Code stringlengths 103 85.9k | Summary listlengths 0 94 |
|---|---|
Please provide a description of the function:def load_molecule(name, format=None):
'''Read a `~chemlab.core.Molecule` from a file.
.. seealso:: `chemlab.io.datafile`
'''
mol = datafile(name, format=format).read('molecule')
display_system(System([mol])) | [] |
Please provide a description of the function:def load_remote_trajectory(url, format=None):
'''Load a trajectory file from a remote location specified by *url*.
.. seealso:: load_remote_system
'''
from urllib import urlretrieve
filename, headers = urlretrieve(url)
load_trajectory(filename, ... | [] |
Please provide a description of the function:def write_system(filename, format=None):
'''Write the system currently displayed to a file.'''
datafile(filename, format=format, mode='w').write('system',
current_system()) | [] |
Please provide a description of the function:def write_molecule(filename, format=None):
'''Write the system displayed in a file as a molecule.'''
datafile(filename, format=format,
mode='w').write('molecule',current_system()) | [] |
Please provide a description of the function:def goto_time(timeval):
'''Go to a specific time (in nanoseconds) in the current
trajectory.
'''
i = bisect.bisect(viewer.frame_times, timeval * 1000)
goto_frame(i) | [] |
Please provide a description of the function:def load_trajectory(name, skip=1, format=None):
'''Load a trajectory file into chemlab. You should call this
command after you load a `~chemlab.core.System` through
load_system or load_remote_system.
'''
df = datafile(name, format=format)
dt, coords ... | [] |
Please provide a description of the function:def merge_systems(sysa, sysb, bounding=0.2):
'''Generate a system by merging *sysa* and *sysb*.
Overlapping molecules are removed by cutting the molecules of
*sysa* that have atoms near the atoms of *sysb*. The cutoff distance
is defined by the *bounding* pa... | [] |
Please provide a description of the function:def minimum_image(self):
if self.box_vectors is None:
raise ValueError('No periodic vectors defined')
else:
self.r_array = minimum_image(self.r_array, self.box_vectors.diagonal())
return self | [
"Align the system according to the minimum image convention"
] |
Please provide a description of the function:def remove_atoms(self, indices):
mol_indices = self.atom_to_molecule_indices(indices)
self.copy_from(self.sub(molecule_index=mol_indices)) | [
"Remove the atoms positioned at *indices*. The molecule\n containing the atom is removed as well.\n\n If you have a system of 10 water molecules (and 30 atoms), if\n you remove the atoms at indices 0, 1 and 29 you will remove\n the first and last water molecules.\n\n **Parameters*... |
Please provide a description of the function:def where(self, within_of=None, inplace=False, **kwargs):
masks = super(System, self).where(inplace=inplace, **kwargs)
def index_to_mask(index, n):
val = np.zeros(n, dtype='bool')
val[index] = True
return ... | [
"Return indices that met the conditions"
] |
Please provide a description of the function:def cartesian_to_spherical(cartesian):
xyz = cartesian
xy = xyz[:,0]**2 + xyz[:,1]**2
r = np.sqrt(xy + xyz[:,2]**2)
phi = np.arctan2(np.sqrt(xy), xyz[:,2]) # for elevation angle defined from Z-axis down
#ptsnew[:,4] = np.arctan2(xyz[:,2], np.sqrt(xy)... | [
"Convert cartesian to spherical coordinates passed as (N,3) shaped arrays."
] |
Please provide a description of the function:def binomial(n,k):
if n==k: return 1
assert n>k, "Attempting to call binomial(%d,%d)" % (n,k)
return factorial(n)//(factorial(k)*factorial(n-k)) | [
"\n Binomial coefficient\n >>> binomial(5,2)\n 10\n >>> binomial(10,5)\n 252\n "
] |
Please provide a description of the function:def Fgamma(m,x):
SMALL=1e-12
x = max(x,SMALL)
return 0.5*pow(x,-m-0.5)*gamm_inc(m+0.5,x) | [
"\n Incomplete gamma function\n >>> np.isclose(Fgamma(0,0),1.0)\n True\n "
] |
Please provide a description of the function:def gamm_inc(a,x):
assert (x > 0 and a >= 0), "Invalid arguments in routine gamm_inc: %s,%s" % (x,a)
if x < (a+1.0): #Use the series representation
gam,gln = _gser(a,x)
else: #Use continued fractions
gamc,gln = _gcf(a,x)
gam = 1-gamc... | [
"\n Incomple gamma function \\gamma; computed from NumRec routine gammp.\n >>> np.isclose(gamm_inc(0.5,1),1.49365)\n True\n >>> np.isclose(gamm_inc(1.5,2),0.6545103)\n True\n >>> np.isclose(gamm_inc(2.5,1e-12),0)\n True\n "
] |
Please provide a description of the function:def _gser(a,x):
"Series representation of Gamma. NumRec sect 6.1."
ITMAX=100
EPS=3.e-7
gln=lgamma(a)
assert(x>=0),'x < 0 in gser'
if x == 0 : return 0,gln
ap = a
delt = sum = 1./a
for i in range(ITMAX):
ap=ap+1.
delt=delt... | [] |
Please provide a description of the function:def _gcf(a,x):
"Continued fraction representation of Gamma. NumRec sect 6.1"
ITMAX=100
EPS=3.e-7
FPMIN=1.e-30
gln=lgamma(a)
b=x+1.-a
c=1./FPMIN
d=1./b
h=d
for i in range(1,ITMAX+1):
an=-i*(i-a)
b=b+2.
d=an*d+b
... | [] |
Please provide a description of the function:def dmat(c,nocc):
"Form the density matrix from the first nocc orbitals of c"
return np.dot(c[:,:nocc],c[:,:nocc].T) | [] |
Please provide a description of the function:def symorth(S):
"Symmetric orthogonalization"
E,U = np.linalg.eigh(S)
n = len(E)
Shalf = np.identity(n,'d')
for i in range(n):
Shalf[i,i] /= np.sqrt(E[i])
return simx(Shalf,U,True) | [] |
Please provide a description of the function:def canorth(S):
"Canonical orthogonalization U/sqrt(lambda)"
E,U = np.linalg.eigh(S)
for i in range(len(E)):
U[:,i] = U[:,i] / np.sqrt(E[i])
return U | [] |
Please provide a description of the function:def cholorth(S):
"Cholesky orthogonalization"
return np.linalg.inv(np.linalg.cholesky(S)).T | [] |
Please provide a description of the function:def simx(A,B,transpose=False):
"Similarity transform B^T(AB) or B(AB^T) (if transpose)"
if transpose:
return np.dot(B,np.dot(A,B.T))
return np.dot(B.T,np.dot(A,B)) | [] |
Please provide a description of the function:def geigh(H,S):
"Solve the generalized eigensystem Hc = ESc"
A = cholorth(S)
E,U = np.linalg.eigh(simx(H,A))
return E,np.dot(A,U) | [] |
Please provide a description of the function:def parseline(line,format):
xlat = {'x':None,'s':str,'f':float,'d':int,'i':int}
result = []
words = line.split()
for i in range(len(format)):
f = format[i]
trans = xlat.get(f,None)
if trans: result.append(trans(words[i]))
if l... | [
"\\\n Given a line (a string actually) and a short string telling\n how to format it, return a list of python objects that result.\n\n The format string maps words (as split by line.split()) into\n python code:\n x -> Nothing; skip this word\n s -> Return this word as a string\n i -... |
Please provide a description of the function:def colorscale(mag, cmin, cmax):
# Normalize to 0-1
try:
x = float(mag-cmin)/(cmax-cmin)
except ZeroDivisionError:
x = 0.5 # cmax == cmin
blue = min((max((4*(0.75-x), 0.)), 1.))
red = min((max((4*(x-0.25), 0.)), 1.))
green = min(... | [
"\n Return a tuple of floats between 0 and 1 for R, G, and B.\n From Python Cookbook (9.11?)\n "
] |
Please provide a description of the function:def from_fields(cls, **kwargs):
'''
Create an `Atom` instance from a set of fields. This is a
slightly faster way to initialize an Atom.
**Example**
>>> Atom.from_fields(type='Ar',
r_array=np.arra... | [] |
Please provide a description of the function:def _check_periodic(periodic):
'''Validate periodic input'''
periodic = np.array(periodic)
# If it is a matrix
if len(periodic.shape) == 2:
assert periodic.shape[0] == periodic.shape[1], 'periodic shoud be a square matrix or a flat array'
ret... | [] |
Please provide a description of the function:def nearest_neighbors(coordinates_a, coordinates_b, periodic, r=None, n=None):
'''Nearest neighbor search between two arrays of coordinates. Notice that
you can control the result by selecting neighbors either by radius *r* or
by number *n*. The algorithm uses a ... | [] |
Please provide a description of the function:def count_neighbors(coordinates_a, coordinates_b, periodic, r):
'''Count the neighbours number of neighbors.
:param np.ndarray coordinates_a: Either an array of coordinates of shape (N,3)
or a single point of shape (3,)
:para... | [] |
Please provide a description of the function:def change_background(color):
viewer.widget.background_color = colors.any_to_rgb(color)
viewer.update() | [
"Setup the background color to *color*. \n \n Example::\n\n change_background('black')\n change_background('white')\n change_background('#ffffff')\n \n You can call this function interactively by using::\n\n change_color.interactive()\n \n A new dialog will popup with a color... |
Please provide a description of the function:def scale_atoms(fac):
'''Scale the currently selected atoms atoms by a certain factor
*fac*.
Use the value *fac=1.0* to reset the scale.
'''
rep = current_representation()
atms = selected_atoms()
rep.scale_factors[atms] = fac
rep.update... | [] |
Please provide a description of the function:def change_color(color):
rep = current_representation()
# Let's parse the color first
if isinstance(color, str):
# The color should be a string
col = color_from_string(color)
if isinstance(color, tuple):
col = color
... | [
"Change the color of the currently selected objects. *color* is\n represented as a string. Otherwise color can be passed as an rgba\n tuple of values between 0, 255\n\n Reset the color by passing *color=None*.\n \n You can call this function interactively by using::\n\n change_color.interactiv... |
Please provide a description of the function:def change_default_radii(def_map):
s = current_system()
rep = current_representation()
rep.radii_state.default = [def_map[t] for t in s.type_array]
rep.radii_state.reset() | [
"Change the default radii\n "
] |
Please provide a description of the function:def screenshot(filename, width=None, height=None):
'''Make a screenshot of the current view. You can tweak the
resolution up to what your GPU memory supports.
By defaults it uses the current window resolution.
Example::
screenshot('screen.png... | [] |
Please provide a description of the function:def add_post_processing(effect, **options):
from chemlab.graphics.postprocessing import SSAOEffect, OutlineEffect, FXAAEffect, GammaCorrectionEffect
pp_map = {'ssao': SSAOEffect,
'outline': OutlineEffect,
'fxaa': FXAAEffect,
... | [
"Apply a post processing effect.\n\n **Parameters**\n \n effect: string\n The effect to be applied, choose between ``ssao``,\n ``outline``, ``fxaa``, ``gamma``.\n \n **options:\n Options used to initialize the effect, check the\n :doc:`chemlab.graphics.postprocessing` for ... |
Please provide a description of the function:def greplines(pattern, lines):
res = []
for line in lines:
match = re.search(pattern, line)
if match is not None:
res.append(line)
return res | [
"Given a list of strings *lines* return the lines that match\n pattern.\n\n "
] |
Please provide a description of the function:def sections(start, end, text, line=True):
if not line:
return re.findall(start+"(.*?)"+end, text, re.DOTALL)
lines = text.splitlines()
# This is a state-machine with the states MATCHING = True/False
MATCHING = False
section_list = ... | [
"Given the *text* to analyze return the section the start and\n end matchers. If line=True return the lines between the line that\n matches *start* and the line that matches *end* regexps.\n\n If line=False return the text between the matching start and end\n \n The match is in the regexp lingo *ungr... |
Please provide a description of the function:def grep_split(pattern, text):
'''Take the lines in *text* and split them each time the pattern
matches a line.
'''
lines = text.splitlines()
indices = [i for i, line in enumerate(lines)
if re.search(pattern, line)]
return ['\n'.j... | [] |
Please provide a description of the function:def unit_vector(x):
y = np.array(x, dtype='float')
return y/norm(y) | [
"Return a unit vector in the same direction as x."
] |
Please provide a description of the function:def angle(x, y):
return arccos(dot(x, y)/(norm(x)*norm(y)))*180./pi | [
"Return the angle between vectors a and b in degrees."
] |
Please provide a description of the function:def cell_to_cellpar(cell):
va, vb, vc = cell
a = np.linalg.norm(va)
b = np.linalg.norm(vb)
c = np.linalg.norm(vc)
alpha = 180.0/pi*arccos(dot(vb, vc)/(b*c))
beta = 180.0/pi*arccos(dot(vc, va)/(c*a))
gamma = 180.0/pi*arccos(dot(va, vb)/(a*b))... | [
"Returns the cell parameters [a, b, c, alpha, beta, gamma] as a\n numpy array."
] |
Please provide a description of the function:def cellpar_to_cell(cellpar, ab_normal=(0,0,1), a_direction=None):
if a_direction is None:
if np.linalg.norm(np.cross(ab_normal, (1,0,0))) < 1e-5:
a_direction = (0,0,1)
else:
a_direction = (1,0,0)
# Define rotated X,Y,Z-s... | [
"Return a 3x3 cell matrix from `cellpar` = [a, b, c, alpha,\n beta, gamma]. The returned cell is orientated such that a and b\n are normal to `ab_normal` and a is parallel to the projection of\n `a_direction` in the a-b plane.\n\n Default `a_direction` is (1,0,0), unless this is parallel to\n `ab_no... |
Please provide a description of the function:def metric_from_cell(cell):
cell = np.asarray(cell, dtype=float)
return np.dot(cell, cell.T) | [
"Calculates the metric matrix from cell, which is given in the\n Cartesian system."
] |
Please provide a description of the function:def add_default_handler(ioclass, format, extension=None):
if format in _handler_map:
print("Warning: format {} already present.".format(format))
_handler_map[format] = ioclass
if extension in _extensions_map:
print("Warning: extension {} al... | [
"Register a new data handler for a given format in\n the default handler list.\n\n This is a convenience function used internally to setup the\n default handlers. It can be used to add other handlers at\n runtime even if this isn't a suggested practice.\n\n **Parameters**\n\n ioc... |
Please provide a description of the function:def get_handler_class(ext):
if ext in _extensions_map:
format = _extensions_map[ext]
else:
raise ValueError("Unknown format for %s extension." % ext)
if format in _handler_map:
hc = _handler_map[format]
return hc
else:
... | [
"Get the IOHandler that can handle the extension *ext*."
] |
Please provide a description of the function:def datafile(filename, mode="rb", format=None):
filename = os.path.expanduser(filename)
base, ext = os.path.splitext(filename)
if format is None:
hc = get_handler_class(ext)
else:
hc = _handler_map.get(format)
if hc is None:
... | [
"Initialize the appropriate\n :py:class:`~chemlab.io.iohandler.IOHandler` for a given file\n extension or file format.\n\n The *datafile* function can be conveniently used to quickly read\n or write data in a certain format::\n\n >>> handler = datafile(\"molecule.pdb\")\n >>> mol = handler... |
Please provide a description of the function:def remotefile(url, format=None):
if format is None:
res = urlparse(url)
filename, ext = os.path.splitext(res.path)
hc = get_handler_class(ext)
else:
hc = _handler_map.get(format)
if hc is None:
raise ValueEr... | [
"The usage of *remotefile* is equivalent to\n :func:`chemlab.io.datafile` except you can download a file from a\n remote url.\n\n **Example**\n\n mol = remotefile(\"https://github.com/chemlab/chemlab-testdata/blob/master/3ZJE.pdb\").read(\"molecule\")\n\n "
] |
Please provide a description of the function:def minimum_image(coords, pbc):
# This will do the broadcasting
coords = np.array(coords)
pbc = np.array(pbc)
# For each coordinate this number represents which box we are in
image_number = np.floor(coords / pbc)
wrap = coords - pbc * image_num... | [
"\n Wraps a vector collection of atom positions into the central periodic\n image or primary simulation cell.\n\n Parameters\n ----------\n pos : :class:`numpy.ndarray`, (Nx3)\n Vector collection of atom positions.\n\n Returns\n -------\n wrap : :class:`numpy.ndarray`, (Nx3)\n Returns ... |
Please provide a description of the function:def noperiodic(r_array, periodic, reference=None):
'''Rearrange the array of coordinates *r_array* in a way that doensn't
cross the periodic boundary.
Parameters
----------
r_array : :class:`numpy.ndarray`, (Nx3)
Array of 3D coordinate... | [] |
Please provide a description of the function:def subtract_vectors(a, b, periodic):
'''Returns the difference of the points vec_a - vec_b subject
to the periodic boundary conditions.
'''
r = a - b
delta = np.abs(r)
sign = np.sign(r)
return np.where(delta > 0.5 * periodic, sign * (periodi... | [] |
Please provide a description of the function:def add_vectors(vec_a, vec_b, periodic):
'''Returns the sum of the points vec_a - vec_b subject
to the periodic boundary conditions.
'''
moved = noperiodic(np.array([vec_a, vec_b]), periodic)
return vec_a + vec_b | [] |
Please provide a description of the function:def distance_matrix(a, b, periodic):
'''Calculate a distrance matrix between coordinates sets a and b
'''
a = a
b = b[:, np.newaxis]
return periodic_distance(a, b, periodic) | [] |
Please provide a description of the function:def periodic_distance(a, b, periodic):
'''
Periodic distance between two arrays. Periodic is a 3
dimensional array containing the 3 box sizes.
'''
a = np.array(a)
b = np.array(b)
periodic = np.array(periodic)
delta = np.abs(a - b)
delta ... | [] |
Please provide a description of the function:def geometric_center(coords, periodic):
'''Geometric center taking into account periodic boundaries'''
max_vals = periodic
theta = 2 * np.pi * (coords / max_vals)
eps = np.cos(theta) * max_vals / (2 * np.pi)
zeta = np.sin(theta) * max_vals / (2 * np.pi)
... | [] |
Please provide a description of the function:def radius_of_gyration(coords, periodic):
'''Calculate the square root of the mean distance squared from the center of gravity.
'''
gc = geometric_center(coords, periodic)
return (periodic_distance(coords, gc, periodic) ** 2).sum() / len(coords) | [] |
Please provide a description of the function:def find(query):
assert type(query) == str or type(query) == str, 'query not a string object'
searchurl = 'http://www.chemspider.com/Search.asmx/SimpleSearch?query=%s&token=%s' % (urlquote(query), TOKEN)
response = urlopen(searchurl)
tree = ET.parse(resp... | [
" Search by Name, SMILES, InChI, InChIKey, etc. Returns first 100 Compounds "
] |
Please provide a description of the function:def imageurl(self):
if self._imageurl is None:
self._imageurl = 'http://www.chemspider.com/ImagesHandler.ashx?id=%s' % self.csid
return self._imageurl | [
" Return the URL of a png image of the 2D structure "
] |
Please provide a description of the function:def loadextendedcompoundinfo(self):
apiurl = 'http://www.chemspider.com/MassSpecAPI.asmx/GetExtendedCompoundInfo?CSID=%s&token=%s' % (self.csid,TOKEN)
response = urlopen(apiurl)
tree = ET.parse(response)
mf = tree.find('{http://www.ch... | [
" Load extended compound info from the Mass Spec API "
] |
Please provide a description of the function:def image(self):
if self._image is None:
apiurl = 'http://www.chemspider.com/Search.asmx/GetCompoundThumbnail?id=%s&token=%s' % (self.csid,TOKEN)
response = urlopen(apiurl)
tree = ET.parse(response)
self._image... | [
" Return string containing PNG binary image data of 2D structure image "
] |
Please provide a description of the function:def mol(self):
if self._mol is None:
apiurl = 'http://www.chemspider.com/MassSpecAPI.asmx/GetRecordMol?csid=%s&calc3d=false&token=%s' % (self.csid,TOKEN)
response = urlopen(apiurl)
tree = ET.parse(response)
sel... | [
" Return record in MOL format "
] |
Please provide a description of the function:def mol3d(self):
if self._mol3d is None:
apiurl = 'http://www.chemspider.com/MassSpecAPI.asmx/GetRecordMol?csid=%s&calc3d=true&token=%s' % (self.csid,TOKEN)
response = urlopen(apiurl)
tree = ET.parse(response)
... | [
" Return record in MOL format with 3D coordinates calculated "
] |
Please provide a description of the function:def update_positions(self, r_array):
'''Update the coordinate array r_array'''
self.ar.update_positions(r_array)
if self.has_bonds:
self.br.update_positions(r_array) | [] |
Please provide a description of the function:def write(self, feature, value, *args, **kwargs):
if 'w' not in self.fd.mode and 'x' not in self.fd.mode:
raise Exception("The file is not opened in writing mode. If you're using datafile, add the 'w' option.\ndatafile(filename, 'w')")
... | [
"Same as :py:meth:`~chemlab.io.iohandler.IOHandler.read`. You have to pass\n also a *value* to write and you may pass any additional \n arguments.\n \n **Example**\n \n ::\n \n class XyzIO(IOHandler):\n can_write = ['molecule']\n \n ... |
Please provide a description of the function:def check_feature(self, feature, readwrite):
if readwrite == "read":
features = self.can_read
if readwrite == "write":
features = self.can_write
if feature not in features:
matches = difflib.g... | [
"Check if the *feature* is supported in the handler and\n raise an exception otherwise.\n\n **Parameters**\n \n feature: str\n Identifier for a certain feature.\n readwrite: \"read\" or \"write\"\n Check if the feature is available for reading or writing.\n ... |
Please provide a description of the function:def concatenate_attributes(attributes):
'''Concatenate InstanceAttribute to return a bigger one.'''
# We get a template/
tpl = attributes[0]
attr = InstanceAttribute(tpl.name, tpl.shape,
tpl.dtype, tpl.dim, alias=None)
#... | [] |
Please provide a description of the function:def concatenate_fields(fields, dim):
'Create an INstanceAttribute from a list of InstnaceFields'
if len(fields) == 0:
raise ValueError('fields cannot be an empty list')
if len(set((f.name, f.shape, f.dtype) for f in fields)) != 1:
raise Value... | [] |
Please provide a description of the function:def normalize_index(index):
index = np.asarray(index)
if len(index) == 0:
return index.astype('int')
if index.dtype == 'bool':
index = index.nonzero()[0]
elif index.dtype == 'int':
pass
else:
raise ValueError... | [
"normalize numpy index"
] |
Please provide a description of the function:def has_attribute(self, name, alias=False):
prop_dict = merge_dicts(self.__attributes__,
self.__fields__,
self.__relations__)
if alias:
prop_dict.update({v.alias : v for v in... | [
"Check if the entity contains the attribute *name*"
] |
Please provide a description of the function:def to_dict(self):
ret = merge_dicts(self.__attributes__, self.__relations__, self.__fields__)
ret = {k : v.value for k,v in ret.items()}
ret['maps'] = {k : v.value for k,v in self.maps.items()}
return ret | [
"Return a dict representing the ChemicalEntity that can be read back\n using from_dict.\n \n "
] |
Please provide a description of the function:def from_json(cls, string):
exp_dict = json_to_data(string)
version = exp_dict.get('version', 0)
if version == 0:
return cls.from_dict(exp_dict)
elif version == 1:
return cls.from_dict(exp_dict)
else:
... | [
"Create a ChemicalEntity from a json string \n "
] |
Please provide a description of the function:def copy(self):
inst = super(type(self), type(self)).empty(**self.dimensions)
# Need to copy all attributes, fields, relations
inst.__attributes__ = {k: v.copy() for k, v in self.__attributes__.items()}
inst.__fields__ = {k: ... | [
"Create a copy of this ChemicalEntity\n \n "
] |
Please provide a description of the function:def copy_from(self, other):
# Need to copy all attributes, fields, relations
self.__attributes__ = {k: v.copy() for k, v in other.__attributes__.items()}
self.__fields__ = {k: v.copy() for k, v in other.__fields__.items()}
self.__rela... | [
"Copy properties from another ChemicalEntity\n \n "
] |
Please provide a description of the function:def update(self, dictionary):
allowed_attrs = list(self.__attributes__.keys())
allowed_attrs += [a.alias for a in self.__attributes__.values()]
for k in dictionary:
# We only update existing attributes
if k in allowed_... | [
"Update the current chemical entity from a dictionary of attributes"
] |
Please provide a description of the function:def subentity(self, Entity, index):
dim = Entity.__dimension__
entity = Entity.empty()
if index >= self.dimensions[dim]:
raise ValueError('index {} out of bounds for dimension {} (size {})'
.f... | [
"Return child entity"
] |
Please provide a description of the function:def sub_dimension(self, index, dimension, propagate=True, inplace=False):
filter_ = self._propagate_dim(index, dimension, propagate)
return self.subindex(filter_, inplace) | [
"Return a ChemicalEntity sliced through a dimension.\n \n If other dimensions depend on this one those are updated accordingly.\n "
] |
Please provide a description of the function:def expand_dimension(self, newdim, dimension, maps={}, relations={}):
''' When we expand we need to provide new maps and relations as those
can't be inferred '''
for name, attr in self.__attributes__.items():
if attr.dim == dimens... | [] |
Please provide a description of the function:def concat(self, other, inplace=False):
'''Concatenate two ChemicalEntity of the same kind'''
# Create new entity
if inplace:
obj = self
else:
obj = self.copy()
# Stitch every attribute
... | [] |
Please provide a description of the function:def where(self, inplace=False, **kwargs):
masks = {k: np.ones(v, dtype='bool') for k,v in self.dimensions.items()}
def index_to_mask(index, n):
val = np.zeros(n, dtype='bool')
val[index] = True
return val... | [
"Return indices over every dimension that met the conditions. \n \n Condition syntax:\n \n *attribute* = value\n \n Return indices that satisfy the condition where the attribute is equal\n to the value\n \n e.g. type_array = 'H'\n \n *attr... |
Please provide a description of the function:def sub(self, inplace=False, **kwargs):
filter_ = self.where(**kwargs)
return self.subindex(filter_, inplace) | [
"Return a entity where the conditions are met"
] |
Please provide a description of the function:def batch(self):
_batch = []
yield _batch
if _batch:
new_part = super(type(self), type(self)).empty()
new_part._from_entities(_batch, _batch[0].__dimension__)
self.concat(new_part, inplace=True) | [
"Batch initialization"
] |
Please provide a description of the function:def sub(self, index):
index = np.asarray(index)
if index.dtype == 'bool':
index = index.nonzero()[0]
if self.size < len(index):
raise ValueError('Can\'t subset "{}": index ({}) is bigger than the number of ele... | [
"Return a sub-attribute"
] |
Please provide a description of the function:def resolve(input, representation, resolvers=None, **kwargs):
resultdict = query(input, representation, resolvers, **kwargs)
result = resultdict[0]['value'] if resultdict else None
if result and len(result) == 1:
result = result[0]
return result | [
" Resolve input to the specified output representation "
] |
Please provide a description of the function:def query(input, representation, resolvers=None, **kwargs):
apiurl = API_BASE+'/%s/%s/xml' % (urlquote(input), representation)
if resolvers:
kwargs['resolver'] = ",".join(resolvers)
if kwargs:
apiurl+= '?%s' % urlencode(kwargs)
result = [... | [
" Get all results for resolving input to the specified output representation "
] |
Please provide a description of the function:def download(input, filename, format='sdf', overwrite=False, resolvers=None, **kwargs):
kwargs['format'] = format
if resolvers:
kwargs['resolver'] = ",".join(resolvers)
url = API_BASE+'/%s/file?%s' % (urlquote(input), urlencode(kwargs))
try:
... | [
" Resolve and download structure as a file "
] |
Please provide a description of the function:def download(self, filename, format='sdf', overwrite=False, resolvers=None, **kwargs):
download(self.input, filename, format, overwrite, resolvers, **kwargs) | [
" Download the resolved structure as a file "
] |
Please provide a description of the function:def guess_bonds(r_array, type_array, threshold=0.1, maxradius=0.3, radii_dict=None):
'''Detect bonds given the coordinates (r_array) and types of the
atoms involved (type_array), based on their covalent radii.
To fine-tune the detection, it is possible to s... | [] |
Please provide a description of the function:def move_to(self, r):
'''Translate the molecule to a new position *r*.
'''
dx = r - self.r_array[0]
self.r_array += dx | [] |
Please provide a description of the function:def periodic_distance(a, b, periodic):
'''Periodic distance between two arrays. Periodic is a 3
dimensional array containing the 3 box sizes.
'''
delta = np.abs(a - b)
delta = np.where(delta > 0.5 * periodic, periodic - delta, delta)
return np.sqrt((... | [] |
Please provide a description of the function:def dipole_moment(r_array, charge_array):
'''Return the dipole moment of a neutral system.
'''
return np.sum(r_array * charge_array[:, np.newaxis], axis=0) | [] |
Please provide a description of the function:def parse_gro_lines(lines):
'''Reusable parsing'''
title = lines.pop(0)
natoms = int(lines.pop(0))
atomlist = []
# I need r_array, type_array
datalist = []
for l in lines:
fields = l.split()
line_length = len(l)
if line_l... | [] |
Please provide a description of the function:def distances_within(coords_a, coords_b, cutoff,
periodic=False, method="simple"):
mat = distance_matrix(coords_a, coords_b, cutoff, periodic, method)
return mat[mat.nonzero()] | [
"Calculate distances between the array of coordinates *coord_a*\n and *coord_b* within a certain cutoff.\n \n This function is a wrapper around different routines and data structures\n for distance searches. It return a np.ndarray containing the distances.\n \n **Parameters**\n\n coords_a: np.n... |
Please provide a description of the function:def distance_matrix(coords_a, coords_b, cutoff,
periodic=False, method="simple"):
coords_a = np.array(coords_a)
coords_b = np.array(coords_b)
if method=="simple":
if periodic is not False:
return distance_array(coords_... | [
"Calculate distances matrix the array of coordinates *coord_a*\n and *coord_b* within a certain cutoff.\n \n This function is a wrapper around different routines and data structures\n for distance searches. It return a np.ndarray containing the distances.\n \n Returns a matrix with all the compute... |
Please provide a description of the function:def overlapping_points(coords_a, coords_b, cutoff, periodic=False):
'''Return the indices of *coords_b* points that overlap with
*coords_a* points. The overlap is calculated based on *cutoff*.
**Parameters**
coords_a: np.ndarray((NA, 3))
coords... | [] |
Please provide a description of the function:def random_lattice_box(mol_list, mol_number, size,
spacing=np.array([0.3, 0.3, 0.3])):
'''Make a box by placing the molecules specified in *mol_list* on
random points of an evenly spaced lattice.
Using a lattice automatically ensures that ... | [] |
Please provide a description of the function:def random_box(molecules, total=None, proportions=None, size=[1.,1.,1.], maxtries=100):
'''Create a System made of a series of random molecules.
Parameters:
total:
molecules:
proportions:
'''
# Setup proportions to be right
if p... | [] |
Please provide a description of the function:def schedule(self, callback, timeout=100):
'''Schedule a function to be called repeated time.
This method can be used to perform animations.
**Example**
This is a typical way to perform an animation, just::
... | [] |
Please provide a description of the function:def add_renderer(self, klass, *args, **kwargs):
'''Add a renderer to the current scene.
**Parameter**
klass: renderer class
The renderer class to be added
args, kwargs:
Arguments used by the renderer c... | [] |
Please provide a description of the function:def remove_renderer(self, rend):
'''Remove a renderer from the current view.
**Example**
::
rend = v.add_renderer(AtomRenderer)
v.remove_renderer(rend)
.. versionadded:: 0.3
'''
if re... | [] |
Please provide a description of the function:def add_ui(self, klass, *args, **kwargs):
'''Add an UI element for the current scene. The approach is
the same as renderers.
.. warning:: The UI api is not yet finalized
'''
ui = klass(self.widget, *args, **kwargs)
self.widge... | [] |
Please provide a description of the function:def add_post_processing(self, klass, *args, **kwargs):
'''Add a post processing effect to the current scene.
The usage is as following::
from chemlab.graphics.qt import QtViewer
from chemlab.graphics.postprocessing im... | [] |
Please provide a description of the function:def crystal(positions, molecules, group,
cellpar=[1.0, 1.0, 1.0, 90, 90, 90], repetitions=[1, 1, 1]):
'''Build a crystal from atomic positions, space group and cell
parameters.
**Parameters**
positions: list of coordinates
A list of ... | [] |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.