chemprop.data.datapoints ======================== .. py:module:: chemprop.data.datapoints Attributes ---------- .. autoapisummary:: chemprop.data.datapoints.MoleculeFeaturizer Classes ------- .. autoapisummary:: chemprop.data.datapoints.MoleculeDatapoint chemprop.data.datapoints.LazyMoleculeDatapoint chemprop.data.datapoints.MolAtomBondDatapoint chemprop.data.datapoints.ReactionDatapoint Module Contents --------------- .. py:data:: MoleculeFeaturizer .. py:class:: MoleculeDatapoint Bases: :py:obj:`_DatapointMixin`, :py:obj:`_MoleculeDatapointMixin` A :class:`MoleculeDatapoint` contains a single molecule and its associated features and targets. .. py:attribute:: V_f :type: numpy.ndarray | None :value: None A numpy array of shape ``V x d_vf``, where ``V`` is the number of atoms in the molecule, and ``d_vf`` is the number of additional features that will be concatenated to atom-level features *before* message passing .. py:attribute:: E_f :type: numpy.ndarray | None :value: None A numpy array of shape ``E x d_ef``, where ``E`` is the number of bonds in the molecule, and ``d_ef`` is the number of additional features containing additional features that will be concatenated to bond-level features *before* message passing .. py:attribute:: V_d :type: numpy.ndarray | None :value: None A numpy array of shape ``V x d_vd``, where ``V`` is the number of atoms in the molecule, and ``d_vd`` is the number of additional descriptors that will be concatenated to atom-level descriptors *after* message passing .. py:method:: __post_init__() .. py:method:: __len__() .. py:class:: LazyMoleculeDatapoint Bases: :py:obj:`_DatapointMixin`, :py:obj:`_LazyMoleculeDatapointMixin` A :class:`LazyMoleculeDatapoint` contains a single SMILES string, and all attributes need to form a `rdkit.Chem.Mol` object. The molecule is computed lazily when the attribute `mol` is accessed. .. py:attribute:: V_f :type: numpy.ndarray | None :value: None A numpy array of shape ``V x d_vf``, where ``V`` is the number of atoms in the molecule, and ``d_vf`` is the number of additional features that will be concatenated to atom-level features *before* message passing .. py:attribute:: E_f :type: numpy.ndarray | None :value: None A numpy array of shape ``E x d_ef``, where ``E`` is the number of bonds in the molecule, and ``d_ef`` is the number of additional features containing additional features that will be concatenated to bond-level features *before* message passing .. py:attribute:: V_d :type: numpy.ndarray | None :value: None A numpy array of shape ``V x d_vd``, where ``V`` is the number of atoms in the molecule, and ``d_vd`` is the number of additional descriptors that will be concatenated to atom-level descriptors *after* message passing .. py:method:: __post_init__() .. py:method:: __len__() .. py:class:: MolAtomBondDatapoint Bases: :py:obj:`MoleculeDatapoint` A :class:`MoleculeDatapoint` contains a single molecule and its associated features and targets. .. py:attribute:: E_d :type: numpy.ndarray | None :value: None A numpy array of shape ``E x d_ed``, where ``E`` is the number of bonds in the molecule, and ``d_ed`` is the number of additional descriptors that will be concatenated to edge-level descriptors *after* message passing .. py:attribute:: atom_y :type: numpy.ndarray | None :value: None A numpy array of shape ``V x v_t``, where ``V`` is the number of atoms in the molecule, and ``v_t`` is the number of atom targets. The order of atoms in the array should match the order of atoms in the mol. Unknown targets are indicated by `nan`s. .. py:attribute:: atom_gt_mask :type: numpy.ndarray | None :value: None Indicates whether the atom targets are an inequality regression target of the form `x` .. py:attribute:: bond_y :type: numpy.ndarray | None :value: None A numpy array of shape ``E x e_t``, where ``V`` is the number of bonds in the molecule, and ``e_t`` is the number of bond targets. The order of bonds in the array should match the order of bonds in the mol. Unknown targets are indicated by `nan`s. .. py:attribute:: bond_gt_mask :type: numpy.ndarray | None :value: None Indicates whether the bond targets are an inequality regression target of the form `x` .. py:attribute:: atom_constraint :type: numpy.ndarray | None :value: None A numpy array of shape ``1 x v_t`` containing the values that the atom property predictions should be constrained to sum to, with np.nan indicating no constraint for that property .. py:attribute:: bond_constraint :type: numpy.ndarray | None :value: None A numpy array of shape ``1 x e_t`` containing the values that the bond property predictions should be constrained to sum to, with np.nan indicating no constraint for that property .. py:method:: __post_init__() .. py:method:: from_smi(smi, *args, keep_h = False, add_h = False, ignore_stereo = False, reorder_atoms = True, **kwargs) :classmethod: .. py:class:: ReactionDatapoint Bases: :py:obj:`_DatapointMixin`, :py:obj:`_ReactionDatapointMixin` A :class:`ReactionDatapoint` contains a single reaction and its associated features and targets. .. py:method:: __post_init__() .. py:method:: __len__()