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woolfson-group/isambard | isambard/ampal/specifications/assembly_specs/nucleic_acid_duplex.py | DNADuplex.from_sequence | def from_sequence(cls, sequence, phos_3_prime=False):
"""Creates a DNA duplex from a nucleotide sequence.
Parameters
----------
sequence: str
Nucleotide sequence.
phos_3_prime: bool, optional
If false the 5' and the 3' phosphor will be omitted.
""... | python | def from_sequence(cls, sequence, phos_3_prime=False):
"""Creates a DNA duplex from a nucleotide sequence.
Parameters
----------
sequence: str
Nucleotide sequence.
phos_3_prime: bool, optional
If false the 5' and the 3' phosphor will be omitted.
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woolfson-group/isambard | isambard/ampal/specifications/assembly_specs/nucleic_acid_duplex.py | DNADuplex.from_start_and_end | def from_start_and_end(cls, start, end, sequence, phos_3_prime=False):
"""Creates a DNA duplex from a start and end point.
Parameters
----------
start: [float, float, float]
Start of the build axis.
end: [float, float, float]
End o... | python | def from_start_and_end(cls, start, end, sequence, phos_3_prime=False):
"""Creates a DNA duplex from a start and end point.
Parameters
----------
start: [float, float, float]
Start of the build axis.
end: [float, float, float]
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woolfson-group/isambard | isambard/ampal/specifications/assembly_specs/nucleic_acid_duplex.py | DNADuplex.generate_complementary_strand | def generate_complementary_strand(strand1):
"""Takes a SingleStrandHelix and creates the antisense strand."""
rise_adjust = (
strand1.rise_per_nucleotide * strand1.axis.unit_tangent) * 2
strand2 = NucleicAcidStrand.from_start_and_end(
strand1.helix_end - rise_adjust, stra... | python | def generate_complementary_strand(strand1):
"""Takes a SingleStrandHelix and creates the antisense strand."""
rise_adjust = (
strand1.rise_per_nucleotide * strand1.axis.unit_tangent) * 2
strand2 = NucleicAcidStrand.from_start_and_end(
strand1.helix_end - rise_adjust, stra... | [
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woolfson-group/isambard | isambard/external_programs/naccess.py | total_accessibility | def total_accessibility(in_rsa, path=True):
"""Parses rsa file for the total surface accessibility data.
Parameters
----------
in_rsa : str
Path to naccess rsa file.
path : bool
Indicates if in_rsa is a path or a string.
Returns
-------
dssp_residues : 5-tuple(float)
... | python | def total_accessibility(in_rsa, path=True):
"""Parses rsa file for the total surface accessibility data.
Parameters
----------
in_rsa : str
Path to naccess rsa file.
path : bool
Indicates if in_rsa is a path or a string.
Returns
-------
dssp_residues : 5-tuple(float)
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woolfson-group/isambard | isambard/tools/amino_acids.py | get_aa_code | def get_aa_code(aa_letter):
""" Get three-letter aa code if possible. If not, return None.
If three-letter code is None, will have to find this later from the filesystem.
Parameters
----------
aa_letter : str
One-letter amino acid code.
Returns
-------
aa_code : str, or None
... | python | def get_aa_code(aa_letter):
""" Get three-letter aa code if possible. If not, return None.
If three-letter code is None, will have to find this later from the filesystem.
Parameters
----------
aa_letter : str
One-letter amino acid code.
Returns
-------
aa_code : str, or None
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woolfson-group/isambard | isambard/tools/amino_acids.py | get_aa_letter | def get_aa_letter(aa_code):
""" Get one-letter version of aa_code if possible. If not, return 'X'.
Parameters
----------
aa_code : str
Three-letter amino acid code.
Returns
-------
aa_letter : str
One-letter aa code.
Default value is 'X'.
"""
aa_letter = 'X'... | python | def get_aa_letter(aa_code):
""" Get one-letter version of aa_code if possible. If not, return 'X'.
Parameters
----------
aa_code : str
Three-letter amino acid code.
Returns
-------
aa_letter : str
One-letter aa code.
Default value is 'X'.
"""
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woolfson-group/isambard | isambard/tools/amino_acids.py | get_aa_info | def get_aa_info(code):
"""Get dictionary of information relating to a new amino acid code not currently in the database.
Notes
-----
Use this function to get a dictionary that is then to be sent to the function add_amino_acid_to_json().
use to fill in rows of amino_acid table for new amino acid cod... | python | def get_aa_info(code):
"""Get dictionary of information relating to a new amino acid code not currently in the database.
Notes
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Use this function to get a dictionary that is then to be sent to the function add_amino_acid_to_json().
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woolfson-group/isambard | isambard/tools/amino_acids.py | add_amino_acid_to_json | def add_amino_acid_to_json(code, description, letter='X', modified=None, force_add=False):
""" Add an amino acid to the amino_acids.json file used to populate the amino_acid table.
Parameters
----------
code : str
New code to be added to amino acid table.
description : str
Descripti... | python | def add_amino_acid_to_json(code, description, letter='X', modified=None, force_add=False):
""" Add an amino acid to the amino_acids.json file used to populate the amino_acid table.
Parameters
----------
code : str
New code to be added to amino acid table.
description : str
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woolfson-group/isambard | isambard/ampal/specifications/assembly_specs/coiledcoil.py | CoiledCoil.from_polymers | def from_polymers(cls, polymers):
"""Creates a `CoiledCoil` from a list of `HelicalHelices`.
Parameters
----------
polymers : [HelicalHelix]
List of `HelicalHelices`.
"""
n = len(polymers)
instance = cls(n=n, auto_build=False)
instance.major_r... | python | def from_polymers(cls, polymers):
"""Creates a `CoiledCoil` from a list of `HelicalHelices`.
Parameters
----------
polymers : [HelicalHelix]
List of `HelicalHelices`.
"""
n = len(polymers)
instance = cls(n=n, auto_build=False)
instance.major_r... | [
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woolfson-group/isambard | isambard/ampal/specifications/assembly_specs/coiledcoil.py | CoiledCoil.from_parameters | def from_parameters(cls, n, aa=28, major_radius=None, major_pitch=None,
phi_c_alpha=26.42, minor_helix_type='alpha',
auto_build=True):
"""Creates a `CoiledCoil` from defined super-helical parameters.
Parameters
----------
n : int
... | python | def from_parameters(cls, n, aa=28, major_radius=None, major_pitch=None,
phi_c_alpha=26.42, minor_helix_type='alpha',
auto_build=True):
"""Creates a `CoiledCoil` from defined super-helical parameters.
Parameters
----------
n : int
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woolfson-group/isambard | isambard/ampal/specifications/assembly_specs/coiledcoil.py | CoiledCoil.tropocollagen | def tropocollagen(
cls, aa=28, major_radius=5.0, major_pitch=85.0, auto_build=True):
"""Creates a model of a collagen triple helix.
Parameters
----------
aa : int, optional
Number of amino acids per minor helix.
major_radius : float, optional
... | python | def tropocollagen(
cls, aa=28, major_radius=5.0, major_pitch=85.0, auto_build=True):
"""Creates a model of a collagen triple helix.
Parameters
----------
aa : int, optional
Number of amino acids per minor helix.
major_radius : float, optional
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woolfson-group/isambard | isambard/ampal/specifications/assembly_specs/coiledcoil.py | CoiledCoil.build | def build(self):
"""Builds a model of a coiled coil protein using input parameters."""
monomers = [HelicalHelix(major_pitch=self.major_pitches[i],
major_radius=self.major_radii[i],
major_handedness=self.major_handedness[i],
... | python | def build(self):
"""Builds a model of a coiled coil protein using input parameters."""
monomers = [HelicalHelix(major_pitch=self.major_pitches[i],
major_radius=self.major_radii[i],
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woolfson-group/isambard | isambard/buff/force_field.py | BuffForceField.find_max_rad_npnp | def find_max_rad_npnp(self):
"""Finds the maximum radius and npnp in the force field.
Returns
-------
(max_rad, max_npnp): (float, float)
Maximum radius and npnp distance in the loaded force field.
"""
max_rad = 0
max_npnp = 0
for res, atoms i... | python | def find_max_rad_npnp(self):
"""Finds the maximum radius and npnp in the force field.
Returns
-------
(max_rad, max_npnp): (float, float)
Maximum radius and npnp distance in the loaded force field.
"""
max_rad = 0
max_npnp = 0
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woolfson-group/isambard | isambard/buff/force_field.py | BuffForceField.parameter_struct_dict | def parameter_struct_dict(self):
"""Dictionary containing PyAtomData structs for the force field."""
if self._parameter_struct_dict is None:
self._parameter_struct_dict = self._make_ff_params_dict()
elif self.auto_update_f_params:
new_hash = hash(
tuple([t... | python | def parameter_struct_dict(self):
"""Dictionary containing PyAtomData structs for the force field."""
if self._parameter_struct_dict is None:
self._parameter_struct_dict = self._make_ff_params_dict()
elif self.auto_update_f_params:
new_hash = hash(
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woolfson-group/isambard | isambard/external_programs/reduce.py | run_reduce | def run_reduce(input_file, path=True):
""" Runs reduce on a pdb or mmol file at the specified path.
Notes
-----
Runs Reduce programme to add missing protons to a PDB file.
Parameters
----------
input_file : str
Path to file to add protons to or structure in mmol/pdb format.
pat... | python | def run_reduce(input_file, path=True):
""" Runs reduce on a pdb or mmol file at the specified path.
Notes
-----
Runs Reduce programme to add missing protons to a PDB file.
Parameters
----------
input_file : str
Path to file to add protons to or structure in mmol/pdb format.
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woolfson-group/isambard | isambard/external_programs/reduce.py | reduce_output_path | def reduce_output_path(path=None, pdb_name=None):
"""Defines location of Reduce output files relative to input files."""
if not path:
if not pdb_name:
raise NameError(
"Cannot save an output for a temporary file without a PDB"
"code specified")
pdb_nam... | python | def reduce_output_path(path=None, pdb_name=None):
"""Defines location of Reduce output files relative to input files."""
if not path:
if not pdb_name:
raise NameError(
"Cannot save an output for a temporary file without a PDB"
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woolfson-group/isambard | isambard/external_programs/reduce.py | output_reduce | def output_reduce(input_file, path=True, pdb_name=None, force=False):
"""Runs Reduce on a pdb or mmol file and creates a new file with the output.
Parameters
----------
input_file : str or pathlib.Path
Path to file to run Reduce on.
path : bool
True if input_file is a path.
pdb_n... | python | def output_reduce(input_file, path=True, pdb_name=None, force=False):
"""Runs Reduce on a pdb or mmol file and creates a new file with the output.
Parameters
----------
input_file : str or pathlib.Path
Path to file to run Reduce on.
path : bool
True if input_file is a path.
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woolfson-group/isambard | isambard/external_programs/reduce.py | output_reduce_list | def output_reduce_list(path_list, force=False):
"""Generates structure file with protons from a list of structure files."""
output_paths = []
for path in path_list:
output_path = output_reduce(path, force=force)
if output_path:
output_paths.append(output_path)
return output_p... | python | def output_reduce_list(path_list, force=False):
"""Generates structure file with protons from a list of structure files."""
output_paths = []
for path in path_list:
output_path = output_reduce(path, force=force)
if output_path:
output_paths.append(output_path)
return output_p... | [
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woolfson-group/isambard | isambard/external_programs/reduce.py | assembly_plus_protons | def assembly_plus_protons(input_file, path=True, pdb_name=None,
save_output=False, force_save=False):
"""Returns an Assembly with protons added by Reduce.
Notes
-----
Looks for a pre-existing Reduce output in the standard location before
running Reduce. If the protein cont... | python | def assembly_plus_protons(input_file, path=True, pdb_name=None,
save_output=False, force_save=False):
"""Returns an Assembly with protons added by Reduce.
Notes
-----
Looks for a pre-existing Reduce output in the standard location before
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woolfson-group/isambard | isambard/ampal/specifications/polymer_specs/helix.py | Helix.from_start_and_end | def from_start_and_end(cls, start, end, aa=None, helix_type='alpha'):
"""Creates a `Helix` between `start` and `end`.
Parameters
----------
start : 3D Vector (tuple or list or numpy.array)
The coordinate of the start of the helix primitive.
end : 3D Vector (tuple or ... | python | def from_start_and_end(cls, start, end, aa=None, helix_type='alpha'):
"""Creates a `Helix` between `start` and `end`.
Parameters
----------
start : 3D Vector (tuple or list or numpy.array)
The coordinate of the start of the helix primitive.
end : 3D Vector (tuple or ... | [
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The coordinate of the start of the helix primitive.
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woolfson-group/isambard | isambard/ampal/specifications/polymer_specs/helix.py | Helix.build | def build(self):
"""Build straight helix along z-axis, starting with CA1 on x-axis"""
ang_per_res = (2 * numpy.pi) / self.residues_per_turn
atom_offsets = _atom_offsets[self.helix_type]
if self.handedness == 'l':
handedness = -1
else:
handedness = 1
... | python | def build(self):
"""Build straight helix along z-axis, starting with CA1 on x-axis"""
ang_per_res = (2 * numpy.pi) / self.residues_per_turn
atom_offsets = _atom_offsets[self.helix_type]
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handedness = -1
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woolfson-group/isambard | isambard/ampal/specifications/polymer_specs/helix.py | HelicalHelix.from_start_and_end | def from_start_and_end(cls, start, end, aa=None, major_pitch=225.8,
major_radius=5.07, major_handedness='l',
minor_helix_type='alpha', orientation=1,
phi_c_alpha=0.0, minor_repeat=None):
"""Creates a `HelicalHelix` between a `start... | python | def from_start_and_end(cls, start, end, aa=None, major_pitch=225.8,
major_radius=5.07, major_handedness='l',
minor_helix_type='alpha', orientation=1,
phi_c_alpha=0.0, minor_repeat=None):
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woolfson-group/isambard | isambard/ampal/specifications/polymer_specs/helix.py | HelicalHelix.curve | def curve(self):
"""Curve of the super helix."""
return HelicalCurve.pitch_and_radius(
self.major_pitch, self.major_radius,
handedness=self.major_handedness) | python | def curve(self):
"""Curve of the super helix."""
return HelicalCurve.pitch_and_radius(
self.major_pitch, self.major_radius,
handedness=self.major_handedness) | [
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woolfson-group/isambard | isambard/ampal/specifications/polymer_specs/helix.py | HelicalHelix.curve_primitive | def curve_primitive(self):
"""`Primitive` of the super-helical curve."""
curve = self.curve
curve.axis_start = self.helix_start
curve.axis_end = self.helix_end
coords = curve.get_coords(
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if... | python | def curve_primitive(self):
"""`Primitive` of the super-helical curve."""
curve = self.curve
curve.axis_start = self.helix_start
curve.axis_end = self.helix_end
coords = curve.get_coords(
n_points=(self.num_monomers + 1), spacing=self.minor_rise_per_residue)
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woolfson-group/isambard | isambard/ampal/specifications/polymer_specs/helix.py | HelicalHelix.major_rise_per_monomer | def major_rise_per_monomer(self):
"""Rise along super-helical axis per monomer."""
return numpy.cos(numpy.deg2rad(self.curve.alpha)) * self.minor_rise_per_residue | python | def major_rise_per_monomer(self):
"""Rise along super-helical axis per monomer."""
return numpy.cos(numpy.deg2rad(self.curve.alpha)) * self.minor_rise_per_residue | [
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woolfson-group/isambard | isambard/ampal/specifications/polymer_specs/helix.py | HelicalHelix.minor_residues_per_turn | def minor_residues_per_turn(self, minor_repeat=None):
"""Calculates the number of residues per turn of the minor helix.
Parameters
----------
minor_repeat : float, optional
Hydrophobic repeat of the minor helix.
Returns
-------
minor_rpt : float
... | python | def minor_residues_per_turn(self, minor_repeat=None):
"""Calculates the number of residues per turn of the minor helix.
Parameters
----------
minor_repeat : float, optional
Hydrophobic repeat of the minor helix.
Returns
-------
minor_rpt : float
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woolfson-group/isambard | isambard/ampal/specifications/polymer_specs/helix.py | HelicalHelix.build | def build(self):
"""Builds the `HelicalHelix`."""
helical_helix = Polypeptide()
primitive_coords = self.curve_primitive.coordinates
helices = [Helix.from_start_and_end(start=primitive_coords[i],
end=primitive_coords[i + 1],
... | python | def build(self):
"""Builds the `HelicalHelix`."""
helical_helix = Polypeptide()
primitive_coords = self.curve_primitive.coordinates
helices = [Helix.from_start_and_end(start=primitive_coords[i],
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woolfson-group/isambard | isambard/ampal/specifications/polymer_specs/helix.py | HelicalHelix.rotate_monomers | def rotate_monomers(self, angle, radians=False):
""" Rotates each Residue in the Polypeptide.
Notes
-----
Each monomer is rotated about the axis formed between its
corresponding primitive `PseudoAtom` and that of the
subsequent `Monomer`.
Parameters
---... | python | def rotate_monomers(self, angle, radians=False):
""" Rotates each Residue in the Polypeptide.
Notes
-----
Each monomer is rotated about the axis formed between its
corresponding primitive `PseudoAtom` and that of the
subsequent `Monomer`.
Parameters
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] | ebc33b48a28ad217e18f93b910dfba46e6e71e07 | https://github.com/woolfson-group/isambard/blob/ebc33b48a28ad217e18f93b910dfba46e6e71e07/isambard/ampal/specifications/polymer_specs/helix.py#L538-L560 | train | 60,027 |
woolfson-group/isambard | isambard/add_ons/knobs_into_holes.py | side_chain_centres | def side_chain_centres(assembly, masses=False):
""" PseudoGroup containing side_chain centres of each Residue in each Polypeptide in Assembly.
Notes
-----
Each PseudoAtom is a side-chain centre.
There is one PseudoMonomer per chain in ampal (each containing len(chain) PseudoAtoms).
The PseudoGr... | python | def side_chain_centres(assembly, masses=False):
""" PseudoGroup containing side_chain centres of each Residue in each Polypeptide in Assembly.
Notes
-----
Each PseudoAtom is a side-chain centre.
There is one PseudoMonomer per chain in ampal (each containing len(chain) PseudoAtoms).
The PseudoGr... | [
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Each PseudoAtom is a side-chain centre.
There is one PseudoMonomer per chain in ampal (each containing len(chain) PseudoAtoms).
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woolfson-group/isambard | isambard/add_ons/knobs_into_holes.py | cluster_helices | def cluster_helices(helices, cluster_distance=12.0):
""" Clusters helices according to the minimum distance between the line segments representing their backbone.
Notes
-----
Each helix is represented as a line segement joining the CA of its first Residue to the CA if its final Residue.
The minimal... | python | def cluster_helices(helices, cluster_distance=12.0):
""" Clusters helices according to the minimum distance between the line segments representing their backbone.
Notes
-----
Each helix is represented as a line segement joining the CA of its first Residue to the CA if its final Residue.
The minimal... | [
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woolfson-group/isambard | isambard/add_ons/knobs_into_holes.py | find_kihs | def find_kihs(assembly, hole_size=4, cutoff=7.0):
""" KnobIntoHoles between residues of different chains in assembly.
Notes
-----
A KnobIntoHole is a found when the side-chain centre of a Residue a chain is close than (cutoff) Angstroms from at
least (hole_size) side-chain centres of Residues of a ... | python | def find_kihs(assembly, hole_size=4, cutoff=7.0):
""" KnobIntoHoles between residues of different chains in assembly.
Notes
-----
A KnobIntoHole is a found when the side-chain centre of a Residue a chain is close than (cutoff) Angstroms from at
least (hole_size) side-chain centres of Residues of a ... | [
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Notes
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A KnobIntoHole is a found when the side-chain centre of a Residue a chain is close than (cutoff) Angstroms from at
least (hole_size) side-chain centres of Residues of a different chain.
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] | ebc33b48a28ad217e18f93b910dfba46e6e71e07 | https://github.com/woolfson-group/isambard/blob/ebc33b48a28ad217e18f93b910dfba46e6e71e07/isambard/add_ons/knobs_into_holes.py#L114-L151 | train | 60,030 |
woolfson-group/isambard | isambard/add_ons/knobs_into_holes.py | find_contiguous_packing_segments | def find_contiguous_packing_segments(polypeptide, residues, max_dist=10.0):
""" Assembly containing segments of polypeptide, divided according to separation of contiguous residues.
Parameters
----------
polypeptide : Polypeptide
residues : iterable containing Residues
max_dist : float
S... | python | def find_contiguous_packing_segments(polypeptide, residues, max_dist=10.0):
""" Assembly containing segments of polypeptide, divided according to separation of contiguous residues.
Parameters
----------
polypeptide : Polypeptide
residues : iterable containing Residues
max_dist : float
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woolfson-group/isambard | isambard/add_ons/knobs_into_holes.py | gen_reference_primitive | def gen_reference_primitive(polypeptide, start, end):
""" Generates a reference Primitive for a Polypeptide given start and end coordinates.
Notes
-----
Uses the rise_per_residue of the Polypeptide primitive to define the separation of points on the line joining
start and end.
Parameters
-... | python | def gen_reference_primitive(polypeptide, start, end):
""" Generates a reference Primitive for a Polypeptide given start and end coordinates.
Notes
-----
Uses the rise_per_residue of the Polypeptide primitive to define the separation of points on the line joining
start and end.
Parameters
-... | [
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polypeptide : Polypeptide
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woolfson-group/isambard | isambard/add_ons/knobs_into_holes.py | KnobGroup.from_helices | def from_helices(cls, assembly, cutoff=7.0, min_helix_length=8):
""" Generate KnobGroup from the helices in the assembly - classic socket functionality.
Notes
-----
Socket identifies knobs-into-holes (KIHs) packing motifs in protein structures.
The following resources can provid... | python | def from_helices(cls, assembly, cutoff=7.0, min_helix_length=8):
""" Generate KnobGroup from the helices in the assembly - classic socket functionality.
Notes
-----
Socket identifies knobs-into-holes (KIHs) packing motifs in protein structures.
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woolfson-group/isambard | isambard/add_ons/knobs_into_holes.py | KnobGroup.knob_subgroup | def knob_subgroup(self, cutoff=7.0):
""" KnobGroup where all KnobsIntoHoles have max_kh_distance <= cutoff. """
if cutoff > self.cutoff:
raise ValueError("cutoff supplied ({0}) cannot be greater than self.cutoff ({1})".format(cutoff,
... | python | def knob_subgroup(self, cutoff=7.0):
""" KnobGroup where all KnobsIntoHoles have max_kh_distance <= cutoff. """
if cutoff > self.cutoff:
raise ValueError("cutoff supplied ({0}) cannot be greater than self.cutoff ({1})".format(cutoff,
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woolfson-group/isambard | isambard/add_ons/knobs_into_holes.py | KnobGroup.graph | def graph(self):
""" Returns MultiDiGraph from kihs. Nodes are helices and edges are kihs. """
g = networkx.MultiDiGraph()
edge_list = [(x.knob_helix, x.hole_helix, x.id, {'kih': x}) for x in self.get_monomers()]
g.add_edges_from(edge_list)
return g | python | def graph(self):
""" Returns MultiDiGraph from kihs. Nodes are helices and edges are kihs. """
g = networkx.MultiDiGraph()
edge_list = [(x.knob_helix, x.hole_helix, x.id, {'kih': x}) for x in self.get_monomers()]
g.add_edges_from(edge_list)
return g | [
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woolfson-group/isambard | isambard/add_ons/knobs_into_holes.py | KnobGroup.filter_graph | def filter_graph(g, cutoff=7.0, min_kihs=2):
""" Get subgraph formed from edges that have max_kh_distance < cutoff.
Parameters
----------
g : MultiDiGraph representing KIHs
g is the output from graph_from_protein
cutoff : float
Socket cutoff in Angstroms.... | python | def filter_graph(g, cutoff=7.0, min_kihs=2):
""" Get subgraph formed from edges that have max_kh_distance < cutoff.
Parameters
----------
g : MultiDiGraph representing KIHs
g is the output from graph_from_protein
cutoff : float
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woolfson-group/isambard | isambard/add_ons/knobs_into_holes.py | KnobGroup.get_coiledcoil_region | def get_coiledcoil_region(self, cc_number=0, cutoff=7.0, min_kihs=2):
""" Assembly containing only assigned regions (i.e. regions with contiguous KnobsIntoHoles. """
g = self.filter_graph(self.graph, cutoff=cutoff, min_kihs=min_kihs)
ccs = sorted(networkx.connected_component_subgraphs(g, copy=Tr... | python | def get_coiledcoil_region(self, cc_number=0, cutoff=7.0, min_kihs=2):
""" Assembly containing only assigned regions (i.e. regions with contiguous KnobsIntoHoles. """
g = self.filter_graph(self.graph, cutoff=cutoff, min_kihs=min_kihs)
ccs = sorted(networkx.connected_component_subgraphs(g, copy=Tr... | [
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woolfson-group/isambard | isambard/add_ons/knobs_into_holes.py | KnobGroup.daisy_chain_graph | def daisy_chain_graph(self):
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g = networkx.DiGraph()
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g.add_edge(x.knob, h)
return g | python | def daisy_chain_graph(self):
""" Directed graph with edges from knob residue to each hole residue for each KnobIntoHole in self. """
g = networkx.DiGraph()
for x in self.get_monomers():
for h in x.hole:
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woolfson-group/isambard | isambard/add_ons/knobs_into_holes.py | KnobIntoHole.knob_end | def knob_end(self):
""" Coordinates of the end of the knob residue (atom in side-chain furthest from CB atom.
Returns CA coordinates for GLY.
"""
side_chain_atoms = self.knob_residue.side_chain
if not side_chain_atoms:
return self.knob_residue['CA']
distances ... | python | def knob_end(self):
""" Coordinates of the end of the knob residue (atom in side-chain furthest from CB atom.
Returns CA coordinates for GLY.
"""
side_chain_atoms = self.knob_residue.side_chain
if not side_chain_atoms:
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woolfson-group/isambard | isambard/add_ons/knobs_into_holes.py | KnobIntoHole.max_knob_end_distance | def max_knob_end_distance(self):
""" Maximum distance between knob_end and each of the hole side-chain centres. """
return max([distance(self.knob_end, h) for h in self.hole]) | python | def max_knob_end_distance(self):
""" Maximum distance between knob_end and each of the hole side-chain centres. """
return max([distance(self.knob_end, h) for h in self.hole]) | [
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woolfson-group/isambard | isambard/configure.py | base_install | def base_install():
"""Generates configuration setting for required functionality of ISAMBARD."""
# scwrl
scwrl = {}
print('{BOLD}{HEADER}Generating configuration files for ISAMBARD.{END_C}\n'
'All required input can use tab completion for paths.\n'
'{BOLD}Setting up SCWRL 4.0 (Recom... | python | def base_install():
"""Generates configuration setting for required functionality of ISAMBARD."""
# scwrl
scwrl = {}
print('{BOLD}{HEADER}Generating configuration files for ISAMBARD.{END_C}\n'
'All required input can use tab completion for paths.\n'
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woolfson-group/isambard | isambard/configure.py | optional_install | def optional_install():
"""Generates configuration settings for optional functionality of ISAMBARD."""
# reduce
print('{BOLD}Setting up Reduce (optional){END_C}'.format(**text_colours))
reduce = {}
reduce_path = get_user_path('Please provide a path to your reduce executable.', required=False)
re... | python | def optional_install():
"""Generates configuration settings for optional functionality of ISAMBARD."""
# reduce
print('{BOLD}Setting up Reduce (optional){END_C}'.format(**text_colours))
reduce = {}
reduce_path = get_user_path('Please provide a path to your reduce executable.', required=False)
re... | [
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woolfson-group/isambard | isambard/ampal/pseudo_atoms.py | PseudoMonomer.pdb | def pdb(self):
"""Generates a PDB string for the `PseudoMonomer`."""
pdb_str = write_pdb(
[self], ' ' if not self.tags['chain_id'] else self.tags['chain_id'])
return pdb_str | python | def pdb(self):
"""Generates a PDB string for the `PseudoMonomer`."""
pdb_str = write_pdb(
[self], ' ' if not self.tags['chain_id'] else self.tags['chain_id'])
return pdb_str | [
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woolfson-group/isambard | isambard/ampal/pseudo_atoms.py | Primitive.from_coordinates | def from_coordinates(cls, coordinates):
"""Creates a `Primitive` from a list of coordinates."""
prim = cls()
for coord in coordinates:
pm = PseudoMonomer(ampal_parent=prim)
pa = PseudoAtom(coord, ampal_parent=pm)
pm.atoms = OrderedDict([('CA', pa)])
... | python | def from_coordinates(cls, coordinates):
"""Creates a `Primitive` from a list of coordinates."""
prim = cls()
for coord in coordinates:
pm = PseudoMonomer(ampal_parent=prim)
pa = PseudoAtom(coord, ampal_parent=pm)
pm.atoms = OrderedDict([('CA', pa)])
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woolfson-group/isambard | isambard/ampal/pseudo_atoms.py | Primitive.rise_per_residue | def rise_per_residue(self):
"""The rise per residue at each point on the Primitive.
Notes
-----
Each element of the returned list is the rise per residue,
at a point on the Primitive. Element i is the distance
between primitive[i] and primitive[i + 1]. The final value
... | python | def rise_per_residue(self):
"""The rise per residue at each point on the Primitive.
Notes
-----
Each element of the returned list is the rise per residue,
at a point on the Primitive. Element i is the distance
between primitive[i] and primitive[i + 1]. The final value
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woolfson-group/isambard | isambard/ampal/nucleic_acid.py | Polynucleotide.sequence | def sequence(self):
"""Returns the sequence of the `Polynucleotide` as a string.
Returns
-------
sequence : str
String of the monomer sequence of the `Polynucleotide`.
"""
seq = [x.mol_code for x in self._monomers]
return ' '.join(seq) | python | def sequence(self):
"""Returns the sequence of the `Polynucleotide` as a string.
Returns
-------
sequence : str
String of the monomer sequence of the `Polynucleotide`.
"""
seq = [x.mol_code for x in self._monomers]
return ' '.join(seq) | [
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String of the monomer sequence of the `Polynucleotide`. | [
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woolfson-group/isambard | isambard/external_programs/dssp.py | run_dssp | def run_dssp(pdb, path=True, outfile=None):
"""Uses DSSP to find helices and extracts helices from a pdb file or string.
Parameters
----------
pdb : str
Path to pdb file or string.
path : bool, optional
Indicates if pdb is a path or a string.
outfile : str, optional
File... | python | def run_dssp(pdb, path=True, outfile=None):
"""Uses DSSP to find helices and extracts helices from a pdb file or string.
Parameters
----------
pdb : str
Path to pdb file or string.
path : bool, optional
Indicates if pdb is a path or a string.
outfile : str, optional
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woolfson-group/isambard | isambard/external_programs/dssp.py | extract_solvent_accessibility_dssp | def extract_solvent_accessibility_dssp(in_dssp, path=True):
"""Uses DSSP to extract solvent accessibilty information on every residue.
Notes
-----
For more information on the solvent accessibility metrics used in dssp, see:
http://swift.cmbi.ru.nl/gv/dssp/HTML/descrip.html#ACC
In the dssp files... | python | def extract_solvent_accessibility_dssp(in_dssp, path=True):
"""Uses DSSP to extract solvent accessibilty information on every residue.
Notes
-----
For more information on the solvent accessibility metrics used in dssp, see:
http://swift.cmbi.ru.nl/gv/dssp/HTML/descrip.html#ACC
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woolfson-group/isambard | isambard/external_programs/dssp.py | extract_helices_dssp | def extract_helices_dssp(in_pdb):
"""Uses DSSP to find alpha-helices and extracts helices from a pdb file.
Returns a length 3 list with a helix id, the chain id and a dict
containing the coordinates of each residues CA.
Parameters
----------
in_pdb : string
Path to a PDB file.
"""
... | python | def extract_helices_dssp(in_pdb):
"""Uses DSSP to find alpha-helices and extracts helices from a pdb file.
Returns a length 3 list with a helix id, the chain id and a dict
containing the coordinates of each residues CA.
Parameters
----------
in_pdb : string
Path to a PDB file.
"""
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woolfson-group/isambard | isambard/external_programs/dssp.py | extract_pp_helices | def extract_pp_helices(in_pdb):
"""Uses DSSP to find polyproline helices in a pdb file.
Returns a length 3 list with a helix id, the chain id and a dict
containing the coordinates of each residues CA.
Parameters
----------
in_pdb : string
Path to a PDB file.
"""
t_phi = -75.0
... | python | def extract_pp_helices(in_pdb):
"""Uses DSSP to find polyproline helices in a pdb file.
Returns a length 3 list with a helix id, the chain id and a dict
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Parameters
----------
in_pdb : string
Path to a PDB file.
"""
t_phi = -75.0
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travispavek/testrail-python | examples/end_to_end_example.py | main | def main():
""" This will offer a step by step guide to create a new run in TestRail,
update tests in the run with results, and close the run
"""
# Parse command line arguments
args = get_args()
# Instantiate the TestRail client
# Use the CLI argument to identify which project to work w... | python | def main():
""" This will offer a step by step guide to create a new run in TestRail,
update tests in the run with results, and close the run
"""
# Parse command line arguments
args = get_args()
# Instantiate the TestRail client
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GGiecold/DBSCAN_multiplex | DBSCAN_multiplex.py | memory | def memory():
"""Determine the machine's memory specifications.
Returns
-------
mem_info : dictonary
Holds the current values for the total, free and used memory of the system.
"""
mem_info = {}
if platform.linux_distribution()[0]:
with open('/proc/meminfo') as file:
... | python | def memory():
"""Determine the machine's memory specifications.
Returns
-------
mem_info : dictonary
Holds the current values for the total, free and used memory of the system.
"""
mem_info = {}
if platform.linux_distribution()[0]:
with open('/proc/meminfo') as file:
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GGiecold/DBSCAN_multiplex | DBSCAN_multiplex.py | get_chunk_size | def get_chunk_size(N, n):
"""Given a dimension of size 'N', determine the number of rows or columns
that can fit into memory.
Parameters
----------
N : int
The size of one of the dimension of a two-dimensional array.
n : int
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"""Given a dimension of size 'N', determine the number of rows or columns
that can fit into memory.
Parameters
----------
N : int
The size of one of the dimension of a two-dimensional array.
n : int
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Wiredcraft/dopy | dopy/manager.py | DoManager.all_floating_ips | def all_floating_ips(self):
"""
Lists all of the Floating IPs available on the account.
"""
if self.api_version == 2:
json = self.request('/floating_ips')
return json['floating_ips']
else:
raise DoError(v2_api_required_str) | python | def all_floating_ips(self):
"""
Lists all of the Floating IPs available on the account.
"""
if self.api_version == 2:
json = self.request('/floating_ips')
return json['floating_ips']
else:
raise DoError(v2_api_required_str) | [
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Wiredcraft/dopy | dopy/manager.py | DoManager.new_floating_ip | def new_floating_ip(self, **kwargs):
"""
Creates a Floating IP and assigns it to a Droplet or reserves it to a region.
"""
droplet_id = kwargs.get('droplet_id')
region = kwargs.get('region')
if self.api_version == 2:
if droplet_id is not None and region is no... | python | def new_floating_ip(self, **kwargs):
"""
Creates a Floating IP and assigns it to a Droplet or reserves it to a region.
"""
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region = kwargs.get('region')
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Wiredcraft/dopy | dopy/manager.py | DoManager.destroy_floating_ip | def destroy_floating_ip(self, ip_addr):
"""
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"""
Deletes a Floating IP and removes it from the account.
"""
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self.request('/floating_ips/' + ip_addr, method='DELETE')
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Wiredcraft/dopy | dopy/manager.py | DoManager.assign_floating_ip | def assign_floating_ip(self, ip_addr, droplet_id):
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Assigns a Floating IP to a Droplet.
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params = {'type': 'assign','droplet_id': droplet_id}
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Wiredcraft/dopy | dopy/manager.py | DoManager.unassign_floating_ip | def unassign_floating_ip(self, ip_addr):
"""
Unassign a Floating IP from a Droplet.
The Floating IP will be reserved in the region but not assigned to a Droplet.
"""
if self.api_version == 2:
params = {'type': 'unassign'}
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"""
Unassign a Floating IP from a Droplet.
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"""
if self.api_version == 2:
params = {'type': 'unassign'}
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Wiredcraft/dopy | dopy/manager.py | DoManager.list_floating_ip_actions | def list_floating_ip_actions(self, ip_addr):
"""
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"""
if self.api_version == 2:
json = self.request('/floating_ips/' + ip_addr + '/actions')
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else:
ra... | python | def list_floating_ip_actions(self, ip_addr):
"""
Retrieve a list of all actions that have been executed on a Floating IP.
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Wiredcraft/dopy | dopy/manager.py | DoManager.get_floating_ip_action | def get_floating_ip_action(self, ip_addr, action_id):
"""
Retrieve the status of a Floating IP action.
"""
if self.api_version == 2:
json = self.request('/floating_ips/' + ip_addr + '/actions/' + action_id)
return json['action']
else:
raise DoE... | python | def get_floating_ip_action(self, ip_addr, action_id):
"""
Retrieve the status of a Floating IP action.
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if self.api_version == 2:
json = self.request('/floating_ips/' + ip_addr + '/actions/' + action_id)
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etoccalino/django-rest-framework-httpsignature | utils/sign3.py | raw_sign | def raw_sign(message, secret):
"""Sign a message."""
digest = hmac.new(secret, message, hashlib.sha256).digest()
return base64.b64encode(digest) | python | def raw_sign(message, secret):
"""Sign a message."""
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etoccalino/django-rest-framework-httpsignature | rest_framework_httpsignature/authentication.py | SignatureAuthentication.get_signature_from_signature_string | def get_signature_from_signature_string(self, signature):
"""Return the signature from the signature header or None."""
match = self.SIGNATURE_RE.search(signature)
if not match:
return None
return match.group(1) | python | def get_signature_from_signature_string(self, signature):
"""Return the signature from the signature header or None."""
match = self.SIGNATURE_RE.search(signature)
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etoccalino/django-rest-framework-httpsignature | rest_framework_httpsignature/authentication.py | SignatureAuthentication.get_headers_from_signature | def get_headers_from_signature(self, signature):
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etoccalino/django-rest-framework-httpsignature | rest_framework_httpsignature/authentication.py | SignatureAuthentication.header_canonical | def header_canonical(self, header_name):
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# Translate as stated in the docs:
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"""Translate HTTP headers to Django header names."""
# Translate as stated in the docs:
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etoccalino/django-rest-framework-httpsignature | rest_framework_httpsignature/authentication.py | SignatureAuthentication.build_dict_to_sign | def build_dict_to_sign(self, request, signature_headers):
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ivankliuk/duckduckpy | duckduckpy/utils.py | camel_to_snake_case | def camel_to_snake_case(string):
"""Converts 'string' presented in camel case to snake case.
e.g.: CamelCase => snake_case
"""
s = _1.sub(r'\1_\2', string)
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query_string: Query to be passed to DuckDuckGo API.
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ivankliuk/duckduckpy | duckduckpy/core.py | query | def query(query_string, secure=False, container='namedtuple', verbose=False,
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Generates and sends a query to DuckDuckGo API.
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wickman/pystachio | pystachio/container.py | ListFactory.create | def create(type_dict, *type_parameters):
"""
Construct a List containing type 'klazz'.
"""
assert len(type_parameters) == 1
klazz = TypeFactory.new(type_dict, *type_parameters[0])
assert isclass(klazz)
assert issubclass(klazz, Object)
return TypeMetaclass('%sList' % klazz.__name__, (Li... | python | def create(type_dict, *type_parameters):
"""
Construct a List containing type 'klazz'.
"""
assert len(type_parameters) == 1
klazz = TypeFactory.new(type_dict, *type_parameters[0])
assert isclass(klazz)
assert issubclass(klazz, Object)
return TypeMetaclass('%sList' % klazz.__name__, (Li... | [
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jeffh/sniffer | sniffer/scent_picker.py | load_file | def load_file(filename):
"Runs the given scent.py file."
mod_name = '.'.join(os.path.basename(filename).split('.')[:-1])
mod_path = os.path.dirname(filename)
if mod_name in sys.modules:
del sys.modules[mod_name]
if mod_path not in set(sys.modules.keys()):
sys.path.insert(0, mod_path... | python | def load_file(filename):
"Runs the given scent.py file."
mod_name = '.'.join(os.path.basename(filename).split('.')[:-1])
mod_path = os.path.dirname(filename)
if mod_name in sys.modules:
del sys.modules[mod_name]
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wickman/pystachio | pystachio/typing.py | TypeFactory.new | def new(type_dict, type_factory, *type_parameters):
"""
Create a fully reified type from a type schema.
"""
type_tuple = (type_factory,) + type_parameters
if type_tuple not in type_dict:
factory = TypeFactory.get_factory(type_factory)
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"""
Create a fully reified type from a type schema.
"""
type_tuple = (type_factory,) + type_parameters
if type_tuple not in type_dict:
factory = TypeFactory.get_factory(type_factory)
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"""Convert a Python class into a type signature."""
if isclass(sig) and issubclass(sig, Object):
return TypeSignature(sig)
elif isinstance(sig, TypeSignature):
return sig | python | def wrap(sig):
"""Convert a Python class into a type signature."""
if isclass(sig) and issubclass(sig, Object):
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jeffh/sniffer | sniffer/scanner/base.py | BaseScanner.trigger_modified | def trigger_modified(self, filepath):
"""Triggers modified event if the given filepath mod time is newer."""
mod_time = self._get_modified_time(filepath)
if mod_time > self._watched_files.get(filepath, 0):
self._trigger('modified', filepath)
self._watched_files[filepath] ... | python | def trigger_modified(self, filepath):
"""Triggers modified event if the given filepath mod time is newer."""
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jeffh/sniffer | sniffer/scanner/base.py | BaseScanner.trigger_created | def trigger_created(self, filepath):
"""Triggers created event if file exists."""
if os.path.exists(filepath):
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"""Triggers created event if file exists."""
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jeffh/sniffer | sniffer/scanner/base.py | BaseScanner.trigger_deleted | def trigger_deleted(self, filepath):
"""Triggers deleted event if the flie doesn't exist."""
if not os.path.exists(filepath):
self._trigger('deleted', filepath) | python | def trigger_deleted(self, filepath):
"""Triggers deleted event if the flie doesn't exist."""
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jeffh/sniffer | sniffer/scanner/base.py | BaseScanner.log | def log(self, *message):
"""
Logs a messate to a defined io stream if available.
"""
if self._logger is None:
return
s = " ".join([str(m) for m in message])
self._logger.write(s+'\n')
self._logger.flush() | python | def log(self, *message):
"""
Logs a messate to a defined io stream if available.
"""
if self._logger is None:
return
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self._logger.write(s+'\n')
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jeffh/sniffer | sniffer/scanner/base.py | BaseScanner.in_repo | def in_repo(self, filepath):
"""
This excludes repository directories because they cause some exceptions
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"""
filepath = set(filepath.replace('\\', '/').split('/'))
for p in ('.git', '.hg', '.svn', '.cvs', '.bzr'):
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... | python | def in_repo(self, filepath):
"""
This excludes repository directories because they cause some exceptions
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"""
filepath = set(filepath.replace('\\', '/').split('/'))
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jeffh/sniffer | sniffer/scanner/base.py | BaseScanner._modify_event | def _modify_event(self, event_name, method, func):
"""
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"""
if event_name not in self.ALL_EVENTS:
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... | python | def _modify_event(self, event_name, method, func):
"""
Wrapper to call a list's method from one of the events
"""
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jeffh/sniffer | sniffer/scanner/base.py | PollingScanner._watch_file | def _watch_file(self, filepath, trigger_event=True):
"""Adds the file's modified time into its internal watchlist."""
is_new = filepath not in self._watched_files
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self.trigger_created(filepath)
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jeffh/sniffer | sniffer/scanner/base.py | PollingScanner._unwatch_file | def _unwatch_file(self, filepath, trigger_event=True):
"""
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"""
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return
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self.trigger_deleted(filepath)
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Removes the file from the internal watchlist if exists.
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jeffh/sniffer | sniffer/scanner/base.py | PollingScanner._is_modified | def _is_modified(self, filepath):
"""
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Will return False if the file has not been seen before.
"""
if self._is_new(filepath):
return False
mtime = self._get_modified_time(filepath)
return self.... | python | def _is_modified(self, filepath):
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Returns True if the file has been modified since last seen.
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jeffh/sniffer | sniffer/scanner/base.py | PollingScanner.loop | def loop(self, sleep_time=1, callback=None):
"""
Goes into a blocking IO loop. If polling is used, the sleep_time is
the interval, in seconds, between polls.
"""
self.log("No supported libraries found: using polling-method.")
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self.trigger_ini... | python | def loop(self, sleep_time=1, callback=None):
"""
Goes into a blocking IO loop. If polling is used, the sleep_time is
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"""
self.log("No supported libraries found: using polling-method.")
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jeffh/sniffer | sniffer/main.py | run | def run(sniffer_instance=None, wait_time=0.5, clear=True, args=(),
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"""
Runs the auto tester loop. Internally, the runner instanciates the sniffer_cls and
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] | 8e4c3e77743aef08109ea0225b4a6536d4e60270 | https://github.com/jeffh/sniffer/blob/8e4c3e77743aef08109ea0225b4a6536d4e60270/sniffer/main.py#L17-L48 | train | 60,084 |
jeffh/sniffer | sniffer/main.py | main | def main(sniffer_instance=None, test_args=(), progname=sys.argv[0],
args=sys.argv[1:]):
"""
Runs the program. This is used when you want to run this program standalone.
``sniffer_instance`` A class (usually subclassed of Sniffer) that hooks into the
scanner and handles running ... | python | def main(sniffer_instance=None, test_args=(), progname=sys.argv[0],
args=sys.argv[1:]):
"""
Runs the program. This is used when you want to run this program standalone.
``sniffer_instance`` A class (usually subclassed of Sniffer) that hooks into the
scanner and handles running ... | [
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jeffh/sniffer | sniffer/runner.py | Sniffer.set_up | def set_up(self, test_args=(), clear=True, debug=False):
"""
Sets properties right before calling run.
``test_args`` The arguments to pass to the test runner.
``clear`` Boolean. Set to True if we should clear console before
running the tests.
``... | python | def set_up(self, test_args=(), clear=True, debug=False):
"""
Sets properties right before calling run.
``test_args`` The arguments to pass to the test runner.
``clear`` Boolean. Set to True if we should clear console before
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jeffh/sniffer | sniffer/runner.py | Sniffer.observe_scanner | def observe_scanner(self, scanner):
"""
Hooks into multiple events of a scanner.
"""
scanner.observe(scanner.ALL_EVENTS,
self.absorb_args(self.modules.restore))
if self.clear:
scanner.observe(scanner.ALL_EVENTS,
self... | python | def observe_scanner(self, scanner):
"""
Hooks into multiple events of a scanner.
"""
scanner.observe(scanner.ALL_EVENTS,
self.absorb_args(self.modules.restore))
if self.clear:
scanner.observe(scanner.ALL_EVENTS,
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jeffh/sniffer | sniffer/runner.py | Sniffer.clear_on_run | def clear_on_run(self, prefix="Running Tests:"):
"""Clears console before running the tests."""
if platform.system() == 'Windows':
os.system('cls')
else:
os.system('clear')
if prefix:
print(prefix) | python | def clear_on_run(self, prefix="Running Tests:"):
"""Clears console before running the tests."""
if platform.system() == 'Windows':
os.system('cls')
else:
os.system('clear')
if prefix:
print(prefix) | [
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jeffh/sniffer | sniffer/runner.py | Sniffer.run | def run(self):
"""
Runs the unit test framework. Can be overridden to run anything.
Returns True on passing and False on failure.
"""
try:
import nose
arguments = [sys.argv[0]] + list(self.test_args)
return nose.run(argv=arguments)
exce... | python | def run(self):
"""
Runs the unit test framework. Can be overridden to run anything.
Returns True on passing and False on failure.
"""
try:
import nose
arguments = [sys.argv[0]] + list(self.test_args)
return nose.run(argv=arguments)
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jeffh/sniffer | sniffer/runner.py | ScentSniffer.run | def run(self):
"""
Runs the CWD's scent file.
"""
if not self.scent or len(self.scent.runners) == 0:
print("Did not find 'scent.py', running nose:")
return super(ScentSniffer, self).run()
else:
print("Using scent:")
arguments = [sys... | python | def run(self):
"""
Runs the CWD's scent file.
"""
if not self.scent or len(self.scent.runners) == 0:
print("Did not find 'scent.py', running nose:")
return super(ScentSniffer, self).run()
else:
print("Using scent:")
arguments = [sys... | [
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wickman/pystachio | pystachio/base.py | Object.copy | def copy(self):
"""
Return a copy of this object.
"""
self_copy = self.dup()
self_copy._scopes = copy.copy(self._scopes)
return self_copy | python | def copy(self):
"""
Return a copy of this object.
"""
self_copy = self.dup()
self_copy._scopes = copy.copy(self._scopes)
return self_copy | [
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wickman/pystachio | pystachio/base.py | Object.bind | def bind(self, *args, **kw):
"""
Bind environment variables into this object's scope.
"""
new_self = self.copy()
new_scopes = Object.translate_to_scopes(*args, **kw)
new_self._scopes = tuple(reversed(new_scopes)) + new_self._scopes
return new_self | python | def bind(self, *args, **kw):
"""
Bind environment variables into this object's scope.
"""
new_self = self.copy()
new_scopes = Object.translate_to_scopes(*args, **kw)
new_self._scopes = tuple(reversed(new_scopes)) + new_self._scopes
return new_self | [
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wickman/pystachio | pystachio/base.py | Object.check | def check(self):
"""
Type check this object.
"""
try:
si, uninterp = self.interpolate()
# TODO(wickman) This should probably be pushed out to the interpolate leaves.
except (Object.CoercionError, MustacheParser.Uninterpolatable) as e:
return TypeCheck(False, "Unable to interpolate:... | python | def check(self):
"""
Type check this object.
"""
try:
si, uninterp = self.interpolate()
# TODO(wickman) This should probably be pushed out to the interpolate leaves.
except (Object.CoercionError, MustacheParser.Uninterpolatable) as e:
return TypeCheck(False, "Unable to interpolate:... | [
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jeffh/sniffer | sniffer/modules_restore_point.py | ModulesRestorePoint.restore | def restore(self):
"""
Unloads all modules that weren't loaded when save_modules was called.
"""
sys = set(self._sys_modules.keys())
for mod_name in sys.difference(self._saved_modules):
del self._sys_modules[mod_name] | python | def restore(self):
"""
Unloads all modules that weren't loaded when save_modules was called.
"""
sys = set(self._sys_modules.keys())
for mod_name in sys.difference(self._saved_modules):
del self._sys_modules[mod_name] | [
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wickman/pystachio | pystachio/parsing.py | MustacheParser.join | def join(cls, splits, *namables):
"""
Interpolate strings.
:params splits: The output of Parser.split(string)
:params namables: A sequence of Namable objects in which the interpolation should take place.
Returns 2-tuple containing:
joined string, list of unbound object ids (potenti... | python | def join(cls, splits, *namables):
"""
Interpolate strings.
:params splits: The output of Parser.split(string)
:params namables: A sequence of Namable objects in which the interpolation should take place.
Returns 2-tuple containing:
joined string, list of unbound object ids (potenti... | [
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numirias/firefed | firefed/output.py | outitem | def outitem(title, elems, indent=4):
"""Output formatted as list item."""
out(title)
max_key_len = max(len(key) for key, _ in elems) + 1
for key, val in elems:
key_spaced = ('%s:' % key).ljust(max_key_len)
out('%s%s %s' % (indent * ' ', key_spaced, val))
out() | python | def outitem(title, elems, indent=4):
"""Output formatted as list item."""
out(title)
max_key_len = max(len(key) for key, _ in elems) + 1
for key, val in elems:
key_spaced = ('%s:' % key).ljust(max_key_len)
out('%s%s %s' % (indent * ' ', key_spaced, val))
out() | [
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numirias/firefed | firefed/util.py | profile_dir | def profile_dir(name):
"""Return path to FF profile for a given profile name or path."""
if name:
possible_path = Path(name)
if possible_path.exists():
return possible_path
profiles = list(read_profiles())
try:
if name:
profile = next(p for p in profiles i... | python | def profile_dir(name):
"""Return path to FF profile for a given profile name or path."""
if name:
possible_path = Path(name)
if possible_path.exists():
return possible_path
profiles = list(read_profiles())
try:
if name:
profile = next(p for p in profiles i... | [
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numirias/firefed | firefed/feature/feature.py | formatter | def formatter(name, default=False):
"""Decorate a Feature method to register it as an output formatter.
All formatters are picked up by the argument parser so that they can be
listed and selected on the CLI via the -f, --format argument.
"""
def decorator(func):
func._output_format = dict(n... | python | def formatter(name, default=False):
"""Decorate a Feature method to register it as an output formatter.
All formatters are picked up by the argument parser so that they can be
listed and selected on the CLI via the -f, --format argument.
"""
def decorator(func):
func._output_format = dict(n... | [
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numirias/firefed | firefed/feature/feature.py | FeatureHelpersMixin.load_sqlite | def load_sqlite(self, db, query=None, table=None, cls=None,
column_map=None):
"""Load data from sqlite db and return as list of specified objects."""
if column_map is None:
column_map = {}
db_path = self.profile_path(db, must_exist=True)
def obj_factory(c... | python | def load_sqlite(self, db, query=None, table=None, cls=None,
column_map=None):
"""Load data from sqlite db and return as list of specified objects."""
if column_map is None:
column_map = {}
db_path = self.profile_path(db, must_exist=True)
def obj_factory(c... | [
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