id int32 0 252k | repo stringlengths 7 55 | path stringlengths 4 127 | func_name stringlengths 1 88 | original_string stringlengths 75 19.8k | language stringclasses 1
value | code stringlengths 51 19.8k | code_tokens list | docstring stringlengths 3 17.3k | docstring_tokens list | sha stringlengths 40 40 | url stringlengths 87 242 |
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229,600 | mosdef-hub/mbuild | mbuild/compound.py | Compound.translate | def translate(self, by):
"""Translate the Compound by a vector
Parameters
----------
by : np.ndarray, shape=(3,), dtype=float
"""
new_positions = _translate(self.xyz_with_ports, by)
self.xyz_with_ports = new_positions | python | def translate(self, by):
new_positions = _translate(self.xyz_with_ports, by)
self.xyz_with_ports = new_positions | [
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Parameters
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by : np.ndarray, shape=(3,), dtype=float | [
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229,601 | mosdef-hub/mbuild | mbuild/compound.py | Compound.rotate | def rotate(self, theta, around):
"""Rotate Compound around an arbitrary vector.
Parameters
----------
theta : float
The angle by which to rotate the Compound, in radians.
around : np.ndarray, shape=(3,), dtype=float
The vector about which to rotate the Compound.
"""
new_positions = _rotate(self.xyz_with_ports, theta, around)
self.xyz_with_ports = new_positions | python | def rotate(self, theta, around):
new_positions = _rotate(self.xyz_with_ports, theta, around)
self.xyz_with_ports = new_positions | [
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Parameters
----------
theta : float
The angle by which to rotate the Compound, in radians.
around : np.ndarray, shape=(3,), dtype=float
The vector about which to rotate the Compound. | [
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229,602 | mosdef-hub/mbuild | mbuild/compound.py | Compound.spin | def spin(self, theta, around):
"""Rotate Compound in place around an arbitrary vector.
Parameters
----------
theta : float
The angle by which to rotate the Compound, in radians.
around : np.ndarray, shape=(3,), dtype=float
The axis about which to spin the Compound.
"""
around = np.asarray(around).reshape(3)
center_pos = self.center
self.translate(-center_pos)
self.rotate(theta, around)
self.translate(center_pos) | python | def spin(self, theta, around):
around = np.asarray(around).reshape(3)
center_pos = self.center
self.translate(-center_pos)
self.rotate(theta, around)
self.translate(center_pos) | [
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Parameters
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theta : float
The angle by which to rotate the Compound, in radians.
around : np.ndarray, shape=(3,), dtype=float
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229,603 | mosdef-hub/mbuild | mbuild/compound.py | Compound.from_trajectory | def from_trajectory(self, traj, frame=-1, coords_only=False):
"""Extract atoms and bonds from a md.Trajectory.
Will create sub-compounds for every chain if there is more than one
and sub-sub-compounds for every residue.
Parameters
----------
traj : mdtraj.Trajectory
The trajectory to load.
frame : int, optional, default=-1 (last)
The frame to take coordinates from.
coords_only : bool, optional, default=False
Only read coordinate information
"""
if coords_only:
if traj.n_atoms != self.n_particles:
raise ValueError('Number of atoms in {traj} does not match'
' {self}'.format(**locals()))
atoms_particles = zip(traj.topology.atoms,
self.particles(include_ports=False))
if None in self._particles(include_ports=False):
raise ValueError('Some particles are None')
for mdtraj_atom, particle in atoms_particles:
particle.pos = traj.xyz[frame, mdtraj_atom.index]
return
atom_mapping = dict()
for chain in traj.topology.chains:
if traj.topology.n_chains > 1:
chain_compound = Compound()
self.add(chain_compound, 'chain[$]')
else:
chain_compound = self
for res in chain.residues:
for atom in res.atoms:
new_atom = Particle(name=str(atom.name),
pos=traj.xyz[frame, atom.index])
chain_compound.add(
new_atom, label='{0}[$]'.format(
atom.name))
atom_mapping[atom] = new_atom
for mdtraj_atom1, mdtraj_atom2 in traj.topology.bonds:
atom1 = atom_mapping[mdtraj_atom1]
atom2 = atom_mapping[mdtraj_atom2]
self.add_bond((atom1, atom2))
if np.any(traj.unitcell_lengths) and np.any(traj.unitcell_lengths[0]):
self.periodicity = traj.unitcell_lengths[0]
else:
self.periodicity = np.array([0., 0., 0.]) | python | def from_trajectory(self, traj, frame=-1, coords_only=False):
if coords_only:
if traj.n_atoms != self.n_particles:
raise ValueError('Number of atoms in {traj} does not match'
' {self}'.format(**locals()))
atoms_particles = zip(traj.topology.atoms,
self.particles(include_ports=False))
if None in self._particles(include_ports=False):
raise ValueError('Some particles are None')
for mdtraj_atom, particle in atoms_particles:
particle.pos = traj.xyz[frame, mdtraj_atom.index]
return
atom_mapping = dict()
for chain in traj.topology.chains:
if traj.topology.n_chains > 1:
chain_compound = Compound()
self.add(chain_compound, 'chain[$]')
else:
chain_compound = self
for res in chain.residues:
for atom in res.atoms:
new_atom = Particle(name=str(atom.name),
pos=traj.xyz[frame, atom.index])
chain_compound.add(
new_atom, label='{0}[$]'.format(
atom.name))
atom_mapping[atom] = new_atom
for mdtraj_atom1, mdtraj_atom2 in traj.topology.bonds:
atom1 = atom_mapping[mdtraj_atom1]
atom2 = atom_mapping[mdtraj_atom2]
self.add_bond((atom1, atom2))
if np.any(traj.unitcell_lengths) and np.any(traj.unitcell_lengths[0]):
self.periodicity = traj.unitcell_lengths[0]
else:
self.periodicity = np.array([0., 0., 0.]) | [
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Will create sub-compounds for every chain if there is more than one
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Parameters
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traj : mdtraj.Trajectory
The trajectory to load.
frame : int, optional, default=-1 (last)
The frame to take coordinates from.
coords_only : bool, optional, default=False
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229,604 | mosdef-hub/mbuild | mbuild/compound.py | Compound.to_trajectory | def to_trajectory(self, show_ports=False, chains=None,
residues=None, box=None):
"""Convert to an md.Trajectory and flatten the compound.
Parameters
----------
show_ports : bool, optional, default=False
Include all port atoms when converting to trajectory.
chains : mb.Compound or list of mb.Compound
Chain types to add to the topology
residues : str of list of str
Labels of residues in the Compound. Residues are assigned by
checking against Compound.name.
box : mb.Box, optional, default=self.boundingbox (with buffer)
Box information to be used when converting to a `Trajectory`.
If 'None', a bounding box is used with a 0.5nm buffer in each
dimension. to avoid overlapping atoms, unless `self.periodicity`
is not None, in which case those values are used for the
box lengths.
Returns
-------
trajectory : md.Trajectory
See also
--------
_to_topology
"""
atom_list = [particle for particle in self.particles(show_ports)]
top = self._to_topology(atom_list, chains, residues)
# Coordinates.
xyz = np.ndarray(shape=(1, top.n_atoms, 3), dtype='float')
for idx, atom in enumerate(atom_list):
xyz[0, idx] = atom.pos
# Unitcell information.
unitcell_angles = [90.0, 90.0, 90.0]
if box is None:
unitcell_lengths = np.empty(3)
for dim, val in enumerate(self.periodicity):
if val:
unitcell_lengths[dim] = val
else:
unitcell_lengths[dim] = self.boundingbox.lengths[dim] + 0.5
else:
unitcell_lengths = box.lengths
unitcell_angles = box.angles
return md.Trajectory(xyz, top, unitcell_lengths=unitcell_lengths,
unitcell_angles=unitcell_angles) | python | def to_trajectory(self, show_ports=False, chains=None,
residues=None, box=None):
atom_list = [particle for particle in self.particles(show_ports)]
top = self._to_topology(atom_list, chains, residues)
# Coordinates.
xyz = np.ndarray(shape=(1, top.n_atoms, 3), dtype='float')
for idx, atom in enumerate(atom_list):
xyz[0, idx] = atom.pos
# Unitcell information.
unitcell_angles = [90.0, 90.0, 90.0]
if box is None:
unitcell_lengths = np.empty(3)
for dim, val in enumerate(self.periodicity):
if val:
unitcell_lengths[dim] = val
else:
unitcell_lengths[dim] = self.boundingbox.lengths[dim] + 0.5
else:
unitcell_lengths = box.lengths
unitcell_angles = box.angles
return md.Trajectory(xyz, top, unitcell_lengths=unitcell_lengths,
unitcell_angles=unitcell_angles) | [
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Parameters
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Include all port atoms when converting to trajectory.
chains : mb.Compound or list of mb.Compound
Chain types to add to the topology
residues : str of list of str
Labels of residues in the Compound. Residues are assigned by
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Box information to be used when converting to a `Trajectory`.
If 'None', a bounding box is used with a 0.5nm buffer in each
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Returns
-------
trajectory : md.Trajectory
See also
--------
_to_topology | [
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229,605 | mosdef-hub/mbuild | mbuild/compound.py | Compound._to_topology | def _to_topology(self, atom_list, chains=None, residues=None):
"""Create a mdtraj.Topology from a Compound.
Parameters
----------
atom_list : list of mb.Compound
Atoms to include in the topology
chains : mb.Compound or list of mb.Compound
Chain types to add to the topology
residues : str of list of str
Labels of residues in the Compound. Residues are assigned by
checking against Compound.name.
Returns
-------
top : mdtraj.Topology
See Also
--------
mdtraj.Topology : Details on the mdtraj Topology object
"""
from mdtraj.core.topology import Topology
if isinstance(chains, string_types):
chains = [chains]
if isinstance(chains, (list, set)):
chains = tuple(chains)
if isinstance(residues, string_types):
residues = [residues]
if isinstance(residues, (list, set)):
residues = tuple(residues)
top = Topology()
atom_mapping = {}
default_chain = top.add_chain()
default_residue = top.add_residue('RES', default_chain)
compound_residue_map = dict()
atom_residue_map = dict()
compound_chain_map = dict()
atom_chain_map = dict()
for atom in atom_list:
# Chains
if chains:
if atom.name in chains:
current_chain = top.add_chain()
compound_chain_map[atom] = current_chain
else:
for parent in atom.ancestors():
if chains and parent.name in chains:
if parent not in compound_chain_map:
current_chain = top.add_chain()
compound_chain_map[parent] = current_chain
current_residue = top.add_residue(
'RES', current_chain)
break
else:
current_chain = default_chain
else:
current_chain = default_chain
atom_chain_map[atom] = current_chain
# Residues
if residues:
if atom.name in residues:
current_residue = top.add_residue(atom.name, current_chain)
compound_residue_map[atom] = current_residue
else:
for parent in atom.ancestors():
if residues and parent.name in residues:
if parent not in compound_residue_map:
current_residue = top.add_residue(
parent.name, current_chain)
compound_residue_map[parent] = current_residue
break
else:
current_residue = default_residue
else:
if chains:
try: # Grab the default residue from the custom chain.
current_residue = next(current_chain.residues)
except StopIteration: # Add the residue to the current chain
current_residue = top.add_residue('RES', current_chain)
else: # Grab the default chain's default residue
current_residue = default_residue
atom_residue_map[atom] = current_residue
# Add the actual atoms
try:
elem = get_by_symbol(atom.name)
except KeyError:
elem = get_by_symbol("VS")
at = top.add_atom(atom.name, elem, atom_residue_map[atom])
at.charge = atom.charge
atom_mapping[atom] = at
# Remove empty default residues.
chains_to_remove = [
chain for chain in top.chains if chain.n_atoms == 0]
residues_to_remove = [res for res in top.residues if res.n_atoms == 0]
for chain in chains_to_remove:
top._chains.remove(chain)
for res in residues_to_remove:
for chain in top.chains:
try:
chain._residues.remove(res)
except ValueError: # Already gone.
pass
for atom1, atom2 in self.bonds():
# Ensure that both atoms are part of the compound. This becomes an
# issue if you try to convert a sub-compound to a topology which is
# bonded to a different subcompound.
if all(a in atom_mapping.keys() for a in [atom1, atom2]):
top.add_bond(atom_mapping[atom1], atom_mapping[atom2])
return top | python | def _to_topology(self, atom_list, chains=None, residues=None):
from mdtraj.core.topology import Topology
if isinstance(chains, string_types):
chains = [chains]
if isinstance(chains, (list, set)):
chains = tuple(chains)
if isinstance(residues, string_types):
residues = [residues]
if isinstance(residues, (list, set)):
residues = tuple(residues)
top = Topology()
atom_mapping = {}
default_chain = top.add_chain()
default_residue = top.add_residue('RES', default_chain)
compound_residue_map = dict()
atom_residue_map = dict()
compound_chain_map = dict()
atom_chain_map = dict()
for atom in atom_list:
# Chains
if chains:
if atom.name in chains:
current_chain = top.add_chain()
compound_chain_map[atom] = current_chain
else:
for parent in atom.ancestors():
if chains and parent.name in chains:
if parent not in compound_chain_map:
current_chain = top.add_chain()
compound_chain_map[parent] = current_chain
current_residue = top.add_residue(
'RES', current_chain)
break
else:
current_chain = default_chain
else:
current_chain = default_chain
atom_chain_map[atom] = current_chain
# Residues
if residues:
if atom.name in residues:
current_residue = top.add_residue(atom.name, current_chain)
compound_residue_map[atom] = current_residue
else:
for parent in atom.ancestors():
if residues and parent.name in residues:
if parent not in compound_residue_map:
current_residue = top.add_residue(
parent.name, current_chain)
compound_residue_map[parent] = current_residue
break
else:
current_residue = default_residue
else:
if chains:
try: # Grab the default residue from the custom chain.
current_residue = next(current_chain.residues)
except StopIteration: # Add the residue to the current chain
current_residue = top.add_residue('RES', current_chain)
else: # Grab the default chain's default residue
current_residue = default_residue
atom_residue_map[atom] = current_residue
# Add the actual atoms
try:
elem = get_by_symbol(atom.name)
except KeyError:
elem = get_by_symbol("VS")
at = top.add_atom(atom.name, elem, atom_residue_map[atom])
at.charge = atom.charge
atom_mapping[atom] = at
# Remove empty default residues.
chains_to_remove = [
chain for chain in top.chains if chain.n_atoms == 0]
residues_to_remove = [res for res in top.residues if res.n_atoms == 0]
for chain in chains_to_remove:
top._chains.remove(chain)
for res in residues_to_remove:
for chain in top.chains:
try:
chain._residues.remove(res)
except ValueError: # Already gone.
pass
for atom1, atom2 in self.bonds():
# Ensure that both atoms are part of the compound. This becomes an
# issue if you try to convert a sub-compound to a topology which is
# bonded to a different subcompound.
if all(a in atom_mapping.keys() for a in [atom1, atom2]):
top.add_bond(atom_mapping[atom1], atom_mapping[atom2])
return top | [
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"... | Create a mdtraj.Topology from a Compound.
Parameters
----------
atom_list : list of mb.Compound
Atoms to include in the topology
chains : mb.Compound or list of mb.Compound
Chain types to add to the topology
residues : str of list of str
Labels of residues in the Compound. Residues are assigned by
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Returns
-------
top : mdtraj.Topology
See Also
--------
mdtraj.Topology : Details on the mdtraj Topology object | [
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229,606 | mosdef-hub/mbuild | mbuild/compound.py | Compound.from_parmed | def from_parmed(self, structure, coords_only=False):
"""Extract atoms and bonds from a pmd.Structure.
Will create sub-compounds for every chain if there is more than one
and sub-sub-compounds for every residue.
Parameters
----------
structure : pmd.Structure
The structure to load.
coords_only : bool
Set preexisting atoms in compound to coordinates given by structure.
"""
if coords_only:
if len(structure.atoms) != self.n_particles:
raise ValueError(
'Number of atoms in {structure} does not match'
' {self}'.format(
**locals()))
atoms_particles = zip(structure.atoms,
self.particles(include_ports=False))
if None in self._particles(include_ports=False):
raise ValueError('Some particles are None')
for parmed_atom, particle in atoms_particles:
particle.pos = np.array([parmed_atom.xx,
parmed_atom.xy,
parmed_atom.xz]) / 10
return
atom_mapping = dict()
chain_id = None
chains = defaultdict(list)
for residue in structure.residues:
chains[residue.chain].append(residue)
for chain, residues in chains.items():
if len(chains) > 1:
chain_compound = Compound()
self.add(chain_compound, chain_id)
else:
chain_compound = self
for residue in residues:
for atom in residue.atoms:
pos = np.array([atom.xx, atom.xy, atom.xz]) / 10
new_atom = Particle(name=str(atom.name), pos=pos)
chain_compound.add(
new_atom, label='{0}[$]'.format(
atom.name))
atom_mapping[atom] = new_atom
for bond in structure.bonds:
atom1 = atom_mapping[bond.atom1]
atom2 = atom_mapping[bond.atom2]
self.add_bond((atom1, atom2))
if structure.box is not None:
# Convert from A to nm
self.periodicity = 0.1 * structure.box[0:3]
else:
self.periodicity = np.array([0., 0., 0.]) | python | def from_parmed(self, structure, coords_only=False):
if coords_only:
if len(structure.atoms) != self.n_particles:
raise ValueError(
'Number of atoms in {structure} does not match'
' {self}'.format(
**locals()))
atoms_particles = zip(structure.atoms,
self.particles(include_ports=False))
if None in self._particles(include_ports=False):
raise ValueError('Some particles are None')
for parmed_atom, particle in atoms_particles:
particle.pos = np.array([parmed_atom.xx,
parmed_atom.xy,
parmed_atom.xz]) / 10
return
atom_mapping = dict()
chain_id = None
chains = defaultdict(list)
for residue in structure.residues:
chains[residue.chain].append(residue)
for chain, residues in chains.items():
if len(chains) > 1:
chain_compound = Compound()
self.add(chain_compound, chain_id)
else:
chain_compound = self
for residue in residues:
for atom in residue.atoms:
pos = np.array([atom.xx, atom.xy, atom.xz]) / 10
new_atom = Particle(name=str(atom.name), pos=pos)
chain_compound.add(
new_atom, label='{0}[$]'.format(
atom.name))
atom_mapping[atom] = new_atom
for bond in structure.bonds:
atom1 = atom_mapping[bond.atom1]
atom2 = atom_mapping[bond.atom2]
self.add_bond((atom1, atom2))
if structure.box is not None:
# Convert from A to nm
self.periodicity = 0.1 * structure.box[0:3]
else:
self.periodicity = np.array([0., 0., 0.]) | [
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structure : pmd.Structure
The structure to load.
coords_only : bool
Set preexisting atoms in compound to coordinates given by structure. | [
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229,607 | mosdef-hub/mbuild | mbuild/compound.py | Compound.to_networkx | def to_networkx(self, names_only=False):
"""Create a NetworkX graph representing the hierarchy of a Compound.
Parameters
----------
names_only : bool, optional, default=False Store only the names of the
compounds in the graph. When set to False, the default behavior,
the nodes are the compounds themselves.
Returns
-------
G : networkx.DiGraph
"""
nx = import_('networkx')
nodes = list()
edges = list()
if names_only:
nodes.append(self.name)
else:
nodes.append(self)
nodes, edges = self._iterate_children(nodes, edges, names_only=names_only)
graph = nx.DiGraph()
graph.add_nodes_from(nodes)
graph.add_edges_from(edges)
return graph | python | def to_networkx(self, names_only=False):
nx = import_('networkx')
nodes = list()
edges = list()
if names_only:
nodes.append(self.name)
else:
nodes.append(self)
nodes, edges = self._iterate_children(nodes, edges, names_only=names_only)
graph = nx.DiGraph()
graph.add_nodes_from(nodes)
graph.add_edges_from(edges)
return graph | [
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Returns
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229,608 | mosdef-hub/mbuild | mbuild/compound.py | Compound.to_intermol | def to_intermol(self, molecule_types=None):
"""Create an InterMol system from a Compound.
Parameters
----------
molecule_types : list or tuple of subclasses of Compound
Returns
-------
intermol_system : intermol.system.System
"""
from intermol.atom import Atom as InterMolAtom
from intermol.molecule import Molecule
from intermol.system import System
import simtk.unit as u
if isinstance(molecule_types, list):
molecule_types = tuple(molecule_types)
elif molecule_types is None:
molecule_types = (type(self),)
intermol_system = System()
last_molecule_compound = None
for atom_index, atom in enumerate(self.particles()):
for parent in atom.ancestors():
# Don't want inheritance via isinstance().
if type(parent) in molecule_types:
# Check if we have encountered this molecule type before.
if parent.name not in intermol_system.molecule_types:
self._add_intermol_molecule_type(
intermol_system, parent)
if parent != last_molecule_compound:
last_molecule_compound = parent
last_molecule = Molecule(name=parent.name)
intermol_system.add_molecule(last_molecule)
break
else:
# Should never happen if molecule_types only contains
# type(self)
raise ValueError(
'Found an atom {} that is not part of any of '
'the specified molecule types {}'.format(
atom, molecule_types))
# Add the actual intermol atoms.
intermol_atom = InterMolAtom(atom_index + 1, name=atom.name,
residue_index=1, residue_name='RES')
intermol_atom.position = atom.pos * u.nanometers
last_molecule.add_atom(intermol_atom)
return intermol_system | python | def to_intermol(self, molecule_types=None):
from intermol.atom import Atom as InterMolAtom
from intermol.molecule import Molecule
from intermol.system import System
import simtk.unit as u
if isinstance(molecule_types, list):
molecule_types = tuple(molecule_types)
elif molecule_types is None:
molecule_types = (type(self),)
intermol_system = System()
last_molecule_compound = None
for atom_index, atom in enumerate(self.particles()):
for parent in atom.ancestors():
# Don't want inheritance via isinstance().
if type(parent) in molecule_types:
# Check if we have encountered this molecule type before.
if parent.name not in intermol_system.molecule_types:
self._add_intermol_molecule_type(
intermol_system, parent)
if parent != last_molecule_compound:
last_molecule_compound = parent
last_molecule = Molecule(name=parent.name)
intermol_system.add_molecule(last_molecule)
break
else:
# Should never happen if molecule_types only contains
# type(self)
raise ValueError(
'Found an atom {} that is not part of any of '
'the specified molecule types {}'.format(
atom, molecule_types))
# Add the actual intermol atoms.
intermol_atom = InterMolAtom(atom_index + 1, name=atom.name,
residue_index=1, residue_name='RES')
intermol_atom.position = atom.pos * u.nanometers
last_molecule.add_atom(intermol_atom)
return intermol_system | [
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Parameters
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molecule_types : list or tuple of subclasses of Compound
Returns
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intermol_system : intermol.system.System | [
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229,609 | mosdef-hub/mbuild | mbuild/compound.py | Compound._add_intermol_molecule_type | def _add_intermol_molecule_type(intermol_system, parent):
"""Create a molecule type for the parent and add bonds. """
from intermol.moleculetype import MoleculeType
from intermol.forces.bond import Bond as InterMolBond
molecule_type = MoleculeType(name=parent.name)
intermol_system.add_molecule_type(molecule_type)
for index, parent_atom in enumerate(parent.particles()):
parent_atom.index = index + 1
for atom1, atom2 in parent.bonds():
intermol_bond = InterMolBond(atom1.index, atom2.index)
molecule_type.bonds.add(intermol_bond) | python | def _add_intermol_molecule_type(intermol_system, parent):
from intermol.moleculetype import MoleculeType
from intermol.forces.bond import Bond as InterMolBond
molecule_type = MoleculeType(name=parent.name)
intermol_system.add_molecule_type(molecule_type)
for index, parent_atom in enumerate(parent.particles()):
parent_atom.index = index + 1
for atom1, atom2 in parent.bonds():
intermol_bond = InterMolBond(atom1.index, atom2.index)
molecule_type.bonds.add(intermol_bond) | [
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229,610 | mosdef-hub/mbuild | mbuild/utils/validation.py | assert_port_exists | def assert_port_exists(port_name, compound):
"""Ensure that a Port label exists in a Compound. """
if port_name in compound.labels:
return True
else:
from mbuild.port import Port
available_ports = [name for name in compound.labels
if isinstance(compound.labels[name], Port)]
compound_name = compound.__class__.__name__
raise ValueError("No port named '{port_name}' in {compound_name}'s"
" labels. Labeled Ports in {compound_name} are:"
" {available_ports}".format(**locals())) | python | def assert_port_exists(port_name, compound):
if port_name in compound.labels:
return True
else:
from mbuild.port import Port
available_ports = [name for name in compound.labels
if isinstance(compound.labels[name], Port)]
compound_name = compound.__class__.__name__
raise ValueError("No port named '{port_name}' in {compound_name}'s"
" labels. Labeled Ports in {compound_name} are:"
" {available_ports}".format(**locals())) | [
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229,611 | mosdef-hub/mbuild | mbuild/lib/recipes/silica_interface.py | SilicaInterface._cleave_interface | def _cleave_interface(self, bulk_silica, tile_x, tile_y, thickness):
"""Carve interface from bulk silica.
Also includes a buffer of O's above and below the surface to ensure the
interface is coated.
"""
O_buffer = self._O_buffer
tile_z = int(math.ceil((thickness + 2*O_buffer) / bulk_silica.periodicity[2]))
bulk = mb.recipes.TiledCompound(bulk_silica, n_tiles=(tile_x, tile_y, tile_z))
interface = mb.Compound(periodicity=(bulk.periodicity[0],
bulk.periodicity[1],
0.0))
for i, particle in enumerate(bulk.particles()):
if ((particle.name == 'Si' and O_buffer < particle.pos[2] < (thickness + O_buffer)) or
(particle.name == 'O' and particle.pos[2] < (thickness + 2*O_buffer))):
interface_particle = mb.Compound(name=particle.name, pos=particle.pos)
interface.add(interface_particle, particle.name + "_{}".format(i))
self.add(interface) | python | def _cleave_interface(self, bulk_silica, tile_x, tile_y, thickness):
O_buffer = self._O_buffer
tile_z = int(math.ceil((thickness + 2*O_buffer) / bulk_silica.periodicity[2]))
bulk = mb.recipes.TiledCompound(bulk_silica, n_tiles=(tile_x, tile_y, tile_z))
interface = mb.Compound(periodicity=(bulk.periodicity[0],
bulk.periodicity[1],
0.0))
for i, particle in enumerate(bulk.particles()):
if ((particle.name == 'Si' and O_buffer < particle.pos[2] < (thickness + O_buffer)) or
(particle.name == 'O' and particle.pos[2] < (thickness + 2*O_buffer))):
interface_particle = mb.Compound(name=particle.name, pos=particle.pos)
interface.add(interface_particle, particle.name + "_{}".format(i))
self.add(interface) | [
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229,612 | mosdef-hub/mbuild | mbuild/lib/recipes/silica_interface.py | SilicaInterface._strip_stray_atoms | def _strip_stray_atoms(self):
"""Remove stray atoms and surface pieces. """
components = self.bond_graph.connected_components()
major_component = max(components, key=len)
for atom in list(self.particles()):
if atom not in major_component:
self.remove(atom) | python | def _strip_stray_atoms(self):
components = self.bond_graph.connected_components()
major_component = max(components, key=len)
for atom in list(self.particles()):
if atom not in major_component:
self.remove(atom) | [
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229,613 | mosdef-hub/mbuild | mbuild/lib/recipes/silica_interface.py | SilicaInterface._bridge_dangling_Os | def _bridge_dangling_Os(self, oh_density, thickness):
"""Form Si-O-Si bridges to yield desired density of reactive surface sites.
References
----------
.. [1] Hartkamp, R., Siboulet, B., Dufreche, J.-F., Boasne, B.
"Ion-specific adsorption and electroosmosis in charged
amorphous porous silica." (2015) Phys. Chem. Chem. Phys.
17, 24683-24695
"""
area = self.periodicity[0] * self.periodicity[1]
target = int(oh_density * area)
dangling_Os = [atom for atom in self.particles()
if atom.name == 'O' and
atom.pos[2] > thickness and
len(self.bond_graph.neighbors(atom)) == 1]
n_bridges = int((len(dangling_Os) - target) / 2)
for _ in range(n_bridges):
bridged = False
while not bridged:
O1 = random.choice(dangling_Os)
Si1 = self.bond_graph.neighbors(O1)[0]
for O2 in dangling_Os:
if O2 == O1:
continue
Si2 = self.bond_graph.neighbors(O2)[0]
if Si1 == Si2:
continue
if any(neigh in self.bond_graph.neighbors(Si2)
for neigh in self.bond_graph.neighbors(Si1)):
continue
r = self.min_periodic_distance(Si1.pos, Si2.pos)
if r < 0.45:
bridged = True
self.add_bond((O1, Si2))
dangling_Os.remove(O1)
dangling_Os.remove(O2)
self.remove(O2)
break | python | def _bridge_dangling_Os(self, oh_density, thickness):
area = self.periodicity[0] * self.periodicity[1]
target = int(oh_density * area)
dangling_Os = [atom for atom in self.particles()
if atom.name == 'O' and
atom.pos[2] > thickness and
len(self.bond_graph.neighbors(atom)) == 1]
n_bridges = int((len(dangling_Os) - target) / 2)
for _ in range(n_bridges):
bridged = False
while not bridged:
O1 = random.choice(dangling_Os)
Si1 = self.bond_graph.neighbors(O1)[0]
for O2 in dangling_Os:
if O2 == O1:
continue
Si2 = self.bond_graph.neighbors(O2)[0]
if Si1 == Si2:
continue
if any(neigh in self.bond_graph.neighbors(Si2)
for neigh in self.bond_graph.neighbors(Si1)):
continue
r = self.min_periodic_distance(Si1.pos, Si2.pos)
if r < 0.45:
bridged = True
self.add_bond((O1, Si2))
dangling_Os.remove(O1)
dangling_Os.remove(O2)
self.remove(O2)
break | [
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"Ion-specific adsorption and electroosmosis in charged
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229,614 | mosdef-hub/mbuild | mbuild/lib/recipes/silica_interface.py | SilicaInterface._identify_surface_sites | def _identify_surface_sites(self, thickness):
"""Label surface sites and add ports above them. """
for atom in self.particles():
if len(self.bond_graph.neighbors(atom)) == 1:
if atom.name == 'O' and atom.pos[2] > thickness:
atom.name = 'OS'
port = mb.Port(anchor=atom)
port.spin(np.pi/2, [1, 0, 0])
port.translate(np.array([0.0, 0.0, 0.1]))
self.add(port, "port_{}".format(len(self.referenced_ports()))) | python | def _identify_surface_sites(self, thickness):
for atom in self.particles():
if len(self.bond_graph.neighbors(atom)) == 1:
if atom.name == 'O' and atom.pos[2] > thickness:
atom.name = 'OS'
port = mb.Port(anchor=atom)
port.spin(np.pi/2, [1, 0, 0])
port.translate(np.array([0.0, 0.0, 0.1]))
self.add(port, "port_{}".format(len(self.referenced_ports()))) | [
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229,615 | mosdef-hub/mbuild | mbuild/packing.py | fill_region | def fill_region(compound, n_compounds, region, overlap=0.2,
seed=12345, edge=0.2, fix_orientation=False, temp_file=None):
"""Fill a region of a box with a compound using packmol.
Parameters
----------
compound : mb.Compound or list of mb.Compound
Compound or list of compounds to be put in region.
n_compounds : int or list of int
Number of compounds to be put in region.
region : mb.Box or list of mb.Box
Region to be filled by compounds.
overlap : float, units nm, default=0.2
Minimum separation between atoms of different molecules.
seed : int, default=12345
Random seed to be passed to PACKMOL.
edge : float, units nm, default=0.2
Buffer at the edge of the region to not place molecules. This is
necessary in some systems because PACKMOL does not account for
periodic boundary conditions in its optimization.
fix_orientation : bool or list of bools
Specify that compounds should not be rotated when filling the box,
default=False.
temp_file : str, default=None
File name to write PACKMOL's raw output to.
Returns
-------
filled : mb.Compound
If using mulitple regions and compounds, the nth value in each
list are used in order.
For example, if the third compound will be put in the third
region using the third value in n_compounds.
"""
_check_packmol(PACKMOL)
if not isinstance(compound, (list, set)):
compound = [compound]
if not isinstance(n_compounds, (list, set)):
n_compounds = [n_compounds]
if not isinstance(fix_orientation, (list, set)):
fix_orientation = [fix_orientation]*len(compound)
if compound is not None and n_compounds is not None:
if len(compound) != len(n_compounds):
msg = ("`compound` and `n_compounds` must be of equal length.")
raise ValueError(msg)
if compound is not None:
if len(compound) != len(fix_orientation):
msg = ("`compound`, `n_compounds`, and `fix_orientation` must be of equal length.")
raise ValueError(msg)
# See if region is a single region or list
if isinstance(region, Box): # Cannot iterate over boxes
region = [region]
elif not any(isinstance(reg, (list, set, Box)) for reg in region):
region = [region]
region = [_validate_box(reg) for reg in region]
# In angstroms for packmol.
overlap *= 10
# Build the input file and call packmol.
filled_xyz = _new_xyz_file()
# List to hold file handles for the temporary compounds
compound_xyz_list = list()
try:
input_text = PACKMOL_HEADER.format(overlap, filled_xyz.name, seed)
for comp, m_compounds, reg, rotate in zip(compound, n_compounds, region, fix_orientation):
m_compounds = int(m_compounds)
compound_xyz = _new_xyz_file()
compound_xyz_list.append(compound_xyz)
comp.save(compound_xyz.name, overwrite=True)
reg_mins = reg.mins * 10
reg_maxs = reg.maxs * 10
reg_maxs -= edge * 10 # Apply edge buffer
input_text += PACKMOL_BOX.format(compound_xyz.name, m_compounds,
reg_mins[0], reg_mins[1],
reg_mins[2], reg_maxs[0],
reg_maxs[1], reg_maxs[2],
PACKMOL_CONSTRAIN if rotate else "")
_run_packmol(input_text, filled_xyz, temp_file)
# Create the topology and update the coordinates.
filled = Compound()
filled = _create_topology(filled, compound, n_compounds)
filled.update_coordinates(filled_xyz.name)
finally:
for file_handle in compound_xyz_list:
file_handle.close()
os.unlink(file_handle.name)
filled_xyz.close()
os.unlink(filled_xyz.name)
return filled | python | def fill_region(compound, n_compounds, region, overlap=0.2,
seed=12345, edge=0.2, fix_orientation=False, temp_file=None):
_check_packmol(PACKMOL)
if not isinstance(compound, (list, set)):
compound = [compound]
if not isinstance(n_compounds, (list, set)):
n_compounds = [n_compounds]
if not isinstance(fix_orientation, (list, set)):
fix_orientation = [fix_orientation]*len(compound)
if compound is not None and n_compounds is not None:
if len(compound) != len(n_compounds):
msg = ("`compound` and `n_compounds` must be of equal length.")
raise ValueError(msg)
if compound is not None:
if len(compound) != len(fix_orientation):
msg = ("`compound`, `n_compounds`, and `fix_orientation` must be of equal length.")
raise ValueError(msg)
# See if region is a single region or list
if isinstance(region, Box): # Cannot iterate over boxes
region = [region]
elif not any(isinstance(reg, (list, set, Box)) for reg in region):
region = [region]
region = [_validate_box(reg) for reg in region]
# In angstroms for packmol.
overlap *= 10
# Build the input file and call packmol.
filled_xyz = _new_xyz_file()
# List to hold file handles for the temporary compounds
compound_xyz_list = list()
try:
input_text = PACKMOL_HEADER.format(overlap, filled_xyz.name, seed)
for comp, m_compounds, reg, rotate in zip(compound, n_compounds, region, fix_orientation):
m_compounds = int(m_compounds)
compound_xyz = _new_xyz_file()
compound_xyz_list.append(compound_xyz)
comp.save(compound_xyz.name, overwrite=True)
reg_mins = reg.mins * 10
reg_maxs = reg.maxs * 10
reg_maxs -= edge * 10 # Apply edge buffer
input_text += PACKMOL_BOX.format(compound_xyz.name, m_compounds,
reg_mins[0], reg_mins[1],
reg_mins[2], reg_maxs[0],
reg_maxs[1], reg_maxs[2],
PACKMOL_CONSTRAIN if rotate else "")
_run_packmol(input_text, filled_xyz, temp_file)
# Create the topology and update the coordinates.
filled = Compound()
filled = _create_topology(filled, compound, n_compounds)
filled.update_coordinates(filled_xyz.name)
finally:
for file_handle in compound_xyz_list:
file_handle.close()
os.unlink(file_handle.name)
filled_xyz.close()
os.unlink(filled_xyz.name)
return filled | [
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Parameters
----------
compound : mb.Compound or list of mb.Compound
Compound or list of compounds to be put in region.
n_compounds : int or list of int
Number of compounds to be put in region.
region : mb.Box or list of mb.Box
Region to be filled by compounds.
overlap : float, units nm, default=0.2
Minimum separation between atoms of different molecules.
seed : int, default=12345
Random seed to be passed to PACKMOL.
edge : float, units nm, default=0.2
Buffer at the edge of the region to not place molecules. This is
necessary in some systems because PACKMOL does not account for
periodic boundary conditions in its optimization.
fix_orientation : bool or list of bools
Specify that compounds should not be rotated when filling the box,
default=False.
temp_file : str, default=None
File name to write PACKMOL's raw output to.
Returns
-------
filled : mb.Compound
If using mulitple regions and compounds, the nth value in each
list are used in order.
For example, if the third compound will be put in the third
region using the third value in n_compounds. | [
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"."
] | dcb80a2becd5d0e6a7e3e7bcb1b59793c46a2dd3 | https://github.com/mosdef-hub/mbuild/blob/dcb80a2becd5d0e6a7e3e7bcb1b59793c46a2dd3/mbuild/packing.py#L220-L319 |
229,616 | mosdef-hub/mbuild | mbuild/packing.py | solvate | def solvate(solute, solvent, n_solvent, box, overlap=0.2,
seed=12345, edge=0.2, fix_orientation=False, temp_file=None):
"""Solvate a compound in a box of solvent using packmol.
Parameters
----------
solute : mb.Compound
Compound to be placed in a box and solvated.
solvent : mb.Compound
Compound to solvate the box.
n_solvent : int
Number of solvents to be put in box.
box : mb.Box
Box to be filled by compounds.
overlap : float, units nm, default=0.2
Minimum separation between atoms of different molecules.
seed : int, default=12345
Random seed to be passed to PACKMOL.
edge : float, units nm, default=0.2
Buffer at the edge of the box to not place molecules. This is necessary
in some systems because PACKMOL does not account for periodic boundary
conditions in its optimization.
fix_orientation : bool
Specify if solvent should not be rotated when filling box,
default=False.
temp_file : str, default=None
File name to write PACKMOL's raw output to.
Returns
-------
solvated : mb.Compound
"""
_check_packmol(PACKMOL)
box = _validate_box(box)
if not isinstance(solvent, (list, set)):
solvent = [solvent]
if not isinstance(n_solvent, (list, set)):
n_solvent = [n_solvent]
if not isinstance(fix_orientation, (list, set)):
fix_orientation = [fix_orientation] * len(solvent)
if len(solvent) != len(n_solvent):
msg = ("`n_solvent` and `n_solvent` must be of equal length.")
raise ValueError(msg)
# In angstroms for packmol.
box_mins = box.mins * 10
box_maxs = box.maxs * 10
overlap *= 10
center_solute = (box_maxs + box_mins) / 2
# Apply edge buffer
box_maxs -= edge * 10
# Build the input file for each compound and call packmol.
solvated_xyz = _new_xyz_file()
solute_xyz = _new_xyz_file()
# generate list of temp files for the solvents
solvent_xyz_list = list()
try:
solute.save(solute_xyz.name, overwrite=True)
input_text = (PACKMOL_HEADER.format(overlap, solvated_xyz.name, seed) +
PACKMOL_SOLUTE.format(solute_xyz.name, *center_solute))
for solv, m_solvent, rotate in zip(solvent, n_solvent, fix_orientation):
m_solvent = int(m_solvent)
solvent_xyz = _new_xyz_file()
solvent_xyz_list.append(solvent_xyz)
solv.save(solvent_xyz.name, overwrite=True)
input_text += PACKMOL_BOX.format(solvent_xyz.name, m_solvent,
box_mins[0], box_mins[1],
box_mins[2], box_maxs[0],
box_maxs[1], box_maxs[2],
PACKMOL_CONSTRAIN if rotate else "")
_run_packmol(input_text, solvated_xyz, temp_file)
# Create the topology and update the coordinates.
solvated = Compound()
solvated.add(solute)
solvated = _create_topology(solvated, solvent, n_solvent)
solvated.update_coordinates(solvated_xyz.name)
finally:
for file_handle in solvent_xyz_list:
file_handle.close()
os.unlink(file_handle.name)
solvated_xyz.close()
solute_xyz.close()
os.unlink(solvated_xyz.name)
os.unlink(solute_xyz.name)
return solvated | python | def solvate(solute, solvent, n_solvent, box, overlap=0.2,
seed=12345, edge=0.2, fix_orientation=False, temp_file=None):
_check_packmol(PACKMOL)
box = _validate_box(box)
if not isinstance(solvent, (list, set)):
solvent = [solvent]
if not isinstance(n_solvent, (list, set)):
n_solvent = [n_solvent]
if not isinstance(fix_orientation, (list, set)):
fix_orientation = [fix_orientation] * len(solvent)
if len(solvent) != len(n_solvent):
msg = ("`n_solvent` and `n_solvent` must be of equal length.")
raise ValueError(msg)
# In angstroms for packmol.
box_mins = box.mins * 10
box_maxs = box.maxs * 10
overlap *= 10
center_solute = (box_maxs + box_mins) / 2
# Apply edge buffer
box_maxs -= edge * 10
# Build the input file for each compound and call packmol.
solvated_xyz = _new_xyz_file()
solute_xyz = _new_xyz_file()
# generate list of temp files for the solvents
solvent_xyz_list = list()
try:
solute.save(solute_xyz.name, overwrite=True)
input_text = (PACKMOL_HEADER.format(overlap, solvated_xyz.name, seed) +
PACKMOL_SOLUTE.format(solute_xyz.name, *center_solute))
for solv, m_solvent, rotate in zip(solvent, n_solvent, fix_orientation):
m_solvent = int(m_solvent)
solvent_xyz = _new_xyz_file()
solvent_xyz_list.append(solvent_xyz)
solv.save(solvent_xyz.name, overwrite=True)
input_text += PACKMOL_BOX.format(solvent_xyz.name, m_solvent,
box_mins[0], box_mins[1],
box_mins[2], box_maxs[0],
box_maxs[1], box_maxs[2],
PACKMOL_CONSTRAIN if rotate else "")
_run_packmol(input_text, solvated_xyz, temp_file)
# Create the topology and update the coordinates.
solvated = Compound()
solvated.add(solute)
solvated = _create_topology(solvated, solvent, n_solvent)
solvated.update_coordinates(solvated_xyz.name)
finally:
for file_handle in solvent_xyz_list:
file_handle.close()
os.unlink(file_handle.name)
solvated_xyz.close()
solute_xyz.close()
os.unlink(solvated_xyz.name)
os.unlink(solute_xyz.name)
return solvated | [
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Parameters
----------
solute : mb.Compound
Compound to be placed in a box and solvated.
solvent : mb.Compound
Compound to solvate the box.
n_solvent : int
Number of solvents to be put in box.
box : mb.Box
Box to be filled by compounds.
overlap : float, units nm, default=0.2
Minimum separation between atoms of different molecules.
seed : int, default=12345
Random seed to be passed to PACKMOL.
edge : float, units nm, default=0.2
Buffer at the edge of the box to not place molecules. This is necessary
in some systems because PACKMOL does not account for periodic boundary
conditions in its optimization.
fix_orientation : bool
Specify if solvent should not be rotated when filling box,
default=False.
temp_file : str, default=None
File name to write PACKMOL's raw output to.
Returns
-------
solvated : mb.Compound | [
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] | dcb80a2becd5d0e6a7e3e7bcb1b59793c46a2dd3 | https://github.com/mosdef-hub/mbuild/blob/dcb80a2becd5d0e6a7e3e7bcb1b59793c46a2dd3/mbuild/packing.py#L472-L567 |
229,617 | mosdef-hub/mbuild | mbuild/packing.py | _create_topology | def _create_topology(container, comp_to_add, n_compounds):
"""Return updated mBuild compound with new coordinates.
Parameters
----------
container : mb.Compound, required
Compound containing the updated system generated by PACKMOL.
comp_to_add : mb.Compound or list of mb.Compounds, required
Compound(s) to add to the container.
container : int or list of int, required
Amount of comp_to_add to container.
Return
------
container : mb.Compound
Compound with added compounds from PACKMOL.
"""
for comp, m_compound in zip(comp_to_add, n_compounds):
for _ in range(m_compound):
container.add(clone(comp))
return container | python | def _create_topology(container, comp_to_add, n_compounds):
for comp, m_compound in zip(comp_to_add, n_compounds):
for _ in range(m_compound):
container.add(clone(comp))
return container | [
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Parameters
----------
container : mb.Compound, required
Compound containing the updated system generated by PACKMOL.
comp_to_add : mb.Compound or list of mb.Compounds, required
Compound(s) to add to the container.
container : int or list of int, required
Amount of comp_to_add to container.
Return
------
container : mb.Compound
Compound with added compounds from PACKMOL. | [
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] | dcb80a2becd5d0e6a7e3e7bcb1b59793c46a2dd3 | https://github.com/mosdef-hub/mbuild/blob/dcb80a2becd5d0e6a7e3e7bcb1b59793c46a2dd3/mbuild/packing.py#L596-L617 |
229,618 | mosdef-hub/mbuild | mbuild/formats/gsdwriter.py | _write_pair_information | def _write_pair_information(gsd_file, structure):
"""Write the special pairs in the system.
Parameters
----------
gsd_file :
The file object of the GSD file being written
structure : parmed.Structure
Parmed structure object holding system information
"""
pair_types = []
pair_typeid = []
pairs = []
for ai in structure.atoms:
for aj in ai.dihedral_partners:
#make sure we don't double add
if ai.idx > aj.idx:
ps = '-'.join(sorted([ai.type, aj.type], key=natural_sort))
if ps not in pair_types:
pair_types.append(ps)
pair_typeid.append(pair_types.index(ps))
pairs.append((ai.idx, aj.idx))
gsd_file.pairs.types = pair_types
gsd_file.pairs.typeid = pair_typeid
gsd_file.pairs.group = pairs
gsd_file.pairs.N = len(pairs) | python | def _write_pair_information(gsd_file, structure):
pair_types = []
pair_typeid = []
pairs = []
for ai in structure.atoms:
for aj in ai.dihedral_partners:
#make sure we don't double add
if ai.idx > aj.idx:
ps = '-'.join(sorted([ai.type, aj.type], key=natural_sort))
if ps not in pair_types:
pair_types.append(ps)
pair_typeid.append(pair_types.index(ps))
pairs.append((ai.idx, aj.idx))
gsd_file.pairs.types = pair_types
gsd_file.pairs.typeid = pair_typeid
gsd_file.pairs.group = pairs
gsd_file.pairs.N = len(pairs) | [
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"dihedral... | Write the special pairs in the system.
Parameters
----------
gsd_file :
The file object of the GSD file being written
structure : parmed.Structure
Parmed structure object holding system information | [
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] | dcb80a2becd5d0e6a7e3e7bcb1b59793c46a2dd3 | https://github.com/mosdef-hub/mbuild/blob/dcb80a2becd5d0e6a7e3e7bcb1b59793c46a2dd3/mbuild/formats/gsdwriter.py#L134-L159 |
229,619 | mosdef-hub/mbuild | mbuild/formats/gsdwriter.py | _write_dihedral_information | def _write_dihedral_information(gsd_file, structure):
"""Write the dihedrals in the system.
Parameters
----------
gsd_file :
The file object of the GSD file being written
structure : parmed.Structure
Parmed structure object holding system information
"""
gsd_file.dihedrals.N = len(structure.rb_torsions)
unique_dihedral_types = set()
for dihedral in structure.rb_torsions:
t1, t2 = dihedral.atom1.type, dihedral.atom2.type
t3, t4 = dihedral.atom3.type, dihedral.atom4.type
if [t2, t3] == sorted([t2, t3], key=natural_sort):
dihedral_type = ('-'.join((t1, t2, t3, t4)))
else:
dihedral_type = ('-'.join((t4, t3, t2, t1)))
unique_dihedral_types.add(dihedral_type)
unique_dihedral_types = sorted(list(unique_dihedral_types), key=natural_sort)
gsd_file.dihedrals.types = unique_dihedral_types
dihedral_typeids = []
dihedral_groups = []
for dihedral in structure.rb_torsions:
t1, t2 = dihedral.atom1.type, dihedral.atom2.type
t3, t4 = dihedral.atom3.type, dihedral.atom4.type
if [t2, t3] == sorted([t2, t3], key=natural_sort):
dihedral_type = ('-'.join((t1, t2, t3, t4)))
else:
dihedral_type = ('-'.join((t4, t3, t2, t1)))
dihedral_typeids.append(unique_dihedral_types.index(dihedral_type))
dihedral_groups.append((dihedral.atom1.idx, dihedral.atom2.idx,
dihedral.atom3.idx, dihedral.atom4.idx))
gsd_file.dihedrals.typeid = dihedral_typeids
gsd_file.dihedrals.group = dihedral_groups | python | def _write_dihedral_information(gsd_file, structure):
gsd_file.dihedrals.N = len(structure.rb_torsions)
unique_dihedral_types = set()
for dihedral in structure.rb_torsions:
t1, t2 = dihedral.atom1.type, dihedral.atom2.type
t3, t4 = dihedral.atom3.type, dihedral.atom4.type
if [t2, t3] == sorted([t2, t3], key=natural_sort):
dihedral_type = ('-'.join((t1, t2, t3, t4)))
else:
dihedral_type = ('-'.join((t4, t3, t2, t1)))
unique_dihedral_types.add(dihedral_type)
unique_dihedral_types = sorted(list(unique_dihedral_types), key=natural_sort)
gsd_file.dihedrals.types = unique_dihedral_types
dihedral_typeids = []
dihedral_groups = []
for dihedral in structure.rb_torsions:
t1, t2 = dihedral.atom1.type, dihedral.atom2.type
t3, t4 = dihedral.atom3.type, dihedral.atom4.type
if [t2, t3] == sorted([t2, t3], key=natural_sort):
dihedral_type = ('-'.join((t1, t2, t3, t4)))
else:
dihedral_type = ('-'.join((t4, t3, t2, t1)))
dihedral_typeids.append(unique_dihedral_types.index(dihedral_type))
dihedral_groups.append((dihedral.atom1.idx, dihedral.atom2.idx,
dihedral.atom3.idx, dihedral.atom4.idx))
gsd_file.dihedrals.typeid = dihedral_typeids
gsd_file.dihedrals.group = dihedral_groups | [
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Parameters
----------
gsd_file :
The file object of the GSD file being written
structure : parmed.Structure
Parmed structure object holding system information | [
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] | dcb80a2becd5d0e6a7e3e7bcb1b59793c46a2dd3 | https://github.com/mosdef-hub/mbuild/blob/dcb80a2becd5d0e6a7e3e7bcb1b59793c46a2dd3/mbuild/formats/gsdwriter.py#L242-L282 |
229,620 | mosdef-hub/mbuild | mbuild/utils/io.py | import_ | def import_(module):
"""Import a module, and issue a nice message to stderr if the module isn't installed.
Parameters
----------
module : str
The module you'd like to import, as a string
Returns
-------
module : {module, object}
The module object
Examples
--------
>>> # the following two lines are equivalent. the difference is that the
>>> # second will check for an ImportError and print you a very nice
>>> # user-facing message about what's wrong (where you can install the
>>> # module from, etc) if the import fails
>>> import tables
>>> tables = import_('tables')
"""
try:
return importlib.import_module(module)
except ImportError as e:
try:
message = MESSAGES[module]
except KeyError:
message = 'The code at {filename}:{line_number} requires the ' + module + ' package'
e = ImportError('No module named %s' % module)
frame, filename, line_number, function_name, lines, index = \
inspect.getouterframes(inspect.currentframe())[1]
m = message.format(filename=os.path.basename(filename), line_number=line_number)
m = textwrap.dedent(m)
bar = '\033[91m' + '#' * max(len(line) for line in m.split(os.linesep)) + '\033[0m'
print('', file=sys.stderr)
print(bar, file=sys.stderr)
print(m, file=sys.stderr)
print(bar, file=sys.stderr)
raise DelayImportError(m) | python | def import_(module):
try:
return importlib.import_module(module)
except ImportError as e:
try:
message = MESSAGES[module]
except KeyError:
message = 'The code at {filename}:{line_number} requires the ' + module + ' package'
e = ImportError('No module named %s' % module)
frame, filename, line_number, function_name, lines, index = \
inspect.getouterframes(inspect.currentframe())[1]
m = message.format(filename=os.path.basename(filename), line_number=line_number)
m = textwrap.dedent(m)
bar = '\033[91m' + '#' * max(len(line) for line in m.split(os.linesep)) + '\033[0m'
print('', file=sys.stderr)
print(bar, file=sys.stderr)
print(m, file=sys.stderr)
print(bar, file=sys.stderr)
raise DelayImportError(m) | [
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module : str
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Returns
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module : {module, object}
The module object
Examples
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>>> # the following two lines are equivalent. the difference is that the
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>>> # user-facing message about what's wrong (where you can install the
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>>> import tables
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229,621 | mosdef-hub/mbuild | mbuild/utils/io.py | get_fn | def get_fn(name):
"""Get the full path to one of the reference files shipped for utils.
In the source distribution, these files are in ``mbuild/utils/reference``,
but on installation, they're moved to somewhere in the user's python
site-packages directory.
Parameters
----------
name : str
Name of the file to load (with respect to the reference/ folder).
"""
fn = resource_filename('mbuild', os.path.join('utils', 'reference', name))
if not os.path.exists(fn):
raise IOError('Sorry! {} does not exists.'.format(fn))
return fn | python | def get_fn(name):
fn = resource_filename('mbuild', os.path.join('utils', 'reference', name))
if not os.path.exists(fn):
raise IOError('Sorry! {} does not exists.'.format(fn))
return fn | [
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229,622 | mosdef-hub/mbuild | mbuild/coordinate_transform.py | angle | def angle(u, v, w=None):
"""Returns the angle in radians between two vectors. """
if w is not None:
u = u - v
v = w - v
c = np.dot(u, v) / norm(u) / norm(v)
return np.arccos(np.clip(c, -1, 1)) | python | def angle(u, v, w=None):
if w is not None:
u = u - v
v = w - v
c = np.dot(u, v) / norm(u) / norm(v)
return np.arccos(np.clip(c, -1, 1)) | [
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229,623 | mosdef-hub/mbuild | mbuild/coordinate_transform.py | _create_equivalence_transform | def _create_equivalence_transform(equiv):
"""Compute an equivalence transformation that transforms this compound
to another compound's coordinate system.
Parameters
----------
equiv : np.ndarray, shape=(n, 3), dtype=float
Array of equivalent points.
Returns
-------
T : CoordinateTransform
Transform that maps this point cloud to the other point cloud's
coordinates system.
"""
from mbuild.compound import Compound
self_points = np.array([])
self_points.shape = (0, 3)
other_points = np.array([])
other_points.shape = (0, 3)
for pair in equiv:
if not isinstance(pair, tuple) or len(pair) != 2:
raise ValueError('Equivalence pair not a 2-tuple')
if not (isinstance(pair[0], Compound) and isinstance(pair[1], Compound)):
raise ValueError('Equivalence pair type mismatch: pair[0] is a {0} '
'and pair[1] is a {1}'.format(type(pair[0]),
type(pair[1])))
# TODO: vstack is slow, replace with list concatenation
if not pair[0].children:
self_points = np.vstack([self_points, pair[0].pos])
other_points = np.vstack([other_points, pair[1].pos])
else:
for atom0 in pair[0]._particles(include_ports=True):
self_points = np.vstack([self_points, atom0.pos])
for atom1 in pair[1]._particles(include_ports=True):
other_points = np.vstack([other_points, atom1.pos])
T = RigidTransform(self_points, other_points)
return T | python | def _create_equivalence_transform(equiv):
from mbuild.compound import Compound
self_points = np.array([])
self_points.shape = (0, 3)
other_points = np.array([])
other_points.shape = (0, 3)
for pair in equiv:
if not isinstance(pair, tuple) or len(pair) != 2:
raise ValueError('Equivalence pair not a 2-tuple')
if not (isinstance(pair[0], Compound) and isinstance(pair[1], Compound)):
raise ValueError('Equivalence pair type mismatch: pair[0] is a {0} '
'and pair[1] is a {1}'.format(type(pair[0]),
type(pair[1])))
# TODO: vstack is slow, replace with list concatenation
if not pair[0].children:
self_points = np.vstack([self_points, pair[0].pos])
other_points = np.vstack([other_points, pair[1].pos])
else:
for atom0 in pair[0]._particles(include_ports=True):
self_points = np.vstack([self_points, atom0.pos])
for atom1 in pair[1]._particles(include_ports=True):
other_points = np.vstack([other_points, atom1.pos])
T = RigidTransform(self_points, other_points)
return T | [
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Array of equivalent points.
Returns
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T : CoordinateTransform
Transform that maps this point cloud to the other point cloud's
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229,624 | mosdef-hub/mbuild | mbuild/coordinate_transform.py | _choose_correct_port | def _choose_correct_port(from_port, to_port):
"""Chooses the direction when using an equivalence transform on two Ports.
Each Port object actually contains 2 sets of 4 atoms, either of which can be
used to make a connection with an equivalence transform. This function
chooses the set of 4 atoms that makes the anchor atoms not overlap which is
the intended behavior for most use-cases.
TODO: -Increase robustness for cases where the anchors are a different
distance from their respective ports.
-Provide options in `force_overlap` to override this behavior.
Parameters
----------
from_port : mb.Port
to_port : mb.Port
Returns
-------
equivalence_pairs : tuple of Ports, shape=(2,)
Technically, a tuple of the Ports' sub-Compounds ('up' or 'down')
that are used to make the correct connection between components.
"""
# First we try matching the two 'up' ports.
T1 = _create_equivalence_transform([(from_port['up'], to_port['up'])])
new_position = T1.apply_to(np.array(from_port.anchor.pos, ndmin=2))
dist_between_anchors_up_up = norm(new_position[0] - to_port.anchor.pos)
# Then matching a 'down' with an 'up' port.
T2 = _create_equivalence_transform([(from_port['down'], to_port['up'])])
new_position = T2.apply_to(np.array(from_port.anchor.pos, ndmin=2))
# Determine which transform places the anchors further away from each other.
dist_between_anchors_down_up = norm(new_position[0] - to_port.anchor.pos)
difference_between_distances = dist_between_anchors_down_up - dist_between_anchors_up_up
if difference_between_distances > 0:
correct_port = from_port['down']
T = T2
else:
correct_port = from_port['up']
T = T1
return [(correct_port, to_port['up'])], T | python | def _choose_correct_port(from_port, to_port):
# First we try matching the two 'up' ports.
T1 = _create_equivalence_transform([(from_port['up'], to_port['up'])])
new_position = T1.apply_to(np.array(from_port.anchor.pos, ndmin=2))
dist_between_anchors_up_up = norm(new_position[0] - to_port.anchor.pos)
# Then matching a 'down' with an 'up' port.
T2 = _create_equivalence_transform([(from_port['down'], to_port['up'])])
new_position = T2.apply_to(np.array(from_port.anchor.pos, ndmin=2))
# Determine which transform places the anchors further away from each other.
dist_between_anchors_down_up = norm(new_position[0] - to_port.anchor.pos)
difference_between_distances = dist_between_anchors_down_up - dist_between_anchors_up_up
if difference_between_distances > 0:
correct_port = from_port['down']
T = T2
else:
correct_port = from_port['up']
T = T1
return [(correct_port, to_port['up'])], T | [
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TODO: -Increase robustness for cases where the anchors are a different
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-Provide options in `force_overlap` to override this behavior.
Parameters
----------
from_port : mb.Port
to_port : mb.Port
Returns
-------
equivalence_pairs : tuple of Ports, shape=(2,)
Technically, a tuple of the Ports' sub-Compounds ('up' or 'down')
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229,625 | mosdef-hub/mbuild | mbuild/coordinate_transform.py | translate | def translate(compound, pos):
"""Translate a compound by a vector.
Parameters
----------
compound : mb.Compound
The compound being translated.
pos : np.ndarray, shape=(3,), dtype=float
The vector to translate the compound by.
"""
atom_positions = compound.xyz_with_ports
atom_positions = Translation(pos).apply_to(atom_positions)
compound.xyz_with_ports = atom_positions | python | def translate(compound, pos):
atom_positions = compound.xyz_with_ports
atom_positions = Translation(pos).apply_to(atom_positions)
compound.xyz_with_ports = atom_positions | [
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The compound being translated.
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The vector to translate the compound by. | [
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229,626 | mosdef-hub/mbuild | mbuild/coordinate_transform.py | translate_to | def translate_to(compound, pos):
"""Translate a compound to a coordinate.
Parameters
----------
compound : mb.Compound
The compound being translated.
pos : np.ndarray, shape=(3,), dtype=float
The coordinate to translate the compound to.
"""
atom_positions = compound.xyz_with_ports
atom_positions -= compound.center
atom_positions = Translation(pos).apply_to(atom_positions)
compound.xyz_with_ports = atom_positions | python | def translate_to(compound, pos):
atom_positions = compound.xyz_with_ports
atom_positions -= compound.center
atom_positions = Translation(pos).apply_to(atom_positions)
compound.xyz_with_ports = atom_positions | [
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229,627 | mosdef-hub/mbuild | mbuild/coordinate_transform.py | _translate_to | def _translate_to(coordinates, to):
"""Translate a set of coordinates to a location.
Parameters
----------
coordinates : np.ndarray, shape=(n,3), dtype=float
The coordinates being translated.
to : np.ndarray, shape=(3,), dtype=float
The new average position of the coordinates.
"""
coordinates -= np.mean(coordinates, axis=0)
return Translation(to).apply_to(coordinates) | python | def _translate_to(coordinates, to):
coordinates -= np.mean(coordinates, axis=0)
return Translation(to).apply_to(coordinates) | [
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229,628 | mosdef-hub/mbuild | mbuild/coordinate_transform.py | _rotate | def _rotate(coordinates, theta, around):
"""Rotate a set of coordinates around an arbitrary vector.
Parameters
----------
coordinates : np.ndarray, shape=(n,3), dtype=float
The coordinates being rotated.
theta : float
The angle by which to rotate the coordinates, in radians.
around : np.ndarray, shape=(3,), dtype=float
The vector about which to rotate the coordinates.
"""
around = np.asarray(around).reshape(3)
if np.array_equal(around, np.zeros(3)):
raise ValueError('Cannot rotate around a zero vector')
return Rotation(theta, around).apply_to(coordinates) | python | def _rotate(coordinates, theta, around):
around = np.asarray(around).reshape(3)
if np.array_equal(around, np.zeros(3)):
raise ValueError('Cannot rotate around a zero vector')
return Rotation(theta, around).apply_to(coordinates) | [
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229,629 | mosdef-hub/mbuild | mbuild/coordinate_transform.py | rotate | def rotate(compound, theta, around):
"""Rotate a compound around an arbitrary vector.
Parameters
----------
compound : mb.Compound
The compound being rotated.
theta : float
The angle by which to rotate the compound, in radians.
around : np.ndarray, shape=(3,), dtype=float
The vector about which to rotate the compound.
"""
around = np.asarray(around).reshape(3)
if np.array_equal(around, np.zeros(3)):
raise ValueError('Cannot rotate around a zero vector')
atom_positions = compound.xyz_with_ports
atom_positions = Rotation(theta, around).apply_to(atom_positions)
compound.xyz_with_ports = atom_positions | python | def rotate(compound, theta, around):
around = np.asarray(around).reshape(3)
if np.array_equal(around, np.zeros(3)):
raise ValueError('Cannot rotate around a zero vector')
atom_positions = compound.xyz_with_ports
atom_positions = Rotation(theta, around).apply_to(atom_positions)
compound.xyz_with_ports = atom_positions | [
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229,630 | mosdef-hub/mbuild | mbuild/coordinate_transform.py | spin | def spin(compound, theta, around):
"""Rotate a compound in place around an arbitrary vector.
Parameters
----------
compound : mb.Compound
The compound being rotated.
theta : float
The angle by which to rotate the compound, in radians.
around : np.ndarray, shape=(3,), dtype=float
The axis about which to spin the compound.
"""
around = np.asarray(around).reshape(3)
if np.array_equal(around, np.zeros(3)):
raise ValueError('Cannot spin around a zero vector')
center_pos = compound.center
translate(compound, -center_pos)
rotate(compound, theta, around)
translate(compound, center_pos) | python | def spin(compound, theta, around):
around = np.asarray(around).reshape(3)
if np.array_equal(around, np.zeros(3)):
raise ValueError('Cannot spin around a zero vector')
center_pos = compound.center
translate(compound, -center_pos)
rotate(compound, theta, around)
translate(compound, center_pos) | [
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] | dcb80a2becd5d0e6a7e3e7bcb1b59793c46a2dd3 | https://github.com/mosdef-hub/mbuild/blob/dcb80a2becd5d0e6a7e3e7bcb1b59793c46a2dd3/mbuild/coordinate_transform.py#L555-L574 |
229,631 | mosdef-hub/mbuild | mbuild/coordinate_transform.py | _spin | def _spin(coordinates, theta, around):
"""Rotate a set of coordinates in place around an arbitrary vector.
Parameters
----------
coordinates : np.ndarray, shape=(n,3), dtype=float
The coordinates being spun.
theta : float
The angle by which to spin the coordinates, in radians.
around : np.ndarray, shape=(3,), dtype=float
The axis about which to spin the coordinates.
"""
around = np.asarray(around).reshape(3)
if np.array_equal(around, np.zeros(3)):
raise ValueError('Cannot spin around a zero vector')
center_pos = np.mean(coordinates, axis=0)
coordinates -= center_pos
coordinates = _rotate(coordinates, theta, around)
coordinates += center_pos
return coordinates | python | def _spin(coordinates, theta, around):
around = np.asarray(around).reshape(3)
if np.array_equal(around, np.zeros(3)):
raise ValueError('Cannot spin around a zero vector')
center_pos = np.mean(coordinates, axis=0)
coordinates -= center_pos
coordinates = _rotate(coordinates, theta, around)
coordinates += center_pos
return coordinates | [
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229,632 | mosdef-hub/mbuild | mbuild/coordinate_transform.py | x_axis_transform | def x_axis_transform(compound, new_origin=None,
point_on_x_axis=None,
point_on_xy_plane=None):
"""Move a compound such that the x-axis lies on specified points.
Parameters
----------
compound : mb.Compound
The compound to move.
new_origin : mb.Compound or list-like of size 3, optional, default=[0.0, 0.0, 0.0]
Where to place the new origin of the coordinate system.
point_on_x_axis : mb.Compound or list-like of size 3, optional, default=[1.0, 0.0, 0.0]
A point on the new x-axis.
point_on_xy_plane : mb.Compound, or list-like of size 3, optional, default=[1.0, 0.0, 0.0]
A point on the new xy-plane.
"""
import mbuild as mb
if new_origin is None:
new_origin = np.array([0, 0, 0])
elif isinstance(new_origin, mb.Compound):
new_origin = new_origin.pos
elif isinstance(new_origin, (tuple, list,np.ndarray)):
new_origin = np.asarray(new_origin)
else:
raise TypeError('x_axis_transform, y_axis_transform, and z_axis_transform only accept'
' mb.Compounds, list-like of length 3 or None for the new_origin'
' parameter. User passed type: {}.'.format(type(new_origin)))
if point_on_x_axis is None:
point_on_x_axis = np.array([1.0, 0.0, 0.0])
elif isinstance(point_on_x_axis, mb.Compound):
point_on_x_axis = point_on_x_axis.pos
elif isinstance(point_on_x_axis, (list, tuple, np.ndarray)):
point_on_x_axis = np.asarray(point_on_x_axis)
else:
raise TypeError('x_axis_transform, y_axis_transform, and z_axis_transform only accept'
' mb.Compounds, list-like of size 3, or None for the point_on_x_axis'
' parameter. User passed type: {}.'.format(type(point_on_x_axis)))
if point_on_xy_plane is None:
point_on_xy_plane = np.array([1.0, 1.0, 0.0])
elif isinstance(point_on_xy_plane, mb.Compound):
point_on_xy_plane = point_on_xy_plane.pos
elif isinstance(point_on_xy_plane, (list, tuple, np.ndarray)):
point_on_xy_plane = np.asarray(point_on_xy_plane)
else:
raise TypeError('x_axis_transform, y_axis_transform, and z_axis_transform only accept'
' mb.Compounds, list-like of size 3, or None for the point_on_xy_plane'
' parameter. User passed type: {}.'.format(type(point_on_xy_plane)))
atom_positions = compound.xyz_with_ports
transform = AxisTransform(new_origin=new_origin,
point_on_x_axis=point_on_x_axis,
point_on_xy_plane=point_on_xy_plane)
atom_positions = transform.apply_to(atom_positions)
compound.xyz_with_ports = atom_positions | python | def x_axis_transform(compound, new_origin=None,
point_on_x_axis=None,
point_on_xy_plane=None):
import mbuild as mb
if new_origin is None:
new_origin = np.array([0, 0, 0])
elif isinstance(new_origin, mb.Compound):
new_origin = new_origin.pos
elif isinstance(new_origin, (tuple, list,np.ndarray)):
new_origin = np.asarray(new_origin)
else:
raise TypeError('x_axis_transform, y_axis_transform, and z_axis_transform only accept'
' mb.Compounds, list-like of length 3 or None for the new_origin'
' parameter. User passed type: {}.'.format(type(new_origin)))
if point_on_x_axis is None:
point_on_x_axis = np.array([1.0, 0.0, 0.0])
elif isinstance(point_on_x_axis, mb.Compound):
point_on_x_axis = point_on_x_axis.pos
elif isinstance(point_on_x_axis, (list, tuple, np.ndarray)):
point_on_x_axis = np.asarray(point_on_x_axis)
else:
raise TypeError('x_axis_transform, y_axis_transform, and z_axis_transform only accept'
' mb.Compounds, list-like of size 3, or None for the point_on_x_axis'
' parameter. User passed type: {}.'.format(type(point_on_x_axis)))
if point_on_xy_plane is None:
point_on_xy_plane = np.array([1.0, 1.0, 0.0])
elif isinstance(point_on_xy_plane, mb.Compound):
point_on_xy_plane = point_on_xy_plane.pos
elif isinstance(point_on_xy_plane, (list, tuple, np.ndarray)):
point_on_xy_plane = np.asarray(point_on_xy_plane)
else:
raise TypeError('x_axis_transform, y_axis_transform, and z_axis_transform only accept'
' mb.Compounds, list-like of size 3, or None for the point_on_xy_plane'
' parameter. User passed type: {}.'.format(type(point_on_xy_plane)))
atom_positions = compound.xyz_with_ports
transform = AxisTransform(new_origin=new_origin,
point_on_x_axis=point_on_x_axis,
point_on_xy_plane=point_on_xy_plane)
atom_positions = transform.apply_to(atom_positions)
compound.xyz_with_ports = atom_positions | [
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The compound to move.
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Where to place the new origin of the coordinate system.
point_on_x_axis : mb.Compound or list-like of size 3, optional, default=[1.0, 0.0, 0.0]
A point on the new x-axis.
point_on_xy_plane : mb.Compound, or list-like of size 3, optional, default=[1.0, 0.0, 0.0]
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229,633 | mosdef-hub/mbuild | mbuild/coordinate_transform.py | y_axis_transform | def y_axis_transform(compound, new_origin=None,
point_on_y_axis=None,
point_on_xy_plane=None):
"""Move a compound such that the y-axis lies on specified points.
Parameters
----------
compound : mb.Compound
The compound to move.
new_origin : mb.Compound or like-like of size 3, optional, default=[0.0, 0.0, 0.0]
Where to place the new origin of the coordinate system.
point_on_y_axis : mb.Compound or list-like of size 3, optional, default=[0.0, 1.0, 0.0]
A point on the new y-axis.
point_on_xy_plane : mb.Compound or list-like of size 3, optional, default=[0.0, 1.0, 0.0]
A point on the new xy-plane.
"""
x_axis_transform(compound, new_origin=new_origin,
point_on_x_axis=point_on_y_axis,
point_on_xy_plane=point_on_xy_plane)
rotate_around_z(compound, np.pi / 2) | python | def y_axis_transform(compound, new_origin=None,
point_on_y_axis=None,
point_on_xy_plane=None):
x_axis_transform(compound, new_origin=new_origin,
point_on_x_axis=point_on_y_axis,
point_on_xy_plane=point_on_xy_plane)
rotate_around_z(compound, np.pi / 2) | [
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The compound to move.
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Where to place the new origin of the coordinate system.
point_on_y_axis : mb.Compound or list-like of size 3, optional, default=[0.0, 1.0, 0.0]
A point on the new y-axis.
point_on_xy_plane : mb.Compound or list-like of size 3, optional, default=[0.0, 1.0, 0.0]
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229,634 | mosdef-hub/mbuild | mbuild/coordinate_transform.py | z_axis_transform | def z_axis_transform(compound, new_origin=None,
point_on_z_axis=None,
point_on_zx_plane=None):
"""Move a compound such that the z-axis lies on specified points.
Parameters
----------
compound : mb.Compound
The compound to move.
new_origin : mb.Compound or list-like of size 3, optional, default=[0.0, 0.0, 0.0]
Where to place the new origin of the coordinate system.
point_on_z_axis : mb.Compound or list-like of size 3, optional, default=[0.0, 0.0, 1.0]
A point on the new z-axis.
point_on_zx_plane : mb.Compound or list-like of size 3, optional, default=[0.0, 0.0, 1.0]
A point on the new xz-plane.
"""
x_axis_transform(compound, new_origin=new_origin,
point_on_x_axis=point_on_z_axis,
point_on_xy_plane=point_on_zx_plane)
rotate_around_y(compound, np.pi * 3 / 2) | python | def z_axis_transform(compound, new_origin=None,
point_on_z_axis=None,
point_on_zx_plane=None):
x_axis_transform(compound, new_origin=new_origin,
point_on_x_axis=point_on_z_axis,
point_on_xy_plane=point_on_zx_plane)
rotate_around_y(compound, np.pi * 3 / 2) | [
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Where to place the new origin of the coordinate system.
point_on_z_axis : mb.Compound or list-like of size 3, optional, default=[0.0, 0.0, 1.0]
A point on the new z-axis.
point_on_zx_plane : mb.Compound or list-like of size 3, optional, default=[0.0, 0.0, 1.0]
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229,635 | mosdef-hub/mbuild | mbuild/coordinate_transform.py | CoordinateTransform.apply_to | def apply_to(self, A):
"""Apply the coordinate transformation to points in A. """
if A.ndim == 1:
A = np.expand_dims(A, axis=0)
rows, cols = A.shape
A_new = np.hstack([A, np.ones((rows, 1))])
A_new = np.transpose(self.T.dot(np.transpose(A_new)))
return A_new[:, 0:cols] | python | def apply_to(self, A):
if A.ndim == 1:
A = np.expand_dims(A, axis=0)
rows, cols = A.shape
A_new = np.hstack([A, np.ones((rows, 1))])
A_new = np.transpose(self.T.dot(np.transpose(A_new)))
return A_new[:, 0:cols] | [
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229,636 | mosdef-hub/mbuild | mbuild/lib/recipes/tiled_compound.py | TiledCompound._add_tile | def _add_tile(self, new_tile, ijk):
"""Add a tile with a label indicating its tiling position. """
tile_label = "{0}_{1}".format(self.name, '-'.join(str(d) for d in ijk))
self.add(new_tile, label=tile_label, inherit_periodicity=False) | python | def _add_tile(self, new_tile, ijk):
tile_label = "{0}_{1}".format(self.name, '-'.join(str(d) for d in ijk))
self.add(new_tile, label=tile_label, inherit_periodicity=False) | [
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229,637 | mosdef-hub/mbuild | mbuild/lib/recipes/tiled_compound.py | TiledCompound._find_particle_image | def _find_particle_image(self, query, match, all_particles):
"""Find particle with the same index as match in a neighboring tile. """
_, idxs = self.particle_kdtree.query(query.pos, k=10)
neighbors = all_particles[idxs]
for particle in neighbors:
if particle.index == match.index:
return particle
raise MBuildError('Unable to find matching particle image while'
' stitching bonds.') | python | def _find_particle_image(self, query, match, all_particles):
_, idxs = self.particle_kdtree.query(query.pos, k=10)
neighbors = all_particles[idxs]
for particle in neighbors:
if particle.index == match.index:
return particle
raise MBuildError('Unable to find matching particle image while'
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229,638 | mosdef-hub/mbuild | mbuild/utils/conversion.py | RB_to_OPLS | def RB_to_OPLS(c0, c1, c2, c3, c4, c5):
"""Converts Ryckaert-Bellemans type dihedrals to OPLS type.
Parameters
----------
c0, c1, c2, c3, c4, c5 : Ryckaert-Belleman coefficients (in kcal/mol)
Returns
-------
opls_coeffs : np.array, shape=(4,)
Array containing the OPLS dihedrals coeffs f1, f2, f3, and f4
(in kcal/mol)
"""
f1 = (-1.5 * c3) - (2 * c1)
f2 = c0 + c1 + c3
f3 = -0.5 * c3
f4 = -0.25 * c4
return np.array([f1, f2, f3, f4]) | python | def RB_to_OPLS(c0, c1, c2, c3, c4, c5):
f1 = (-1.5 * c3) - (2 * c1)
f2 = c0 + c1 + c3
f3 = -0.5 * c3
f4 = -0.25 * c4
return np.array([f1, f2, f3, f4]) | [
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c0, c1, c2, c3, c4, c5 : Ryckaert-Belleman coefficients (in kcal/mol)
Returns
-------
opls_coeffs : np.array, shape=(4,)
Array containing the OPLS dihedrals coeffs f1, f2, f3, and f4
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229,639 | mosdef-hub/mbuild | mbuild/formats/hoomdxml.py | write_hoomdxml | def write_hoomdxml(structure, filename, ref_distance=1.0, ref_mass=1.0,
ref_energy=1.0, rigid_bodies=None, shift_coords=True,
auto_scale=False):
"""Output a HOOMD XML file.
Parameters
----------
structure : parmed.Structure
ParmEd structure object
filename : str
Path of the output file.
ref_distance : float, optional, default=1.0, units=nanometers
Reference distance for conversion to reduced units
ref_mass : float, optional, default=1.0, units=amu
Reference mass for conversion to reduced units
ref_energy : float, optional, default=1.0, units=kJ/mol
Reference energy for conversion to reduced units
rigid_bodies : list
List of rigid body information. An integer value is required
for each particle corresponding to the number of the rigid body with
which the particle should be included. A value of None indicates the
particle is not part of any rigid body.
shift_coords : bool, optional, default=True
Shift coordinates from (0, L) to (-L/2, L/2) if necessary.
auto_scale : bool, optional, default=False
Automatically use largest sigma value as ref_distance, largest mass value
as ref_mass and largest epsilon value as ref_energy.
Returns
-------
ReferenceValues : namedtuple
Values used in scaling
Example
-------
ref_values = ethane.save(filename='ethane-opls.hoomdxml', forcefield_name='oplsaa', auto_scale=True)
print(ref_values.mass, ref_values.distance, ref_values.energy)
Notes
-----
The following elements are always written:
* **position** : particle positions
* **type** : particle types
* **mass** : particle masses (default 1.0)
* **charge** : particle charges
The following elements may be written if applicable:
* **pair_coeffs** : Pair coefficients for each particle type (assumes a 12-6 LJ pair style). The following information is written for each particle type:
* type : particle type
* epsilon : LJ epsilon
* sigma : LJ sigma
* **bond_coeffs** : Coefficients for each bond type (assumes a harmonic bond style). The following information is written for each bond type:
* type : bond type
* k : force constant (units of energy/distance^2)
* r0 : bond rest length (units of distance)
* **bond** : system bonds
* **angle_coeffs** : Coefficients for each angle type (assumes a harmonic angle style). The following information is written for each angle type:
* type : angle type
* k : force constant (units of energy/radians^2)
* theta : rest angle (units of radians)
* **angle** : system angles
* **dihedral_coeffs** : Coefficients for each dihedral type (assumes an OPLS dihedral style). The following information is written for each dihedral type:
* type : dihedral type
* k1, k2, k3, k4 : force coefficients (units of energy)
* **dihedral** : system dihedrals
* **body** : ID of the rigid body to which each particle belongs
"""
ref_distance *= 10 # Parmed unit hack
ref_energy /= 4.184 # Parmed unit hack
forcefield = True
if structure[0].type == '':
forcefield = False
if auto_scale and forcefield:
ref_mass = max([atom.mass for atom in structure.atoms])
pair_coeffs = list(set((atom.type,
atom.epsilon,
atom.sigma) for atom in structure.atoms))
ref_energy = max(pair_coeffs, key=operator.itemgetter(1))[1]
ref_distance = max(pair_coeffs, key=operator.itemgetter(2))[2]
xyz = np.array([[atom.xx, atom.xy, atom.xz] for atom in structure.atoms])
if shift_coords:
xyz = coord_shift(xyz, structure.box[:3])
with open(filename, 'w') as xml_file:
xml_file.write('<?xml version="1.2" encoding="UTF-8"?>\n')
xml_file.write('<hoomd_xml version="1.2">\n')
xml_file.write('<!-- ref_distance (nm) ref_mass (amu) ref_energy (kJ/mol) -->\n')
xml_file.write('<!-- {} {} {} -->\n'.format(ref_distance, ref_mass, ref_energy))
xml_file.write('<configuration time_step="0">\n')
_write_box_information(xml_file, structure, ref_distance)
_write_particle_information(xml_file, structure, xyz, forcefield,
ref_distance, ref_mass, ref_energy)
_write_bond_information(xml_file, structure, ref_distance, ref_energy)
_write_angle_information(xml_file, structure, ref_energy)
_write_dihedral_information(xml_file, structure, ref_energy)
_write_rigid_information(xml_file, rigid_bodies)
xml_file.write('</configuration>\n')
xml_file.write('</hoomd_xml>')
ReferenceValues = namedtuple("ref_values", ["distance", "mass", "energy"])
return ReferenceValues(ref_distance, ref_mass, ref_energy) | python | def write_hoomdxml(structure, filename, ref_distance=1.0, ref_mass=1.0,
ref_energy=1.0, rigid_bodies=None, shift_coords=True,
auto_scale=False):
ref_distance *= 10 # Parmed unit hack
ref_energy /= 4.184 # Parmed unit hack
forcefield = True
if structure[0].type == '':
forcefield = False
if auto_scale and forcefield:
ref_mass = max([atom.mass for atom in structure.atoms])
pair_coeffs = list(set((atom.type,
atom.epsilon,
atom.sigma) for atom in structure.atoms))
ref_energy = max(pair_coeffs, key=operator.itemgetter(1))[1]
ref_distance = max(pair_coeffs, key=operator.itemgetter(2))[2]
xyz = np.array([[atom.xx, atom.xy, atom.xz] for atom in structure.atoms])
if shift_coords:
xyz = coord_shift(xyz, structure.box[:3])
with open(filename, 'w') as xml_file:
xml_file.write('<?xml version="1.2" encoding="UTF-8"?>\n')
xml_file.write('<hoomd_xml version="1.2">\n')
xml_file.write('<!-- ref_distance (nm) ref_mass (amu) ref_energy (kJ/mol) -->\n')
xml_file.write('<!-- {} {} {} -->\n'.format(ref_distance, ref_mass, ref_energy))
xml_file.write('<configuration time_step="0">\n')
_write_box_information(xml_file, structure, ref_distance)
_write_particle_information(xml_file, structure, xyz, forcefield,
ref_distance, ref_mass, ref_energy)
_write_bond_information(xml_file, structure, ref_distance, ref_energy)
_write_angle_information(xml_file, structure, ref_energy)
_write_dihedral_information(xml_file, structure, ref_energy)
_write_rigid_information(xml_file, rigid_bodies)
xml_file.write('</configuration>\n')
xml_file.write('</hoomd_xml>')
ReferenceValues = namedtuple("ref_values", ["distance", "mass", "energy"])
return ReferenceValues(ref_distance, ref_mass, ref_energy) | [
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Parameters
----------
structure : parmed.Structure
ParmEd structure object
filename : str
Path of the output file.
ref_distance : float, optional, default=1.0, units=nanometers
Reference distance for conversion to reduced units
ref_mass : float, optional, default=1.0, units=amu
Reference mass for conversion to reduced units
ref_energy : float, optional, default=1.0, units=kJ/mol
Reference energy for conversion to reduced units
rigid_bodies : list
List of rigid body information. An integer value is required
for each particle corresponding to the number of the rigid body with
which the particle should be included. A value of None indicates the
particle is not part of any rigid body.
shift_coords : bool, optional, default=True
Shift coordinates from (0, L) to (-L/2, L/2) if necessary.
auto_scale : bool, optional, default=False
Automatically use largest sigma value as ref_distance, largest mass value
as ref_mass and largest epsilon value as ref_energy.
Returns
-------
ReferenceValues : namedtuple
Values used in scaling
Example
-------
ref_values = ethane.save(filename='ethane-opls.hoomdxml', forcefield_name='oplsaa', auto_scale=True)
print(ref_values.mass, ref_values.distance, ref_values.energy)
Notes
-----
The following elements are always written:
* **position** : particle positions
* **type** : particle types
* **mass** : particle masses (default 1.0)
* **charge** : particle charges
The following elements may be written if applicable:
* **pair_coeffs** : Pair coefficients for each particle type (assumes a 12-6 LJ pair style). The following information is written for each particle type:
* type : particle type
* epsilon : LJ epsilon
* sigma : LJ sigma
* **bond_coeffs** : Coefficients for each bond type (assumes a harmonic bond style). The following information is written for each bond type:
* type : bond type
* k : force constant (units of energy/distance^2)
* r0 : bond rest length (units of distance)
* **bond** : system bonds
* **angle_coeffs** : Coefficients for each angle type (assumes a harmonic angle style). The following information is written for each angle type:
* type : angle type
* k : force constant (units of energy/radians^2)
* theta : rest angle (units of radians)
* **angle** : system angles
* **dihedral_coeffs** : Coefficients for each dihedral type (assumes an OPLS dihedral style). The following information is written for each dihedral type:
* type : dihedral type
* k1, k2, k3, k4 : force coefficients (units of energy)
* **dihedral** : system dihedrals
* **body** : ID of the rigid body to which each particle belongs | [
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] | dcb80a2becd5d0e6a7e3e7bcb1b59793c46a2dd3 | https://github.com/mosdef-hub/mbuild/blob/dcb80a2becd5d0e6a7e3e7bcb1b59793c46a2dd3/mbuild/formats/hoomdxml.py#L16-L131 |
229,640 | mosdef-hub/mbuild | mbuild/formats/hoomdxml.py | _write_dihedral_information | def _write_dihedral_information(xml_file, structure, ref_energy):
"""Write dihedrals in the system.
Parameters
----------
xml_file : file object
The file object of the hoomdxml file being written
structure : parmed.Structure
Parmed structure object
ref_energy : float, default=1.0
Reference energy for conversion to reduced units
"""
unique_dihedral_types = set()
xml_file.write('<dihedral>\n')
for dihedral in structure.rb_torsions:
t1, t2 = dihedral.atom1.type, dihedral.atom2.type,
t3, t4 = dihedral.atom3.type, dihedral.atom4.type
if [t2, t3] == sorted([t2, t3]):
types_in_dihedral = '-'.join((t1, t2, t3, t4))
else:
types_in_dihedral = '-'.join((t4, t3, t2, t1))
dihedral_type = (types_in_dihedral, dihedral.type.c0,
dihedral.type.c1, dihedral.type.c2, dihedral.type.c3, dihedral.type.c4,
dihedral.type.c5, dihedral.type.scee, dihedral.type.scnb)
unique_dihedral_types.add(dihedral_type)
xml_file.write('{} {} {} {} {}\n'.format(
dihedral_type[0], dihedral.atom1.idx, dihedral.atom2.idx,
dihedral.atom3.idx, dihedral.atom4.idx))
xml_file.write('</dihedral>\n')
xml_file.write('<dihedral_coeffs>\n')
xml_file.write('<!-- type k1 k2 k3 k4 -->\n')
for dihedral_type, c0, c1, c2, c3, c4, c5, scee, scnb in unique_dihedral_types:
opls_coeffs = RB_to_OPLS(c0, c1, c2, c3, c4, c5)
opls_coeffs /= ref_energy
xml_file.write('{} {:.5f} {:.5f} {:.5f} {:.5f}\n'.format(
dihedral_type, *opls_coeffs))
xml_file.write('</dihedral_coeffs>\n') | python | def _write_dihedral_information(xml_file, structure, ref_energy):
unique_dihedral_types = set()
xml_file.write('<dihedral>\n')
for dihedral in structure.rb_torsions:
t1, t2 = dihedral.atom1.type, dihedral.atom2.type,
t3, t4 = dihedral.atom3.type, dihedral.atom4.type
if [t2, t3] == sorted([t2, t3]):
types_in_dihedral = '-'.join((t1, t2, t3, t4))
else:
types_in_dihedral = '-'.join((t4, t3, t2, t1))
dihedral_type = (types_in_dihedral, dihedral.type.c0,
dihedral.type.c1, dihedral.type.c2, dihedral.type.c3, dihedral.type.c4,
dihedral.type.c5, dihedral.type.scee, dihedral.type.scnb)
unique_dihedral_types.add(dihedral_type)
xml_file.write('{} {} {} {} {}\n'.format(
dihedral_type[0], dihedral.atom1.idx, dihedral.atom2.idx,
dihedral.atom3.idx, dihedral.atom4.idx))
xml_file.write('</dihedral>\n')
xml_file.write('<dihedral_coeffs>\n')
xml_file.write('<!-- type k1 k2 k3 k4 -->\n')
for dihedral_type, c0, c1, c2, c3, c4, c5, scee, scnb in unique_dihedral_types:
opls_coeffs = RB_to_OPLS(c0, c1, c2, c3, c4, c5)
opls_coeffs /= ref_energy
xml_file.write('{} {:.5f} {:.5f} {:.5f} {:.5f}\n'.format(
dihedral_type, *opls_coeffs))
xml_file.write('</dihedral_coeffs>\n') | [
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Parameters
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xml_file : file object
The file object of the hoomdxml file being written
structure : parmed.Structure
Parmed structure object
ref_energy : float, default=1.0
Reference energy for conversion to reduced units | [
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229,641 | mosdef-hub/mbuild | mbuild/formats/hoomdxml.py | _write_rigid_information | def _write_rigid_information(xml_file, rigid_bodies):
"""Write rigid body information.
Parameters
----------
xml_file : file object
The file object of the hoomdxml file being written
rigid_bodies : list, len=n_particles
The rigid body that each particle belongs to (-1 for none)
"""
if not all(body is None for body in rigid_bodies):
xml_file.write('<body>\n')
for body in rigid_bodies:
if body is None:
body = -1
xml_file.write('{}\n'.format(int(body)))
xml_file.write('</body>\n') | python | def _write_rigid_information(xml_file, rigid_bodies):
if not all(body is None for body in rigid_bodies):
xml_file.write('<body>\n')
for body in rigid_bodies:
if body is None:
body = -1
xml_file.write('{}\n'.format(int(body)))
xml_file.write('</body>\n') | [
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Parameters
----------
xml_file : file object
The file object of the hoomdxml file being written
rigid_bodies : list, len=n_particles
The rigid body that each particle belongs to (-1 for none) | [
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229,642 | mosdef-hub/mbuild | mbuild/formats/hoomdxml.py | _write_box_information | def _write_box_information(xml_file, structure, ref_distance):
"""Write box information.
Parameters
----------
xml_file : file object
The file object of the hoomdxml file being written
structure : parmed.Structure
Parmed structure object
ref_energy : float, default=1.0
Reference energy for conversion to reduced units
"""
if np.allclose(structure.box[3:6], np.array([90, 90, 90])):
box_str = '<box units="sigma" Lx="{}" Ly="{}" Lz="{}"/>\n'
xml_file.write(box_str.format(*structure.box[:3] / ref_distance))
else:
a, b, c = structure.box[0:3] / ref_distance
alpha, beta, gamma = np.radians(structure.box[3:6])
lx = a
xy = b * np.cos(gamma)
xz = c * np.cos(beta)
ly = np.sqrt(b**2 - xy**2)
yz = (b*c*np.cos(alpha) - xy*xz) / ly
lz = np.sqrt(c**2 - xz**2 - yz**2)
box_str = '<box units="sigma" Lx="{}" Ly="{}" Lz="{}" xy="{}" xz="{}" yz="{}"/>\n'
xml_file.write(box_str.format(lx, ly, lz, xy, xz, yz)) | python | def _write_box_information(xml_file, structure, ref_distance):
if np.allclose(structure.box[3:6], np.array([90, 90, 90])):
box_str = '<box units="sigma" Lx="{}" Ly="{}" Lz="{}"/>\n'
xml_file.write(box_str.format(*structure.box[:3] / ref_distance))
else:
a, b, c = structure.box[0:3] / ref_distance
alpha, beta, gamma = np.radians(structure.box[3:6])
lx = a
xy = b * np.cos(gamma)
xz = c * np.cos(beta)
ly = np.sqrt(b**2 - xy**2)
yz = (b*c*np.cos(alpha) - xy*xz) / ly
lz = np.sqrt(c**2 - xz**2 - yz**2)
box_str = '<box units="sigma" Lx="{}" Ly="{}" Lz="{}" xy="{}" xz="{}" yz="{}"/>\n'
xml_file.write(box_str.format(lx, ly, lz, xy, xz, yz)) | [
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Parameters
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xml_file : file object
The file object of the hoomdxml file being written
structure : parmed.Structure
Parmed structure object
ref_energy : float, default=1.0
Reference energy for conversion to reduced units | [
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229,643 | mosdef-hub/mbuild | mbuild/port.py | Port.access_labels | def access_labels(self):
"""List of labels used to access the Port
Returns
-------
list of str
Strings that can be used to access this Port relative to self.root
"""
access_labels = []
for referrer in self.referrers:
referrer_labels = [key for key, val in self.root.labels.items()
if val == referrer]
port_labels = [key for key, val in referrer.labels.items()
if val == self]
if referrer is self.root:
for label in port_labels:
access_labels.append("['{}']".format(label))
for label in itertools.product(referrer_labels, port_labels):
access_labels.append("['{}']".format("']['".join(label)))
return access_labels | python | def access_labels(self):
access_labels = []
for referrer in self.referrers:
referrer_labels = [key for key, val in self.root.labels.items()
if val == referrer]
port_labels = [key for key, val in referrer.labels.items()
if val == self]
if referrer is self.root:
for label in port_labels:
access_labels.append("['{}']".format(label))
for label in itertools.product(referrer_labels, port_labels):
access_labels.append("['{}']".format("']['".join(label)))
return access_labels | [
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Returns
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list of str
Strings that can be used to access this Port relative to self.root | [
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229,644 | GeospatialPython/pyshp | shapefile.py | signed_area | def signed_area(coords):
"""Return the signed area enclosed by a ring using the linear time
algorithm. A value >= 0 indicates a counter-clockwise oriented ring.
"""
xs, ys = map(list, zip(*coords))
xs.append(xs[1])
ys.append(ys[1])
return sum(xs[i]*(ys[i+1]-ys[i-1]) for i in range(1, len(coords)))/2.0 | python | def signed_area(coords):
xs, ys = map(list, zip(*coords))
xs.append(xs[1])
ys.append(ys[1])
return sum(xs[i]*(ys[i+1]-ys[i-1]) for i in range(1, len(coords)))/2.0 | [
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229,645 | GeospatialPython/pyshp | shapefile.py | Reader.load | def load(self, shapefile=None):
"""Opens a shapefile from a filename or file-like
object. Normally this method would be called by the
constructor with the file name as an argument."""
if shapefile:
(shapeName, ext) = os.path.splitext(shapefile)
self.shapeName = shapeName
self.load_shp(shapeName)
self.load_shx(shapeName)
self.load_dbf(shapeName)
if not (self.shp or self.dbf):
raise ShapefileException("Unable to open %s.dbf or %s.shp." % (shapeName, shapeName))
if self.shp:
self.__shpHeader()
if self.dbf:
self.__dbfHeader() | python | def load(self, shapefile=None):
if shapefile:
(shapeName, ext) = os.path.splitext(shapefile)
self.shapeName = shapeName
self.load_shp(shapeName)
self.load_shx(shapeName)
self.load_dbf(shapeName)
if not (self.shp or self.dbf):
raise ShapefileException("Unable to open %s.dbf or %s.shp." % (shapeName, shapeName))
if self.shp:
self.__shpHeader()
if self.dbf:
self.__dbfHeader() | [
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229,646 | GeospatialPython/pyshp | shapefile.py | Reader.load_shp | def load_shp(self, shapefile_name):
"""
Attempts to load file with .shp extension as both lower and upper case
"""
shp_ext = 'shp'
try:
self.shp = open("%s.%s" % (shapefile_name, shp_ext), "rb")
except IOError:
try:
self.shp = open("%s.%s" % (shapefile_name, shp_ext.upper()), "rb")
except IOError:
pass | python | def load_shp(self, shapefile_name):
shp_ext = 'shp'
try:
self.shp = open("%s.%s" % (shapefile_name, shp_ext), "rb")
except IOError:
try:
self.shp = open("%s.%s" % (shapefile_name, shp_ext.upper()), "rb")
except IOError:
pass | [
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229,647 | GeospatialPython/pyshp | shapefile.py | Reader.load_shx | def load_shx(self, shapefile_name):
"""
Attempts to load file with .shx extension as both lower and upper case
"""
shx_ext = 'shx'
try:
self.shx = open("%s.%s" % (shapefile_name, shx_ext), "rb")
except IOError:
try:
self.shx = open("%s.%s" % (shapefile_name, shx_ext.upper()), "rb")
except IOError:
pass | python | def load_shx(self, shapefile_name):
shx_ext = 'shx'
try:
self.shx = open("%s.%s" % (shapefile_name, shx_ext), "rb")
except IOError:
try:
self.shx = open("%s.%s" % (shapefile_name, shx_ext.upper()), "rb")
except IOError:
pass | [
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229,648 | GeospatialPython/pyshp | shapefile.py | Reader.load_dbf | def load_dbf(self, shapefile_name):
"""
Attempts to load file with .dbf extension as both lower and upper case
"""
dbf_ext = 'dbf'
try:
self.dbf = open("%s.%s" % (shapefile_name, dbf_ext), "rb")
except IOError:
try:
self.dbf = open("%s.%s" % (shapefile_name, dbf_ext.upper()), "rb")
except IOError:
pass | python | def load_dbf(self, shapefile_name):
dbf_ext = 'dbf'
try:
self.dbf = open("%s.%s" % (shapefile_name, dbf_ext), "rb")
except IOError:
try:
self.dbf = open("%s.%s" % (shapefile_name, dbf_ext.upper()), "rb")
except IOError:
pass | [
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229,649 | GeospatialPython/pyshp | shapefile.py | Reader.__getFileObj | def __getFileObj(self, f):
"""Checks to see if the requested shapefile file object is
available. If not a ShapefileException is raised."""
if not f:
raise ShapefileException("Shapefile Reader requires a shapefile or file-like object.")
if self.shp and self.shpLength is None:
self.load()
if self.dbf and len(self.fields) == 0:
self.load()
return f | python | def __getFileObj(self, f):
if not f:
raise ShapefileException("Shapefile Reader requires a shapefile or file-like object.")
if self.shp and self.shpLength is None:
self.load()
if self.dbf and len(self.fields) == 0:
self.load()
return f | [
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229,650 | GeospatialPython/pyshp | shapefile.py | Reader.__restrictIndex | def __restrictIndex(self, i):
"""Provides list-like handling of a record index with a clearer
error message if the index is out of bounds."""
if self.numRecords:
rmax = self.numRecords - 1
if abs(i) > rmax:
raise IndexError("Shape or Record index out of range.")
if i < 0: i = range(self.numRecords)[i]
return i | python | def __restrictIndex(self, i):
if self.numRecords:
rmax = self.numRecords - 1
if abs(i) > rmax:
raise IndexError("Shape or Record index out of range.")
if i < 0: i = range(self.numRecords)[i]
return i | [
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229,651 | GeospatialPython/pyshp | shapefile.py | Reader.iterShapes | def iterShapes(self):
"""Serves up shapes in a shapefile as an iterator. Useful
for handling large shapefiles."""
shp = self.__getFileObj(self.shp)
shp.seek(0,2)
self.shpLength = shp.tell()
shp.seek(100)
while shp.tell() < self.shpLength:
yield self.__shape() | python | def iterShapes(self):
shp = self.__getFileObj(self.shp)
shp.seek(0,2)
self.shpLength = shp.tell()
shp.seek(100)
while shp.tell() < self.shpLength:
yield self.__shape() | [
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229,652 | GeospatialPython/pyshp | shapefile.py | Reader.iterRecords | def iterRecords(self):
"""Serves up records in a dbf file as an iterator.
Useful for large shapefiles or dbf files."""
if self.numRecords is None:
self.__dbfHeader()
f = self.__getFileObj(self.dbf)
f.seek(self.__dbfHdrLength)
for i in xrange(self.numRecords):
r = self.__record()
if r:
yield r | python | def iterRecords(self):
if self.numRecords is None:
self.__dbfHeader()
f = self.__getFileObj(self.dbf)
f.seek(self.__dbfHdrLength)
for i in xrange(self.numRecords):
r = self.__record()
if r:
yield r | [
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229,653 | GeospatialPython/pyshp | shapefile.py | Writer.close | def close(self):
"""
Write final shp, shx, and dbf headers, close opened files.
"""
# Check if any of the files have already been closed
shp_open = self.shp and not (hasattr(self.shp, 'closed') and self.shp.closed)
shx_open = self.shx and not (hasattr(self.shx, 'closed') and self.shx.closed)
dbf_open = self.dbf and not (hasattr(self.dbf, 'closed') and self.dbf.closed)
# Balance if already not balanced
if self.shp and shp_open and self.dbf and dbf_open:
if self.autoBalance:
self.balance()
if self.recNum != self.shpNum:
raise ShapefileException("When saving both the dbf and shp file, "
"the number of records (%s) must correspond "
"with the number of shapes (%s)" % (self.recNum, self.shpNum))
# Fill in the blank headers
if self.shp and shp_open:
self.__shapefileHeader(self.shp, headerType='shp')
if self.shx and shx_open:
self.__shapefileHeader(self.shx, headerType='shx')
# Update the dbf header with final length etc
if self.dbf and dbf_open:
self.__dbfHeader()
# Close files, if target is a filepath
if self.target:
for attribute in (self.shp, self.shx, self.dbf):
if hasattr(attribute, 'close'):
try:
attribute.close()
except IOError:
pass | python | def close(self):
# Check if any of the files have already been closed
shp_open = self.shp and not (hasattr(self.shp, 'closed') and self.shp.closed)
shx_open = self.shx and not (hasattr(self.shx, 'closed') and self.shx.closed)
dbf_open = self.dbf and not (hasattr(self.dbf, 'closed') and self.dbf.closed)
# Balance if already not balanced
if self.shp and shp_open and self.dbf and dbf_open:
if self.autoBalance:
self.balance()
if self.recNum != self.shpNum:
raise ShapefileException("When saving both the dbf and shp file, "
"the number of records (%s) must correspond "
"with the number of shapes (%s)" % (self.recNum, self.shpNum))
# Fill in the blank headers
if self.shp and shp_open:
self.__shapefileHeader(self.shp, headerType='shp')
if self.shx and shx_open:
self.__shapefileHeader(self.shx, headerType='shx')
# Update the dbf header with final length etc
if self.dbf and dbf_open:
self.__dbfHeader()
# Close files, if target is a filepath
if self.target:
for attribute in (self.shp, self.shx, self.dbf):
if hasattr(attribute, 'close'):
try:
attribute.close()
except IOError:
pass | [
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229,654 | GeospatialPython/pyshp | shapefile.py | Writer.__getFileObj | def __getFileObj(self, f):
"""Safety handler to verify file-like objects"""
if not f:
raise ShapefileException("No file-like object available.")
elif hasattr(f, "write"):
return f
else:
pth = os.path.split(f)[0]
if pth and not os.path.exists(pth):
os.makedirs(pth)
return open(f, "wb+") | python | def __getFileObj(self, f):
if not f:
raise ShapefileException("No file-like object available.")
elif hasattr(f, "write"):
return f
else:
pth = os.path.split(f)[0]
if pth and not os.path.exists(pth):
os.makedirs(pth)
return open(f, "wb+") | [
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229,655 | GeospatialPython/pyshp | shapefile.py | Writer.balance | def balance(self):
"""Adds corresponding empty attributes or null geometry records depending
on which type of record was created to make sure all three files
are in synch."""
while self.recNum > self.shpNum:
self.null()
while self.recNum < self.shpNum:
self.record() | python | def balance(self):
while self.recNum > self.shpNum:
self.null()
while self.recNum < self.shpNum:
self.record() | [
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229,656 | GeospatialPython/pyshp | shapefile.py | Writer.point | def point(self, x, y):
"""Creates a POINT shape."""
shapeType = POINT
pointShape = Shape(shapeType)
pointShape.points.append([x, y])
self.shape(pointShape) | python | def point(self, x, y):
shapeType = POINT
pointShape = Shape(shapeType)
pointShape.points.append([x, y])
self.shape(pointShape) | [
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229,657 | GeospatialPython/pyshp | shapefile.py | Writer.multipoint | def multipoint(self, points):
"""Creates a MULTIPOINT shape.
Points is a list of xy values."""
shapeType = MULTIPOINT
points = [points] # nest the points inside a list to be compatible with the generic shapeparts method
self._shapeparts(parts=points, shapeType=shapeType) | python | def multipoint(self, points):
shapeType = MULTIPOINT
points = [points] # nest the points inside a list to be compatible with the generic shapeparts method
self._shapeparts(parts=points, shapeType=shapeType) | [
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229,658 | GeospatialPython/pyshp | shapefile.py | Writer.line | def line(self, lines):
"""Creates a POLYLINE shape.
Lines is a collection of lines, each made up of a list of xy values."""
shapeType = POLYLINE
self._shapeparts(parts=lines, shapeType=shapeType) | python | def line(self, lines):
shapeType = POLYLINE
self._shapeparts(parts=lines, shapeType=shapeType) | [
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229,659 | GeospatialPython/pyshp | shapefile.py | Writer.poly | def poly(self, polys):
"""Creates a POLYGON shape.
Polys is a collection of polygons, each made up of a list of xy values.
Note that for ordinary polygons the coordinates must run in a clockwise direction.
If some of the polygons are holes, these must run in a counterclockwise direction."""
shapeType = POLYGON
self._shapeparts(parts=polys, shapeType=shapeType) | python | def poly(self, polys):
shapeType = POLYGON
self._shapeparts(parts=polys, shapeType=shapeType) | [
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229,660 | jrmontag/STLDecompose | stldecompose/stl.py | forecast | def forecast(stl, fc_func, steps=10, seasonal=False, **fc_func_kwargs):
"""Forecast the given decomposition ``stl`` forward by ``steps`` steps using the forecasting
function ``fc_func``, optionally including the calculated seasonality.
This is an additive model, Y[t] = T[t] + S[t] + e[t]
Args:
stl (a modified statsmodels.tsa.seasonal.DecomposeResult): STL decomposition of observed time
series created using the ``stldecompose.decompose()`` method.
fc_func (function): Function which takes an array of observations and returns a single
valued forecast for the next point.
steps (int, optional): Number of forward steps to include in the forecast
seasonal (bool, optional): Include seasonal component in forecast
fc_func_kwargs: keyword arguments
All remaining arguments are passed to the forecasting function ``fc_func``
Returns:
forecast_frame (pd.Dataframe): A ``pandas.Dataframe`` containing forecast values and a
DatetimeIndex matching the observed index.
"""
# container for forecast values
forecast_array = np.array([])
# forecast trend
# unpack precalculated trend array stl frame
trend_array = stl.trend
# iteratively forecast trend ("seasonally adjusted") component
# note: this loop can be slow
for step in range(steps):
# make this prediction on all available data
pred = fc_func(np.append(trend_array, forecast_array), **fc_func_kwargs)
# add this prediction to current array
forecast_array = np.append(forecast_array, pred)
col_name = fc_func.__name__
# forecast start and index are determined by observed data
observed_timedelta = stl.observed.index[-1] - stl.observed.index[-2]
forecast_idx_start = stl.observed.index[-1] + observed_timedelta
forecast_idx = pd.date_range(start=forecast_idx_start,
periods=steps,
freq=pd.tseries.frequencies.to_offset(observed_timedelta))
# (optionally) forecast seasonal & combine
if seasonal:
# track index and value of max correlation
seasonal_ix = 0
max_correlation = -np.inf
# loop over indexes=length of period avgs
detrended_array = np.asanyarray(stl.observed - stl.trend).squeeze()
for i, x in enumerate(stl.period_averages):
# work slices backward from end of detrended observations
if i == 0:
# slicing w/ [x:-0] doesn't work
detrended_slice = detrended_array[-len(stl.period_averages):]
else:
detrended_slice = detrended_array[-(len(stl.period_averages) + i):-i]
# calculate corr b/w period_avgs and detrend_slice
this_correlation = np.correlate(detrended_slice, stl.period_averages)[0]
if this_correlation > max_correlation:
# update ix and max correlation
max_correlation = this_correlation
seasonal_ix = i
# roll seasonal signal to matching phase
rolled_period_averages = np.roll(stl.period_averages, -seasonal_ix)
# tile as many time as needed to reach "steps", then truncate
tiled_averages = np.tile(rolled_period_averages,
(steps // len(stl.period_averages) + 1))[:steps]
# add seasonal values to previous forecast
forecast_array += tiled_averages
col_name += '+seasonal'
# combine data array with index into named dataframe
forecast_frame = pd.DataFrame(data=forecast_array, index=forecast_idx)
forecast_frame.columns = [col_name]
return forecast_frame | python | def forecast(stl, fc_func, steps=10, seasonal=False, **fc_func_kwargs):
# container for forecast values
forecast_array = np.array([])
# forecast trend
# unpack precalculated trend array stl frame
trend_array = stl.trend
# iteratively forecast trend ("seasonally adjusted") component
# note: this loop can be slow
for step in range(steps):
# make this prediction on all available data
pred = fc_func(np.append(trend_array, forecast_array), **fc_func_kwargs)
# add this prediction to current array
forecast_array = np.append(forecast_array, pred)
col_name = fc_func.__name__
# forecast start and index are determined by observed data
observed_timedelta = stl.observed.index[-1] - stl.observed.index[-2]
forecast_idx_start = stl.observed.index[-1] + observed_timedelta
forecast_idx = pd.date_range(start=forecast_idx_start,
periods=steps,
freq=pd.tseries.frequencies.to_offset(observed_timedelta))
# (optionally) forecast seasonal & combine
if seasonal:
# track index and value of max correlation
seasonal_ix = 0
max_correlation = -np.inf
# loop over indexes=length of period avgs
detrended_array = np.asanyarray(stl.observed - stl.trend).squeeze()
for i, x in enumerate(stl.period_averages):
# work slices backward from end of detrended observations
if i == 0:
# slicing w/ [x:-0] doesn't work
detrended_slice = detrended_array[-len(stl.period_averages):]
else:
detrended_slice = detrended_array[-(len(stl.period_averages) + i):-i]
# calculate corr b/w period_avgs and detrend_slice
this_correlation = np.correlate(detrended_slice, stl.period_averages)[0]
if this_correlation > max_correlation:
# update ix and max correlation
max_correlation = this_correlation
seasonal_ix = i
# roll seasonal signal to matching phase
rolled_period_averages = np.roll(stl.period_averages, -seasonal_ix)
# tile as many time as needed to reach "steps", then truncate
tiled_averages = np.tile(rolled_period_averages,
(steps // len(stl.period_averages) + 1))[:steps]
# add seasonal values to previous forecast
forecast_array += tiled_averages
col_name += '+seasonal'
# combine data array with index into named dataframe
forecast_frame = pd.DataFrame(data=forecast_array, index=forecast_idx)
forecast_frame.columns = [col_name]
return forecast_frame | [
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Args:
stl (a modified statsmodels.tsa.seasonal.DecomposeResult): STL decomposition of observed time
series created using the ``stldecompose.decompose()`` method.
fc_func (function): Function which takes an array of observations and returns a single
valued forecast for the next point.
steps (int, optional): Number of forward steps to include in the forecast
seasonal (bool, optional): Include seasonal component in forecast
fc_func_kwargs: keyword arguments
All remaining arguments are passed to the forecasting function ``fc_func``
Returns:
forecast_frame (pd.Dataframe): A ``pandas.Dataframe`` containing forecast values and a
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229,661 | jrmontag/STLDecompose | stldecompose/forecast_funcs.py | mean | def mean(data, n=3, **kwargs):
"""The mean forecast for the next point is the mean value of the previous ``n`` points in
the series.
Args:
data (np.array): Observed data, presumed to be ordered in time.
n (int): period over which to calculate the mean
Returns:
float: a single-valued forecast for the next value in the series.
"""
# don't start averaging until we've seen n points
if len(data[-n:]) < n:
forecast = np.nan
else:
# nb: we'll keep the forecast as a float
forecast = np.mean(data[-n:])
return forecast | python | def mean(data, n=3, **kwargs):
# don't start averaging until we've seen n points
if len(data[-n:]) < n:
forecast = np.nan
else:
# nb: we'll keep the forecast as a float
forecast = np.mean(data[-n:])
return forecast | [
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229,662 | jrmontag/STLDecompose | stldecompose/forecast_funcs.py | drift | def drift(data, n=3, **kwargs):
"""The drift forecast for the next point is a linear extrapolation from the previous ``n``
points in the series.
Args:
data (np.array): Observed data, presumed to be ordered in time.
n (int): period over which to calculate linear model for extrapolation
Returns:
float: a single-valued forecast for the next value in the series.
"""
yi = data[-n]
yf = data[-1]
slope = (yf - yi) / (n - 1)
forecast = yf + slope
return forecast | python | def drift(data, n=3, **kwargs):
yi = data[-n]
yf = data[-1]
slope = (yf - yi) / (n - 1)
forecast = yf + slope
return forecast | [
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229,663 | soundcloud/soundcloud-python | soundcloud/client.py | Client.exchange_token | def exchange_token(self, code):
"""Given the value of the code parameter, request an access token."""
url = '%s%s/oauth2/token' % (self.scheme, self.host)
options = {
'grant_type': 'authorization_code',
'redirect_uri': self._redirect_uri(),
'client_id': self.options.get('client_id'),
'client_secret': self.options.get('client_secret'),
'code': code,
}
options.update({
'verify_ssl': self.options.get('verify_ssl', True),
'proxies': self.options.get('proxies', None)
})
self.token = wrapped_resource(
make_request('post', url, options))
self.access_token = self.token.access_token
return self.token | python | def exchange_token(self, code):
url = '%s%s/oauth2/token' % (self.scheme, self.host)
options = {
'grant_type': 'authorization_code',
'redirect_uri': self._redirect_uri(),
'client_id': self.options.get('client_id'),
'client_secret': self.options.get('client_secret'),
'code': code,
}
options.update({
'verify_ssl': self.options.get('verify_ssl', True),
'proxies': self.options.get('proxies', None)
})
self.token = wrapped_resource(
make_request('post', url, options))
self.access_token = self.token.access_token
return self.token | [
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229,664 | soundcloud/soundcloud-python | soundcloud/client.py | Client._authorization_code_flow | def _authorization_code_flow(self):
"""Build the the auth URL so the user can authorize the app."""
options = {
'scope': getattr(self, 'scope', 'non-expiring'),
'client_id': self.options.get('client_id'),
'response_type': 'code',
'redirect_uri': self._redirect_uri()
}
url = '%s%s/connect' % (self.scheme, self.host)
self._authorize_url = '%s?%s' % (url, urlencode(options)) | python | def _authorization_code_flow(self):
options = {
'scope': getattr(self, 'scope', 'non-expiring'),
'client_id': self.options.get('client_id'),
'response_type': 'code',
'redirect_uri': self._redirect_uri()
}
url = '%s%s/connect' % (self.scheme, self.host)
self._authorize_url = '%s?%s' % (url, urlencode(options)) | [
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229,665 | soundcloud/soundcloud-python | soundcloud/client.py | Client._refresh_token_flow | def _refresh_token_flow(self):
"""Given a refresh token, obtain a new access token."""
url = '%s%s/oauth2/token' % (self.scheme, self.host)
options = {
'grant_type': 'refresh_token',
'client_id': self.options.get('client_id'),
'client_secret': self.options.get('client_secret'),
'refresh_token': self.options.get('refresh_token')
}
options.update({
'verify_ssl': self.options.get('verify_ssl', True),
'proxies': self.options.get('proxies', None)
})
self.token = wrapped_resource(
make_request('post', url, options))
self.access_token = self.token.access_token | python | def _refresh_token_flow(self):
url = '%s%s/oauth2/token' % (self.scheme, self.host)
options = {
'grant_type': 'refresh_token',
'client_id': self.options.get('client_id'),
'client_secret': self.options.get('client_secret'),
'refresh_token': self.options.get('refresh_token')
}
options.update({
'verify_ssl': self.options.get('verify_ssl', True),
'proxies': self.options.get('proxies', None)
})
self.token = wrapped_resource(
make_request('post', url, options))
self.access_token = self.token.access_token | [
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229,666 | soundcloud/soundcloud-python | soundcloud/client.py | Client._request | def _request(self, method, resource, **kwargs):
"""Given an HTTP method, a resource name and kwargs, construct a
request and return the response.
"""
url = self._resolve_resource_name(resource)
if hasattr(self, 'access_token'):
kwargs.update(dict(oauth_token=self.access_token))
if hasattr(self, 'client_id'):
kwargs.update(dict(client_id=self.client_id))
kwargs.update({
'verify_ssl': self.options.get('verify_ssl', True),
'proxies': self.options.get('proxies', None)
})
return wrapped_resource(make_request(method, url, kwargs)) | python | def _request(self, method, resource, **kwargs):
url = self._resolve_resource_name(resource)
if hasattr(self, 'access_token'):
kwargs.update(dict(oauth_token=self.access_token))
if hasattr(self, 'client_id'):
kwargs.update(dict(client_id=self.client_id))
kwargs.update({
'verify_ssl': self.options.get('verify_ssl', True),
'proxies': self.options.get('proxies', None)
})
return wrapped_resource(make_request(method, url, kwargs)) | [
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229,667 | soundcloud/soundcloud-python | soundcloud/request.py | extract_files_from_dict | def extract_files_from_dict(d):
"""Return any file objects from the provided dict.
>>> extract_files_from_dict({
... 'oauth_token': 'foo',
... 'track': {
... 'title': 'bar',
... 'asset_data': open('setup.py', 'rb')
... }}) # doctest:+ELLIPSIS
{'track': {'asset_data': <...}}
"""
files = {}
for key, value in six.iteritems(d):
if isinstance(value, dict):
files[key] = extract_files_from_dict(value)
elif is_file_like(value):
files[key] = value
return files | python | def extract_files_from_dict(d):
files = {}
for key, value in six.iteritems(d):
if isinstance(value, dict):
files[key] = extract_files_from_dict(value)
elif is_file_like(value):
files[key] = value
return files | [
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229,668 | soundcloud/soundcloud-python | soundcloud/request.py | remove_files_from_dict | def remove_files_from_dict(d):
"""Return the provided dict with any file objects removed.
>>> remove_files_from_dict({
... 'oauth_token': 'foo',
... 'track': {
... 'title': 'bar',
... 'asset_data': open('setup.py', 'rb')
... }
... }) == {'track': {'title': 'bar'}, 'oauth_token': 'foo'}
... # doctest:+ELLIPSIS
True
"""
file_free = {}
for key, value in six.iteritems(d):
if isinstance(value, dict):
file_free[key] = remove_files_from_dict(value)
elif not is_file_like(value):
if hasattr(value, '__iter__'):
file_free[key] = value
else:
if hasattr(value, 'encode'):
file_free[key] = value.encode('utf-8')
else:
file_free[key] = str(value)
return file_free | python | def remove_files_from_dict(d):
file_free = {}
for key, value in six.iteritems(d):
if isinstance(value, dict):
file_free[key] = remove_files_from_dict(value)
elif not is_file_like(value):
if hasattr(value, '__iter__'):
file_free[key] = value
else:
if hasattr(value, 'encode'):
file_free[key] = value.encode('utf-8')
else:
file_free[key] = str(value)
return file_free | [
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... 'oauth_token': 'foo',
... 'track': {
... 'title': 'bar',
... 'asset_data': open('setup.py', 'rb')
... }
... }) == {'track': {'title': 'bar'}, 'oauth_token': 'foo'}
... # doctest:+ELLIPSIS
True | [
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229,669 | soundcloud/soundcloud-python | soundcloud/request.py | namespaced_query_string | def namespaced_query_string(d, prefix=""):
"""Transform a nested dict into a string with namespaced query params.
>>> namespaced_query_string({
... 'oauth_token': 'foo',
... 'track': {'title': 'bar', 'sharing': 'private'}}) == {
... 'track[sharing]': 'private',
... 'oauth_token': 'foo',
... 'track[title]': 'bar'} # doctest:+ELLIPSIS
True
"""
qs = {}
prefixed = lambda k: prefix and "%s[%s]" % (prefix, k) or k
for key, value in six.iteritems(d):
if isinstance(value, dict):
qs.update(namespaced_query_string(value, prefix=key))
else:
qs[prefixed(key)] = value
return qs | python | def namespaced_query_string(d, prefix=""):
qs = {}
prefixed = lambda k: prefix and "%s[%s]" % (prefix, k) or k
for key, value in six.iteritems(d):
if isinstance(value, dict):
qs.update(namespaced_query_string(value, prefix=key))
else:
qs[prefixed(key)] = value
return qs | [
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... 'track[sharing]': 'private',
... 'oauth_token': 'foo',
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229,670 | soundcloud/soundcloud-python | soundcloud/request.py | make_request | def make_request(method, url, params):
"""Make an HTTP request, formatting params as required."""
empty = []
# TODO
# del params[key]
# without list
for key, value in six.iteritems(params):
if value is None:
empty.append(key)
for key in empty:
del params[key]
# allow caller to disable automatic following of redirects
allow_redirects = params.get('allow_redirects', True)
kwargs = {
'allow_redirects': allow_redirects,
'headers': {
'User-Agent': soundcloud.USER_AGENT
}
}
# options, not params
if 'verify_ssl' in params:
if params['verify_ssl'] is False:
kwargs['verify'] = params['verify_ssl']
del params['verify_ssl']
if 'proxies' in params:
kwargs['proxies'] = params['proxies']
del params['proxies']
if 'allow_redirects' in params:
del params['allow_redirects']
params = hashconversions.to_params(params)
files = namespaced_query_string(extract_files_from_dict(params))
data = namespaced_query_string(remove_files_from_dict(params))
request_func = getattr(requests, method, None)
if request_func is None:
raise TypeError('Unknown method: %s' % (method,))
if method == 'get':
kwargs['headers']['Accept'] = 'application/json'
qs = urlencode(data)
if '?' in url:
url_qs = '%s&%s' % (url, qs)
else:
url_qs = '%s?%s' % (url, qs)
result = request_func(url_qs, **kwargs)
else:
kwargs['data'] = data
if files:
kwargs['files'] = files
result = request_func(url, **kwargs)
# if redirects are disabled, don't raise for 301 / 302
if result.status_code in (301, 302):
if allow_redirects:
result.raise_for_status()
else:
result.raise_for_status()
return result | python | def make_request(method, url, params):
empty = []
# TODO
# del params[key]
# without list
for key, value in six.iteritems(params):
if value is None:
empty.append(key)
for key in empty:
del params[key]
# allow caller to disable automatic following of redirects
allow_redirects = params.get('allow_redirects', True)
kwargs = {
'allow_redirects': allow_redirects,
'headers': {
'User-Agent': soundcloud.USER_AGENT
}
}
# options, not params
if 'verify_ssl' in params:
if params['verify_ssl'] is False:
kwargs['verify'] = params['verify_ssl']
del params['verify_ssl']
if 'proxies' in params:
kwargs['proxies'] = params['proxies']
del params['proxies']
if 'allow_redirects' in params:
del params['allow_redirects']
params = hashconversions.to_params(params)
files = namespaced_query_string(extract_files_from_dict(params))
data = namespaced_query_string(remove_files_from_dict(params))
request_func = getattr(requests, method, None)
if request_func is None:
raise TypeError('Unknown method: %s' % (method,))
if method == 'get':
kwargs['headers']['Accept'] = 'application/json'
qs = urlencode(data)
if '?' in url:
url_qs = '%s&%s' % (url, qs)
else:
url_qs = '%s?%s' % (url, qs)
result = request_func(url_qs, **kwargs)
else:
kwargs['data'] = data
if files:
kwargs['files'] = files
result = request_func(url, **kwargs)
# if redirects are disabled, don't raise for 301 / 302
if result.status_code in (301, 302):
if allow_redirects:
result.raise_for_status()
else:
result.raise_for_status()
return result | [
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229,671 | soundcloud/soundcloud-python | soundcloud/resource.py | wrapped_resource | def wrapped_resource(response):
"""Return a response wrapped in the appropriate wrapper type.
Lists will be returned as a ```ResourceList``` instance,
dicts will be returned as a ```Resource``` instance.
"""
# decode response text, assuming utf-8 if unset
response_content = response.content.decode(response.encoding or 'utf-8')
try:
content = json.loads(response_content)
except ValueError:
# not JSON
content = response_content
if isinstance(content, list):
result = ResourceList(content)
else:
result = Resource(content)
if hasattr(result, 'collection'):
result.collection = ResourceList(result.collection)
result.raw_data = response_content
for attr in ('encoding', 'url', 'status_code', 'reason'):
setattr(result, attr, getattr(response, attr))
return result | python | def wrapped_resource(response):
# decode response text, assuming utf-8 if unset
response_content = response.content.decode(response.encoding or 'utf-8')
try:
content = json.loads(response_content)
except ValueError:
# not JSON
content = response_content
if isinstance(content, list):
result = ResourceList(content)
else:
result = Resource(content)
if hasattr(result, 'collection'):
result.collection = ResourceList(result.collection)
result.raw_data = response_content
for attr in ('encoding', 'url', 'status_code', 'reason'):
setattr(result, attr, getattr(response, attr))
return result | [
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229,672 | soundcloud/soundcloud-python | soundcloud/hashconversions.py | normalize_param | def normalize_param(key, value):
"""Convert a set of key, value parameters into a dictionary suitable for
passing into requests. This will convert lists into the syntax required
by SoundCloud. Heavily lifted from HTTParty.
>>> normalize_param('playlist', {
... 'title': 'foo',
... 'sharing': 'private',
... 'tracks': [
... {id: 1234}, {id: 4567}
... ]}) == {
... u'playlist[tracks][][<built-in function id>]': [1234, 4567],
... u'playlist[sharing]': 'private',
... u'playlist[title]': 'foo'} # doctest:+ELLIPSIS
True
>>> normalize_param('oauth_token', 'foo')
{'oauth_token': 'foo'}
>>> normalize_param('playlist[tracks]', [1234, 4567]) == {
... u'playlist[tracks][]': [1234, 4567]}
True
"""
params = {}
stack = []
if isinstance(value, list):
normalized = [normalize_param(u"{0[key]}[]".format(dict(key=key)), e) for e in value]
keys = [item for sublist in tuple(h.keys() for h in normalized) for item in sublist]
lists = {}
if len(keys) != len(set(keys)):
duplicates = [x for x, y in collections.Counter(keys).items() if y > 1]
for dup in duplicates:
lists[dup] = [h[dup] for h in normalized]
for h in normalized:
del h[dup]
params.update(dict((k, v) for d in normalized for (k, v) in d.items()))
params.update(lists)
elif isinstance(value, dict):
stack.append([key, value])
else:
params.update({key: value})
for (parent, hash) in stack:
for (key, value) in six.iteritems(hash):
if isinstance(value, dict):
stack.append([u"{0[parent]}[{0[key]}]".format(dict(parent=parent, key=key)), value])
else:
params.update(normalize_param(u"{0[parent]}[{0[key]}]".format(dict(parent=parent, key=key)), value))
return params | python | def normalize_param(key, value):
params = {}
stack = []
if isinstance(value, list):
normalized = [normalize_param(u"{0[key]}[]".format(dict(key=key)), e) for e in value]
keys = [item for sublist in tuple(h.keys() for h in normalized) for item in sublist]
lists = {}
if len(keys) != len(set(keys)):
duplicates = [x for x, y in collections.Counter(keys).items() if y > 1]
for dup in duplicates:
lists[dup] = [h[dup] for h in normalized]
for h in normalized:
del h[dup]
params.update(dict((k, v) for d in normalized for (k, v) in d.items()))
params.update(lists)
elif isinstance(value, dict):
stack.append([key, value])
else:
params.update({key: value})
for (parent, hash) in stack:
for (key, value) in six.iteritems(hash):
if isinstance(value, dict):
stack.append([u"{0[parent]}[{0[key]}]".format(dict(parent=parent, key=key)), value])
else:
params.update(normalize_param(u"{0[parent]}[{0[key]}]".format(dict(parent=parent, key=key)), value))
return params | [
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... {id: 1234}, {id: 4567}
... ]}) == {
... u'playlist[tracks][][<built-in function id>]': [1234, 4567],
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>>> normalize_param('oauth_token', 'foo')
{'oauth_token': 'foo'}
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... u'playlist[tracks][]': [1234, 4567]}
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229,673 | psd-tools/psd-tools | src/psd_tools/api/smart_object.py | SmartObject.open | def open(self, external_dir=None):
"""
Open the smart object as binary IO.
:param external_dir: Path to the directory of the external file.
Example::
with layer.smart_object.open() as f:
data = f.read()
"""
if self.kind == 'data':
with io.BytesIO(self._data.data) as f:
yield f
elif self.kind == 'external':
filepath = self._data.linked_file[b'fullPath'].value
filepath = filepath.replace('\x00', '').replace('file://', '')
if not os.path.exists(filepath):
filepath = self._data.linked_file[b'relPath'].value
filepath = filepath.replace('\x00', '')
if external_dir is not None:
filepath = os.path.join(external_dir, filepath)
if not os.path.exists(filepath):
raise FileNotFoundError(filepath)
with open(filepath, 'rb') as f:
yield f
else:
raise NotImplementedError('alias is not supported.') | python | def open(self, external_dir=None):
if self.kind == 'data':
with io.BytesIO(self._data.data) as f:
yield f
elif self.kind == 'external':
filepath = self._data.linked_file[b'fullPath'].value
filepath = filepath.replace('\x00', '').replace('file://', '')
if not os.path.exists(filepath):
filepath = self._data.linked_file[b'relPath'].value
filepath = filepath.replace('\x00', '')
if external_dir is not None:
filepath = os.path.join(external_dir, filepath)
if not os.path.exists(filepath):
raise FileNotFoundError(filepath)
with open(filepath, 'rb') as f:
yield f
else:
raise NotImplementedError('alias is not supported.') | [
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229,674 | psd-tools/psd-tools | src/psd_tools/api/smart_object.py | SmartObject.data | def data(self):
"""Embedded file content, or empty if kind is `external` or `alias`"""
if self.kind == 'data':
return self._data.data
else:
with self.open() as f:
return f.read() | python | def data(self):
if self.kind == 'data':
return self._data.data
else:
with self.open() as f:
return f.read() | [
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229,675 | psd-tools/psd-tools | src/psd_tools/api/smart_object.py | SmartObject.filesize | def filesize(self):
"""File size of the object."""
if self.kind == 'data':
return len(self._data.data)
return self._data.filesize | python | def filesize(self):
if self.kind == 'data':
return len(self._data.data)
return self._data.filesize | [
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229,676 | psd-tools/psd-tools | src/psd_tools/api/smart_object.py | SmartObject.save | def save(self, filename=None):
"""
Save the smart object to a file.
:param filename: File name to export. If None, use the embedded name.
"""
if filename is None:
filename = self.filename
with open(filename, 'wb') as f:
f.write(self.data) | python | def save(self, filename=None):
if filename is None:
filename = self.filename
with open(filename, 'wb') as f:
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229,677 | psd-tools/psd-tools | src/psd_tools/psd/base.py | BaseElement._traverse | def _traverse(element, condition=None):
"""
Traversal API intended for debugging.
"""
if condition is None or condition(element):
yield element
if isinstance(element, DictElement):
for child in element.values():
for _ in BaseElement._traverse(child, condition):
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elif isinstance(element, ListElement):
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yield _
elif attr.has(element.__class__):
for field in attr.fields(element.__class__):
child = getattr(element, field.name)
for _ in BaseElement._traverse(child, condition):
yield _ | python | def _traverse(element, condition=None):
if condition is None or condition(element):
yield element
if isinstance(element, DictElement):
for child in element.values():
for _ in BaseElement._traverse(child, condition):
yield _
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for _ in BaseElement._traverse(child, condition):
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229,678 | psd-tools/psd-tools | src/psd_tools/psd/descriptor.py | read_length_and_key | def read_length_and_key(fp):
"""
Helper to read descriptor key.
"""
length = read_fmt('I', fp)[0]
key = fp.read(length or 4)
if length == 0 and key not in _TERMS:
logger.debug('Unknown term: %r' % (key))
_TERMS.add(key)
return key | python | def read_length_and_key(fp):
length = read_fmt('I', fp)[0]
key = fp.read(length or 4)
if length == 0 and key not in _TERMS:
logger.debug('Unknown term: %r' % (key))
_TERMS.add(key)
return key | [
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229,679 | psd-tools/psd-tools | src/psd_tools/psd/descriptor.py | write_length_and_key | def write_length_and_key(fp, value):
"""
Helper to write descriptor key.
"""
written = write_fmt(fp, 'I', 0 if value in _TERMS else len(value))
written += write_bytes(fp, value)
return written | python | def write_length_and_key(fp, value):
written = write_fmt(fp, 'I', 0 if value in _TERMS else len(value))
written += write_bytes(fp, value)
return written | [
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229,680 | psd-tools/psd-tools | src/psd_tools/__main__.py | main | def main(argv=None):
"""
psd-tools command line utility.
Usage:
psd-tools export <input_file> <output_file> [options]
psd-tools show <input_file> [options]
psd-tools debug <input_file> [options]
psd-tools -h | --help
psd-tools --version
Options:
-v --verbose Be more verbose.
Example:
psd-tools show example.psd # Show the file content
psd-tools export example.psd example.png # Export as PNG
psd-tools export example.psd[0] example-0.png # Export layer as PNG
"""
args = docopt.docopt(main.__doc__, version=__version__, argv=argv)
if args['--verbose']:
logger.setLevel(logging.DEBUG)
else:
logger.setLevel(logging.INFO)
if args['export']:
input_parts = args['<input_file>'].split('[')
input_file = input_parts[0]
if len(input_parts) > 1:
indices = [int(x.rstrip(']')) for x in input_parts[1:]]
else:
indices = []
layer = PSDImage.open(input_file)
for index in indices:
layer = layer[index]
if isinstance(layer, PSDImage) and layer.has_preview():
image = layer.topil()
else:
image = layer.compose()
image.save(args['<output_file>'])
elif args['show']:
psd = PSDImage.open(args['<input_file>'])
pprint(psd)
elif args['debug']:
psd = PSDImage.open(args['<input_file>'])
pprint(psd._record) | python | def main(argv=None):
args = docopt.docopt(main.__doc__, version=__version__, argv=argv)
if args['--verbose']:
logger.setLevel(logging.DEBUG)
else:
logger.setLevel(logging.INFO)
if args['export']:
input_parts = args['<input_file>'].split('[')
input_file = input_parts[0]
if len(input_parts) > 1:
indices = [int(x.rstrip(']')) for x in input_parts[1:]]
else:
indices = []
layer = PSDImage.open(input_file)
for index in indices:
layer = layer[index]
if isinstance(layer, PSDImage) and layer.has_preview():
image = layer.topil()
else:
image = layer.compose()
image.save(args['<output_file>'])
elif args['show']:
psd = PSDImage.open(args['<input_file>'])
pprint(psd)
elif args['debug']:
psd = PSDImage.open(args['<input_file>'])
pprint(psd._record) | [
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Usage:
psd-tools export <input_file> <output_file> [options]
psd-tools show <input_file> [options]
psd-tools debug <input_file> [options]
psd-tools -h | --help
psd-tools --version
Options:
-v --verbose Be more verbose.
Example:
psd-tools show example.psd # Show the file content
psd-tools export example.psd example.png # Export as PNG
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229,681 | psd-tools/psd-tools | src/psd_tools/api/psd_image.py | PSDImage.new | def new(cls, mode, size, color=0, depth=8, **kwargs):
"""
Create a new PSD document.
:param mode: The color mode to use for the new image.
:param size: A tuple containing (width, height) in pixels.
:param color: What color to use for the image. Default is black.
:return: A :py:class:`~psd_tools.api.psd_image.PSDImage` object.
"""
header = cls._make_header(mode, size, depth)
image_data = ImageData.new(header, color=color, **kwargs)
# TODO: Add default metadata.
return cls(PSD(
header=header,
image_data=image_data,
image_resources=ImageResources.new(),
)) | python | def new(cls, mode, size, color=0, depth=8, **kwargs):
header = cls._make_header(mode, size, depth)
image_data = ImageData.new(header, color=color, **kwargs)
# TODO: Add default metadata.
return cls(PSD(
header=header,
image_data=image_data,
image_resources=ImageResources.new(),
)) | [
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229,682 | psd-tools/psd-tools | src/psd_tools/api/psd_image.py | PSDImage.frompil | def frompil(cls, image, compression=Compression.PACK_BITS):
"""
Create a new PSD document from PIL Image.
:param image: PIL Image object.
:param compression: ImageData compression option. See
:py:class:`~psd_tools.constants.Compression`.
:return: A :py:class:`~psd_tools.api.psd_image.PSDImage` object.
"""
header = cls._make_header(image.mode, image.size)
# TODO: Add default metadata.
# TODO: Perhaps make this smart object.
image_data = ImageData(compression=compression)
image_data.set_data([channel.tobytes() for channel in image.split()],
header)
return cls(PSD(
header=header,
image_data=image_data,
image_resources=ImageResources.new(),
)) | python | def frompil(cls, image, compression=Compression.PACK_BITS):
header = cls._make_header(image.mode, image.size)
# TODO: Add default metadata.
# TODO: Perhaps make this smart object.
image_data = ImageData(compression=compression)
image_data.set_data([channel.tobytes() for channel in image.split()],
header)
return cls(PSD(
header=header,
image_data=image_data,
image_resources=ImageResources.new(),
)) | [
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229,683 | psd-tools/psd-tools | src/psd_tools/api/psd_image.py | PSDImage.open | def open(cls, fp):
"""
Open a PSD document.
:param fp: filename or file-like object.
:return: A :py:class:`~psd_tools.api.psd_image.PSDImage` object.
"""
if hasattr(fp, 'read'):
self = cls(PSD.read(fp))
else:
with open(fp, 'rb') as f:
self = cls(PSD.read(f))
return self | python | def open(cls, fp):
if hasattr(fp, 'read'):
self = cls(PSD.read(fp))
else:
with open(fp, 'rb') as f:
self = cls(PSD.read(f))
return self | [
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:param fp: filename or file-like object.
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229,684 | psd-tools/psd-tools | src/psd_tools/api/psd_image.py | PSDImage.save | def save(self, fp, mode='wb'):
"""
Save the PSD file.
:param fp: filename or file-like object.
:param mode: file open mode, default 'wb'.
"""
if hasattr(fp, 'write'):
self._record.write(fp)
else:
with open(fp, mode) as f:
self._record.write(f) | python | def save(self, fp, mode='wb'):
if hasattr(fp, 'write'):
self._record.write(fp)
else:
with open(fp, mode) as f:
self._record.write(f) | [
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229,685 | psd-tools/psd-tools | src/psd_tools/api/psd_image.py | PSDImage.topil | def topil(self, **kwargs):
"""
Get PIL Image.
:return: :py:class:`PIL.Image`, or `None` if the composed image is not
available.
"""
if self.has_preview():
return pil_io.convert_image_data_to_pil(self._record, **kwargs)
return None | python | def topil(self, **kwargs):
if self.has_preview():
return pil_io.convert_image_data_to_pil(self._record, **kwargs)
return None | [
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:return: :py:class:`PIL.Image`, or `None` if the composed image is not
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] | 4952b57bcf1cf2c1f16fd9d6d51d4fa0b53bce4e | https://github.com/psd-tools/psd-tools/blob/4952b57bcf1cf2c1f16fd9d6d51d4fa0b53bce4e/src/psd_tools/api/psd_image.py#L117-L126 |
229,686 | psd-tools/psd-tools | src/psd_tools/api/psd_image.py | PSDImage.compose | def compose(self, force=False, bbox=None, **kwargs):
"""
Compose the PSD image.
See :py:func:`~psd_tools.compose` for available extra arguments.
:param bbox: Viewport tuple (left, top, right, bottom).
:return: :py:class:`PIL.Image`, or `None` if there is no pixel.
"""
from psd_tools.api.composer import compose
image = None
if not force or len(self) == 0:
image = self.topil(**kwargs)
if image is None:
image = compose(
self, bbox=bbox or self.viewbox, force=force, **kwargs
)
return image | python | def compose(self, force=False, bbox=None, **kwargs):
from psd_tools.api.composer import compose
image = None
if not force or len(self) == 0:
image = self.topil(**kwargs)
if image is None:
image = compose(
self, bbox=bbox or self.viewbox, force=force, **kwargs
)
return image | [
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:param bbox: Viewport tuple (left, top, right, bottom).
:return: :py:class:`PIL.Image`, or `None` if there is no pixel. | [
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229,687 | psd-tools/psd-tools | src/psd_tools/api/psd_image.py | PSDImage.bbox | def bbox(self):
"""
Minimal bounding box that contains all the visible layers.
Use :py:attr:`~psd_tools.api.psd_image.PSDImage.viewbox` to get
viewport bounding box. When the psd is empty, bbox is equal to the
canvas bounding box.
:return: (left, top, right, bottom) `tuple`.
"""
bbox = super(PSDImage, self).bbox
if bbox == (0, 0, 0, 0):
bbox = self.viewbox
return bbox | python | def bbox(self):
bbox = super(PSDImage, self).bbox
if bbox == (0, 0, 0, 0):
bbox = self.viewbox
return bbox | [
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canvas bounding box.
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229,688 | psd-tools/psd-tools | src/psd_tools/api/psd_image.py | PSDImage.viewbox | def viewbox(self):
"""
Return bounding box of the viewport.
:return: (left, top, right, bottom) `tuple`.
"""
return self.left, self.top, self.right, self.bottom | python | def viewbox(self):
return self.left, self.top, self.right, self.bottom | [
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229,689 | psd-tools/psd-tools | src/psd_tools/api/psd_image.py | PSDImage.thumbnail | def thumbnail(self):
"""
Returns a thumbnail image in PIL.Image. When the file does not
contain an embedded thumbnail image, returns None.
"""
if 'THUMBNAIL_RESOURCE' in self.image_resources:
return pil_io.convert_thumbnail_to_pil(
self.image_resources.get_data('THUMBNAIL_RESOURCE')
)
elif 'THUMBNAIL_RESOURCE_PS4' in self.image_resources:
return pil_io.convert_thumbnail_to_pil(
self.image_resources.get_data('THUMBNAIL_RESOURCE_PS4'), 'BGR'
)
return None | python | def thumbnail(self):
if 'THUMBNAIL_RESOURCE' in self.image_resources:
return pil_io.convert_thumbnail_to_pil(
self.image_resources.get_data('THUMBNAIL_RESOURCE')
)
elif 'THUMBNAIL_RESOURCE_PS4' in self.image_resources:
return pil_io.convert_thumbnail_to_pil(
self.image_resources.get_data('THUMBNAIL_RESOURCE_PS4'), 'BGR'
)
return None | [
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229,690 | psd-tools/psd-tools | src/psd_tools/api/psd_image.py | PSDImage._get_pattern | def _get_pattern(self, pattern_id):
"""Get pattern item by id."""
for key in ('PATTERNS1', 'PATTERNS2', 'PATTERNS3'):
if key in self.tagged_blocks:
data = self.tagged_blocks.get_data(key)
for pattern in data:
if pattern.pattern_id == pattern_id:
return pattern
return None | python | def _get_pattern(self, pattern_id):
for key in ('PATTERNS1', 'PATTERNS2', 'PATTERNS3'):
if key in self.tagged_blocks:
data = self.tagged_blocks.get_data(key)
for pattern in data:
if pattern.pattern_id == pattern_id:
return pattern
return None | [
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".... | Get pattern item by id. | [
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] | 4952b57bcf1cf2c1f16fd9d6d51d4fa0b53bce4e | https://github.com/psd-tools/psd-tools/blob/4952b57bcf1cf2c1f16fd9d6d51d4fa0b53bce4e/src/psd_tools/api/psd_image.py#L442-L450 |
229,691 | psd-tools/psd-tools | src/psd_tools/api/psd_image.py | PSDImage._init | def _init(self):
"""Initialize layer structure."""
group_stack = [self]
clip_stack = []
last_layer = None
for record, channels in self._record._iter_layers():
current_group = group_stack[-1]
blocks = record.tagged_blocks
end_of_group = False
divider = blocks.get_data('SECTION_DIVIDER_SETTING', None)
divider = blocks.get_data('NESTED_SECTION_DIVIDER_SETTING',
divider)
if divider is not None:
if divider.kind == SectionDivider.BOUNDING_SECTION_DIVIDER:
layer = Group(self, None, None, current_group)
group_stack.append(layer)
elif divider.kind in (SectionDivider.OPEN_FOLDER,
SectionDivider.CLOSED_FOLDER):
layer = group_stack.pop()
assert layer is not self
layer._record = record
layer._channels = channels
for key in (
'ARTBOARD_DATA1', 'ARTBOARD_DATA2', 'ARTBOARD_DATA3'
):
if key in blocks:
layer = Artboard._move(layer)
end_of_group = True
elif (
'TYPE_TOOL_OBJECT_SETTING' in blocks or
'TYPE_TOOL_INFO' in blocks
):
layer = TypeLayer(self, record, channels, current_group)
elif (
record.flags.pixel_data_irrelevant and (
'VECTOR_ORIGINATION_DATA' in blocks or
'VECTOR_MASK_SETTING1' in blocks or
'VECTOR_MASK_SETTING2' in blocks or
'VECTOR_STROKE_DATA' in blocks or
'VECTOR_STROKE_CONTENT_DATA' in blocks
)
):
layer = ShapeLayer(self, record, channels, current_group)
elif (
'SMART_OBJECT_LAYER_DATA1' in blocks or
'SMART_OBJECT_LAYER_DATA2' in blocks or
'PLACED_LAYER1' in blocks or
'PLACED_LAYER2' in blocks
):
layer = SmartObjectLayer(self, record, channels,
current_group)
else:
layer = None
for key in adjustments.TYPES.keys():
if key in blocks:
layer = adjustments.TYPES[key](
self, record, channels, current_group
)
break
# If nothing applies, this is a pixel layer.
if layer is None:
layer = PixelLayer(
self, record, channels, current_group
)
if record.clipping == Clipping.NON_BASE:
clip_stack.append(layer)
else:
if clip_stack:
last_layer._clip_layers = clip_stack
clip_stack = []
if not end_of_group:
current_group._layers.append(layer)
last_layer = layer
if clip_stack and last_layer:
last_layer._clip_layers = clip_stack | python | def _init(self):
group_stack = [self]
clip_stack = []
last_layer = None
for record, channels in self._record._iter_layers():
current_group = group_stack[-1]
blocks = record.tagged_blocks
end_of_group = False
divider = blocks.get_data('SECTION_DIVIDER_SETTING', None)
divider = blocks.get_data('NESTED_SECTION_DIVIDER_SETTING',
divider)
if divider is not None:
if divider.kind == SectionDivider.BOUNDING_SECTION_DIVIDER:
layer = Group(self, None, None, current_group)
group_stack.append(layer)
elif divider.kind in (SectionDivider.OPEN_FOLDER,
SectionDivider.CLOSED_FOLDER):
layer = group_stack.pop()
assert layer is not self
layer._record = record
layer._channels = channels
for key in (
'ARTBOARD_DATA1', 'ARTBOARD_DATA2', 'ARTBOARD_DATA3'
):
if key in blocks:
layer = Artboard._move(layer)
end_of_group = True
elif (
'TYPE_TOOL_OBJECT_SETTING' in blocks or
'TYPE_TOOL_INFO' in blocks
):
layer = TypeLayer(self, record, channels, current_group)
elif (
record.flags.pixel_data_irrelevant and (
'VECTOR_ORIGINATION_DATA' in blocks or
'VECTOR_MASK_SETTING1' in blocks or
'VECTOR_MASK_SETTING2' in blocks or
'VECTOR_STROKE_DATA' in blocks or
'VECTOR_STROKE_CONTENT_DATA' in blocks
)
):
layer = ShapeLayer(self, record, channels, current_group)
elif (
'SMART_OBJECT_LAYER_DATA1' in blocks or
'SMART_OBJECT_LAYER_DATA2' in blocks or
'PLACED_LAYER1' in blocks or
'PLACED_LAYER2' in blocks
):
layer = SmartObjectLayer(self, record, channels,
current_group)
else:
layer = None
for key in adjustments.TYPES.keys():
if key in blocks:
layer = adjustments.TYPES[key](
self, record, channels, current_group
)
break
# If nothing applies, this is a pixel layer.
if layer is None:
layer = PixelLayer(
self, record, channels, current_group
)
if record.clipping == Clipping.NON_BASE:
clip_stack.append(layer)
else:
if clip_stack:
last_layer._clip_layers = clip_stack
clip_stack = []
if not end_of_group:
current_group._layers.append(layer)
last_layer = layer
if clip_stack and last_layer:
last_layer._clip_layers = clip_stack | [
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229,692 | psd-tools/psd-tools | src/psd_tools/api/effects.py | _AngleMixin.angle | def angle(self):
"""Angle value."""
if self.use_global_light:
return self._image_resources.get_data('global_angle', 30.0)
return self.value.get(Key.LocalLightingAngle).value | python | def angle(self):
if self.use_global_light:
return self._image_resources.get_data('global_angle', 30.0)
return self.value.get(Key.LocalLightingAngle).value | [
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229,693 | psd-tools/psd-tools | src/psd_tools/api/pil_io.py | get_color_mode | def get_color_mode(mode):
"""Convert PIL mode to ColorMode."""
name = mode.upper()
name = name.rstrip('A') # Trim alpha.
name = {'1': 'BITMAP', 'L': 'GRAYSCALE'}.get(name, name)
return getattr(ColorMode, name) | python | def get_color_mode(mode):
name = mode.upper()
name = name.rstrip('A') # Trim alpha.
name = {'1': 'BITMAP', 'L': 'GRAYSCALE'}.get(name, name)
return getattr(ColorMode, name) | [
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229,694 | psd-tools/psd-tools | src/psd_tools/api/pil_io.py | get_pil_mode | def get_pil_mode(value, alpha=False):
"""Get PIL mode from ColorMode."""
name = {
'GRAYSCALE': 'L',
'BITMAP': '1',
'DUOTONE': 'L',
'INDEXED': 'P',
}.get(value, value)
if alpha and name in ('L', 'RGB'):
name += 'A'
return name | python | def get_pil_mode(value, alpha=False):
name = {
'GRAYSCALE': 'L',
'BITMAP': '1',
'DUOTONE': 'L',
'INDEXED': 'P',
}.get(value, value)
if alpha and name in ('L', 'RGB'):
name += 'A'
return name | [
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229,695 | psd-tools/psd-tools | src/psd_tools/api/pil_io.py | convert_image_data_to_pil | def convert_image_data_to_pil(psd, apply_icc=True, **kwargs):
"""Convert ImageData to PIL Image.
.. note:: Image resources contain extra alpha channels in these keys:
`ALPHA_NAMES_UNICODE`, `ALPHA_NAMES_PASCAL`, `ALPHA_IDENTIFIERS`.
"""
from PIL import Image, ImageOps
header = psd.header
size = (header.width, header.height)
channels = []
for channel_data in psd.image_data.get_data(header):
channels.append(_create_channel(size, channel_data, header.depth))
alpha = _get_alpha_use(psd)
mode = get_pil_mode(header.color_mode.name)
if mode == 'P':
image = Image.merge('L', channels[:get_pil_channels(mode)])
image.putpalette(psd.color_mode_data.interleave())
elif mode == 'MULTICHANNEL':
image = channels[0] # Multi-channel mode is a collection of alpha.
else:
image = Image.merge(mode, channels[:get_pil_channels(mode)])
if mode == 'CMYK':
image = image.point(lambda x: 255 - x)
if apply_icc and 'ICC_PROFILE' in psd.image_resources:
image = _apply_icc(image, psd.image_resources.get_data('ICC_PROFILE'))
if alpha and mode in ('L', 'RGB'):
image.putalpha(channels[-1])
return _remove_white_background(image) | python | def convert_image_data_to_pil(psd, apply_icc=True, **kwargs):
from PIL import Image, ImageOps
header = psd.header
size = (header.width, header.height)
channels = []
for channel_data in psd.image_data.get_data(header):
channels.append(_create_channel(size, channel_data, header.depth))
alpha = _get_alpha_use(psd)
mode = get_pil_mode(header.color_mode.name)
if mode == 'P':
image = Image.merge('L', channels[:get_pil_channels(mode)])
image.putpalette(psd.color_mode_data.interleave())
elif mode == 'MULTICHANNEL':
image = channels[0] # Multi-channel mode is a collection of alpha.
else:
image = Image.merge(mode, channels[:get_pil_channels(mode)])
if mode == 'CMYK':
image = image.point(lambda x: 255 - x)
if apply_icc and 'ICC_PROFILE' in psd.image_resources:
image = _apply_icc(image, psd.image_resources.get_data('ICC_PROFILE'))
if alpha and mode in ('L', 'RGB'):
image.putalpha(channels[-1])
return _remove_white_background(image) | [
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229,696 | psd-tools/psd-tools | src/psd_tools/api/pil_io.py | convert_layer_to_pil | def convert_layer_to_pil(layer, apply_icc=True, **kwargs):
"""Convert Layer to PIL Image."""
from PIL import Image
header = layer._psd._record.header
if header.color_mode == ColorMode.BITMAP:
raise NotImplementedError
width, height = layer.width, layer.height
channels, alpha = [], None
for ci, cd in zip(layer._record.channel_info, layer._channels):
if ci.id in (ChannelID.USER_LAYER_MASK,
ChannelID.REAL_USER_LAYER_MASK):
continue
channel = cd.get_data(width, height, header.depth, header.version)
channel_image = _create_channel(
(width, height), channel, header.depth
)
if ci.id == ChannelID.TRANSPARENCY_MASK:
alpha = channel_image
else:
channels.append(channel_image)
mode = get_pil_mode(header.color_mode.name)
channels = _check_channels(channels, header.color_mode)
image = Image.merge(mode, channels)
if mode == 'CMYK':
image = image.point(lambda x: 255 - x)
if alpha is not None:
if mode in ('RGB', 'L'):
image.putalpha(alpha)
else:
logger.debug('Alpha channel is not supported in %s' % (mode))
if apply_icc and 'ICC_PROFILE' in layer._psd.image_resources:
image = _apply_icc(
image, layer._psd.image_resources.get_data('ICC_PROFILE')
)
return image | python | def convert_layer_to_pil(layer, apply_icc=True, **kwargs):
from PIL import Image
header = layer._psd._record.header
if header.color_mode == ColorMode.BITMAP:
raise NotImplementedError
width, height = layer.width, layer.height
channels, alpha = [], None
for ci, cd in zip(layer._record.channel_info, layer._channels):
if ci.id in (ChannelID.USER_LAYER_MASK,
ChannelID.REAL_USER_LAYER_MASK):
continue
channel = cd.get_data(width, height, header.depth, header.version)
channel_image = _create_channel(
(width, height), channel, header.depth
)
if ci.id == ChannelID.TRANSPARENCY_MASK:
alpha = channel_image
else:
channels.append(channel_image)
mode = get_pil_mode(header.color_mode.name)
channels = _check_channels(channels, header.color_mode)
image = Image.merge(mode, channels)
if mode == 'CMYK':
image = image.point(lambda x: 255 - x)
if alpha is not None:
if mode in ('RGB', 'L'):
image.putalpha(alpha)
else:
logger.debug('Alpha channel is not supported in %s' % (mode))
if apply_icc and 'ICC_PROFILE' in layer._psd.image_resources:
image = _apply_icc(
image, layer._psd.image_resources.get_data('ICC_PROFILE')
)
return image | [
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229,697 | psd-tools/psd-tools | src/psd_tools/api/pil_io.py | convert_mask_to_pil | def convert_mask_to_pil(mask, real=True):
"""Convert Mask to PIL Image."""
from PIL import Image
header = mask._layer._psd._record.header
channel_ids = [ci.id for ci in mask._layer._record.channel_info]
if real and mask._has_real():
width = mask._data.real_right - mask._data.real_left
height = mask._data.real_bottom - mask._data.real_top
channel = mask._layer._channels[
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]
else:
width = mask._data.right - mask._data.left
height = mask._data.bottom - mask._data.top
channel = mask._layer._channels[
channel_ids.index(ChannelID.USER_LAYER_MASK)
]
data = channel.get_data(width, height, header.depth, header.version)
return _create_channel((width, height), data, header.depth) | python | def convert_mask_to_pil(mask, real=True):
from PIL import Image
header = mask._layer._psd._record.header
channel_ids = [ci.id for ci in mask._layer._record.channel_info]
if real and mask._has_real():
width = mask._data.real_right - mask._data.real_left
height = mask._data.real_bottom - mask._data.real_top
channel = mask._layer._channels[
channel_ids.index(ChannelID.REAL_USER_LAYER_MASK)
]
else:
width = mask._data.right - mask._data.left
height = mask._data.bottom - mask._data.top
channel = mask._layer._channels[
channel_ids.index(ChannelID.USER_LAYER_MASK)
]
data = channel.get_data(width, height, header.depth, header.version)
return _create_channel((width, height), data, header.depth) | [
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229,698 | psd-tools/psd-tools | src/psd_tools/api/pil_io.py | convert_pattern_to_pil | def convert_pattern_to_pil(pattern, version=1):
"""Convert Pattern to PIL Image."""
from PIL import Image
mode = get_pil_mode(pattern.image_mode.name, False)
# The order is different here.
size = pattern.data.rectangle[3], pattern.data.rectangle[2]
channels = [
_create_channel(size, c.get_data(version), c.pixel_depth).convert('L')
for c in pattern.data.channels if c.is_written
]
if len(channels) == len(mode) + 1:
mode += 'A' # TODO: Perhaps doesn't work for some modes.
if mode == 'P':
image = channels[0]
image.putpalette([x for rgb in pattern.color_table for x in rgb])
else:
image = Image.merge(mode, channels)
if mode == 'CMYK':
image = image.point(lambda x: 255 - x)
return image | python | def convert_pattern_to_pil(pattern, version=1):
from PIL import Image
mode = get_pil_mode(pattern.image_mode.name, False)
# The order is different here.
size = pattern.data.rectangle[3], pattern.data.rectangle[2]
channels = [
_create_channel(size, c.get_data(version), c.pixel_depth).convert('L')
for c in pattern.data.channels if c.is_written
]
if len(channels) == len(mode) + 1:
mode += 'A' # TODO: Perhaps doesn't work for some modes.
if mode == 'P':
image = channels[0]
image.putpalette([x for rgb in pattern.color_table for x in rgb])
else:
image = Image.merge(mode, channels)
if mode == 'CMYK':
image = image.point(lambda x: 255 - x)
return image | [
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229,699 | psd-tools/psd-tools | src/psd_tools/api/pil_io.py | convert_thumbnail_to_pil | def convert_thumbnail_to_pil(thumbnail, mode='RGB'):
"""Convert thumbnail resource."""
from PIL import Image
if thumbnail.fmt == 0:
size = (thumbnail.width, thumbnail.height)
stride = thumbnail.widthbytes
return Image.frombytes('RGBX', size, thumbnail.data, 'raw', mode,
stride)
elif thumbnail.fmt == 1:
return Image.open(io.BytesIO(thumbnail.data))
else:
raise ValueError('Unknown thumbnail format %d' % (thumbnail.fmt)) | python | def convert_thumbnail_to_pil(thumbnail, mode='RGB'):
from PIL import Image
if thumbnail.fmt == 0:
size = (thumbnail.width, thumbnail.height)
stride = thumbnail.widthbytes
return Image.frombytes('RGBX', size, thumbnail.data, 'raw', mode,
stride)
elif thumbnail.fmt == 1:
return Image.open(io.BytesIO(thumbnail.data))
else:
raise ValueError('Unknown thumbnail format %d' % (thumbnail.fmt)) | [
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"resource",
"."
] | 4952b57bcf1cf2c1f16fd9d6d51d4fa0b53bce4e | https://github.com/psd-tools/psd-tools/blob/4952b57bcf1cf2c1f16fd9d6d51d4fa0b53bce4e/src/psd_tools/api/pil_io.py#L163-L174 |
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