[Rdkit-discuss] Stereo information lost

Hi, I am using the following C++ script to read a molecule from a SD file (with defined stereochemistry), but the information about the stereochemistry gets lost. The file I am using is from glucose (ZINC03833800; http://zinc.docking.org/substance/3833800

Re: [Rdkit-discuss] Explicit hydrogens in substructure search

Hi Greg, Does this depend on removeHs() function? I mean, to make MergeQueryHs() work, should I do removeHs=False first for all compounds in my database, to preserve implicit\explicit hydrogens in their structure? Thank you! Andrew 30.11.2017 22:26, Andrey >That's awesome,

[Rdkit-discuss] read sdf file without removing hydrogen atoms.

Dear RDkit Users, Rdkit would delete all hydrogen atoms when read in a sdf file. Since I want to use charge information of all atoms in sdf file, I want to keep all hydrogen atoms when readin. Is there something like Chem.SmilesParserParams() for sdfsupplier ? Many thanks for your help. Best,

Re: [Rdkit-discuss] read sdf file without removing hydrogen atoms.

On 12/13/2017 11:03 AM, Chicago Ji wrote: > Dear RDkit Users, > > Rdkit would delete all hydrogen atoms when read in a sdf file. > Since I want to use charge information of all atoms in sdf file, I want > to keep all hydrogen atoms when readin. > Is there something like  Chem.SmilesParserParams()

Re: [Rdkit-discuss] Similarity maps using machine learning

I know that Michal has done some work with this as part of the beta for the new ChEMBL interface. @Michal: do you have a bit of time to explain what you did in order to get images that you could serve via the web? On Tue, Dec 12, 2017 at 1:50 PM, Bruno Neves wrote: >

Re: [Rdkit-discuss] Explicit hydrogens in substructure search

On Tue, Dec 12, 2017 at 7:28 PM, Andrey wrote: > > Does this depend on removeHs() function? I mean, to make MergeQueryHs() > work, should I do removeHs=False first for all compounds in my database, to > preserve implicit\explicit hydrogens in their structure? > The MergeQueryHs()

[Rdkit-discuss] Similarity maps using machine learning

Dear colleagues I want to develop mechanistically interpretable machine learning models (i.e., using similarity maps) and implement them in web services. I've already managed to generate a map from a smiles. However, I can not generate maps for multiple molecules in a data set (CSV ou SDF). I’m