Python rdkit.Chem.GetPeriodicTable() Examples

The following are 4 code examples of rdkit.Chem.GetPeriodicTable(). You can vote up the ones you like or vote down the ones you don't like, and go to the original project or source file by following the links above each example. You may also want to check out all available functions/classes of the module rdkit.Chem , or try the search function .
Example #1
Source File: xyz2mol.py    From xyz2mol with MIT License 5 votes vote down vote up 
def get_AC(mol, covalent_factor=1.3):
    """

    Generate adjacent matrix from atoms and coordinates.

    AC is a (num_atoms, num_atoms) matrix with 1 being covalent bond and 0 is not


    covalent_factor - 1.3 is an arbitrary factor

    args:
        mol - rdkit molobj with 3D conformer

    optional
        covalent_factor - increase covalent bond length threshold with facto

    returns:
        AC - adjacent matrix

    """

    # Calculate distance matrix
    dMat = Chem.Get3DDistanceMatrix(mol)

    pt = Chem.GetPeriodicTable()
    num_atoms = mol.GetNumAtoms()
    AC = np.zeros((num_atoms, num_atoms), dtype=int)

    for i in range(num_atoms):
        a_i = mol.GetAtomWithIdx(i)
        Rcov_i = pt.GetRcovalent(a_i.GetAtomicNum()) * covalent_factor
        for j in range(i + 1, num_atoms):
            a_j = mol.GetAtomWithIdx(j)
            Rcov_j = pt.GetRcovalent(a_j.GetAtomicNum()) * covalent_factor
            if dMat[i, j] <= Rcov_i + Rcov_j:
                AC[i, j] = 1
                AC[j, i] = 1

    return AC
Example #2
Source File: estate.py    From PyBioMed with BSD 3-Clause "New" or "Revised" License 5 votes vote down vote up 
def _CalculateEState(mol, skipH=1):
    """
    #################################################################
    **Internal used only**

    Get the EState value of each atom in a molecule
    #################################################################
    """
    mol = Chem.AddHs(mol)
    if skipH == 1:
        mol = Chem.RemoveHs(mol)
    tb1 = Chem.GetPeriodicTable()
    nAtoms = mol.GetNumAtoms()
    Is = numpy.zeros(nAtoms, numpy.float)
    for i in range(nAtoms):
        at = mol.GetAtomWithIdx(i)
        atNum = at.GetAtomicNum()
        d = at.GetDegree()
        if d > 0:
            h = at.GetTotalNumHs()
            dv = tb1.GetNOuterElecs(atNum) - h
            # dv=numpy.array(_AtomHKDeltas(at),'d')
            N = _GetPrincipleQuantumNumber(atNum)
            Is[i] = (4.0 / (N * N) * dv + 1) / d
    dists = Chem.GetDistanceMatrix(mol, useBO=0, useAtomWts=0)
    dists += 1
    accum = numpy.zeros(nAtoms, numpy.float)
    for i in range(nAtoms):
        for j in range(i + 1, nAtoms):
            p = dists[i, j]
            if p < 1e6:
                temp = (Is[i] - Is[j]) / (p * p)
                accum[i] += temp
                accum[j] -= temp
    res = accum + Is
    return res
Example #3
Source File: xyz2mol.py    From BCAI_kaggle_CHAMPS with MIT License 5 votes vote down vote up 
def xyz2AC(atomicNumList,xyz):
    import numpy as np
    mol = get_proto_mol(atomicNumList)

    conf = Chem.Conformer(mol.GetNumAtoms())
    for i in range(mol.GetNumAtoms()):
        conf.SetAtomPosition(i,(xyz[i][0],xyz[i][1],xyz[i][2]))
    mol.AddConformer(conf)

    dMat = Chem.Get3DDistanceMatrix(mol)
    pt = Chem.GetPeriodicTable()

    num_atoms = len(atomicNumList)
    AC = np.zeros((num_atoms,num_atoms)).astype(int)

    for i in range(num_atoms):
        a_i = mol.GetAtomWithIdx(i)
        Rcov_i = pt.GetRcovalent(a_i.GetAtomicNum())*1.30
        for j in range(i+1,num_atoms):
            a_j = mol.GetAtomWithIdx(j)
            Rcov_j = pt.GetRcovalent(a_j.GetAtomicNum())*1.30
            if dMat[i,j] <= Rcov_i + Rcov_j:
                AC[i,j] = 1
                AC[j,i] = 1

    return AC,mol
Example #4
Source File: fprinter.py    From e3fp with GNU Lesser General Public License v3.0 5 votes vote down vote up 
def rdkit_invariants_from_atom(atom):
    """Get the 6 atom invariants RDKit uses for its Morgan fingerprints.

    Parameters
    ----------
    atom : RDKit Atom
        Input atom

    Returns
    -------
    1-D array if int64: Array of 6 invariants
    """
    delta_mass = int(
        atom.GetMass()
        - Chem.GetPeriodicTable().GetAtomicWeight(atom.GetAtomicNum())
    )
    return np.array(
        [
            atom.GetAtomicNum(),
            atom.GetTotalDegree(),
            atom.GetTotalNumHs(),
            atom.GetFormalCharge(),
            delta_mass,
            int(atom.IsInRing()),
        ],
        dtype=IDENT_DTYPE,
    )