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molmod/molmod | molmod/io/atrj.py | SectionFile._skip_section | def _skip_section(self):
"""Skip a section"""
self._last = self._f.readline()
while len(self._last) > 0 and len(self._last[0].strip()) == 0:
self._last = self._f.readline() | python | def _skip_section(self):
"""Skip a section"""
self._last = self._f.readline()
while len(self._last) > 0 and len(self._last[0].strip()) == 0:
self._last = self._f.readline() | [
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molmod/molmod | molmod/io/atrj.py | SectionFile._read_section | def _read_section(self):
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while len(self._last) > 0 and len(self._last[0].strip()) == 0:
lines.append(self._last)
self._last = self._f.readline()
... | python | def _read_section(self):
"""Read and return an entire section"""
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self._last = self._f.readline()
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molmod/molmod | molmod/io/atrj.py | SectionFile.get_next | def get_next(self, label):
"""Get the next section with the given label"""
while self._get_current_label() != label:
self._skip_section()
return self._read_section() | python | def get_next(self, label):
"""Get the next section with the given label"""
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molmod/molmod | molmod/io/atrj.py | ATRJReader._read_frame | def _read_frame(self):
"""Read a single frame from the trajectory"""
self._secfile.get_next("Frame Number")
frame = ATRJFrame()
# Read the time and energy
energy_lines = self._secfile.get_next("Time/Energy")
energy_words = energy_lines[0].split()
frame.time = floa... | python | def _read_frame(self):
"""Read a single frame from the trajectory"""
self._secfile.get_next("Frame Number")
frame = ATRJFrame()
# Read the time and energy
energy_lines = self._secfile.get_next("Time/Energy")
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molmod/molmod | molmod/io/cube.py | get_cube_points | def get_cube_points(origin, axes, nrep):
'''Generate the Cartesian coordinates of the points in a cube file
*Arguemnts:*
origin
The cartesian coordinate for the origin of the grid.
axes
The 3 by 3 array with the grid spacings as rows.
nrep
The numb... | python | def get_cube_points(origin, axes, nrep):
'''Generate the Cartesian coordinates of the points in a cube file
*Arguemnts:*
origin
The cartesian coordinate for the origin of the grid.
axes
The 3 by 3 array with the grid spacings as rows.
nrep
The numb... | [
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molmod/molmod | molmod/io/cube.py | Cube.from_file | def from_file(cls, filename):
'''Create a cube object by loading data from a file.
*Arguemnts:*
filename
The file to load. It must contain the header with the
description of the grid and the molecule.
'''
with open(filename) as f:
... | python | def from_file(cls, filename):
'''Create a cube object by loading data from a file.
*Arguemnts:*
filename
The file to load. It must contain the header with the
description of the grid and the molecule.
'''
with open(filename) as f:
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molmod/molmod | molmod/io/cube.py | Cube.write_to_file | def write_to_file(self, fn):
'''Write the cube to a file in the Gaussian cube format.'''
with open(fn, 'w') as f:
f.write(' {}\n'.format(self.molecule.title))
f.write(' {}\n'.format(self.subtitle))
def write_grid_line(n, v):
f.write('%5i % 11.6f % 11.... | python | def write_to_file(self, fn):
'''Write the cube to a file in the Gaussian cube format.'''
with open(fn, 'w') as f:
f.write(' {}\n'.format(self.molecule.title))
f.write(' {}\n'.format(self.subtitle))
def write_grid_line(n, v):
f.write('%5i % 11.6f % 11.... | [
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molmod/molmod | molmod/io/cube.py | Cube.copy | def copy(self, newdata=None):
'''Return a copy of the cube with optionally new data.'''
if newdata is None:
newdata = self.data.copy()
return self.__class__(
self.molecule, self.origin.copy(), self.axes.copy(),
self.nrep.copy(), newdata, self.subtitle, self.nu... | python | def copy(self, newdata=None):
'''Return a copy of the cube with optionally new data.'''
if newdata is None:
newdata = self.data.copy()
return self.__class__(
self.molecule, self.origin.copy(), self.axes.copy(),
self.nrep.copy(), newdata, self.subtitle, self.nu... | [
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molmod/molmod | molmod/io/cp2k.py | CP2KSection._consistent | def _consistent(self):
"""Checks the constency between self.__index and self.__order"""
if len(self.__order) != sum(len(values) for values in self.__index.values()):
return False
import copy
tmp = copy.copy(self.__order)
for key, values in self.__index.items():
... | python | def _consistent(self):
"""Checks the constency between self.__index and self.__order"""
if len(self.__order) != sum(len(values) for values in self.__index.values()):
return False
import copy
tmp = copy.copy(self.__order)
for key, values in self.__index.items():
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molmod/molmod | molmod/io/cp2k.py | CP2KSection.append | def append(self, child):
"""Add a child section or keyword"""
if not (isinstance(child, CP2KSection) or isinstance(child, CP2KKeyword)):
raise TypeError("The child must be a CP2KSection or a CP2KKeyword, got: %s." % child)
l = self.__index.setdefault(child.name, [])
l.append(... | python | def append(self, child):
"""Add a child section or keyword"""
if not (isinstance(child, CP2KSection) or isinstance(child, CP2KKeyword)):
raise TypeError("The child must be a CP2KSection or a CP2KKeyword, got: %s." % child)
l = self.__index.setdefault(child.name, [])
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molmod/molmod | molmod/io/cp2k.py | CP2KSection.dump_children | def dump_children(self, f, indent=''):
"""Dump the children of the current section to a file-like object"""
for child in self.__order:
child.dump(f, indent+' ') | python | def dump_children(self, f, indent=''):
"""Dump the children of the current section to a file-like object"""
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molmod/molmod | molmod/io/cp2k.py | CP2KSection.dump | def dump(self, f, indent=''):
"""Dump this section and its children to a file-like object"""
print(("%s&%s %s" % (indent, self.__name, self.section_parameters)).rstrip(), file=f)
self.dump_children(f, indent)
print("%s&END %s" % (indent, self.__name), file=f) | python | def dump(self, f, indent=''):
"""Dump this section and its children to a file-like object"""
print(("%s&%s %s" % (indent, self.__name, self.section_parameters)).rstrip(), file=f)
self.dump_children(f, indent)
print("%s&END %s" % (indent, self.__name), file=f) | [
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molmod/molmod | molmod/io/cp2k.py | CP2KSection.readline | def readline(self, f):
"""A helper method that only reads uncommented lines"""
while True:
line = f.readline()
if len(line) == 0:
raise EOFError
line = line[:line.find('#')]
line = line.strip()
if len(line) > 0:
... | python | def readline(self, f):
"""A helper method that only reads uncommented lines"""
while True:
line = f.readline()
if len(line) == 0:
raise EOFError
line = line[:line.find('#')]
line = line.strip()
if len(line) > 0:
... | [
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molmod/molmod | molmod/io/cp2k.py | CP2KSection.load_children | def load_children(self, f):
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while True:
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if line[0] == '&':
if line[1:].startswith("END"):
check_name = line[4:].strip().upper()
if check... | python | def load_children(self, f):
"""Load the children of this section from a file-like object"""
while True:
line = self.readline(f)
if line[0] == '&':
if line[1:].startswith("END"):
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molmod/molmod | molmod/io/cp2k.py | CP2KSection.load | def load(self, f, line=None):
"""Load this section from a file-like object"""
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self.__name = words[0].upper()
... | python | def load(self, f, line=None):
"""Load this section from a file-like object"""
if line is None:
# in case the file contains only a fragment of an input file,
# this is useful.
line = f.readlin()
words = line[1:].split()
self.__name = words[0].upper()
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molmod/molmod | molmod/io/cp2k.py | CP2KKeyword.dump | def dump(self, f, indent=''):
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if self.__unit is None:
print(("%s%s %s" % (indent, self.__name, self.__value)).rstrip(), file=f)
else:
print(("%s%s [%s] %s" % (indent, self.__name, self.__unit, self.__value)).rstrip(), file=f) | python | def dump(self, f, indent=''):
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if self.__unit is None:
print(("%s%s %s" % (indent, self.__name, self.__value)).rstrip(), file=f)
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molmod/molmod | molmod/io/cp2k.py | CP2KKeyword.load | def load(self, line):
"""Load this keyword from a file-like object"""
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try:
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except ValueError:
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if len(words) > 2 ... | python | def load(self, line):
"""Load this keyword from a file-like object"""
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"""Set the value associated with the keyword"""
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"""Set the value associated with the keyword"""
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molmod/molmod | molmod/io/cp2k.py | CP2KInputFile.read_from_file | def read_from_file(filename):
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| ``filename`` -- the filename of the input file
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>>> if = CP2KInputFile.read_from_file("somefile.inp")
>>> for section in if:
... print section.name
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Arguments:
| ``filename`` -- the filename of the input file
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"""Read and return the next time frame"""
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vel = np.zeros((self.num_atoms, 3), float)
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molmod/molmod | molmod/transformations.py | check_matrix | def check_matrix(m):
"""Check the sanity of the given 4x4 transformation matrix"""
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raise ValueError("The argument must be a 4x4 array.")
if max(abs(m[3, 0:3])) > eps:
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"""Check the sanity of the given 4x4 transformation matrix"""
if m.shape != (4, 4):
raise ValueError("The argument must be a 4x4 array.")
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molmod/molmod | molmod/transformations.py | superpose | def superpose(ras, rbs, weights=None):
"""Compute the transformation that minimizes the RMSD between the points ras and rbs
Arguments:
| ``ras`` -- a ``np.array`` with 3D coordinates of geometry A,
shape=(N,3)
| ``rbs`` -- a ``np.array`` with 3D coordinates of geom... | python | def superpose(ras, rbs, weights=None):
"""Compute the transformation that minimizes the RMSD between the points ras and rbs
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molmod/molmod | molmod/transformations.py | fit_rmsd | def fit_rmsd(ras, rbs, weights=None):
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Arguments:
| ``ras`` -- a numpy array with 3D coordinates of geometry A,
shape=(N,3)
| ``rbs`` -- a numpy array with 3D coordinates of geometry B,
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molmod/molmod | molmod/transformations.py | Translation.inv | def inv(self):
"""The inverse translation"""
result = Translation(-self.t)
result._cache_inv = self
return result | python | def inv(self):
"""The inverse translation"""
result = Translation(-self.t)
result._cache_inv = self
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molmod/molmod | molmod/transformations.py | Translation.apply_to | def apply_to(self, x, columns=False):
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* ``np.array`` with shape (N, 3)
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molmod/molmod | molmod/transformations.py | Translation.compare | def compare(self, other, t_threshold=1e-3):
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translations are almost identical.
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molmod/molmod | molmod/transformations.py | Rotation._check_r | def _check_r(self, r):
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np.dot(r[:, 1], r[:, 2]) ... | python | def _check_r(self, r):
"""the columns must orthogonal"""
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molmod/molmod | molmod/transformations.py | Rotation.random | def random(cls):
"""Return a random rotation"""
axis = random_unit()
angle = np.random.uniform(0,2*np.pi)
invert = bool(np.random.randint(0,2))
return Rotation.from_properties(angle, axis, invert) | python | def random(cls):
"""Return a random rotation"""
axis = random_unit()
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molmod/molmod | molmod/transformations.py | Rotation.from_properties | def from_properties(cls, angle, axis, invert):
"""Initialize a rotation based on the properties"""
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x = axis[0] / norm
y = axis[1] / norm
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molmod/molmod | molmod/transformations.py | Rotation.properties | def properties(self):
"""Rotation properties: angle, axis, invert"""
# determine wether an inversion rotation has been applied
invert = (np.linalg.det(self.r) < 0)
factor = {True: -1, False: 1}[invert]
# get the rotation data
# trace(r) = 1+2*cos(angle)
cos_angle ... | python | def properties(self):
"""Rotation properties: angle, axis, invert"""
# determine wether an inversion rotation has been applied
invert = (np.linalg.det(self.r) < 0)
factor = {True: -1, False: 1}[invert]
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molmod/molmod | molmod/transformations.py | Rotation.matrix | def matrix(self):
"""The 4x4 matrix representation of this rotation"""
result = np.identity(4, float)
result[0:3, 0:3] = self.r
return result | python | def matrix(self):
"""The 4x4 matrix representation of this rotation"""
result = np.identity(4, float)
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molmod/molmod | molmod/transformations.py | Rotation.inv | def inv(self):
"""The inverse rotation"""
result = Rotation(self.r.transpose())
result._cache_inv = self
return result | python | def inv(self):
"""The inverse rotation"""
result = Rotation(self.r.transpose())
result._cache_inv = self
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molmod/molmod | molmod/transformations.py | Rotation.apply_to | def apply_to(self, x, columns=False):
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molmod/molmod | molmod/transformations.py | Rotation.compare | def compare(self, other, r_threshold=1e-3):
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is True when the RMSD is below the threshold, i.e. when the two
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molmod/molmod | molmod/transformations.py | Complete.from_properties | def from_properties(cls, angle, axis, invert, translation):
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molmod/molmod | molmod/transformations.py | Complete.properties | def properties(self):
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molmod/molmod | molmod/transformations.py | Complete.inv | def inv(self):
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molmod/molmod | molmod/io/lammps.py | LAMMPSDumpReader._read_frame | def _read_frame(self):
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molmod/molmod | molmod/io/lammps.py | LAMMPSDumpReader._skip_frame | def _skip_frame(self):
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molmod/molmod | molmod/periodic.py | PeriodicData._add_atom_info | def _add_atom_info(self, atom_info):
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molmod/molmod | molmod/clusters.py | RuleCluster.update | def update(self, other):
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molmod/molmod | molmod/clusters.py | ClusterFactory.add_related | def add_related(self, *objects):
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molmod/molmod | molmod/io/dlpoly.py | DLPolyHistoryReader._read_frame | def _read_frame(self):
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molmod/molmod | molmod/io/dlpoly.py | DLPolyOutputReader.goto_next_frame | def goto_next_frame(self):
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molmod/molmod | molmod/io/xyz.py | XYZReader._read_frame | def _read_frame(self):
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molmod/molmod | molmod/io/xyz.py | XYZReader.get_first_molecule | def get_first_molecule(self):
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molmod/molmod | molmod/io/xyz.py | XYZWriter.dump | def dump(self, title, coordinates):
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| ``coordinates`` -- a numpy array with coordinates in atomic units
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molmod/molmod | molmod/io/xyz.py | XYZFile.get_molecule | def get_molecule(self, index=0):
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Optional argument:
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molmod/molmod | molmod/minimizer.py | ConjugateGradient.update | def update(self, gradient, step):
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molmod/molmod | molmod/minimizer.py | ConjugateGradient._update_cg | def _update_cg(self):
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molmod/molmod | molmod/minimizer.py | GoldenLineSearch._bracket | def _bracket(self, qinit, f0, fun):
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molmod/molmod | molmod/minimizer.py | GoldenLineSearch._golden | def _golden(self, triplet, fun):
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molmod/molmod | molmod/minimizer.py | Preconditioner.update | def update(self, counter, f, x_orig, gradient_orig):
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molmod/molmod | molmod/minimizer.py | DiagonalPreconditioner.update | def update(self, counter, f, x_orig, gradient_orig):
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molmod/molmod | molmod/minimizer.py | FullPreconditioner.update | def update(self, counter, f, x_orig, gradient_orig):
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molmod/molmod | molmod/minimizer.py | FullPreconditioner.do | def do(self, x_orig):
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molmod/molmod | molmod/minimizer.py | FullPreconditioner.undo | def undo(self, x_prec):
"""Transform the unknowns to original coordinates
This method also transforms the gradient to preconditioned coordinates
"""
if self.scales is None:
return x_prec
else:
return np.dot(self.rotation, x_prec/self.scales) | python | def undo(self, x_prec):
"""Transform the unknowns to original coordinates
This method also transforms the gradient to preconditioned coordinates
"""
if self.scales is None:
return x_prec
else:
return np.dot(self.rotation, x_prec/self.scales) | [
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molmod/molmod | molmod/minimizer.py | ConvergenceCondition.get_header | def get_header(self):
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"""Returns the header for screen logging of the minimization"""
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molmod/molmod | molmod/minimizer.py | LineWrapper.configure | def configure(self, x0, axis):
"""Configure the 1D function for a line search
Arguments:
x0 -- the reference point (q=0)
axis -- a unit vector in the direction of the line search
"""
self.x0 = x0
self.axis = axis | python | def configure(self, x0, axis):
"""Configure the 1D function for a line search
Arguments:
x0 -- the reference point (q=0)
axis -- a unit vector in the direction of the line search
"""
self.x0 = x0
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molmod/molmod | molmod/minimizer.py | Constraints._compute_equations | def _compute_equations(self, x, verbose=False):
'''Compute the values and the normals (gradients) of active constraints.
Arguments:
| ``x`` -- The unknowns.
'''
# compute the error and the normals.
normals = []
values = []
signs = []
error ... | python | def _compute_equations(self, x, verbose=False):
'''Compute the values and the normals (gradients) of active constraints.
Arguments:
| ``x`` -- The unknowns.
'''
# compute the error and the normals.
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molmod/molmod | molmod/minimizer.py | Constraints._rough_shake | def _rough_shake(self, x, normals, values, error):
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| ``x`` -- The unknowns.
| ``normals`` -- A numpy array with the gradients of the active
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| ``x`` -- The unknowns.
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molmod/molmod | molmod/minimizer.py | Constraints._fast_shake | def _fast_shake(self, x, normals, values, error):
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| ``x`` -- The unknowns.
| ``normals`` -- A numpy array with the gradients of the active
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molmod/molmod | molmod/minimizer.py | Constraints.free_shake | def free_shake(self, x):
'''Brings unknowns to the constraints.
Arguments:
| ``x`` -- The unknowns.
'''
self.lock[:] = False
normals, values, error = self._compute_equations(x)[:-1]
counter = 0
while True:
if error <= self.threshold:
... | python | def free_shake(self, x):
'''Brings unknowns to the constraints.
Arguments:
| ``x`` -- The unknowns.
'''
self.lock[:] = False
normals, values, error = self._compute_equations(x)[:-1]
counter = 0
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molmod/molmod | molmod/minimizer.py | Constraints.safe_shake | def safe_shake(self, x, fun, fmax):
'''Brings unknowns to the constraints, without increasing fun above fmax.
Arguments:
| ``x`` -- The unknowns.
| ``fun`` -- The function being minimized.
| ``fmax`` -- The highest allowed value of the function being
... | python | def safe_shake(self, x, fun, fmax):
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| ``x`` -- The unknowns.
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molmod/molmod | molmod/minimizer.py | Constraints.project | def project(self, x, vector):
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Arguments:
| ``x`` -- The unknowns.
| ``vector`` -- A numpy array with a direction or a gradient.
The return value is a gradient or direction, where the components... | python | def project(self, x, vector):
'''Project a vector (gradient or direction) on the active constraints.
Arguments:
| ``x`` -- The unknowns.
| ``vector`` -- A numpy array with a direction or a gradient.
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molmod/molmod | molmod/minimizer.py | Minimizer.get_final | def get_final(self):
"""Return the final solution in the original coordinates"""
if self.prec is None:
return self.x
else:
return self.prec.undo(self.x) | python | def get_final(self):
"""Return the final solution in the original coordinates"""
if self.prec is None:
return self.x
else:
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molmod/molmod | molmod/minimizer.py | Minimizer._run | def _run(self):
"""Run the iterative optimizer"""
success = self.initialize()
while success is None:
success = self.propagate()
return success | python | def _run(self):
"""Run the iterative optimizer"""
success = self.initialize()
while success is None:
success = self.propagate()
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molmod/molmod | molmod/minimizer.py | Minimizer._print_header | def _print_header(self):
"""Print the header for screen logging"""
header = " Iter Dir "
if self.constraints is not None:
header += ' SC CC'
header += " Function"
if self.convergence_condition is not None:
header += self.convergence_condition.ge... | python | def _print_header(self):
"""Print the header for screen logging"""
header = " Iter Dir "
if self.constraints is not None:
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header += " Function"
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molmod/molmod | molmod/minimizer.py | Minimizer._screen | def _screen(self, s, newline=False):
"""Print something on screen when self.verbose == True"""
if self.verbose:
if newline:
print(s)
else:
print(s, end=' ') | python | def _screen(self, s, newline=False):
"""Print something on screen when self.verbose == True"""
if self.verbose:
if newline:
print(s)
else:
print(s, end=' ') | [
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molmod/molmod | molmod/minimizer.py | Minimizer._line_opt | def _line_opt(self):
"""Perform a line search along the current direction"""
direction = self.search_direction.direction
if self.constraints is not None:
try:
direction = self.constraints.project(self.x, direction)
except ConstraintError:
s... | python | def _line_opt(self):
"""Perform a line search along the current direction"""
direction = self.search_direction.direction
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direction = self.constraints.project(self.x, direction)
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molmod/molmod | molmod/graphs.py | Graph.edge_index | def edge_index(self):
"""A map to look up the index of a edge"""
return dict((edge, index) for index, edge in enumerate(self.edges)) | python | def edge_index(self):
"""A map to look up the index of a edge"""
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molmod/molmod | molmod/graphs.py | Graph.neighbors | def neighbors(self):
"""A dictionary with neighbors
The dictionary will have the following form:
``{vertexX: (vertexY1, vertexY2, ...), ...}``
This means that vertexX and vertexY1 are connected etc. This also
implies that the following elements are part of the dictio... | python | def neighbors(self):
"""A dictionary with neighbors
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``{vertexX: (vertexY1, vertexY2, ...), ...}``
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molmod/molmod | molmod/graphs.py | Graph.distances | def distances(self):
"""The matrix with the all-pairs shortest path lenghts"""
from molmod.ext import graphs_floyd_warshall
distances = np.zeros((self.num_vertices,)*2, dtype=int)
#distances[:] = -1 # set all -1, which is just a very big integer
#distances.ravel()[::len(distances... | python | def distances(self):
"""The matrix with the all-pairs shortest path lenghts"""
from molmod.ext import graphs_floyd_warshall
distances = np.zeros((self.num_vertices,)*2, dtype=int)
#distances[:] = -1 # set all -1, which is just a very big integer
#distances.ravel()[::len(distances... | [
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molmod/molmod | molmod/graphs.py | Graph.central_vertices | def central_vertices(self):
"""Vertices that have the lowest maximum distance to any other vertex"""
max_distances = self.distances.max(0)
max_distances_min = max_distances[max_distances > 0].min()
return (max_distances == max_distances_min).nonzero()[0] | python | def central_vertices(self):
"""Vertices that have the lowest maximum distance to any other vertex"""
max_distances = self.distances.max(0)
max_distances_min = max_distances[max_distances > 0].min()
return (max_distances == max_distances_min).nonzero()[0] | [
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molmod/molmod | molmod/graphs.py | Graph.independent_vertices | def independent_vertices(self):
"""Lists of vertices that are only interconnected within each list
This means that there is no path from a vertex in one list to a
vertex in another list. In case of a molecular graph, this would
yield the atoms that belong to individual molecule... | python | def independent_vertices(self):
"""Lists of vertices that are only interconnected within each list
This means that there is no path from a vertex in one list to a
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molmod/molmod | molmod/graphs.py | Graph.fingerprint | def fingerprint(self):
"""A total graph fingerprint
The result is invariant under permutation of the vertex indexes. The
chance that two different (molecular) graphs yield the same
fingerprint is small but not zero. (See unit tests.)"""
if self.num_vertices == 0:
... | python | def fingerprint(self):
"""A total graph fingerprint
The result is invariant under permutation of the vertex indexes. The
chance that two different (molecular) graphs yield the same
fingerprint is small but not zero. (See unit tests.)"""
if self.num_vertices == 0:
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molmod/molmod | molmod/graphs.py | Graph.vertex_fingerprints | def vertex_fingerprints(self):
"""A fingerprint for each vertex
The result is invariant under permutation of the vertex indexes.
Vertices that are symmetrically equivalent will get the same
fingerprint, e.g. the hydrogens in methane would get the same
fingerprint.
... | python | def vertex_fingerprints(self):
"""A fingerprint for each vertex
The result is invariant under permutation of the vertex indexes.
Vertices that are symmetrically equivalent will get the same
fingerprint, e.g. the hydrogens in methane would get the same
fingerprint.
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molmod/molmod | molmod/graphs.py | Graph.equivalent_vertices | def equivalent_vertices(self):
"""A dictionary with symmetrically equivalent vertices."""
level1 = {}
for i, row in enumerate(self.vertex_fingerprints):
key = row.tobytes()
l = level1.get(key)
if l is None:
l = set([i])
level1[k... | python | def equivalent_vertices(self):
"""A dictionary with symmetrically equivalent vertices."""
level1 = {}
for i, row in enumerate(self.vertex_fingerprints):
key = row.tobytes()
l = level1.get(key)
if l is None:
l = set([i])
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molmod/molmod | molmod/graphs.py | Graph.symmetries | def symmetries(self):
"""Graph symmetries (permutations) that map the graph onto itself."""
symmetry_cycles = set([])
symmetries = set([])
for match in GraphSearch(EqualPattern(self))(self):
match.cycles = match.get_closed_cycles()
if match.cycles in symmetry_cyc... | python | def symmetries(self):
"""Graph symmetries (permutations) that map the graph onto itself."""
symmetry_cycles = set([])
symmetries = set([])
for match in GraphSearch(EqualPattern(self))(self):
match.cycles = match.get_closed_cycles()
if match.cycles in symmetry_cyc... | [
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molmod/molmod | molmod/graphs.py | Graph.symmetry_cycles | def symmetry_cycles(self):
"""The cycle representations of the graph symmetries"""
result = set([])
for symmetry in self.symmetries:
result.add(symmetry.cycles)
return result | python | def symmetry_cycles(self):
"""The cycle representations of the graph symmetries"""
result = set([])
for symmetry in self.symmetries:
result.add(symmetry.cycles)
return result | [
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molmod/molmod | molmod/graphs.py | Graph.canonical_order | def canonical_order(self):
"""The vertices in a canonical or normalized order.
This routine will return a list of vertices in an order that does not
depend on the initial order, but only depends on the connectivity and
the return values of the function self.get_vertex_string.
... | python | def canonical_order(self):
"""The vertices in a canonical or normalized order.
This routine will return a list of vertices in an order that does not
depend on the initial order, but only depends on the connectivity and
the return values of the function self.get_vertex_string.
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molmod/molmod | molmod/graphs.py | Graph.iter_breadth_first | def iter_breadth_first(self, start=None, do_paths=False, do_duplicates=False):
"""Iterate over the vertices with the breadth first algorithm.
See http://en.wikipedia.org/wiki/Breadth-first_search for more info.
If not start vertex is given, the central vertex is taken.
By defa... | python | def iter_breadth_first(self, start=None, do_paths=False, do_duplicates=False):
"""Iterate over the vertices with the breadth first algorithm.
See http://en.wikipedia.org/wiki/Breadth-first_search for more info.
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molmod/molmod | molmod/graphs.py | Graph.iter_breadth_first_edges | def iter_breadth_first_edges(self, start=None):
"""Iterate over the edges with the breadth first convention.
We need this for the pattern matching algorithms, but a quick look at
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The edges are yielded one by one, togethe... | python | def iter_breadth_first_edges(self, start=None):
"""Iterate over the edges with the breadth first convention.
We need this for the pattern matching algorithms, but a quick look at
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The edges are yielded one by one, togethe... | [
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molmod/molmod | molmod/graphs.py | Graph.get_subgraph | def get_subgraph(self, subvertices, normalize=False):
"""Constructs a subgraph of the current graph
Arguments:
| ``subvertices`` -- The vertices that should be retained.
| ``normalize`` -- Whether or not the vertices should renumbered and
reduced to the given... | python | def get_subgraph(self, subvertices, normalize=False):
"""Constructs a subgraph of the current graph
Arguments:
| ``subvertices`` -- The vertices that should be retained.
| ``normalize`` -- Whether or not the vertices should renumbered and
reduced to the given... | [
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molmod/molmod | molmod/graphs.py | Graph.get_vertex_fingerprints | def get_vertex_fingerprints(self, vertex_strings, edge_strings, num_iter=None):
"""Return an array with fingerprints for each vertex"""
import hashlib
def str2array(x):
"""convert a hash string to a numpy array of bytes"""
if len(x) == 0:
return np.zeros(0... | python | def get_vertex_fingerprints(self, vertex_strings, edge_strings, num_iter=None):
"""Return an array with fingerprints for each vertex"""
import hashlib
def str2array(x):
"""convert a hash string to a numpy array of bytes"""
if len(x) == 0:
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molmod/molmod | molmod/graphs.py | Graph.get_halfs | def get_halfs(self, vertex1, vertex2):
"""Split the graph in two halfs by cutting the edge: vertex1-vertex2
If this is not possible (due to loops connecting both ends), a
GraphError is raised.
Returns the vertices in both halfs.
"""
def grow(origin, other):
... | python | def get_halfs(self, vertex1, vertex2):
"""Split the graph in two halfs by cutting the edge: vertex1-vertex2
If this is not possible (due to loops connecting both ends), a
GraphError is raised.
Returns the vertices in both halfs.
"""
def grow(origin, other):
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molmod/molmod | molmod/graphs.py | Graph.get_part | def get_part(self, vertex_in, vertices_border):
"""List all vertices that are connected to vertex_in, but are not
included in or 'behind' vertices_border.
"""
vertices_new = set(self.neighbors[vertex_in])
vertices_part = set([vertex_in])
while len(vertices_new) > 0:
... | python | def get_part(self, vertex_in, vertices_border):
"""List all vertices that are connected to vertex_in, but are not
included in or 'behind' vertices_border.
"""
vertices_new = set(self.neighbors[vertex_in])
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molmod/molmod | molmod/graphs.py | Graph.get_halfs_double | def get_halfs_double(self, vertex_a1, vertex_b1, vertex_a2, vertex_b2):
"""Compute the two parts separated by ``(vertex_a1, vertex_b1)`` and ``(vertex_a2, vertex_b2)``
Raise a GraphError when ``(vertex_a1, vertex_b1)`` and
``(vertex_a2, vertex_b2)`` do not separate the graph in two
... | python | def get_halfs_double(self, vertex_a1, vertex_b1, vertex_a2, vertex_b2):
"""Compute the two parts separated by ``(vertex_a1, vertex_b1)`` and ``(vertex_a2, vertex_b2)``
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