本文整理匯總了Python中rdkit.Chem.GetPeriodicTable方法的典型用法代碼示例。如果您正苦於以下問題：Python Chem.GetPeriodicTable方法的具體用法？Python Chem.GetPeriodicTable怎麽用？Python Chem.GetPeriodicTable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.GetPeriodicTable方法的4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: get_AC
# 需要導入模塊: from rdkit import Chem [as 別名]
# 或者: from rdkit.Chem import GetPeriodicTable [as 別名]
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 示例2: _CalculateEState
# 需要導入模塊: from rdkit import Chem [as 別名]
# 或者: from rdkit.Chem import GetPeriodicTable [as 別名]
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 示例3: xyz2AC
# 需要導入模塊: from rdkit import Chem [as 別名]
# 或者: from rdkit.Chem import GetPeriodicTable [as 別名]
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 示例4: rdkit_invariants_from_atom
# 需要導入模塊: from rdkit import Chem [as 別名]
# 或者: from rdkit.Chem import GetPeriodicTable [as 別名]
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,
)