Re: [Rdkit-discuss] MolFromPDBBlock and heterocycles
Hi Steven,
The PDB reader in the RDKit doesn’t determine any bond orders - everything
is read as a single bond.
In order to set the bond orders, you need to call the
AssignBondOrdersFromTemplate() function using a reference molecule
generated from SMILES (or SDF).
Here is some example code from the docs:
>>> from rdkit.Chem import AllChem
>>> template = AllChem.MolFromSmiles("CN1C(=NC(C1=O)(c2c2)c3c3)N")
>>> mol = AllChem.MolFromPDBFile(os.path.join(RDConfig.RDCodeDir, 'Chem',
'test_data', '4DJU_lig.pdb'))
>>> len([1 for b in template.GetBonds() if b.GetBondTypeAsDouble() == 1.0])
8
>>> len([1 for b in mol.GetBonds() if b.GetBondTypeAsDouble() == 1.0])
22
Now assign the bond orders based on the template molecule
>>> newMol = AllChem.AssignBondOrdersFromTemplate(template, mol)
>>> len([1 for b in newMol.GetBonds() if b.GetBondTypeAsDouble() == 1.0])
8
Note that the template molecule should have no explicit hydrogens
else the algorithm will fail.
Hope this helps.
Best,
Sereina
2016-09-07 17:16 GMT+02:00 Steven Combs :
> Hello!
>
> I have a pdb block that I am working with, which is attached to this
> email. The ligand has aromatic ring structures in it; however, when it is
> read into RDKit and converted into a smiles string, the aromatic rings are
> converted into aliphatic rings. Any thoughts?
>
> Here is the python code:
>
> def extract_data( filename):
> extracted_info = ""
> with open(filename) as f:
> for line in f.readlines():
> if "HETATM" in line:
> extracted_info += ( line)
> return extracted_info
>
> for index, filename in enumerate(solution_pdb_filenames):
> row = extract_data( filename)
> m = Chem.MolFromPDBBlock(row, sanitize=True, removeHs=False )
> Chem.SetHybridization(m)
> Chem.SetAromaticity(m)
> Chem.SanitizeMol(m,
> sanitizeOps=Chem.rdmolops.SanitizeFlags.SANITIZE_ALL)
> #not needed since sanitizing during read in, but trying to figure out if it
> actually worked
> print ("Parsing file " + str(index) + " of " +
> str(len(solution_pdb_filenames)))
> print (Chem.MolToSmiles(m, kekuleSmiles=True, allHsExplicit=True))
>
> The output smile string is:
>
> [H][O][CH]1[NH][CH]([C]([H])([H])[CH]([OH])[OH])[CH]([C]([H]
> )([H])[C]([H])([H])[H])[CH]([CH]([OH])[CH]2[CH]([H])[CH]([
> H])[CH]([H])[CH]([N]([H])[H])[CH]2[H])[CH]1[N]([C]([H])([H])
> [H])[C]([H])([H])[H]
>
> Steven Combs
>
>
>
>
> --
>
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Re: [Rdkit-discuss] MolFromPDBBlock and heterocycles
Hi Steven,
The PDB reader in the RDKit doesn’t determine any bond orders - everything is
read as a single bond.
In order to set the bond orders, you need to call the
AssignBondOrdersFromTemplate() function using a reference molecule generated
from SMILES (or SDF).
Here is some example code from the docs:
>>> from rdkit.Chem import AllChem
>>> template = AllChem.MolFromSmiles("CN1C(=NC(C1=O)(c2c2)c3c3)N")
>>> mol = AllChem.MolFromPDBFile(os.path.join(RDConfig.RDCodeDir, 'Chem',
>>> 'test_data', '4DJU_lig.pdb'))
>>> len([1 for b in template.GetBonds() if b.GetBondTypeAsDouble() == 1.0])
8
>>> len([1 for b in mol.GetBonds() if b.GetBondTypeAsDouble() == 1.0])
22
Now assign the bond orders based on the template molecule
>>> newMol = AllChem.AssignBondOrdersFromTemplate(template, mol)
>>> len([1 for b in newMol.GetBonds() if b.GetBondTypeAsDouble() == 1.0])
8
Note that the template molecule should have no explicit hydrogens
else the algorithm will fail.
Hope this helps.
Best,
Sereina
On 07 Sep 2016, at 17:16, Steven Combs wrote:
> Hello!
>
> I have a pdb block that I am working with, which is attached to this email.
> The ligand has aromatic ring structures in it; however, when it is read into
> RDKit and converted into a smiles string, the aromatic rings are converted
> into aliphatic rings. Any thoughts?
>
> Here is the python code:
>
> def extract_data( filename):
> extracted_info = ""
> with open(filename) as f:
> for line in f.readlines():
> if "HETATM" in line:
> extracted_info += ( line)
> return extracted_info
>
> for index, filename in enumerate(solution_pdb_filenames):
> row = extract_data( filename)
> m = Chem.MolFromPDBBlock(row, sanitize=True, removeHs=False )
> Chem.SetHybridization(m)
> Chem.SetAromaticity(m)
> Chem.SanitizeMol(m,
> sanitizeOps=Chem.rdmolops.SanitizeFlags.SANITIZE_ALL) #not needed since
> sanitizing during read in, but trying to figure out if it actually worked
> print ("Parsing file " + str(index) + " of " +
> str(len(solution_pdb_filenames)))
> print (Chem.MolToSmiles(m, kekuleSmiles=True, allHsExplicit=True))
>
> The output smile string is:
>
> [H][O][CH]1[NH][CH]([C]([H])([H])[CH]([OH])[OH])[CH]([C]([H])([H])[C]([H])([H])[H])[CH]([CH]([OH])[CH]2[CH]([H])[CH]([H])[CH]([H])[CH]([N]([H])[H])[CH]2[H])[CH]1[N]([C]([H])([H])[H])[C]([H])([H])[H]
>
> Steven Combs
>
>
> --
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[Rdkit-discuss] MolFromPDBBlock and heterocycles
Hello!
I have a pdb block that I am working with, which is attached to this email.
The ligand has aromatic ring structures in it; however, when it is read
into RDKit and converted into a smiles string, the aromatic rings are
converted into aliphatic rings. Any thoughts?
Here is the python code:
def extract_data( filename):
extracted_info = ""
with open(filename) as f:
for line in f.readlines():
if "HETATM" in line:
extracted_info += ( line)
return extracted_info
for index, filename in enumerate(solution_pdb_filenames):
row = extract_data( filename)
m = Chem.MolFromPDBBlock(row, sanitize=True, removeHs=False )
Chem.SetHybridization(m)
Chem.SetAromaticity(m)
Chem.SanitizeMol(m,
sanitizeOps=Chem.rdmolops.SanitizeFlags.SANITIZE_ALL) #not needed since
sanitizing during read in, but trying to figure out if it actually worked
print ("Parsing file " + str(index) + " of " +
str(len(solution_pdb_filenames)))
print (Chem.MolToSmiles(m, kekuleSmiles=True, allHsExplicit=True))
The output smile string is:
[H][O][CH]1[NH][CH]([C]([H])([H])[CH]([OH])[OH])[CH]([C]([H])([H])[C]([H])([H])[H])[CH]([CH]([OH])[CH]2[CH]([H])[CH]([H])[CH]([H])[CH]([N]([H])[H])[CH]2[H])[CH]1[N]([C]([H])([H])[H])[C]([H])([H])[H]
Steven Combs
test.pdb
Description: Protein Databank data
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