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How to get the SMILES of all compounds on PubChem?
Pubchem, InChI, SMILES, and uniquenessPubchem: list all compounds for which Kovats retention indices are availableSoftware for compound database creationenumerationInferring bond breakage in a reaction from InChI strings of reactans?Finding vendor information programmaticallyWhat is the best way to convert SMILES strings to file names?How to index molecules in computer programs?Is it possible to build or embed the SMILES representation of compounds in 3D?
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I would like to download all the compounds from ChEMBL and PubChem. For ChEMBL this is easy using their webUI. Nevertheless, for PubChem, it isn't clear how to download all the compounds on the database including their SMILES representations.
I am also not sure how pubchem has 33,000,000 compounds where ChEMBL has "only" 2,000,000.
aromatic-compounds cheminformatics
asked 14 hours ago
0x900x90
3191 silver badge13 bronze badges
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add a comment
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$begingroup$
I would like to download all the compounds from ChEMBL and PubChem. For ChEMBL this is easy using their webUI. Nevertheless, for PubChem, it isn't clear how to download all the compounds on the database including their SMILES representations.
I am also not sure how pubchem has 33,000,000 compounds where ChEMBL has "only" 2,000,000.
aromatic-compounds cheminformatics
asked 14 hours ago
0x900x90
3191 silver badge13 bronze badges
$endgroup$
1
$begingroup$
Have a look at github.com/mcs07/PubChemPy. Maybe you can find some application of it. And related for ChemSpider: github.com/mcs07/ChemSpiPy
$endgroup$
– Martin - マーチン♦
10 hours ago
add a comment
|
$begingroup$
I would like to download all the compounds from ChEMBL and PubChem. For ChEMBL this is easy using their webUI. Nevertheless, for PubChem, it isn't clear how to download all the compounds on the database including their SMILES representations.
I am also not sure how pubchem has 33,000,000 compounds where ChEMBL has "only" 2,000,000.
aromatic-compounds cheminformatics
asked 14 hours ago
0x900x90
3191 silver badge13 bronze badges
$endgroup$
I would like to download all the compounds from ChEMBL and PubChem. For ChEMBL this is easy using their webUI. Nevertheless, for PubChem, it isn't clear how to download all the compounds on the database including their SMILES representations.
I am also not sure how pubchem has 33,000,000 compounds where ChEMBL has "only" 2,000,000.
aromatic-compounds cheminformatics
aromatic-compounds cheminformatics
asked 14 hours ago
0x900x90
3191 silver badge13 bronze badges
asked 14 hours ago
0x900x90
3191 silver badge13 bronze badges
edited 10 hours ago
0x90
asked 14 hours ago
0x900x90
3191 silver badge13 bronze badges
asked 14 hours ago
0x900x90
3191 silver badge13 bronze badges
asked 14 hours ago
0x900x90
3191 silver badge13 bronze badges
3191 silver badge13 bronze badges
1
$begingroup$
Have a look at github.com/mcs07/PubChemPy. Maybe you can find some application of it. And related for ChemSpider: github.com/mcs07/ChemSpiPy
$endgroup$
– Martin - マーチン♦
10 hours ago
add a comment
|
1
$begingroup$
Have a look at github.com/mcs07/PubChemPy. Maybe you can find some application of it. And related for ChemSpider: github.com/mcs07/ChemSpiPy
$endgroup$
– Martin - マーチン♦
10 hours ago
1
1
$begingroup$
Have a look at github.com/mcs07/PubChemPy. Maybe you can find some application of it. And related for ChemSpider: github.com/mcs07/ChemSpiPy
$endgroup$
– Martin - マーチン♦
10 hours ago
$begingroup$
Have a look at github.com/mcs07/PubChemPy. Maybe you can find some application of it. And related for ChemSpider: github.com/mcs07/ChemSpiPy
$endgroup$
– Martin - マーチン♦
10 hours ago
add a comment
|
1 Answer
1
active
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votes
$begingroup$
The best way to download bulk data from PubChem is actually FTP, as documented in their documentation.
For example, if you want the unfiltered SMILES of every CID in PubChem, the URL is ftp://ftp.ncbi.nlm.nih.gov/pubchem/Compound/Extras/CID-SMILES.gz
You can also download subsets using the PubChem Structure Download service
And as mentioned above, there are Python and other tools to access both PubChem and ChemSpider through their documented web APIs.
answered 9 hours ago
Geoff HutchisonGeoff Hutchison
21.7k3 gold badges56 silver badges117 bronze badges
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1
$begingroup$
One thing to keep in mind.. PubChem intentionally has duplicates - there are SMILES with no stereochemical information and the same SMILES with correct stereo. So depending on your use, you may want to do some level of standardization, filtering and validation.
$endgroup$
– Geoff Hutchison
9 hours ago
add a comment
|
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1 Answer
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1 Answer
1
active
oldest
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active
oldest
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active
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votes
$begingroup$
The best way to download bulk data from PubChem is actually FTP, as documented in their documentation.
For example, if you want the unfiltered SMILES of every CID in PubChem, the URL is ftp://ftp.ncbi.nlm.nih.gov/pubchem/Compound/Extras/CID-SMILES.gz
You can also download subsets using the PubChem Structure Download service
And as mentioned above, there are Python and other tools to access both PubChem and ChemSpider through their documented web APIs.
answered 9 hours ago
Geoff HutchisonGeoff Hutchison
21.7k3 gold badges56 silver badges117 bronze badges
$endgroup$
1
$begingroup$
One thing to keep in mind.. PubChem intentionally has duplicates - there are SMILES with no stereochemical information and the same SMILES with correct stereo. So depending on your use, you may want to do some level of standardization, filtering and validation.
$endgroup$
– Geoff Hutchison
9 hours ago
add a comment
|
$begingroup$
The best way to download bulk data from PubChem is actually FTP, as documented in their documentation.
For example, if you want the unfiltered SMILES of every CID in PubChem, the URL is ftp://ftp.ncbi.nlm.nih.gov/pubchem/Compound/Extras/CID-SMILES.gz
You can also download subsets using the PubChem Structure Download service
And as mentioned above, there are Python and other tools to access both PubChem and ChemSpider through their documented web APIs.
answered 9 hours ago
Geoff HutchisonGeoff Hutchison
21.7k3 gold badges56 silver badges117 bronze badges
$endgroup$
1
$begingroup$
One thing to keep in mind.. PubChem intentionally has duplicates - there are SMILES with no stereochemical information and the same SMILES with correct stereo. So depending on your use, you may want to do some level of standardization, filtering and validation.
$endgroup$
– Geoff Hutchison
9 hours ago
add a comment
|
$begingroup$
The best way to download bulk data from PubChem is actually FTP, as documented in their documentation.
For example, if you want the unfiltered SMILES of every CID in PubChem, the URL is ftp://ftp.ncbi.nlm.nih.gov/pubchem/Compound/Extras/CID-SMILES.gz
You can also download subsets using the PubChem Structure Download service
And as mentioned above, there are Python and other tools to access both PubChem and ChemSpider through their documented web APIs.
answered 9 hours ago
Geoff HutchisonGeoff Hutchison
21.7k3 gold badges56 silver badges117 bronze badges
$endgroup$
The best way to download bulk data from PubChem is actually FTP, as documented in their documentation.
For example, if you want the unfiltered SMILES of every CID in PubChem, the URL is ftp://ftp.ncbi.nlm.nih.gov/pubchem/Compound/Extras/CID-SMILES.gz
You can also download subsets using the PubChem Structure Download service
And as mentioned above, there are Python and other tools to access both PubChem and ChemSpider through their documented web APIs.
answered 9 hours ago
Geoff HutchisonGeoff Hutchison
21.7k3 gold badges56 silver badges117 bronze badges
answered 9 hours ago
Geoff HutchisonGeoff Hutchison
21.7k3 gold badges56 silver badges117 bronze badges
answered 9 hours ago
Geoff HutchisonGeoff Hutchison
21.7k3 gold badges56 silver badges117 bronze badges
answered 9 hours ago
Geoff HutchisonGeoff Hutchison
21.7k3 gold badges56 silver badges117 bronze badges
21.7k3 gold badges56 silver badges117 bronze badges
1
$begingroup$
One thing to keep in mind.. PubChem intentionally has duplicates - there are SMILES with no stereochemical information and the same SMILES with correct stereo. So depending on your use, you may want to do some level of standardization, filtering and validation.
$endgroup$
– Geoff Hutchison
9 hours ago
add a comment
|
1
$begingroup$
One thing to keep in mind.. PubChem intentionally has duplicates - there are SMILES with no stereochemical information and the same SMILES with correct stereo. So depending on your use, you may want to do some level of standardization, filtering and validation.
$endgroup$
– Geoff Hutchison
9 hours ago
1
1
$begingroup$
One thing to keep in mind.. PubChem intentionally has duplicates - there are SMILES with no stereochemical information and the same SMILES with correct stereo. So depending on your use, you may want to do some level of standardization, filtering and validation.
$endgroup$
– Geoff Hutchison
9 hours ago
$begingroup$
One thing to keep in mind.. PubChem intentionally has duplicates - there are SMILES with no stereochemical information and the same SMILES with correct stereo. So depending on your use, you may want to do some level of standardization, filtering and validation.
$endgroup$
– Geoff Hutchison
9 hours ago
add a comment
|
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Have a look at github.com/mcs07/PubChemPy. Maybe you can find some application of it. And related for ChemSpider: github.com/mcs07/ChemSpiPy
$endgroup$
– Martin - マーチン♦
10 hours ago