rdkit.Chem.TemplateAlign module

rdkit.Chem.TemplateAlign.AlignMolToTemplate2D(mol, template, match=None, clearConfs=False, templateConfId=-1)

Parameters:

• mol (-) – the molecule to be aligned

• template (-) – the template to align to

• match (-) –

  If provided, this should be a sequence of integers containing the indices of the atoms in mol that match those in template. This is the result of calling:

  mol.GetSubstructMatch(template)

• clearConfs (-) –

  toggles removing any existing conformers on mol

  Returns the confId of the conformer containing the depiction

  >>> patt = Chem.MolFromSmiles('C1CC1')
  >>> rdDepictor.Compute2DCoords(patt)
  0
  >>> mol = Chem.MolFromSmiles('OC1CC1CC1CCC1')
  >>> rdDepictor.Compute2DCoords(mol)
  0
  >>> pc = patt.GetConformer(0)
  >>> mc = mol.GetConformer(0)
  

  We start out with the molecules not aligned:

  >>> vs = [abs(pc.GetAtomPosition(i).x-mc.GetAtomPosition(i+1).x) for i in range(pc.GetNumAtoms())]
  >>> [x<1e-4 for x in vs]
  [False, False, False]
  

  But then we can replace the conformer of mol:

  >>> AlignMolToTemplate2D(mol,patt,clearConfs=True)
  0
  >>> mol.GetNumConformers()
  1
  >>> pc = patt.GetConformer(0)
  >>> mc = mol.GetConformer(0)
  >>> vs = [abs(pc.GetAtomPosition(i).x-mc.GetAtomPosition(i+1).x) for i in range(pc.GetNumAtoms())]
  >>> [x<1e-4 for x in vs]
  [True, True, True]
  

  If we like, we can specify the atom map explicitly in order to align to the second matching ring in the probe molecule:

  >>> match = (5,6,7)
  >>> AlignMolToTemplate2D(mol,patt,clearConfs=True,match=match)
  0
  >>> mol.GetNumConformers()
  1
  >>> pc = patt.GetConformer(0)
  >>> mc = mol.GetConformer(0)
  >>> vs = [abs(pc.GetAtomPosition(i).x-mc.GetAtomPosition(i+1).x) for i in range(pc.GetNumAtoms())]
  >>> [x<1e-4 for x in vs]
  [False, False, False]
  >>> vs = [abs(pc.GetAtomPosition(i).x-mc.GetAtomPosition(i+5).x) for i in range(pc.GetNumAtoms())]
  >>> [x<1e-4 for x in vs]
  [True, True, True]