def main():
natoms = 5
X1 = np.random.uniform(-1,1,[natoms*3])*(float(natoms))**(1./3)
X2 = np.random.uniform(-1,1,[natoms*3])*(float(natoms))**(1./3)
#X1 = np.array( [ 0., 0., 0., 1., 0., 0., 0., 0., 1.,] )
#X2 = np.array( [ 0., 0., 0., 1., 0., 0., 0., 1., 0.,] )
import copy
X1i = copy.copy(X1)
X2i = copy.copy(X2)
distinit = np.linalg.norm(X1-X2)
print "distinit", distinit
dist, X1, X2 = minDist(X1,X2)
distfinal = np.linalg.norm(X1-X2)
print "dist from eigenvalue", dist
print "distfinal", distfinal
import pygmin.printing.print_atoms_xyz as printxyz
with open("out.xyz", "w") as fout:
CoMToOrigin(X1i)
CoMToOrigin(X2i)
printxyz.printAtomsXYZ(fout, X1i )
printxyz.printAtomsXYZ(fout, X2i )
printxyz.printAtomsXYZ(fout, X1 )
printxyz.printAtomsXYZ(fout, X2 )
def test_multiple(self):
"""test hungarian, munkres, and OPTIM algorithms agains each other"""
import pygmin.defaults as defaults
from pygmin.mindist import CoMToOrigin
X1 = np.copy(self.X1)
X2 = np.random.uniform(-1,1,[self.natoms*3])*(float(self.natoms))**(1./3)/2
X2 = CoMToOrigin(X2)
X1 = CoMToOrigin(X1)
X2i = X2.copy()
d1, X11, X21 = findBestPermutationListHungarian(X1, X2, self.permlist[0])
d1calc = np.linalg.norm(X11-X21)
X2 = X2i.copy()
d2, X12, X22 = findBestPermutationListOPTIM(X1, X2, self.permlist[0])
d2calc = np.linalg.norm(X12-X22)
X2 = X2i.copy()
d3, X13, X23 = findBestPermutationListMunkres(X1, X2, self.permlist[0])
d3calc = np.linalg.norm(X13-X23)
self.assertAlmostEqual(d1, d2, 5)
self.assertAlmostEqual(d1, d1calc, 5)
self.assertAlmostEqual(d2, d2calc, 5)
self.assertAlmostEqual(d1, d3, 5)
self.assertAlmostEqual(d3, d3calc, 5)
def load_coords_pymol(self, coordslist, oname, index=1):
"""load the coords into pymol
the new object must be named oname so we can manipulate it later
Parameters
----------
coordslist : list of arrays
oname : str
the new pymol object must be named oname so it can be manipulated
later
index : int
we can have more than one molecule on the screen at one time. index tells
which one to draw. They are viewed at the same time, so should be
visually distinct, e.g. different colors. accepted values are 1 or 2
Notes
-----
the implementation here is a bit hacky. we create a temporary xyz file from coords
and load the molecule in pymol from this file.
"""
#pymol is imported here so you can do, e.g. basinhopping without installing pymol
import pymol
#create the temporary file
suffix = ".pdb"
f = tempfile.NamedTemporaryFile(mode="w", suffix=suffix)
fname = f.name
from simtk.openmm.app import pdbfile as openmmpdb
#write the coords into pdb file
from pygmin.mindist import CoMToOrigin
ct = 0
for coords in coordslist:
ct = ct + 1
coords = CoMToOrigin(coords.copy())
self.potential.copyToLocalCoords(coords)
# openmmpdb.PDBFile.writeFile(self.potential.prmtop.topology , self.potential.localCoords * openmm_angstrom , file=sys.stdout, modelIndex=1)
openmmpdb.PDBFile.writeModel(self.potential.prmtop.topology , self.potential.localCoords * openmm_angstrom , file=f, modelIndex=ct)
print "closing file"
f.flush()
#load the molecule from the temporary file
pymol.cmd.load(fname)
#get name of the object just created and change it to oname
objects = pymol.cmd.get_object_list()
objectname = objects[-1]
pymol.cmd.set_name(objectname, oname)
#set the representation
pymol.cmd.hide("everything", oname)
pymol.cmd.show("lines", oname)
def load_coords_pymol(self, coordslist, oname, index=1):
"""load the coords into pymol
the new object must be named oname so we can manipulate it later
Parameters
----------
coordslist : list of arrays
oname : str
the new pymol object must be named oname so it can be manipulated
later
index : int
we can have more than one molecule on the screen at one time. index tells
which one to draw. They are viewed at the same time, so should be
visually distinct, e.g. different colors. accepted values are 1 or 2
Notes
-----
the implementation here is a bit hacky. we create a temporary xyz file from coords
and load the molecule in pymol from this file.
"""
#pymol is imported here so you can do, e.g. basinhopping without installing pymol
import pymol
#create the temporary file
suffix = ".pdb"
f = tempfile.NamedTemporaryFile(mode="w", suffix=suffix)
fname = f.name
from simtk.openmm.app import pdbfile as openmmpdb
#write the coords into pdb file
from pygmin.mindist import CoMToOrigin
ct = 0
for coords in coordslist:
ct = ct + 1
coords = CoMToOrigin(coords.copy())
self.potential.copyToLocalCoords(coords)
# openmmpdb.PDBFile.writeFile(self.potential.prmtop.topology , self.potential.localCoords * openmm_angstrom , file=sys.stdout, modelIndex=1)
openmmpdb.PDBFile.writeModel(self.potential.prmtop.topology , self.potential.localCoords * openmm_angstrom , file=f, modelIndex=ct)
print "closing file"
f.flush()
#load the molecule from the temporary file
pymol.cmd.load(fname)
#get name of the object just created and change it to oname
objects = pymol.cmd.get_object_list()
objectname = objects[-1]
pymol.cmd.set_name(objectname, oname)
#set the representation
pymol.cmd.hide("everything", oname)
pymol.cmd.show("lines", oname)
def load_coords_pymol(self, coordslist, oname, index=1):
"""load the coords into pymol
the new object must be named oname so we can manipulate it later
Parameters
----------
coordslist : list of arrays
oname : str
the new pymol object must be named oname so it can be manipulated
later
index : int
we can have more than one molecule on the screen at one time. index tells
which one to draw. They are viewed at the same time, so should be
visually distinct, e.g. different colors. accepted values are 1 or 2
Notes
-----
the implementation here is a bit hacky. we create a temporary xyz file from coords
and load the molecule in pymol from this file.
"""
#pymol is imported here so you can do, e.g. basinhopping without installing pymol
import pymol
#create the temporary file
suffix = ".xyz"
f = tempfile.NamedTemporaryFile(mode="w", suffix=suffix)
fname = f.name
#write the coords into the xyz file
from pygmin.mindist import CoMToOrigin
for coords in coordslist:
coords = CoMToOrigin(coords.copy())
write_xyz(f, coords, title=oname, atomtypes=["LA"])
f.flush()
#load the molecule from the temporary file
pymol.cmd.load(fname)
#get name of the object just create and change it to oname
objects = pymol.cmd.get_object_list()
objectname = objects[-1]
pymol.cmd.set_name(objectname, oname)
#set the representation
pymol.cmd.hide("everything", oname)
pymol.cmd.show("spheres", oname)
#set the color according to index
if index == 1:
pymol.cmd.color("red", oname)
else:
pymol.cmd.color("gray", oname)
def load_coords_pymol(self, coordslist, oname, index=1):
"""load the coords into pymol
the new object must be named oname so we can manipulate it later
Parameters
----------
coordslist : list of arrays
oname : str
the new pymol object must be named oname so it can be manipulated
later
index : int
we can have more than one molecule on the screen at one time. index tells
which one to draw. They are viewed at the same time, so should be
visually distinct, e.g. different colors. accepted values are 1 or 2
Notes
-----
the implementation here is a bit hacky. we create a temporary xyz file from coords
and load the molecule in pymol from this file.
"""
#pymol is imported here so you can do, e.g. basinhopping without installing pymol
import pymol
#create the temporary file
suffix = ".xyz"
f = tempfile.NamedTemporaryFile(mode="w", suffix=suffix)
fname = f.name
#write the coords into the xyz file
from pygmin.mindist import CoMToOrigin
for coords in coordslist:
coords = CoMToOrigin(coords.copy())
write_xyz(f, coords, title=oname, atomtypes=["LA"])
f.flush()
#load the molecule from the temporary file
pymol.cmd.load(fname)
#get name of the object just create and change it to oname
objects = pymol.cmd.get_object_list()
objectname = objects[-1]
pymol.cmd.set_name(objectname, oname)
#set the representation
pymol.cmd.hide("everything", oname)
pymol.cmd.show("spheres", oname)
#set the color according to index
if index == 1:
pymol.cmd.color("red", oname)
else:
pymol.cmd.color("gray", oname)
def minDist(X1, X2):
"""
Minimize the distance between two clusters. The following symmetries
will be accounted for.
Translational symmetry
Global rotational symmetry
"""
#alignCoM(X1, X2)
X1 = CoMToOrigin(X1)
X2 = CoMToOrigin(X2)
#align rotation degrees of freedom
dist, X2 = alignRotation(X1, X2)
return dist, X1, X2
def setUp(self):
from pygmin.potentials import LJ
from pygmin import defaults
from pygmin.mindist import CoMToOrigin
self.natoms = 15
self.pot = LJ(self.natoms)
self.permlist = [range(self.natoms)]
self.X1 = np.random.uniform(-1,1,[self.natoms*3])*(float(self.natoms))**(1./3)/2
ret = defaults.quenchRoutine(self.X1, self.pot.getEnergyGradient, tol=.1)
self.X1 = ret[0]
self.X1 = CoMToOrigin(self.X1)
def minPermDistStochastic(X1,
X2,
niter=100,
permlist=None,
verbose=False,
accuracy=0.01,
check_inversion=True,
use_quench=False):
"""
Minimize the distance between two clusters.
Parameters
----------
X1, X2 :
the structures to align. X2 will be aligned with X1, both
the center of masses will be shifted to the origin
niter : int
the number of basinhopping iterations to perform
permlist : a list of lists of atoms
A list of lists of atoms which are interchangable.
e.g. if all the atoms are interchangable
permlist = [range(natoms)]
For a 50/50 binary mixture,
permlist = [range(1,natoms/2), range(natoms/2,natoms)]
verbose :
whether to print status information
accuracy :
accuracy for determining if the structures are identical
check_inversion :
if true, account for point inversion symmetry
use_quench :
for each step of the iteration, minimize a permutationally invariant
distance metric. This slows the algorithm, but can potentially make
it more accurate.
Notes
-----
The following symmetries will be accounted for::
1. Translational symmetry
#. Global rotational symmetry
#. Permutational symmetry
#. Point inversion symmetry
The algorithm here to find the best distance is
for i in range(niter):
random_rotation(coords)
findBestPermutation(coords)
alignRotation(coords)
"""
natoms = len(X1) / 3
if permlist is None:
permlist = [range(natoms)]
X1init = X1
X2init = X2
X1 = np.copy(X1)
X2 = np.copy(X2)
#first check for exact match
exactmatch = ExactMatchCluster(accuracy=accuracy, permlist=permlist)
if exactmatch(X1, X2):
#this is kind of cheating, I would prefer to return
#X2 in best alignment and the actual (small) distance
return 0.0, X1, X1.copy()
#bring center of mass of x1 and x2 to the origin
#save the center of mass of X1 for later
X1com = X1.reshape([-1, 3]).sum(0) / natoms
X1 = CoMToOrigin(X1)
X2 = CoMToOrigin(X2)
#print "X2.shape", X2.shape
#find the best rotation stochastically
X20 = X2.copy()
distbest, mxbest = _optimizePermRot(X1,
X2,
niter,
permlist,
verbose=verbose,
use_quench=use_quench)
use_inversion = False
if check_inversion:
X20i = -X20.copy()
X2 = X20i.copy()
distbest1, mxbest1 = _optimizePermRot(X1,
X2,
niter,
permlist,
verbose=verbose,
use_quench=use_quench)
if distbest1 < distbest:
if verbose:
print "using inversion in minpermdist"
use_inversion = True
distbest = distbest1
mxbest = mxbest1
#now we know the best rotation
if use_inversion: X20 = X20i
X2 = applyRotation(mxbest, X20)
dist, X1, X2 = findBestPermutation(X1, X2, permlist)
dist, X2 = alignRotation(X1, X2)
if dist > distbest + 0.001:
print "ERROR: minPermDistRanRot: dist is different from distbest %f %f" % (
dist, distbest)
if verbose:
print "finaldist", dist, "distmin", distbest
#add back in the center of mass of X1
X1 = X1.reshape([-1, 3])
X2 = X2.reshape([-1, 3])
X1 += X1com
X2 += X1com
X1 = X1.reshape(-1)
X2 = X2.reshape(-1)
return dist, X1, X2
def minPermDistStochastic(X1, X2, niter=100, permlist=None, verbose=False, accuracy=0.01,
check_inversion=True, use_quench=False):
"""
Minimize the distance between two clusters.
Parameters
----------
X1, X2 :
the structures to align. X2 will be aligned with X1, both
the center of masses will be shifted to the origin
niter : int
the number of basinhopping iterations to perform
permlist : a list of lists of atoms
A list of lists of atoms which are interchangable.
e.g. if all the atoms are interchangable
permlist = [range(natoms)]
For a 50/50 binary mixture,
permlist = [range(1,natoms/2), range(natoms/2,natoms)]
verbose :
whether to print status information
accuracy :
accuracy for determining if the structures are identical
check_inversion :
if true, account for point inversion symmetry
use_quench :
for each step of the iteration, minimize a permutationally invariant
distance metric. This slows the algorithm, but can potentially make
it more accurate.
Notes
-----
The following symmetries will be accounted for::
1. Translational symmetry
#. Global rotational symmetry
#. Permutational symmetry
#. Point inversion symmetry
The algorithm here to find the best distance is
for i in range(niter):
random_rotation(coords)
findBestPermutation(coords)
alignRotation(coords)
"""
natoms = len(X1) / 3
if permlist is None:
permlist = [range(natoms)]
X1init = X1
X2init = X2
X1 = np.copy(X1)
X2 = np.copy(X2)
#first check for exact match
exactmatch = ExactMatchCluster(accuracy=accuracy, permlist=permlist)
if exactmatch(X1, X2):
#this is kind of cheating, I would prefer to return
#X2 in best alignment and the actual (small) distance
return 0.0, X1, X1.copy()
#bring center of mass of x1 and x2 to the origin
#save the center of mass of X1 for later
X1com = X1.reshape([-1,3]).sum(0) / natoms
X1 = CoMToOrigin(X1)
X2 = CoMToOrigin(X2)
#print "X2.shape", X2.shape
#find the best rotation stochastically
X20 = X2.copy()
distbest, mxbest = _optimizePermRot(X1, X2, niter, permlist, verbose=verbose, use_quench=use_quench)
use_inversion = False
if check_inversion:
X20i = -X20.copy()
X2 = X20i.copy()
distbest1, mxbest1 = _optimizePermRot(X1, X2, niter, permlist, verbose=verbose, use_quench=use_quench)
if distbest1 < distbest:
if verbose:
print "using inversion in minpermdist"
use_inversion = True
distbest = distbest1
mxbest = mxbest1
#now we know the best rotation
if use_inversion: X20 = X20i
X2 = applyRotation(mxbest, X20)
dist, X1, X2 = findBestPermutation(X1, X2, permlist)
dist, X2 = alignRotation(X1, X2)
if dist > distbest+0.001:
print "ERROR: minPermDistRanRot: dist is different from distbest %f %f" % (dist, distbest)
if verbose:
print "finaldist", dist, "distmin", distbest
#add back in the center of mass of X1
X1 = X1.reshape([-1,3])
X2 = X2.reshape([-1,3])
X1 += X1com
X2 += X1com
X1 = X1.reshape(-1)
X2 = X2.reshape(-1)
return dist, X1, X2