class exANM(ANMBase):
"""Class for explicit ANM (exANM) method ([FT00]_).
Optional arguments build a membrane lattice permit analysis of membrane
effect on elastic network models in *exANM* method described in [TL12]_.
.. [TL12] Lezon TR, Bahar I, Constraints Imposed by the Membrane
Selectively Guide the Alternating Access Dynamics of the Glutamate
Transporter GltPh
"""
def __init__(self, name='Unknown'):
super(exANM, self).__init__(name)
self._membrane = None
self._combined = None
def buildMembrane(self, coords, **kwargs):
"""Build Hessian matrix for given coordinate set.
:arg coords: a coordinate set or an object with ``getCoords`` method
:type coords: :class:`numpy.ndarray`
:arg membrane_hi: the maximum z coordinate of the pdb default is 13.0
:type membrane_hi: float
:arg membrane_lo: the minimum z coordinate of the pdb default is -13.0
:type membrane_lo: float
:arg R: radius of all membrane in x-y direction default is 80.
:type R: float
:arg r: radius of individual barrel-type membrane protein default is 2.5.
:type
:arg lat: lattice type which could be FCC(face-centered-cubic)(default),
SC(simple cubic), SH(simple hexagonal)
:type lat: str
"""
if type(coords) is AtomGroup:
buildAg = True
else:
buildAg = False
try:
coords = (coords._getCoords()
if hasattr(coords, '_getCoords') else coords.getCoords())
except AttributeError:
try:
checkCoords(coords)
except TypeError:
raise TypeError('coords must be a Numpy array or an object '
'with `getCoords` method')
self._n_atoms = natoms = int(coords.shape[0])
pxlo = min(np.append(coords[:, 0], 10000))
pxhi = max(np.append(coords[:, 0], -10000))
pylo = min(np.append(coords[:, 1], 10000))
pyhi = max(np.append(coords[:, 1], -10000))
pzlo = min(np.append(coords[:, 2], 10000))
pzhi = max(np.append(coords[:, 2], -10000))
membrane_hi = float(kwargs.get('membrane_hi', 13.0))
membrane_lo = float(kwargs.get('membrane_lo', -13.0))
R = float(kwargs.get('R', 80))
r = float(kwargs.get('r', 5))
lat = str(kwargs.get('lat', 'FCC'))
lpv = assign_lpvs(lat)
imax = (R + lpv[0, 2] * (membrane_hi - membrane_lo) / 2.) / r
jmax = (R + lpv[1, 2] * (membrane_hi - membrane_lo) / 2.) / r
kmax = (R + lpv[2, 2] * (membrane_hi - membrane_lo) / 2.) / r
#print pxlo, pxhi, pylo, pyhi, pzlo, pzhi
#print lpv[0,2],lpv[1,2],lpv[2,2]
#print R,r,imax,jmax,kmax
membrane = zeros((1, 3))
LOGGER.timeit('_membrane')
membrane = zeros((1, 3))
atm = 0
for i in range(-int(imax), int(imax + 1)):
for j in range(-int(jmax), int(jmax + 1)):
for k in range(-int(kmax), int(kmax + 1)):
X = zeros((1, 3))
for p in range(3):
X[0, p] = 2. * r * (i * lpv[0, p] + j * lpv[1, p] +
k * lpv[2, p])
dd = 0
for p in range(3):
dd += X[0, p]**2
if dd < R**2 and X[0,
2] > membrane_lo and X[0,
2] < membrane_hi:
if X[0, 0] > pxlo - R / 2 and X[
0, 0] < pxhi + R / 2 and X[
0, 1] > pylo - R / 2 and X[
0, 1] < pyhi + R / 2 and X[
0, 2] > pzlo and X[0, 2] < pzhi:
if checkClash(X, coords[:natoms, :], radius=5):
if atm == 0:
membrane = X
else:
membrane = np.append(membrane, X, axis=0)
atm = atm + 1
#print atm
self._membrane = AtomGroup(title="Membrane")
self._membrane.setCoords(membrane)
self._membrane.setResnums(list(range(atm)))
self._membrane.setResnames(["NE1" for i in range(atm)])
self._membrane.setChids(["Q" for i in range(atm)])
self._membrane.setElements(["Q1" for i in range(atm)])
self._membrane.setNames(["Q1" for i in range(atm)])
LOGGER.report('Membrane was built in %2.fs.', label='_membrane')
def buildHessian(self, coords, cutoff=15., gamma=1., **kwargs):
"""Build Hessian matrix for given coordinate set.
:arg coords: a coordinate set or an object with ``getCoords`` method
:type coords: :class:`numpy.ndarray`
:arg cutoff: cutoff distance (Å) for pairwise interactions,
default is 15.0 Å
:type cutoff: float
:arg gamma: spring constant, default is 1.0
:type gamma: float
:arg membrane_hi: the maximum z coordinate of the pdb default is 13.0
:type membrane_hi: float
:arg membrane_lo: the minimum z coordinate of the pdb default is -13.0
:type membrane_lo: float
:arg R: radius of all membrane in x-y direction default is 80.
:type R: float
:arg r: radius of individual barrel-type membrane protein default is 2.5.
:type
:arg lat: lattice type which could be FCC(face-centered-cubic)(default),
SC(simple cubic), SH(simple hexagonal)
:type lat: str
"""
try:
coords = (coords._getCoords()
if hasattr(coords, '_getCoords') else coords.getCoords())
except AttributeError:
try:
checkCoords(coords)
except TypeError:
raise TypeError('coords must be a Numpy array or an object '
'with `getCoords` method')
self._n_atoms = natoms = int(coords.shape[0])
if self._membrane is None:
membrane_hi = float(kwargs.get('membrane_hi', 13.0))
membrane_lo = float(kwargs.get('membrane_lo', -13.0))
R = float(kwargs.get('R', 80))
r = float(kwargs.get('r', 5))
lat = str(kwargs.get('lat', 'FCC'))
self.buildMembrane(coords,
membrane_hi=membrane_hi,
membrane_lo=membrane_lo,
R=R,
r=r,
lat=lat)
LOGGER.timeit('_exanm')
coords = np.concatenate((coords, self._membrane.getCoords()), axis=0)
self._combined_coords = coords
total_natoms = int(coords.shape[0])
self._hessian = np.zeros((natoms * 3, natoms * 3), float)
total_hessian = np.zeros((total_natoms * 3, total_natoms * 3), float)
cutoff, g, gamma = checkENMParameters(cutoff, gamma)
cutoff2 = cutoff * cutoff
for i in range(total_natoms):
res_i3 = i * 3
res_i33 = res_i3 + 3
i_p1 = i + 1
i2j_all = coords[i_p1:, :] - coords[i]
for j, dist2 in enumerate((i2j_all**2).sum(1)):
if dist2 > cutoff2:
continue
i2j = i2j_all[j]
j += i_p1
g = gamma(dist2, i, j)
res_j3 = j * 3
res_j33 = res_j3 + 3
super_element = np.outer(i2j, i2j) * (-g / dist2)
total_hessian[res_i3:res_i33, res_j3:res_j33] = super_element
total_hessian[res_j3:res_j33, res_i3:res_i33] = super_element
total_hessian[res_i3:res_i33, res_i3:res_i33] = total_hessian[
res_i3:res_i33, res_i3:res_i33] - super_element
total_hessian[res_j3:res_j33, res_j3:res_j33] = total_hessian[
res_j3:res_j33, res_j3:res_j33] - super_element
ss = total_hessian[:natoms * 3, :natoms * 3]
so = total_hessian[:natoms * 3, natoms * 3 + 1:]
os = total_hessian[natoms * 3 + 1:, :natoms * 3]
oo = total_hessian[natoms * 3 + 1:, natoms * 3 + 1:]
self._hessian = ss - np.dot(so, np.dot(linalg.inv(oo), os))
LOGGER.report('Hessian was built in %.2fs.', label='_exanm')
self._dof = self._hessian.shape[0]
def calcModes(self, n_modes=20, zeros=False, turbo=True):
"""Calculate normal modes. This method uses :func:`scipy.linalg.eigh`
function to diagonalize the Hessian matrix. When Scipy is not found,
:func:`numpy.linalg.eigh` is used.
:arg n_modes: number of non-zero eigenvalues/vectors to calculate.
If ``None`` is given, all modes will be calculated.
:type n_modes: int or None, default is 20
:arg zeros: If ``True``, modes with zero eigenvalues will be kept.
:type zeros: bool, default is ``False``
:arg turbo: Use a memory intensive, but faster way to calculate modes.
:type turbo: bool, default is ``True``
"""
super(exANM, self).calcModes(n_modes, zeros, turbo)
def getMembrane(self):
"""Returns a copy of the membrane coordinates."""
if self._membrane is not None:
return self._membrane.copy()
def _getMembrane(self):
return self._membrane
def combineMembraneProtein(self, coords):
try:
if type(coords) is AtomGroup:
self._combined = coords + self._membrane
except TypeError:
raise TypeError('coords must be an AtomGroup object '
'with `getCoords` method')
def writeCombinedPDB(self, filename):
""" Given membrane coordinates it will write a pdb file with membrane coordinates.
:arg filename: filename for the pdb file.
:type filename: str
:arg membrane: membrane coordinates or the membrane structure.
:type membrane: nd.array
"""
if self._combined is None:
combineMembraneProtein(self, coords)
try:
writePDB(filename, self._combined)
except TypeError:
raise "Membrane not found. Use buildMembrane() function."
class exANM(ANMBase):
"""Class for explicit ANM (exANM) method ([FT00]_).
Optional arguments build a membrane lattice permit analysis of membrane
effect on elastic network models in *exANM* method described in [TL12]_.
.. [TL12] Lezon TR, Bahar I, Constraints Imposed by the Membrane
Selectively Guide the Alternating Access Dynamics of the Glutamate
Transporter GltPh
"""
def __init__(self, name='Unknown'):
super(exANM, self).__init__(name)
self._membrane = None
self._combined = None
def buildMembrane(self, coords, **kwargs):
"""Build Hessian matrix for given coordinate set.
:arg coords: a coordinate set or an object with ``getCoords`` method
:type coords: :class:`numpy.ndarray`
:arg membrane_hi: the maximum z coordinate of the pdb default is 13.0
:type membrane_hi: float
:arg membrane_lo: the minimum z coordinate of the pdb default is -13.0
:type membrane_lo: float
:arg R: radius of all membrane in x-y direction default is 80.
:type R: float
:arg r: radius of individual barrel-type membrane protein default is 2.5.
:type
:arg lat: lattice type which could be FCC(face-centered-cubic)(default),
SC(simple cubic), SH(simple hexagonal)
:type lat: str
"""
if type(coords) is AtomGroup:
buildAg = True
else:
buildAg = False
try:
coords = (coords._getCoords() if hasattr(coords, '_getCoords') else
coords.getCoords())
except AttributeError:
try:
checkCoords(coords)
except TypeError:
raise TypeError('coords must be a Numpy array or an object '
'with `getCoords` method')
self._n_atoms = natoms = int(coords.shape[0])
pxlo = min(np.append(coords[:,0],10000))
pxhi = max(np.append(coords[:,0],-10000))
pylo = min(np.append(coords[:,1],10000))
pyhi = max(np.append(coords[:,1],-10000))
pzlo = min(np.append(coords[:,2],10000))
pzhi = max(np.append(coords[:,2],-10000))
membrane_hi = float(kwargs.get('membrane_hi', 13.0))
membrane_lo = float(kwargs.get('membrane_lo', -13.0))
R = float(kwargs.get('R', 80))
r = float(kwargs.get('r', 5))
lat = str(kwargs.get('lat', 'FCC'))
lpv = assign_lpvs(lat)
imax = (R + lpv[0,2] * (membrane_hi - membrane_lo)/2.)/r
jmax = (R + lpv[1,2] * (membrane_hi - membrane_lo)/2.)/r
kmax = (R + lpv[2,2] * (membrane_hi - membrane_lo)/2.)/r
#print pxlo, pxhi, pylo, pyhi, pzlo, pzhi
#print lpv[0,2],lpv[1,2],lpv[2,2]
#print R,r,imax,jmax,kmax
membrane = zeros((1,3))
LOGGER.timeit('_membrane')
membrane = zeros((1,3))
atm = 0
for i in range(-int(imax),int(imax+1)):
for j in range(-int(jmax),int(jmax+1)):
for k in range(-int(kmax),int(kmax+1)):
X = zeros((1,3))
for p in range(3):
X[0,p]=2.*r*(i*lpv[0,p]+j*lpv[1,p]+k*lpv[2,p])
dd=0
for p in range(3):
dd += X[0,p] ** 2
if dd<R**2 and X[0,2]>membrane_lo and X[0,2]<membrane_hi:
if X[0,0]>pxlo-R/2 and X[0,0]<pxhi+R/2 and X[0,1]>pylo-R/2 and X[0,1]<pyhi+R/2 and X[0,2]>pzlo and X[0,2]<pzhi:
if checkClash(X, coords[:natoms,:], radius=5):
if atm == 0:
membrane = X
else:
membrane = np.append(membrane, X, axis=0)
atm = atm + 1
#print atm
self._membrane = AtomGroup(title="Membrane")
self._membrane.setCoords(membrane)
self._membrane.setResnums(range(atm))
self._membrane.setResnames(["NE1" for i in range(atm)])
self._membrane.setChids(["Q" for i in range(atm)])
self._membrane.setElements(["Q1" for i in range(atm)])
self._membrane.setNames(["Q1" for i in range(atm)])
LOGGER.report('Membrane was built in %2.fs.', label='_membrane')
def buildHessian(self, coords, cutoff=15., gamma=1., **kwargs):
"""Build Hessian matrix for given coordinate set.
:arg coords: a coordinate set or an object with ``getCoords`` method
:type coords: :class:`numpy.ndarray`
:arg cutoff: cutoff distance (Å) for pairwise interactions,
default is 15.0 Å
:type cutoff: float
:arg gamma: spring constant, default is 1.0
:type gamma: float
:arg membrane_hi: the maximum z coordinate of the pdb default is 13.0
:type membrane_hi: float
:arg membrane_lo: the minimum z coordinate of the pdb default is -13.0
:type membrane_lo: float
:arg R: radius of all membrane in x-y direction default is 80.
:type R: float
:arg r: radius of individual barrel-type membrane protein default is 2.5.
:type
:arg lat: lattice type which could be FCC(face-centered-cubic)(default),
SC(simple cubic), SH(simple hexagonal)
:type lat: str
"""
try:
coords = (coords._getCoords() if hasattr(coords, '_getCoords') else
coords.getCoords())
except AttributeError:
try:
checkCoords(coords)
except TypeError:
raise TypeError('coords must be a Numpy array or an object '
'with `getCoords` method')
self._n_atoms = natoms = int(coords.shape[0])
if self._membrane is None:
membrane_hi = float(kwargs.get('membrane_hi', 13.0))
membrane_lo = float(kwargs.get('membrane_lo', -13.0))
R = float(kwargs.get('R', 80))
r = float(kwargs.get('r', 5))
lat = str(kwargs.get('lat', 'FCC'))
buildMembrane(self,coords,membrane_hi=membrane_hi, membrane_lo=membrane_lo,R=R,r=r,lat=lat)
LOGGER.timeit('_exanm')
coords = np.concatenate((coords,self._membrane.getCoords()),axis=0)
self._combined_coords = coords
total_natoms = int(coords.shape[0])
self._hessian = np.zeros((natoms*3, natoms*3), float)
total_hessian = np.zeros((total_natoms*3, total_natoms*3), float)
cutoff, g, gamma = checkENMParameters(cutoff, gamma)
cutoff2 = cutoff * cutoff
for i in range(total_natoms):
res_i3 = i*3
res_i33 = res_i3+3
i_p1 = i+1
i2j_all = coords[i_p1:, :] - coords[i]
for j, dist2 in enumerate((i2j_all ** 2).sum(1)):
if dist2 > cutoff2:
continue
i2j = i2j_all[j]
j += i_p1
g = gamma(dist2, i, j)
res_j3 = j*3
res_j33 = res_j3+3
super_element = np.outer(i2j, i2j) * (- g / dist2)
total_hessian[res_i3:res_i33, res_j3:res_j33] = super_element
total_hessian[res_j3:res_j33, res_i3:res_i33] = super_element
total_hessian[res_i3:res_i33, res_i3:res_i33] = total_hessian[res_i3:res_i33, res_i3:res_i33] - super_element
total_hessian[res_j3:res_j33, res_j3:res_j33] = total_hessian[res_j3:res_j33, res_j3:res_j33] - super_element
ss = total_hessian[:natoms*3, :natoms*3]
so = total_hessian[:natoms*3, natoms*3+1:]
os = total_hessian[natoms*3+1:,:natoms*3]
oo = total_hessian[natoms*3+1:, natoms*3+1:]
self._hessian = ss - np.dot(so, np.dot(linalg.inv(oo), os))
LOGGER.report('Hessian was built in %.2fs.', label='_exanm')
self._dof = self._hessian.shape[0]
def calcModes(self, n_modes=20, zeros=False, turbo=True):
"""Calculate normal modes. This method uses :func:`scipy.linalg.eigh`
function to diagonalize the Hessian matrix. When Scipy is not found,
:func:`numpy.linalg.eigh` is used.
:arg n_modes: number of non-zero eigenvalues/vectors to calculate.
If ``None`` is given, all modes will be calculated.
:type n_modes: int or None, default is 20
:arg zeros: If ``True``, modes with zero eigenvalues will be kept.
:type zeros: bool, default is ``False``
:arg turbo: Use a memory intensive, but faster way to calculate modes.
:type turbo: bool, default is ``True``
"""
super(exANM, self).calcModes(n_modes, zeros, turbo)
def getMembrane(self):
"""Returns a copy of the membrane coordinates."""
if self._membrane is not None:
return self._membrane.copy()
def _getMembrane(self):
return self._membrane
def combineMembraneProtein(self, coords):
try:
if type(coords) is AtomGroup:
self._combined = coords + self._membrane
except TypeError:
raise TypeError('coords must be an AtomGroup object '
'with `getCoords` method')
def writeCombinedPDB(self,filename):
""" Given membrane coordinates it will write a pdb file with membrane coordinates.
:arg filename: filename for the pdb file.
:type filename: str
:arg membrane: membrane coordinates or the membrane structure.
:type membrane: nd.array
"""
if self._combined is None:
combineMembraneProtein(self,coords)
try:
writePDB(filename,self._combined)
except TypeError:
raise "Membrane not found. Use buildMembrane() function."
class exANM(ANM):
"""Class for explicit ANM (exANM) method ([FT00]_).
Optional arguments build a membrane lattice permit analysis of membrane
effect on elastic network models in *exANM* method described in [TL12]_.
.. [TL12] Lezon TR, Bahar I, Constraints Imposed by the Membrane
Selectively Guide the Alternating Access Dynamics of the Glutamate
Transporter GltPh
"""
def __init__(self, name='Unknown'):
super(exANM, self).__init__(name)
self._membrane = None
self._combined = None
def buildMembrane(self, coords, **kwargs):
"""Build membrane lattice around **coords**.
:arg coords: a coordinate set or an object with ``getCoords`` method
:type coords: :class:`numpy.ndarray`
:arg membrane_high: the maximum z coordinate of the membrane. Default is **13.0**
:type membrane_high: float
:arg membrane_low: the minimum z coordinate of the membrane. Default is **-13.0**
:type membrane_low: float
:arg R: radius of all membrane in x-y direction. Default is **80**
:type R: float
:arg Ri: inner radius of the membrane in x-y direction if it needs to be hollow.
Default is **0**, which is not hollow
:type Ri: float
:arg r: radius of each membrane node. Default is **3.1**
:type r: float
:arg lat: lattice type which could be **FCC** (face-centered-cubic, default),
**SC** (simple cubic), **SH** (simple hexagonal)
:type lat: str
:arg exr: exclusive radius of each protein node. Default is **5.0**
:type exr: float
:arg hull: whether use convex hull to determine the protein's interior.
Turn it off if protein is multimer. Default is **True**
:type hull: bool
:arg center: whether transform the structure to the origin (only x- and y-axis).
Default is **True**
:type center: bool
"""
atoms = coords
try:
coords = (coords._getCoords()
if hasattr(coords, '_getCoords') else coords.getCoords())
except AttributeError:
try:
checkCoords(coords)
except TypeError:
raise TypeError('coords must be a Numpy array or an object '
'with `getCoords` method')
self._n_atoms = int(coords.shape[0])
LOGGER.timeit('_membrane')
depth = kwargs.pop('depth', None)
h = depth / 2 if depth is not None else None
h = kwargs.pop('h', h)
if h is not None:
h = float(h)
hu = h
hl = -h
else:
hu = kwargs.pop('membrane_high', 13.0)
hu = kwargs.pop('high', hu)
hu = float(hu)
hl = kwargs.pop('membrane_low', -13.0)
hl = kwargs.pop('low', hl)
hl = float(hl)
R = float(kwargs.pop('R', 80.))
Ri = float(kwargs.pop('Ri', 0.))
r = float(kwargs.pop('r', 3.1))
lat = str(kwargs.pop('lat', 'FCC'))
exr = float(kwargs.pop('exr', 5.))
use_hull = kwargs.pop('hull', True)
centering = kwargs.pop('center', True)
V = assign_lpvs(lat)
if centering:
c0 = coords.mean(axis=0)
c0[-1] = 0.
coords -= c0
# determine transmembrane part
torf = np.logical_and(coords[:, -1] < hu, coords[:, -1] > hl)
transmembrane = coords[torf, :]
if not np.any(torf):
raise ValueError(
'No region was identified as membrane. Please use a structure from opm/ppm.'
)
if use_hull:
from scipy.spatial import ConvexHull
hull = ConvexHull(transmembrane)
else:
hull = transmembrane
## determine the bound for ijk
imax = (R + V[0, 2] * (hu - hl) / 2.) / r
jmax = (R + V[1, 2] * (hu - hl) / 2.) / r
kmax = (R + V[2, 2] * (hu - hl) / 2.) / r
imax = int(ceil(imax))
jmax = int(ceil(jmax))
kmax = int(ceil(kmax))
membrane = []
atm = 0
for i in range(-imax, imax):
for j in range(-jmax, jmax):
for k in range(-kmax, kmax):
c = array([i, j, k])
xyz = 2. * r * dot(c, V)
if xyz[2]>hl and xyz[2]<hu and \
xyz[0]>-R and xyz[0]<R and \
xyz[1]>-R and xyz[1]<R:
dd = norm(xyz[:2])
if dd < R and dd > Ri:
if checkClash(xyz, hull, radius=exr):
membrane.append(xyz)
atm = atm + 1
membrane = array(membrane)
if len(membrane) == 0:
self._membrane = None
LOGGER.warn(
'no membrane is built. The protein should be transformed to the correct origin as in OPM'
)
return coords
else:
self._membrane = AtomGroup(title="Membrane")
self._membrane.setCoords(membrane)
self._membrane.setResnums(range(atm))
self._membrane.setResnames(["NE1" for i in range(atm)])
self._membrane.setChids(["Q" for i in range(atm)])
self._membrane.setElements(["Q1" for i in range(atm)])
self._membrane.setNames(["Q1" for i in range(atm)])
LOGGER.report('Membrane was built in %2.fs.', label='_membrane')
coords = self._combineMembraneProtein(atoms)
return coords
def buildHessian(self, coords, cutoff=15., gamma=1., **kwargs):
"""Build Hessian matrix for given coordinate set.
**kwargs** are passed to :method:`.buildMembrane`.
:arg coords: a coordinate set or an object with ``getCoords`` method
:type coords: :class:`numpy.ndarray`
:arg cutoff: cutoff distance (Å) for pairwise interactions,
default is 15.0 Å
:type cutoff: float
:arg gamma: spring constant, default is 1.0
:type gamma: float
"""
atoms = coords
turbo = kwargs.pop('turbo', True)
try:
coords = (coords._getCoords()
if hasattr(coords, '_getCoords') else coords.getCoords())
except AttributeError:
try:
checkCoords(coords)
except TypeError:
raise TypeError('coords must be a Numpy array or an object '
'with `getCoords` method')
n_atoms = int(coords.shape[0])
if self._membrane is None:
coords = self.buildMembrane(atoms, **kwargs)
else:
coords = self._combined.getCoords()
system = zeros(coords.shape[0], dtype=bool)
system[:n_atoms] = True
LOGGER.timeit('_exanm')
if turbo:
self._hessian = buildReducedHessian(coords, system, cutoff, gamma,
**kwargs)
else:
super(exANM, self).buildHessian(coords, cutoff, gamma, **kwargs)
system = np.repeat(system, 3)
self._hessian = _reduceModel(self._hessian, system)
LOGGER.report('Hessian was built in %.2fs.', label='_exanm')
self._dof = self._hessian.shape[0]
self._n_atoms = n_atoms
def calcModes(self, n_modes=20, zeros=False, turbo=True):
"""Calculate normal modes. This method uses :func:`scipy.linalg.eigh`
function to diagonalize the Hessian matrix. When Scipy is not found,
:func:`numpy.linalg.eigh` is used.
:arg n_modes: number of non-zero eigenvalues/vectors to calculate.
If **None** is given, all modes will be calculated.
:type n_modes: int or None, default is 20
:arg zeros: If **True**, modes with zero eigenvalues will be kept.
:type zeros: bool, default is **True**
:arg turbo: Use a memory intensive, but faster way to calculate modes.
:type turbo: bool, default is **True**
"""
super(exANM, self).calcModes(n_modes, zeros, turbo)
def getMembrane(self):
"""Returns a copy of the membrane coordinates."""
return self._membrane
def getCombined(self):
"""Returns a copy of the combined atoms or coordinates."""
return self._combined
def _combineMembraneProtein(self, coords):
if self._membrane is not None:
if isinstance(coords, Atomic):
self._combined = coords.copy() + self._membrane
coords = self._combined.getCoords()
else:
self._combined = coords = np.concatenate(
(coords, self._membrane.getCoords()), axis=0)
else:
self._combined = coords = copy(coords)
return coords
