Re: [BlueObelisk-discuss] Software for ligands

2016-08-19 Thread Rzepa, Henry S 
I guess  Rasmol must be coming up/already celebrated  its  25th  anniversary, 
which shows that such projects can have longevity.

It would indeed be an interesting story to track what has happened to  Rasmol 
and its successors over this  25 year period, and indeed the impact it has had 
in this area, inspiring no doubt many others.

>Well, some of these tools have risen this way - RasMol was Roger Sayle's final 
>year project in biophysics (I think).  If the tool is useful, then the student 
>or supervisor may take it up. We can't command - or fund - so we have to 
>encourage and publicise.



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Re: [BlueObelisk-discuss] Software for ligands

2016-08-19 Thread Peter Murray-Rust 
On Fri, Aug 19, 2016 at 8:44 AM, Greg Landrum 
wrote:

>
>
>
> Even if it were possible for an MSc student to develop a decent editor in
> the time available to them, someone would need to take over ongoing
> ownership and support of the tool. This seems to be more of a problem.
>

Well, some of these tools have risen this way - RasMol was Roger Sayle's
final year project in biophysics (I think).  If the tool is useful, then
the student or supervisor may take it up. We can't command - or fund - so
we have to encourage and publicise.



>
> -greg
>



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Re: [BlueObelisk-discuss] Software for ligands

2016-08-19 Thread Greg Landrum 
On Fri, Aug 19, 2016 at 9:36 AM, Peter Murray-Rust  wrote:

>
> On Thu, Aug 18, 2016 at 7:51 PM, Geoffrey Hutchison 
> wrote:
>
>> > I have suggested that there are Open tools that they may not yet have
>> discovered. They have needs for (at least):
>> >  * 2-D chemical editor and display
>>
>> I do not think such a thing currently exists. The ChemDoodle tool, while
>> not open, is at least low cost, and they do support open source web
>> components (http://web.chemdoodle.com/)
>>
>> This is a sorely lacking area.
>>
>>
> It might be useful to categorize those areas where more effort would be
> valuable. Did John May put effort into JChempaint - what I saw was
> certainly improved from when I last visited it. Is it a useful tool, being
> used? And if not is it capable of being developed.
> It's a pity that JME is not open - after about 20 years.
>

Agreed.

There's also Alex Clark's SketchEl (http://sketchel.sourceforge.net/) and
EPAMs (formerly GGA) ketcher (
http://lifescience.opensource.epam.com/ketcher/index.html). I haven't made
extensive use of either, but I believe that both are still being actively
developed.


> Graphics libraries have improved - a good MSc student could develop an
> editor - should we have a wish list that could be distributed?
>

Even if it were possible for an MSc student to develop a decent editor in
the time available to them, someone would need to take over ongoing
ownership and support of the tool. This seems to be more of a problem.

-greg
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Re: [BlueObelisk-discuss] Software for ligands

2016-08-19 Thread Peter Murray-Rust 
Thanks everyone - and keep suggestions coming.

On Thu, Aug 18, 2016 at 7:51 PM, Geoffrey Hutchison  wrote:

> > I have suggested that there are Open tools that they may not yet have
> discovered. They have needs for (at least):
> >  * 2-D chemical editor and display
>
> I do not think such a thing currently exists. The ChemDoodle tool, while
> not open, is at least low cost, and they do support open source web
> components (http://web.chemdoodle.com/)
>
> This is a sorely lacking area.
>
>
It might be useful to categorize those areas where more effort would be
valuable. Did John May put effort into JChempaint - what I saw was
certainly improved from when I last visited it. Is it a useful tool, being
used? And if not is it capable of being developed.
It's a pity that JME is not open - after about 20 years.

Graphics libraries have improved - a good MSc student could develop an
editor - should we have a wish list that could be distributed?



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University of Cambridge
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Re: [BlueObelisk-discuss] Software for ligands

2016-08-18 Thread Geoffrey Hutchison 
> I have suggested that there are Open tools that they may not yet have 
> discovered. They have needs for (at least):
>  * 2-D chemical editor and display

I do not think such a thing currently exists. The ChemDoodle tool, while not 
open, is at least low cost, and they do support open source web components 
(http://web.chemdoodle.com/)

This is a sorely lacking area.

>  * 3-D editor 

I humbly suggest Avogadro. :-)

> I am not up-to-date with all the Open software. Do we have a list of tools in 
> this area? If not, perhaps people can respond to the list? It would be a 
> useful update.

Multiple people have suggested the recent review, which also lives online (and 
open):
https://opensourcemolecularmodeling.github.io

Cheers,
-Geoff
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Re: [BlueObelisk-discuss] Software for ligands

2016-08-18 Thread Wibe de Jong 
That's a nice overview paper. Started to look more into descriptors, so
happy to see the listing of tools one can start from.

Some of the web components have been integrated into MongoChem (
https://openchemistry.kitware.com/). Here we use a greatly extended version
of Marcus' Chemical Json (reusing some of the CML naming conventions) to
generate data and populate a MongoDB. The computational chemistry app used
here is NWChem, for which we now have a CJson writer directly in the code
(using an open source son fortran writer) and an extensive Python script
(which I need to integrate into cclib at some point in the near future).

Bert

On Thu, Aug 18, 2016 at 5:06 AM, Rajarshi Guha 
wrote:

> There is a nice listing of open tools by Pirhadi et al and covers the
> spectrum from cheminformatics to computational chemistry
>
> http://www.sciencedirect.com/science/article/pii/S1093326316301188
>
> On Thu, Aug 18, 2016 at 5:13 AM, Peter Murray-Rust 
> wrote:
>
>> I have been talking with the Computational Crystallography group in
>> Cambridge/LMB who develop ligand dictionaries for protein crystallography
>> and are building their system with Open software (and Open data from
>> Crystallography Open Database).
>>
>> I have suggested that there are Open tools that they may not yet have
>> discovered. They have needs for (at least):
>>  * 2-D chemical editor and display
>>  * 3-D editor
>>  * atom typing
>>  * computational chemistry (e.g. DFT)
>>  * chemical database software
>>
>> They have filled some of this themselves, and use RDKIT, but would
>> benefit from other components. I pointed them at JChempaint - which has
>> matured a lot since I last used it. I have also suggested NWChem.
>>
>> I am not up-to-date with all the Open software. Do we have a list of
>> tools in this area? If not, perhaps people can respond to the list? It
>> would be a useful update.
>>
>>
>> --
>> Peter Murray-Rust
>> Reader in Molecular Informatics
>> Unilever Centre, Dep. Of Chemistry
>> University of Cambridge
>> CB2 1EW, UK
>> +44-1223-763069
>>
>> 
>> --
>>
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>>
>>
>
>
> --
> Rajarshi Guha | http://blog.rguha.net
> NIH Center for Advancing Translational Science
>
> 
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>
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Re: [BlueObelisk-discuss] Software for ligands

2016-08-18 Thread Greg Landrum 
Orca does indeed look interesting.

For those who care about such things, however, orca is unfortunately not
open-source. It falls into the category that Pirhadi et al. refer to as
"source-available" licenses:
https://orcaforum.cec.mpg.de/license.html


-greg


On Thu, Aug 18, 2016 at 2:38 PM, jay patel  wrote:

> Thanks for referencing Pirhadi et al's recent paper, it looks like one of
> the the most comprehensive list I have come across.
>
> I can highly recommend ORCA (https://orcaforum.cec.mpg.de/) for
> performing all kinds of DFT and ab initio calculations. I have used it on a
> standalone basis as well as with a GUI called gabedit (
> http://gabedit.sourceforge.net/). I saw Pirhadi's paper mention couple of
> other GUI for ORCA too but I haven't had a chance to use it yet.
>
> On Thu, Aug 18, 2016 at 8:06 AM, Rajarshi Guha 
> wrote:
>
>> There is a nice listing of open tools by Pirhadi et al and covers the
>> spectrum from cheminformatics to computational chemistry
>>
>> http://www.sciencedirect.com/science/article/pii/S1093326316301188
>>
>> On Thu, Aug 18, 2016 at 5:13 AM, Peter Murray-Rust 
>> wrote:
>>
>>> I have been talking with the Computational Crystallography group in
>>> Cambridge/LMB who develop ligand dictionaries for protein crystallography
>>> and are building their system with Open software (and Open data from
>>> Crystallography Open Database).
>>>
>>> I have suggested that there are Open tools that they may not yet have
>>> discovered. They have needs for (at least):
>>>  * 2-D chemical editor and display
>>>  * 3-D editor
>>>  * atom typing
>>>  * computational chemistry (e.g. DFT)
>>>  * chemical database software
>>>
>>> They have filled some of this themselves, and use RDKIT, but would
>>> benefit from other components. I pointed them at JChempaint - which has
>>> matured a lot since I last used it. I have also suggested NWChem.
>>>
>>> I am not up-to-date with all the Open software. Do we have a list of
>>> tools in this area? If not, perhaps people can respond to the list? It
>>> would be a useful update.
>>>
>>>
>>> --
>>> Peter Murray-Rust
>>> Reader in Molecular Informatics
>>> Unilever Centre, Dep. Of Chemistry
>>> University of Cambridge
>>> CB2 1EW, UK
>>> +44-1223-763069
>>>
>>> 
>>> --
>>>
>>> ___
>>> Blueobelisk-discuss mailing list
>>> Blueobelisk-discuss@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
>>>
>>>
>>
>>
>> --
>> Rajarshi Guha | http://blog.rguha.net
>> NIH Center for Advancing Translational Science
>>
>> 
>> --
>>
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>>
>
> 
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Re: [BlueObelisk-discuss] Software for ligands

2016-08-18 Thread Peter Murray-Rust 
Many thanks,

This is impressive! and very welcome to see how much Open Source there is
now.


On Thu, Aug 18, 2016 at 1:06 PM, Rajarshi Guha 
wrote:

> There is a nice listing of open tools by Pirhadi et al and covers the
> spectrum from cheminformatics to computational chemistry
>
> http://www.sciencedirect.com/science/article/pii/S1093326316301188
>
> On Thu, Aug 18, 2016 at 5:13 AM, Peter Murray-Rust 
> wrote:
>
>> I have been talking with the Computational Crystallography group in
>> Cambridge/LMB who develop ligand dictionaries for protein crystallography
>> and are building their system with Open software (and Open data from
>> Crystallography Open Database).
>>
>> I have suggested that there are Open tools that they may not yet have
>> discovered. They have needs for (at least):
>>  * 2-D chemical editor and display
>>  * 3-D editor
>>  * atom typing
>>  * computational chemistry (e.g. DFT)
>>  * chemical database software
>>
>> They have filled some of this themselves, and use RDKIT, but would
>> benefit from other components. I pointed them at JChempaint - which has
>> matured a lot since I last used it. I have also suggested NWChem.
>>
>> I am not up-to-date with all the Open software. Do we have a list of
>> tools in this area? If not, perhaps people can respond to the list? It
>> would be a useful update.
>>
>>
>> --
>> Peter Murray-Rust
>> Reader in Molecular Informatics
>> Unilever Centre, Dep. Of Chemistry
>> University of Cambridge
>> CB2 1EW, UK
>> +44-1223-763069
>>
>> 
>> --
>>
>> ___
>> Blueobelisk-discuss mailing list
>> Blueobelisk-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
>>
>>
>
>
> --
> Rajarshi Guha | http://blog.rguha.net
> NIH Center for Advancing Translational Science
>



-- 
Peter Murray-Rust
Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge
CB2 1EW, UK
+44-1223-763069
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Re: [BlueObelisk-discuss] Software for ligands

2016-08-18 Thread Rajarshi Guha 
There is a nice listing of open tools by Pirhadi et al and covers the
spectrum from cheminformatics to computational chemistry

http://www.sciencedirect.com/science/article/pii/S1093326316301188

On Thu, Aug 18, 2016 at 5:13 AM, Peter Murray-Rust  wrote:

> I have been talking with the Computational Crystallography group in
> Cambridge/LMB who develop ligand dictionaries for protein crystallography
> and are building their system with Open software (and Open data from
> Crystallography Open Database).
>
> I have suggested that there are Open tools that they may not yet have
> discovered. They have needs for (at least):
>  * 2-D chemical editor and display
>  * 3-D editor
>  * atom typing
>  * computational chemistry (e.g. DFT)
>  * chemical database software
>
> They have filled some of this themselves, and use RDKIT, but would benefit
> from other components. I pointed them at JChempaint - which has matured a
> lot since I last used it. I have also suggested NWChem.
>
> I am not up-to-date with all the Open software. Do we have a list of tools
> in this area? If not, perhaps people can respond to the list? It would be a
> useful update.
>
>
> --
> Peter Murray-Rust
> Reader in Molecular Informatics
> Unilever Centre, Dep. Of Chemistry
> University of Cambridge
> CB2 1EW, UK
> +44-1223-763069
>
> 
> --
>
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> Blueobelisk-discuss mailing list
> Blueobelisk-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
>
>


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