Re: [Rdkit-discuss] RDkit and Pubchem

2017-12-01 Thread Sundar
Hi Jason, Thanks for the info. That's exactly what I want. I want to download the compound in any format (smiles/mol/sdf) for which I only have the Substance ID. Sundar On Fri, Dec 1, 2017 at 8:06 PM, Jason Biggs wrote: > Sundar, > What you do will depend on whether

Re: [Rdkit-discuss] RDkit and Pubchem

2017-12-01 Thread Sundar
I would like to download at least SMILES (great if I can also download mol files). And the same is true for Pubchem Compound ID or using Substance ID. Or even download the whole data set using an assay id. Anything could help. Thanks, Jubi On Fri, Dec 1, 2017 at 11:55 AM, Tim Dudgeon

Re: [Rdkit-discuss] RDkit and Pubchem

2017-12-01 Thread Scalfani, Vincent
Hi Jubi, If you need the entire dataset and are not creating queries via the API, you can download all PubChem Data via ftp here: ftp://ftp.ncbi.nlm.nih.gov/pubchem/ Then download the SDFs, and extract out SMILES (I’ve used regular expressions that match the appropriate data tag with good

[Rdkit-discuss] Cartridge upgrades

2017-12-01 Thread Tim Dudgeon
If upgrading PostgreSQL to a new version of the RDKit cartridge is any maintenance needed? Either rebuild the indexes or regenerate the fingerprints and rebuild the indexes? -- Check out the vibrant tech community

Re: [Rdkit-discuss] RDkit and Pubchem

2017-12-01 Thread Dimitri Maziuk
On 12/01/2017 11:55 AM, Tim Dudgeon wrote: > In what way? Given a single PubChem compound or substance ID you just > want to pull the smiles or molfile into RDKit? Furthermore what's your definition of "a compound"? If it includes stereochemistry, pubchem usually has 3d mol files, except where it

Re: [Rdkit-discuss] RDkit and Pubchem

2017-12-01 Thread Michał Nowotka
Hi, If you would like get compounds from ChEMBL instead of PubChem you can use this Python client: https://github.com/chembl/chembl_webresource_client and get access to 1.7M+ unique compounds as molfiles, smiles, inchis, inch keys and images. Cheers, Michał On Fri, Dec 1, 2017 at 6:51 PM,

Re: [Rdkit-discuss] RDkit and Pubchem

2017-12-01 Thread Jason Biggs
Pubchem has an easy to use rest API, described here: https://pubchemdocs.ncbi.nlm.nih.gov/pug-rest If you have a compound ID, you can query properties via something https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/2244/property/CanonicalSMILES,IsomericSMILES,InChI/JSON It comes back in

Re: [Rdkit-discuss] RPM distros

2017-12-01 Thread Tim Dudgeon
Maciek The 'cpack -G RPM' command does not seem to create a rdkit_package_file.rpm. The ones that are created are: RDKit-2018.03.1.dev1-Linux-Development.rpm RDKit-2018.03.1.dev1-Linux-Extras.rpm RDKit-2018.03.1.dev1-Linux-Python.rpm RDKit-2018.03.1.dev1-Linux-Runtime.rpm Tim On 28/11/2017

Re: [Rdkit-discuss] RPM distros

2017-12-01 Thread Gianluca Sforna
On Fri, Dec 1, 2017 at 6:04 PM, Tim Dudgeon wrote: > Maciek > > The 'cpack -G RPM' command does not seem to create a rdkit_package_file.rpm. > The ones that are created are: > > RDKit-2018.03.1.dev1-Linux-Development.rpm > RDKit-2018.03.1.dev1-Linux-Extras.rpm >

Re: [Rdkit-discuss] RDkit and Pubchem

2017-12-01 Thread Tim Dudgeon
In what way? Given a single PubChem compound or substance ID you just want to pull the smiles or molfile into RDKit? Tim On 01/12/17 17:26, Sundar wrote: Hi RDkit users, I was wondering if RDkit has a means of downloading compounds from Pubchem. Also let me other ways that helps here.

Re: [Rdkit-discuss] bad coordinates for acetylenic hydrogens

2017-12-01 Thread Malitha Kabir
Hi Jason, I hope the following codes will help you a little. from rdkit import Chem from rdkit.Chem import Draw from rdkit.Chem import AllChem size = (120, 120) m = Chem.MolFromSmiles('C#C') m2=Chem.rdmolops.AddHs(m) AllChem.EmbedMolecule(m2, AllChem.ETKDG()) Draw.MolToMPL(m2, size=size) ***

Re: [Rdkit-discuss] bad coordinates for acetylenic hydrogens

2017-12-01 Thread Jason Biggs
Thank you Malitha, If I'm understanding the Draw code (not a given, my python ist nicht gut), then MolToMPL (or MolToImage) is just using the 3D conformation generated by EmbedMolecule. Is it just chopping off the z-coordinate? For acetylene, this works out because it gets embedded mostly in

Re: [Rdkit-discuss] bad coordinates for acetylenic hydrogens

2017-12-01 Thread Malitha Kabir
Dear Jason, The geometry that you/me visualized in a 2D plot necessarily doesn't exist in real world except a few planner molecules. To view 3D geometry of a molecule, 2D representation doesn't work. Please feel free to do whatever you want to do with your molecule while producing 2D graph.

[Rdkit-discuss] RDkit and Pubchem

2017-12-01 Thread Sundar
Hi RDkit users, I was wondering if RDkit has a means of downloading compounds from Pubchem. Also let me other ways that helps here. Thanks, Jubi -- Check out the vibrant tech community on one of the world's most engaging

Re: [Rdkit-discuss] RPM distros

2017-12-01 Thread Tim Dudgeon
Francois, I'm assuming you are meaning to install those packages on the debian system prior to installing the RDKit-2018.03.1.dev1-Linux-*.deb files. Unfortunately that didn't help. Tim On 27/11/2017 23:50, Francois BERENGER wrote: On 11/28/2017 12:42 AM, Tim Dudgeon wrote: I see exactly

Re: [Rdkit-discuss] RPM distros

2017-12-01 Thread Tim Dudgeon
Read back to the top of this thread for all the details, but the key bit is this: In the bugtracker, there is an issue about the .deb: https://github.com/rdkit/rdkit/issues/911 and there is a pull request by Patrick Avery to fix them: https://github.com/rdkit/rdkit/pull/1580 Tim On

Re: [Rdkit-discuss] RDkit and Pubchem

2017-12-01 Thread Sundar
Hi Jason, This is great. I would really benefit from this. At present I am looking for a way to download smiles or mol data of a few compound which only have SIDs and CIDs. Can we do it? I failed after trying the following,

Re: [Rdkit-discuss] RDkit and Pubchem

2017-12-01 Thread Jason Biggs
Sundar, What you do will depend on whether you have an SID or a CID number. Read https://pubchemblog.ncbi.nlm.nih.gov/2014/06/19/what-is-the-difference-between-a-substance-and-a-compound-in-pubchem/ for more info. In PubChem terminology, a *substance* is a chemical sample description > provided