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utils.py
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utils.py
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from typing import Tuple, Union, Iterable, Dict, Optional, List
import uuid
from io import StringIO
from IPython.display import SVG
from openff.toolkit.topology import FrozenMolecule
from rdkit import Chem
from rdkit.Chem import Draw
from rdkit.Chem.rdDepictor import Compute2DCoords
import numpy as np
import nglview
from nglview.base_adaptor import Structure, Trajectory
from openff.units import unit
from openff.toolkit import Molecule, ForceField, Topology
from openff.toolkit.typing.engines.smirnoff.parameters import BondType, ParameterType
from openff.toolkit.utils.exceptions import ParameterLookupError
AMBER_COLOR = np.array([255, 192, 0]) / 255
SAGE_COLOR = np.array([141, 208, 169]) / 255
NEW_PARAM_COLOR = np.array([191, 192, 238]) / 255
WHITE = np.array([255, 255, 255]) / 255
DEFAULT_WIDTH = 980
DEFAULT_HEIGHT = 400
Color = Iterable[float]
BondIndices = Tuple[int, int]
MOLECULE_DEFAULT_REPS = [
dict(type="licorice", params=dict(radius=0.25, multipleBond=True))
]
def in_ff(handler: str, param: ParameterType, ff: ForceField) -> bool:
"""
True if param is in ff[handler], false if not
"""
smirks = param.smirks
try:
ff_param = ff[handler][smirks]
except ParameterLookupError:
return False
return ff_param.__dict__ == param.__dict__
def bond_in_ff(bond: BondType, ff: ForceField) -> bool:
return in_ff("Bonds", bond, ff)
def blend_colors(a: Color, b: Color, t: float = 0.5, w: float = 0.0) -> Color:
"""
Blend two colors with white.
By default, produces a color with an even mix of ``a`` and ``b`` and no
white.
Parameters
==========
a
The first color.
b
The second color.
t
The proportion of ``a`` in the final mix.
w
The proportion of white in the final mix.
"""
a = np.asarray(a)
b = np.asarray(b)
return np.sqrt(w * WHITE**2 + t * a**2 + (1 - t - w) * b**2)
def draw_molecule(
molecule: Union[str, Molecule, Chem.Mol],
image_width: int = DEFAULT_WIDTH,
image_height: int = DEFAULT_HEIGHT,
highlight_atoms: Optional[Union[List[int], Dict[int, Color]]] = None,
highlight_bonds: Optional[
Union[List[BondIndices], Dict[BondIndices, Color]]
] = None,
atom_notes: Optional[Dict[int, str]] = None,
bond_notes: Optional[Dict[BondIndices, str]] = None,
explicit_hydrogens: Optional[bool] = None,
color_by_element: Optional[bool] = None,
) -> SVG:
"""Draw a molecule
Parameters
==========
molecule
The molecule to draw.
image_width
The width of the resulting image in pixels.
image_height
The height of the resulting image in pixels.
highlight_atoms
A list of atom indices to highlight, or a map from indices to colors.
Colors should be given as triplets of floats between 0.0 and 1.0.
highlight_atoms
A list of pairs of atom indices indicating bonds to highlight, or a map
from index pairs to colors. Colors should be given as triplets of floats
between 0.0 and 1.0.
atom_notes
A map from atom indices to a string that should be printed near the
atom.
bond_notes
A map from atom index pairs to a string that should be printed near the
bond.
explicit_hydrogens
If ``False``, allow uncharged monovalent hydrogens to be hidden. If
``True``, make all hydrogens explicit. If ``None``
color_by_element
If True, color heteroatoms according to their element; if False, the
image will be black and white. By default, uses black and white when
highlight_atoms or highlight_bonds is provided, and color otherwise.
Raises
======
KeyError
When an atom or bond in highlight_atoms or highlight_bonds is missing
from the image, including when it is present in the molecule but hidden.
"""
if isinstance(molecule, FrozenMolecule):
rdmol = molecule.to_rdkit()
elif isinstance(molecule, str):
rdmol = Molecule.from_smiles(molecule).to_rdkit()
else:
rdmol = molecule
if color_by_element is None:
color_by_element = highlight_atoms is None and highlight_bonds is None
if explicit_hydrogens is None:
idx_map = {i: i for i in range(rdmol.GetNumAtoms())}
elif explicit_hydrogens:
idx_map = {i: i for i in range(rdmol.GetNumAtoms())}
rdmol = Chem.AddHs(rdmol, explicitOnly=True)
else:
idx_map = {
old: new
for new, old in enumerate(
a.GetIdx()
for a in rdmol.GetAtoms()
if a.GetAtomicNum() != 1 and a.GetMass() != 1
)
}
rdmol = Chem.RemoveHs(rdmol, updateExplicitCount=True)
if highlight_atoms is None:
highlight_atoms = []
highlight_atom_colors = None
elif isinstance(highlight_atoms, dict):
highlight_atom_colors = {
idx_map[i]: tuple(c) for i, c in highlight_atoms.items() if i in idx_map
}
highlight_atoms = list(highlight_atoms.keys())
else:
highlight_atoms = [idx_map[i] for i in highlight_atoms if i in idx_map]
highlight_atom_colors = None
if highlight_bonds is None:
highlight_bonds = []
highlight_bond_colors = None
elif isinstance(highlight_bonds, dict):
highlight_bond_colors = {
rdmol.GetBondBetweenAtoms(idx_map[i_a], idx_map[i_b]).GetIdx(): tuple(v)
for (i_a, i_b), v in highlight_bonds.items()
if i_a in idx_map and i_b in idx_map
}
highlight_bonds = list(highlight_bond_colors.keys())
else:
highlight_bonds = [
rdmol.GetBondBetweenAtoms(idx_map[i_a], idx_map[i_b])
for i_a, i_b in highlight_bonds
if i_a in idx_map and i_b in idx_map
]
highlight_bond_colors = None
if bond_notes is not None:
for (i_a, i_b), note in bond_notes.items():
if i_a not in idx_map or i_b not in idx_map:
continue
rdbond = rdmol.GetBondBetweenAtoms(idx_map[i_a], idx_map[i_b])
rdbond.SetProp("bondNote", note)
if atom_notes is not None:
for i, note in atom_notes.items():
if i not in idx_map:
continue
rdatom = rdmol.GetAtomWithIdx(idx_map[i])
rdatom.SetProp("atomNote", note)
Compute2DCoords(rdmol)
drawer = Draw.MolDraw2DSVG(image_width, image_height)
draw_options = drawer.drawOptions()
if not color_by_element:
draw_options.useBWAtomPalette()
drawer.DrawMolecule(
rdmol,
highlightAtoms=highlight_atoms,
highlightAtomColors=highlight_atom_colors,
highlightBonds=highlight_bonds,
highlightBondColors=highlight_bond_colors,
)
drawer.FinishDrawing()
svg_contents = drawer.GetDrawingText()
return SVG(svg_contents)
def depict_charges(
offmol: Molecule,
force_field: ForceField,
image_width: int = DEFAULT_WIDTH,
image_height: int = DEFAULT_HEIGHT,
) -> SVG:
"""
Draw the library charges next to each atom
"""
labels = force_field.label_molecules(offmol.to_topology())
atom_notes = {}
for indices, charge_type in labels[0]["LibraryCharges"].items():
for charge_idx, atom_idx in enumerate(indices, start=1):
charge = getattr(charge_type, f"charge{charge_idx}")
atom_notes[atom_idx] = f"{charge.m:.1}"
return draw_molecule(
offmol,
atom_notes=atom_notes,
image_height=image_height,
image_width=image_width,
)
def depict_charge_source(
offmol: Molecule,
force_field: ForceField,
image_width: int = DEFAULT_WIDTH,
image_height: int = DEFAULT_HEIGHT,
) -> SVG:
"""
Color each atom according to where it gets its charges from
"""
labels = force_field.label_molecules(offmol.to_topology())
highlight_atom_colors = {}
for indices, charge_type in labels[0]["LibraryCharges"].items():
# We don't assign IDs, but ff14sb does:
if isinstance(charge_type.id, str):
this_color = tuple(AMBER_COLOR)
elif charge_type.id is None:
this_color = tuple(NEW_PARAM_COLOR)
else:
continue
for i in indices:
highlight_atom_colors[i] = this_color
return draw_molecule(
offmol,
highlight_atoms=highlight_atom_colors,
image_height=image_height,
image_width=image_width,
)
def depict_bonds_source(
offmol: Molecule,
force_field: ForceField,
image_width: int = DEFAULT_WIDTH,
image_height: int = DEFAULT_HEIGHT,
show_smirks: bool = False,
) -> SVG:
"""
Color each bond according to where it gets its torsions from
"""
labels = force_field.label_molecules(offmol.to_topology())
sage = ForceField("openff-2.0.0.offxml")
ff14sb = ForceField("ff14sb_off_impropers_0.0.3.offxml")
highlight_bond_colors = {}
bond_notes = {}
for indices, bond_type in labels[0]["Bonds"].items():
if bond_in_ff(bond_type, ff14sb):
highlight_bond_colors[indices] = tuple(AMBER_COLOR)
elif bond_in_ff(bond_type, sage):
highlight_bond_colors[indices] = tuple(SAGE_COLOR)
if show_smirks:
bond_notes[indices] = bond_type.smirks
return draw_molecule(
offmol,
highlight_bonds=highlight_bond_colors,
bond_notes=bond_notes,
image_height=image_height,
image_width=image_width,
)
def depict_torsions_source(
offmol: Molecule,
force_field: ForceField,
image_width: int = DEFAULT_WIDTH,
image_height: int = DEFAULT_HEIGHT,
show_smirks: bool = False,
) -> SVG:
"""
Color each torsion according to where it gets its torsions from
"""
labels = force_field.label_molecules(offmol.to_topology())
sage = ForceField("openff-2.0.0.offxml")
ff14sb = ForceField("ff14sb_off_impropers_0.0.3.offxml")
torsions_per_ff = {}
bond_notes: Dict[Tuple[int, int], str] = {}
for indices, torsion_type in labels[0]["ProperTorsions"].items():
if in_ff("ProperTorsions", torsion_type, ff14sb):
this_color = np.asarray([1, 0])
elif in_ff("ProperTorsions", torsion_type, sage):
this_color = np.asarray([0, 1])
else:
this_color = np.asarray([0, 0])
bond_index = tuple(sorted(indices[1:3]))
color = torsions_per_ff.setdefault(bond_index, np.zeros(2))
color += this_color
if show_smirks:
bond_notes[bond_index] = torsion_type.smirks
total_available_torsions = np.max([v[0] + v[1] for v in torsions_per_ff.values()])
highlight_torsion_colors = {
k: tuple(
blend_colors(
AMBER_COLOR,
SAGE_COLOR,
t=v[0] / total_available_torsions,
w=1 - (v[0] + v[1]) / total_available_torsions,
)
)
for k, v in torsions_per_ff.items()
}
return draw_molecule(
offmol,
image_width=image_width,
image_height=image_height,
highlight_bonds=highlight_torsion_colors,
bond_notes=bond_notes,
explicit_hydrogens=False,
)
class OpenFFMoleculeTrajectory(Structure, Trajectory):
"""OpenFF Molecule adaptor.
Example
-------
>>> import nglview as nv
>>> import mdtraj as md
>>> mol = Molecule.from_polymer_pdb(pdb_filename)
>>> t = OpenFFMoleculeTrajectory(mol)
>>> w = nv.NGLWidget(t)
>>> w
"""
def __init__(self, molecule: Molecule, ext: str = "MOL2"):
if not molecule.conformers:
raise ValueError(
"Cannot visualize a molecule without conformers with NGLView"
)
self.molecule = molecule
self.ext = ext.lower()
self.params = {}
self.id = str(uuid.uuid4())
def get_coordinates(self, index: int):
return self.molecule.conformers[index].m_as(unit.angstrom)
@property
def n_frames(self):
return len(self.molecule.conformers)
def get_structure_string(self):
with StringIO() as f:
self.molecule.to_file(f, file_format=self.ext)
sdf_str = f.getvalue()
return sdf_str
class OpenFFTopologyStructure(Structure):
"""OpenFF Molecule adaptor.
Example
-------
>>> import nglview as nv
>>> import mdtraj as md
>>> mol = Molecule.from_polymer_pdb(pdb_filename)
>>> t = OpenFFMoleculeTrajectory(mol)
>>> w = nv.NGLWidget(t)
>>> w
"""
def __init__(
self,
topology: Topology,
ext: str,
):
self.topology = topology
self.ext = ext.lower()
self.params = {}
self.id = str(uuid.uuid4())
def get_structure_string(self):
with StringIO() as f:
self.topology.to_file(f, file_format=self.ext)
sdf_str = f.getvalue()
return sdf_str
def visualize(obj: Union[Molecule, Topology], ext=None, representations=None):
"""Visualize a topology or molecule with nglview"""
if isinstance(obj, Molecule):
if representations is None:
representations = MOLECULE_DEFAULT_REPS
if ext is None:
ext = "MOL2"
return nglview.NGLWidget(
OpenFFMoleculeTrajectory(obj, ext=ext), representations=representations
)
elif isinstance(obj, Topology):
if ext is None:
ext = "PDB"
return nglview.NGLWidget(
OpenFFTopologyStructure(obj, ext=ext), representations=representations
)
else:
if ext is not None:
raise ValueError(
"ext parameter only supported for topologies and molecules"
)
return nglview.NGLWidget(structure=obj, representations=representations)