def determineF(self,system):
w2=self.hill.w**2
N=system.natom
self.localGPos=np.zeros((N,3))
self.localVTens=np.zeros((3,3))
if self.hill.id=='volume':
cv=system.cell.volume
g=-np.sum(self.H[:]*self.hill.h*(cv-self.B[:])/w2*np.exp(-(cv-self.B[:])**2/2./w2))
self.localVTens=np.identity(3)*g*cv
self.U=np.sum(self.H[:]*self.hill.h*np.exp(-(cv-self.B[:])**2/2./w2))
elif self.hill.id=='cell':
rvecs=system.cell.rvecs
uc=UnitCell(np.array(rvecs))
abc,abg=uc.parameters
cv=abc[self.hill.atoms]
g=np.zeros((3,3))
g[self.hill.atoms,self.hill.atoms]=-np.sum(self.H[:]*self.hill.h*(cv-self.B[:])/w2*np.exp(-(cv-self.B[:])**2/2./w2))
self.localVTens=np.dot(rvecs,np.dot(g,rvecs.T))/np.linalg.det(rvecs)**2
self.U=np.sum(self.H[:]*self.hill.h*np.exp(-(cv-self.B[:])**2/2./w2))
elif self.hill.id=='angle':
cv,cvderiv=bend_angle(np.array([system.pos[self.hill.atoms[0],:],system.pos[self.hill.atoms[1],:],system.pos[self.hill.atoms[2],:]]),deriv=1)
g=-np.sum(self.H[:]*self.hill.h*(cv-self.B[:])/w2*np.exp(-(cv-self.B[:])**2/2./w2))
for i,a in enumerate(self.hill.atoms):
self.localGPos[a,:]=g*cvderiv[i,:]
self.U=np.sum(self.H[:]*self.hill.h*np.exp(-(cv-self.B[:])**2/2./w2))
else:
raise NotImplementedError
def cart_to_zmat(self, coordinates):
"""Convert cartesian coordinates to ZMatrix format
Argument:
coordinates -- Cartesian coordinates (numpy array Nx3)
The coordinates must match with the graph that was used to initialize
the ZMatrixGenerator object.
"""
N = len(self.graph.numbers)
if coordinates.shape != (N, 3):
raise ValueError("The shape of the coordinates must be (%i, 3)" % N)
result = numpy.zeros(N, dtype=self.dtype)
for i in xrange(N):
ref0 = self.old_index[i]
rel1 = -1
rel2 = -1
rel3 = -1
distance = 0
angle = 0
dihed = 0
if i > 0:
ref1 = self._get_new_ref([ref0])
distance = numpy.linalg.norm(coordinates[ref0]-coordinates[ref1])
rel1 = i - self.new_index[ref1]
if i > 1:
ref2 = self._get_new_ref([ref0, ref1])
angle, = ic.bend_angle(coordinates[[ref0, ref1, ref2]])
rel2 = i - self.new_index[ref2]
if i > 2:
ref3 = self._get_new_ref([ref0, ref1, ref2])
dihed, = ic.dihed_angle(coordinates[[ref0, ref1, ref2, ref3]])
rel3 = i - self.new_index[ref3]
result[i] = (self.graph.numbers[i], distance, rel1, angle, rel2, dihed, rel3)
return result
def cart_to_zmat(self, coordinates):
N = len(self.graph.numbers)
result = numpy.zeros(N, dtype=self.dtype)
for i in xrange(N):
ref0 = self.old_index[i]
rel1 = -1
rel2 = -1
rel3 = -1
distance = 0
angle = 0
dihed = 0
if i > 0:
ref1 = self.get_new_ref([ref0])
distance = numpy.linalg.norm(coordinates[ref0] -
coordinates[ref1])
rel1 = i - self.new_index[ref1]
if i > 1:
ref2 = self.get_new_ref([ref0, ref1])
angle, = ic.bend_angle(coordinates[ref0], coordinates[ref1],
coordinates[ref2])
rel2 = i - self.new_index[ref2]
if i > 2:
ref3 = self.get_new_ref([ref0, ref1, ref2])
dihed, = ic.dihed_angle(coordinates[ref0], coordinates[ref1],
coordinates[ref2], coordinates[ref3])
rel3 = i - self.new_index[ref3]
result[i] = (self.graph.numbers[i], distance, rel1, angle, rel2,
dihed, rel3)
return result
def cart_to_zmat(self, coordinates):
N = len(self.graph.numbers)
result = numpy.zeros(N, dtype=self.dtype)
for i in xrange(N):
ref0 = self.old_index[i]
rel1 = -1
rel2 = -1
rel3 = -1
distance = 0
angle = 0
dihed = 0
if i > 0:
ref1 = self.get_new_ref([ref0])
distance = numpy.linalg.norm(coordinates[ref0]-coordinates[ref1])
rel1 = i - self.new_index[ref1]
if i > 1:
ref2 = self.get_new_ref([ref0, ref1])
angle, = ic.bend_angle(coordinates[ref0], coordinates[ref1], coordinates[ref2])
rel2 = i - self.new_index[ref2]
if i > 2:
ref3 = self.get_new_ref([ref0, ref1, ref2])
dihed, = ic.dihed_angle(coordinates[ref0], coordinates[ref1], coordinates[ref2], coordinates[ref3])
rel3 = i - self.new_index[ref3]
result[i] = (self.graph.numbers[i], distance, rel1, angle, rel2, dihed, rel3)
return result
def determineCV(self,iterative):
if self.hill.id=='volume':
return iterative.ff.system.cell.volume
elif self.hill.id=='cell':
uc=UnitCell(np.array(iterative.ff.system.cell.rvecs))
abc,abg=uc.parameters
return abc[self.hill.atoms]
elif self.hill.id=='angle':
return bend_angle(np.array([iterative.ff.system.pos[self.hill.atoms[0],:],iterative.ff.system.pos[self.hill.atoms[1],:],iterative.ff.system.pos[self.hill.atoms[2],:]]))[0]
else:
raise NotImplementedError
def get_bonds_angles(geometries, atoms):
"""
This functions takes an array with the geometries, and a list with a group of atoms
and returns the bond or angle evolution during the simulation
"""
number_of_steps, number_of_atoms, _ = geometries.shape
colvar = np.empty(number_of_steps)
if len(atoms) == 2:
for frame in range(number_of_steps):
colvar[frame] = bond_length(geometries[frame, atoms])[0]
elif len(atoms) == 3:
for frame in range(number_of_steps):
colvar[frame] = bend_angle(geometries[frame, atoms])[0]
return colvar
def cart_to_zmat(self, coordinates):
"""Convert cartesian coordinates to ZMatrix format
Argument:
coordinates -- Cartesian coordinates (numpy array Nx3)
The coordinates must match with the graph that was used to initialize
the ZMatrixGenerator object.
"""
N = len(self.graph.numbers)
if coordinates.shape != (N, 3):
raise ValueError("The shape of the coordinates must be (%i, 3)" %
N)
result = np.zeros(N, dtype=self.dtype)
for i in range(N):
ref0 = self.old_index[i]
rel1 = -1
rel2 = -1
rel3 = -1
distance = 0
angle = 0
dihed = 0
if i > 0:
ref1 = self._get_new_ref([ref0])
distance = np.linalg.norm(coordinates[ref0] -
coordinates[ref1])
rel1 = i - self.new_index[ref1]
if i > 1:
ref2 = self._get_new_ref([ref0, ref1])
angle, = ic.bend_angle(coordinates[[ref0, ref1, ref2]])
rel2 = i - self.new_index[ref2]
if i > 2:
ref3 = self._get_new_ref([ref0, ref1, ref2])
dihed, = ic.dihed_angle(coordinates[[ref0, ref1, ref2, ref3]])
rel3 = i - self.new_index[ref3]
result[i] = (self.graph.numbers[i], distance, rel1, angle, rel2,
dihed, rel3)
return result
def angle(self, *atoms):
return ic.bend_angle([self.coordinates[i]
for i in atoms])[0] / units.deg
def angle(self, *atoms):
return ic.bend_angle([self.coordinates[i]
for i in atoms])[0] / units.deg
def bend_angle(mol, i0, i1, i2):
c = mol.coordinates
return ic.bend_angle(c[i0], c[i1], c[i2])[0]
def determine_ics_from_topology(self, stretch_pot_kind='harmonic', bend_pot_kind='harmonic'):
#original
# def determine_ics_from_topology(self):
#SHLL end
'''
Method to generate IC instances corresponding to all ics
present in the bonds, bends, dihedrals and opdists attributes.
'''
#SHLL 1508
self.stretch_pot_kind = stretch_pot_kind
self.bend_pot_kind = bend_pot_kind
#SHLL end
self.ics = {}
def sort_ffatypes(ffatypes, kind=''):
if kind != 'opdist':
if ffatypes[0] < ffatypes[-1]:
return ffatypes
elif ffatypes[0]==ffatypes[-1]:
if len(ffatypes)==4:
if ffatypes[1]<ffatypes[2]:
return ffatypes
else:
return ffatypes[::-1]
else:
return ffatypes
else:
return ffatypes[::-1]
else:
result = sorted(ffatypes[:3])
result.append(ffatypes[3])
return result
#Find bonds
number = {}
for bond in self.bonds:
name = 'bond/'+'.'.join(sort_ffatypes([self.ffatypes[at] for at in bond]))
if name not in number.keys():
number[name] = 0
else:
number[name] += 1
#SHLL 1508
#-- unit of spf force constant
if stretch_pot_kind.lower()=='spf':
kunitstr='kjmol'
else:
kunitstr='kjmol/A**2'
ic = IC(
name+str(number[name]), bond, bond_length,
qunit='A', kunit=kunitstr
)
#original
# ic = IC(
# name+str(number[name]), bond, bond_length,
# qunit='A', kunit='kjmol/A**2'
# )
#SHLL end
if name in self.ics.keys():
self.ics[name].append(ic)
else:
self.ics[name] = [ic]
#Find bends
number = {}
for bend in self.bends:
name = 'angle/'+'.'.join(sort_ffatypes([self.ffatypes[at] for at in bend]))
if name not in number.keys():
number[name] = 0
else:
number[name] += 1
#SHLL 1508
#-- unit of harmcos force constant
if bend_pot_kind.lower()=='harmcos':
kunitstr='kjmol'
else:
kunitstr='kjmol/rad**2'
ic = IC(
name+str(number[name]), bend, bend_angle,
qunit='deg', kunit=kunitstr
)
#original
# ic = IC(
# name+str(number[name]), bend, bend_angle,
# qunit='deg', kunit='kjmol/rad**2'
# )
#SHLL end
if name in self.ics.keys():
self.ics[name].append(ic)
else:
self.ics[name] = [ic]
#Find dihedrals
number = {}
for dihed in self.diheds:
if bend_angle(self.ref.coords[dihed[0:3]], deriv=0)[0] > 175*deg \
or bend_angle(self.ref.coords[dihed[1:4]], deriv=0)[0] > 175*deg:
continue
name = 'dihed/'+'.'.join(sort_ffatypes([self.ffatypes[at] for at in dihed]))
if name not in number.keys():
number[name] = 0
else:
number[name] += 1
ic = IC(
name+str(number[name]), dihed, dihed_angle,
qunit='deg', kunit='kjmol'
)
if name in self.ics.keys():
self.ics[name].append(ic)
else:
self.ics[name] = [ic]
#Find out-of-plane distances
number = {}
for opdist in self.opdists:
if bend_angle(self.ref.coords[opdist[0:3]], deriv=0)[0] > 175*deg \
or bend_angle(self.ref.coords[opdist[0:3]], deriv=0)[0] < 5*deg:
continue
name = 'opdist/'+'.'.join(sort_ffatypes([self.ffatypes[at] for at in opdist], kind='opdist'))
if name not in number.keys(): number[name] = 0
else: number[name] += 1
ic = IC(
name+str(number[name]), opdist, opbend_dist,
qunit='A', kunit='kjmol/A**2'
)
if name in self.ics.keys():
self.ics[name].append(ic)
else:
self.ics[name] = [ic]
def bend_angle(mol, i0, i1, i2):
c = mol.coordinates
return ic.bend_angle(c[i0], c[i1], c[i2])[0]
mol = Molecule.from_file(filename)
# setup stuff
mol.set_default_graph()
mol.set_default_symbols()
return mol
if __name__ == "__main__":
# initialize molecule
mol = setup("1IRA_R_B_clean.pdb")
# all bonds of degree 3
for bond in kth_bonds(mol, 3):
# find the coordinates of the bonds
bond_coor = list(map(lambda x: mol.coordinates[x], bond))
# print symbols of bond and bond angle in degrees
to_print = [bond]+symbolify(mol, bond)+[bend_angle(bond_coor)[0]/deg]
pretty(to_print, "\t")
# all bonds of degree 4
for bond in kth_bonds(mol, 4):
# find the coordinates of the bonds
bond_coor = list(map(lambda x: mol.coordinates[x], bond))
# print symbols of bond and dihed angle in degrees
to_print = [bond]+symbolify(mol, bond)+[dihed_angle(bond_coor)[0]/deg]
pretty(to_print, "\t")