Re: [Rdkit-discuss] Information contained in SMARTS and SMILES

2017-04-19 Thread Peter S. Shenkin
On Wed, Apr 19, 2017 at 7:25 PM, Andrew Dalke wrote: > On Apr 19, 2017, at 23:59, Peter S. Shenkin wrote: > > One more thing. The term "Mol" in RDKit and some other tookits does not > really mean "molecule" in the sense that chemists use it. > > ? I

Re: [Rdkit-discuss] Information contained in SMARTS and SMILES

2017-04-19 Thread Andrew Dalke
On Apr 19, 2017, at 23:59, Peter S. Shenkin wrote: > One more thing. The term "Mol" in RDKit and some other tookits does not > really mean "molecule" in the sense that chemists use it. ? I don't see how this is connected to the previous emails. I believe most toolkits use

Re: [Rdkit-discuss] Information contained in SMARTS and SMILES

2017-04-19 Thread Peter S. Shenkin
One more thing. The term "Mol" in RDKit and some other tookits does not really mean "molecule" in the sense that chemists use it. It is used to connote a data structure that can store a SMARTS or a SMILES. Only when a SMILES is used does it really correspond to a chemical "molecule", except, in

Re: [Rdkit-discuss] Information contained in SMARTS and SMILES

2017-04-19 Thread Andrew Dalke
On Apr 19, 2017, at 18:26, Curt Fischer wrote: > From chemistry stack exchange, an answer contributed by user R.M.: > > SMARTS is deliberately designed to be a superset of SMILES. That is, any > valid SMILES depiction should also be a valid SMARTS query, one that will

Re: [Rdkit-discuss] Information contained in SMARTS and SMILES

2017-04-19 Thread Andrew Dalke
On Apr 19, 2017, at 12:03, Thilo Bauer wrote: > is converting SMARTS to SMILES a "lossless" operation, or does one loose > information on doing so? It is obviously not lossless if you include terms that cannot be represented in SMILES. >>> from rdkit import Chem >>>

Re: [Rdkit-discuss] Information contained in SMARTS and SMILES

2017-04-19 Thread Curt Fischer
Hi Thilo, Interesting question. rdkit-discuss members should know you also posted a very similar question to https://chemistry.stackexchange.com/questions/72880/is-converting-smarts-to-smiles-a-lossless-operation . If an interesting answer materializes here, it would be useful to post it there,

[Rdkit-discuss] Information contained in SMARTS and SMILES

2017-04-19 Thread Thilo Bauer
Dear mailinglist-members, is converting SMARTS to SMILES a "lossless" operation, or does one loose information on doing so? Background: I've got three different SMARTS strings representing the same structure - at least when depicting it. Also all three strings result in the exact same SMILES