Re: [Rdkit-discuss] RDkit deficieny in radical chemistry

[Paolo Tosco]

Dear Geun,

currently the resonance structure enumerator does not take into account radical 
species. I hope I can find the time to take into account radical species as 
well in the near future.

Cheers,
p.

> On 19 Aug 2016, at 10:06, Geun Ho Gu  wrote:
> 
> Hello RDkitters, 
> 
> 
> I'm a user interested in the more of the catalytic side of the chemistry 
> involving radical chemistry. I found a couple deficiency in RDkit 
> functionality regarding this. 
> 
> 
> 1. rdqueries module in python wrapper lacks a query for number of radical 
> electrons.
> 
> I can work around this if I know the atomic number of the species and use the 
> default valence with total valence queries, but it's not possible for atom 
> query where atomic number is not well-defined.
> 
> 
> 2. ResonanceMolSupplier module in python wrapper does not enumerate the 
> radical resonance structure. For example,
> 
>  
> 
> mol = Chem.MolFromSmiles('[CH2]C=CC')
> 
> resmols = ResonanceMolSupplier(mol)
> 
> for resmol in resmols:
> 
> print Chem.MolToSmiles(resmol)
> 
> 
> should produce two molecules: [CH2]C=CC and C=C[CH]C. But only produce the 
> original molecule.
> 
> It seems that the enumerator only looks at the resonance structure of charged 
> species, because when I do the same procedure with charged species, (i.e. 
> replace the smiles of the code above to [CH2+]C=CC), it produces [CH2+]C=CC 
> and C=C[CH+]C just fine.
> 
> 
> 
> I apologize for not working on these issues myself. I'm not very familiar 
> with C++, and do not have much time in my hand.. 
> 
> 
> 
> Thank you very much,
> 
> Geun Ho Gu
> 
> 
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Re: [Rdkit-discuss] library name change?

[Igor Filippov]

Paul,

Both or neither - for me it's important that RDKit::foo() is working in my
code, not which specific library it is in or
what other libraries the first lib depends upon. So if I need to use foo()
I'd like to know what to include into my Makefile.
That's why I suggested having a monolithic static library as an option or
an easy way to get a list of libs to add to the linker command.

Igor


On Fri, Aug 19, 2016 at 11:22 AM, Paul Emsley 
wrote:

>
> I'd like to pick apart this comment:
>
> On 19/08/2016 15:45, Igor Filippov wrote:
>
> > It is sometimes a bit of a pain to collect the list of the dependencies.
>
> Do you mean that (for example) if you wanted to link with
> libMolChemicalFeatures, you also
> have to add libSubstructureMatch and libSmilesParse - and it isn't readily
> apparent to you
> which additional libraries you need to add when linking?
>
> > Alternatively some easier way to discover what belongs to what library
> would be appreciated...
>
> Do you mean which libraries depend on which libraries (as above) - or
> which functions are in
> which libraries?
>
>
>
> 
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Re: [Rdkit-discuss] library name change?

[Paul Emsley]

I'd like to pick apart this comment:

On 19/08/2016 15:45, Igor Filippov wrote:

> It is sometimes a bit of a pain to collect the list of the dependencies.

Do you mean that (for example) if you wanted to link with 
libMolChemicalFeatures, you also 
have to add libSubstructureMatch and libSmilesParse - and it isn't readily 
apparent to you 
which additional libraries you need to add when linking?

> Alternatively some easier way to discover what belongs to what library would 
> be appreciated...

Do you mean which libraries depend on which libraries (as above) - or which 
functions are in 
which libraries?



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Re: [Rdkit-discuss] library name change?

[Peter S. Shenkin]

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.
>
>
>
> 
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Re: [Rdkit-discuss] library name change?

[Paul Emsley]

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.



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Re: [Rdkit-discuss] library name change?

[Greg Landrum]

Ok, here's the issue in github:
https://github.com/rdkit/rdkit/issues/1036

These are famous last words, but it looks like adding this, and making it
optional, may be trivial. Cmake is *awesome*.
Let's move any technical discussion to github

-greg


On Fri, Aug 19, 2016 at 2:28 PM, Brian Kelley  wrote:

> Perhaps announce at the RDKit meeting and make the full change for the
> first release of next year?  We could also make it a CMAKE option to
> use/build the old names, but this would be a bit of work.
>
> Cheers,
>  Brian
>
> On Fri, Aug 19, 2016 at 7:52 AM, Greg Landrum 
> wrote:
>
>> Hi Paul,
>>
>> Nice suggestion. It seems logical to me, though I would probably go with
>> RDKit instead of RD as the prefix.
>> It's not a small change for people who are using the C++ libs without
>> cmake (I wouldn't change the names of the cmake projects, so if you're
>> using the RDKit cmake stuff nothing changes), but I suspect there aren't
>> that many of you guys.
>>
>> @Gianluca: what do you think?
>>
>> Anyone else have an opinion?
>>
>> -greg
>>
>>
>>
>> On Fri, Aug 19, 2016 at 1:15 PM, Paul Emsley 
>> wrote:
>>
>>>
>>> Greg,
>>>
>>> RDKit is becoming increasingly popular and is getting picked up by third
>>> parties, including
>>> the Linux distros.  It seems to me that several RDKit library names are
>>> too generic (and
>>> hence confusing) for such an environment: I have in mind libs such as
>>> Alignment, Catalog,
>>> FileParsers (and others).  I suggest that all RDKit libraries are
>>> prefixed with RD (like
>>> RDGeneral and RDInchi). I think that this should be done by at
>>> RDKit-Central rather than by
>>> patches applied by package maintainers at the distros.
>>>
>>> Yes, this will involve some fiddling for us C++ RDKit users, but worth
>>> it, I think.
>>>
>>> Paul.
>>>
>>> 
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>>
>>
>> 
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Re: [Rdkit-discuss] library name change?

[Igor Filippov]

If we are talking about the changes to the way the libs are build is there
a chance to get a (possibly optional) monolithic static library?
It is sometimes a bit of a pain to collect the list of the dependencies.
Alternatively some easier way to discover what belongs to what library
would be appreciated...

Igor


On Fri, Aug 19, 2016 at 10:40 AM, Greg Landrum 
wrote:

> Ok, here's the issue in github:
> https://github.com/rdkit/rdkit/issues/1036
>
> These are famous last words, but it looks like adding this, and making it
> optional, may be trivial. Cmake is *awesome*.
> Let's move any technical discussion to github
>
> -greg
>
>
> On Fri, Aug 19, 2016 at 2:28 PM, Brian Kelley 
> wrote:
>
>> Perhaps announce at the RDKit meeting and make the full change for the
>> first release of next year?  We could also make it a CMAKE option to
>> use/build the old names, but this would be a bit of work.
>>
>> Cheers,
>>  Brian
>>
>> On Fri, Aug 19, 2016 at 7:52 AM, Greg Landrum 
>> wrote:
>>
>>> Hi Paul,
>>>
>>> Nice suggestion. It seems logical to me, though I would probably go with
>>> RDKit instead of RD as the prefix.
>>> It's not a small change for people who are using the C++ libs without
>>> cmake (I wouldn't change the names of the cmake projects, so if you're
>>> using the RDKit cmake stuff nothing changes), but I suspect there aren't
>>> that many of you guys.
>>>
>>> @Gianluca: what do you think?
>>>
>>> Anyone else have an opinion?
>>>
>>> -greg
>>>
>>>
>>>
>>> On Fri, Aug 19, 2016 at 1:15 PM, Paul Emsley 
>>> wrote:
>>>

 Greg,

 RDKit is becoming increasingly popular and is getting picked up by
 third parties, including
 the Linux distros.  It seems to me that several RDKit library names are
 too generic (and
 hence confusing) for such an environment: I have in mind libs such as
 Alignment, Catalog,
 FileParsers (and others).  I suggest that all RDKit libraries are
 prefixed with RD (like
 RDGeneral and RDInchi). I think that this should be done by at
 RDKit-Central rather than by
 patches applied by package maintainers at the distros.

 Yes, this will involve some fiddling for us C++ RDKit users, but worth
 it, I think.

 Paul.

 
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 ___
 Rdkit-discuss mailing list
 Rdkit-discuss@lists.sourceforge.net
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>>>
>>>
>>> 
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>>
>
> 
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Re: [Rdkit-discuss] library name change?

[Rocco Moretti]

On Fri, Aug 19, 2016 at 6:15 AM, Paul Emsley 
wrote:

>
> It seems to me that several RDKit library names are too generic (and
> hence confusing) for such an environment: I have in mind libs such as
> Alignment, Catalog,
> FileParsers (and others).  I suggest that all RDKit libraries are prefixed
> with RD (like
> RDGeneral and RDInchi).
>

To clarify, would this only be for the shared object files?

This wouldn't involve any changes at the Python or C++ code level, right?
(Only changes would be at the build level.)
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Re: [Rdkit-discuss] library name change?

[Greg Landrum]

Correct, it would be just changing the names of the C++ shared and static
libraries. No code changes would be required, just makefiles.

On Fri, Aug 19, 2016 at 4:22 PM, Rocco Moretti 
wrote:

> On Fri, Aug 19, 2016 at 6:15 AM, Paul Emsley 
> wrote:
>
>>
>> It seems to me that several RDKit library names are too generic (and
>> hence confusing) for such an environment: I have in mind libs such as
>> Alignment, Catalog,
>> FileParsers (and others).  I suggest that all RDKit libraries are
>> prefixed with RD (like
>> RDGeneral and RDInchi).
>>
>
> To clarify, would this only be for the shared object files?
>
> This wouldn't involve any changes at the Python or C++ code level, right?
> (Only changes would be at the build level.)
>
>
> 
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Re: [Rdkit-discuss] library name change?

[Greg Landrum]

On Fri, Aug 19, 2016 at 2:54 PM, Gianluca Sforna  wrote:

> On Fri, Aug 19, 2016 at 1:52 PM, Greg Landrum 
> wrote:
>
> Of course, changing names is a bit of a hassle for those usign the
> previous names, as they needs to rebuild dependent packages; however,
> given there are none as of today, I don't think it will be a big
> issue.
>

That sounds like an argument for doing it sooner rather than later...
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Re: [Rdkit-discuss] library name change?

[Gianluca Sforna]

On Fri, Aug 19, 2016 at 1:52 PM, Greg Landrum  wrote:

> Nice suggestion. It seems logical to me, though I would probably go with
> RDKit instead of RD as the prefix.
> It's not a small change for people who are using the C++ libs without cmake
> (I wouldn't change the names of the cmake projects, so if you're using the
> RDKit cmake stuff nothing changes), but I suspect there aren't that many of
> you guys.
>
> @Gianluca: what do you think?

>From the Fedora point of view, clashes happens, and we deal with them
as they are discovered; I could check if some of the common library
names are already in the repositories, but adding some prefix should
fix the issue permanently.

Of course, changing names is a bit of a hassle for those usign the
previous names, as they needs to rebuild dependent packages; however,
given there are none as of today, I don't think it will be a big
issue.

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Re: [Rdkit-discuss] library name change?

[Greg Landrum]

Hi Paul,

Nice suggestion. It seems logical to me, though I would probably go with
RDKit instead of RD as the prefix.
It's not a small change for people who are using the C++ libs without cmake
(I wouldn't change the names of the cmake projects, so if you're using the
RDKit cmake stuff nothing changes), but I suspect there aren't that many of
you guys.

@Gianluca: what do you think?

Anyone else have an opinion?

-greg



On Fri, Aug 19, 2016 at 1:15 PM, Paul Emsley 
wrote:

>
> Greg,
>
> RDKit is becoming increasingly popular and is getting picked up by third
> parties, including
> the Linux distros.  It seems to me that several RDKit library names are
> too generic (and
> hence confusing) for such an environment: I have in mind libs such as
> Alignment, Catalog,
> FileParsers (and others).  I suggest that all RDKit libraries are prefixed
> with RD (like
> RDGeneral and RDInchi). I think that this should be done by at
> RDKit-Central rather than by
> patches applied by package maintainers at the distros.
>
> Yes, this will involve some fiddling for us C++ RDKit users, but worth it,
> I think.
>
> Paul.
>
> 
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[Rdkit-discuss] library name change?

[Paul Emsley]

Greg,

RDKit is becoming increasingly popular and is getting picked up by third 
parties, including 
the Linux distros.  It seems to me that several RDKit library names are too 
generic (and 
hence confusing) for such an environment: I have in mind libs such as 
Alignment, Catalog, 
FileParsers (and others).  I suggest that all RDKit libraries are prefixed with 
RD (like 
RDGeneral and RDInchi). I think that this should be done by at RDKit-Central 
rather than by 
patches applied by package maintainers at the distros.

Yes, this will involve some fiddling for us C++ RDKit users, but worth it, I 
think.

Paul.

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