Python Chem.AddHs方法代碼示例

本文整理匯總了Python中rdkit.Chem.AddHs方法的典型用法代碼示例。如果您正苦於以下問題：Python Chem.AddHs方法的具體用法？Python Chem.AddHs怎麽用？Python Chem.AddHs使用的例子？那麽, 這裏精選的方法代碼示例或許可以為您提供幫助。您也可以進一步了解該方法所在類rdkit.Chem的用法示例。

在下文中一共展示了Chem.AddHs方法的15個代碼示例，這些例子默認根據受歡迎程度排序。您可以為喜歡或者感覺有用的代碼點讚，您的評價將有助於係統推薦出更棒的Python代碼示例。

示例1: generate_structure_from_smiles

# 需要導入模塊: from rdkit import Chem [as 別名]
# 或者: from rdkit.Chem import AddHs [as 別名]
def generate_structure_from_smiles(smiles):

    # Generate a 3D structure from smiles

    mol = Chem.MolFromSmiles(smiles)
    mol = Chem.AddHs(mol)

    status = AllChem.EmbedMolecule(mol)
    status = AllChem.UFFOptimizeMolecule(mol)

    conformer = mol.GetConformer()
    coordinates = conformer.GetPositions()
    coordinates = np.array(coordinates)

    atoms = get_atoms(mol)

    return atoms, coordinates

開發者ID:jensengroup，項目名稱:xyz2mol，代碼行數:19，代碼來源:test.py

示例2: _CalculateElementMaxPCharge

# 需要導入模塊: from rdkit import Chem [as 別名]
# 或者: from rdkit.Chem import AddHs [as 別名]
def _CalculateElementMaxPCharge(mol, AtomicNum=6):
    """
    #################################################################
    **Internal used only**

    Most positive charge on atom with atomic number equal to n
    #################################################################
    """
    Hmol = Chem.AddHs(mol)
    GMCharge.ComputeGasteigerCharges(Hmol, iter_step)
    res = []
    for atom in Hmol.GetAtoms():
        if atom.GetAtomicNum() == AtomicNum:
            res.append(float(atom.GetProp("_GasteigerCharge")))

    if res == []:
        return 0
    else:
        return round(max(res), 3)

開發者ID:gadsbyfly，項目名稱:PyBioMed，代碼行數:21，代碼來源:charge.py

示例3: _CalculateElementMaxNCharge

# 需要導入模塊: from rdkit import Chem [as 別名]
# 或者: from rdkit.Chem import AddHs [as 別名]
def _CalculateElementMaxNCharge(mol, AtomicNum=6):
    """
    #################################################################
    **Internal used only**

    Most negative charge on atom with atomic number equal to n
    #################################################################
    """
    Hmol = Chem.AddHs(mol)
    GMCharge.ComputeGasteigerCharges(Hmol, iter_step)
    res = []
    for atom in Hmol.GetAtoms():
        if atom.GetAtomicNum() == AtomicNum:
            res.append(float(atom.GetProp("_GasteigerCharge")))
    if res == []:
        return 0
    else:
        return round(min(res), 3)

開發者ID:gadsbyfly，項目名稱:PyBioMed，代碼行數:20，代碼來源:charge.py

示例4: CalculateAllMaxPCharge

# 需要導入模塊: from rdkit import Chem [as 別名]
# 或者: from rdkit.Chem import AddHs [as 別名]
def CalculateAllMaxPCharge(mol):
    """
    #################################################################
    Most positive charge on ALL atoms

    -->Qmax

    Usage:

        result=CalculateAllMaxPCharge(mol)

        Input: mol is a molecule object.

        Output: result is a numeric value.
    #################################################################
    """
    Hmol = Chem.AddHs(mol)
    GMCharge.ComputeGasteigerCharges(Hmol, iter_step)
    res = []
    for atom in Hmol.GetAtoms():
        res.append(float(atom.GetProp("_GasteigerCharge")))
    if res == []:
        return 0
    else:
        return round(max(res), 3)

開發者ID:gadsbyfly，項目名稱:PyBioMed，代碼行數:27，代碼來源:charge.py

示例5: CalculateAllMaxNCharge

# 需要導入模塊: from rdkit import Chem [as 別名]
# 或者: from rdkit.Chem import AddHs [as 別名]
def CalculateAllMaxNCharge(mol):
    """
    #################################################################
    Most negative charge on all atoms

    -->Qmin

    Usage:

        result=CalculateAllMaxNCharge(mol)

        Input: mol is a molecule object.

        Output: result is a numeric value.
    #################################################################
    """
    Hmol = Chem.AddHs(mol)
    GMCharge.ComputeGasteigerCharges(Hmol, iter_step)
    res = []
    for atom in Hmol.GetAtoms():
        res.append(float(atom.GetProp("_GasteigerCharge")))
    if res == []:
        return 0
    else:
        return round(min(res), 3)

開發者ID:gadsbyfly，項目名稱:PyBioMed，代碼行數:27，代碼來源:charge.py

示例6: _CalculateElementSumSquareCharge

# 需要導入模塊: from rdkit import Chem [as 別名]
# 或者: from rdkit.Chem import AddHs [as 別名]
def _CalculateElementSumSquareCharge(mol, AtomicNum=6):
    """
    #################################################################
    **Internal used only**

    Ths sum of square Charges on all atoms with atomicnumber equal to n
    #################################################################
    """
    Hmol = Chem.AddHs(mol)
    GMCharge.ComputeGasteigerCharges(Hmol, iter_step)
    res = []
    for atom in Hmol.GetAtoms():
        if atom.GetAtomicNum() == AtomicNum:
            res.append(float(atom.GetProp("_GasteigerCharge")))
    if res == []:
        return 0
    else:
        return round(sum(numpy.square(res)), 3)

開發者ID:gadsbyfly，項目名稱:PyBioMed，代碼行數:20，代碼來源:charge.py

示例7: CalculateHydrogenNumber

# 需要導入模塊: from rdkit import Chem [as 別名]
# 或者: from rdkit.Chem import AddHs [as 別名]
def CalculateHydrogenNumber(mol):

    """
    #################################################################
    Calculation of Number of Hydrogen in a molecule

    ---->nhyd

    Usage:

        result=CalculateHydrogenNumber(mol)

        Input: mol is a molecule object.

        Output: result is a numeric value.
    #################################################################
    """
    i = 0
    Hmol = Chem.AddHs(mol)
    for atom in Hmol.GetAtoms():
        if atom.GetAtomicNum() == 1:
            i = i + 1

    return i

開發者ID:gadsbyfly，項目名稱:PyBioMed，代碼行數:26，代碼來源:constitution.py

示例8: CalculateAllAtomNumber

# 需要導入模塊: from rdkit import Chem [as 別名]
# 或者: from rdkit.Chem import AddHs [as 別名]
def CalculateAllAtomNumber(mol):
    """
    #################################################################
    Calculation of all atom counts in a molecule

    ---->nta

    Usage:

        result=CalculateAllAtomNumber(mol)

        Input: mol is a molecule object.

        Output: result is a numeric value.
    #################################################################
    """

    return Chem.AddHs(mol).GetNumAtoms()

開發者ID:gadsbyfly，項目名稱:PyBioMed，代碼行數:20，代碼來源:constitution.py

示例9: CalculateBasakSIC0

# 需要導入模塊: from rdkit import Chem [as 別名]
# 或者: from rdkit.Chem import AddHs [as 別名]
def CalculateBasakSIC0(mol):
    """
    #################################################################
    Obtain the structural information content with order 0

    proposed by Basak

    ---->SIC0
    #################################################################
    """

    Hmol = Chem.AddHs(mol)
    nAtoms = Hmol.GetNumAtoms()
    IC = CalculateBasakIC0(mol)
    if nAtoms <= 1:
        BasakSIC = 0.0
    else:
        BasakSIC = IC / numpy.log2(nAtoms)

    return BasakSIC

開發者ID:gadsbyfly，項目名稱:PyBioMed，代碼行數:22，代碼來源:basak.py

示例10: CalculateBasakCIC0

# 需要導入模塊: from rdkit import Chem [as 別名]
# 或者: from rdkit.Chem import AddHs [as 別名]
def CalculateBasakCIC0(mol):

    """
    #################################################################
    Obtain the complementary information content with order 0

    proposed by Basak

    ---->CIC0
    #################################################################
    """
    Hmol = Chem.AddHs(mol)
    nAtoms = Hmol.GetNumAtoms()
    IC = CalculateBasakIC0(mol)
    if nAtoms <= 1:
        BasakCIC = 0.0
    else:
        BasakCIC = numpy.log2(nAtoms) - IC

    return BasakCIC

開發者ID:gadsbyfly，項目名稱:PyBioMed，代碼行數:22，代碼來源:basak.py