Re: [Rdkit-discuss] Latest Mac Conda installation advice; was: Boost 1.61 and the RDKit work together.

wrote: > > On Fri, Aug 26, 2016 at 7:43 PM, Peter S. Shenkin <shen...@gmail.com> > wrote: > >> >> I want to install RDKit on my Mac Mini, which I just upgraded to El >> Capitan. It's pretty much a virgin machine (wiped clean, but running >> Yosemite,

[Rdkit-discuss] Latest Mac Conda installation advice; was: Boost 1.61 and the RDKit work together.

Hi, I want to install RDKit on my Mac Mini, which I just upgraded to El Capitan. It's pretty much a virgin machine (wiped clean, but running Yosemite, before I started). I don't need to compile RDKit (unless you say I have to); I want to install an image and have it work with PostgreSQL and the

Re: [Rdkit-discuss] library name change?

Compromise on "RDK"? -P. On Fri, Aug 19, 2016 at 10:50 AM, Paul Emsley wrote: > On 19/08/2016 12:52, Greg Landrum wrote: > > > > It seems logical to me, though I would probably go with RDKit instead of > RD > > as the prefix. > > OK, that's clearer yet. > > > >

Re: [Rdkit-discuss] Incorrect SMARTS from FindMCS

But we have learned that RDKit can do the imparsable -P. On Tue, Jul 5, 2016 at 6:14 AM, Marta Stępniewska-Dziubińska < mart...@ibb.waw.pl> wrote: > Hi Greg, > > To be honest, I expected it to fail :) > > I want to find structures with a defined topology, but allow for > different bond

Re: [Rdkit-discuss] Gobbi hydrogen bond acceptor definition

Speaking from the peanut gallery, that seems to me to be a rather important point, at least as far as pyrrole NH is concerned. I assume there is widespread agreement that these are not acceptors. I think thiophene S is usually regarded as a receptor, albeit a weak one, but F is highly debatable.

Re: [Rdkit-discuss] two versions of RDKit in one python program - static compilation?

Perhaps more of interest is why the old version is still required. Does functionality get deleted when new releases come out? Undocumented side effects that old scripts depended on? Too hard to rewrite the old scripts because the APIs have changed? Or what? -P. On Fri, Apr 29, 2016 at 2:50 AM,

Re: [Rdkit-discuss] Two SMILES that (I think) should canonicalize to the same thing, but don't

Hi, Greg, This is a bit of a meta-comment, so I hope it's appropriate here. I might possibly make more comments on the github site. After this discussion went dead (but before I retired from Schrödinger), I looked into the origin of that bizarre multicyclic structure. It turned out to have

Re: [Rdkit-discuss] compiling error with C++ on maverick

of > headaches! > > Best, > Yingfeng > > On Wed, Mar 16, 2016 at 10:27 AM, Peter S. Shenkin <shen...@gmail.com> > wrote: > >> Yes, that's exactly what I meant. I'm not sure whether this sort of thing >> still works in our troubled times, but it's easy enough to

Re: [Rdkit-discuss] compiling error with C++ on maverick

_static -lLibC_static -lLibA_static -lLibB_static > -lLibC_static > > ? > > So, by this way, we don't need to worry about the order of these three > libraries. > > Best, > Yingfeng > > On Wed, Mar 16, 2016 at 12:36 AM, Peter S. Shenkin <shen...@gmail.com> &

Re: [Rdkit-discuss] compiling error with C++ on maverick

I'm not sure how this works with modern linkers, but "back in the old days", you could kludge it by putting all libraries on the link line twice, This also resolved circular references. -P. On Wed, Mar 16, 2016 at 12:05 AM, Greg Landrum wrote: > Though that would be

Re: [Rdkit-discuss] canonical atom indexing

] != hvyNbrRanks[1]: > res.append(atom.GetIdx()) > return res > > > Is that headed in the right direction? > -greg > > > > On Thu, Mar 10, 2016 at 5:30 PM, Peter S. Shenkin <shen...@gmail.com> > wrote:

Re: [Rdkit-discuss] canonical atom indexing

Is the canonical rank of prochiral H's different or the same? (For example the rank of the H's on C-1 of ethyl chloride.) Thanks, -P. -- Transform Data into Opportunity. Accelerate data analysis in your applications with

Re: [Rdkit-discuss] getting substructure for Morgan fingerprint bit

Just curious here Since every SMILES is a valid SMARTS, - How do you want the SMARTS to differ from the SMARTS the SMILES already is? - What would be the advantage if you could do so? Thanks, -P. On Sat, Mar 5, 2016 at 8:40 PM, Naeem Attari wrote: > Hi, >

Re: [Rdkit-discuss] The Chlorine molfile question

On Wed, Jan 20, 2016 at 7:42 PM, Dimitri Maziuk <dmaz...@bmrb.wisc.edu> wrote: > On 01/20/2016 04:57 PM, Peter S. Shenkin wrote: > > On Wed, Jan 20, 2016 at 5:33 PM, Dimitri Maziuk <dmaz...@bmrb.wisc.edu> > > wrote: > > >> JSON encodes a single string. Tha

Re: [Rdkit-discuss] The Chlorine molfile question

On Wed, Jan 20, 2016 at 3:06 PM, Dimitri Maziuk wrote: > As much as PDB wants the old busted PDB format gone, they are not offering a usable alternative that I know of. Such as: a JSON file with predefined keys for all the bona-fide fields originally defined by the PDB

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