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42,900 | hannes-brt/cudnn-python-wrappers | libcudnn.py | cudnnGetConvolution2dDescriptor | def cudnnGetConvolution2dDescriptor(convDesc):
""""
Get a convolution descriptor.
This function queries a previously initialized 2D convolution descriptor object.
Parameters
----------
convDesc : cudnnConvolutionDescriptor
Handle to a previously created convolution descriptor.
Ret... | python | def cudnnGetConvolution2dDescriptor(convDesc):
""""
Get a convolution descriptor.
This function queries a previously initialized 2D convolution descriptor object.
Parameters
----------
convDesc : cudnnConvolutionDescriptor
Handle to a previously created convolution descriptor.
Ret... | [
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42,901 | hannes-brt/cudnn-python-wrappers | libcudnn.py | cudnnGetConvolution2dForwardOutputDim | def cudnnGetConvolution2dForwardOutputDim(convDesc, inputTensorDesc, wDesc):
""""
Return the dimensions of the output tensor given a convolution descriptor.
This function returns the dimensions of the resulting 4D tensor of a 2D
convolution, given the convolution descriptor, the input tensor descriptor... | python | def cudnnGetConvolution2dForwardOutputDim(convDesc, inputTensorDesc, wDesc):
""""
Return the dimensions of the output tensor given a convolution descriptor.
This function returns the dimensions of the resulting 4D tensor of a 2D
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42,902 | hannes-brt/cudnn-python-wrappers | libcudnn.py | cudnnGetConvolutionForwardAlgorithm | def cudnnGetConvolutionForwardAlgorithm(handle, srcDesc, wDesc,
convDesc, destDesc, preference, memoryLimitInbytes):
""""
This function returns the best algorithm to choose for the forward convolution
depending on the critera expressed in the cudnnConvolutionFwdPrefer... | python | def cudnnGetConvolutionForwardAlgorithm(handle, srcDesc, wDesc,
convDesc, destDesc, preference, memoryLimitInbytes):
""""
This function returns the best algorithm to choose for the forward convolution
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Parameters
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handle : cudnnHandle
Handle to a previously created cuDNN context.
srcDesc : cudnnTensorDescriptor
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42,903 | hannes-brt/cudnn-python-wrappers | libcudnn.py | cudnnGetConvolutionForwardWorkspaceSize | def cudnnGetConvolutionForwardWorkspaceSize(handle, srcDesc, wDesc,
convDesc, destDesc, algo):
""""
This function returns the amount of GPU memory workspace the user needs
to allocate to be able to call cudnnConvolutionForward with the specified algorithm.
Pa... | python | def cudnnGetConvolutionForwardWorkspaceSize(handle, srcDesc, wDesc,
convDesc, destDesc, algo):
""""
This function returns the amount of GPU memory workspace the user needs
to allocate to be able to call cudnnConvolutionForward with the specified algorithm.
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srcDesc : cudnnTensorDescriptor
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42,904 | hannes-brt/cudnn-python-wrappers | libcudnn.py | cudnnSoftmaxForward | def cudnnSoftmaxForward(handle, algorithm, mode, alpha, srcDesc, srcData, beta, destDesc, destData):
""""
This routing computes the softmax function
Parameters
----------
handle : cudnnHandle
Handle to a previously created cuDNN context.
algorithm : cudnnSoftmaxAlgorithm
Enumera... | python | def cudnnSoftmaxForward(handle, algorithm, mode, alpha, srcDesc, srcData, beta, destDesc, destData):
""""
This routing computes the softmax function
Parameters
----------
handle : cudnnHandle
Handle to a previously created cuDNN context.
algorithm : cudnnSoftmaxAlgorithm
Enumera... | [
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handle : cudnnHandle
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algorithm : cudnnSoftmaxAlgorithm
Enumerant to specify the softmax algorithm.
mode : cudnnSoftmaxMode
Enumerant to specify the softmax mode.
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42,905 | hannes-brt/cudnn-python-wrappers | libcudnn.py | cudnnCreatePoolingDescriptor | def cudnnCreatePoolingDescriptor():
""""
Create pooling descriptor.
This function creates a pooling descriptor object by allocating the memory needed to
hold its opaque structure,
Returns
-------
poolingDesc : cudnnPoolingDescriptor
Newly allocated pooling descriptor.
"""
... | python | def cudnnCreatePoolingDescriptor():
""""
Create pooling descriptor.
This function creates a pooling descriptor object by allocating the memory needed to
hold its opaque structure,
Returns
-------
poolingDesc : cudnnPoolingDescriptor
Newly allocated pooling descriptor.
"""
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This function creates a pooling descriptor object by allocating the memory needed to
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42,906 | hannes-brt/cudnn-python-wrappers | libcudnn.py | cudnnSetPooling2dDescriptor | def cudnnSetPooling2dDescriptor(poolingDesc, mode, windowHeight, windowWidth,
verticalPadding, horizontalPadding, verticalStride, horizontalStride):
""""
Initialize a 2D pooling descriptor.
This function initializes a previously created pooling descriptor object.
Parame... | python | def cudnnSetPooling2dDescriptor(poolingDesc, mode, windowHeight, windowWidth,
verticalPadding, horizontalPadding, verticalStride, horizontalStride):
""""
Initialize a 2D pooling descriptor.
This function initializes a previously created pooling descriptor object.
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42,907 | hannes-brt/cudnn-python-wrappers | libcudnn.py | cudnnGetPooling2dDescriptor | def cudnnGetPooling2dDescriptor(poolingDesc):
""""
This function queries a previously created pooling descriptor object.
Parameters
----------
poolingDesc : cudnnPoolingDescriptor
Handle to a previously created 2D pooling descriptor.
Returns
-------
mode : cudnnPoolingMode
... | python | def cudnnGetPooling2dDescriptor(poolingDesc):
""""
This function queries a previously created pooling descriptor object.
Parameters
----------
poolingDesc : cudnnPoolingDescriptor
Handle to a previously created 2D pooling descriptor.
Returns
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mode : cudnnPoolingMode
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42,908 | hannes-brt/cudnn-python-wrappers | libcudnn.py | cudnnActivationBackward | def cudnnActivationBackward(handle, mode, alpha, srcDesc, srcData, srcDiffDesc, srcDiffData,
destDesc, destData, beta, destDiffDesc, destDiffData):
""""
Gradient of activation function.
This routine computes the gradient of a neuron activation function.
In-place operation i... | python | def cudnnActivationBackward(handle, mode, alpha, srcDesc, srcData, srcDiffDesc, srcDiffData,
destDesc, destData, beta, destDiffDesc, destDiffData):
""""
Gradient of activation function.
This routine computes the gradient of a neuron activation function.
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42,909 | xray7224/PyPump | pypump/store.py | AbstractStore.__prefix_key | def __prefix_key(self, key):
""" This will add the prefix to the key if one exists on the store """
# If there isn't a prefix don't bother
if self.prefix is None:
return key
# Don't prefix key if it already has it
if key.startswith(self.prefix + "-"):
ret... | python | def __prefix_key(self, key):
""" This will add the prefix to the key if one exists on the store """
# If there isn't a prefix don't bother
if self.prefix is None:
return key
# Don't prefix key if it already has it
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42,910 | xray7224/PyPump | pypump/store.py | AbstractStore.export | def export(self):
""" Exports as dictionary """
data = {}
for key, value in self.items():
data[key] = value
return data | python | def export(self):
""" Exports as dictionary """
data = {}
for key, value in self.items():
data[key] = value
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42,911 | xray7224/PyPump | pypump/store.py | JSONStore.save | def save(self):
""" Saves dictionary to disk in JSON format. """
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# We need an atomic way of re-writing the settings, we also need to
# prevent only overwriting part of the settings ... | python | def save(self):
""" Saves dictionary to disk in JSON format. """
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42,912 | xray7224/PyPump | pypump/store.py | JSONStore.get_filename | def get_filename(cls):
""" Gets filename of store on disk """
config_home = os.environ.get("XDG_CONFIG_HOME", "~/.config")
config_home = os.path.expanduser(config_home)
base_path = os.path.join(config_home, "PyPump")
if not os.path.isdir(base_path):
os.makedirs(base_... | python | def get_filename(cls):
""" Gets filename of store on disk """
config_home = os.environ.get("XDG_CONFIG_HOME", "~/.config")
config_home = os.path.expanduser(config_home)
base_path = os.path.join(config_home, "PyPump")
if not os.path.isdir(base_path):
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42,913 | xray7224/PyPump | pypump/store.py | JSONStore.load | def load(cls, webfinger, pypump):
""" Load JSON from disk into store object """
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data = json.loads(data)
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42,914 | joeyespo/py-getch | getch/pause.py | pause | def pause(message='Press any key to continue . . . '):
"""
Prints the specified message if it's not None and waits for a keypress.
"""
if message is not None:
print(message, end='')
sys.stdout.flush()
getch()
print() | python | def pause(message='Press any key to continue . . . '):
"""
Prints the specified message if it's not None and waits for a keypress.
"""
if message is not None:
print(message, end='')
sys.stdout.flush()
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42,915 | woolfson-group/isambard | isambard/ampal/interactions.py | covalent_bonds | def covalent_bonds(atoms, threshold=1.1):
"""Returns all the covalent bonds in a list of `Atom` pairs.
Notes
-----
Uses information `element_data`, which can be accessed directly
through this module i.e. `isambard.ampal.interactions.element_data`.
Parameters
----------
atoms : [(`Atom`... | python | def covalent_bonds(atoms, threshold=1.1):
"""Returns all the covalent bonds in a list of `Atom` pairs.
Notes
-----
Uses information `element_data`, which can be accessed directly
through this module i.e. `isambard.ampal.interactions.element_data`.
Parameters
----------
atoms : [(`Atom`... | [
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42,916 | woolfson-group/isambard | isambard/ampal/interactions.py | find_covalent_bonds | def find_covalent_bonds(ampal, max_range=2.2, threshold=1.1, tag=True):
"""Finds all covalent bonds in the AMPAL object.
Parameters
----------
ampal : AMPAL Object
Any AMPAL object with a `get_atoms` method.
max_range : float, optional
Used to define the sector size, so interactions... | python | def find_covalent_bonds(ampal, max_range=2.2, threshold=1.1, tag=True):
"""Finds all covalent bonds in the AMPAL object.
Parameters
----------
ampal : AMPAL Object
Any AMPAL object with a `get_atoms` method.
max_range : float, optional
Used to define the sector size, so interactions... | [
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Used to define the sector size, so interactions at longer ranges
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42,917 | woolfson-group/isambard | isambard/ampal/interactions.py | generate_covalent_bond_graph | def generate_covalent_bond_graph(covalent_bonds):
"""Generates a graph of the covalent bond network described by the interactions.
Parameters
----------
covalent_bonds: [CovalentBond]
List of `CovalentBond`.
Returns
-------
bond_graph: networkx.Graph
A graph of the covalent... | python | def generate_covalent_bond_graph(covalent_bonds):
"""Generates a graph of the covalent bond network described by the interactions.
Parameters
----------
covalent_bonds: [CovalentBond]
List of `CovalentBond`.
Returns
-------
bond_graph: networkx.Graph
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42,918 | woolfson-group/isambard | isambard/ampal/interactions.py | generate_bond_subgraphs_from_break | def generate_bond_subgraphs_from_break(bond_graph, atom1, atom2):
"""Splits the bond graph between two atoms to producing subgraphs.
Notes
-----
This will not work if there are cycles in the bond graph.
Parameters
----------
bond_graph: networkx.Graph
Graph of covalent bond network... | python | def generate_bond_subgraphs_from_break(bond_graph, atom1, atom2):
"""Splits the bond graph between two atoms to producing subgraphs.
Notes
-----
This will not work if there are cycles in the bond graph.
Parameters
----------
bond_graph: networkx.Graph
Graph of covalent bond network... | [
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42,919 | woolfson-group/isambard | isambard/ampal/base_ampal.py | cap | def cap(v, l):
"""Shortens string is above certain length."""
s = str(v)
return s if len(s) <= l else s[-l:] | python | def cap(v, l):
"""Shortens string is above certain length."""
s = str(v)
return s if len(s) <= l else s[-l:] | [
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42,920 | woolfson-group/isambard | isambard/ampal/base_ampal.py | find_atoms_within_distance | def find_atoms_within_distance(atoms, cutoff_distance, point):
"""Returns atoms within the distance from the point.
Parameters
----------
atoms : [ampal.atom]
A list of `ampal.atoms`.
cutoff_distance : float
Maximum distance from point.
point : (float, float, float)
Refe... | python | def find_atoms_within_distance(atoms, cutoff_distance, point):
"""Returns atoms within the distance from the point.
Parameters
----------
atoms : [ampal.atom]
A list of `ampal.atoms`.
cutoff_distance : float
Maximum distance from point.
point : (float, float, float)
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A list of `ampal.atoms`.
cutoff_distance : float
Maximum distance from point.
point : (float, float, float)
Reference point, 3D coordinate.
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42,921 | woolfson-group/isambard | isambard/ampal/base_ampal.py | centre_of_atoms | def centre_of_atoms(atoms, mass_weighted=True):
""" Returns centre point of any list of atoms.
Parameters
----------
atoms : list
List of AMPAL atom objects.
mass_weighted : bool, optional
If True returns centre of mass, otherwise just geometric centre of points.
Returns
--... | python | def centre_of_atoms(atoms, mass_weighted=True):
""" Returns centre point of any list of atoms.
Parameters
----------
atoms : list
List of AMPAL atom objects.
mass_weighted : bool, optional
If True returns centre of mass, otherwise just geometric centre of points.
Returns
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42,922 | woolfson-group/isambard | isambard/ampal/base_ampal.py | BaseAmpal.assign_force_field | def assign_force_field(self, ff, mol2=False):
"""Assigns force field parameters to Atoms in the AMPAL object.
Parameters
----------
ff: BuffForceField
The force field to be used for scoring.
mol2: bool, optional
If true, mol2 style labels will also be use... | python | def assign_force_field(self, ff, mol2=False):
"""Assigns force field parameters to Atoms in the AMPAL object.
Parameters
----------
ff: BuffForceField
The force field to be used for scoring.
mol2: bool, optional
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42,923 | woolfson-group/isambard | isambard/ampal/base_ampal.py | BaseAmpal.update_ff | def update_ff(self, ff, mol2=False, force_ff_assign=False):
"""Manages assigning the force field parameters.
The aim of this method is to avoid unnecessary assignment of the
force field.
Parameters
----------
ff: BuffForceField
The force field to be used for... | python | def update_ff(self, ff, mol2=False, force_ff_assign=False):
"""Manages assigning the force field parameters.
The aim of this method is to avoid unnecessary assignment of the
force field.
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----------
ff: BuffForceField
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42,924 | woolfson-group/isambard | isambard/ampal/base_ampal.py | BaseAmpal.get_internal_energy | def get_internal_energy(self, assign_ff=True, ff=None, mol2=False,
force_ff_assign=False):
"""Calculates the internal energy of the AMPAL object.
This method is assigned to the buff_internal_energy property,
using the default arguments.
Parameters
--... | python | def get_internal_energy(self, assign_ff=True, ff=None, mol2=False,
force_ff_assign=False):
"""Calculates the internal energy of the AMPAL object.
This method is assigned to the buff_internal_energy property,
using the default arguments.
Parameters
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42,925 | woolfson-group/isambard | isambard/ampal/base_ampal.py | BaseAmpal.rotate | def rotate(self, angle, axis, point=None, radians=False, inc_alt_states=True):
"""Rotates every atom in the AMPAL object.
Parameters
----------
angle : float
Angle that AMPAL object will be rotated.
axis : 3D Vector (tuple, list, numpy.array)
Axis about w... | python | def rotate(self, angle, axis, point=None, radians=False, inc_alt_states=True):
"""Rotates every atom in the AMPAL object.
Parameters
----------
angle : float
Angle that AMPAL object will be rotated.
axis : 3D Vector (tuple, list, numpy.array)
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Axis about which the AMPAL object will be rotated.
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42,926 | woolfson-group/isambard | isambard/ampal/base_ampal.py | BaseAmpal.translate | def translate(self, vector, inc_alt_states=True):
"""Translates every atom in the AMPAL object.
Parameters
----------
vector : 3D Vector (tuple, list, numpy.array)
Vector used for translation.
inc_alt_states : bool, optional
If true, will rotate atoms in ... | python | def translate(self, vector, inc_alt_states=True):
"""Translates every atom in the AMPAL object.
Parameters
----------
vector : 3D Vector (tuple, list, numpy.array)
Vector used for translation.
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Vector used for translation.
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42,927 | woolfson-group/isambard | isambard/ampal/base_ampal.py | BaseAmpal.rmsd | def rmsd(self, other, backbone=False):
"""Calculates the RMSD between two AMPAL objects.
Notes
-----
No fitting operation is performs and both AMPAL objects must
have the same number of atoms.
Parameters
----------
other : AMPAL Object
Any AM... | python | def rmsd(self, other, backbone=False):
"""Calculates the RMSD between two AMPAL objects.
Notes
-----
No fitting operation is performs and both AMPAL objects must
have the same number of atoms.
Parameters
----------
other : AMPAL Object
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42,928 | woolfson-group/isambard | isambard/ampal/base_ampal.py | Polymer.append | def append(self, item):
"""Appends a `Monomer to the `Polymer`.
Notes
-----
Does not update labelling.
"""
if isinstance(item, Monomer):
self._monomers.append(item)
else:
raise TypeError(
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"""Appends a `Monomer to the `Polymer`.
Notes
-----
Does not update labelling.
"""
if isinstance(item, Monomer):
self._monomers.append(item)
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] | ebc33b48a28ad217e18f93b910dfba46e6e71e07 | https://github.com/woolfson-group/isambard/blob/ebc33b48a28ad217e18f93b910dfba46e6e71e07/isambard/ampal/base_ampal.py#L449-L461 |
42,929 | woolfson-group/isambard | isambard/ampal/base_ampal.py | Polymer.extend | def extend(self, polymer):
"""Extends the `Polymer` with the contents of another `Polymer`.
Notes
-----
Does not update labelling.
"""
if isinstance(polymer, Polymer):
self._monomers.extend(polymer)
else:
raise TypeError(
'... | python | def extend(self, polymer):
"""Extends the `Polymer` with the contents of another `Polymer`.
Notes
-----
Does not update labelling.
"""
if isinstance(polymer, Polymer):
self._monomers.extend(polymer)
else:
raise TypeError(
'... | [
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42,930 | woolfson-group/isambard | isambard/ampal/base_ampal.py | Polymer.get_monomers | def get_monomers(self, ligands=True):
"""Retrieves all the `Monomers` from the AMPAL object.
Parameters
----------
ligands : bool, optional
If true, will include ligand `Monomers`.
"""
if ligands and self.ligands:
monomers = self._monomers + self.... | python | def get_monomers(self, ligands=True):
"""Retrieves all the `Monomers` from the AMPAL object.
Parameters
----------
ligands : bool, optional
If true, will include ligand `Monomers`.
"""
if ligands and self.ligands:
monomers = self._monomers + self.... | [
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42,931 | woolfson-group/isambard | isambard/ampal/base_ampal.py | Polymer.get_atoms | def get_atoms(self, ligands=True, inc_alt_states=False):
"""Flat list of all the Atoms in the Polymer.
Parameters
----------
inc_alt_states : bool
If true atoms from alternate conformations are included rather
than only the "active" states.
Returns
... | python | def get_atoms(self, ligands=True, inc_alt_states=False):
"""Flat list of all the Atoms in the Polymer.
Parameters
----------
inc_alt_states : bool
If true atoms from alternate conformations are included rather
than only the "active" states.
Returns
... | [
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42,932 | woolfson-group/isambard | isambard/ampal/base_ampal.py | Polymer.relabel_monomers | def relabel_monomers(self, labels=None):
"""Relabels the either in numerically or using a list of labels.
Parameters
----------
labels : list, optional
A list of new labels.
Raises
------
ValueError
Raised if the number of labels does not... | python | def relabel_monomers(self, labels=None):
"""Relabels the either in numerically or using a list of labels.
Parameters
----------
labels : list, optional
A list of new labels.
Raises
------
ValueError
Raised if the number of labels does not... | [
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42,933 | woolfson-group/isambard | isambard/ampal/base_ampal.py | Polymer.relabel_atoms | def relabel_atoms(self, start=1):
"""Relabels all `Atoms` in numerical order.
Parameters
----------
start : int, optional
Offset the labelling by `start` residues.
"""
counter = start
for atom in self.get_atoms():
atom.id = counter
... | python | def relabel_atoms(self, start=1):
"""Relabels all `Atoms` in numerical order.
Parameters
----------
start : int, optional
Offset the labelling by `start` residues.
"""
counter = start
for atom in self.get_atoms():
atom.id = counter
... | [
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Offset the labelling by `start` residues. | [
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42,934 | woolfson-group/isambard | isambard/ampal/base_ampal.py | Polymer.make_pdb | def make_pdb(self, alt_states=False, inc_ligands=True):
"""Generates a PDB string for the `Polymer`.
Parameters
----------
alt_states : bool, optional
Include alternate conformations for `Monomers` in PDB.
inc_ligands : bool, optional
Includes `Ligands` i... | python | def make_pdb(self, alt_states=False, inc_ligands=True):
"""Generates a PDB string for the `Polymer`.
Parameters
----------
alt_states : bool, optional
Include alternate conformations for `Monomers` in PDB.
inc_ligands : bool, optional
Includes `Ligands` i... | [
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42,935 | woolfson-group/isambard | isambard/ampal/base_ampal.py | Atom.rotate | def rotate(self, angle, axis, point=None, radians=False):
"""Rotates `Atom` by `angle`.
Parameters
----------
angle : float
Angle that `Atom` will be rotated.
axis : 3D Vector (tuple, list, numpy.array)
Axis about which the `Atom` will be rotated.
... | python | def rotate(self, angle, axis, point=None, radians=False):
"""Rotates `Atom` by `angle`.
Parameters
----------
angle : float
Angle that `Atom` will be rotated.
axis : 3D Vector (tuple, list, numpy.array)
Axis about which the `Atom` will be rotated.
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42,936 | woolfson-group/isambard | isambard/tools/file_parsing.py | dict_from_mmcif | def dict_from_mmcif(mmcif, path=True):
"""Parse mmcif file into a dictionary.
Notes
-----
Full list of keys/value types, and further information on them can be viewed here:
http://mmcif.wwpdb.org/docs/pdb_to_pdbx_correspondences.html
All values in the returned dict are str or list(str).... | python | def dict_from_mmcif(mmcif, path=True):
"""Parse mmcif file into a dictionary.
Notes
-----
Full list of keys/value types, and further information on them can be viewed here:
http://mmcif.wwpdb.org/docs/pdb_to_pdbx_correspondences.html
All values in the returned dict are str or list(str).... | [
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42,937 | woolfson-group/isambard | isambard/tools/file_parsing.py | get_protein_dict | def get_protein_dict(cif_data):
""" Parse cif_data dict for a subset of its data.
Notes
-----
cif_data dict contains all the data from the .cif file, with values as strings.
This function returns a more 'human readable' dictionary of key-value pairs.
The keys have simpler (and still often more ... | python | def get_protein_dict(cif_data):
""" Parse cif_data dict for a subset of its data.
Notes
-----
cif_data dict contains all the data from the .cif file, with values as strings.
This function returns a more 'human readable' dictionary of key-value pairs.
The keys have simpler (and still often more ... | [
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42,938 | woolfson-group/isambard | isambard/tools/file_parsing.py | parse_PISCES_output | def parse_PISCES_output(pisces_output, path=False):
""" Takes the output list of a PISCES cull and returns in a usable dictionary.
Notes
-----
Designed for outputs of protein sequence redundancy culls conducted using the PISCES server.
http://dunbrack.fccc.edu/PISCES.php
G. Wang and R. L. Dunbr... | python | def parse_PISCES_output(pisces_output, path=False):
""" Takes the output list of a PISCES cull and returns in a usable dictionary.
Notes
-----
Designed for outputs of protein sequence redundancy culls conducted using the PISCES server.
http://dunbrack.fccc.edu/PISCES.php
G. Wang and R. L. Dunbr... | [
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42,939 | woolfson-group/isambard | isambard/tools/file_parsing.py | download_decode | def download_decode(URL, encoding='utf-8', verbose=True):
""" Downloads data from URL and returns decoded contents."""
if verbose:
print("Downloading data from " + URL)
req = Request(URL)
try:
with urlopen(req) as u:
decoded_file = u.read().decode(encoding)
except URLErro... | python | def download_decode(URL, encoding='utf-8', verbose=True):
""" Downloads data from URL and returns decoded contents."""
if verbose:
print("Downloading data from " + URL)
req = Request(URL)
try:
with urlopen(req) as u:
decoded_file = u.read().decode(encoding)
except URLErro... | [
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42,940 | woolfson-group/isambard | isambard/tools/file_parsing.py | olderado_best_model | def olderado_best_model(pdb_id):
""" Checks the Olderado web server and returns the most representative conformation for PDB NMR structures.
Notes
-----
Uses OLDERADO from the EBI.
See http://www.ebi.ac.uk/pdbe/nmr/olderado/ and citations therein.
Parameters
----------
pdb_id : str
... | python | def olderado_best_model(pdb_id):
""" Checks the Olderado web server and returns the most representative conformation for PDB NMR structures.
Notes
-----
Uses OLDERADO from the EBI.
See http://www.ebi.ac.uk/pdbe/nmr/olderado/ and citations therein.
Parameters
----------
pdb_id : str
... | [
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42,941 | woolfson-group/isambard | isambard/optimisation/optimizer.py | buff_eval | def buff_eval(params):
"""Builds and evaluates BUFF energy of model in parallelization
Parameters
----------
params: list
Tuple containing the specification to be built, the sequence,
and the parameters for model building.
Returns
-------
model.bude_score: float
BUF... | python | def buff_eval(params):
"""Builds and evaluates BUFF energy of model in parallelization
Parameters
----------
params: list
Tuple containing the specification to be built, the sequence,
and the parameters for model building.
Returns
-------
model.bude_score: float
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42,942 | woolfson-group/isambard | isambard/optimisation/optimizer.py | buff_internal_eval | def buff_internal_eval(params):
"""Builds and evaluates BUFF internal energy of a model in parallelization
Parameters
----------
params: list
Tuple containing the specification to be built, the sequence
and the parameters for model building.
Returns
-------
model.bude_score... | python | def buff_internal_eval(params):
"""Builds and evaluates BUFF internal energy of a model in parallelization
Parameters
----------
params: list
Tuple containing the specification to be built, the sequence
and the parameters for model building.
Returns
-------
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42,943 | woolfson-group/isambard | isambard/optimisation/optimizer.py | rmsd_eval | def rmsd_eval(rmsd_params):
"""Builds a model and runs profit against a reference model.
Parameters
----------
rmsd_params
Returns
-------
rmsd: float
rmsd against reference model as calculated by profit.
"""
specification, sequence, parsed_ind, reference_pdb = rmsd_params
... | python | def rmsd_eval(rmsd_params):
"""Builds a model and runs profit against a reference model.
Parameters
----------
rmsd_params
Returns
-------
rmsd: float
rmsd against reference model as calculated by profit.
"""
specification, sequence, parsed_ind, reference_pdb = rmsd_params
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42,944 | woolfson-group/isambard | isambard/optimisation/optimizer.py | comparator_eval | def comparator_eval(comparator_params):
"""Gets BUFF score for interaction between two AMPAL objects
"""
top1, top2, params1, params2, seq1, seq2, movements = comparator_params
xrot, yrot, zrot, xtrans, ytrans, ztrans = movements
obj1 = top1(*params1)
obj2 = top2(*params2)
obj2.rotate(xrot, ... | python | def comparator_eval(comparator_params):
"""Gets BUFF score for interaction between two AMPAL objects
"""
top1, top2, params1, params2, seq1, seq2, movements = comparator_params
xrot, yrot, zrot, xtrans, ytrans, ztrans = movements
obj1 = top1(*params1)
obj2 = top2(*params2)
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42,945 | woolfson-group/isambard | isambard/optimisation/optimizer.py | BaseOptimizer.parameters | def parameters(self, sequence, value_means, value_ranges, arrangement):
"""Relates the individual to be evolved to the full parameter string.
Parameters
----------
sequence: str
Full amino acid sequence for specification object to be
optimized. Must be equal to t... | python | def parameters(self, sequence, value_means, value_ranges, arrangement):
"""Relates the individual to be evolved to the full parameter string.
Parameters
----------
sequence: str
Full amino acid sequence for specification object to be
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Full amino acid sequence for specification object to be
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42,946 | woolfson-group/isambard | isambard/optimisation/optimizer.py | BaseScore.make_energy_funnel_data | def make_energy_funnel_data(self, cores=1):
"""Compares models created during the minimisation to the best model.
Returns
-------
energy_rmsd_gen: [(float, float, int)]
A list of triples containing the BUFF score, RMSD to the
top model and generation of a model g... | python | def make_energy_funnel_data(self, cores=1):
"""Compares models created during the minimisation to the best model.
Returns
-------
energy_rmsd_gen: [(float, float, int)]
A list of triples containing the BUFF score, RMSD to the
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42,947 | woolfson-group/isambard | isambard/optimisation/optimizer.py | BaseScore.funnel_rebuild | def funnel_rebuild(psg_trm_spec):
"""Rebuilds a model and compares it to a reference model.
Parameters
----------
psg_trm: (([float], float, int), AMPAL, specification)
A tuple containing the parameters, score and generation for a
model as well as a model of the ... | python | def funnel_rebuild(psg_trm_spec):
"""Rebuilds a model and compares it to a reference model.
Parameters
----------
psg_trm: (([float], float, int), AMPAL, specification)
A tuple containing the parameters, score and generation for a
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42,948 | woolfson-group/isambard | isambard/optimisation/optimizer.py | OptDE.update_pop | def update_pop(self):
"""Updates the population according to crossover and fitness criteria.
"""
candidates = []
for ind in self.population:
candidates.append(self.crossover(ind))
self._params['model_count'] += len(candidates)
self.assign_fitnesses(candidates)... | python | def update_pop(self):
"""Updates the population according to crossover and fitness criteria.
"""
candidates = []
for ind in self.population:
candidates.append(self.crossover(ind))
self._params['model_count'] += len(candidates)
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42,949 | woolfson-group/isambard | isambard/optimisation/optimizer.py | OptPSO.initialize_pop | def initialize_pop(self):
"""Generates initial population with random positions and speeds."""
self.population = self.toolbox.swarm(n=self._params['popsize'])
if self._params['neighbours']:
for i in range(len(self.population)):
self.population[i].ident = i
... | python | def initialize_pop(self):
"""Generates initial population with random positions and speeds."""
self.population = self.toolbox.swarm(n=self._params['popsize'])
if self._params['neighbours']:
for i in range(len(self.population)):
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42,950 | woolfson-group/isambard | isambard/optimisation/optimizer.py | OptGA.initialize_pop | def initialize_pop(self):
"""Assigns initial fitnesses."""
self.toolbox.register("individual", self.generate)
self.toolbox.register("population", tools.initRepeat,
list, self.toolbox.individual)
self.population = self.toolbox.population(n=self._params['popsi... | python | def initialize_pop(self):
"""Assigns initial fitnesses."""
self.toolbox.register("individual", self.generate)
self.toolbox.register("population", tools.initRepeat,
list, self.toolbox.individual)
self.population = self.toolbox.population(n=self._params['popsi... | [
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42,951 | woolfson-group/isambard | isambard/optimisation/mmc_optimizer.py | MMCParameter.randomise_proposed_value | def randomise_proposed_value(self):
"""Creates a randomly the proposed value.
Raises
------
TypeError
Raised if this method is called on a static value.
TypeError
Raised if the parameter type is unknown.
"""
if self.parameter_type is MMCPa... | python | def randomise_proposed_value(self):
"""Creates a randomly the proposed value.
Raises
------
TypeError
Raised if this method is called on a static value.
TypeError
Raised if the parameter type is unknown.
"""
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42,952 | woolfson-group/isambard | isambard/optimisation/mmc_optimizer.py | MMCParameter.accept_proposed_value | def accept_proposed_value(self):
"""Changes the current value to the proposed value."""
if self.proposed_value is not None:
self.current_value = self.proposed_value
self.proposed_value = None
return | python | def accept_proposed_value(self):
"""Changes the current value to the proposed value."""
if self.proposed_value is not None:
self.current_value = self.proposed_value
self.proposed_value = None
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42,953 | woolfson-group/isambard | isambard/optimisation/mmc_optimizer.py | MMCParameterOptimisation.start_optimisation | def start_optimisation(self, rounds, temp=298.15):
"""Begin the optimisation run.
Parameters
----------
rounds : int
The number of rounds of optimisation to perform.
temp : float, optional
The temperature (in K) used during the optimisation.
"""
... | python | def start_optimisation(self, rounds, temp=298.15):
"""Begin the optimisation run.
Parameters
----------
rounds : int
The number of rounds of optimisation to perform.
temp : float, optional
The temperature (in K) used during the optimisation.
"""
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42,954 | woolfson-group/isambard | isambard/optimisation/mmc_optimizer.py | MMCParameterOptimisation._generate_initial_model | def _generate_initial_model(self):
"""Creates the initial model for the optimistation.
Raises
------
TypeError
Raised if the model failed to build. This could be due to
parameters being passed to the specification in the wrong
format.
"""
... | python | def _generate_initial_model(self):
"""Creates the initial model for the optimistation.
Raises
------
TypeError
Raised if the model failed to build. This could be due to
parameters being passed to the specification in the wrong
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42,955 | woolfson-group/isambard | isambard/optimisation/mmc_optimizer.py | MMCParameterOptimisation._mmc_loop | def _mmc_loop(self, rounds, temp=298.15, verbose=True):
"""The main MMC loop.
Parameters
----------
rounds : int
The number of rounds of optimisation to perform.
temp : float, optional
The temperature (in K) used during the optimisation.
verbose :... | python | def _mmc_loop(self, rounds, temp=298.15, verbose=True):
"""The main MMC loop.
Parameters
----------
rounds : int
The number of rounds of optimisation to perform.
temp : float, optional
The temperature (in K) used during the optimisation.
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42,956 | woolfson-group/isambard | isambard/optimisation/evo_optimizers.py | DE._crossover | def _crossover(self, ind):
"""Used by the evolution process to generate a new individual.
Notes
-----
This is a tweaked version of the classical DE crossover
algorithm, the main difference that candidate parameters are
generated using a lognormal distribution. Bound hand... | python | def _crossover(self, ind):
"""Used by the evolution process to generate a new individual.
Notes
-----
This is a tweaked version of the classical DE crossover
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42,957 | woolfson-group/isambard | isambard/optimisation/evo_optimizers.py | PSO._generate | def _generate(self):
"""Generates a particle using the creator function.
Notes
-----
Position and speed are uniformly randomly seeded within
allowed bounds. The particle also has speed limit settings
taken from global values.
Returns
-------
part... | python | def _generate(self):
"""Generates a particle using the creator function.
Notes
-----
Position and speed are uniformly randomly seeded within
allowed bounds. The particle also has speed limit settings
taken from global values.
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-------
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42,958 | woolfson-group/isambard | isambard/optimisation/evo_optimizers.py | PSO.update_particle | def update_particle(self, part, chi=0.729843788, c=2.05):
"""Constriction factor update particle method.
Notes
-----
Looks for a list of neighbours attached to a particle and
uses the particle's best position and that of the best
neighbour.
"""
neighbour_... | python | def update_particle(self, part, chi=0.729843788, c=2.05):
"""Constriction factor update particle method.
Notes
-----
Looks for a list of neighbours attached to a particle and
uses the particle's best position and that of the best
neighbour.
"""
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42,959 | woolfson-group/isambard | isambard/optimisation/evo_optimizers.py | CMAES._make_individual | def _make_individual(self, paramlist):
"""Makes an individual particle."""
part = creator.Individual(paramlist)
part.ident = None
return part | python | def _make_individual(self, paramlist):
"""Makes an individual particle."""
part = creator.Individual(paramlist)
part.ident = None
return part | [
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42,960 | woolfson-group/isambard | isambard/add_ons/filesystem.py | number_of_mmols | def number_of_mmols(code):
""" Number of .mmol files associated with code in the PDBE.
Notes
-----
This function makes a series of calls to the PDBE website using the requests module. This can make it slow!
Parameters
----------
code : str
PDB code.
Returns
-------
num... | python | def number_of_mmols(code):
""" Number of .mmol files associated with code in the PDBE.
Notes
-----
This function makes a series of calls to the PDBE website using the requests module. This can make it slow!
Parameters
----------
code : str
PDB code.
Returns
-------
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code : str
PDB code.
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42,961 | woolfson-group/isambard | isambard/add_ons/filesystem.py | get_mmol | def get_mmol(code, mmol_number=None, outfile=None):
""" Get mmol file from PDBe and return its content as a string. Write to file if outfile given.
Parameters
----------
code : str
PDB code.
mmol_number : int
mmol number (biological assembly number) of file to download. Numbers from... | python | def get_mmol(code, mmol_number=None, outfile=None):
""" Get mmol file from PDBe and return its content as a string. Write to file if outfile given.
Parameters
----------
code : str
PDB code.
mmol_number : int
mmol number (biological assembly number) of file to download. Numbers from... | [
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42,962 | woolfson-group/isambard | isambard/add_ons/filesystem.py | get_mmcif | def get_mmcif(code, outfile=None):
""" Get mmcif file associated with code from PDBE.
Parameters
----------
code : str
PDB code.
outfile : str
Filepath. Writes returned value to this file.
Returns
-------
mmcif_file : str
Filepath to the mmcif file.
"""
... | python | def get_mmcif(code, outfile=None):
""" Get mmcif file associated with code from PDBE.
Parameters
----------
code : str
PDB code.
outfile : str
Filepath. Writes returned value to this file.
Returns
-------
mmcif_file : str
Filepath to the mmcif file.
"""
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42,963 | woolfson-group/isambard | isambard/add_ons/filesystem.py | pdbe_status_code | def pdbe_status_code(code):
"""Check if a PDB code has structure files on the PDBE site.
Parameters
----------
code : str
PDB code to check for on PDBE.
Returns
-------
status_code : int
HTTP status code of PDBE url associated with input code.
"""
url = 'http://www.... | python | def pdbe_status_code(code):
"""Check if a PDB code has structure files on the PDBE site.
Parameters
----------
code : str
PDB code to check for on PDBE.
Returns
-------
status_code : int
HTTP status code of PDBE url associated with input code.
"""
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code : str
PDB code to check for on PDBE.
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status_code : int
HTTP status code of PDBE url associated with input code. | [
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42,964 | woolfson-group/isambard | isambard/add_ons/filesystem.py | preferred_mmol | def preferred_mmol(code):
""" Get mmol number of preferred biological assembly as listed in the PDBe.
Notes
-----
First checks for code in mmols.json.
If code not yet in this json dictionary, uses requests module to scrape the PDBE for the preferred mmol number.
Parameters
----------
c... | python | def preferred_mmol(code):
""" Get mmol number of preferred biological assembly as listed in the PDBe.
Notes
-----
First checks for code in mmols.json.
If code not yet in this json dictionary, uses requests module to scrape the PDBE for the preferred mmol number.
Parameters
----------
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42,965 | woolfson-group/isambard | isambard/add_ons/filesystem.py | current_codes_from_pdb | def current_codes_from_pdb():
""" Get list of all PDB codes currently listed in the PDB.
Returns
-------
pdb_codes : list(str)
List of PDB codes (in lower case).
"""
url = 'http://www.rcsb.org/pdb/rest/getCurrent'
r = requests.get(url)
if r.status_code == 200:
pdb_codes ... | python | def current_codes_from_pdb():
""" Get list of all PDB codes currently listed in the PDB.
Returns
-------
pdb_codes : list(str)
List of PDB codes (in lower case).
"""
url = 'http://www.rcsb.org/pdb/rest/getCurrent'
r = requests.get(url)
if r.status_code == 200:
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42,966 | woolfson-group/isambard | isambard/add_ons/filesystem.py | FileSystem.mmols | def mmols(self):
""" Dict of filepaths for all mmol files associated with code.
Notes
-----
Downloads mmol files if not already present.
Returns
-------
mmols_dict : dict, or None.
Keys : int
mmol number
Values : str
... | python | def mmols(self):
""" Dict of filepaths for all mmol files associated with code.
Notes
-----
Downloads mmol files if not already present.
Returns
-------
mmols_dict : dict, or None.
Keys : int
mmol number
Values : str
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42,967 | woolfson-group/isambard | isambard/add_ons/filesystem.py | FileSystem.dssps | def dssps(self):
""" Dict of filepaths for all dssp files associated with code.
Notes
-----
Runs dssp and stores writes output to files if not already present.
Also downloads mmol files if not already present.
Calls isambard.external_programs.dssp and so needs dssp to be... | python | def dssps(self):
""" Dict of filepaths for all dssp files associated with code.
Notes
-----
Runs dssp and stores writes output to files if not already present.
Also downloads mmol files if not already present.
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42,968 | woolfson-group/isambard | isambard/add_ons/filesystem.py | FileSystem.fastas | def fastas(self, download=False):
""" Dict of filepaths for all fasta files associated with code.
Parameters
----------
download : bool
If True, downloads the fasta file from the PDB.
If False, uses the ampal Protein.fasta property
Defaults to False -... | python | def fastas(self, download=False):
""" Dict of filepaths for all fasta files associated with code.
Parameters
----------
download : bool
If True, downloads the fasta file from the PDB.
If False, uses the ampal Protein.fasta property
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42,969 | woolfson-group/isambard | isambard/add_ons/filesystem.py | FileSystem.mmcif | def mmcif(self):
""" Filepath for mmcif file associated with code.
Notes
-----
Downloads mmcif file if not already present.
Returns
-------
mmcif_file : str
Filepath for the mmcif file.
"""
mmcif_dir = os.path.join(self.parent_dir, 'm... | python | def mmcif(self):
""" Filepath for mmcif file associated with code.
Notes
-----
Downloads mmcif file if not already present.
Returns
-------
mmcif_file : str
Filepath for the mmcif file.
"""
mmcif_dir = os.path.join(self.parent_dir, 'm... | [
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42,970 | woolfson-group/isambard | isambard/ampal/ligands.py | LigandGroup.categories | def categories(self):
"""Returns the categories of `Ligands` in `LigandGroup`."""
category_dict = {}
for ligand in self:
if ligand.category in category_dict:
category_dict[ligand.category].append(ligand)
else:
category_dict[ligand.category]... | python | def categories(self):
"""Returns the categories of `Ligands` in `LigandGroup`."""
category_dict = {}
for ligand in self:
if ligand.category in category_dict:
category_dict[ligand.category].append(ligand)
else:
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42,971 | woolfson-group/isambard | isambard/ampal/ligands.py | LigandGroup.category_count | def category_count(self):
"""Returns the number of categories in `categories`."""
category_dict = self.categories
count_dict = {category: len(
category_dict[category]) for category in category_dict}
return count_dict | python | def category_count(self):
"""Returns the number of categories in `categories`."""
category_dict = self.categories
count_dict = {category: len(
category_dict[category]) for category in category_dict}
return count_dict | [
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42,972 | woolfson-group/isambard | isambard/ampal/analyse_protein.py | sequence_molecular_weight | def sequence_molecular_weight(seq):
"""Returns the molecular weight of the polypeptide sequence.
Notes
-----
Units = Daltons
Parameters
----------
seq : str
Sequence of amino acids.
"""
if 'X' in seq:
warnings.warn(_nc_warning_str, NoncanonicalWarning)
return su... | python | def sequence_molecular_weight(seq):
"""Returns the molecular weight of the polypeptide sequence.
Notes
-----
Units = Daltons
Parameters
----------
seq : str
Sequence of amino acids.
"""
if 'X' in seq:
warnings.warn(_nc_warning_str, NoncanonicalWarning)
return su... | [
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42,973 | woolfson-group/isambard | isambard/ampal/analyse_protein.py | sequence_molar_extinction_280 | def sequence_molar_extinction_280(seq):
"""Returns the molar extinction coefficient of the sequence at 280 nm.
Notes
-----
Units = M/cm
Parameters
----------
seq : str
Sequence of amino acids.
"""
if 'X' in seq:
warnings.warn(_nc_warning_str, NoncanonicalWarning)
... | python | def sequence_molar_extinction_280(seq):
"""Returns the molar extinction coefficient of the sequence at 280 nm.
Notes
-----
Units = M/cm
Parameters
----------
seq : str
Sequence of amino acids.
"""
if 'X' in seq:
warnings.warn(_nc_warning_str, NoncanonicalWarning)
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42,974 | woolfson-group/isambard | isambard/ampal/analyse_protein.py | partial_charge | def partial_charge(aa, pH):
"""Calculates the partial charge of the amino acid.
Parameters
----------
aa : str
Amino acid single-letter code.
pH : float
pH of interest.
"""
difference = pH - residue_pka[aa]
if residue_charge[aa] > 0:
difference *= -1
ratio = ... | python | def partial_charge(aa, pH):
"""Calculates the partial charge of the amino acid.
Parameters
----------
aa : str
Amino acid single-letter code.
pH : float
pH of interest.
"""
difference = pH - residue_pka[aa]
if residue_charge[aa] > 0:
difference *= -1
ratio = ... | [
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42,975 | woolfson-group/isambard | isambard/ampal/analyse_protein.py | sequence_charge | def sequence_charge(seq, pH=7.4):
"""Calculates the total charge of the input polypeptide sequence.
Parameters
----------
seq : str
Sequence of amino acids.
pH : float
pH of interest.
"""
if 'X' in seq:
warnings.warn(_nc_warning_str, NoncanonicalWarning)
adj_prot... | python | def sequence_charge(seq, pH=7.4):
"""Calculates the total charge of the input polypeptide sequence.
Parameters
----------
seq : str
Sequence of amino acids.
pH : float
pH of interest.
"""
if 'X' in seq:
warnings.warn(_nc_warning_str, NoncanonicalWarning)
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Sequence of amino acids.
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42,976 | woolfson-group/isambard | isambard/ampal/analyse_protein.py | charge_series | def charge_series(seq, granularity=0.1):
"""Calculates the charge for pH 1-13.
Parameters
----------
seq : str
Sequence of amino acids.
granularity : float, optional
Granularity of pH values i.e. if 0.1 pH = [1.0, 1.1, 1.2...]
"""
if 'X' in seq:
warnings.warn(_nc_war... | python | def charge_series(seq, granularity=0.1):
"""Calculates the charge for pH 1-13.
Parameters
----------
seq : str
Sequence of amino acids.
granularity : float, optional
Granularity of pH values i.e. if 0.1 pH = [1.0, 1.1, 1.2...]
"""
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42,977 | woolfson-group/isambard | isambard/ampal/analyse_protein.py | sequence_isoelectric_point | def sequence_isoelectric_point(seq, granularity=0.1):
"""Calculates the isoelectric point of the sequence for ph 1-13.
Parameters
----------
seq : str
Sequence of amino acids.
granularity : float, optional
Granularity of pH values i.e. if 0.1 pH = [1.0, 1.1, 1.2...]
"""
if '... | python | def sequence_isoelectric_point(seq, granularity=0.1):
"""Calculates the isoelectric point of the sequence for ph 1-13.
Parameters
----------
seq : str
Sequence of amino acids.
granularity : float, optional
Granularity of pH values i.e. if 0.1 pH = [1.0, 1.1, 1.2...]
"""
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Sequence of amino acids.
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42,978 | woolfson-group/isambard | isambard/ampal/analyse_protein.py | measure_sidechain_torsion_angles | def measure_sidechain_torsion_angles(residue, verbose=True):
"""Calculates sidechain dihedral angles for a residue
Parameters
----------
residue : [ampal.Residue]
`Residue` object.
verbose : bool, optional
If `true`, tells you when a residue does not have any known
dihedral ... | python | def measure_sidechain_torsion_angles(residue, verbose=True):
"""Calculates sidechain dihedral angles for a residue
Parameters
----------
residue : [ampal.Residue]
`Residue` object.
verbose : bool, optional
If `true`, tells you when a residue does not have any known
dihedral ... | [
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`Residue` object.
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If `true`, tells you when a residue does not have any known
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42,979 | woolfson-group/isambard | isambard/ampal/analyse_protein.py | measure_torsion_angles | def measure_torsion_angles(residues):
"""Calculates the dihedral angles for a list of backbone atoms.
Parameters
----------
residues : [ampal.Residue]
List of `Residue` objects.
Returns
-------
torsion_angles : (float, float, float)
One triple for each residue, containing t... | python | def measure_torsion_angles(residues):
"""Calculates the dihedral angles for a list of backbone atoms.
Parameters
----------
residues : [ampal.Residue]
List of `Residue` objects.
Returns
-------
torsion_angles : (float, float, float)
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List of `Residue` objects.
Returns
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torsion_angles : (float, float, float)
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42,980 | woolfson-group/isambard | isambard/ampal/analyse_protein.py | cc_to_local_params | def cc_to_local_params(pitch, radius, oligo):
"""Returns local parameters for an oligomeric assembly.
Parameters
----------
pitch : float
Pitch of assembly
radius : float
Radius of assembly
oligo : int
Oligomeric state of assembly
Returns
-------
pitchloc : ... | python | def cc_to_local_params(pitch, radius, oligo):
"""Returns local parameters for an oligomeric assembly.
Parameters
----------
pitch : float
Pitch of assembly
radius : float
Radius of assembly
oligo : int
Oligomeric state of assembly
Returns
-------
pitchloc : ... | [
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Pitch of assembly
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Radius of assembly
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Oligomeric state of assembly
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Local pitch of assembly (between 2 adja... | [
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42,981 | woolfson-group/isambard | isambard/ampal/analyse_protein.py | residues_per_turn | def residues_per_turn(p):
""" The number of residues per turn at each Monomer in the Polymer.
Notes
-----
Each element of the returned list is the number of residues
per turn, at a point on the Polymer primitive. Calculated using
the relative positions of the CA atoms and the primitive of the
... | python | def residues_per_turn(p):
""" The number of residues per turn at each Monomer in the Polymer.
Notes
-----
Each element of the returned list is the number of residues
per turn, at a point on the Polymer primitive. Calculated using
the relative positions of the CA atoms and the primitive of the
... | [
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42,982 | woolfson-group/isambard | isambard/ampal/analyse_protein.py | polymer_to_reference_axis_distances | def polymer_to_reference_axis_distances(p, reference_axis, tag=True, reference_axis_name='ref_axis'):
"""Returns distances between the primitive of a Polymer and a reference_axis.
Notes
-----
Distances are calculated between each point of the Polymer primitive
and the corresponding point in referen... | python | def polymer_to_reference_axis_distances(p, reference_axis, tag=True, reference_axis_name='ref_axis'):
"""Returns distances between the primitive of a Polymer and a reference_axis.
Notes
-----
Distances are calculated between each point of the Polymer primitive
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42,983 | woolfson-group/isambard | isambard/ampal/analyse_protein.py | crick_angles | def crick_angles(p, reference_axis, tag=True, reference_axis_name='ref_axis'):
"""Returns the Crick angle for each CA atom in the `Polymer`.
Notes
-----
The final value is in the returned list is `None`, since the angle
calculation requires pairs of points on both the primitive and
reference_ax... | python | def crick_angles(p, reference_axis, tag=True, reference_axis_name='ref_axis'):
"""Returns the Crick angle for each CA atom in the `Polymer`.
Notes
-----
The final value is in the returned list is `None`, since the angle
calculation requires pairs of points on both the primitive and
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42,984 | woolfson-group/isambard | isambard/ampal/analyse_protein.py | alpha_angles | def alpha_angles(p, reference_axis, tag=True, reference_axis_name='ref_axis'):
"""Alpha angle calculated using points on the primitive of helix and axis.
Notes
-----
The final value is None, since the angle calculation requires pairs
of points along the primitive and axis. This is a generalisation
... | python | def alpha_angles(p, reference_axis, tag=True, reference_axis_name='ref_axis'):
"""Alpha angle calculated using points on the primitive of helix and axis.
Notes
-----
The final value is None, since the angle calculation requires pairs
of points along the primitive and axis. This is a generalisation
... | [
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42,985 | woolfson-group/isambard | isambard/ampal/analyse_protein.py | reference_axis_from_chains | def reference_axis_from_chains(chains):
"""Average coordinates from a set of primitives calculated from Chains.
Parameters
----------
chains : list(Chain)
Returns
-------
reference_axis : numpy.array
The averaged (x, y, z) coordinates of the primitives for
the list of Chain... | python | def reference_axis_from_chains(chains):
"""Average coordinates from a set of primitives calculated from Chains.
Parameters
----------
chains : list(Chain)
Returns
-------
reference_axis : numpy.array
The averaged (x, y, z) coordinates of the primitives for
the list of Chain... | [
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] | ebc33b48a28ad217e18f93b910dfba46e6e71e07 | https://github.com/woolfson-group/isambard/blob/ebc33b48a28ad217e18f93b910dfba46e6e71e07/isambard/ampal/analyse_protein.py#L525-L563 |
42,986 | woolfson-group/isambard | isambard/ampal/analyse_protein.py | flip_reference_axis_if_antiparallel | def flip_reference_axis_if_antiparallel(
p, reference_axis, start_index=0, end_index=-1):
"""Flips reference axis if direction opposes the direction of the `Polymer`.
Notes
-----
If the angle between the vector for the Polymer and the vector
for the reference_axis is > 90 degrees, then the ... | python | def flip_reference_axis_if_antiparallel(
p, reference_axis, start_index=0, end_index=-1):
"""Flips reference axis if direction opposes the direction of the `Polymer`.
Notes
-----
If the angle between the vector for the Polymer and the vector
for the reference_axis is > 90 degrees, then the ... | [
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If the angle between the vector for the Polymer and the vector
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42,987 | woolfson-group/isambard | isambard/ampal/analyse_protein.py | make_primitive | def make_primitive(cas_coords, window_length=3):
"""Calculates running average of cas_coords with a fixed averaging window_length.
Parameters
----------
cas_coords : list(numpy.array or float or tuple)
Each element of the list must have length 3.
window_length : int, optional
The nu... | python | def make_primitive(cas_coords, window_length=3):
"""Calculates running average of cas_coords with a fixed averaging window_length.
Parameters
----------
cas_coords : list(numpy.array or float or tuple)
Each element of the list must have length 3.
window_length : int, optional
The nu... | [
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window_length : int, optional
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42,988 | woolfson-group/isambard | isambard/ampal/analyse_protein.py | make_primitive_smoothed | def make_primitive_smoothed(cas_coords, smoothing_level=2):
""" Generates smoothed primitive from a list of coordinates.
Parameters
----------
cas_coords : list(numpy.array or float or tuple)
Each element of the list must have length 3.
smoothing_level : int, optional
Number of time... | python | def make_primitive_smoothed(cas_coords, smoothing_level=2):
""" Generates smoothed primitive from a list of coordinates.
Parameters
----------
cas_coords : list(numpy.array or float or tuple)
Each element of the list must have length 3.
smoothing_level : int, optional
Number of time... | [
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42,989 | woolfson-group/isambard | isambard/ampal/analyse_protein.py | make_primitive_extrapolate_ends | def make_primitive_extrapolate_ends(cas_coords, smoothing_level=2):
"""Generates smoothed helix primitives and extrapolates lost ends.
Notes
-----
From an input list of CA coordinates, the running average is
calculated to form a primitive. The smoothing_level dictates how
many times to calculat... | python | def make_primitive_extrapolate_ends(cas_coords, smoothing_level=2):
"""Generates smoothed helix primitives and extrapolates lost ends.
Notes
-----
From an input list of CA coordinates, the running average is
calculated to form a primitive. The smoothing_level dictates how
many times to calculat... | [
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42,990 | woolfson-group/isambard | isambard/ampal/assembly.py | AmpalContainer.extend | def extend(self, ampal_container):
"""Extends an `AmpalContainer` with another `AmpalContainer`."""
if isinstance(ampal_container, AmpalContainer):
self._ampal_objects.extend(ampal_container)
else:
raise TypeError(
'Only AmpalContainer objects may be merge... | python | def extend(self, ampal_container):
"""Extends an `AmpalContainer` with another `AmpalContainer`."""
if isinstance(ampal_container, AmpalContainer):
self._ampal_objects.extend(ampal_container)
else:
raise TypeError(
'Only AmpalContainer objects may be merge... | [
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42,991 | woolfson-group/isambard | isambard/ampal/assembly.py | AmpalContainer.pdb | def pdb(self):
"""Compiles the PDB strings for each state into a single file."""
header_title = '{:<80}\n'.format('HEADER {}'.format(self.id))
data_type = '{:<80}\n'.format('EXPDTA ISAMBARD Model')
pdb_strs = []
for ampal in self:
if isinstance(ampal, Assembly):... | python | def pdb(self):
"""Compiles the PDB strings for each state into a single file."""
header_title = '{:<80}\n'.format('HEADER {}'.format(self.id))
data_type = '{:<80}\n'.format('EXPDTA ISAMBARD Model')
pdb_strs = []
for ampal in self:
if isinstance(ampal, Assembly):... | [
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42,992 | woolfson-group/isambard | isambard/ampal/assembly.py | AmpalContainer.sort_by_tag | def sort_by_tag(self, tag):
"""Sorts the `AmpalContainer` by a tag on the component objects.
Parameters
----------
tag : str
Key of tag used for sorting.
"""
return AmpalContainer(sorted(self, key=lambda x: x.tags[tag])) | python | def sort_by_tag(self, tag):
"""Sorts the `AmpalContainer` by a tag on the component objects.
Parameters
----------
tag : str
Key of tag used for sorting.
"""
return AmpalContainer(sorted(self, key=lambda x: x.tags[tag])) | [
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----------
tag : str
Key of tag used for sorting. | [
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42,993 | woolfson-group/isambard | isambard/ampal/assembly.py | Assembly.append | def append(self, item):
"""Adds a `Polymer` to the `Assembly`.
Raises
------
TypeError
Raised if other is any type other than `Polymer`.
"""
if isinstance(item, Polymer):
self._molecules.append(item)
else:
raise TypeError(
... | python | def append(self, item):
"""Adds a `Polymer` to the `Assembly`.
Raises
------
TypeError
Raised if other is any type other than `Polymer`.
"""
if isinstance(item, Polymer):
self._molecules.append(item)
else:
raise TypeError(
... | [
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Raised if other is any type other than `Polymer`. | [
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42,994 | woolfson-group/isambard | isambard/ampal/assembly.py | Assembly.extend | def extend(self, assembly):
"""Extends the `Assembly` with the contents of another `Assembly`.
Raises
------
TypeError
Raised if other is any type other than `Assembly`.
"""
if isinstance(assembly, Assembly):
self._molecules.extend(assembly)
... | python | def extend(self, assembly):
"""Extends the `Assembly` with the contents of another `Assembly`.
Raises
------
TypeError
Raised if other is any type other than `Assembly`.
"""
if isinstance(assembly, Assembly):
self._molecules.extend(assembly)
... | [
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42,995 | woolfson-group/isambard | isambard/ampal/assembly.py | Assembly.get_monomers | def get_monomers(self, ligands=True, pseudo_group=False):
"""Retrieves all the `Monomers` from the `Assembly` object.
Parameters
----------
ligands : bool, optional
If `true`, will include ligand `Monomers`.
pseudo_group : bool, optional
If `True`, will i... | python | def get_monomers(self, ligands=True, pseudo_group=False):
"""Retrieves all the `Monomers` from the `Assembly` object.
Parameters
----------
ligands : bool, optional
If `true`, will include ligand `Monomers`.
pseudo_group : bool, optional
If `True`, will i... | [
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Parameters
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ligands : bool, optional
If `true`, will include ligand `Monomers`.
pseudo_group : bool, optional
If `True`, will include pseudo atoms. | [
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42,996 | woolfson-group/isambard | isambard/ampal/assembly.py | Assembly.get_ligands | def get_ligands(self, solvent=True):
"""Retrieves all ligands from the `Assembly`.
Parameters
----------
solvent : bool, optional
If `True`, solvent molecules will be included.
"""
if solvent:
ligand_list = [x for x in self.get_monomers()
... | python | def get_ligands(self, solvent=True):
"""Retrieves all ligands from the `Assembly`.
Parameters
----------
solvent : bool, optional
If `True`, solvent molecules will be included.
"""
if solvent:
ligand_list = [x for x in self.get_monomers()
... | [
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----------
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42,997 | woolfson-group/isambard | isambard/ampal/assembly.py | Assembly.get_atoms | def get_atoms(self, ligands=True, pseudo_group=False, inc_alt_states=False):
""" Flat list of all the `Atoms` in the `Assembly`.
Parameters
----------
ligands : bool, optional
Include ligand `Atoms`.
pseudo_group : bool, optional
Include pseudo_group `Ato... | python | def get_atoms(self, ligands=True, pseudo_group=False, inc_alt_states=False):
""" Flat list of all the `Atoms` in the `Assembly`.
Parameters
----------
ligands : bool, optional
Include ligand `Atoms`.
pseudo_group : bool, optional
Include pseudo_group `Ato... | [
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ligands : bool, optional
Include ligand `Atoms`.
pseudo_group : bool, optional
Include pseudo_group `Atoms`.
inc_alt_states : bool, optional
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42,998 | woolfson-group/isambard | isambard/ampal/assembly.py | Assembly.is_within | def is_within(self, cutoff_dist, point, ligands=True):
"""Returns all atoms in AMPAL object within `cut-off` distance from the `point`."""
return find_atoms_within_distance(self.get_atoms(ligands=ligands), cutoff_dist, point) | python | def is_within(self, cutoff_dist, point, ligands=True):
"""Returns all atoms in AMPAL object within `cut-off` distance from the `point`."""
return find_atoms_within_distance(self.get_atoms(ligands=ligands), cutoff_dist, point) | [
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42,999 | woolfson-group/isambard | isambard/ampal/assembly.py | Assembly.relabel_polymers | def relabel_polymers(self, labels=None):
"""Relabels the component Polymers either in alphabetical order or using a list of labels.
Parameters
----------
labels : list, optional
A list of new labels.
Raises
------
ValueError
Raised if the... | python | def relabel_polymers(self, labels=None):
"""Relabels the component Polymers either in alphabetical order or using a list of labels.
Parameters
----------
labels : list, optional
A list of new labels.
Raises
------
ValueError
Raised if the... | [
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Parameters
----------
labels : list, optional
A list of new labels.
Raises
------
ValueError
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