- Forwarded Message -
>From: S.L. Chan
>To: JP
>Sent: Tuesday, January 14, 2014 10:03 PM
>Subject: Re: [Rdkit-discuss] Add a charge to an atom and modify Hs accordingly
>(protonation)
>
>
>
>Hello JP,
>
>You need to bear in mind that by default RDKit does not store the
>hydrogens e
HI,
I guess these are well known but here is some relevant literature. I believe
there is also a section on AutoNom in the Handbook of Cheminformatics.
AutoNom : paper1 and paper2
Automated systematic nomenclature generation for organic compounds:
http://onlinelibrary.wiley.com/doi/10.1002/wcms
Hi there,
This must be really easy -- but anything I am trying is failing and I am
losing my mind. I want to add a charge (+ / -) to an atom and add or
delete a connected H accordingly.
I thought an easy way to do this was to remove all Hs from the molecule
(removeHs), add a charge (SetFormalCha
OPSIN is doing the reverse - converts name to structure, perhaps it's
possible to re-use the algorithm?
Igor
On Tue, Jan 14, 2014 at 1:29 PM, David Hall wrote:
> Certainly, RDKit can help, any cheminformatics toolkit with
> SMARTS/substructures to quickly classify something as a ketone, ester,
To keep it 'simple' let's set some assumptions:
- I would like to cover 'only' organic compounds
- I won't something that works in 95% of compounds, producing some
clear warning for remaining 5%
Now, how can I classify compound as alkane, acid, ester etc. using RDkit?
On Tue, Jan 14, 2014 at 7:2
Certainly, RDKit can help, any cheminformatics toolkit with
SMARTS/substructures to quickly classify something as a ketone, ester,
ether, bond orders, ring finding, path finding, etc. can help.
As for how hard it is, I think for drug discovery, most would start with
the Nomenclature of Organic Che
Yes, I know there is no algorithm for that. This is why I'm wondering
how hard it to write one and how RDkit can help here.
On Tue, Jan 14, 2014 at 4:01 PM, Dimitri Maziuk wrote:
> On 1/14/2014 6:09 AM, Michał Nowotka wrote:
>> Hi,
>>
>> Since there is no open source software converting structure
On 1/14/2014 6:09 AM, Michał Nowotka wrote:
> Hi,
>
> Since there is no open source software converting structure to IUPAC
> name (I'm not talking about web services) I was wandering if one can
> be implemented using RDkit? Which parts of RDKit would help in doing
> that? Any pointers, suggestions?
Hi JP,
However I am unable to get bond orders for the protein side - am I doing
> something wrong or is this the intended behaviour ?
> I imagine I can use AssignBondOrdersFromTemplate() for the 20 amino acids
> and set these myself -- or is there a better way to do this?
>
I don't know why your
Apologies all -- but I am still having problems with this.
Reading
https://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg03485.html
"As far as I understood, the PDB reader assigns bond orders to the amino
acids in a protein, but if a ligand is present it puts all bonds of it to
SING
Hi,
Since there is no open source software converting structure to IUPAC
name (I'm not talking about web services) I was wandering if one can
be implemented using RDkit? Which parts of RDKit would help in doing
that? Any pointers, suggestions?
Regards,
Michal Nowotka
---
On Tue, Jan 14, 2014 at 3:37 AM, Oriol López Massaguer wrote:
>
> I use RDKit from Scala/Java and experienced the same issue.
>
> Despite having GraphMolWrap.so in the LD_LIBRARY_PATH the code fails with
> a UnsatisfiedLinkError.
>
> I've solved it by loading explicitly the native library:
>
> Sys
Hi Matt, all;
I use RDKit from Scala/Java and experienced the same issue.
Despite having GraphMolWrap.so in the LD_LIBRARY_PATH the code fails
with a UnsatisfiedLinkError.
I've solved it by loading explicitly the native library:
System.load("/opt/collector/lib/libGraphMolWrap.so")
I don't k
Hi Matt, all;
I use RDKit from Scala/Java and experienced the same issue.
Despite having GraphMolWrap.so in the LD_LIBRARY_PATH the code fails
with a UnsatisfiedLinkError.
I've solved it by loading explicitly the native library:
System.load("/opt/collector/lib/libGraphMolWrap.so")
I don't k
On Mon, Jan 13, 2014 at 10:58 PM, Matthew Lardy wrote:
> The machine I had been build RDKit was having some major Cmake issues, but I
> am through that now. I did a fresh install of CentOS (this time version
> 6.5) and a new copy of Swig (2.0.10) and things compiled without issue. So,
> I have t
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