[Rdkit-discuss] NYC "RDKit Users and Learners" meetup Monday, Oct. 3

[Peter S. Shenkin]

Hi,

As a reminder to anyone in the NYC area who might be interested, I am
trying to get a few RDKit "users and learners" together via a meetup on
Monday evening, October 3. *More information here
*.
If it makes sense to do so, we can make this a regular thing in the future.

Best,
-P.
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Re: [Rdkit-discuss] The RDKit and modern C++

[Paolo Tosco]

Hi Dimitri,

That can be avoided building the RPMs on older RHEL distributions using the Red 
Hat Developer Toolsets that Greg and others mentioned. These toolsets include 
newer compilers, which however link the binaries against the GLIBC present in 
the distribution they run on, thus maintaining the backwards compatibility. For 
example, devtoolset-4 brings GCC 5.2 to RHEL 6:

http://developers.redhat.com/products/developertoolset/get-started-rhel6-cpp/

Cheers,
p.

> On 29 Sep 2016, at 20:14, Dimitri Maziuk  wrote:
> 
>> On 09/29/2016 10:16 AM, Greg Landrum wrote:
>> 
>> My hope is that all of those people will be able to keep happily
>> using a reasonably up-to-date version of the RDKit.
> 
> Well, that's kinda the point: there are no RPMs that let you run
> binaries linked to GLIBC_2.17 on GLIBC_2.5, nor compile c++-14 code with
> c++-03 compilers.
> 
> -- 
> Dimitri Maziuk
> Programmer/sysadmin
> BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
> 
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Re: [Rdkit-discuss] The RDKit and modern C++

[Dimitri Maziuk]

On 09/29/2016 10:16 AM, Greg Landrum wrote:

> My hope is that all of those people will be able to keep happily
> using a reasonably up-to-date version of the RDKit.

Well, that's kinda the point: there are no RPMs that let you run
binaries linked to GLIBC_2.17 on GLIBC_2.5, nor compile c++-14 code with
c++-03 compilers.

-- 
Dimitri Maziuk
Programmer/sysadmin
BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu



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Re: [Rdkit-discuss] Ring membership

[Marco Stenta]

Hi Greg,
I missed the @ bit for bonds: thanks for the tip: I will definitely use it.
Still not matching donor and acceptors in the same ring is something I need
to achieve.
I'll work on Paul's suggestion and report back if I have any success in it.

Cheers,
m

2016-09-29 17:03 GMT+02:00 Greg Landrum :

> Paul already mentioned an approach using the molecule's RingInfo
> structure, which you could certainly use to see if the RDKit thinks the two
> molecules are part of the same smallest ring.
> I suspect that you might want something a bit more general (apologies that
> I don't have a copy of that paper handy, so I can't read what the Roche
> folks used).
>
> Fortunately, the more general case actually turns out to be easier.
> I believe that what you want is to just determine whether or not the path
> between the two atoms is composed solely of ring bonds.
> You could express this in SMARTS as:
> {DONOR}@*@*@{ACCEPTOR}
> That's the three-bond separation case.
> Where {DONOR} and {ACCEPTOR} are the SMARTS definitions you would like to
> use for those atoms. The "@" in SMARTS means "Ring bond", so this pattern
> corresponds to a donor separated by three ring bonds from an acceptor.
>
> This will, unfortunately, also match the case where the donor and acceptor
> are adjacent to each other in a 5 membered ring. If it's important than you
> not match that, you'll have to do a bit more work.
>
> Best,
> -greg
>
>
>
> _
> From: Marco Stenta 
> Sent: Thursday, September 29, 2016 4:13 PM
> Subject: [Rdkit-discuss] Ring membership
> To: 
>
>
>
> Dear Colleagues,
> I am working on intramolecular hydrogen bonds, formed between
> donor-acceptors separated by 2,3,4 atoms, as described in the Roche paper:
> Kuhn, B.; Mohr, P.; Stahl, M. J. Med. Chem. 2010, 53, 2601.
>
> I will use SMARTS and RDKIT to identify and classify IMHB.
>
> I see from documentation how to identify atoms that are members of a ring,
> how can I identify if two atoms are member of the same ring?
>
>
> Example:
>
> Donor--X-Y---Acceptor
>
> NCC=O
>
> This will match
> C1CC(NC1)C=O
>
> but I would lie to flag if two or more atoms belong to the same ring, as
> this will impact the capability of IMHB to opne and close.
>
>
> Do you have any suggestion?
>
> cheers,
> Marco
>
>
>
>
>
>
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Re: [Rdkit-discuss] The RDKit and modern C++

[Greg Landrum]

Which is, along with the inertia that large companies have, part of the reason 
that RHEL6 will be with us for a while.
Similarly, a year after RHEL8 comes out some of us will be complaining that 
we'll be stuck with RHEL7 forever, others will be clamoring for immediate 
support of all the new features, and a third camp will still be stuck with 
RHEL6. That's just the way things go.
My hope is that all of those people will be able to keep happily using a 
reasonably up-to-date version of the RDKit.
-greg






On Thu, Sep 29, 2016 at 5:01 PM +0200, "Dimitri Maziuk"  
wrote:










On 2016-09-29 00:57, Markus Sitzmann wrote:
> I get the feeling, RH/Centos 6 becomes the next XP kind of story - to
> many legacies that make the update impossible or very hard. Also docker,
> a great technology that could mitigate this problem, is very painful
> under RH/Centos 6.

systemd, corosync/pacemaker, apache 2.4, gnome.whichever are some of 
RH7's "exciting new technologies" a lot of us don't want.

Dimitri



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Re: [Rdkit-discuss] Ring membership

[Greg Landrum]

Paul already mentioned an approach using the molecule's RingInfo structure, 
which you could certainly use to see if the RDKit thinks the two molecules are 
part of the same smallest ring.I suspect that you might want something a bit 
more general (apologies that I don't have a copy of that paper handy, so I 
can't read what the Roche folks used). 
Fortunately, the more general case actually turns out to be easier.I believe 
that what you want is to just determine whether or not the path between the two 
atoms is composed solely of ring bonds.You could express this in SMARTS 
as:{DONOR}@*@*@{ACCEPTOR}That's the three-bond separation case.Where {DONOR} 
and {ACCEPTOR} are the SMARTS definitions you would like to use for those 
atoms. The "@" in SMARTS means "Ring bond", so this pattern corresponds to a 
donor separated by three ring bonds from an acceptor.
This will, unfortunately, also match the case where the donor and acceptor are 
adjacent to each other in a 5 membered ring. If it's important than you not 
match that, you'll have to do a bit more work.
Best,-greg



_
From: Marco Stenta 
Sent: Thursday, September 29, 2016 4:13 PM
Subject: [Rdkit-discuss] Ring membership
To:  


Dear Colleagues,I am working on intramolecular hydrogen bonds, formed between 
donor-acceptors separated by 2,3,4 atoms, as described in the Roche paper:Kuhn, 
B.; Mohr, P.; Stahl, M. J. Med. Chem. 2010, 53, 2601.

I will use SMARTS and RDKIT to identify and classify IMHB.
I see from documentation how to identify atoms that are members of a ring, how 
can I identify if two atoms are member of the same ring?

Example:
Donor--X-Y---Acceptor
NCC=O
This will match C1CC(NC1)C=O

but I would lie to flag if two or more atoms belong to the same ring, as this 
will impact the capability of IMHB to opne and close.

Do you have any suggestion?
cheers,Marco





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Re: [Rdkit-discuss] The RDKit and modern C++

[Dimitri Maziuk]

On 2016-09-29 00:57, Markus Sitzmann wrote:
> I get the feeling, RH/Centos 6 becomes the next XP kind of story - to
> many legacies that make the update impossible or very hard. Also docker,
> a great technology that could mitigate this problem, is very painful
> under RH/Centos 6.

systemd, corosync/pacemaker, apache 2.4, gnome.whichever are some of 
RH7's "exciting new technologies" a lot of us don't want.

Dimitri



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Re: [Rdkit-discuss] Ring membership

[Paul Emsley]

On 29/09/16 15:12, Marco Stenta wrote:
> Dear Colleagues,
> I am working on intramolecular hydrogen bonds, formed between 
> donor-acceptors separated by 2,3,4 atoms, as described in the Roche paper:
> Kuhn, B.; Mohr, P.; Stahl, M. J. Med. Chem. 2010, 53, 2601.
>
> I will use SMARTS and RDKIT to identify and classify IMHB.
>
> I see from documentation how to identify atoms that are members of a 
> ring, how can I identify if two atoms are member of the same ring?

I don't use Python, but you might like to check out
rings = GetRingInfo(mol)

http://www.rdkit.org/Python_Docs/rdkit.Chem.rdchem.Mol-class.html

The documentation says:

 Returns the number of molecule's RingInfo object.


This may be true, but I doubt it.  The C++ function returns a vector of 
vector of atom indices and I suspect that the python version does too 
(or the python equivalent).

Paul.


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[Rdkit-discuss] Ring membership

[Marco Stenta]

Dear Colleagues,
I am working on intramolecular hydrogen bonds, formed between
donor-acceptors separated by 2,3,4 atoms, as described in the Roche paper:
Kuhn, B.; Mohr, P.; Stahl, M. J. Med. Chem. 2010, 53, 2601.

I will use SMARTS and RDKIT to identify and classify IMHB.

I see from documentation how to identify atoms that are members of a ring,
how can I identify if two atoms are member of the same ring?


Example:

Donor--X-Y---Acceptor

NCC=O

This will match
C1CC(NC1)C=O

but I would lie to flag if two or more atoms belong to the same ring, as
this will impact the capability of IMHB to opne and close.


Do you have any suggestion?

cheers,
Marco
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Re: [Rdkit-discuss] The RDKit and modern C++

[Greg Landrum]

I agree that it's going to be a thorn for a while. Still, it's better than 
being stuck with RHEL5. :-S





On Thu, Sep 29, 2016 at 7:58 AM +0200, "Markus Sitzmann" 
 wrote:










I get the feeling, RH/Centos 6 becomes the next XP kind of story - to many 
legacies that make the update impossible or very hard. Also docker, a great 
technology that could mitigate this problem, is very painful under RH/Centos 6.
---Markus Sitzmann

On 29 Sep 2016, at 07:31, Greg Landrum  wrote:


On Thu, Sep 29, 2016 at 7:06 AM, Peter S. Shenkin  wrote:

Thanks... so it sounds like the main effort (aside from what you delicately 
called "professional development" ;-) ) will be to introduce features that 
improve robustness or performance when writing new code and possibly when 
maintaining (fixing, extending) existing code.
Yes, I think that's about right with the one refinement that we'll be using 
some automated tools to convert the existing code to use some of those new 
features.
-greg 
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