rdkit-devel — Developers information and discussion.

Re: [Rdkit-devel] cairo backend not loadable

[Greg L. <gre...@gm...>]

Hi Gianluca,

On Wed, Dec 1, 2010 at 12:58 PM, gi...@gm... <gi...@gm...> wrote:
> I started to work with depictions and noticed the results were a bit
> ugly [1], at least if compared to rdkit generated images I can find
> online[2]
>
> Digging a bit in the code I realized the cairo backend was not being
> used as a result of commit 1515[3], which contained:
>
> -      import cairo
> +      import cairo2
>
> I guess this is just something sneaked into the commit? can we revert
> it before Q4 release?

It's basically a matter of the wrong file getting checked in.

I'll fix it in svn now.

> After fixing it, results are much better [4] but still not matching
> that one from [2]

The better results ([2]) come from using aggdraw, which you'll need to
download and build separately (instructions in the wiki). Aggdraw
really makes for nice pictures.

>
> Am I missing something obvious?

Er no, that was me that checked in the obvious mistake... apologies.

-greg

[Rdkit-devel] cairo backend not loadable

[<gi...@gm...>]

I started to work with depictions and noticed the results were a bit
ugly [1], at least if compared to rdkit generated images I can find
online[2]

Digging a bit in the code I realized the cairo backend was not being
used as a result of commit 1515[3], which contained:

-      import cairo
+      import cairo2

I guess this is just something sneaked into the commit? can we revert
it before Q4 release?

After fixing it, results are much better [4] but still not matching
that one from [2]

Am I missing something obvious?

G.


[1] http://giallu.fedorapeople.org/depict-pidPIL.png
[2] http://ctr.wikia.com/wiki/File:3016_highlighted.rdkit.png
[3] http://rdkit.svn.sourceforge.net/viewvc/rdkit/trunk/rdkit/Chem/Draw/__init__.py?r1=1515&r2=1514&pathrev=1515
[4] http://giallu.fedorapeople.org/depict-cairo.png

-- 
Gianluca Sforna

http://morefedora.blogspot.com
http://identi.ca/giallu - http://twitter.com/giallu

Re: [Rdkit-devel] PostgreSQL cartridge: Function to check whether a SMILES string is valid or not in RDKit

[Greg L. <gre...@gm...>]

Dear Adrian,

Quick one: the svn version of the cartridge code now has the function
is_valid_smiles()

On Fri, Oct 29, 2010 at 5:08 PM, Adrian Schreyer <ma...@ad...> wrote:
>
> Creating the mol types is actually not that slow I thought, compared
> to creating the indexes (based on the latest version of chembl).

The index generation is certainly slower than loading the molecules.

> Simplifying the database creation is definitely worth it, and those
> costly operations are done only once. Another suggestion I had was to
> refactor the naming of the functions in the cartridge to make them
> more similar to the underlying functions in the Python/C++ libraries,
> e.g. mol_in ~ mol_from_smiles / mol_out ~ mol_to_smiles.

I believe that the current naming scheme is more consistent with the
way postgresql does things. That's not an automatic "it has to be done
that way", but I think it is an argument for maintaining the current
naming.

>
> Given the context, maybe it is possible to reduce the number of
> instances where a smiles string cannot be parsed. From what I have
> seen so far, this happens in three cases: the smiles string contains a
> non-daylight extension (not rdkit's fault), exotic inorganic chemistry
> (negligible) or the valence system in rdkit is violated. The last case
> is something where I often encounter problems, for example bromic acid
>
> Chem.MolFromSmiles('OBr(=O)=O')
> [15:21:29] Explicit valence for atom # 1 Br, 5, is greater than permitted
>
> Is there a definition for the valence model used in rdkit somewhere in
> the source tree? I assume the valence model is nothing that can be
> manually changed by the user without breaking other aspects of the
> software.

If you want to allow additional valence states for atoms, you can edit
$RDBASE/Code/GraphMol/atomic_data.cpp, but that's about the only way
to do changes at the moment. The topic of supporting other valences,
like 5 for Br, has come up in the past. If we can identify a limited
number of additional valences that are required, I'd be willing to add
them to the standard RDKit parameters.[1] I'm happy to hear
suggestions about what those additional valences should be. We should
probably do this in a separate thread on the -discuss list.

Best Regards,
-greg
[1] Within reason... I will balk at changing anything in the first row
of the periodic table and will probably resist changing anything in
the second row other than chlorine (to allow chlorate anions).

Re: [Rdkit-devel] PostgreSQL cartridge: Function to check whether a SMILES string is valid or not in RDKit

[Adrian S. <ma...@ad...>]

Hi Greg,

On Thu, Oct 28, 2010 at 14:04, Greg Landrum <gre...@gm...> wrote:
> Dear Adrian,
>
> On Thu, Oct 28, 2010 at 11:34 AM, Adrian Schreyer <am...@ca...> wrote:
>>
>> I moved to PostgreSQL 9.0 recently and installed the RDKit cartridge
>> which was easy to compile and install. It is also one of the fastest
>> cartridges I have used so far, definitely a great extension of RDKit!
>
> Thank! I'm glad to hear that it's useful.
>
>> At the moment I am trying to create rdkit molecules and fingerprints
>> for the latest version of the ChEMBL database, there is however a
>> problem which can be solved easily. Since I already had the ChEMBL
>> database (including the SMILES strings), I added tables to hold the
>> mol and fp types for every compound and tried to populate it through
>> "insert into... select mol_in(ism::cstring)..." which works nicely
>> unless it finds a SMILES string it cannot parse such as this
>> "CCCC1234B567B89%10B%11%12%13B8%14%15B%11%16%17B%12%18%19B59%13B16%18C2%16%19(c%20ccc(Oc%21ccc(cc%21)C(=O)O)cc%20)B3%14%17B47%10%15"
>> (ChEBI: http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI%3A105310).
>> The query will fail then, and the only way to populate these table is
>> to download the SMILES and filter them manually in Python. Is it
>> possible to have a boolean function (is_valid(cstring)?) in the
>> cartridge that simply checks if a SMILES can be parsed with RDKit or
>> not? This would make it possible to add this check to a where clause
>> in a query and as a result make the creation of mol types much easier.
>
> That's one good solution that would be easy to implement. The
> is_valid() function would be a useful thing to have anyway, so I'll go
> ahead and add it sometime in the near future. The downside is that it
> will take more or less twice as long to populate the database (since
> every molecule would have to be processed twice). Another option that
> might be better, but I'll have to check about how feasible it is,
> would be to have the molecule construction functions just return a
> null (or whatever the postgresql equivalent is).

Creating the mol types is actually not that slow I thought, compared
to creating the indexes (based on the latest version of chembl).
Simplifying the database creation is definitely worth it, and those
costly operations are done only once. Another suggestion I had was to
refactor the naming of the functions in the cartridge to make them
more similar to the underlying functions in the Python/C++ libraries,
e.g. mol_in ~ mol_from_smiles / mol_out ~ mol_to_smiles.

Given the context, maybe it is possible to reduce the number of
instances where a smiles string cannot be parsed. From what I have
seen so far, this happens in three cases: the smiles string contains a
non-daylight extension (not rdkit's fault), exotic inorganic chemistry
(negligible) or the valence system in rdkit is violated. The last case
is something where I often encounter problems, for example bromic acid

Chem.MolFromSmiles('OBr(=O)=O')
[15:21:29] Explicit valence for atom # 1 Br, 5, is greater than permitted

Is there a definition for the valence model used in rdkit somewhere in
the source tree? I assume the valence model is nothing that can be
manually changed by the user without breaking other aspects of the
software.

Cheers,

Adrian

Re: [Rdkit-devel] PostgreSQL cartridge: Function to check whether a SMILES string is valid or not in RDKit

[Greg L. <gre...@gm...>]

Dear Adrian,

On Thu, Oct 28, 2010 at 11:34 AM, Adrian Schreyer <am...@ca...> wrote:
>
> I moved to PostgreSQL 9.0 recently and installed the RDKit cartridge
> which was easy to compile and install. It is also one of the fastest
> cartridges I have used so far, definitely a great extension of RDKit!

Thank! I'm glad to hear that it's useful.

> At the moment I am trying to create rdkit molecules and fingerprints
> for the latest version of the ChEMBL database, there is however a
> problem which can be solved easily. Since I already had the ChEMBL
> database (including the SMILES strings), I added tables to hold the
> mol and fp types for every compound and tried to populate it through
> "insert into... select mol_in(ism::cstring)..." which works nicely
> unless it finds a SMILES string it cannot parse such as this
> "CCCC1234B567B89%10B%11%12%13B8%14%15B%11%16%17B%12%18%19B59%13B16%18C2%16%19(c%20ccc(Oc%21ccc(cc%21)C(=O)O)cc%20)B3%14%17B47%10%15"
> (ChEBI: http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI%3A105310).
> The query will fail then, and the only way to populate these table is
> to download the SMILES and filter them manually in Python. Is it
> possible to have a boolean function (is_valid(cstring)?) in the
> cartridge that simply checks if a SMILES can be parsed with RDKit or
> not? This would make it possible to add this check to a where clause
> in a query and as a result make the creation of mol types much easier.

That's one good solution that would be easy to implement. The
is_valid() function would be a useful thing to have anyway, so I'll go
ahead and add it sometime in the near future. The downside is that it
will take more or less twice as long to populate the database (since
every molecule would have to be processed twice). Another option that
might be better, but I'll have to check about how feasible it is,
would be to have the molecule construction functions just return a
null (or whatever the postgresql equivalent is).

Thanks for the suggestion,
-greg

[Rdkit-devel] PostgreSQL cartridge: Function to check whether a SMILES string is valid or not in RDKit

[Adrian S. <am...@ca...>]

Hi Greg,

I moved to PostgreSQL 9.0 recently and installed the RDKit cartridge
which was easy to compile and install. It is also one of the fastest
cartridges I have used so far, definitely a great extension of RDKit!

At the moment I am trying to create rdkit molecules and fingerprints
for the latest version of the ChEMBL database, there is however a
problem which can be solved easily. Since I already had the ChEMBL
database (including the SMILES strings), I added tables to hold the
mol and fp types for every compound and tried to populate it through
"insert into... select mol_in(ism::cstring)..." which works nicely
unless it finds a SMILES string it cannot parse such as this
"CCCC1234B567B89%10B%11%12%13B8%14%15B%11%16%17B%12%18%19B59%13B16%18C2%16%19(c%20ccc(Oc%21ccc(cc%21)C(=O)O)cc%20)B3%14%17B47%10%15"
(ChEBI: http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI%3A105310).
The query will fail then, and the only way to populate these table is
to download the SMILES and filter them manually in Python. Is it
possible to have a boolean function (is_valid(cstring)?) in the
cartridge that simply checks if a SMILES can be parsed with RDKit or
not? This would make it possible to add this check to a where clause
in a query and as a result make the creation of mol types much easier.

Cheers

Adrian

Re: [Rdkit-devel] How to build the RDKit?

[<nik...@no...>]

Hi Sridhar,

congrats on getting things working. One more comment - maybe you want to 
post these kind of questions rather in the discuss than the devel list. It 
is much more populated and you will for sure get replies quicker.

Cheers
Nik




Eddie Cao <cao...@gm...> 
10/19/2010 11:49 PM

To
sri...@th...
cc
rdk...@li...
Subject
Re: [Rdkit-devel] How to build the RDKit?






Hi Sridhar,

Congratulations! If from rdkit import Chem gives you >>>, then it is very 
good sign that things are all in place.

To load molecules from Oracle database, you need a database connector 
called cx_Oracle. After installing this module, you will be able to send 
SQL statement to Oracle to retrieve molecule SMILES or SDF, depending on 
how molecules are stored in your database. You might need to consult your 
database administrator.

To download cx_Oracle: http://cx-oracle.sourceforge.net/
For a simple example about how to use it: 
http://wiki.oracle.com/page/Python

Check Section 14 of the Getting Started in Python Guide for  a complete 
list of descriptors you can calculate using RDKit:

http://rdkit.org/GettingStartedInPython.pdf

Regards,
Eddie

On Oct 19, 2010, at 2:31 PM, sri...@th... 
wrote:

Hi Nik,
Looks like I had a version issue with the RDkit I downloaded. I needed 
Q22010_1 for Python2.5 but I downloaded Q22009_1 in which, it was looking 
for Python2.5 (hardcoded path from one of the libs, looked like) when I 
ran the test command (hence I downloaded and installed Python2.5 and 
removed 2.6).
Now that I have a clean install of Py2.5 and fresh download of RDkit 
Q22010_1 for Py2.5, the test command ran well and passed the test.
 
I just have to go to the next step.
I need to create molLogP, NumHAcceptors, NumHDonors etc.. values for a 
given molecule.
My molecules are actually stored in an Oracle DB.
So, Where do I begin?
 
I just got your other mail. The install is set and OK now as it seems.
I ran the command ?from rdkit import Chem? from the command-line and it 
put me back to the >>> prompt, no add?l msgs.
As for sending to the whole group, it was an honest mistake. I just 
clicked ?Reply?. Some other lists that I subscribed to, send to the list 
automagically. I realized my mistake when I didn?t receive the mail back 
to me and fixed it in this one.
 
Regards,
Sridhar
 
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message to the intended recipient, you are hereby notified that any 
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Re: [Rdkit-devel] How to build the RDKit?

[Eddie C. <cao...@gm...>]

Hi Sridhar,

Congratulations! If from rdkit import Chem gives you >>>, then it is very good sign that things are all in place.

To load molecules from Oracle database, you need a database connector called cx_Oracle. After installing this module, you will be able to send SQL statement to Oracle to retrieve molecule SMILES or SDF, depending on how molecules are stored in your database. You might need to consult your database administrator.

To download cx_Oracle: http://cx-oracle.sourceforge.net/
For a simple example about how to use it: http://wiki.oracle.com/page/Python

Check Section 14 of the Getting Started in Python Guide for  a complete list of descriptors you can calculate using RDKit:

http://rdkit.org/GettingStartedInPython.pdf

Regards,
Eddie

On Oct 19, 2010, at 2:31 PM, sri...@th... wrote:

> Hi Nik,
> Looks like I had a version issue with the RDkit I downloaded. I needed Q22010_1 for Python2.5 but I downloaded Q22009_1 in which, it was looking for Python2.5 (hardcoded path from one of the libs, looked like) when I ran the test command (hence I downloaded and installed Python2.5 and removed 2.6).
> Now that I have a clean install of Py2.5 and fresh download of RDkit Q22010_1 for Py2.5, the test command ran well and passed the test.
>  
> I just have to go to the next step.
> I need to create molLogP, NumHAcceptors, NumHDonors etc.. values for a given molecule.
> My molecules are actually stored in an Oracle DB.
> So, Where do I begin?
>  
> I just got your other mail. The install is set and OK now as it seems.
> I ran the command “from rdkit import Chem” from the command-line and it put me back to the >>> prompt, no add’l msgs.
> As for sending to the whole group, it was an honest mistake. I just clicked “Reply”. Some other lists that I subscribed to, send to the list automagically. I realized my mistake when I didn’t receive the mail back to me and fixed it in this one.
>  
> Regards,
> Sridhar
>  

Re: [Rdkit-devel] How to build the RDKit?

[<sri...@th...>]

Hi Nik,

Looks like I had a version issue with the RDkit I downloaded. I needed
Q22010_1 for Python2.5 but I downloaded Q22009_1 in which, it was
looking for Python2.5 (hardcoded path from one of the libs, looked like)
when I ran the test command (hence I downloaded and installed Python2.5
and removed 2.6).

Now that I have a clean install of Py2.5 and fresh download of RDkit
Q22010_1 for Py2.5, the test command ran well and passed the test.

 

I just have to go to the next step.

I need to create molLogP, NumHAcceptors, NumHDonors etc.. values for a
given molecule.

My molecules are actually stored in an Oracle DB.

So, Where do I begin?

 

I just got your other mail. The install is set and OK now as it seems.

I ran the command "from rdkit import Chem" from the command-line and it
put me back to the >>> prompt, no add'l msgs.

As for sending to the whole group, it was an honest mistake. I just
clicked "Reply". Some other lists that I subscribed to, send to the list
automagically. I realized my mistake when I didn't receive the mail back
to me and fixed it in this one.

 

Regards,

Sridhar

 

From: Kuntamukkula, Sridhar (Hlthcr&Science) 
Sent: Tuesday, October 19, 2010 4:45 PM
To: 'nik...@no...'
Subject: RE: [Rdkit-devel] How to build the RDKit?

 

Hi Nik,

You and Eddie  (thanks to both of you) pointed to the same link which is
what I used to download the RDKit. But haven't any idea whether that was
source or binary. Now I know I downloaded the binary install for
Windows.

And am trying to follow the "install" file's instructions from the
RDBASE folder.

In this process I happened to install the other required
software/utilities such as python, numpy, scipy, PIL, Boost, etc..

But my RDKIT download referred to python2.5, so I had to downgrade to
python2.5 (originally install2.6 and 2.6 utilities)

I have set the ENV vars. For,

PYTHONPATH,

RDBASE,

PATH,

BOOSTHOME (although this is boost 1.44, not 1.36 as the install doc
referred to)

BOOST_BUILD_PATH 

 

But the "install" doc (from the RDBASE) referes to a folder called,
%RDBASE%\Code which is not there in the package I downloaded.

 

In the end, when I follow the test guidelines, with the following
command,

python C:\RDkit\RDKit_Q22009_1\rdkit\testrunner.py test_list.py

 I get the following errors reported.

!-!-!-!-!-!-!-!-!-!-!

        Script: test_list.py.  Failed 3 (of 32) tests in 71.61 seconds

                (.): python UnitTestChem.py

                (.): python UnitTestCatalog.py

                (Pharm3D): python test_list.py

 

It is a bit confusing, to say the least. And now, after the re-install
of python2.5 and removal of python2.6 (in this order), the *.py files
are not opening with python.

Dbl click flashes a command window and disappears. Right click and
choose "Open with IDLE" does nothing.

 

Appreciate any insights (to get me started with RDkit).

-Sridhar

 

From: nik...@no... [mailto:nik...@no...]

Sent: Tuesday, October 19, 2010 3:59 PM
To: Kuntamukkula, Sridhar (Hlthcr&Science)
Cc: rdk...@li...
Subject: Re: [Rdkit-devel] How to build the RDKit?

 


Hi Sridhar, 

are you using the windows binaries or is that a Linux system? Did you
follow the installation instructions on
http://code.google.com/p/rdkit/wiki/GettingStarted ? I guess some more
details is needed to help you out here ... most likely you have not set
any of the important environment variables such as RDBASE etc. 

Cheers 
Nik 



<sri...@th...> 

10/19/2010 05:19 PM 

To

<rdk...@li...> 

cc

	
Subject

[Rdkit-devel] How to build the RDKit?

 

		




Hi, 
I am new to the RDKIT. Just got introduced. The command, "from rdkit
import chem. Gives me an error as below 
Traceback (most recent call last): 
  File "<pyshell#9>", line 1, in <module> 
    from rdkit import chem 
ImportError: No module named rdkit 
  
I have python installed in C:\python26 folder. 
I also have the RDKit unzipped into the same folder. 
  
What else do I need to do? 
Are there step by step instructions online or in the docs somewhere that
could get me going with RDKit? 
  
Many thanks 
  
Sridhar Kuntamukkula
Chemical Prog Analyst Sr 
Healthcare & Science 

Thomson Reuters 
  
Phone: +1-215-823-5657
sri...@th...
<mailto:sri...@th...> 
thomsonreuters.com------------------------------------------------------
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the intended recipient, or the employee or agent responsible for
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communication in error, please notify the sender immediately by e-mail
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Re: [Rdkit-devel] How to build the RDKit?

[<nik...@no...>]

Hi Sridhar,

are you using the windows binaries or is that a Linux system? Did you 
follow the installation instructions on 
http://code.google.com/p/rdkit/wiki/GettingStarted ? I guess some more 
details is needed to help you out here ... most likely you have not set 
any of the important environment variables such as RDBASE etc.

Cheers
Nik




<sri...@th...> 
10/19/2010 05:19 PM

To
<rdk...@li...>
cc

Subject
[Rdkit-devel] How to build the RDKit?






Hi,
I am new to the RDKIT. Just got introduced. The command, ?from rdkit 
import chem. Gives me an error as below
Traceback (most recent call last):
  File "<pyshell#9>", line 1, in <module>
    from rdkit import chem
ImportError: No module named rdkit
 
I have python installed in C:\python26 folder.
I also have the RDKit unzipped into the same folder.
 
What else do I need to do?
Are there step by step instructions online or in the docs somewhere that 
could get me going with RDKit?
 
Many thanks
 
Sridhar Kuntamukkula
Chemical Prog Analyst Sr
Healthcare & Science

Thomson Reuters
 
Phone: +1-215-823-5657
sri...@th...
thomsonreuters.com
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across multiple browsers and platforms. Download your free trials today!
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_______________________________________________
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Rdk...@li...
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CONFIDENTIALITY NOTICE

The information contained in this e-mail message is intended only for the 
exclusive use of the individual or entity named above and may contain 
information that is privileged, confidential or exempt from disclosure 
under applicable law. If the reader of this message is not the intended 
recipient, or the employee or agent responsible for delivery of the 
message to the intended recipient, you are hereby notified that any 
dissemination, distribution or copying of this communication is strictly 
prohibited. If you have received this communication in error, please 
notify the sender immediately by e-mail and delete the material from any 
computer.  Thank you.

[Rdkit-devel] How to build the RDKit?

[<sri...@th...>]

Hi,

I am new to the RDKIT. Just got introduced. The command, "from rdkit
import chem. Gives me an error as below

Traceback (most recent call last):

  File "<pyshell#9>", line 1, in <module>

    from rdkit import chem

ImportError: No module named rdkit

 

I have python installed in C:\python26 folder.

I also have the RDKit unzipped into the same folder.

 

What else do I need to do?

Are there step by step instructions online or in the docs somewhere that
could get me going with RDKit?

 

Many thanks

 

Sridhar Kuntamukkula
Chemical Prog Analyst Sr

Healthcare & Science


Thomson Reuters

 

Phone: +1-215-823-5657
sri...@th...
<mailto:sri...@th...> thomsonreuters.com

Re: [Rdkit-devel] [PATCH] Fix postgresql cartridge compilation

[Greg L. <gre...@gm...>]

Ah, that one slipped through. Thanks for the patch.

-greg


On Wed, Sep 29, 2010 at 11:05 AM, Gianluca Sforna <gi...@gm...> wrote:
> It seems in 2010.09 beta1 release I can't compile the cartridge
> against postgresql 8.4; the following patch fixes the issue:
>
> diff --git a/trunk/Code/PgSQL/rdkit/cache.c b/trunk/Code/PgSQL/rdkit/cache.c
> index 56b38d6..53b4910 100644
> --- a/trunk/Code/PgSQL/rdkit/cache.c
> +++ b/trunk/Code/PgSQL/rdkit/cache.c
> @@ -1,4 +1,4 @@
> -// $Id$
> +// $Id: cache.c 1522 2010-09-21 06:17:39Z glandrum $
>  //
>  //  Copyright (c) 2010, Novartis Institutes for BioMedical Research Inc.
>  //  All rights reserved.
> @@ -275,7 +275,11 @@ createCache(void *cache, struct MemoryContextData * ctx)
>                methodsOrig = ctx->methods;
>                methodsCache = *methodsOrig;
>                methodsCache.reset = resetCacheContext;
> +#if PG_VERSION_NUM>=90000
>                methodsCache.delete_context = deleteCacheContext;
> +#else
> +               methodsCache.delete = deleteCacheContext;
> +#endif
>        }
>
>        /*
>
>
> --
> Gianluca Sforna
>
> http://morefedora.blogspot.com
> http://identi.ca/giallu - http://twitter.com/giallu
>
> ------------------------------------------------------------------------------
> Start uncovering the many advantages of virtual appliances
> and start using them to simplify application deployment and
> accelerate your shift to cloud computing.
> http://p.sf.net/sfu/novell-sfdev2dev
> _______________________________________________
> Rdkit-devel mailing list
> Rdk...@li...
> https://lists.sourceforge.net/lists/listinfo/rdkit-devel
>

[Rdkit-devel] [PATCH] Fix postgresql cartridge compilation

[Gianluca S. <gi...@gm...>]

It seems in 2010.09 beta1 release I can't compile the cartridge
against postgresql 8.4; the following patch fixes the issue:

diff --git a/trunk/Code/PgSQL/rdkit/cache.c b/trunk/Code/PgSQL/rdkit/cache.c
index 56b38d6..53b4910 100644
--- a/trunk/Code/PgSQL/rdkit/cache.c
+++ b/trunk/Code/PgSQL/rdkit/cache.c
@@ -1,4 +1,4 @@
-// $Id$
+// $Id: cache.c 1522 2010-09-21 06:17:39Z glandrum $
 //
 //  Copyright (c) 2010, Novartis Institutes for BioMedical Research Inc.
 //  All rights reserved.
@@ -275,7 +275,11 @@ createCache(void *cache, struct MemoryContextData * ctx)
                methodsOrig = ctx->methods;
                methodsCache = *methodsOrig;
                methodsCache.reset = resetCacheContext;
+#if PG_VERSION_NUM>=90000
                methodsCache.delete_context = deleteCacheContext;
+#else
+               methodsCache.delete = deleteCacheContext;
+#endif
        }

        /*


-- 
Gianluca Sforna

http://morefedora.blogspot.com
http://identi.ca/giallu - http://twitter.com/giallu

Re: [Rdkit-devel] Beta of Q3 2010 release up

[Gianluca S. <gi...@gm...>]

On Tue, Sep 28, 2010 at 11:33 PM, Gianluca Sforna <gi...@gm...> wrote:
> Any chance to have it in this release?

More precisely, this was the proposal, and your reply:

==========
> I suggest you revise how you do name versions; one simple way to avoid
> the issue is to swap year with quarter, so 2010Q4 < 2011Q1. Avoiding
> non numeric versions would be a nice bonus, so you could use to the
> same effect something like "YYYY.MM" (so 2010.12 < 2011.04)

This is ok with me if no one else has objections.
===============


-- 
Gianluca Sforna

http://morefedora.blogspot.com
http://identi.ca/giallu - http://twitter.com/giallu

Re: [Rdkit-devel] Beta of Q3 2010 release up

[Gianluca S. <gi...@gm...>]

On Mon, Sep 27, 2010 at 7:35 AM, Greg Landrum <gre...@gm...> wrote:
>
> As usual: if no problems come up in the next week I will go ahead and
> do the actual release.

Again, not really a problem, but we also discussed an alternate
numbering scheme like  YYYYMM, which is friendlier for packaging
because it always increases.

Any chance to have it in this release?

-- 
Gianluca Sforna

http://morefedora.blogspot.com
http://identi.ca/giallu - http://twitter.com/giallu

Re: [Rdkit-devel] Beta of Q3 2010 release up

[Greg L. <gre...@gm...>]

And now the python2.6 windows binary is up on google code:
http://code.google.com/p/rdkit/downloads/detail?name=RDKit_Q32010_1beta1.win32.py26.zip

Please let me know if you encounter any problems with the new binary.

Best Regards,
-greg

On Mon, Sep 27, 2010 at 7:35 AM, Greg Landrum <gre...@gm...> wrote:
> Dear all,
>
> I have tagged a beta of the Q3 2010 release in svn:
> https://rdkit.svn.sourceforge.net/svnroot/rdkit/tags/Release_Q32010_1beta1
> and uploaded a source distribution to the google code and sourceforge pages:
> http://code.google.com/p/rdkit/downloads
> and
> https://sourceforge.net/projects/rdkit/files/rdkit/Q3_2010/
>
> I will get a windows binary (python 2.6) up sometime in the next day or so.
>
> Draft release notes are here:
> http://rdkit.svn.sourceforge.net/viewvc/rdkit/tags/Release_Q32010_1beta1/ReleaseNotes.txt?view=markup
>
> As usual: if no problems come up in the next week I will go ahead and
> do the actual release.
>
> Thanks to everyone who contributed to this release.
>
> Best regards,
> -greg
>

[Rdkit-devel] Beta of Q3 2010 release up

[Greg L. <gre...@gm...>]

Dear all,

I have tagged a beta of the Q3 2010 release in svn:
https://rdkit.svn.sourceforge.net/svnroot/rdkit/tags/Release_Q32010_1beta1
and uploaded a source distribution to the google code and sourceforge pages:
http://code.google.com/p/rdkit/downloads
and
https://sourceforge.net/projects/rdkit/files/rdkit/Q3_2010/

I will get a windows binary (python 2.6) up sometime in the next day or so.

Draft release notes are here:
http://rdkit.svn.sourceforge.net/viewvc/rdkit/tags/Release_Q32010_1beta1/ReleaseNotes.txt?view=markup

As usual: if no problems come up in the next week I will go ahead and
do the actual release.

Thanks to everyone who contributed to this release.

Best regards,
-greg

Re: [Rdkit-devel] [Packaging] a suggestion to minimize problems

[Gianluca S. <gi...@gm...>]

On Tue, Sep 14, 2010 at 6:21 AM, Greg Landrum <gre...@gm...> wrote:
> I think it's time to merge the branch back to the trunk; sound ok to you guys?

Yes. Less active branches is good.


-- 
Gianluca Sforna

http://morefedora.blogspot.com
http://identi.ca/giallu - http://twitter.com/giallu

Re: [Rdkit-devel] [Packaging] a suggestion to minimize problems

[Greg L. <gre...@gm...>]

On Thu, Sep 9, 2010 at 3:59 PM, Gianluca Sforna <gi...@gm...> wrote:
> On Wed, Sep 8, 2010 at 6:33 AM, Greg Landrum <gre...@gm...> wrote:
>> Dear all,
>>
>> In order to minimize the problems caused by the packaging-related
>> changes, I suggest that we modify the top level CMakeLists.txt file so
>> that RDK_INSTALL_INTREE defaults to ON. This way people will get the
>> old behavior by default, but can easily switch to the new if they
>> wish.
>
> It's ok for me.
>
> I'm just wondering if we could make it ON by default unless a
> CMAKE_INSTALL_PREFIX is passed; that way I would not even need to add
> -DRDK_INSTALL_INTREE:BOOL=OFF to my build.

I'm fine with the idea, but I'm not at all sure how to do this in cmake.

A couple of updates:
- I merged the changes from the trunk onto the packaging branch. The
builds and tests seem to work with both values of RDK_INSTALL_INTREE
- I've added updated build instructions to the wiki, please let me
know what you think: http://code.google.com/p/rdkit/wiki/NewLinuxBuild

I think it's time to merge the branch back to the trunk; sound ok to you guys?

-greg

Re: [Rdkit-devel] [Packaging] a suggestion to minimize problems

[Gianluca S. <gi...@gm...>]

On Wed, Sep 8, 2010 at 6:33 AM, Greg Landrum <gre...@gm...> wrote:
> Dear all,
>
> In order to minimize the problems caused by the packaging-related
> changes, I suggest that we modify the top level CMakeLists.txt file so
> that RDK_INSTALL_INTREE defaults to ON. This way people will get the
> old behavior by default, but can easily switch to the new if they
> wish.

It's ok for me.

I'm just wondering if we could make it ON by default unless a
CMAKE_INSTALL_PREFIX is passed; that way I would not even need to add
-DRDK_INSTALL_INTREE:BOOL=OFF to my build.


-- 
Gianluca Sforna

http://morefedora.blogspot.com
http://identi.ca/giallu - http://twitter.com/giallu

Re: [Rdkit-devel] [Packaging] a suggestion to minimize problems

[Riccardo V. <ric...@gm...>]

Hello all,

On Wed, Sep 8, 2010 at 6:33 AM, Greg Landrum <gre...@gm...> wrote:
> In order to minimize the problems caused by the packaging-related
> changes, I suggest that we modify the top level CMakeLists.txt file so
> that RDK_INSTALL_INTREE defaults to ON. This way people will get the
> old behavior by default, but can easily switch to the new if they
> wish.

no objections on my part, of course. actually, it sounds like a more
user-friendly approach.

--
Riccardo

[Rdkit-devel] [Packaging] a suggestion to minimize problems

[Greg L. <gre...@gm...>]

Dear all,

In order to minimize the problems caused by the packaging-related
changes, I suggest that we modify the top level CMakeLists.txt file so
that RDK_INSTALL_INTREE defaults to ON. This way people will get the
old behavior by default, but can easily switch to the new if they
wish.

Objections?

-greg

Re: [Rdkit-devel] [PATCH 2/2] Install libraries in ${RDKit_LibDir}

[Greg L. <gre...@gm...>]

2010/9/7 Gianluca Sforna <gi...@gm...>:
>
> Running rpmlint on resulting rpms results in some warnings, the list
> is attached.
> Most of them relates to the executable bit being set on some source
> fields, I could fix it during packaging but it's probably a good idea
> to change them in the repository.
> Then it warns about /usr/include/rdkit/GraphMol/BondProps.h and
> /usr/include/rdkit/GraphMol/AtomProps.h being empty.

These should now be taken care of.

I also tested the build on windows and everything seems to work
without problems.

-greg

Re: [Rdkit-devel] [PATCH 2/2] Install libraries in ${RDKit_LibDir}

[Greg L. <gre...@gm...>]

On Tue, Sep 7, 2010 at 9:09 PM, Gianluca Sforna <gi...@gm...> wrote:
>
> On Tue, Sep 7, 2010 at 7:41 PM, Greg Landrum <gre...@gm...> wrote:
> > what about the contents of Contrib and Projects? maybe an rdkit-extras
> > package for those? I'm not sure how many packages one normally does.
>
> good idea. There is no general rule, but one usually appreciate a
> split finer enough to not bloat an installation when you just need a
> library; so splitting Contrib and Projects from rdkit definitely makes
> sense.

good to know.

> What about a rdkit-extras with Contrib, Projects and the Data ?

There are some files in Data that are needed with the python
distribution, Specifically BaseFeatures.fdef, Crippen.txt,
FragmentDescriptors.csv, and FunctionalGroups.txt. The others can go
in rdkit-extras.

-greg

Re: [Rdkit-devel] [PATCH 2/2] Install libraries in ${RDKit_LibDir}

[Gianluca S. <gi...@gm...>]

On Tue, Sep 7, 2010 at 7:41 PM, Greg Landrum <gre...@gm...> wrote:
> what about the contents of Contrib and Projects? maybe an rdkit-extras
> package for those? I'm not sure how many packages one normally does.

good idea. There is no general rule, but one usually appreciate a
split finer enough to not bloat an installation when you just need a
library; so splitting Contrib and Projects from rdkit definitely makes
sense.

What about a rdkit-extras with Contrib, Projects and the Data ?


-- 
Gianluca Sforna

http://morefedora.blogspot.com
http://identi.ca/giallu - http://twitter.com/giallu