_list()
v_xyz_2_post = cmd.get_model('all', state=2).get_coord_list()
self.assertEqual(v_xyz_1_post, v_xyz_1_pre)
self.assertEqual(v_xyz_2_post, v_mock)
def COM(selection='all', center=0, quiet=1):
model = cmd.get_model(selection)
nAtom = len(model.atom)
COM = cpv.get_null()
for a in model.atom:
COM = cpv.add(COM, a.coord)
COM = cpv.scale(COM, 1./nAtom)
if not int(quiet):
print ' COM: [%8.3f,%8.3f,%8.3f]' % tuple(COM)
if int(center):
cmd.alter_state(1, selection, "(x,y,z)=sub((x,y,z), COM)",
space={'COM': COM, 'sub': cpv.sub})
return COM
def simulation():
state = 1
import traceback
try:
while state < n_states:
state = state + 1
for part in particle:
# simplistic Euler intergration
# p = p + v
part[1] = (half_box + part[1] + part[5]) % box_size - half_box
part[2] = (half_box + part[2] + part[6]) % box_size - half_box
part[3] = (half_box + part[3] + part[7]) % box_size - half_box
# v = v + pseudo-gravitational acceleration
factor = max(0.1 * box_size,
0.1 * (part[1]**2 + part[2]**2 + part[3]**2)**1.5)
part[5] = part[5] - part[1] / factor
part[6] = part[6] - part[2] / factor
part[7] = part[7] - part[3] / factor
# copy initial coordinates to a new state
cmd.create("cloud", "cloud", 1, state)
# update the new state coordinates
cmd.alter_state(state,
"cloud",
"(x,y,z) = particle[int(resi)][1:4]",
space=globals())
cmd.forward()
cmd.refresh()
# don't hog the CPU entirely
sleep(0.01)
cmd.mplay()
except:
traceback.print_exc()
def COM(selection='all', center=0, quiet=1):
model = cmd.get_model(selection)
nAtom = len(model.atom)
COM = cpv.get_null()
for a in model.atom:
COM = cpv.add(COM, a.coord)
COM = cpv.scale(COM, 1. / nAtom)
if not int(quiet):
print ' COM: [%8.3f,%8.3f,%8.3f]' % tuple(COM)
if int(center):
cmd.alter_state(1, selection, "(x,y,z)=sub((x,y,z), COM)",
space={'COM': COM, 'sub': cpv.sub})
return COM
def centroid(selection='all', center=0, quiet=1):
model = cmd.get_model(selection)
nAtom = len(model.atom)
centroid = cpv.get_null()
for a in model.atom:
centroid = cpv.add(centroid, a.coord)
centroid = cpv.scale(centroid, 1. / nAtom)
if not int(quiet):
print ' centroid: [%8.3f,%8.3f,%8.3f]' % tuple(centroid)
if int(move):
cmd.alter_state(1, selection, "(x,y,z)=sub((x,y,z), centroid)",
space={'centroid': centroid, 'sub': cpv.sub})
return centroid
def test_atom_state_settings_3f(self, f, data):
m1 = "pseudo01"
lp1, lp2 = lp = map(f, data)
cmd.pseudoatom(m1)
cmd.pseudoatom(m1)
cmd.create(m1, m1, 1, 2)
stored.pos = {}
stored.lp1 = lp1
stored.lp2 = lp2
stored.origp = None
# get origp (should be 0.,0.,0.
cmd.alter("(index 1)", "stored.origp = s['label_placement_offset']")
# change atom-state setting to lp1 for atom in both states
cmd.alter_state(0, "(index 1)",
"s['label_placement_offset']=stored.lp1")
# change atom-level setting for all atoms to something else
cmd.alter("all", "s['label_placement_offset']=stored.lp2")
# get atom-state settings
cmd.iterate_state(
0, "all",
"stored.pos['%s-%s-%s' % (model, state, index)]=s['label_placement_offset']"
)
# atom-state setting should be lp1 for atom 1
self.assertEqual(tuple(lp1), stored.pos['%s-%s-%s' % (m1, 1, 1)])
self.assertEqual(tuple(lp1), stored.pos['%s-%s-%s' % (m1, 2, 1)])
# atom setting should override to lp2 for atom 2 in both states
self.assertEqual(tuple(lp2), stored.pos['%s-%s-%s' % (m1, 1, 2)])
self.assertEqual(tuple(lp2), stored.pos['%s-%s-%s' % (m1, 2, 2)])
# unset all atom-level settings, atom-state settings should still exist
cmd.alter("all", "s['label_placement_offset']=None")
stored.pos = {}
cmd.iterate_state(
0, "all",
"stored.pos['%s-%s-%s' % (model, state, index)]=s['label_placement_offset']"
)
self.assertEqual(tuple(lp1), stored.pos['%s-%s-%s' % (m1, 1, 1)])
self.assertEqual(tuple(lp1), stored.pos['%s-%s-%s' % (m1, 2, 1)])
self.assertEqual(tuple(stored.origp),
stored.pos['%s-%s-%s' % (m1, 1, 2)])
self.assertEqual(tuple(stored.origp),
stored.pos['%s-%s-%s' % (m1, 2, 2)])
def test2667(self):
cmd.fragment('ala', 'm1')
cmd.alter_state(1, '%m1', 's.label_placement_offset = [1., 0., 0.]')
with testing.mktemp('.pse') as filename:
cmd.save(filename)
cmd.set_name('m1', 'm2')
cmd.load(filename, partial=1)
# now we have two copies (m1 m2). If unique ids are converted upon
# loading, then there will be no settings cross-leaking. Otherwise
# changing m1 settings will affect m2.
cmd.alter_state(1, '%m1', 's.label_placement_offset = [0., 1., 0.]')
m2_setting = []
cmd.iterate_state(1,
'first %m2', 'm2_setting.append(s.label_placement_offset)',
space=locals())
self.assertArrayEqual([1., 0., 0.], m2_setting[0], 0.001)
def test2667(self):
cmd.fragment('ala', 'm1')
cmd.alter_state(1, '%m1', 's.label_placement_offset = [1., 0., 0.]')
with testing.mktemp('.pse') as filename:
cmd.save(filename)
cmd.set_name('m1', 'm2')
cmd.load(filename, partial=1)
# now we have two copies (m1 m2). If unique ids are converted upon
# loading, then there will be no settings cross-leaking. Otherwise
# changing m1 settings will affect m2.
cmd.alter_state(1, '%m1', 's.label_placement_offset = [0., 1., 0.]')
m2_setting = []
cmd.iterate_state(1,
'first %m2',
'm2_setting.append(s.label_placement_offset)',
space=locals())
self.assertArrayEqual([1., 0., 0.], m2_setting[0], 0.001)
def simulation():
state = 1
import traceback
try:
while state < n_states:
state = state + 1
for part in particle:
# simplistic Euler intergration
# p = p + v
part[1] = (half_box + part[1] + part[5]) % box_size - half_box
part[2] = (half_box + part[2] + part[6]) % box_size - half_box
part[3] = (half_box + part[3] + part[7]) % box_size - half_box
# v = v + pseudo-gravitational acceleration
factor = max(0.1*box_size, 0.1*(part[1]**2+part[2]**2+part[3]**2)**1.5)
part[5] = part[5] - part[1] / factor
part[6] = part[6] - part[2] / factor
part[7] = part[7] - part[3] / factor
# copy initial coordinates to a new state
cmd.create("cloud","cloud",1,state)
# update the new state coordinates
cmd.alter_state(state,"cloud","(x,y,z) = particle[int(resi)][1:4]",space=globals())
cmd.forward()
cmd.refresh()
# don't hog the CPU entirely
sleep(0.01)
cmd.mplay()
except:
traceback.print_exc()
def testStereo(self):
cmd.fragment('ala')
cmd.remove('hydro')
# default: S configuration
labels = []
cmd.iterate('name CA', 'labels.append(stereo)', space=locals())
self.assertEqual(labels, ['S'])
# load R configuration (moves CB)
ala_conf_R = {
'N' : (-0.67690, -1.23030, -0.49050),
'CA' : (-0.00090, 0.06370, -0.49050),
'C' : ( 1.49910, -0.11030, -0.49050),
'O' : ( 2.03010, -1.22730, -0.50150),
# 'CB' : (-0.50890, 0.85570, 0.72650), # S configuration
'CB' : (-0.33784, 0.82664, -1.78310), # R configuration
}
cmd.alter_state(1, 'ala', '(x,y,z) = ala_conf_R.get(name)', space=locals())
labels = []
cmd.iterate('name CA', 'labels.append(stereo)', space=locals())
self.assertEqual(labels, ['R'])
def testAlterState(self):
self.load_big_example_multistate()
v_count = cmd.count_atoms() * cmd.count_states()
assert v_count > 10**5
xyz = []
with self.timing('i', 5.0):
cmd.iterate_state(0, 'all', 'xyz.append((x,y,z))', space=locals())
self.assertEqual(v_count, len(xyz))
with self.timing('a', 5.0):
cmd.alter_state(0,
'all',
'(x,y,z) = next(xyz_rev)',
space={
'xyz_rev': reversed(xyz),
'next': next
})
cmd.iterate_state(0, 'last all', 'stored.xyz = (x,y,z)')
self.assertEqual(stored.xyz, xyz[0])
def centroid(selection='all', center=0, quiet=1):
model = cmd.get_model(selection)
nAtom = len(model.atom)
centroid = cpv.get_null()
for a in model.atom:
centroid = cpv.add(centroid, a.coord)
centroid = cpv.scale(centroid, 1. / nAtom)
if not int(quiet):
print(' centroid: [%8.3f,%8.3f,%8.3f]' % tuple(centroid))
if int(center):
cmd.alter_state(1,
selection,
"(x,y,z)=sub((x,y,z), centroid)",
space={
'centroid': centroid,
'sub': cpv.sub
})
return centroid
def ens_rmsf(selection,
rmsf_spectrum = False,
mean_structure = False,
mean_per_resi = True,
log_name = None):
'''
DESCRIPTION
Generates and colors structure by RMSF statistics, calculated from mulistate ensembles
USAGE
ens_rmsf selection, sigma_rmsf_spectrum, mean_structure, histogram_number_bins, log_name
ARGUMENTS
sigma_rmsf_spectrum = overwrite q col with sigma RMSF (per atom), color by q
mean_structure = generate new single state structure with mean coords
histogram_number_bins = number of bins for output histograms
log_name = name of log file
EXAMPLE
ens_rmsf protein, True, True, 25, 'ens_rmsf.log'
'''
if log_name == None:
log = LogWriter(sys.stdout, 'log.txt')
else:
log = LogWriter(sys.stdout, log_name+'.txt')
print >> log, "\nEnsemble RMSF"
print >> log, "N.B. waters excluded"
print >> log, "N.B. B column information from first model"
print >> log, "Rmsf (Angstrom) [w.r.t mean structure]"
print >> log, "B_atom (Angstrom^2) [atomic Bfactor used in simulation]"
print >> log, "B_rmsf (Angstrom^2) [rmsf converted to Bfactor]"
# initialize arrays
selection = selection + ' and not resn hoh'
models = []
mean_coords = None
number_models = cmd.count_states(selection)
r_number_models = 1.0 / number_models
# get models, mean coords
for i in range(number_models):
models.append(cmd.get_model(selection,state=i+1))
coords_for_mean = map( lambda x: [x[0]*r_number_models,x[1]*r_number_models,x[2]*r_number_models],models[i].get_coord_list())
if mean_coords == None:
mean_coords = coords_for_mean
else:
n = []
for mean, for_mean in zip(mean_coords, coords_for_mean):
mean = map(sum, zip(mean,for_mean))
n.append(mean)
mean_coords = n
# calculate RMSF w.r.t. mean structure
rmsf_coord = [0.0]*len(mean_coords)
for i in range(number_models):
coord_array = models[i].get_coord_list()
for i_seq, xyz in enumerate(coord_array):
rmsf_coord[i_seq] += distance(xyz, mean_coords[i_seq])**2
rmsf_coord = map(lambda x: (x / number_models)**0.5, rmsf_coord)
# Generate new model object with average xyz coord
if mean_structure:
mean_structure_name = 'mean_xyz_'+selection
cmd.create(mean_structure_name, selection, 1)
stored.xyz = map(lambda v:[v[0],v[1],v[2]],mean_coords)
cmd.alter_state(1, mean_structure_name,'(x,y,z) = stored.xyz.pop(0)')
# convert to B factor (A^2)
rmsf_as_b_coord = map(lambda x: x**2 * ((8.0 * math.pi**2) / 3.0), rmsf_coord)
# get atomic b factor info
atom_b = [at.b for at in models[0].atom]
b_atom_plus_b_rsmf = map(sum,zip(atom_b,rmsf_as_b_coord))
# Colour by rmsf
if rmsf_spectrum:
# cmd.color('grey', 'all')
# cmd.alter('all','q=0')
atom = models[0].atom
for n, atom in enumerate(models[0].atom):
atom_sel = 'id ' + str(atom.id)
atom_action = 'q = ' + str(rmsf_sigma[n])
cmd.alter(atom_sel,atom_action)
print "\n\nQ infomation updated with RMSF sigma\n"
cmd.spectrum('q',selection = selection)
if mean_structure:
cmd.spectrum('q', selection = mean_structure_name)
else:
for n, atom in enumerate(models[0].atom):
atom_sel = 'id ' + str(atom.id)
atom_action = 'q = ' + str(rmsf_coord[n])
cmd.alter(atom_sel,atom_action)
print "\n\nQ infomation updated with RMSF (Angstrom)\n"
cmd.spectrum('q',selection = selection)
# array stats
print >> log, '\nB_atom (A^2): '
print_array_stats(array = atom_b,
log = log)
print >> log, '\nRmsf (A): '
print_array_stats(array = rmsf_coord,
log = log)
print >> log, '\nB_rmsf (A^2): '
print_array_stats(array = rmsf_as_b_coord,
log = log)
print >> log, '\nB_atom + B_rmsf (A^2):'
print_array_stats(array = b_atom_plus_b_rsmf,
log = log)
# individual atom stats
print >> log, '\n\n Resi | Name | Chain | Rmsf | B_rmsf | B_atom | B_rmsf+B_atom\n'
for i_seq, b_factor in enumerate(atom_b):
print >> log, ' %7s %7s %7s | %8.3f | %8.3f %8.3f | %8.3f'%(
models[0].atom[i_seq].resi,
models[0].atom[i_seq].name,
models[0].atom[i_seq].chain,
rmsf_coord[i_seq],
rmsf_as_b_coord[i_seq],
b_factor,
b_atom_plus_b_rsmf[i_seq])
if mean_per_resi:
print >> log, '\nMean per residue'
# update atom to include info
for n, atom in enumerate(models[0].atom):
atom.rmsf = rmsf_coord[n]
atom.b_rmsf = rmsf_as_b_coord[n]
atom.b_atom_plus_b_rsmf = atom.b + atom.b_rmsf
print >> log, ' Resi Resn | Atoms | Atom_rmsf | B_atom B_rmsf B_atom+B_rmsf'
def print_mean_residue():
print >> log, ' %4s %5s| %3d | %8.3f | %8.3f %8.3f %8.3f '%(
current_resi,
current_resn,
len(res_b),
sum(res_rmsf) / len(res_rmsf),
sum(res_b) / len(res_b),
sum(res_b_rmsf) / len(res_b_rmsf),
sum(res_b_atom_plus_b_rsmf) / len(res_b_atom_plus_b_rsmf) )
current_resi = models[0].atom[0].resi
current_resn = models[0].atom[0].resn
res_rmsf = []
res_b = []
res_b_rmsf = []
res_b_atom_plus_b_rsmf = []
for atom in models[0].atom:
if atom.resi == current_resi:
assert atom.resn == current_resn
res_rmsf.append(atom.rmsf)
res_b.append(atom.b)
res_b_rmsf.append(atom.b_rmsf)
res_b_atom_plus_b_rsmf.append(atom.b_atom_plus_b_rsmf)
else:
print_mean_residue()
current_resi = atom.resi
current_resn = atom.resn
res_rmsf = [atom.rmsf]
res_b = [atom.b]
res_b_rmsf = [atom.b_rmsf]
res_b_atom_plus_b_rsmf = [atom.b_atom_plus_b_rsmf]
print_mean_residue()
def update(self):
self.center = cmd.get_position()
cmd.alter_state(0, self.center_name, "(x, y, z) = p", space={'p': self.center})
cmd.isomesh(self.name, self.map_name, self.level, self.center_name, carve=self.radius)
def avgStates(object='all',object_sel=None,first=1,last=0,newobj=None,fitverdict='no',\
verb=0,pairs=1,writefiles=1):
'''
ARGUMENTS:
object (string [defaults to 'all']):
Starting PyMOL molecular object consisting of >1 states to be averaged
object_sel (string [defaults to "name CA"]):
An optional subset of atoms on which to operate (e.g., "name CA and resi 20-50")
first (int [defaults to 1]):
number of the first state to include in averaging
last (int [defaults to last state]):
Number of the last state to include in averaging. A value of '0' (zero)
means use the last state in the object.
newobj (string [defaults to name of object with string "_avg_AtoZ" appended,
where A and Z are the numbers of the first and last frames included
in the averaging]):
Desired name of the new output pymol object (i.e., averaged structure)
fitverdict (string [defaults to "no", any value != "no" is taken as a "yes"]):
Use the pymol function intra_fit() to fit all the states of "object & object_sel"
before calculating the average structure and RMSDs??
'no' = NO, !'no' = yes
verb (int [defaults to 0]):
Verbosity level of output. 0 = quiet, !0 = verbose (e.g., write position-specific
RMSDs to standard output).
pairs (int [default 1]):
Also calculate average pairwise RMSD for each residue position?? 0 = no, !0 = yes
writefiles (int [default 1]):
Write the calculated RMSD data to plaintext files?? 0 = no, !0 = yes
NOTES:
The state specified as 'first' is taken as the reference state for the (optional)
intra_fit() alignment. If no selection is given, the string "and name CA" will be
appended to the object and the averaging and rmsd calculations will be restricted
to "object and name CA" (i.e., C-alpha atoms). To avoid this default behavior,
specify a valid pymol atom selection for the object_sel argument (e.g., "name CA"
or "name CA and resi 20-50" or whatever).
'''
object = str(object)
object_sel = str(object_sel)
first=int(first)
last=int(last)
num_states_tot = cmd.count_states(object)
if last<1:
last=num_states_tot
num_states2avg = last - first + 1
if newobj==None or newobj=='':
newobj = "%s_avg_%dto%d"%(object,first,last)
cmd.create(newobj,object,first,1)
if writefiles:
print '%s'%('-'*80)
datfileprefix = '%s_%dto%d'%(replace(object,' ','_'),first,last)
avg_rmsd_file = datfileprefix + '.avg_rmsd.dat'
avg_file = open(avg_rmsd_file,'w')
print 'Opened "%s" file for writing residue-specific RMSDs to average structure...'%avg_rmsd_file
if pairs:
pair_rmsd_file = datfileprefix + '.pair_rmsd.dat'
pair_file = open(pair_rmsd_file,'w')
print 'Opened "%s" file for writing averaged residue-specific pairwise RMSDs...'%pair_rmsd_file
print '%s'%('-'*80)
else:
avg_file = open('/dev/null','w') # just do this instead of evaluating conditionals each time
if pairs:
pair_file = open('/dev/null','w') # through the atom loops (below)...
obj_sel_string = (lambda o,s: (o and s and "%s and %s"%(o,s)) or \
(o and not s and "%s and name CA"%o))(object,object_sel)
newobj_sel_string = (lambda o,s: (o and s and "%s and %s"%(o,s)) or \
(o and not s and "%s and name CA"%o))(newobj,object_sel)
print '%s'%('-'*80)
print 'Averaging %d states [%d, %d] of object "%s" (%d total states) to get new single-state object "%s"...' \
% (num_states2avg,first,last,obj_sel_string,num_states_tot,newobj)
print '%s'%('-'*80)
tmpobject='%s_tmp4avg_%dto%d'%(object,first,last)
i=0
for eachstate in range(first,last+1):
i+=1 # because pymol states are indexed starting from 1 (not 0)
cmd.create(tmpobject,obj_sel_string,eachstate,i)
if fitverdict != 'no':
print "-> proceeding WITH FITTING to reference state..."
tmpobject_intrafit_rmsds = cmd.intra_fit(tmpobject,1)
if verb:
print ' intrafit_rmsds = ',
print tmpobject_intrafit_rmsds
else:
print "-> proceeding WITHOUT FITTING to reference state..."
# create an atom index map between original (complete) object and subset to be averaged:
atindex_map = [None]
for at in cmd.get_model(newobj_sel_string,1).atom:
atindex_map.append(at.index)
if verb:
print "-> atom index_map = ",
print atindex_map
newobj_chempy = cmd.get_model(tmpobject,1)
for at in newobj_chempy.atom:
this_at_idx = at.index
sum_x = sum_y = sum_z = 0.0
avg_x = avg_y = avg_z = 0.0
state_coords=[]
rmsd_sum = rmsd = 0.0
for s in range(1,num_states2avg+1):
this_x = cmd.get_model(tmpobject,s).atom[this_at_idx-1].coord[0]
this_y = cmd.get_model(tmpobject,s).atom[this_at_idx-1].coord[1]
this_z = cmd.get_model(tmpobject,s).atom[this_at_idx-1].coord[2]
sum_x += this_x
sum_y += this_y
sum_z += this_z
state_coords.append([this_x,this_y,this_z])
avg_x = sum_x / num_states2avg
avg_y = sum_y / num_states2avg
avg_z = sum_z / num_states2avg
cmd.alter_state(1,'%s and id %d'%(newobj,atindex_map[this_at_idx]),'x=%f'%avg_x)
cmd.alter_state(1,'%s and id %d'%(newobj,atindex_map[this_at_idx]),'y=%f'%avg_y)
cmd.alter_state(1,'%s and id %d'%(newobj,atindex_map[this_at_idx]),'z=%f'%avg_z)
# position-specific RMSDs with respect to average structure:
for somept in state_coords:
rmsd_sum += pow(calcDist(somept,[avg_x,avg_y,avg_z]),2.0)
rmsd = sqrt(rmsd_sum / num_states2avg)
# DEBUG:
# DEBUG print 'newobj = %s / id = %d / b = %0.3f'%(newobj,atindex_map[this_at_idx],rmsd)
cmd.alter('%s and id %d'%(newobj,atindex_map[this_at_idx]),'b=%0.3f'%rmsd)
if verb:
print '"%s" index = %d'%(obj_sel_string,this_at_idx)
print 'rmsd = %0.3f'%rmsd
avg_file.write('%d\t%0.3f\n'%(atindex_map[this_at_idx],rmsd))
# position-specific RMSDs averaged pairwise over the bundle:
if pairs:
for at in newobj_chempy.atom:
this_at_idx = at.index
loop_counter = 0
running_sum = 0.0
for s1 in range(1,num_states2avg+1):
for s2 in range(s1+1,num_states2avg+1):
#DB print 'computing position %d, %d x %d'%(this_at_idx,s1,s2)
pos1 = [ cmd.get_model(tmpobject,s1).atom[this_at_idx-1].coord[0],
cmd.get_model(tmpobject,s1).atom[this_at_idx-1].coord[1],
cmd.get_model(tmpobject,s1).atom[this_at_idx-1].coord[2] ]
pos2 = [ cmd.get_model(tmpobject,s2).atom[this_at_idx-1].coord[0],
cmd.get_model(tmpobject,s2).atom[this_at_idx-1].coord[1],
cmd.get_model(tmpobject,s2).atom[this_at_idx-1].coord[2] ]
loop_counter += 1
running_sum += pow(calcDist(pos1,pos2),2.0)
# print '%s'%('.'*s2)
pairwise_rmsd = sqrt(running_sum / loop_counter)
if verb: print 'calculated pairwise RMSD for %d pairs at position %d = %0.3f' % \
(loop_counter,atindex_map[this_at_idx],pairwise_rmsd)
pair_file.write('%d\t%0.3f\n'%(atindex_map[this_at_idx],pairwise_rmsd))
if writefiles:
avg_file.close()
if pairs:
pair_file.close()
from pymol import cmd from pymol import stored stored.xyz = [] cmd.iterate_state(1,"pept","stored.xyz.append([x,y,z])") # at this point, stored.xyz is a native Python array holding # the coordinates, which you can modify as required stored.xyz = map(lambda v:[-v[1],v[0],v[2]],stored.xyz) # and now you can update the internal coordinate sets cmd.alter_state(1,"pept","(x,y,z)=stored.xyz.pop(0)")
def do_library(self):
cmd = self.cmd
pymol = cmd._pymol
if not (
(cmd.count_atoms("(%s) and name n" % src_sele) == 1)
and (cmd.count_atoms("(%s) and name c" % src_sele) == 1)
and (cmd.count_atoms("(%s) and name o" % src_sele) == 1)
):
self.clear()
return 1
cmd.feedback("push")
cmd.feedback("disable", "selector", "everythin")
cmd.feedback("disable", "editor", "actions")
self.prompt = ["Loading rotamers..."]
pymol.stored.name = "residue"
cmd.iterate("first (%s)" % src_sele, 'stored.name=model+"/"+segi+"/"+chain+"/"+resn+"`"+resi')
self.res_text = pymol.stored.name
cmd.select("_seeker_hilight", src_sele)
auto_zoom = cmd.get_setting_text("auto_zoom")
cmd.set("auto_zoom", "0", quiet=1)
cmd.frame(0)
cmd.delete(frag_name)
if self.auto_center:
cmd.center(src_sele, animate=-1)
self.lib_mode = self.mode
if self.lib_mode == "current":
pymol.stored.resn = ""
cmd.iterate("(%s and n;ca)" % src_sele, "stored.resn=resn")
rot_type = _rot_type_xref.get(pymol.stored.resn, pymol.stored.resn)
if (self.c_cap != "none") or (self.n_cap != "none") or (self.hyd != "auto"):
self.lib_mode = rot_type # force fragment-based load
else:
cmd.create(frag_name, src_sele, 1, 1)
if self.c_cap == "open":
cmd.remove("%s and name OXT" % frag_name)
if self.lib_mode != "current":
rot_type = self.lib_mode
frag_type = self.lib_mode
if (self.n_cap == "posi") and (frag_type[0:3] != "NT_"):
if not (cmd.count_atoms("elem c & !(%s) & (bto. (n;n & (%s))) &! r. ace" % (src_sele, src_sele))):
# use N-terminal fragment
frag_type = "NT_" + frag_type
if (self.c_cap == "nega") and (frag_type[0:3] != "CT_"):
if not (cmd.count_atoms("elem n & !(%s) & (bto. (n;c & (%s))) & !r. nme+nhh" % (src_sele, src_sele))):
# use C-terminal fragment
frag_type = "CT_" + frag_type
if rot_type[0:3] in ["NT_", "CT_"]:
rot_type = rot_type[3:]
rot_type = _rot_type_xref.get(rot_type, rot_type)
cmd.fragment(string.lower(frag_type), frag_name)
# trim off hydrogens
if self.hyd == "none":
cmd.remove("(" + frag_name + " and hydro)")
elif self.hyd == "auto":
if cmd.count_atoms("(" + src_sele + ") and hydro") == 0:
cmd.remove("(" + frag_name + " and hydro)")
# copy identifying information
cmd.iterate("(%s and n;ca)" % src_sele, "stored.chain=chain")
cmd.alter("(%s)" % frag_name, "chain=stored.chain")
cmd.iterate("(%s and n;ca)" % src_sele, "stored.resi=resi")
cmd.alter("(%s)" % frag_name, "resi=stored.resi")
cmd.iterate("(%s and n;ca)" % src_sele, "stored.segi=segi")
cmd.alter("(%s)" % frag_name, "segi=stored.segi")
cmd.iterate("(%s and n;ca)" % src_sele, "stored.ss=ss")
cmd.alter("(%s)" % frag_name, "ss=stored.ss")
# move the fragment
if (cmd.count_atoms("(%s and n;cb)" % frag_name) == 1) and (
cmd.count_atoms("(%s and n;cb)" % src_sele) == 1
):
cmd.pair_fit(
"(%s and n;ca)" % frag_name,
"(%s and n;ca)" % src_sele,
"(%s and n;cb)" % frag_name,
"(%s and n;cb)" % src_sele,
"(%s and n;c)" % frag_name,
"(%s and n;c)" % src_sele,
"(%s and n;n)" % frag_name,
"(%s and n;n)" % src_sele,
)
else:
cmd.pair_fit(
"(%s and n;ca)" % frag_name,
"(%s and n;ca)" % src_sele,
"(%s and n;c)" % frag_name,
"(%s and n;c)" % src_sele,
"(%s and n;n)" % frag_name,
"(%s and n;n)" % src_sele,
)
# fix the carbonyl position...
cmd.iterate_state(1, "(%s and n;o)" % src_sele, "stored.list=[x,y,z]")
cmd.alter_state(1, "(%s and n;o)" % frag_name, "(x,y,z)=stored.list")
if cmd.count_atoms("(%s and n;oxt)" % src_sele):
cmd.iterate_state(1, "(%s and n;oxt)" % src_sele, "stored.list=[x,y,z]")
cmd.alter_state(1, "(%s and n;oxt)" % frag_name, "(x,y,z)=stored.list")
elif cmd.count_atoms("(%s and n;oxt)" % frag_name): # place OXT if no template exists
angle = cmd.get_dihedral(
"(%s and n;n)" % frag_name,
"(%s and n;ca)" % frag_name,
"(%s and n;c)" % frag_name,
"(%s and n;o)" % frag_name,
)
cmd.protect("(%s and n;o)" % frag_name)
cmd.set_dihedral(
"(%s and n;n)" % frag_name,
"(%s and n;ca)" % frag_name,
"(%s and n;c)" % frag_name,
"(%s and n;oxt)" % frag_name,
180.0 + angle,
)
cmd.deprotect(frag_name)
# fix the hydrogen position (if any)
if cmd.count_atoms("(elem h and bound_to (n;n and (%s)))" % frag_name) == 1:
if cmd.count_atoms("(elem h and bound_to (n;n and (%s)))" % src_sele) == 1:
cmd.iterate_state(1, "(elem h and bound_to (n;n and (%s)))" % src_sele, "stored.list=[x,y,z]")
cmd.alter_state(1, "(elem h and bound_to (n;n and (%s)))" % frag_name, "(x,y,z)=stored.list")
elif cmd.select(tmp_sele1, "(n;c and bound_to (%s and e;n))" % src_sele) == 1:
# position hydro based on location of the carbonyl
angle = cmd.get_dihedral(
"(%s and n;c)" % frag_name, "(%s and n;ca)" % frag_name, "(%s and n;n)" % frag_name, tmp_sele1
)
cmd.set_dihedral(
"(%s and n;c)" % frag_name,
"(%s and n;ca)" % frag_name,
"(%s and n;n)" % frag_name,
"(%s and n;h)" % frag_name,
180.0 + angle,
)
cmd.delete(tmp_sele1)
# add c-cap (if appropriate)
if self.c_cap in ["amin", "nmet"]:
if not cmd.count_atoms("elem n & !(%s) & (bto. (n;c & (%s))) & !r. nme+nhh" % (src_sele, src_sele)):
if cmd.count_atoms("n;c & (%s)" % (frag_name)) == 1:
if self.c_cap == "amin":
editor.attach_amino_acid("n;c & (%s)" % (frag_name), "nhh")
elif self.c_cap == "nmet":
editor.attach_amino_acid("n;c & (%s)" % (frag_name), "nme")
if cmd.count_atoms("hydro & bound_to (n;n & bound_to (n;c & (%s)))" % frag_name):
cmd.h_fix("n;n & bound_to (n;c & (%s))" % frag_name)
# trim hydrogens
if self.hyd == "none":
cmd.remove("(" + frag_name + " and hydro)")
elif self.hyd == "auto":
if cmd.count_atoms("(" + src_sele + ") and hydro") == 0:
cmd.remove("(" + frag_name + " and hydro)")
# add n-cap (if appropriate)
if self.n_cap in ["acet"]:
if not cmd.count_atoms("elem c & !(%s) & (bto. (n;n & (%s))) & !r. ace " % (src_sele, src_sele)):
if cmd.count_atoms("n;n & (%s)" % (frag_name)) == 1:
if self.n_cap == "acet":
editor.attach_amino_acid("n;n & (%s)" % (frag_name), "ace")
if cmd.count_atoms("hydro & bound_to (n;n & bound_to (n;c & (%s)))" % frag_name):
cmd.h_fix("n;n & (%s)" % frag_name)
# trim hydrogens
if self.hyd == "none":
cmd.remove("(" + frag_name + " and hydro)")
elif self.hyd == "auto":
if cmd.count_atoms("(" + src_sele + ") and hydro") == 0:
cmd.remove("(" + frag_name + " and hydro)")
cartoon = cmd.count_atoms("(%s and n;ca and rep cartoon)" % src_sele) > 0
sticks = cmd.count_atoms("(%s and n;ca and rep sticks)" % src_sele) > 0
cmd.delete(obj_name)
key = rot_type
lib = None
if self.dep == "dep":
try:
result = cmd.phi_psi("%s" % src_sele)
if len(result) == 1:
(phi, psi) = result[result.keys()[0]]
(phi, psi) = (int(10 * round(phi / 10)), int(10 * (round(psi / 10))))
key = (rot_type, phi, psi)
if not self.dep_library.has_key(key):
(phi, psi) = (int(20 * round(phi / 20)), int(20 * (round(psi / 20))))
key = (rot_type, phi, psi)
if not self.dep_library.has_key(key):
(phi, psi) = (int(60 * round(phi / 60)), int(60 * (round(psi / 60))))
key = (rot_type, phi, psi)
lib = self.dep_library.get(key, None)
except:
pass
if lib == None:
key = rot_type
lib = self.ind_library.get(key, None)
if (lib != None) and self.dep == "dep":
print " Mutagenesis: no phi/psi, using backbone-independent rotamers."
if lib != None:
state = 1
for a in lib:
cmd.create(obj_name, frag_name, 1, state)
if state == 1:
cmd.select(mut_sele, "(byres (%s like %s))" % (obj_name, src_sele))
if rot_type == "PRO":
cmd.unbond("(%s & name N)" % mut_sele, "(%s & name CD)" % mut_sele)
for b in a.keys():
if b != "FREQ":
cmd.set_dihedral(
"(%s & n;%s)" % (mut_sele, b[0]),
"(%s & n;%s)" % (mut_sele, b[1]),
"(%s & n;%s)" % (mut_sele, b[2]),
"(%s & n;%s)" % (mut_sele, b[3]),
a[b],
state=state,
)
else:
cmd.set_title(obj_name, state, "%1.1f%%" % (a[b] * 100))
if rot_type == "PRO":
cmd.bond("(%s & name N)" % mut_sele, "(%s & name CD)" % mut_sele)
state = state + 1
cmd.delete(frag_name)
print " Mutagenesis: %d rotamers loaded." % len(lib)
if self.bump_check:
cmd.delete(bump_name)
cmd.create(
bump_name,
"(((byobj %s) within 6 of (%s and not name n+c+ca+o+h+ha)) and (not (%s)))|(%s)"
% (src_sele, mut_sele, src_sele, mut_sele),
singletons=1,
)
cmd.color("gray50", bump_name + " and elem c")
cmd.set("seq_view", 0, bump_name, quiet=1)
cmd.hide("everything", bump_name)
if (cmd.select(tmp_sele1, "(n;N and (%s in (neighbor %s)))" % (bump_name, src_sele)) == 1) and (
cmd.select(tmp_sele2, "(n;C and (%s in %s))" % (bump_name, mut_sele)) == 1
):
cmd.bond(tmp_sele1, tmp_sele2)
if (cmd.select(tmp_sele1, "(n;C and (%s in (neighbor %s)))" % (bump_name, src_sele)) == 1) and (
cmd.select(tmp_sele2, "(n;N and (%s in %s))" % (bump_name, mut_sele)) == 1
):
cmd.bond(tmp_sele1, tmp_sele2)
cmd.delete(tmp_sele1)
cmd.delete(tmp_sele2)
cmd.protect("%s and not (%s in (%s and not name n+c+ca+o+h+ha))" % (bump_name, bump_name, mut_sele))
cmd.sculpt_activate(bump_name)
cmd.show("cgo", bump_name)
# draw the bumps
cmd.set("sculpt_vdw_vis_mode", 1, bump_name)
state = 1
for a in lib:
cmd.sculpt_iterate(bump_name, state=state)
state = state + 1
cmd.delete(mut_sele)
else:
cmd.create(obj_name, frag_name, 1, 1)
print " Mutagenesis: no rotamers found in library."
cmd.set("seq_view", 0, obj_name, quiet=1)
pymol.util.cbaw(obj_name)
cmd.hide("(" + obj_name + ")")
cmd.show(self.rep, obj_name)
cmd.show("lines", obj_name) # neighbor always show lines
if cartoon:
cmd.show("cartoon", obj_name)
if sticks:
cmd.show("sticks", obj_name)
cmd.set("auto_zoom", auto_zoom, quiet=1)
cmd.delete(frag_name)
cmd.frame(0)
cmd.unpick()
cmd.feedback("pop")
def avg_states(object='all',
object_sel=None,
first=1,
last=0,
newobj=None,
fitverdict='no',
verb=0,
pairs=1,
writefiles=1):
"""
ARGUMENTS:
object (string [defaults to 'all']):
Starting PyMOL molecular object consisting of >1 states to be averaged
object_sel (string [defaults to "name CA"]):
An optional subset of atoms on which to operate (e.g., "name CA and
resi 20-50")
first (int [defaults to 1]):
number of the first state to include in averaging
last (int [defaults to last state]):
Number of the last state to include in averaging. A value of '0' (zero)
means use the last state in the object.
newobj (string [defaults to name of object with string "_avg_AtoZ"
appended,
where A and Z are the numbers of the first and last frames included
in the averaging]):
Desired name of the new output pymol object (i.e., averaged structure)
fitverdict (string [defaults to "no", any value != "no" is taken as a
"yes"]):
Use the pymol function intra_fit() to fit all the states of "object &
object_sel"
before calculating the average structure and RMSDs??
'no' = NO, !'no' = yes
verb (int [defaults to 0]):
Verbosity level of output. 0 = quiet, !0 = verbose (e.g., write
position-specific
RMSDs to standard output).
pairs (int [default 1]):
Also calculate average pairwise RMSD for each residue position??
0 = no, !0 = yes
writefiles (int [default 1]):
Write the calculated RMSD data to plaintext files?? 0 = no, !0 = yes
NOTES:
The state specified as 'first' is taken as the reference state for
the (optional)
intra_fit() alignment. If no selection is given, the string "and name
CA" will be
appended to the object and the averaging and rmsd calculations will be
restricted
to "object and name CA" (i.e., C-alpha atoms). To avoid this default
behavior,
specify a valid pymol atom selection for the object_sel argument (e.g.,
"name CA"
or "name CA and resi 20-50" or whatever).
"""
pair_file = None
object = str(object)
object_sel = str(object_sel)
first = int(first)
last = int(last)
num_states_tot = cmd.count_states(object)
if last < 1:
last = num_states_tot
num_states2avg = last - first + 1
if newobj is None or newobj == '':
newobj = "%s_avg_%dto%d" % (object, first, last)
cmd.create(newobj, object, first, 1)
if writefiles:
print('%s' % ('-' * 80))
datfileprefix = '%s_%dto%d' % (replace(object, ' ', '_'), first, last)
avg_rmsd_file = datfileprefix + '.avg_rmsd.dat'
avg_file = open(avg_rmsd_file, 'w')
print('Opened "%s" file for writing residue-specific RMSDs to '
'average structure...' % avg_rmsd_file)
if pairs:
pair_rmsd_file = datfileprefix + '.pair_rmsd.dat'
pair_file = open(pair_rmsd_file, 'w')
print('Opened "%s" file for writing averaged residue-specific '
'pairwise RMSDs...' % pair_rmsd_file)
print('%s' % ('-' * 80))
else:
# just do this instead of evaluating conditionals each time
avg_file = open('/dev/null', 'w')
if pairs:
pair_file = open('/dev/null',
'w') # through the atom loops (below)...
obj_sel_string = (lambda o, sel: (o and sel and "%s and %s" % (o, sel)) or
(o and not sel and "%s and name CA" % o))(object,
object_sel)
newobj_sel_string = (lambda o, sel: (o and sel and "%s and %s" %
(o, sel)) or
(o and not sel and "%s and name CA" % o))(newobj,
object_sel)
print('%s' % ('-' * 80))
print(
'Averaging %d states [%d, %d] of object "%s" (%d total states) '
'to get new single-state object "%s"...' %
(num_states2avg, first, last, obj_sel_string, num_states_tot, newobj))
print('%s' % ('-' * 80))
tmpobject = '%s_tmp4avg_%dto%d' % (object, first, last)
i = 0
for eachstate in range(first, last + 1):
i += 1 # because pymol states are indexed starting from 1 (not 0)
cmd.create(tmpobject, obj_sel_string, eachstate, i)
if fitverdict != 'no':
print("-> proceeding WITH FITTING to reference state...")
tmpobject_intrafit_rmsds = cmd.intra_fit(tmpobject)
if verb:
print(' intrafit_rmsds = ', )
print(tmpobject_intrafit_rmsds)
else:
print("-> proceeding WITHOUT FITTING to reference state...")
# create an atom index map between original (complete) object and subset
# to be averaged:
atindex_map = [None]
for at in cmd.get_model(newobj_sel_string).atom:
atindex_map.append(at.index)
if verb:
print("-> atom index_map = ", )
print(atindex_map)
newobj_chempy = cmd.get_model(tmpobject)
for at in newobj_chempy.atom:
this_at_idx = at.index
sum_x = sum_y = sum_z = 0.0
# avg_x = avg_y = avg_z = 0.0
state_coords = []
# rmsd_sum = rmsd = 0.0
rmsd_sum = 0.0
for s in range(1, num_states2avg + 1):
this_x = cmd.get_model(tmpobject, s).atom[this_at_idx - 1].coord[0]
this_y = cmd.get_model(tmpobject, s).atom[this_at_idx - 1].coord[1]
this_z = cmd.get_model(tmpobject, s).atom[this_at_idx - 1].coord[2]
sum_x += this_x
sum_y += this_y
sum_z += this_z
state_coords.append([this_x, this_y, this_z])
avg_x = sum_x / num_states2avg
avg_y = sum_y / num_states2avg
avg_z = sum_z / num_states2avg
cmd.alter_state(
1, '{0:s} and id {1:d}'.format(newobj, atindex_map[this_at_idx]),
'x=%f' % avg_x)
cmd.alter_state(
1, '{0:s} and id {1:d}'.format(newobj, atindex_map[this_at_idx]),
'y=%f' % avg_y)
cmd.alter_state(
1, '{0:s} and id {1:d}'.format(newobj, atindex_map[this_at_idx]),
'z=%f' % avg_z)
# position-specific RMSDs with respect to average structure:
for somept in state_coords:
rmsd_sum += pow(calcDist(somept, [avg_x, avg_y, avg_z]), 2.0)
rmsd = sqrt(rmsd_sum / num_states2avg)
# DEBUG:
# DEBUG print('newobj = %sel / id = %d / b = %0.3f'
# %(newobj,atindex_map[this_at_idx],rmsd)
cmd.alter(
'{0:s} and id {1:d}'.format(newobj, atindex_map[this_at_idx]),
'b=%0.3f' % rmsd)
if verb:
print('"%s" index = %d' % (obj_sel_string, this_at_idx))
print('rmsd = %0.3f' % rmsd)
avg_file.write('{0:d}\t{1:0.3f}\n'.format(atindex_map[this_at_idx],
rmsd))
# position-specific RMSDs averaged pairwise over the bundle:
if pairs:
for at in newobj_chempy.atom:
this_at_idx = at.index
loop_counter = 0
running_sum = 0.0
for s1 in range(1, num_states2avg + 1):
for s2 in range(s1 + 1, num_states2avg + 1):
# print('computing position %d, %d x %d'%(this_at_idx,s1,s2)
pos1 = [
cmd.get_model(tmpobject,
s1).atom[this_at_idx - 1].coord[0],
cmd.get_model(tmpobject,
s1).atom[this_at_idx - 1].coord[1],
cmd.get_model(tmpobject,
s1).atom[this_at_idx - 1].coord[2]
]
pos2 = [
cmd.get_model(tmpobject,
s2).atom[this_at_idx - 1].coord[0],
cmd.get_model(tmpobject,
s2).atom[this_at_idx - 1].coord[1],
cmd.get_model(tmpobject,
s2).atom[this_at_idx - 1].coord[2]
]
loop_counter += 1
running_sum += pow(calcDist(pos1, pos2), 2.0)
pairwise_rmsd = sqrt(running_sum / loop_counter)
if verb:
print('calculated pairwise RMSD for {0:d} pairs at '
'position {0:d} = {1:0.3f}'.format(
loop_counter, atindex_map[this_at_idx],
pairwise_rmsd))
pair_file.write('{0:d}\t{1:0.3f}\n'.format(
atindex_map[this_at_idx], pairwise_rmsd))
if writefiles:
avg_file.close()
if pairs:
pair_file.close()
cmd.delete(tmpobject)
return newobj
def GenNM(obj, nmids, mode, inp=None, amp=50., nframes=20, dump_file=False, \
prmtop=None):
nmids=[int(i) for i in nmids.split()]
amp = float(amp)
nframes=int(nframes)
mode=int(mode)
stored.NMA = {}
stored.NMA[obj] = {}
if mode==1:
if not inp:
print "Please specify cpptraj covariance matrix file"
return 0
if (not prmtop):
print "Please specify prmtop file for proper mass reweighing of vectors."
return 0
print "Attempting to read mwcov matrix %s" %inp
mwcvmat=genfromtxt(inp)
print "Diagonalizing covariance matrix."
w,v = linalg.eig(mwcvmat)
#sort from largest eigenvvalue to smallest
si=argsort(w)[::-1]
w=w[si]
v=v[:,si]
#convert to cm-1
for i in range(len(w)):
if w[i]<0: w[i]= -108.587*sqrt(-0.6/w[i])
elif w[i]>0: w[i]= 108.587*sqrt(0.6/w[i])
else: w[i]=0
#get masses and un-mass weigh the modes
m=raf.prmtop(prmtop).Get_Masses()
m=[[i]*3 for i in m]
m=[item for sublist in m for item in sublist]
for vec in range(v.shape[1]):
v[:,vec]=v[:,vec]/sqrt(m)
#store
stored.NMA[obj]['w'] = w
stored.NMA[obj]['v'] = v
elif mode==2:
if not inp:
print "Please specify evecs frequency/eigenvector file"
return 0
print "Attempting to read evecs file %s" %inp
stored.NMA[obj]['w'], stored.NMA[obj]['v'] = ReadEvecs(inp)
elif mode==3:
if not inp:
print "Please specify pickled normal mode object"
return 0
print "Attempting to read pickle file %s" %inp
stored.NMA[obj]=pickle.load( open(inp,"rb"))
if dump_file:
print "Dumping eigenvalues and modes to pickle file."
pickle.dump(stored.NMA[obj], open(dump_file,"wb") )
w = stored.NMA[obj]['w']
v = stored.NMA[obj]['v']
print "%7s%20s%20s" % ('NMID', 'f Hz', 'f cm^-1')
for i in range(min(w.size,20)):
print "%7d%20.5e\t%20.5f" % (i, w[i]*2.99792458e10, w[i]),
if i in nmids:
print "*"
else:
print ""
for nmid in nmids:
newobj = "%s-nm_%d" % (obj, nmid)
cmd.delete(newobj)
nm = real(v[:,nmid])
nm *= amp/sqrt((nm**2).sum())
for ifr in range(nframes):
cmd.create(newobj, obj, 1, ifr+1)
stored.nm = nm*sin(2.*pi*ifr/nframes)
cmd.alter_state(ifr+1, newobj, "x,y,z = x+stored.nm[(ID-1)*3], y+stored.nm[(ID-1)*3+1], z+stored.nm[(ID-1)*3+2]")
def do_library(self):
cmd=self.cmd
pymol=cmd._pymol
if not ((cmd.count_atoms("(%s) and name N"%src_sele)==1) and
(cmd.count_atoms("(%s) and name C"%src_sele)==1) and
(cmd.count_atoms("(%s) and name O"%src_sele)==1)):
self.clear()
return 1
cmd.feedback("push")
cmd.feedback("disable","selector","everythin")
cmd.feedback("disable","editor","actions")
self.prompt = [ 'Loading rotamers...']
self.bump_scores = []
state_best = 0
pymol.stored.name = 'residue'
cmd.iterate("first (%s)"%src_sele,'stored.name=model+"/"+segi+"/"+chain+"/"+resn+"`"+resi')
self.res_text = pymol.stored.name
cmd.select("_seeker_hilight",src_sele)
auto_zoom = cmd.get_setting_text('auto_zoom')
cmd.set('auto_zoom',"0",quiet=1)
cmd.frame(0)
cmd.delete(frag_name)
if self.auto_center:
cmd.center(src_sele,animate=-1)
self.lib_mode = self.mode
if self.lib_mode=="current":
pymol.stored.resn=""
cmd.iterate("(%s & name CA)"%src_sele,"stored.resn=resn")
rot_type = _rot_type_xref.get(pymol.stored.resn,pymol.stored.resn)
if (self.c_cap!='none') or (self.n_cap!='none') or (self.hyd != 'auto'):
self.lib_mode = rot_type # force fragment-based load
else:
cmd.create(frag_name,src_sele,1,1)
if self.c_cap=='open':
cmd.remove("%s and name OXT"%frag_name)
if self.lib_mode!='current':
rot_type = self.lib_mode
frag_type = self.lib_mode
if (self.n_cap == 'posi') and (frag_type[0:3]!='NT_'):
if not ( cmd.count_atoms(
"elem C & !(%s) & (bto. (name N & (%s))) &! resn ACE"%
(src_sele,src_sele))):
# use N-terminal fragment
frag_type ="NT_"+frag_type
if (self.c_cap == 'nega') and (frag_type[0:3]!='CT_'):
if not ( cmd.count_atoms("elem N & !(%s) & (bto. (name C & (%s))) & !resn NME+NHH"%
(src_sele,src_sele))):
# use C-terminal fragment
frag_type ="CT_"+frag_type
if rot_type[0:3] in [ 'NT_', 'CT_' ]:
rot_type = rot_type[3:]
rot_type = _rot_type_xref.get(rot_type, rot_type)
cmd.fragment(frag_type.lower(), frag_name, origin=0)
# trim off hydrogens
if (self.hyd == 'none'):
cmd.remove("("+frag_name+" and hydro)")
elif (self.hyd == 'auto'):
if cmd.count_atoms("("+src_sele+") and hydro")==0:
cmd.remove("("+frag_name+" and hydro)")
# copy identifying information
cmd.alter("?%s & name CA" % src_sele, "stored.identifiers = (segi, chain, resi, ss, color)", space=self.space)
cmd.alter("?%s" % frag_name, "(segi, chain, resi, ss) = stored.identifiers[:4]", space=self.space)
# move the fragment
if ((cmd.count_atoms("(%s & name CB)"%frag_name)==1) and
(cmd.count_atoms("(%s & name CB)"%src_sele)==1)):
cmd.pair_fit("(%s & name CA)"%frag_name,
"(%s & name CA)"%src_sele,
"(%s & name CB)"%frag_name,
"(%s & name CB)"%src_sele,
"(%s & name C)"%frag_name,
"(%s & name C)"%src_sele,
"(%s & name N)"%frag_name,
"(%s & name N)"%src_sele)
else:
cmd.pair_fit("(%s & name CA)"%frag_name,
"(%s & name CA)"%src_sele,
"(%s & name C)"%frag_name,
"(%s & name C)"%src_sele,
"(%s & name N)"%frag_name,
"(%s & name N)"%src_sele)
# fix the carbonyl position...
cmd.iterate_state(1,"(%s & name O)"%src_sele,"stored.list=[x,y,z]")
cmd.alter_state(1,"(%s & name O)"%frag_name,"(x,y,z)=stored.list")
if cmd.count_atoms("(%s & name OXT)"%src_sele):
cmd.iterate_state(1,"(%s & name OXT)"%src_sele,"stored.list=[x,y,z]")
cmd.alter_state(1,"(%s & name OXT)"%frag_name,"(x,y,z)=stored.list")
elif cmd.count_atoms("(%s & name OXT)"%frag_name): # place OXT if no template exists
angle = cmd.get_dihedral("(%s & name N)"%frag_name,
"(%s & name CA)"%frag_name,
"(%s & name C)"%frag_name,
"(%s & name O)"%frag_name)
cmd.protect("(%s & name O)"%frag_name)
cmd.set_dihedral("(%s & name N)"%frag_name,
"(%s & name CA)"%frag_name,
"(%s & name C)"%frag_name,
"(%s & name OXT)"%frag_name,180.0+angle)
cmd.deprotect(frag_name)
# fix the hydrogen position (if any)
if cmd.count_atoms("(hydro and bound_to (name N & (%s)))"%frag_name)==1:
if cmd.count_atoms("(hydro and bound_to (name N & (%s)))"%src_sele)==1:
cmd.iterate_state(1,"(hydro and bound_to (name N & (%s)))"%src_sele,
"stored.list=[x,y,z]")
cmd.alter_state(1,"(hydro and bound_to (name N & (%s)))"%frag_name,
"(x,y,z)=stored.list")
elif cmd.select(tmp_sele1,"(name C & bound_to (%s and elem N))"%src_sele)==1:
# position hydro based on location of the carbonyl
angle = cmd.get_dihedral("(%s & name C)"%frag_name,
"(%s & name CA)"%frag_name,
"(%s & name N)"%frag_name,
tmp_sele1)
cmd.set_dihedral("(%s & name C)"%frag_name,
"(%s & name CA)"%frag_name,
"(%s & name N)"%frag_name,
"(%s & name H)"%frag_name,180.0+angle)
cmd.delete(tmp_sele1)
# add c-cap (if appropriate)
if self.c_cap in [ 'amin', 'nmet' ]:
if not cmd.count_atoms("elem N & !(%s) & (bto. (name C & (%s))) & !resn NME+NHH"%
(src_sele,src_sele)):
if cmd.count_atoms("name C & (%s)"%(frag_name))==1:
if self.c_cap == 'amin':
editor.attach_amino_acid("name C & (%s)"%(frag_name), 'nhh')
elif self.c_cap == 'nmet':
editor.attach_amino_acid("name C & (%s)"%(frag_name), 'nme')
if cmd.count_atoms("hydro & bound_to (name N & bound_to (name C & (%s)))"%frag_name):
cmd.h_fix("name N & bound_to (name C & (%s))"%frag_name)
# trim hydrogens
if (self.hyd == 'none'):
cmd.remove("("+frag_name+" and hydro)")
elif (self.hyd == 'auto'):
if cmd.count_atoms("("+src_sele+") and hydro")==0:
cmd.remove("("+frag_name+" and hydro)")
# add n-cap (if appropriate)
if self.n_cap in [ 'acet' ]:
if not cmd.count_atoms("elem C & !(%s) & (bto. (name N & (%s))) & !resn ACE "%
(src_sele,src_sele)):
if cmd.count_atoms("name N & (%s)"%(frag_name))==1:
if self.n_cap == 'acet':
editor.attach_amino_acid("name N & (%s)"%(frag_name), 'ace')
if cmd.count_atoms("hydro & bound_to (name N & bound_to (name C & (%s)))"%frag_name):
cmd.h_fix("name N & (%s)"%frag_name)
# trim hydrogens
if (self.hyd == 'none'):
cmd.remove("("+frag_name+" and hydro)")
elif (self.hyd == 'auto'):
if cmd.count_atoms("("+src_sele+") and hydro")==0:
cmd.remove("("+frag_name+" and hydro)")
cartoon = (cmd.count_atoms("(%s & name CA & rep cartoon)"%src_sele)>0)
sticks = (cmd.count_atoms("(%s & name CA & rep sticks)"%src_sele)>0)
cmd.delete(obj_name)
key = rot_type
lib = None
if self.dep == 'dep':
try:
result = cmd.phi_psi("%s"%src_sele)
if len(result)==1:
(phi,psi) = list(result.values())[0]
(phi,psi) = (int(10*round(phi/10)),int(10*(round(psi/10))))
key = (rot_type,phi,psi)
if key not in self.dep_library:
(phi,psi) = (int(20*round(phi/20)),int(20*(round(psi/20))))
key = (rot_type,phi,psi)
if key not in self.dep_library:
(phi,psi) = (int(60*round(phi/60)),int(60*(round(psi/60))))
key = (rot_type,phi,psi)
lib = self.dep_library.get(key,None)
except:
pass
if lib == None:
key = rot_type
lib = self.ind_library.get(key,None)
if (lib!= None) and self.dep == 'dep':
print(' Mutagenesis: no phi/psi, using backbone-independent rotamers.')
if lib != None:
state = 1
for a in lib:
cmd.create(obj_name,frag_name,1,state)
if state == 1:
cmd.select(mut_sele,"(byres (%s like %s))"%(obj_name,src_sele))
if rot_type=='PRO':
cmd.unbond("(%s & name N)"%mut_sele,"(%s & name CD)"%mut_sele)
for b in a.keys():
if b!='FREQ':
cmd.set_dihedral("(%s & n;%s)"%(mut_sele,b[0]),
"(%s & n;%s)"%(mut_sele,b[1]),
"(%s & n;%s)"%(mut_sele,b[2]),
"(%s & n;%s)"%(mut_sele,b[3]),
a[b],state=state)
else:
cmd.set_title(obj_name,state,"%1.1f%%"%(a[b]*100))
if rot_type=='PRO':
cmd.bond("(%s & name N)"%mut_sele,"(%s & name CD)"%mut_sele)
state = state + 1
cmd.delete(frag_name)
print(" Mutagenesis: %d rotamers loaded."%len(lib))
if self.bump_check:
cmd.delete(bump_name)
cmd.create(bump_name,
"(((byobj %s) within 6 of (%s and not name N+C+CA+O+H+HA)) and (not (%s)))|(%s)"%
(src_sele,mut_sele,src_sele,mut_sele),singletons=1)
cmd.color("gray50",bump_name+" and elem C")
cmd.set("seq_view",0,bump_name,quiet=1)
cmd.hide("everything",bump_name)
if ((cmd.select(tmp_sele1, "(name N & (%s in (neighbor %s)))"%
(bump_name,src_sele)) == 1) and
(cmd.select(tmp_sele2, "(name C & (%s in %s))"%
(bump_name,mut_sele)) == 1)):
cmd.bond(tmp_sele1,tmp_sele2)
if ((cmd.select(tmp_sele1,"(name C & (%s in (neighbor %s)))"%
(bump_name,src_sele)) == 1) and
(cmd.select(tmp_sele2,"(name N & (%s in %s))"%
(bump_name,mut_sele)) == 1)):
cmd.bond(tmp_sele1,tmp_sele2)
cmd.delete(tmp_sele1)
cmd.delete(tmp_sele2)
cmd.protect("%s and not (%s in (%s and not name N+C+CA+O+H+HA))"%
(bump_name,bump_name,mut_sele))
cmd.sculpt_activate(bump_name)
cmd.show("cgo",bump_name)
# draw the bumps
cmd.set("sculpt_vdw_vis_mode",1,bump_name)
state = 1
score_best = 1e6
for a in lib:
score = cmd.sculpt_iterate(bump_name, state, 1)
self.bump_scores.append(score)
if score < score_best:
state_best = state
score_best = score
state = state + 1
cmd.delete(mut_sele)
else:
cmd.create(obj_name,frag_name,1,1)
print(" Mutagenesis: no rotamers found in library.")
cmd.set("seq_view",0,obj_name,quiet=1)
pymol.util.cbaw(obj_name)
cmd.hide("("+obj_name+")")
cmd.show(self.rep,obj_name)
cmd.show('lines',obj_name) #neighbor always show lines
if cartoon:
cmd.show("cartoon",obj_name)
if sticks:
cmd.show("sticks",obj_name)
cmd.set('auto_zoom',auto_zoom,quiet=1)
cmd.delete(frag_name)
cmd.frame(state_best)
cmd.unpick()
cmd.feedback("pop")
def optAlign( sel1, sel2 ):
"""
optAlign performs the Kabsch alignment algorithm upon the alpha-carbons of two selections.
Example: optAlign MOL1 and i. 20-40, MOL2 and i. 102-122
Example 2: optAlign 1GGZ and i. 4-146 and n. CA, 1CLL and i. 4-146 and n. CA
Two RMSDs are returned. One comes from the Kabsch algorithm and the other from
PyMol based upon your selections.
By default, this program will optimally align the ALPHA CARBONS of the selections provided.
To turn off this feature remove the lines between the commented "REMOVE ALPHA CARBONS" below.
@param sel1: First PyMol selection with N-atoms
@param sel2: Second PyMol selection with N-atoms
"""
cmd.reset()
# make the lists for holding coordinates
# partial lists
stored.sel1 = []
stored.sel2 = []
# full lists
stored.mol1 = []
stored.mol2 = []
# -- CUT HERE
sel1 += " and N. CA"
sel2 += " and N. CA"
# -- CUT HERE
# Get the selected coordinates. We
# align these coords.
cmd.iterate_state(1, selector.process(sel1), "stored.sel1.append([x,y,z])")
cmd.iterate_state(1, selector.process(sel2), "stored.sel2.append([x,y,z])")
# get molecule name
mol1 = cmd.identify(sel1,1)[0][0]
mol2 = cmd.identify(sel2,1)[0][0]
# Get all molecule coords. We do this because
# we have to rotate the whole molcule, not just
# the aligned selection
cmd.iterate_state(1, mol1, "stored.mol1.append([x,y,z])")
cmd.iterate_state(1, mol2, "stored.mol2.append([x,y,z])")
# check for consistency
assert len(stored.sel1) == len(stored.sel2)
L = len(stored.sel1)
assert L > 0
# must alway center the two proteins to avoid
# affine transformations. Center the two proteins
# to their selections.
COM1 = numpy.sum(stored.sel1,axis=0) / float(L)
COM2 = numpy.sum(stored.sel2,axis=0) / float(L)
stored.sel1 -= COM1
stored.sel2 -= COM2
# Initial residual, see Kabsch.
E0 = numpy.sum( numpy.sum(stored.sel1 * stored.sel1,axis=0),axis=0) + numpy.sum( numpy.sum(stored.sel2 * stored.sel2,axis=0),axis=0)
#
# This beautiful step provides the answer. V and Wt are the orthonormal
# bases that when multiplied by each other give us the rotation matrix, U.
# S, (Sigma, from SVD) provides us with the error! Isn't SVD great!
V, S, Wt = numpy.linalg.svd( numpy.dot( numpy.transpose(stored.sel2), stored.sel1))
# we already have our solution, in the results from SVD.
# we just need to check for reflections and then produce
# the rotation. V and Wt are orthonormal, so their det's
# are +/-1.
reflect = float(str(float(numpy.linalg.det(V) * numpy.linalg.det(Wt))))
if reflect == -1.0:
S[-1] = -S[-1]
V[:,-1] = -V[:,-1]
RMSD = E0 - (2.0 * sum(S))
RMSD = numpy.sqrt(abs(RMSD / L))
#U is simply V*Wt
U = numpy.dot(V, Wt)
# rotate and translate the molecule
stored.sel2 = numpy.dot((stored.mol2 - COM2), U)
stored.sel2 = stored.sel2.tolist()
# center the molecule
stored.sel1 = stored.mol1 - COM1
stored.sel1 = stored.sel1.tolist()
# let PyMol know about the changes to the coordinates
cmd.alter_state(1,mol1,"(x,y,z)=stored.sel1.pop(0)")
cmd.alter_state(1,mol2,"(x,y,z)=stored.sel2.pop(0)")
print "RMSD=%f" % RMSD
# make the alignment OBVIOUS
cmd.hide('everything')
cmd.show('ribbon', sel1 + ' or ' + sel2)
cmd.color('gray70', mol1 )
cmd.color('paleyellow', mol2 )
cmd.color('red', 'visible')
cmd.show('ribbon', 'not visible')
cmd.center('visible')
cmd.orient()
cmd.zoom('visible')
def simpAlign( mat1, mat2, name1, name2, mol1=None, mol2=None, align=0, L=0 ): """ optAlign performs the Kabsch alignment algorithm upon the alpha-carbons of two selections. Example: optAlign MOL1 and i. 20-40, MOL2 and i. 102-122 Example 2: optAlign 1GGZ and i. 4-146 and n. CA, 1CLL and i. 4-146 and n. CA Two RMSDs are returned. One comes from the Kabsch algorithm and the other from PyMol based upon your selections. By default, this program will optimally align the ALPHA CARBONS of the selections provided. To turn off this feature remove the lines between the commented "REMOVE ALPHA CARBONS" below. @param sel1: First PyMol selection with N-atoms @param sel2: Second PyMol selection with N-atoms """ # check for consistency assert(len(mat1) == len(mat2)) # must alway center the two proteins to avoid # affine transformations. Center the two proteins # to their selections. COM1 = numpy.sum(mat1,axis=0) / float(L) COM2 = numpy.sum(mat2,axis=0) / float(L) mat1 = mat1 - COM1 mat2 = mat2 - COM2 # Initial residual, see Kabsch. E0 = numpy.sum( numpy.sum(mat1 * mat1,axis=0),axis=0) + numpy.sum( numpy.sum(mat2 * mat2,axis=0),axis=0) # # This beautiful step provides the answer. V and Wt are the orthonormal # bases that when multiplied by each other give us the rotation matrix, U. # S, (Sigma, from SVD) provides us with the error! Isn't SVD great! V, S, Wt = numpy.linalg.svd( numpy.dot( numpy.transpose(mat2), mat1)) # we already have our solution, in the results from SVD. # we just need to check for reflections and then produce # the rotation. V and Wt are orthonormal, so their det's # are +/-1. reflect = float(str(float(numpy.linalg.det(V) * numpy.linalg.det(Wt)))) if reflect == -1.0: S[-1] = -S[-1] V[:,-1] = -V[:,-1] RMSD = E0 - (2.0 * sum(S)) RMSD = numpy.sqrt(abs(RMSD / L)) if ( align == 0 ): return RMSD; assert(mol1 != None) assert(mol2 != None) #U is simply V*Wt U = numpy.dot(V, Wt) # rotate and translate the molecule mat2 = numpy.dot((mol2 - COM2), U) + COM1 stored.sel2 = mat2.tolist() # let PyMol know about the changes to the coordinates cmd.alter_state(1,name2,"(x,y,z)=stored.sel2.pop(0)") print "NumAligned=%d" % L print "RMSD=%f" % RMSD
def affineStretch(selection, stretch):
# stretch molecule using affine transformations
stored.altered = []
cmd.iterate_state(1, selector.process(selection),
f"stored.altered.append([x,{stretch}*y,z])")
cmd.alter_state(1, selection, "(x,y,z) = stored.altered.pop(0)")
# Load frames
cmd.set('all_states', 0)
print "Loading frames..."
for iteration in range(niterations):
# Set coordinates
print "iteration %8d / %8d" % (iteration, niterations)
positions = (10.0 * ncfile.variables['positions'][iteration, replica, :, :]).squeeze()
positions[:,:] = positions[pdb_mapping,:]
xyz = positions.tolist()
xyz_iter = iter(xyz)
#cmd.load_model(model, 'complex', state=iteration+1)
#cmd.frame(iteration+1)
#model = cmd.get_model('complex', state=1)
#cmd.load_model(model, 'complex', state=iteration+1)
cmd.create('complex', 'complex', 1, iteration+1)
cmd.alter_state(iteration+1, 'complex', '(x,y,z) = xyz_iter.next()', space=locals())
#for pdb_index in range(natoms):
#if (pdb_index % 100)==0: print pdb_index
#model_index = model_mapping[pdb_index]
#model.atom[model_index].coord = (10 * ncfile.variables['positions'][iteration, replica, pdb_index, :]).squeeze().tolist()
#for k in range(3):
# model.atom[model_index].coord[k] = float(ncfile.variables['positions'][iteration, replica, pdb_index, k]) * 10.0 # convert to angstroms
#cmd.load_model(model, 'complex', state=iteration+1)
#cmd.load_model(model, 'complex')
print "done"
# Align all states
cmd.intra_fit('all')
def updateColor(self):
selection = 'all'
stored.atoms_charge = []
stored.atoms_colors = []
cmd.map_new('chargyc_map', selection="(all)")
if not self.colorNeutral:
tkMessageBox.showerror("Error", "Set Neutral Color, Please")
return
if not self.colorNegative:
tkMessageBox.showerror("Error", "Set Negative Color, Please")
return
if not self.colorPositive:
tkMessageBox.showerror("Error", "Set Positive Color, Please")
return
cmd.iterate_state(1, '(' + selection + ')',
'stored.atoms_charge.append(partial_charge)')
_i = 0
minValue = None
maxValue = None
while _i < len(stored.atoms_charge):
color = []
if _i == 0:
maxValue = stored.atoms_charge[_i]
minValue = stored.atoms_charge[_i]
if(stored.atoms_charge[_i] > maxValue):
maxValue = stored.atoms_charge[_i]
if stored.atoms_charge[_i] < minValue:
minValue = stored.atoms_charge[_i]
_i += 1
self.minNegativeLbl["text"] = 'Min Found: ' + str(round(minValue, 3))
self.maxPositiveLbl["text"] = 'Max Found: ' + str(round(maxValue, 3))
if(self.scaleNegative == 0.0 and self.scalePositive == 0.0):
self.scaleNegative = round(minValue, 3)
self.scalePositive = round(maxValue, 3)
self.sclSelectNegative.delete(0, "end")
self.sclSelectPositive.delete(0, "end")
self.sclSelectNegative.insert(0, round(minValue, 3))
self.sclSelectPositive.insert(0, round(maxValue, 3))
else:
self.scaleNegative = float(self.sclSelectNegative.get())
self.scalePositive = float(self.sclSelectPositive.get())
minValue = float(self.sclSelectNegative.get())
maxValue = float(self.sclSelectPositive.get())
self.scaleLbl["text"] = 'Scale: ' + str(
self.scaleNegative) + ' to ' + str(self.scalePositive)
middleValue = 0
if(maxValue < 0):
maxValue = 0
if(minValue > 0):
minValue = 0
_i = 0
while _i < len(stored.atoms_charge):
color = []
cmd.set_color("neutral_color", self.colorNeutral[0])
cmd.set_color("positive_color", self.colorPositive[0])
cmd.set_color("negative_color", self.colorNegative[0])
if(stored.atoms_charge[_i] >= middleValue):
if(stored.atoms_charge[_i] == middleValue):
cmd.set_color(str(_i) + "_color", self.colorNeutral[0])
else:
cmd.set_color(str(_i) + "_color", self.getColor(
self.colorNeutral[0], self.colorPositive[0], maxValue, stored.atoms_charge[_i] if stored.atoms_charge[_i] < maxValue else maxValue))
else:
cmd.set_color(str(_i) + "_color", self.getColor(
self.colorNeutral[0], self.colorNegative[0], abs(minValue), abs(stored.atoms_charge[_i]) if abs(stored.atoms_charge[_i]) < abs(minValue) else abs(minValue)))
index = cmd.get_color_index(str(_i) + "_color")
stored.atoms_colors.append(index)
_i += 1
cmd.alter_state(1, '(' + selection + ')',
"color=stored.atoms_colors.pop(0)")
cmd.ramp_new('chargy_ramp', 'chargyc_map', range=[self.scaleNegative, ((self.scaleNegative+self.scalePositive)/2.0), self.scalePositive],
color=['negative_color', 'neutral_color', 'positive_color'])
def eigenfacs_iter(mode):
x = modes[mode-1].array
return iter(x.take(z, 0))
for mode in range(first, min(last, len(modes)) + 1):
name = prefix + '%d' % mode
cmd.delete(name)
if not quiet:
print ' normalmodes: object "%s" for mode %d with freq. %.6f' % \
(name, mode, frequencies[mode-1])
for state in range(1, states+1):
cmd.create(name, selection, 1, state, zoom=0)
cmd.alter_state(state, name,
'(x,y,z) = cpv.add([x,y,z], cpv.scale(myit.next(), myfac))',
space={'cpv': cpv, 'myit': eigenfacs_iter(mode),
'myfac': 1e2 * factor * ((state-1.0)/(states-1.0) - 0.5)})
cmd.delete(selection)
if model == 'calpha':
cmd.set('ribbon_trace_atoms', 1, prefix + '*')
cmd.show_as('ribbon', prefix + '*')
else:
cmd.show_as('lines', prefix + '*')
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.
def optAlignRNA( sel1, sel2 ):
"""
optAlignRNA performs the Kabsch alignment algorithm upon the C1' carbons of two selections.
Example: optAlignRNA 1JU7 and i. 1-16 and n. C1', 1CLL and i. 4-146 and n. C1'
Two RMSDs are returned. One comes from the Kabsch algorithm and the other from
PyMOL based upon your selections.
This function can be run in a for loop to fit multiple structures with a common prefix name:
for x in cmd.get_names(): optAlignRNA(x, "1JU7_0001")
or get the rmsds for all combinations, do the following:
[[optAlignRNA(x, y) for x in cmd.get_names()] for y in cmd.get_names()]
"""
cmd.reset()
# make the lists for holding coordinates
# partial lists
stored.sel1 = []
stored.sel2 = []
# full lists
stored.mol1 = []
stored.mol2 = []
# -- CUT HERE
sel1 += " and N. C1'"
sel2 += " and N. C1'"
# -- CUT HERE
# Get the selected coordinates. We
# align these coords.
cmd.iterate_state(1, selector.process(sel1), "stored.sel1.append([x,y,z])")
cmd.iterate_state(1, selector.process(sel2), "stored.sel2.append([x,y,z])")
# get molecule name
mol1 = cmd.identify(sel1,1)[0][0]
mol2 = cmd.identify(sel2,1)[0][0]
# Get all molecule coords. We do this because
# we have to rotate the whole molcule, not just
# the aligned selection
cmd.iterate_state(1, mol1, "stored.mol1.append([x,y,z])")
cmd.iterate_state(1, mol2, "stored.mol2.append([x,y,z])")
# check for consistency
assert len(stored.sel1) == len(stored.sel2)
L = len(stored.sel1)
assert L > 0
# must alway center the two proteins to avoid
# affine transformations. Center the two proteins
# to their selections.
COM1 = numpy.sum(stored.sel1,axis=0) / float(L)
COM2 = numpy.sum(stored.sel2,axis=0) / float(L)
stored.sel1 -= COM1
stored.sel2 -= COM2
# Initial residual, see Kabsch.
E0 = numpy.sum( numpy.sum(stored.sel1 * stored.sel1,axis=0),axis=0) + numpy.sum( numpy.sum(stored.sel2 * stored.sel2,axis=0),axis=0)
#
# This beautiful step provides the answer. V and Wt are the orthonormal
# bases that when multiplied by each other give us the rotation matrix, U.
# S, (Sigma, from SVD) provides us with the error! Isn't SVD great!
V, S, Wt = numpy.linalg.svd( numpy.dot( numpy.transpose(stored.sel2), stored.sel1))
# we already have our solution, in the results from SVD.
# we just need to check for reflections and then produce
# the rotation. V and Wt are orthonormal, so their det's
# are +/-1.
reflect = float(str(float(numpy.linalg.det(V) * numpy.linalg.det(Wt))))
if reflect == -1.0:
S[-1] = -S[-1]
V[:,-1] = -V[:,-1]
RMSD = E0 - (2.0 * sum(S))
RMSD = numpy.sqrt(abs(RMSD / L))
#U is simply V*Wt
U = numpy.dot(V, Wt)
# rotate and translate the molecule
stored.sel2 = numpy.dot((stored.mol2 - COM2), U)
stored.sel2 = stored.sel2.tolist()
# center the molecule
stored.sel1 = stored.mol1 - COM1
stored.sel1 = stored.sel1.tolist()
# let PyMol know about the changes to the coordinates
cmd.alter_state(1,mol1,"(x,y,z)=stored.sel1.pop(0)")
cmd.alter_state(1,mol2,"(x,y,z)=stored.sel2.pop(0)")
#print("Moved: %s Reference: %s RMSD = %f" % mol1, mol2, RMSD)
print("% s, % s,% 5.3f" % (mol1, mol2, RMSD))
# make the alignment OBVIOUS
cmd.hide("everything")
cmd.show("ribbon", sel1 + " or " + sel2)
cmd.color("gray70", mol1 )
cmd.color("magenta", mol2 )
cmd.color("red", "visible")
cmd.show("ribbon", "not visible")
cmd.center("visible")
cmd.orient()
cmd.zoom("visible")
def _normalmodes(selection, cutoff, force, mass,
first, last, choose, substruct, blocksize,
exe, diag_exe, prefix, states, factor, clean, quiet, wiz=None):
import tempfile, subprocess, os, shutil, sys
from chempy import cpv
cutoff, force = float(cutoff), float(force)
first, last, blocksize = int(first), int(last), int(blocksize)
clean, quiet = int(clean), int(quiet)
exe = cmd.exp_path(exe)
diag_exe = cmd.exp_path(diag_exe)
tempdir = tempfile.mkdtemp()
if not quiet:
print ' normalmodes: Temporary directory is', tempdir
try:
sele_name = cmd.get_unused_name('__pdbmat')
except AttributeError:
sele_name = '__pdbmat'
try:
filename = os.path.join(tempdir, 'mobile.pdb')
commandfile = os.path.join(tempdir, 'pdbmat.dat')
cmd.select(sele_name, '(%s) and not hetatm' % (selection))
cmd.save(filename, sele_name)
f = open(commandfile, 'w')
f.write('''! pdbmat file
Coordinate FILENAME = %s
MATRIx FILENAME = matrix.sdijb
INTERACtion DISTance CUTOF = %.3f
INTERACtion FORCE CONStant = %.3f
Origin of MASS values = %s
Output PRINTing level = 0
MATRix FORMat = BINA
''' % (filename, cutoff, force, mass.upper()))
f.close()
if not quiet:
print ' normalmodes: running', exe, '...'
if wiz is not None:
wiz.message[1] = 'running pdbmat'
cmd.refresh_wizard()
process = subprocess.Popen([exe], cwd=tempdir,
stderr=subprocess.STDOUT, stdout=subprocess.PIPE)
for line in process.stdout:
if not quiet:
sys.stdout.write(line)
natoms = len(open(os.path.join(tempdir, 'pdbmat.xyzm')).readlines())
if natoms != cmd.count_atoms(sele_name):
print 'Error: pdbmat did not recognize all atoms'
raise CmdException
commandfile = os.path.join(tempdir, 'diagrtb.dat')
f = open(commandfile, 'w')
f.write('''! diagrtb file
MATRIx FILENAME = matrix.sdijb
COORdinates filename = pdbmat.xyzm
Eigenvector OUTPut filename= diagrtb.eigenfacs
Nb of VECTors required = %d
EigeNVALues chosen = %s
Type of SUBStructuring = %s
Nb of residues per BLOck = %d
Origin of MASS values = %s
Temporary files cleaning = ALL
MATRix FORMat = BINA
Output PRINting level = 0
''' % (last, choose.upper(), substruct.upper(), blocksize, mass.upper()))
f.close()
exe = diag_exe
if not quiet:
print ' normalmodes: running', exe, '...'
if wiz is not None:
wiz.message[1] = 'running diagrtb'
cmd.refresh_wizard()
process = subprocess.Popen([exe], cwd=tempdir,
stderr=subprocess.STDOUT, stdout=subprocess.PIPE)
for line in process.stdout:
if not quiet:
sys.stdout.write(line)
eigenfacs, frequencies = parse_eigenfacs(
os.path.join(tempdir, 'diagrtb.eigenfacs'), last)
if wiz is not None:
wiz.message[1] = 'generating objects'
cmd.refresh_wizard()
states = int(states)
factor = float(factor)
if factor < 0:
factor = natoms**0.5
for mode in range(first, last+1):
name = prefix + '%d' % mode
cmd.delete(name)
if not quiet:
print ' normalmodes: object "%s" for mode %d with freq. %.6f' % \
(name, mode, frequencies[mode-1])
for state in range(1, states+1):
cmd.create(name, sele_name, 1, state, zoom=0)
cmd.alter_state(state, name,
'(x,y,z) = cpv.add([x,y,z], cpv.scale(myit.next(), myfac))',
space={'cpv': cpv, 'myit': iter(eigenfacs[mode-1]),
'myfac': factor * (state - (states+1)/2.0)})
# if CA only selection, show ribbon trace
if natoms == cmd.count_atoms('(%s) and name CA' % sele_name):
cmd.set('ribbon_trace_atoms', 1, prefix + '*')
cmd.show_as('ribbon', prefix + '*')
# store results
if not hasattr(stored, 'nma_results'):
stored.nma_results = []
stored.nma_results.append({
'facs': eigenfacs,
'freq': frequencies,
'sele': sele_name,
})
except OSError:
print 'Cannot execute "%s", please provide full path to executable' % (exe)
except CmdException, e:
print ' normalmodes: failed!', e
def display_graphpool(pdb_id, pdb_path):
'''
'''
# Load PDB
cmd.bg_color('white')
cmd.load(pdb_path + pdb_id[:-2] + '.pdb')
cmd.split_chains(pdb_id[:-2])
for name in cmd.get_names('objects', 0, '(all)'):
if not name.endswith(pdb_id[-1].upper()) and name.startswith(
pdb_id[:4]):
cmd.delete(name)
else:
zero_residues(name)
cmd.reset()
pdb_id2 = pdb_id + 'copy'
cmd.create(pdb_id2, pdb_id)
cmd.color('grey', pdb_id)
cmd.hide('everything', pdb_id)
cmd.show_as('lines', pdb_id + ' and (name ca)')
cmd.set('line_width', 5)
cmd.set_bond('line_width', 5, pdb_id + ' and (name ca)')
cmd.show('spheres', pdb_id + ' and name ca')
cmd.set('sphere_transparency', 0.0, pdb_id + ' and name ca')
cmd.set('sphere_scale', 0.5, pdb_id + ' and name ca')
data = cmd.get_coords(selection=pdb_id + ' and name ca', state=1)
data_ = []
cmd.set('dash_color', 'marine')
cmd.set('dash_width', 1.0)
j = 55
for i in range(len(data)):
if i % 2 == 0 and i + 1 < len(data):
data[i] = np.mean(data[i:i + 2], axis=0)
data[i + 1] = np.array([10000, 10000, 10000])
#cmd.distance('d'+str(i)+str(j), pdb_id + ' and name ca and res ' + str(i), pdb_id + ' and name ca and res ' + str(j))
#cmd.hide('labels', 'd'+str(i)+str(j))
cmd.color('red', pdb_id2)
cmd.hide('everything', pdb_id2)
cmd.show_as('lines', pdb_id2 + ' and (name ca)')
cmd.set('line_width', 5)
cmd.set_bond('line_width', 5, pdb_id2 + ' and (name ca)')
cmd.show('spheres', pdb_id2 + ' and name ca')
cmd.set('sphere_transparency', 0.0, pdb_id2 + ' and name ca')
cmd.set('sphere_scale', 0.5, pdb_id2 + ' and name ca')
for i in range(len(data)):
if i % 2 == 0 and i + 1 < len(data):
cmd.alter_state(1, pdb_id2 + ' and name ca and res ' + str(i),
'(x,y,z)=' + str(tuple(data[i])))
else:
cmd.hide('spheres', pdb_id2 + ' and name ca and res ' + str(i))
pdb_id3 = pdb_id + 'copy2'
cmd.create(pdb_id3, pdb_id2)
cmd.color('red', pdb_id3)
cmd.hide('everything', pdb_id3)
cmd.show_as('lines', pdb_id3 + ' and (name ca)')
cmd.set('line_width', 5)
cmd.set_bond('line_width', 5, pdb_id3 + ' and (name ca)')
cmd.show('spheres', pdb_id3 + ' and name ca')
cmd.set('sphere_transparency', 0.8, pdb_id3 + ' and name ca')
for i in range(len(data)):
if i % 2 == 0 and i + 1 < len(data):
cmd.set('sphere_scale', np.random.uniform(1.0, 4.5),
pdb_id3 + ' and name ca and res ' + str(i))
else:
cmd.hide('spheres', pdb_id2 + ' and name ca and res ' + str(i))
def _normalmodes(selection,
cutoff,
force,
mass,
first,
last,
choose,
substruct,
blocksize,
exe,
diag_exe,
prefix,
states,
factor,
clean,
quiet,
wiz=None):
import tempfile, subprocess, os, shutil, sys
from chempy import cpv
cutoff, force = float(cutoff), float(force)
first, last, blocksize = int(first), int(last), int(blocksize)
clean, quiet = int(clean), int(quiet)
exe = cmd.exp_path(exe)
diag_exe = cmd.exp_path(diag_exe)
tempdir = tempfile.mkdtemp()
if not quiet:
print(' normalmodes: Temporary directory is', tempdir)
try:
sele_name = cmd.get_unused_name('__pdbmat')
except AttributeError:
sele_name = '__pdbmat'
try:
filename = os.path.join(tempdir, 'mobile.pdb')
commandfile = os.path.join(tempdir, 'pdbmat.dat')
cmd.select(sele_name, '(%s) and not hetatm' % (selection))
cmd.save(filename, sele_name)
f = open(commandfile, 'w')
f.write('''! pdbmat file
Coordinate FILENAME = %s
MATRIx FILENAME = matrix.sdijb
INTERACtion DISTance CUTOF = %.3f
INTERACtion FORCE CONStant = %.3f
Origin of MASS values = %s
Output PRINTing level = 0
MATRix FORMat = BINA
''' % (filename, cutoff, force, mass.upper()))
f.close()
if not quiet:
print(' normalmodes: running', exe, '...')
if wiz is not None:
wiz.message[1] = 'running pdbmat'
cmd.refresh_wizard()
process = subprocess.Popen([exe],
cwd=tempdir,
universal_newlines=True,
stderr=subprocess.STDOUT,
stdout=subprocess.PIPE)
for line in process.stdout:
if not quiet:
sys.stdout.write(line)
try:
natoms = len(
open(os.path.join(tempdir, 'pdbmat.xyzm')).readlines())
except Exception as e:
print(e)
natoms = cmd.count_atoms(sele_name)
if natoms != cmd.count_atoms(sele_name):
print('Error: pdbmat did not recognize all atoms')
raise CmdException
commandfile = os.path.join(tempdir, 'diagrtb.dat')
f = open(commandfile, 'w')
f.write('''! diagrtb file
MATRIx FILENAME = matrix.sdijb
COORdinates filename = %s
Eigenvector OUTPut filename= diagrtb.eigenfacs
Nb of VECTors required = %d
EigeNVALues chosen = %s
Type of SUBStructuring = %s
Nb of residues per BLOck = %d
Origin of MASS values = %s
Temporary files cleaning = ALL
MATRix FORMat = BINA
Output PRINting level = 0
''' % (filename, last, choose.upper(), substruct.upper(), blocksize,
mass.upper()))
f.close()
exe = diag_exe
if not quiet:
print(' normalmodes: running', exe, '...')
if wiz is not None:
wiz.message[1] = 'running diagrtb'
cmd.refresh_wizard()
process = subprocess.Popen([exe],
cwd=tempdir,
universal_newlines=True,
stderr=subprocess.STDOUT,
stdout=subprocess.PIPE)
for line in process.stdout:
if not quiet:
sys.stdout.write(line)
eigenfacs, frequencies = parse_eigenfacs(
os.path.join(tempdir, 'diagrtb.eigenfacs'), last)
if wiz is not None:
wiz.message[1] = 'generating objects'
cmd.refresh_wizard()
states = int(states)
factor = float(factor)
if factor < 0:
factor = natoms**0.5
for mode in range(first, last + 1):
name = prefix + '%d' % mode
cmd.delete(name)
if not quiet:
print(' normalmodes: object "%s" for mode %d with freq. %.6f' % \
(name, mode, frequencies[mode-1]))
for state in range(1, states + 1):
cmd.create(name, sele_name, 1, state, zoom=0)
cmd.alter_state(
state,
name,
'(x,y,z) = cpv.add([x,y,z], cpv.scale(next(myit), myfac))',
space={
'cpv': cpv,
'myit': iter(eigenfacs[mode - 1]),
'next': next,
'myfac': factor * (state - (states + 1) / 2.0)
})
# if CA only selection, show ribbon trace
if natoms == cmd.count_atoms('(%s) and name CA' % sele_name):
cmd.set('ribbon_trace_atoms', 1, prefix + '*')
cmd.show_as('ribbon', prefix + '*')
# store results
if not hasattr(stored, 'nma_results'):
stored.nma_results = []
stored.nma_results.append({
'facs': eigenfacs,
'freq': frequencies,
'sele': sele_name,
})
except OSError:
print('Cannot execute "%s", please provide full path to executable' %
(exe))
except CmdException as e:
print(' normalmodes: failed!', e)
finally:
if clean:
shutil.rmtree(tempdir)
elif not quiet:
print(' normalmodes: Working directory "%s" not removed!' %
(tempdir))
# cmd.delete(sele_name)
if wiz is not None:
cmd.set_wizard_stack(
[w for w in cmd.get_wizard_stack() if w != wiz])
for mode in range(first, min(last, len(modes)) + 1):
name = prefix + '%d' % mode
cmd.delete(name)
if not quiet:
print(' normalmodes: object "%s" for mode %d with freq. %.6f' % \
(name, mode, frequencies[mode-1]))
for state in range(1, states + 1):
cmd.create(name, selection, 1, state, zoom=0)
cmd.alter_state(
state,
name,
'(x,y,z) = cpv.add([x,y,z], cpv.scale(myit.next(), myfac))',
space={
'cpv': cpv,
'myit': eigenfacs_iter(mode),
'myfac':
1e2 * factor * ((state - 1.0) / (states - 1.0) - 0.5)
})
cmd.delete(selection)
if model == 'calpha':
cmd.set('ribbon_trace_atoms', 1, prefix + '*')
cmd.show_as('ribbon', prefix + '*')
else:
cmd.show_as('lines', prefix + '*')
def normalmodes_prody(selection,
cutoff=15,
def normalmodes_mmtk(selection,
cutoff=12.0,
ff='Deformation',
first=7,
last=10,
prefix='mmtk',
states=7,
factor=-1,
quiet=1):
'''
DESCRIPTION
Fast normal modes for large proteins using an elastic network model (CA only)
Based on:
http://dirac.cnrs-orleans.fr/MMTK/using-mmtk/mmtk-example-scripts/normal-modes/
'''
try:
import MMTK
except ImportError:
print('Failed to import MMTK, please add to PYTHONPATH')
raise CmdException
selection = selector.process(selection)
cutoff = float(cutoff)
first, last = int(first), int(last)
states, factor, quiet = int(states), float(factor), int(quiet)
from math import log
from chempy import cpv
from MMTK import InfiniteUniverse
from MMTK.PDB import PDBConfiguration
from MMTK.Proteins import Protein
from MMTK.NormalModes import NormalModes
from MMTK.ForceFields import DeformationForceField, CalphaForceField
from MMTK.FourierBasis import FourierBasis, estimateCutoff
from MMTK.NormalModes import NormalModes, SubspaceNormalModes
model = 'calpha'
ff = ff.lower()
if 'deformationforcefield'.startswith(ff):
forcefield = DeformationForceField(cutoff=cutoff / 10.)
elif 'calphaforcefield'.startswith(ff):
forcefield = CalphaForceField(cutoff=cutoff / 10.)
elif 'amber94forcefield'.startswith(ff):
from MMTK.ForceFields import Amber94ForceField
forcefield = Amber94ForceField()
model = 'all'
else:
raise NotImplementedError('unknown ff = ' + str(ff))
if not quiet:
print(' Forcefield:', forcefield.__class__.__name__)
if model == 'calpha':
selection = '(%s) and polymer and name CA' % (selection)
f = StringIO(cmd.get_pdbstr(selection))
conf = PDBConfiguration(f)
items = conf.createPeptideChains(model)
universe = InfiniteUniverse(forcefield)
universe.protein = Protein(*items)
nbasis = max(10, universe.numberOfAtoms() / 5)
cutoff, nbasis = estimateCutoff(universe, nbasis)
if not quiet:
print(" Calculating %d low-frequency modes." % nbasis)
if cutoff is None:
modes = NormalModes(universe)
else:
subspace = FourierBasis(universe, cutoff)
modes = SubspaceNormalModes(universe, subspace)
natoms = modes.array.shape[1]
frequencies = modes.frequencies
if factor < 0:
factor = log(natoms)
if not quiet:
print(' set factor to %.2f' % (factor))
if True: # cmd.count_atoms(selection) != natoms:
import tempfile, os
from MMTK import DCD
filename = tempfile.mktemp(suffix='.pdb')
sequence = DCD.writePDB(universe, None, filename)
z = [a.index for a in sequence]
selection = cmd.get_unused_name('_')
cmd.load(filename, selection, zoom=0)
os.remove(filename)
if cmd.count_atoms(selection) != natoms:
print('hmm... still wrong number of atoms')
def eigenfacs_iter(mode):
x = modes[mode - 1].array
return iter(x.take(z, 0))
for mode in range(first, min(last, len(modes)) + 1):
name = prefix + '%d' % mode
cmd.delete(name)
if not quiet:
print(' normalmodes: object "%s" for mode %d with freq. %.6f' % \
(name, mode, frequencies[mode-1]))
for state in range(1, states + 1):
cmd.create(name, selection, 1, state, zoom=0)
cmd.alter_state(
state,
name,
'(x,y,z) = cpv.add([x,y,z], cpv.scale(next(myit), myfac))',
space={
'cpv': cpv,
'myit': eigenfacs_iter(mode),
'next': next,
'myfac':
1e2 * factor * ((state - 1.0) / (states - 1.0) - 0.5)
})
cmd.delete(selection)
if model == 'calpha':
cmd.set('ribbon_trace_atoms', 1, prefix + '*')
cmd.show_as('ribbon', prefix + '*')
else:
cmd.show_as('lines', prefix + '*')
def symset(prefix="sym", object=-1, x=0, y=0, z=0, opList=[]):
if object == -1:
object = cmd.get_names()[0]
cell = [float(x), float(y), float(z)]
view = cmd.get_view()
cmd.show("lines", object)
sgInfo = cmd.get_symmetry(object)
raw_ops = []
for s in sgtbx.space_group_info(sgInfo[6]).group():
raw_ops.append(str(s))
if len(opList) == 0:
for i in range(len(raw_ops)):
opList.append(i)
opMatrices = []
vars = ["x", "y", "z"]
#CREATE 4X4 MATRICES FOR SYMMETRY OPERATORS
for i, raw_op in enumerate(raw_ops):
ops = raw_op.split(",")
matrix = [[0, 0, 0, 0], [0, 0, 0, 0], [0, 0, 0, 0], [0, 0, 0, 1]]
for j in range(len(ops)):
for k in range(len(vars)):
index = ops[j].find(vars[k])
if index != -1:
if index == 0:
matrix[k][j] = 1
elif ops[j][index - 1] == "-":
matrix[k][j] = -1
else:
matrix[k][j] = 1
index = ops[j].find("/")
if index != -1:
matrix[3][j] = float(ops[j][index - 1]) / float(
ops[j][index + 1])
opMatrices.append(matrix)
a, b, c, alpha, beta, gamma = sgInfo[0:6]
ca = math.cos(math.radians(alpha))
cb = math.cos(math.radians(beta))
cg = math.cos(math.radians(gamma))
sb = math.sin(math.radians(beta))
sg = math.sin(math.radians(gamma))
fracToOrt = N.array([[a, b * cg, c * cb, 0.0],
[0.0, b * sg, c * (ca - cb * cg) / sg, 0.0],
[
0.0, 0.0,
c * sb * math.sqrt(1.0 - ((cb * cg - ca) /
(sb * sg))**2), 0.0
], [0.0, 0.0, 0.0, 1.0]])
fracToOrt = fracToOrt.transpose()
ortToFrac = inv(fracToOrt)
stored.atoms = []
cmd.iterate_state(1, object, "stored.atoms.append([x,y,z,1])")
stored.atoms = N.array(stored.atoms)
fracCoords = N.dot(stored.atoms, ortToFrac)
for i in opList:
try:
op = opMatrices[i]
except:
print("Bad symmetry partner numbers. Try again.")
quit()
copy = "%s%02d_%d_%d_%d" % (prefix, i, x, y, z)
cmd.copy(copy, object)
newCoordsFrac = N.dot(fracCoords, op)
stored.newCoords = N.dot(newCoordsFrac, fracToOrt)
stored.j = 0
cmd.alter_state(
1, copy,
"x,y,z = stored.newCoords[stored.j][0], stored.newCoords[stored.j][1], stored.newCoords[stored.j][2]; stored.j = stored.j + 1"
)
xSum = ySum = zSum = 0.0
for a, b, c in newCoordsFrac:
xSum += a
ySum += b
zSum += c
center = N.array([xSum, ySum, zSum])
center = center / len(stored.newCoords)
shift = [
cell[0] - math.floor(center[0]), cell[1] - math.floor(center[1]),
cell[2] - math.floor(center[2])
]
cell_shift(copy, shift[0], shift[1], shift[2], 0)
'''
#COPIES COORDINATES OF EACH ATOM TO CORRESPONDING ONE IN GIVEN SYMMETRY PARTNER
#cmd.alter_state(1, copy, "x,y,z = cmd.sym_partner([x,y,z], stored.tmpOp)")
#MOVES SYMMETRY PARTNER TO PROPER LATTICE COORDINATES AND CORRECTS FOR NATIVE LATTICE POSITION ERROR
#stored.xSum,stored.ySum,stored.zSum = 0.0,0.0,0.0
#atoms = cmd.count_atoms(copy)
#cmd.iterate_state(1, copy, "stored.xSum = stored.xSum + x; stored.ySum = stored.ySum + y; stored.zSum = stored.zSum + z")
#xMean = stored.xSum / atoms
#yMean = stored.ySum / atoms
#zMean = stored.zSum / atoms
#xError, yError, zError = N.dot(N.array([xMean,yMean,zMean]), stored.ortToFrac)
#dX,dY,dZ = cell[0]-math.floor(xError), cell[1]-math.floor(yError), cell[2]-math.floor(zError)
#cell_shift(copy,dX,dY,dZ, 0)
'''
cmd.hide("everything", object)
cmd.set_view(view)
def do_library(self):
cmd=self.cmd
pymol=cmd._pymol
if not ((cmd.count_atoms("(%s) and name N"%src_sele)==1) and
(cmd.count_atoms("(%s) and name C"%src_sele)==1) and
(cmd.count_atoms("(%s) and name O"%src_sele)==1)):
self.clear()
return 1
cmd.feedback("push")
cmd.feedback("disable","selector","everythin")
cmd.feedback("disable","editor","actions")
self.prompt = [ 'Loading rotamers...']
self.bump_scores = []
state_best = 0
pymol.stored.name = 'residue'
cmd.iterate("first (%s)"%src_sele,'stored.name=model+"/"+segi+"/"+chain+"/"+resn+"`"+resi')
self.res_text = pymol.stored.name
cmd.select("_seeker_hilight",src_sele)
auto_zoom = cmd.get_setting_text('auto_zoom')
cmd.set('auto_zoom',"0",quiet=1)
cmd.frame(0)
cmd.delete(frag_name)
if self.auto_center:
cmd.center(src_sele,animate=-1)
self.lib_mode = self.mode
if self.lib_mode=="current":
pymol.stored.resn=""
cmd.iterate("(%s & name CA)"%src_sele,"stored.resn=resn")
rot_type = _rot_type_xref.get(pymol.stored.resn,pymol.stored.resn)
if (self.c_cap!='none') or (self.n_cap!='none') or (self.hyd != 'auto'):
self.lib_mode = rot_type # force fragment-based load
else:
cmd.create(frag_name,src_sele,1,1)
if self.c_cap=='open':
cmd.remove("%s and name OXT"%frag_name)
if self.lib_mode!='current':
rot_type = self.lib_mode
frag_type = self.lib_mode
if (self.n_cap == 'posi') and (frag_type[0:3]!='NT_'):
if not ( cmd.count_atoms(
"elem C & !(%s) & (bto. (name N & (%s))) &! resn ACE"%
(src_sele,src_sele))):
# use N-terminal fragment
frag_type ="NT_"+frag_type
if (self.c_cap == 'nega') and (frag_type[0:3]!='CT_'):
if not ( cmd.count_atoms("elem N & !(%s) & (bto. (name C & (%s))) & !resn NME+NHH"%
(src_sele,src_sele))):
# use C-terminal fragment
frag_type ="CT_"+frag_type
if rot_type[0:3] in [ 'NT_', 'CT_' ]:
rot_type = rot_type[3:]
rot_type = _rot_type_xref.get(rot_type, rot_type)
cmd.fragment(frag_type.lower(), frag_name, origin=0)
# trim off hydrogens
if (self.hyd == 'none'):
cmd.remove("("+frag_name+" and hydro)")
elif (self.hyd == 'auto'):
if cmd.count_atoms("("+src_sele+") and hydro")==0:
cmd.remove("("+frag_name+" and hydro)")
# copy identifying information
cmd.alter("?%s & name CA" % src_sele, "stored.identifiers = (segi, chain, resi, ss, color)", space=self.space)
cmd.alter("?%s" % frag_name, "(segi, chain, resi, ss) = stored.identifiers[:4]", space=self.space)
# move the fragment
if ((cmd.count_atoms("(%s & name CB)"%frag_name)==1) and
(cmd.count_atoms("(%s & name CB)"%src_sele)==1)):
cmd.pair_fit("(%s & name CA)"%frag_name,
"(%s & name CA)"%src_sele,
"(%s & name CB)"%frag_name,
"(%s & name CB)"%src_sele,
"(%s & name C)"%frag_name,
"(%s & name C)"%src_sele,
"(%s & name N)"%frag_name,
"(%s & name N)"%src_sele)
else:
cmd.pair_fit("(%s & name CA)"%frag_name,
"(%s & name CA)"%src_sele,
"(%s & name C)"%frag_name,
"(%s & name C)"%src_sele,
"(%s & name N)"%frag_name,
"(%s & name N)"%src_sele)
# fix the carbonyl position...
cmd.iterate_state(1,"(%s & name O)"%src_sele,"stored.list=[x,y,z]")
cmd.alter_state(1,"(%s & name O)"%frag_name,"(x,y,z)=stored.list")
if cmd.count_atoms("(%s & name OXT)"%src_sele):
cmd.iterate_state(1,"(%s & name OXT)"%src_sele,"stored.list=[x,y,z]")
cmd.alter_state(1,"(%s & name OXT)"%frag_name,"(x,y,z)=stored.list")
elif cmd.count_atoms("(%s & name OXT)"%frag_name): # place OXT if no template exists
angle = cmd.get_dihedral("(%s & name N)"%frag_name,
"(%s & name CA)"%frag_name,
"(%s & name C)"%frag_name,
"(%s & name O)"%frag_name)
cmd.protect("(%s & name O)"%frag_name)
cmd.set_dihedral("(%s & name N)"%frag_name,
"(%s & name CA)"%frag_name,
"(%s & name C)"%frag_name,
"(%s & name OXT)"%frag_name,180.0+angle)
cmd.deprotect(frag_name)
# fix the hydrogen position (if any)
if cmd.count_atoms("(hydro and bound_to (name N & (%s)))"%frag_name)==1:
if cmd.count_atoms("(hydro and bound_to (name N & (%s)))"%src_sele)==1:
cmd.iterate_state(1,"(hydro and bound_to (name N & (%s)))"%src_sele,
"stored.list=[x,y,z]")
cmd.alter_state(1,"(hydro and bound_to (name N & (%s)))"%frag_name,
"(x,y,z)=stored.list")
elif cmd.select(tmp_sele1,"(name C & bound_to (%s and elem N))"%src_sele)==1:
# position hydro based on location of the carbonyl
angle = cmd.get_dihedral("(%s & name C)"%frag_name,
"(%s & name CA)"%frag_name,
"(%s & name N)"%frag_name,
tmp_sele1)
cmd.set_dihedral("(%s & name C)"%frag_name,
"(%s & name CA)"%frag_name,
"(%s & name N)"%frag_name,
"(%s & name H)"%frag_name,180.0+angle)
cmd.delete(tmp_sele1)
# add c-cap (if appropriate)
if self.c_cap in [ 'amin', 'nmet' ]:
if not cmd.count_atoms("elem N & !(%s) & (bto. (name C & (%s))) & !resn NME+NHH"%
(src_sele,src_sele)):
if cmd.count_atoms("name C & (%s)"%(frag_name))==1:
if self.c_cap == 'amin':
editor.attach_amino_acid("name C & (%s)"%(frag_name), 'nhh')
elif self.c_cap == 'nmet':
editor.attach_amino_acid("name C & (%s)"%(frag_name), 'nme')
if cmd.count_atoms("hydro & bound_to (name N & bound_to (name C & (%s)))"%frag_name):
cmd.h_fix("name N & bound_to (name C & (%s))"%frag_name)
# trim hydrogens
if (self.hyd == 'none'):
cmd.remove("("+frag_name+" and hydro)")
elif (self.hyd == 'auto'):
if cmd.count_atoms("("+src_sele+") and hydro")==0:
cmd.remove("("+frag_name+" and hydro)")
# add n-cap (if appropriate)
if self.n_cap in [ 'acet' ]:
if not cmd.count_atoms("elem C & !(%s) & (bto. (name N & (%s))) & !resn ACE "%
(src_sele,src_sele)):
if cmd.count_atoms("name N & (%s)"%(frag_name))==1:
if self.n_cap == 'acet':
editor.attach_amino_acid("name N & (%s)"%(frag_name), 'ace')
if cmd.count_atoms("hydro & bound_to (name N & bound_to (name C & (%s)))"%frag_name):
cmd.h_fix("name N & (%s)"%frag_name)
# trim hydrogens
if (self.hyd == 'none'):
cmd.remove("("+frag_name+" and hydro)")
elif (self.hyd == 'auto'):
if cmd.count_atoms("("+src_sele+") and hydro")==0:
cmd.remove("("+frag_name+" and hydro)")
cartoon = (cmd.count_atoms("(%s & name CA & rep cartoon)"%src_sele)>0)
sticks = (cmd.count_atoms("(%s & name CA & rep sticks)"%src_sele)>0)
cmd.delete(obj_name)
key = rot_type
lib = None
if self.dep == 'dep':
try:
result = cmd.phi_psi("%s"%src_sele)
if len(result)==1:
(phi,psi) = list(result.values())[0]
(phi,psi) = (int(10*round(phi/10)),int(10*(round(psi/10))))
key = (rot_type,phi,psi)
if key not in self.dep_library:
(phi,psi) = (int(20*round(phi/20)),int(20*(round(psi/20))))
key = (rot_type,phi,psi)
if key not in self.dep_library:
(phi,psi) = (int(60*round(phi/60)),int(60*(round(psi/60))))
key = (rot_type,phi,psi)
lib = self.dep_library.get(key,None)
except:
pass
if lib is None:
key = rot_type
lib = self.ind_library.get(key,None)
if (lib is not None) and self.dep == 'dep':
print(' Mutagenesis: no phi/psi, using backbone-independent rotamers.')
if lib is not None:
state = 1
for a in lib:
cmd.create(obj_name,frag_name,1,state)
if state == 1:
cmd.select(mut_sele,"(byres (%s like %s))"%(obj_name,src_sele))
if rot_type=='PRO':
cmd.unbond("(%s & name N)"%mut_sele,"(%s & name CD)"%mut_sele)
for b in a.keys():
if b!='FREQ':
cmd.set_dihedral("(%s & n;%s)"%(mut_sele,b[0]),
"(%s & n;%s)"%(mut_sele,b[1]),
"(%s & n;%s)"%(mut_sele,b[2]),
"(%s & n;%s)"%(mut_sele,b[3]),
a[b],state=state)
else:
cmd.set_title(obj_name,state,"%1.1f%%"%(a[b]*100))
if rot_type=='PRO':
cmd.bond("(%s & name N)"%mut_sele,"(%s & name CD)"%mut_sele)
state = state + 1
cmd.delete(frag_name)
print(" Mutagenesis: %d rotamers loaded."%len(lib))
if self.bump_check:
cmd.delete(bump_name)
cmd.create(bump_name,
"(((byobj %s) within 6 of (%s and not name N+C+CA+O+H+HA)) and (not (%s)))|(%s)"%
(src_sele,mut_sele,src_sele,mut_sele),singletons=1)
cmd.color("gray50",bump_name+" and elem C")
cmd.set("seq_view",0,bump_name,quiet=1)
cmd.hide("everything",bump_name)
if ((cmd.select(tmp_sele1, "(name N & (%s in (neighbor %s)))"%
(bump_name,src_sele)) == 1) and
(cmd.select(tmp_sele2, "(name C & (%s in %s))"%
(bump_name,mut_sele)) == 1)):
cmd.bond(tmp_sele1,tmp_sele2)
if ((cmd.select(tmp_sele1,"(name C & (%s in (neighbor %s)))"%
(bump_name,src_sele)) == 1) and
(cmd.select(tmp_sele2,"(name N & (%s in %s))"%
(bump_name,mut_sele)) == 1)):
cmd.bond(tmp_sele1,tmp_sele2)
cmd.delete(tmp_sele1)
cmd.delete(tmp_sele2)
cmd.protect("%s and not (%s in (%s and not name N+C+CA+O+H+HA))"%
(bump_name,bump_name,mut_sele))
cmd.sculpt_activate(bump_name)
cmd.show("cgo",bump_name)
# draw the bumps
cmd.set("sculpt_vdw_vis_mode",1,bump_name)
state = 1
score_best = 1e6
for a in lib:
score = cmd.sculpt_iterate(bump_name, state, 1)
self.bump_scores.append(score)
if score < score_best:
state_best = state
score_best = score
state = state + 1
cmd.delete(mut_sele)
else:
cmd.create(obj_name,frag_name,1,1)
print(" Mutagenesis: no rotamers found in library.")
cmd.set("seq_view",0,obj_name,quiet=1)
pymol.util.cbaw(obj_name)
cmd.hide("("+obj_name+")")
cmd.show(self.rep,obj_name)
cmd.show('lines',obj_name) #neighbor always show lines
if cartoon:
cmd.show("cartoon",obj_name)
if sticks:
cmd.show("sticks",obj_name)
cmd.set('auto_zoom',auto_zoom,quiet=1)
cmd.delete(frag_name)
cmd.frame(state_best)
cmd.unpick()
cmd.feedback("pop")
from random import random, seed
print "BEGIN-LOG"
seed(123)
print "the 1st random number should be %8.3f\notherwise the rest of the test is meaningless...\n" % pymol.random()
pymol.random = random
cmd.load("dat/pept.pdb", "ref")
for a in xrange(1, 11):
cmd.create("trg", "ref", 1, a, quiet=0)
cmd.alter_state(a, "trg", "x=x+random()/2")
cmd.alter_state(a, "trg", "y=y+random()/2")
cmd.alter_state(a, "trg", "z=z+random()/2", quiet=0)
cmd.frame(1)
print "%8.3f" % cmd.fit("ref", "trg")
# asdf
for a in xrange(1, 14):
print a,
print "%8.3f" % cmd.fit("ref and resi %d" % a, "trg"),
print "%8.3f" % cmd.rms("ref", "trg"),
print "%8.3f" % cmd.rms_cur("ref", "trg")
def symset(prefix = "sym", object = -1, x=0,y=0,z=0, opList = []):
if object == -1:
object = cmd.get_names()[0]
cell = [float(x),float(y),float(z)]
view = cmd.get_view()
cmd.show("lines", object)
sgInfo = cmd.get_symmetry(object)
raw_ops = []
for s in sgtbx.space_group_info(sgInfo[6]).group():
raw_ops.append(str(s))
if (len(opList) == 0):
for i in range(len(raw_ops)):
opList.append(i)
opMatrices = []
vars = ["x","y","z"]
i = 0
j = 0
k = 0
#CREATE 4X4 MATRICES FOR SYMMETRY OPERATORS
for raw_op in raw_ops:
ops = raw_op.split(",")
matrix = [[0,0,0,0],[0,0,0,0],[0,0,0,0],[0,0,0,1]]
for j in range(len(ops)):
for k in range(len(vars)):
index = ops[j].find(vars[k])
if index != -1:
if index == 0:
matrix[k][j] = 1
elif ops[j][index - 1] == "-":
matrix[k][j] = -1
else:
matrix[k][j] = 1
index = ops[j].find("/")
if index != -1:
matrix[3][j] = float(ops[j][index - 1]) / float(ops[j][index + 1])
opMatrices.append(matrix)
i=i+1
a,b,c,alpha,beta,gamma = sgInfo[0:6]
ca = math.cos(math.radians(alpha))
cb = math.cos(math.radians(beta))
cg = math.cos(math.radians(gamma))
sb = math.sin(math.radians(beta))
sg = math.sin(math.radians(gamma))
fracToOrt = N.array([[a, b * cg, c * cb, 0.0],
[0.0, b * sg, c * (ca - cb * cg) / sg, 0.0],
[0.0, 0.0, c * sb * math.sqrt(1.0 - ((cb * cg - ca) / (sb * sg))**2), 0.0],
[0.0,0.0,0.0,1.0]])
fracToOrt = fracToOrt.transpose()
ortToFrac = inv(fracToOrt)
stored.atoms = []
cmd.iterate_state(1,object,"stored.atoms.append([x,y,z,1])")
stored.atoms = N.array(stored.atoms)
fracCoords = N.dot(stored.atoms,ortToFrac)
for i in opList:
try:
op = opMatrices[i]
except:
print "Bad symmetry partner numbers. Try again."
quit()
if i > 9:
copy = prefix + str(i) + "_" + str(x) + "_" + str(y) + "_" + str(z)
else:
copy = prefix + "0" + str(i) + "_" + str(x) + "_" + str(y) + "_" + str(z)
cmd.copy(copy, object)
newCoordsFrac = N.dot(fracCoords, op)
stored.newCoords = N.dot(newCoordsFrac, fracToOrt)
stored.j = 0
cmd.alter_state(1,copy,"x,y,z = stored.newCoords[stored.j][0], stored.newCoords[stored.j][1], stored.newCoords[stored.j][2]; stored.j = stored.j + 1")
xSum=ySum=zSum=0.0
for k in range(len(newCoordsFrac)):
xSum = newCoordsFrac[k][0] + xSum
ySum = newCoordsFrac[k][1] + ySum
zSum = newCoordsFrac[k][2] + zSum
center = N.array([xSum,ySum,zSum])
center = center/len(stored.newCoords)
shift = [-math.floor(center[0]) + cell[0], -math.floor(center[1]) + cell[1], -math.floor(center[2]) + cell[2]]
cell_shift(copy,shift[0],shift[1],shift[2],0)
'''
#COPIES COORDINATES OF EACH ATOM TO CORRESPONDING ONE IN GIVEN SYMMETRY PARTNER
#cmd.alter_state(1, copy, "x,y,z = cmd.sym_partner([x,y,z], stored.tmpOp)")
#MOVES SYMMETRY PARTNER TO PROPER LATTICE COORDINATES AND CORRECTS FOR NATIVE LATTICE POSITION ERROR
#stored.xSum,stored.ySum,stored.zSum = 0.0,0.0,0.0
#atoms = cmd.count_atoms(copy)
#cmd.iterate_state(1, copy, "stored.xSum = stored.xSum + x; stored.ySum = stored.ySum + y; stored.zSum = stored.zSum + z")
#xMean = (stored.xSum / atoms)
#yMean = (stored.ySum / atoms)
#zMean = (stored.zSum / atoms)
#xError, yError, zError = N.dot(N.array([xMean,yMean,zMean]), stored.ortToFrac)
#dX,dY,dZ = -math.floor(xError) + cell[0], -math.floor(yError) + cell[1], -math.floor(zError) + cell[2]
#cell_shift(copy,dX,dY,dZ, 0)
'''
cmd.hide("everything", object)
cmd.set_view(view)
for iteration in range(niterations):
# Set coordinates
print "iteration %8d / %8d" % (iteration, niterations)
positions = (
10.0 *
ncfile.variables['positions'][iteration, replica, :, :]).squeeze()
positions = positions[pdb_mapping, :]
xyz = positions.tolist()
xyz_iter = iter(xyz)
#cmd.load_model(model, 'complex', state=iteration+1)
#cmd.frame(iteration+1)
#model = cmd.get_model('complex', state=1)
#cmd.load_model(model, 'complex', state=iteration+1)
cmd.create('complex', 'complex', 1, iteration + 1)
cmd.alter_state(iteration + 1,
'complex',
'(x,y,z) = xyz_iter.next()',
space=locals())
#for pdb_index in range(natoms):
#if (pdb_index % 100)==0: print pdb_index
#model_index = model_mapping[pdb_index]
#model.atom[model_index].coord = (10 * ncfile.variables['positions'][iteration, replica, pdb_index, :]).squeeze().tolist()
#for k in range(3):
# model.atom[model_index].coord[k] = float(ncfile.variables['positions'][iteration, replica, pdb_index, k]) * 10.0 # convert to angstroms
#cmd.load_model(model, 'complex', state=iteration+1)
#cmd.load_model(model, 'complex')
print "done"
# Align all states
cmd.intra_fit('all')
def optAlign( sel1, sel2 ):
"""
optAlign performs the Kabsch alignment algorithm upon the alpha-carbons of two selections.
Example: optAlign MOL1 and i. 20-40, MOL2 and i. 102-122
Example 2: optAlign 1GGZ and i. 4-146 and n. CA, 1CLL and i. 4-146 and n. CA
Two RMSDs are returned. One comes from the Kabsch algorithm and the other from
PyMol based upon your selections.
By default, this program will optimally align the ALPHA CARBONS of the selections provided.
To turn off this feature remove the lines between the commented "REMOVE ALPHA CARBONS" below.
@param sel1: First PyMol selection with N-atoms
@param sel2: Second PyMol selection with N-atoms
"""
cmd.reset()
# make the lists for holding coordinates
# partial lists
stored.sel1 = []
stored.sel2 = []
# full lists
stored.mol1 = []
stored.mol2 = []
# now put the coordinates into a list
# partials
# -- REMOVE ALPHA CARBONS
sel1 = sel1 + " and N. CA"
sel2 = sel2 + " and N. CA"
# -- REMOVE ALPHA CARBONS
cmd.iterate_state(1, selector.process(sel1), "stored.sel1.append([x,y,z])")
cmd.iterate_state(1, selector.process(sel2), "stored.sel2.append([x,y,z])")
# full molecule
mol1 = cmd.identify(sel1,1)[0][0]
mol2 = cmd.identify(sel2,1)[0][0]
cmd.iterate_state(1, mol1, "stored.mol1.append([x,y,z])")
cmd.iterate_state(1, mol2, "stored.mol2.append([x,y,z])")
K = kabsch()
U, T1, T2, RMSD, c1, c2 = K.align(stored.sel1, stored.sel2, [])
stored.mol2 = map(lambda v:[T2[0]+((v[0]*U[0][0])+(v[1]*U[1][0])+(v[2]*U[2][0])),T2[1]+((v[0]*U[0][1])+(v[1]*U[1][1])+(v[2]*U[2][1])),T2[2]+((v[0]*U[0][2])+(v[1]*U[1][2])+(v[2]*U[2][2]))],stored.mol2)
#stored.mol1 = map(lambda v:[ v[0]+T1[0], v[1]+T1[1], v[2]+T1[2] ], stored.mol1)
stored.mol1 = map(lambda v:[ v[0]+T1[0], v[1]+T1[1], v[2]+T1[2] ], stored.mol1)
cmd.alter_state(1,mol1,"(x,y,z)=stored.mol1.pop(0)")
cmd.alter_state(1,mol2,"(x,y,z)=stored.mol2.pop(0)")
cmd.alter( 'all',"segi=''")
cmd.alter('all', "chain=''")
print "RMSD=%f" % cmd.rms_cur(sel1, sel2)
print "MY RMSD=%f" % RMSD
cmd.hide('everything')
cmd.show('ribbon', sel1 + ' or ' + sel2)
cmd.color('gray70', mol1 )
cmd.color('paleyellow', mol2 )
cmd.color('red', 'visible')
cmd.show('ribbon', 'not visible')
cmd.center('visible')
cmd.orient()
cmd.zoom('visible')