MolecularDiffusion.utils.shepherd_utils¶

Attributes¶

`COULOMB_SCALING`
`PT`
`P_TYPES`
`SMARTS_FEATURES_FDEF`
`logger`
`o3d`

Functions¶

`GetAcceptorFeatVects`(conf, featAtoms[, scale])
`GetAromaticFeatVects`(conf, featAtoms, featLoc[, ...])
`GetDonorFeatVects`(conf, featAtoms[, scale, exclude])
`GetHalogenFeatVects`(conf, featAtoms[, scale])
`find_hydrophobes`(mol[, cluster_hydrophobic])
`get_atomic_vdw_radii`(→ numpy.ndarray)
`get_electrostatics_given_point_charges`(→ numpy.ndarray)
`get_molecular_surface`(→ numpy.ndarray)
`get_pharmacophores`(→ Tuple[numpy.ndarray, ...)
`sample_molecular_surface_with_radius_fibonacci`(...)
`update_mol_coordinates`(mol, pos)

Module Contents¶

MolecularDiffusion.utils.shepherd_utils.GetAcceptorFeatVects(conf, featAtoms, scale=1.0)¶

MolecularDiffusion.utils.shepherd_utils.GetAromaticFeatVects(conf, featAtoms, featLoc, return_both: bool = False, scale=1.0)¶

MolecularDiffusion.utils.shepherd_utils.GetDonorFeatVects(conf, featAtoms, scale=1.0, exclude=[])¶

MolecularDiffusion.utils.shepherd_utils.GetHalogenFeatVects(conf, featAtoms, scale=1.0)¶

MolecularDiffusion.utils.shepherd_utils.find_hydrophobes(mol, cluster_hydrophobic: bool = True)¶

MolecularDiffusion.utils.shepherd_utils.get_atomic_vdw_radii(mol) → numpy.ndarray¶

MolecularDiffusion.utils.shepherd_utils.get_electrostatics_given_point_charges(charges: numpy.ndarray, positions: numpy.ndarray, points: numpy.ndarray) → numpy.ndarray¶

MolecularDiffusion.utils.shepherd_utils.get_molecular_surface(centers: numpy.ndarray, radii: numpy.ndarray, num_points: int | None = None, num_samples_per_atom: int = 25, probe_radius: float = 1.2) → numpy.ndarray¶

MolecularDiffusion.utils.shepherd_utils.get_pharmacophores(mol, multi_vector: bool = True, exclude: List[int] = [], check_access: bool = False, scale: float = 1.0) → Tuple[numpy.ndarray, numpy.ndarray, numpy.ndarray]¶

MolecularDiffusion.utils.shepherd_utils.sample_molecular_surface_with_radius_fibonacci(centers: numpy.ndarray, radii: numpy.ndarray, probe_radius: float = 1.2, num_samples_per_atom: int = 20) → numpy.ndarray¶

MolecularDiffusion.utils.shepherd_utils.update_mol_coordinates(mol, pos)¶

MolecularDiffusion.utils.shepherd_utils.COULOMB_SCALING¶

MolecularDiffusion.utils.shepherd_utils.PT¶

MolecularDiffusion.utils.shepherd_utils.P_TYPES = ('Acceptor', 'Donor', 'Aromatic', 'Hydrophobe', 'Halogen', 'Cation', 'Anion', 'ZnBinder', 'Dummy')¶

MolecularDiffusion.utils.shepherd_utils.SMARTS_FEATURES_FDEF = Multiline-String¶

Show Value

"""
AtomType AromR4 [a;r4,!R1&r3]
DefineFeature Arom4 [{AromR4}]1:[{AromR4}]:[{AromR4}]:[{AromR4}]:1
 Family Aromatic
 Weights 1,1,1,1
EndFeature
AtomType AromR5 [a;r5,!R1&r4,!R1&r3]
DefineFeature Arom5 [{AromR5}]1:[{AromR5}]:[{AromR5}]:[{AromR5}]:[{AromR5}]:1
 Family Aromatic
 Weights 1,1,1,1,1
EndFeature
AtomType AromR6 [a;r6,!R1&r5,!R1&r4,!R1&r3]
DefineFeature Arom6 [{AromR6}]1:[{AromR6}]:[{AromR6}]:[{AromR6}]:[{AromR6}]:[{AromR6}]:1
 Family Aromatic
 Weights 1,1,1,1,1,1
EndFeature
AtomType AromR7 [a;r7,!R1&r6,!R1&r5,!R1&r4,!R1&r3]
DefineFeature Arom7 [{AromR7}]1:[{AromR7}]:[{AromR7}]:[{AromR7}]:[{AromR7}]:[{AromR7}]:[{AromR7}]:1
 Family Aromatic
 Weights 1,1,1,1,1,1,1
EndFeature
AtomType AromR8 [a;r8,!R1&r7,!R1&r6,!R1&r5,!R1&r4,!R1&r3]
DefineFeature Arom8 [{AromR8}]1:[{AromR8}]:[{AromR8}]:[{AromR8}]:[{AromR8}]:[{AromR8}]:[{AromR8}]:[{AromR8}]:1
 Family Aromatic
 Weights 1,1,1,1,1,1,1,1
EndFeature
DefineFeature ZnBinder1 [S;D1]-[#6]
  Family ZnBinder
  Weights 1,0
EndFeature
DefineFeature ZnBinder2 [#6]-C(=O)-C-[S;D1]
  Family ZnBinder
  Weights 0,0,1,0,1
EndFeature
DefineFeature ZnBinder3 [#6]-C(=O)-C-C-[S;D1]
  Family ZnBinder
  Weights 0,0,1,0,0,1
EndFeature
DefineFeature ZnBinder4 [#6]-C(=O)-N-[O;D1]
  Family ZnBinder
  Weights 0,0,1,0,1
EndFeature
DefineFeature ZnBinder5 [#6]-C(=O)-[O;D1]
  Family ZnBinder
  Weights 0,0,1,1
EndFeature
DefineFeature ZnBinder6 [#6]-P(=O)(-O)-[C,O,N]-[C,H]
  Family ZnBinder
  Weights 0,0,1,1,0,0
EndFeature
DefineFeature N_HBD [#7!H0&!$(N-[SX4](=O)(=O)[CX4](F)(F)F)]
  Family Donor
  Weights 1
EndFeature
DefineFeature O_HBD [#8!H0&!$([OH][C,S,P]=O)]
  Family Donor
  Weights 1
EndFeature
DefineFeature S_HBD [#16!H0]
  Family Donor
  Weights 1
EndFeature
DefineFeature ChalcDonor [O,S;H1;+0]
  Family Donor
  Weights 1
EndFeature
AtomType N_HBA [#7&!$([nX3])&!$([NX3]-*=[!#6])&!$([NX3]-[a])&!$([NX4])&!$(N=C([C,N])N)]
AtomType O_HBA [$([O])&!$([OX2](C)C=O)&!$(*(~a)~a)]
AtomType ChalcAcceptor [O;H0;v2;!$(O=N-*)]
Atomtype ChalcAcceptor [O;-;!$(*-N=O)]
Atomtype ChalcAcceptor [o;+0]
AtomType Hydroxyl [O;H1;v2]
DefineFeature HBA [{Hydroxyl},{ChalcAcceptor},{O_HBA},{N_HBA}]
  Family Acceptor
  Weights 1
EndFeature
DefineFeature N_positive [$([NX3+]([CX4])([CX4,#1])[CX4,#1])&!$([NX3]-*=[!#6])]
  Family Cation
  Weights 1
EndFeature
DefineFeature amidino_positive1 [CX3](=[N+])(-N)[!N]
  Family Cation
  Weights 1,1,1,1
EndFeature
DefineFeature amidino_positive2 [CX3](=N)(-[N+])[!N]
  Family Cation
  Weights 1,1,1,1
EndFeature
DefineFeature guanidino_positive1 [N+]=[CX3](N)-N
  Family Cation
  Weights 1,1,1,1
EndFeature
DefineFeature guanidino_positive2 [N+]=[CX3](N)-N
  Family Cation
  Weights 1,1,1,1
EndFeature
DefineFeature guanidino_positive3 N=[CX3]([N+])-N
  Family Cation
  Weights 1,1,1,1
EndFeature
DefineFeature charged_positive [$([+,+2,+3])&!$(*[-,-2,-3])]
  Family Cation
  Weights 1
EndFeature
DefineFeature tetrazole_negative c1nn[nH1]n1
  Family Anion
  Weights 1,1,1,1,1
EndFeature
DefineFeature SP_v4_negative [$([SX4,PX4](=O)(=O)[O-])](=O)(=O)[O-]
  Family Anion
  Weights 1,1,1,1
EndFeature
DefineFeature CSP_v3_negative [$([CX3,SX3,PX3](=O)[O-])](=O)[O-]
  Family Anion
  Weights 1,1,1
EndFeature
DefineFeature charged_negative [$([-,-2,-3])&!$(*[+,+2,+3])]
  Family Anion
  Weights 1
EndFeature
AtomType Fluorine [F;$(F-[#6]);!$(FC[F,Cl,Br,I])]
AtomType Chlorine [Cl;$(Cl-[#6]);!$(FC[F,Cl,Br,I])]
AtomType Bromine [Br;$(Br-[#6]);!$(FC[F,Cl,Br,I])]
AtomType Iodine [I;$(I-[#6]);!$(FC[F,Cl,Br,I])]
DefineFeature Halogen [{Fluorine},{Chlorine},{Bromine},{Iodine}]
  Family Halogen
  Weights 1
EndFeature
"""

MolecularDiffusion.utils.shepherd_utils.logger¶

MolecularDiffusion.utils.shepherd_utils.o3d = None¶