import torch
from rdkit import Chem
from .utils import one_hot, is_one
METAL =["LI","NA","K","RB","CS","MG","TL","CU","AG","BE","NI","PT","ZN","CO",\
"PD","AG","CR","FE","V","MN","HG",'GA',"CD","YB","CA","SN","PB","EU",\
"SR","SM","BA","RA","AL","IN","TL","Y","LA","CE","PR","ND","GD","TB",\
"DY","ER","TM","LU","HF","ZR","CE","U","PU","TH","AU"]
PERIODIC_table = '''H __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ He
Li Be __ __ __ __ __ __ __ __ __ __ B C N O F Ne
Na Mg __ __ __ __ __ __ __ __ __ __ Al Si P S Cl Ar
K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr
Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te I Xe'''
PERIODIC = {}
for i, per in enumerate(PERIODIC_table.split('\n')):
for j, atom in enumerate(per.split()):
if atom != '__':
PERIODIC[atom] = (i, j)
electronegativity_table = '''2.20 ____ ____ ____ ____ ____ ____ ____ ____ ____ ____ ____ ____ ____ ____ ____ ____ ____
0.98 1.57 ____ ____ ____ ____ ____ ____ ____ ____ ____ ____ 2.04 2.55 3.04 3.44 3.98 ____
0.93 1.31 ____ ____ ____ ____ ____ ____ ____ ____ ____ ____ 1.61 1.90 2.19 2.58 3.16 ____
0.82 1.00 1.36 1.54 1.63 1.66 1.55 1.83 1.88 1.91 1.90 1.65 1.81 2.01 2.18 2.55 2.96 3.00
0.82 0.95 1.22 1.33 1.60 2.16 1.90 2.20 2.28 2.20 1.93 1.69 1.78 1.96 2.05 2.10 2.66 2.60'''
ELECTRONEGATIVITY = {}
for i, per in enumerate(electronegativity_table.split('\n')):
for j, atom_electronegativity in enumerate(per.split()):
if atom_electronegativity != '____':
ELECTRONEGATIVITY[(i, j)] = float(atom_electronegativity)
allowable_atom = ['C', 'O', 'N', 'S', 'P', 'Se', 'F', 'Cl', 'Br', 'I', 'METAL']
allowable_period = [ i for i in range(5) ]
allowable_group = [ i for i in range(18) ]
allowable_degree = [ i for i in range(7) ]
allowable_totalHs = [ i for i in range(5) ]
allowable_hybrid = [ Chem.rdchem.HybridizationType.SP,
Chem.rdchem.HybridizationType.SP2,
Chem.rdchem.HybridizationType.SP3,
Chem.rdchem.HybridizationType.SP3D,
Chem.rdchem.HybridizationType.SP3D2,
Chem.rdchem.HybridizationType.UNSPECIFIED ]
allowable_bond = [ Chem.rdchem.BondType.SINGLE,
Chem.rdchem.BondType.DOUBLE,
Chem.rdchem.BondType.TRIPLE,
Chem.rdchem.BondType.AROMATIC ]
allowable_streo = [ Chem.rdchem.BondStereo.STEREOANY,
Chem.rdchem.BondStereo.STEREOCIS,
Chem.rdchem.BondStereo.STEREOE,
Chem.rdchem.BondStereo.STEREONONE,
Chem.rdchem.BondStereo.STEREOTRANS,
Chem.rdchem.BondStereo.STEREOZ ]
def get_mol_coordinate(mol):
return torch.tensor( mol.GetConformer().GetPositions() ).float()
def atom_feature(atom):
symbol = atom.GetSymbol()
period, group = PERIODIC[ symbol ]
negativity = [ ELECTRONEGATIVITY[(period, group)] / 4 ]
period = one_hot( period, allowable_period )
group = one_hot( group, allowable_group )
symbol = one_hot( symbol, allowable_atom)
degree = one_hot( atom.GetDegree(), allowable_degree )
total_H = one_hot( atom.GetTotalNumHs(), allowable_totalHs )
hybrid = one_hot( atom.GetHybridization(), allowable_hybrid )
aromatic = [ atom.GetIsAromatic() ]
isinring = [ atom.IsInRing() ]
radical = [ atom.GetNumRadicalElectrons() ]
formal_charge = [ atom.GetFormalCharge() * 0.2 ]
return period + group + symbol + degree + total_H + hybrid + aromatic + isinring + radical + formal_charge + negativity
def bond_feature(bond):
bond_type = one_hot( bond.GetBondType(), allowable_bond )
bond_streo = one_hot( bond.GetStereo(), allowable_streo )
isinring = [ bond.IsInRing() ]
conjugated = [ bond.GetIsConjugated() ]
return bond_type + bond_streo + isinring + conjugated
def get_atom_feature(mol):
return torch.tensor( [ atom_feature(atom) for atom in mol.GetAtoms() ] ).float()
def get_indices(mol, smarts):
return torch.tensor( mol.GetSubstructMatches( Chem.MolFromSmarts( smarts ) ) )
def get_bond_feature(mol):
adj = torch.tensor( Chem.GetAdjacencyMatrix(mol) )
rotate = get_indices(mol, "[!$(*#*)&!D1]-!@[!$(*#*)&!D1]")
index = torch.where(adj != 0)
adj = adj.unsqueeze(2)
adj = torch.where(adj > 0, torch.zeros(13), torch.zeros(13))
for i, j in zip(index[0], index[1]):
bf = bond_feature( mol.GetBondBetweenAtoms( int(i), int(j) ) )
rf = [ 1 if len(rotate) != 0 and torch.tensor( [i, j] ) in rotate else 0 ]
adj[i, j] = torch.tensor( bf + rf )
return adj.float()
def get_distance_feature( distance ):
scale_list = [ 1.5 ** x for x in range(15) ]
center_list = [ 0 for _ in range(15) ]
scaled_distance = torch.stack( [ torch.exp( -(( distance - center) ** 2) / float(scale))
for scale, center in zip(scale_list, center_list)], axis=1 )
return scaled_distance
def get_indices(mol, smarts):
return torch.tensor( mol.GetSubstructMatches( Chem.MolFromSmarts( smarts ) ) )
def get_indices_sparse(sparse, indices):
if torch.sum(indices) == 0:
return torch.zeros( len(sparse) )
else:
indices = torch.where( sparse == indices, 1, 0)
indices = torch.sum( indices, dim=-2 )
return indices
def get_smarts_feature(mol, smarts, index):
indices = get_indices(mol, smarts)
indices = get_indices_sparse( index, indices )
return indices
def get_interact_feature(pmol, lmol, protein_node_idx, ligand_node_idx):
hydrogen_accept_smarts = "[!$([#6,F,Cl,Br,I,o,s,nX3,#7v5,#15v5,#16v4,#16v6,*+1,*+2,*+3])]"
hydrogen_donor_smarts = "[!$([#6,H0,-,-2,-3])]"
electron_accept_smarts = "[!H0;F,Cl,Br,I,N+,$([OH]-*=[!#6]),+]"
electron_donor_smarts = "[#7;+,$([N;H2&+0][$([C,a]);!$([C,a](=O))]),$([N;H1&+0]([$([C,a]);!$([C,a](=O))])[$([C,a]);!$([C,a](=O))]),$([N;H0&+0]([C;!$(C(=O))])([C;!$(C(=O))])[C;!$(C(=O))])]"
hydrophobic_smarts = "[C,c,S&H0&v2,F,Cl,Br,I&!$(C=[O,N,P,S])&!$(C#N);!$(C=O)]"
l_hydrogen_accpt = get_smarts_feature( lmol, hydrogen_accept_smarts, ligand_node_idx)
p_hydrogen_accpt = get_smarts_feature( pmol, hydrogen_accept_smarts, protein_node_idx)
l_hydrogen_donor = get_smarts_feature( lmol, hydrogen_donor_smarts, ligand_node_idx)
p_hydrogen_donor = get_smarts_feature( pmol, hydrogen_donor_smarts, protein_node_idx)
l_electron_accpt = get_smarts_feature( lmol, electron_accept_smarts, ligand_node_idx)
p_electron_accpt = get_smarts_feature( pmol, electron_accept_smarts, protein_node_idx)
l_electron_donor = get_smarts_feature( lmol, electron_donor_smarts, ligand_node_idx)
p_electron_donor = get_smarts_feature( pmol, electron_donor_smarts, protein_node_idx)
l_hydrophobic = get_smarts_feature( lmol, hydrophobic_smarts, ligand_node_idx)
p_hydrophobic = get_smarts_feature( pmol, hydrophobic_smarts, protein_node_idx)
interact_adj = torch.stack( [ l_hydrogen_accpt, l_hydrogen_donor, p_hydrogen_accpt, p_hydrogen_donor,
l_electron_accpt, l_electron_donor, p_electron_accpt, p_electron_donor,
l_hydrophobic, p_hydrophobic ], dim=1 )
return interact_adj
import torch
from rdkit import Chem
from .utils import one_hot, is_one
METAL =["LI","NA","K","RB","CS","MG","TL","CU","AG","BE","NI","PT","ZN","CO",\
"PD","AG","CR","FE","V","MN","HG",'GA',"CD","YB","CA","SN","PB","EU",\
"SR","SM","BA","RA","AL","IN","TL","Y","LA","CE","PR","ND","GD","TB",\
"DY","ER","TM","LU","HF","ZR","CE","U","PU","TH","AU"]
PERIODIC_table = '''H __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ He
Li Be __ __ __ __ __ __ __ __ __ __ B C N O F Ne
Na Mg __ __ __ __ __ __ __ __ __ __ Al Si P S Cl Ar
K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr
Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te I Xe'''
PERIODIC = {}
for i, per in enumerate(PERIODIC_table.split('\n')):
for j, atom in enumerate(per.split()):
if atom != '__':
PERIODIC[atom] = (i, j)
electronegativity_table = '''2.20 ____ ____ ____ ____ ____ ____ ____ ____ ____ ____ ____ ____ ____ ____ ____ ____ ____
0.98 1.57 ____ ____ ____ ____ ____ ____ ____ ____ ____ ____ 2.04 2.55 3.04 3.44 3.98 ____
0.93 1.31 ____ ____ ____ ____ ____ ____ ____ ____ ____ ____ 1.61 1.90 2.19 2.58 3.16 ____
0.82 1.00 1.36 1.54 1.63 1.66 1.55 1.83 1.88 1.91 1.90 1.65 1.81 2.01 2.18 2.55 2.96 3.00
0.82 0.95 1.22 1.33 1.60 2.16 1.90 2.20 2.28 2.20 1.93 1.69 1.78 1.96 2.05 2.10 2.66 2.60'''
ELECTRONEGATIVITY = {}
for i, per in enumerate(electronegativity_table.split('\n')):
for j, atom_electronegativity in enumerate(per.split()):
if atom_electronegativity != '____':
ELECTRONEGATIVITY[(i, j)] = float(atom_electronegativity)
allowable_atom = ['C', 'O', 'N', 'S', 'P', 'Se', 'F', 'Cl', 'Br', 'I', 'METAL']
allowable_period = [ i for i in range(5) ]
allowable_group = [ i for i in range(18) ]
allowable_degree = [ i for i in range(7) ]
allowable_totalHs = [ i for i in range(5) ]
allowable_hybrid = [ Chem.rdchem.HybridizationType.SP,
Chem.rdchem.HybridizationType.SP2,
Chem.rdchem.HybridizationType.SP3,
Chem.rdchem.HybridizationType.SP3D,
Chem.rdchem.HybridizationType.SP3D2,
Chem.rdchem.HybridizationType.UNSPECIFIED ]
allowable_bond = [ Chem.rdchem.BondType.SINGLE,
Chem.rdchem.BondType.DOUBLE,
Chem.rdchem.BondType.TRIPLE,
Chem.rdchem.BondType.AROMATIC ]
allowable_streo = [ Chem.rdchem.BondStereo.STEREOANY,
Chem.rdchem.BondStereo.STEREOCIS,
Chem.rdchem.BondStereo.STEREOE,
Chem.rdchem.BondStereo.STEREONONE,
Chem.rdchem.BondStereo.STEREOTRANS,
Chem.rdchem.BondStereo.STEREOZ ]
[docs]
def get_mol_coordinate(mol):
return torch.tensor( mol.GetConformer().GetPositions() ).float()
[docs]
def atom_feature(atom):
symbol = atom.GetSymbol()
period, group = PERIODIC[ symbol ]
negativity = [ ELECTRONEGATIVITY[(period, group)] / 4 ]
period = one_hot( period, allowable_period )
group = one_hot( group, allowable_group )
symbol = one_hot( symbol, allowable_atom)
degree = one_hot( atom.GetDegree(), allowable_degree )
total_H = one_hot( atom.GetTotalNumHs(), allowable_totalHs )
hybrid = one_hot( atom.GetHybridization(), allowable_hybrid )
aromatic = [ atom.GetIsAromatic() ]
isinring = [ atom.IsInRing() ]
radical = [ atom.GetNumRadicalElectrons() ]
formal_charge = [ atom.GetFormalCharge() * 0.2 ]
return period + group + symbol + degree + total_H + hybrid + aromatic + isinring + radical + formal_charge + negativity
[docs]
def bond_feature(bond):
bond_type = one_hot( bond.GetBondType(), allowable_bond )
bond_streo = one_hot( bond.GetStereo(), allowable_streo )
isinring = [ bond.IsInRing() ]
conjugated = [ bond.GetIsConjugated() ]
return bond_type + bond_streo + isinring + conjugated
[docs]
def get_atom_feature(mol):
return torch.tensor( [ atom_feature(atom) for atom in mol.GetAtoms() ] ).float()
def get_indices(mol, smarts):
return torch.tensor( mol.GetSubstructMatches( Chem.MolFromSmarts( smarts ) ) )
[docs]
def get_bond_feature(mol):
adj = torch.tensor( Chem.GetAdjacencyMatrix(mol) )
rotate = get_indices(mol, "[!$(*#*)&!D1]-!@[!$(*#*)&!D1]")
index = torch.where(adj != 0)
adj = adj.unsqueeze(2)
adj = torch.where(adj > 0, torch.zeros(13), torch.zeros(13))
for i, j in zip(index[0], index[1]):
bf = bond_feature( mol.GetBondBetweenAtoms( int(i), int(j) ) )
rf = [ 1 if len(rotate) != 0 and torch.tensor( [i, j] ) in rotate else 0 ]
adj[i, j] = torch.tensor( bf + rf )
return adj.float()
[docs]
def get_distance_feature( distance ):
scale_list = [ 1.5 ** x for x in range(15) ]
center_list = [ 0 for _ in range(15) ]
scaled_distance = torch.stack( [ torch.exp( -(( distance - center) ** 2) / float(scale))
for scale, center in zip(scale_list, center_list)], axis=1 )
return scaled_distance
[docs]
def get_indices(mol, smarts):
return torch.tensor( mol.GetSubstructMatches( Chem.MolFromSmarts( smarts ) ) )
[docs]
def get_indices_sparse(sparse, indices):
if torch.sum(indices) == 0:
return torch.zeros( len(sparse) )
else:
indices = torch.where( sparse == indices, 1, 0)
indices = torch.sum( indices, dim=-2 )
return indices
[docs]
def get_smarts_feature(mol, smarts, index):
indices = get_indices(mol, smarts)
indices = get_indices_sparse( index, indices )
return indices
[docs]
def get_interact_feature(pmol, lmol, protein_node_idx, ligand_node_idx):
hydrogen_accept_smarts = "[!$([#6,F,Cl,Br,I,o,s,nX3,#7v5,#15v5,#16v4,#16v6,*+1,*+2,*+3])]"
hydrogen_donor_smarts = "[!$([#6,H0,-,-2,-3])]"
electron_accept_smarts = "[!H0;F,Cl,Br,I,N+,$([OH]-*=[!#6]),+]"
electron_donor_smarts = "[#7;+,$([N;H2&+0][$([C,a]);!$([C,a](=O))]),$([N;H1&+0]([$([C,a]);!$([C,a](=O))])[$([C,a]);!$([C,a](=O))]),$([N;H0&+0]([C;!$(C(=O))])([C;!$(C(=O))])[C;!$(C(=O))])]"
hydrophobic_smarts = "[C,c,S&H0&v2,F,Cl,Br,I&!$(C=[O,N,P,S])&!$(C#N);!$(C=O)]"
l_hydrogen_accpt = get_smarts_feature( lmol, hydrogen_accept_smarts, ligand_node_idx)
p_hydrogen_accpt = get_smarts_feature( pmol, hydrogen_accept_smarts, protein_node_idx)
l_hydrogen_donor = get_smarts_feature( lmol, hydrogen_donor_smarts, ligand_node_idx)
p_hydrogen_donor = get_smarts_feature( pmol, hydrogen_donor_smarts, protein_node_idx)
l_electron_accpt = get_smarts_feature( lmol, electron_accept_smarts, ligand_node_idx)
p_electron_accpt = get_smarts_feature( pmol, electron_accept_smarts, protein_node_idx)
l_electron_donor = get_smarts_feature( lmol, electron_donor_smarts, ligand_node_idx)
p_electron_donor = get_smarts_feature( pmol, electron_donor_smarts, protein_node_idx)
l_hydrophobic = get_smarts_feature( lmol, hydrophobic_smarts, ligand_node_idx)
p_hydrophobic = get_smarts_feature( pmol, hydrophobic_smarts, protein_node_idx)
interact_adj = torch.stack( [ l_hydrogen_accpt, l_hydrogen_donor, p_hydrogen_accpt, p_hydrogen_donor,
l_electron_accpt, l_electron_donor, p_electron_accpt, p_electron_donor,
l_hydrophobic, p_hydrophobic ], dim=1 )
return interact_adj