On Wed, Dec 7, 2011 at 5:06 AM, Greg Landrum wrote:
> Dear JP,
>
>> I do not see how AddHs will help me when replacing [OH] with [O-], but
>> that might just be me being thick.
>> My problem is that ps = AllChem.ReplaceSubstructs(mol, patt, repl,
>> replaceAll=True) in my original attached code th
Dear JP,
On Tue, Nov 29, 2011 at 5:47 PM, JP wrote:
>
> I am not sure that is what I need/I explained myself well.
>
> My question is: If you have a 3D molecule, and you replace a part of
> it with a new group based on some SMARTS expression (with no 3D
> coorinates) - what is the best way to kee
Just bumping this up ...
On 29 November 2011 16:47, JP wrote:
> Dear Greg,
>
> I am not sure that is what I need/I explained myself well.
>
> My question is: If you have a 3D molecule, and you replace a part of
> it with a new group based on some SMARTS expression (with no 3D
> coorinates) - what
Dear Greg,
I am not sure that is what I need/I explained myself well.
My question is: If you have a 3D molecule, and you replace a part of
it with a new group based on some SMARTS expression (with no 3D
coorinates) - what is the best way to keep all the 3D info for the
atoms in the molecule which
Dear JP,
On Tue, Nov 29, 2011 at 3:36 PM, JP wrote:
> Sorry for the repeated posting -- I had asked a similar question for
> 2D some time ago
> (http://www.mail-archive.com/[email protected]/msg01916.html),
> but now I need the 3D case and I am stuck.
>
> Using RDKit 2011_09_01.
Sorry for the repeated posting -- I had asked a similar question for
2D some time ago
(http://www.mail-archive.com/[email protected]/msg01916.html),
but now I need the 3D case and I am stuck.
Using RDKit 2011_09_01.
I am simply protonating a molecule via some simple SMART replac
> It's kind of interesting (and encouraging) that the optimizer doesn't
> completely freak out when you hand it a 2D conformer. :-)
>
>
Ah... :)
>> What makes 3D coordinates? (I'm guessing it's a one-liner somewhere...)
>>
> It is indeed a one-liner (two lines with a bit of error chec
Hi Paul,
On Fri, Sep 10, 2010 at 7:29 PM, Paul Emsley wrote:
>
> I've been tinkering a bit more with RDKit and having fun.
Glad to hear it.
> I have hit a problem though. I am trying to reproduce Greg's "Generating
> 3D coordinates" in RDKit-overview.pdf in C++:
>
> This is what I have (mostly
Hi All,
I've been tinkering a bit more with RDKit and having fun.
I have hit a problem though. I am trying to reproduce Greg's "Generating
3D coordinates" in RDKit-overview.pdf in C++:
This is what I have (mostly via cut 'n paste):
int
main(int argc, char **argv) {
std::string smiles_s
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