def writeDeformProfile(stiffness, pdb, filename='dp_out', \
select='protein and name CA', \
pdb_selstr='protein', loadToVMD=False):
"""Calculate deformability (plasticity) profile of molecule based on mechanical
stiffness matrix (see [EB08]_).
:arg model: this is an 3-dimensional NMA instance from a :class:`.ANM
calculations
:type model: :class:`.ANM`
:arg pdb: a coordinate set or an object with ``getCoords`` method
:type pdb: :class:`numpy.ndarray`
Note: selection can be done using ``select`` and ``pdb_selstr``.
``select`` defines ``model`` selection (used for building :class:`.ANM` model)
and ``pdb_selstr`` will be used in VMD program for visualization.
By default files are saved as *filename* and loaded to VMD program. To change
it use ``loadToVMD=False``.
Mean value of mechanical stiffness for molecule can be found in occupancy column
in PDB file.
"""
_, pdb = sliceAtoms(pdb, pdb_selstr)
_, coords = sliceAtoms(pdb, select)
meanStiff = np.mean(stiffness, axis=0)
out_mean = open(filename+'_mean.txt','w') # mean value of Kij for each residue
for nr_i, i in enumerate(meanStiff):
out_mean.write("{} {}\n".format(nr_i, i))
out_mean.close()
from collections import Counter
aa_counter = Counter(pdb.getResindices())
meanStiff_all = []
for i in range(coords.numAtoms()):
meanStiff_all.extend(list(aa_counter.values())[i]*[round(meanStiff[i], 2)])
writePDB(filename, pdb, occupancy=meanStiff_all)
LOGGER.info('PDB file with deformability profile has been saved.')
LOGGER.info('Creating TCL file.')
out_tcl = open(filename+'.tcl','w')
out_tcl.write('display resetview \nmol addrep 0 \ndisplay resetview \n')
out_tcl.write('mol new {./'+filename+'.pdb} type {pdb} first 0 last -1 step 1 waitfor 1 \n')
out_tcl.write('animate style Loop \ndisplay projection Orthographic \n')
out_tcl.write('display depthcue off \ndisplay rendermode GLSL \naxes location Off \n')
out_tcl.write('color Display Background white \n')
out_tcl.write('mol modstyle 0 0 NewCartoon 0.300000 10.000000 4.100000 0 \n')
out_tcl.write('mol modmaterial 0 0 Diffuse \nmol modcolor 0 0 Occupancy \n')
out_tcl.write('menu colorscalebar on \n')
out_tcl.close()
if loadToVMD:
from prody import pathVMD
LOGGER.info('File will be loaded to VMD program.')
os.system(pathVMD()+" -e "+str(filename)+".tcl")
def writeDeformProfile(stiffness, pdb, filename='dp_out', \
select='protein and name CA', \
pdb_selstr='protein', loadToVMD=False):
"""Calculate deformability (plasticity) profile of molecule based on mechanical
stiffness matrix (see [EB08]_).
:arg stiffness: mechanical stiffness matrix
:type stiffness: :class:`~numpy.ndarray
:arg pdb: a coordinate set or an object with ``getCoords`` method
:type pdb: :class:`~numpy.ndarray`
Note: selection can be done using ``select`` and ``pdb_selstr``.
``select`` defines ``model`` selection (used for building :class:`.ANM` model)
and ``pdb_selstr`` will be used in VMD program for visualization.
By default files are saved as *filename* and loaded to VMD program. To change
it use ``loadToVMD=False``.
Mean value of mechanical stiffness for molecule can be found in occupancy column
in PDB file.
"""
_, pdb = sliceAtoms(pdb, pdb_selstr)
_, coords = sliceAtoms(pdb, select)
meanStiff = np.mean(stiffness, axis=0)
out_mean = open(filename+'_mean.txt','w') # mean value of Kij for each residue
for nr_i, i in enumerate(meanStiff):
out_mean.write("{} {}\n".format(nr_i, i))
out_mean.close()
from collections import Counter
aa_counter = Counter(pdb.getResindices())
meanStiff_all = []
for i in range(coords.numAtoms()):
meanStiff_all.extend(list(aa_counter.values())[i]*[round(meanStiff[i], 2)])
writePDB(filename, pdb, occupancy=meanStiff_all)
LOGGER.info('PDB file with deformability profile has been saved.')
LOGGER.info('Creating TCL file.')
out_tcl = open(filename+'.tcl','w')
out_tcl.write('display resetview \nmol addrep 0 \ndisplay resetview \n')
out_tcl.write('mol new {./'+filename+'.pdb} type {pdb} first 0 last -1 step 1 waitfor 1 \n')
out_tcl.write('animate style Loop \ndisplay projection Orthographic \n')
out_tcl.write('display depthcue off \ndisplay rendermode GLSL \naxes location Off \n')
out_tcl.write('color Display Background white \n')
out_tcl.write('mol modstyle 0 0 NewCartoon 0.300000 10.000000 4.100000 0 \n')
out_tcl.write('mol modmaterial 0 0 Diffuse \nmol modcolor 0 0 Occupancy \n')
out_tcl.write('menu colorscalebar on \n')
out_tcl.close()
if loadToVMD:
from prody import pathVMD
LOGGER.info('File will be loaded to VMD program.')
os.system(pathVMD()+" -e "+str(filename)+".tcl")
def sliceMode(mode, atoms, select):
"""Returns part of the *mode* for *atoms* matching *select*. This works
slightly different from :func:`.sliceVector`. Mode array (eigenvector) is
multiplied by square-root of the variance along the mode. If mode is from
an elastic network model, variance is defined as the inverse of the
eigenvalue. Note that returned :class:`.Vector` instance is not
normalized.
:arg mode: mode instance to be sliced
:type mode: :class:`.Mode`
:arg atoms: atoms for which *mode* describes a deformation, motion, etc.
:type atoms: :class:`.Atomic`
:arg select: an atom selection or a selection string
:type select: :class:`.Selection`, str
:returns: (:class:`.Vector`, :class:`.Selection`)"""
if not isinstance(mode, Mode):
raise TypeError('mode must be a Mode instance, not {0}'.format(
type(mode)))
if not isinstance(atoms, Atomic):
raise TypeError('atoms must be an Atomic instance, not {0}'.format(
type(atoms)))
if atoms.numAtoms() != mode.numAtoms():
raise ValueError('number of atoms in model and atoms must be equal')
which, sel = sliceAtoms(atoms, select)
vec = Vector(
mode.getArrayNx3()[which, :].flatten() * mode.getVariance()**0.5,
'{0} slice {1}'.format(str(mode), select), mode.is3d())
return (vec, sel)
def sliceVector(vector, atoms, select):
"""Returns part of the *vector* for *atoms* matching *select*. Note that
returned :class:`.Vector` instance is not normalized.
:arg vector: vector instance to be sliced
:type vector: :class:`.VectorBase`
:arg atoms: atoms for which *vector* describes a deformation, motion, etc.
:type atoms: :class:`.Atomic`
:arg select: an atom selection or a selection string
:type select: :class:`.Selection`, str
:returns: (:class:`.Vector`, :class:`.Selection`)"""
if not isinstance(vector, VectorBase):
raise TypeError('vector must be a VectorBase instance, not {0}'
.format(type(vector)))
if not isinstance(atoms, Atomic):
raise TypeError('atoms must be an Atomic instance, not {0}'
.format(type(atoms)))
if atoms.numAtoms() != vector.numAtoms():
raise ValueError('number of atoms in model and atoms must be equal')
which, sel = sliceAtoms(atoms, select)
vec = Vector(vector.getArrayNx3()[
which, :].flatten(),
'{0} slice {1}'.format(str(vector), select),
vector.is3d())
return (vec, sel)
def sliceVector(vector, atoms, select):
"""Returns part of the *vector* for *atoms* matching *select*. Note that
returned :class:`.Vector` instance is not normalized.
:arg vector: vector instance to be sliced
:type vector: :class:`.VectorBase`
:arg atoms: atoms for which *vector* describes a deformation, motion, etc.
:type atoms: :class:`.Atomic`
:arg select: an atom selection or a selection string
:type select: :class:`.Selection`, str
:returns: (:class:`.Vector`, :class:`.Selection`)"""
if not isinstance(vector, VectorBase):
raise TypeError('vector must be a VectorBase instance, not {0}'.format(
type(vector)))
if not isinstance(atoms, Atomic):
raise TypeError('atoms must be an Atomic instance, not {0}'.format(
type(atoms)))
if atoms.numAtoms() != vector.numAtoms():
raise ValueError('number of atoms in model and atoms must be equal')
which, sel = sliceAtoms(atoms, select)
vec = Vector(vector.getArrayNx3()[which, :].flatten(),
'{0} slice {1}'.format(str(vector), select), vector.is3d())
return (vec, sel)
def sliceModel(model, atoms, select):
"""Returns a part of the *model* (modes calculated) for *atoms* matching *select*.
Note that normal modes are sliced instead the connectivity matrix. Sliced normal
modes (eigenvectors) are not normalized.
:arg mode: NMA model instance to be sliced
:type mode: :class:`.NMA`
:arg atoms: atoms for which the *model* was built
:type atoms: :class:`.Atomic`
:arg select: an atom selection or a selection string
:type select: :class:`.Selection`, str
:returns: (:class:`.NMA`, :class:`.Selection`)"""
if not isinstance(model, NMA):
raise TypeError('mode must be a NMA instance, not {0}'.format(
type(model)))
if not isinstance(atoms, Atomic):
raise TypeError('atoms must be an Atomic instance, not {0}'.format(
type(atoms)))
if atoms.numAtoms() != model.numAtoms():
raise ValueError('number of atoms in model and atoms must be equal')
which, sel = sliceAtoms(atoms, select)
nma = sliceModelByMask(model, which)
return (nma, sel)
def sliceMode(mode, atoms, select):
"""Returns part of the *mode* for *atoms* matching *select*. This works
slightly different from :func:`.sliceVector`. Mode array (eigenvector) is
multiplied by square-root of the variance along the mode. If mode is from
an elastic network model, variance is defined as the inverse of the
eigenvalue. Note that returned :class:`.Vector` instance is not
normalized.
:arg mode: mode instance to be sliced
:type mode: :class:`.Mode`
:arg atoms: atoms for which *mode* describes a deformation, motion, etc.
:type atoms: :class:`.Atomic`
:arg select: an atom selection or a selection string
:type select: :class:`.Selection`, str
:returns: (:class:`.Vector`, :class:`.Selection`)"""
if not isinstance(mode, Mode):
raise TypeError('mode must be a Mode instance, not {0}'
.format(type(mode)))
if not isinstance(atoms, Atomic):
raise TypeError('atoms must be an Atomic instance, not {0}'
.format(type(atoms)))
if atoms.numAtoms() != mode.numAtoms():
raise ValueError('number of atoms in model and atoms must be equal')
which, sel = sliceAtoms(atoms, select)
vec = Vector(mode.getArrayNx3()[which, :].flatten() *
mode.getVariance()**0.5,
'{0} slice {1}'.format(str(mode), select), mode.is3d())
return (vec, sel)
def trimModel(model, atoms, select):
"""Returns a part of the *model* for *atoms* matching *select*. This method removes
columns and rows in the connectivity matrix and fix the diagonal sums. Normal modes
need to be calculated again after the trim.
:arg mode: NMA model instance to be sliced
:type mode: :class:`.NMA`
:arg atoms: atoms for which the *model* was built
:type atoms: :class:`.Atomic`
:arg select: an atom selection or a selection string
:type select: :class:`.Selection`, str
:returns: (:class:`.NMA`, :class:`.Selection`)"""
if not isinstance(model, NMA):
raise TypeError('mode must be a NMA instance, not {0}'.format(
type(model)))
if not isinstance(atoms, Atomic):
raise TypeError('atoms must be an Atomic instance, not {0}'.format(
type(atoms)))
if atoms.numAtoms() != model.numAtoms():
raise ValueError('number of atoms in model and atoms must be equal')
which, sel = sliceAtoms(atoms, select)
nma = trimModelByMask(model, which)
return (nma, sel)
def setAtoms(self, atoms):
"""Set *atoms* or specify a selection of atoms to be considered in
calculations and coordinate requests. When a selection is set,
corresponding subset of coordinates will be considered in, for
example, alignments and RMSD calculations. Setting atoms also
allows some functions to access atomic data when needed. For
example, :class:`.Ensemble` and :class:`.Conformation` instances
become suitable arguments for :func:`.writePDB`. Passing **None**
as *atoms* argument will deselect atoms."""
if atoms is None:
self._atoms = self._indices = None
return
try:
atoms.getACSIndex()
except AttributeError:
raise TypeError('atoms must be an Atomic instance')
n_atoms = self._n_atoms
if n_atoms:
if atoms.numAtoms() > n_atoms:
raise ValueError('atoms must be same size or smaller than '
'the ensemble')
try:
dummies = atoms.numDummies()
except AttributeError:
pass
else:
if dummies:
raise ValueError('atoms must not have any dummies')
else:
indices = atoms._getIndices()
if any(indices != unique(indices)):
raise ValueError('atoms must be ordered by indices')
if atoms.numAtoms(
) == n_atoms: # atoms is a complete set (AtomSubset can be a complete set)
self._atoms = atoms
self._indices = None
else: # atoms is a subset
if not self._atoms:
try:
ag = atoms.getAtomGroup()
except AttributeError:
ag = atoms
if ag.numAtoms() != n_atoms:
raise ValueError(
'size mismatch between this ensemble ({0} atoms) and atoms ({1} atoms)'
.format(n_atoms, ag.numAtoms()))
self._atoms = ag
self._indices, _ = sliceAtoms(self._atoms, atoms)
else: # if assigning atoms to a new ensemble
self._n_atoms = atoms.numAtoms()
self._atoms = atoms
self._indices = None
def setAtoms(self, atoms):
"""Set *atoms* or specify a selection of atoms to be considered in
calculations and coordinate requests. When a selection is set,
corresponding subset of coordinates will be considered in, for
example, alignments and RMSD calculations. Setting atoms also
allows some functions to access atomic data when needed. For
example, :class:`.Ensemble` and :class:`.Conformation` instances
become suitable arguments for :func:`.writePDB`. Passing **None**
as *atoms* argument will deselect atoms."""
if atoms is None:
self._atoms = self._indices = None
return
try:
atoms.getACSIndex()
except AttributeError:
raise TypeError('atoms must be an Atomic instance')
n_atoms = self._n_atoms
if n_atoms:
if atoms.numAtoms() > n_atoms:
raise ValueError('atoms must be same size or smaller than '
'the ensemble')
try:
dummies = atoms.numDummies()
except AttributeError:
pass
else:
if dummies:
raise ValueError('atoms must not have any dummies')
else:
indices = atoms._getIndices()
if any(indices != unique(indices)):
raise ValueError('atoms must be ordered by indices')
if atoms.numAtoms() == n_atoms: # atoms is a complete set (AtomSubset can be a complete set)
self._atoms = atoms
self._indices = None
else: # atoms is a subset
if not self._atoms:
try:
ag = atoms.getAtomGroup()
except AttributeError:
ag = atoms
if ag.numAtoms() != n_atoms:
raise ValueError('size mismatch between this ensemble ({0} atoms) and atoms ({1} atoms)'
.format(n_atoms, ag.numAtoms()))
self._atoms = ag
self._indices, _ = sliceAtoms(self._atoms, atoms)
else: # if assigning atoms to a new ensemble
self._n_atoms = atoms.numAtoms()
self._atoms = atoms
self._indices = None
def reduceModel(model, atoms, select):
"""Returns reduced NMA model. Reduces a :class:`.NMA` model to a subset of
*atoms* matching *select*. This function behaves differently depending on
the type of the *model* argument. For :class:`.ANM` and :class:`.GNM` or
other :class:`.NMA` models, force constant matrix for system of interest
(specified by the *select*) is derived from the force constant matrix for
the *model* by assuming that for any given displacement of the system of
interest, other atoms move along in such a way as to minimize the potential
energy. This is based on the formulation in [KH00]_. For :class:`.PCA`
models, this function simply takes the sub-covariance matrix for selection.
.. [KH00] Hinsen K, Petrescu A-J, Dellerue S, Bellissent-Funel M-C, Kneller GR.
Harmonicity in slow protein dynamics. *Chem Phys* **2000** 261:25-37.
:arg model: dynamics model
:type model: :class:`.ANM`, :class:`.GNM`, or :class:`.PCA`
:arg atoms: atoms that were used to build the model
:type atoms: :class:`.Atomic`
:arg select: an atom selection or a selection string
:type select: :class:`.Selection`, str
:returns: (:class:`.NMA`, :class:`.Selection`)"""
if not isinstance(model, NMA):
raise TypeError('model must be an NMA instance, not {0}'.format(
type(model)))
if not isinstance(atoms, (AtomGroup, AtomSubset, AtomMap)):
raise TypeError('atoms type is not valid')
if len(atoms) <= 1:
raise TypeError('atoms must contain more than 1 atoms')
if isinstance(model, GNM):
matrix = model._kirchhoff
elif isinstance(model, ANM):
matrix = model._hessian
elif isinstance(model, PCA):
matrix = model._cov
else:
raise TypeError('model does not have a valid type derived from NMA')
if matrix is None:
raise ValueError('model matrix (Hessian/Kirchhoff/Covariance) is not '
'built')
which, select = sliceAtoms(atoms, select)
nma = reduceModelByMask(model, which)
return nma, select
def sliceModel(model, atoms, select):
"""Returns a part of the *model* for *atoms* matching *select*. Note that
normal modes (eigenvectors) are not normalized.
:arg mode: NMA model instance to be sliced
:type mode: :class:`.NMA`
:arg atoms: atoms for which the *model* was built
:type atoms: :class:`.Atomic`
:arg select: an atom selection or a selection string
:type select: :class:`.Selection`, str
:returns: (:class:`.NMA`, :class:`.Selection`)"""
if not isinstance(model, NMA):
raise TypeError('mode must be a NMA instance, not {0}'
.format(type(model)))
if not isinstance(atoms, Atomic):
raise TypeError('atoms must be an Atomic instance, not {0}'
.format(type(atoms)))
if atoms.numAtoms() != model.numAtoms():
raise ValueError('number of atoms in model and atoms must be equal')
array = model._getArray()
which, sel = sliceAtoms(atoms, select)
nma = type(model)('{0} slice {1}'
.format(model.getTitle(), select))
if model.is3d():
which = [which.reshape((len(which), 1))*3]
which.append(which[0]+1)
which.append(which[0]+2)
which = np.concatenate(which, 1).flatten()
nma.setEigens(array[which, :], model.getEigvals())
return (nma, sel)
def sliceModel(model, atoms, select):
"""Returns a part of the *model* for *atoms* matching *select*. Note that
normal modes (eigenvectors) are not normalized.
:arg mode: NMA model instance to be sliced
:type mode: :class:`.NMA`
:arg atoms: atoms for which the *model* was built
:type atoms: :class:`.Atomic`
:arg select: an atom selection or a selection string
:type select: :class:`.Selection`, str
:returns: (:class:`.NMA`, :class:`.Selection`)"""
if not isinstance(model, NMA):
raise TypeError('mode must be a NMA instance, not {0}'
.format(type(model)))
if not isinstance(atoms, Atomic):
raise TypeError('atoms must be an Atomic instance, not {0}'
.format(type(atoms)))
if atoms.numAtoms() != model.numAtoms():
raise ValueError('number of atoms in model and atoms must be equal')
array = model._getArray()
which, sel = sliceAtoms(atoms, select)
nma = type(model)('{0} slice {1}'
.format(model.getTitle(), select))
if model.is3d():
which = [which.reshape((len(which), 1))*3]
which.append(which[0]+1)
which.append(which[0]+2)
which = np.concatenate(which, 1).flatten()
nma.setEigens(array[which, :], model.getEigvals())
return (nma, sel)
def reduceModel(model, atoms, select):
"""Returns reduced NMA model. Reduces a :class:`.NMA` model to a subset of
*atoms* matching *select*. This function behaves differently depending on
the type of the *model* argument. For :class:`.ANM` and :class:`.GNM` or
other :class:`.NMA` models, force constant matrix for system of interest
(specified by the *select*) is derived from the force constant matrix for
the *model* by assuming that for any given displacement of the system of
interest, other atoms move along in such a way as to minimize the potential
energy. This is based on the formulation in [KH00]_. For :class:`.PCA`
models, this function simply takes the sub-covariance matrix for selection.
.. [KH00] Hinsen K, Petrescu A-J, Dellerue S, Bellissent-Funel M-C, Kneller GR.
Harmonicity in slow protein dynamics. *Chem Phys* **2000** 261:25-37.
:arg model: dynamics model
:type model: :class:`.ANM`, :class:`.GNM`, or :class:`.PCA`
:arg atoms: atoms that were used to build the model
:type atoms: :class:`.Atomic`
:arg select: an atom selection or a selection string
:type select: :class:`.Selection`, str
:returns: (:class:`.NMA`, :class:`.Selection`)"""
linalg = importLA()
if not isinstance(model, NMA):
raise TypeError('model must be an NMA instance, not {0}'
.format(type(model)))
if not isinstance(atoms, (AtomGroup, AtomSubset, AtomMap)):
raise TypeError('atoms type is not valid')
if len(atoms) <= 1:
raise TypeError('atoms must contain more than 1 atoms')
if isinstance(model, GNM):
matrix = model._kirchhoff
elif isinstance(model, ANM):
matrix = model._hessian
elif isinstance(model, PCA):
matrix = model._cov
else:
raise TypeError('model does not have a valid type derived from NMA')
if matrix is None:
raise ValueError('model matrix (Hessian/Kirchhoff/Covariance) is not '
'built')
which, select = sliceAtoms(atoms, select)
system = np.zeros(model.numAtoms(), dtype=bool)
system[which] = True
other = np.invert(system)
if model.is3d():
system = np.repeat(system, 3)
other = np.repeat(other, 3)
ss = matrix[system, :][:, system]
if isinstance(model, PCA):
eda = PCA(model.getTitle() + ' reduced')
eda.setCovariance(ss)
return eda, system
so = matrix[system, :][:, other]
os = matrix[other, :][:, system]
oo = matrix[other, :][:, other]
try:
invoo = linalg.inv(oo)
except:
invoo = linalg.pinv(oo)
matrix = ss - np.dot(so, np.dot(invoo, os))
if isinstance(model, GNM):
gnm = GNM(model.getTitle() + ' reduced')
gnm.setKirchhoff(matrix)
return gnm, select
elif isinstance(model, ANM):
anm = ANM(model.getTitle() + ' reduced')
anm.setHessian(matrix)
return anm, select
elif isinstance(model, PCA):
eda = PCA(model.getTitle() + ' reduced')
eda.setCovariance(matrix)
return eda, select
def reduceModel(model, atoms, select):
"""Returns reduced NMA model. Reduces a :class:`.NMA` model to a subset of
*atoms* matching *select*. This function behaves differently depending on
the type of the *model* argument. For :class:`.ANM` and :class:`.GNM` or
other :class:`.NMA` models, force constant matrix for system of interest
(specified by the *select*) is derived from the force constant matrix for
the *model* by assuming that for any given displacement of the system of
interest, other atoms move along in such a way as to minimize the potential
energy. This is based on the formulation in [KH00]_. For :class:`.PCA`
models, this function simply takes the sub-covariance matrix for selection.
.. [KH00] Hinsen K, Petrescu A-J, Dellerue S, Bellissent-Funel M-C, Kneller GR.
Harmonicity in slow protein dynamics. *Chem Phys* **2000** 261:25-37.
:arg model: dynamics model
:type model: :class:`.ANM`, :class:`.GNM`, or :class:`.PCA`
:arg atoms: atoms that were used to build the model
:type atoms: :class:`.Atomic`
:arg select: an atom selection or a selection string
:type select: :class:`.Selection`, str
:returns: (:class:`.NMA`, :class:`.Selection`)"""
linalg = importLA()
if not isinstance(model, NMA):
raise TypeError('model must be an NMA instance, not {0}'
.format(type(model)))
if not isinstance(atoms, (AtomGroup, AtomSubset, AtomMap)):
raise TypeError('atoms type is not valid')
if len(atoms) <= 1:
raise TypeError('atoms must contain more than 1 atoms')
if isinstance(model, GNM):
matrix = model._kirchhoff
elif isinstance(model, ANM):
matrix = model._hessian
elif isinstance(model, PCA):
matrix = model._cov
else:
raise TypeError('model does not have a valid type derived from NMA')
if matrix is None:
raise ValueError('model matrix (Hessian/Kirchhoff/Covariance) is not '
'built')
which, select = sliceAtoms(atoms, select)
system = np.zeros(model.numAtoms(), dtype=bool)
system[which] = True
other = np.invert(system)
if model.is3d():
system = np.repeat(system, 3)
other = np.repeat(other, 3)
ss = matrix[system, :][:, system]
if isinstance(model, PCA):
eda = PCA(model.getTitle() + ' reduced')
eda.setCovariance(ss)
return eda, system
so = matrix[system, :][:, other]
os = matrix[other, :][:, system]
oo = matrix[other, :][:, other]
if other.any():
try:
invoo = linalg.inv(oo)
except:
invoo = linalg.pinv(oo)
matrix = ss - np.dot(so, np.dot(invoo, os))
else:
matrix = ss
if isinstance(model, GNM):
gnm = GNM(model.getTitle() + ' reduced')
gnm.setKirchhoff(matrix)
return gnm, select
elif isinstance(model, ANM):
anm = ANM(model.getTitle() + ' reduced')
anm.setHessian(matrix)
return anm, select
elif isinstance(model, PCA):
eda = PCA(model.getTitle() + ' reduced')
eda.setCovariance(matrix)
return eda, select
def writeVMDstiffness(stiffness, pdb, indices, k_range, filename='vmd_out', \
select='protein and name CA', loadToVMD=False):
"""
Returns three files starting with the provided filename and having
their own extensions:
(1) A PDB file that can be used in the TCL script.
(2) TCL file containing vmd commands for loading PDB file with accurate
vmd representation. Pair of residues with selected *k_range* of
effective spring constant are shown in VMD respresentation with
solid line between them. If more than one residue is selected in
*indices*, different pair for each residue will be colored in the
different colors.
(3) TXT file containing pair of residues with effective spring constant
in selected range *k_range*.
.. note::
#. This function skips modes with zero eigenvalues.
#. If a :class:`.Vector` instance is given, it will be normalized
before it is written. It's length before normalization will be
written as the scaling factor of the vector.
:arg stiffness: mechanical stiffness profile calculated with
:func:`.calcMechStiff`
:type stiffness: :class:`~numpy.ndarray`
:arg pdb: a coordinate set or an object with ``getCoords`` method
:type pdb: :class:`~numpy.ndarray`, :class:`.Atomic`
:arg indices: an amino acid number or a pair of amino acid numbers
:type indices: list
:arg k_range: effective force constant value or range of values
:type k_range: int, float, list
:arg select: a selection or selection string
default is 'protein and name CA'
:type select: :class:`.Select`, str
:arg loadToVMD: whether to load VMD and run the tcl file
default is False
:type loadToVMD: bool
"""
if not isinstance(filename, str):
raise TypeError('filename should be a string')
try:
_, coords_sel = sliceAtoms(pdb, select)
resnum_list = coords_sel.getResnums()
coords = (coords_sel._getCoords() if hasattr(coords_sel, '_getCoords') else
coords_sel.getCoords())
except AttributeError:
try:
checkCoords(coords_sel)
except TypeError:
raise TypeError('pdb must be a Numpy array or an object '
'with `getCoords` method')
if len(indices) == 0:
raise ValueError('indices cannot be an empty array')
if len(indices) == 1:
indices0 = indices[0] - resnum_list[0]
indices1 = indices[0] - resnum_list[0]
elif len(indices) == 2:
indices0 = indices[0] - resnum_list[0]
indices1 = indices[1] - resnum_list[0]
out = openFile(addext(filename, '.tcl'), 'w')
out_txt = openFile(addext(filename,'.txt'), 'w')
writePDB(filename + '.pdb', pdb)
LOGGER.info('Creating VMD file.')
out.write('display rendermode GLSL \n')
out.write('display projection orthographic\n')
out.write('color Display Background white\n')
out.write('display shadows on\n')
out.write('display depthcue off\n')
out.write('axes location off\n')
out.write('stage location off\n')
out.write('light 0 on\n')
out.write('light 1 on\n')
out.write('light 2 off\n')
out.write('light 3 on\n')
out.write('mol addrep 0\n')
out.write('display resetview\n')
out.write('mol new {./'+str(filename)+'.pdb} type {pdb} first 0 last -1 step 1 waitfor 1\n')
out.write('mol modselect 0 0 protein\n')
out.write('mol modstyle 0 0 NewCartoon 0.300000 10.000000 4.100000 0\n')
out.write('mol modcolor 0 0 Structure\n')
out.write('mol color Structure\n')
out.write('mol representation NewCartoon 0.300000 10.000000 4.100000 0\n')
out.write('mol selection protein\n')
out.write('mol material Opaque\n')
colors = ['blue', 'red', 'gray', 'orange','yellow', 'tan','silver', 'green', \
'white', 'pink', 'cyan', 'purple', 'lime', 'mauve', 'ochre', 'iceblue', 'black', \
'yellow2','yellow3','green2','green3','cyan2','cyan3','blue2','blue3','violet', \
'violet2','magenta','magenta2','red2','red3','orange2','orange3']*50
color_nr = 1 # starting from red color in VMD
ResCounter = []
for r in range(indices0, indices1 + 1):
baza_col = [] # Value of Kij is here for each residue
nr_baza_col = [] # Resid of aa are here
out.write("draw color "+str(colors[color_nr])+"\n")
for nr_i, i in enumerate(stiffness[r]):
if k_range[0] < float(i) < k_range[1]:
baza_col.append(i)
nr_baza_col.append(nr_i+resnum_list[0])
resid_r = str(coords_sel.getResnames()[r])+str(r+resnum_list[0])
resid_r2 = str(coords_sel.getResnames()[nr_i])+str(nr_i+resnum_list[0])
if len(baza_col) == 0: # if base is empty then it will not change the color
color_nr = 0
else:
out.write("draw line "+'{'+str(coords[r])[1:-1]+'} {'+\
str(coords[nr_i])[1:-1]+'} width 3 style solid \n')
out_txt.write(resid_r + '\t' + resid_r2 + '\t' + str(i) + '\n')
ResCounter.append(len(baza_col))
else: pass
if len(baza_col) != 0:
out.write('mol addrep 0\n')
out.write('mol modselect '+str(color_nr+1)+' 0 protein and name CA and resid '+ \
str(r+resnum_list[0])+' '+str(nr_baza_col)[1:-1].replace(',','')+'\n')
out.write('mol modcolor '+str(color_nr+1)+' 0 ColorID '+str(color_nr)+'\n')
out.write('mol modstyle '+str(color_nr+1)+' 0 VDW 0.600000 12.000000\n')
out.write('mol color ColorID '+str(color_nr)+'\n')
out.write('mol representation VDW 1.000000 12.000000 \n')
out.write('mol selection protein and name CA and resid '+ \
str(r+resnum_list[0])+' '+str(nr_baza_col)[1:-1].replace(',','')+'\n')
out.write('mol material Opaque \n')
color_nr = color_nr + 1
out.write('mol addrep 0\n')
out.close()
out_txt.close()
if loadToVMD:
from prody import pathVMD
LOGGER.info('File will be loaded to VMD program.')
os.system(pathVMD()+" -e "+str(filename)+".tcl")
if len(ResCounter) > 0:
return out
elif len(ResCounter) == 0:
LOGGER.info('There is no residue pair in this Kij range.')
return 'None'
def writeVMDstiffness(stiffness, pdb, indices, k_range, filename='vmd_out', \
select='protein and name CA', loadToVMD=False):
"""
Returns three files starting with the provided filename and having
their own extensions:
(1) A PDB file that can be used in the TCL script.
(2) TCL file containing vmd commands for loading PDB file with accurate
vmd representation. Pair of residues with selected *k_range* of
effective spring constant are shown in VMD respresentation with
solid line between them. If more than one residue is selected in
*indices*, different pair for each residue will be colored in the
different colors.
(3) TXT file containing pair of residues with effective spring constant
in selected range *k_range*.
.. note::
#. This function skips modes with zero eigenvalues.
#. If a :class:`.Vector` instance is given, it will be normalized
before it is written. It's length before normalization will be
written as the scaling factor of the vector.
:arg stiffness: mechanical stiffness profile calculated with
:func:`.calcMechStiff`
:type stiffness: :class:`~numpy.ndarray`
:arg pdb: a coordinate set or an object with ``getCoords`` method
:type pdb: :class:`~numpy.ndarray`, :class:`.Atomic`
:arg indices: an amino acid number or a pair of amino acid numbers
:type indices: list
:arg k_range: effective force constant value or range of values
:type k_range: int, float, list
:arg select: a selection or selection string
default is 'protein and name CA'
:type select: :class:`.Select`, str
:arg loadToVMD: whether to load VMD and run the tcl file
default is False
:type loadToVMD: bool
"""
if not isinstance(filename, str):
raise TypeError('filename should be a string')
try:
_, coords_sel = sliceAtoms(pdb, select)
resnum_list = coords_sel.getResnums()
coords = (coords_sel._getCoords() if hasattr(coords_sel, '_getCoords')
else coords_sel.getCoords())
except AttributeError:
try:
checkCoords(coords_sel)
except TypeError:
raise TypeError('pdb must be a Numpy array or an object '
'with `getCoords` method')
if len(indices) == 0:
raise ValueError('indices cannot be an empty array')
if len(indices) == 1:
indices0 = indices[0] - resnum_list[0]
indices1 = indices[0] - resnum_list[0]
elif len(indices) == 2:
indices0 = indices[0] - resnum_list[0]
indices1 = indices[1] - resnum_list[0]
out = openFile(addext(filename, '.tcl'), 'w')
out_txt = openFile(addext(filename, '.txt'), 'w')
writePDB(filename + '.pdb', pdb)
LOGGER.info('Creating VMD file.')
out.write('display rendermode GLSL \n')
out.write('display projection orthographic\n')
out.write('color Display Background white\n')
out.write('display shadows on\n')
out.write('display depthcue off\n')
out.write('axes location off\n')
out.write('stage location off\n')
out.write('light 0 on\n')
out.write('light 1 on\n')
out.write('light 2 off\n')
out.write('light 3 on\n')
out.write('mol addrep 0\n')
out.write('display resetview\n')
out.write('mol new {./' + str(filename) +
'.pdb} type {pdb} first 0 last -1 step 1 waitfor 1\n')
out.write('mol modselect 0 0 protein\n')
out.write('mol modstyle 0 0 NewCartoon 0.300000 10.000000 4.100000 0\n')
out.write('mol modcolor 0 0 Structure\n')
out.write('mol color Structure\n')
out.write('mol representation NewCartoon 0.300000 10.000000 4.100000 0\n')
out.write('mol selection protein\n')
out.write('mol material Opaque\n')
colors = ['blue', 'red', 'gray', 'orange','yellow', 'tan','silver', 'green', \
'white', 'pink', 'cyan', 'purple', 'lime', 'mauve', 'ochre', 'iceblue', 'black', \
'yellow2','yellow3','green2','green3','cyan2','cyan3','blue2','blue3','violet', \
'violet2','magenta','magenta2','red2','red3','orange2','orange3']*50
color_nr = 1 # starting from red color in VMD
ResCounter = []
for r in range(indices0, indices1 + 1):
baza_col = [] # Value of Kij is here for each residue
nr_baza_col = [] # Resid of aa are here
out.write("draw color " + str(colors[color_nr]) + "\n")
for nr_i, i in enumerate(stiffness[r]):
if k_range[0] < float(i) < k_range[1]:
baza_col.append(i)
nr_baza_col.append(nr_i + resnum_list[0])
resid_r = str(
coords_sel.getResnames()[r]) + str(r + resnum_list[0])
resid_r2 = str(
coords_sel.getResnames()[nr_i]) + str(nr_i +
resnum_list[0])
if len(
baza_col
) == 0: # if base is empty then it will not change the color
color_nr = 0
else:
out.write("draw line "+'{'+str(coords[r])[1:-1]+'} {'+\
str(coords[nr_i])[1:-1]+'} width 3 style solid \n')
out_txt.write(resid_r + '\t' + resid_r2 + '\t' + str(i) +
'\n')
ResCounter.append(len(baza_col))
else:
pass
if len(baza_col) != 0:
out.write('mol addrep 0\n')
out.write('mol modselect '+str(color_nr+1)+' 0 protein and name CA and resid '+ \
str(r+resnum_list[0])+' '+str(nr_baza_col)[1:-1].replace(',','')+'\n')
out.write('mol modcolor ' + str(color_nr + 1) + ' 0 ColorID ' +
str(color_nr) + '\n')
out.write('mol modstyle ' + str(color_nr + 1) +
' 0 VDW 0.600000 12.000000\n')
out.write('mol color ColorID ' + str(color_nr) + '\n')
out.write('mol representation VDW 1.000000 12.000000 \n')
out.write('mol selection protein and name CA and resid '+ \
str(r+resnum_list[0])+' '+str(nr_baza_col)[1:-1].replace(',','')+'\n')
out.write('mol material Opaque \n')
color_nr = color_nr + 1
out.write('mol addrep 0\n')
out.close()
out_txt.close()
if loadToVMD:
from prody import pathVMD
LOGGER.info('File will be loaded to VMD program.')
os.system(pathVMD() + " -e " + str(filename) + ".tcl")
if len(ResCounter) > 0:
return out
elif len(ResCounter) == 0:
LOGGER.info('There is no residue pair in this Kij range.')
return 'None'
