Convert list of smiles strings ['x', 'y', 'z'] to mol files or MDL mol blocks using RDKit
I have generated a list of smiles strings and defined them as 'result'
I'd like to convert each SMILES string in the list to separate mol files using RDKit. My current code is this:
m = Chem.MolFromSmiles('result')
print(Chem.MolToMolBlock(m))
This script does not work and returns:
ArgumentError: Python argument types in
rdkit.Chem.rdmolfiles.MolToMolBlock(NoneType) did not match C++ signature:
MolToMolBlock(RDKit::ROMol mol, bool includeStereo=True, int confId=-1, bool kekulize=True, bool forceV3000=False)
How would I go about correcting this?
Thanks!
python-3.x spyder rdkit
edited Nov 12 '18 at 3:05
Graham
3,533123559
asked Nov 12 '18 at 0:50
Matt Hostetler
62
add a comment |
I have generated a list of smiles strings and defined them as 'result'
I'd like to convert each SMILES string in the list to separate mol files using RDKit. My current code is this:
m = Chem.MolFromSmiles('result')
print(Chem.MolToMolBlock(m))
This script does not work and returns:
ArgumentError: Python argument types in
rdkit.Chem.rdmolfiles.MolToMolBlock(NoneType) did not match C++ signature:
MolToMolBlock(RDKit::ROMol mol, bool includeStereo=True, int confId=-1, bool kekulize=True, bool forceV3000=False)
How would I go about correcting this?
Thanks!
python-3.x spyder rdkit
edited Nov 12 '18 at 3:05
Graham
3,533123559
asked Nov 12 '18 at 0:50
Matt Hostetler
62
add a comment |
I have generated a list of smiles strings and defined them as 'result'
I'd like to convert each SMILES string in the list to separate mol files using RDKit. My current code is this:
m = Chem.MolFromSmiles('result')
print(Chem.MolToMolBlock(m))
This script does not work and returns:
ArgumentError: Python argument types in
rdkit.Chem.rdmolfiles.MolToMolBlock(NoneType) did not match C++ signature:
MolToMolBlock(RDKit::ROMol mol, bool includeStereo=True, int confId=-1, bool kekulize=True, bool forceV3000=False)
How would I go about correcting this?
Thanks!
python-3.x spyder rdkit
edited Nov 12 '18 at 3:05
Graham
3,533123559
asked Nov 12 '18 at 0:50
Matt Hostetler
62
I have generated a list of smiles strings and defined them as 'result'
I'd like to convert each SMILES string in the list to separate mol files using RDKit. My current code is this:
m = Chem.MolFromSmiles('result')
print(Chem.MolToMolBlock(m))
This script does not work and returns:
ArgumentError: Python argument types in
rdkit.Chem.rdmolfiles.MolToMolBlock(NoneType) did not match C++ signature:
MolToMolBlock(RDKit::ROMol mol, bool includeStereo=True, int confId=-1, bool kekulize=True, bool forceV3000=False)
How would I go about correcting this?
Thanks!
python-3.x spyder rdkit
python-3.x spyder rdkit
edited Nov 12 '18 at 3:05
Graham
3,533123559
asked Nov 12 '18 at 0:50
Matt Hostetler
62
edited Nov 12 '18 at 3:05
Graham
3,533123559
asked Nov 12 '18 at 0:50
Matt Hostetler
62
edited Nov 12 '18 at 3:05
Graham
3,533123559
edited Nov 12 '18 at 3:05
Graham
3,533123559
edited Nov 12 '18 at 3:05
Graham
3,533123559
3,533123559
asked Nov 12 '18 at 0:50
Matt Hostetler
62
asked Nov 12 '18 at 0:50
Matt Hostetler
62
asked Nov 12 '18 at 0:50
Matt Hostetler
62
62
add a comment |
add a comment |
1 Answer
1
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oldest
votes
You converted the string 'result' to a RDKit mol object. And this could not not be transformed to a Molblock.
Variable names are not strings, so don't use them with quotes.
First you have to convert the SMILES one by one to mol objects.
from rdkit import Chem
result = ['C', 'CC', 'CCC']
mo = [Chem.MolFromSmiles(r) for r in result]
Then you can print the Molblocks one by one.
for m in mo:
print(Chem.MolToMolBlock(m))
That will give you this:
RDKit 2D
1 0 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
M END
RDKit 2D
2 1 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.2990 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
M END
RDKit 2D
3 2 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.2990 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.5981 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 1 0
M END
answered Nov 12 '18 at 17:37
rapelpy
146115
add a comment |
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1 Answer
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oldest
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1 Answer
1
active
oldest
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active
oldest
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active
oldest
votes
You converted the string 'result' to a RDKit mol object. And this could not not be transformed to a Molblock.
Variable names are not strings, so don't use them with quotes.
First you have to convert the SMILES one by one to mol objects.
from rdkit import Chem
result = ['C', 'CC', 'CCC']
mo = [Chem.MolFromSmiles(r) for r in result]
Then you can print the Molblocks one by one.
for m in mo:
print(Chem.MolToMolBlock(m))
That will give you this:
RDKit 2D
1 0 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
M END
RDKit 2D
2 1 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.2990 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
M END
RDKit 2D
3 2 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.2990 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.5981 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 1 0
M END
answered Nov 12 '18 at 17:37
rapelpy
146115
add a comment |
You converted the string 'result' to a RDKit mol object. And this could not not be transformed to a Molblock.
Variable names are not strings, so don't use them with quotes.
First you have to convert the SMILES one by one to mol objects.
from rdkit import Chem
result = ['C', 'CC', 'CCC']
mo = [Chem.MolFromSmiles(r) for r in result]
Then you can print the Molblocks one by one.
for m in mo:
print(Chem.MolToMolBlock(m))
That will give you this:
RDKit 2D
1 0 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
M END
RDKit 2D
2 1 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.2990 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
M END
RDKit 2D
3 2 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.2990 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.5981 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 1 0
M END
answered Nov 12 '18 at 17:37
rapelpy
146115
add a comment |
You converted the string 'result' to a RDKit mol object. And this could not not be transformed to a Molblock.
Variable names are not strings, so don't use them with quotes.
First you have to convert the SMILES one by one to mol objects.
from rdkit import Chem
result = ['C', 'CC', 'CCC']
mo = [Chem.MolFromSmiles(r) for r in result]
Then you can print the Molblocks one by one.
for m in mo:
print(Chem.MolToMolBlock(m))
That will give you this:
RDKit 2D
1 0 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
M END
RDKit 2D
2 1 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.2990 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
M END
RDKit 2D
3 2 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.2990 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.5981 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 1 0
M END
answered Nov 12 '18 at 17:37
rapelpy
146115
You converted the string 'result' to a RDKit mol object. And this could not not be transformed to a Molblock.
Variable names are not strings, so don't use them with quotes.
First you have to convert the SMILES one by one to mol objects.
from rdkit import Chem
result = ['C', 'CC', 'CCC']
mo = [Chem.MolFromSmiles(r) for r in result]
Then you can print the Molblocks one by one.
for m in mo:
print(Chem.MolToMolBlock(m))
That will give you this:
RDKit 2D
1 0 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
M END
RDKit 2D
2 1 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.2990 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
M END
RDKit 2D
3 2 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.2990 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.5981 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 1 0
M END
answered Nov 12 '18 at 17:37
rapelpy
146115
answered Nov 12 '18 at 17:37
rapelpy
146115
answered Nov 12 '18 at 17:37
rapelpy
146115
answered Nov 12 '18 at 17:37
rapelpy
146115
146115
add a comment |
add a comment |
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