Loading deepchem/dock/docking.py +2 −1 Original line number Diff line number Diff line Loading @@ -102,7 +102,8 @@ class Docker(object): """ if self.scoring_model is not None and use_pose_generator_scores: raise ValueError( "Cannot set use_pose_generator_scores=True when self.scoring_model is set (since both generator scores for complexes)." "Cannot set use_pose_generator_scores=True " "when self.scoring_model is set (since both generator scores for complexes)." ) outputs = self.pose_generator.generate_poses( Loading deepchem/hyper/base_classes.py +1 −1 Original line number Diff line number Diff line Loading @@ -8,7 +8,7 @@ from deepchem.metrics import Metric logger = logging.getLogger(__name__) def _convert_hyperparam_dict_to_filename(hyper_params: Dict) -> str: def _convert_hyperparam_dict_to_filename(hyper_params: Dict[str, Any]) -> str: """Helper function that converts a dictionary of hyperparameters to a string that can be a filename. Parameters Loading deepchem/hyper/gaussian_process.py +5 −1 Original line number Diff line number Diff line Loading @@ -120,6 +120,10 @@ class GaussianProcessHyperparamOpt(HyperparamOpt): ... dropouts=dropout ... ) >>> optimizer = dc.hyper.GaussianProcessHyperparamOpt(model_builder) Note ---- This class requires pyGPGO to be installed. """ # NOTE: mypy prohibits changing the number of arguments Loading Loading @@ -309,7 +313,7 @@ class GaussianProcessHyperparamOpt(HyperparamOpt): if param_range[hp][0] == "int": hyper_parameters[hp] = int(hp_opt[hp]) else: # Incompatible types in assignment # FIXME: Incompatible types in assignment hyper_parameters[hp] = float(hp_opt[hp]) # type: ignore hp_str = _convert_hyperparam_dict_to_filename(hyper_parameters) Loading deepchem/utils/coordinate_box_utils.py +15 −15 Original line number Diff line number Diff line Loading @@ -20,17 +20,17 @@ class CoordinateBox(object): of atoms that live in this box alongside their coordinates. """ def __init__(self, x_range: Tuple[int, int], y_range: Tuple[int, int], z_range: Tuple[int, int]): def __init__(self, x_range: Tuple[float, float], y_range: Tuple[float, float], z_range: Tuple[float, float]): """Initialize this box. Parameters ---------- x_range: Tuple[int] x_range: Tuple[float] A tuple of `(x_min, x_max)` with max and min x-coordinates. y_range: Tuple[int] y_range: Tuple[float] A tuple of `(y_min, y_max)` with max and min y-coordinates. z_range: Tuple[int] z_range: Tuple[float] A tuple of `(z_min, z_max)` with max and min z-coordinates. Raises Loading Loading @@ -70,7 +70,7 @@ class CoordinateBox(object): """Create a string representation of this box.""" return self.__repr__() def __contains__(self, point: Sequence[int]) -> bool: def __contains__(self, point: Sequence[float]) -> bool: """Check whether a point is in this box. Parameters Loading Loading @@ -144,12 +144,12 @@ class CoordinateBox(object): return (x_min + (x_max - x_min) / 2, y_min + (y_max - y_min) / 2, z_min + (z_max - z_min) / 2) def volume(self) -> int: def volume(self) -> float: """Computes and returns the volume of this box. Returns ------- int, the volume of this box. Can be 0 if box is empty float, the volume of this box. Can be 0 if box is empty Examples -------- Loading Loading @@ -193,20 +193,20 @@ class CoordinateBox(object): self_z_min <= other_z_min and other_z_max <= self_z_max) def intersect_interval(interval1: Tuple[int, int], interval2: Tuple[int, int]) -> Tuple[int, int]: def intersect_interval(interval1: Tuple[float, float], interval2: Tuple[float, float]) -> Tuple[float, float]: """Computes the intersection of two intervals. Parameters ---------- interval1: Tuple[int] interval1: Tuple[float] Should be `(x1_min, x1_max)` interval2: Tuple[int] interval2: Tuple[float] Should be `(x2_min, x2_max)` Returns ------- x_intersect: Tuple[int] x_intersect: Tuple[float] Should be the intersection. If the intersection is empty returns `(0, 0)` to represent the empty set. Otherwise is `(max(x1_min, x2_min), min(x1_max, x2_max))`. Loading Loading @@ -304,7 +304,7 @@ def merge_overlapping_boxes(boxes: List[CoordinateBox], return outputs def get_face_boxes(coords: np.ndarray, pad: int = 5) -> List[CoordinateBox]: def get_face_boxes(coords: np.ndarray, pad: float = 5.0) -> List[CoordinateBox]: """For each face of the convex hull, compute a coordinate box around it. The convex hull of a macromolecule will have a series of triangular Loading @@ -322,7 +322,7 @@ def get_face_boxes(coords: np.ndarray, pad: int = 5) -> List[CoordinateBox]: ---------- coords: np.ndarray Of shape `(N, 3)`. The coordinates of a molecule. pad: int, optional (default 5) pad: float, optional (default 5.0) The number of angstroms to pad. Returns Loading Loading
deepchem/dock/docking.py +2 −1 Original line number Diff line number Diff line Loading @@ -102,7 +102,8 @@ class Docker(object): """ if self.scoring_model is not None and use_pose_generator_scores: raise ValueError( "Cannot set use_pose_generator_scores=True when self.scoring_model is set (since both generator scores for complexes)." "Cannot set use_pose_generator_scores=True " "when self.scoring_model is set (since both generator scores for complexes)." ) outputs = self.pose_generator.generate_poses( Loading
deepchem/hyper/base_classes.py +1 −1 Original line number Diff line number Diff line Loading @@ -8,7 +8,7 @@ from deepchem.metrics import Metric logger = logging.getLogger(__name__) def _convert_hyperparam_dict_to_filename(hyper_params: Dict) -> str: def _convert_hyperparam_dict_to_filename(hyper_params: Dict[str, Any]) -> str: """Helper function that converts a dictionary of hyperparameters to a string that can be a filename. Parameters Loading
deepchem/hyper/gaussian_process.py +5 −1 Original line number Diff line number Diff line Loading @@ -120,6 +120,10 @@ class GaussianProcessHyperparamOpt(HyperparamOpt): ... dropouts=dropout ... ) >>> optimizer = dc.hyper.GaussianProcessHyperparamOpt(model_builder) Note ---- This class requires pyGPGO to be installed. """ # NOTE: mypy prohibits changing the number of arguments Loading Loading @@ -309,7 +313,7 @@ class GaussianProcessHyperparamOpt(HyperparamOpt): if param_range[hp][0] == "int": hyper_parameters[hp] = int(hp_opt[hp]) else: # Incompatible types in assignment # FIXME: Incompatible types in assignment hyper_parameters[hp] = float(hp_opt[hp]) # type: ignore hp_str = _convert_hyperparam_dict_to_filename(hyper_parameters) Loading
deepchem/utils/coordinate_box_utils.py +15 −15 Original line number Diff line number Diff line Loading @@ -20,17 +20,17 @@ class CoordinateBox(object): of atoms that live in this box alongside their coordinates. """ def __init__(self, x_range: Tuple[int, int], y_range: Tuple[int, int], z_range: Tuple[int, int]): def __init__(self, x_range: Tuple[float, float], y_range: Tuple[float, float], z_range: Tuple[float, float]): """Initialize this box. Parameters ---------- x_range: Tuple[int] x_range: Tuple[float] A tuple of `(x_min, x_max)` with max and min x-coordinates. y_range: Tuple[int] y_range: Tuple[float] A tuple of `(y_min, y_max)` with max and min y-coordinates. z_range: Tuple[int] z_range: Tuple[float] A tuple of `(z_min, z_max)` with max and min z-coordinates. Raises Loading Loading @@ -70,7 +70,7 @@ class CoordinateBox(object): """Create a string representation of this box.""" return self.__repr__() def __contains__(self, point: Sequence[int]) -> bool: def __contains__(self, point: Sequence[float]) -> bool: """Check whether a point is in this box. Parameters Loading Loading @@ -144,12 +144,12 @@ class CoordinateBox(object): return (x_min + (x_max - x_min) / 2, y_min + (y_max - y_min) / 2, z_min + (z_max - z_min) / 2) def volume(self) -> int: def volume(self) -> float: """Computes and returns the volume of this box. Returns ------- int, the volume of this box. Can be 0 if box is empty float, the volume of this box. Can be 0 if box is empty Examples -------- Loading Loading @@ -193,20 +193,20 @@ class CoordinateBox(object): self_z_min <= other_z_min and other_z_max <= self_z_max) def intersect_interval(interval1: Tuple[int, int], interval2: Tuple[int, int]) -> Tuple[int, int]: def intersect_interval(interval1: Tuple[float, float], interval2: Tuple[float, float]) -> Tuple[float, float]: """Computes the intersection of two intervals. Parameters ---------- interval1: Tuple[int] interval1: Tuple[float] Should be `(x1_min, x1_max)` interval2: Tuple[int] interval2: Tuple[float] Should be `(x2_min, x2_max)` Returns ------- x_intersect: Tuple[int] x_intersect: Tuple[float] Should be the intersection. If the intersection is empty returns `(0, 0)` to represent the empty set. Otherwise is `(max(x1_min, x2_min), min(x1_max, x2_max))`. Loading Loading @@ -304,7 +304,7 @@ def merge_overlapping_boxes(boxes: List[CoordinateBox], return outputs def get_face_boxes(coords: np.ndarray, pad: int = 5) -> List[CoordinateBox]: def get_face_boxes(coords: np.ndarray, pad: float = 5.0) -> List[CoordinateBox]: """For each face of the convex hull, compute a coordinate box around it. The convex hull of a macromolecule will have a series of triangular Loading @@ -322,7 +322,7 @@ def get_face_boxes(coords: np.ndarray, pad: int = 5) -> List[CoordinateBox]: ---------- coords: np.ndarray Of shape `(N, 3)`. The coordinates of a molecule. pad: int, optional (default 5) pad: float, optional (default 5.0) The number of angstroms to pad. Returns Loading
