date:20140226

Re: [Rdkit-discuss] rdkit RPM for CentOS 5.3 ?

2014-02-26 Thread Gianluca Sforna

On Tue, Feb 25, 2014 at 9:40 PM, Jan Holst Jensen j...@biochemfusion.com 
wrote:

 I am testing if rdkit can be used from Oracle on a customer (test!)
 database. And said database runs on a CentOS 5.3 server - no OS upgrade
 in the near future. First step is to get rdkit working in Python 2.4 on
 that server.

For a start, you can make your life easier by adding the EPEL
repository and pulling python26 package from there.

IIRC the only real blocker that prevented me from building RDKit
against CentOS5 + EPEL was flex

-- 
Gianluca Sforna

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

--
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Re: [Rdkit-discuss] rdkit RPM for CentOS 5.3 ?

2014-02-26 Thread Greg Landrum

On Wed, Feb 26, 2014 at 10:56 AM, Gianluca Sforna gia...@gmail.com wrote:

 On Tue, Feb 25, 2014 at 9:40 PM, Jan Holst Jensen j...@biochemfusion.com
 wrote:

  I am testing if rdkit can be used from Oracle on a customer (test!)
  database. And said database runs on a CentOS 5.3 server - no OS upgrade
  in the near future. First step is to get rdkit working in Python 2.4 on
  that server.

 For a start, you can make your life easier by adding the EPEL
 repository and pulling python26 package from there.


Yeah, I am pretty sure that there is python code that is not going to work
with 2.4


 IIRC the only real blocker that prevented me from building RDKit
 against CentOS5 + EPEL was flex


Fortunately, flex is no longer required, so that one is gone.

-greg
--
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Re: [Rdkit-discuss] rdkit RPM for CentOS 5.3 ?

2014-02-26 Thread Jan Holst Jensen


  
  
On 2014-02-26 11:04, Greg Landrum
  wrote:


  

  
  On Wed, Feb 26, 2014 at 10:56 AM,
Gianluca Sforna gia...@gmail.com wrote:

  On Tue, Feb 25, 2014 at 9:40 PM, Jan Holst
Jensen j...@biochemfusion.com
wrote:

 I am testing if rdkit can be used from Oracle on a
customer (test!)
 database. And said database runs on a CentOS 5.3
server - no OS upgrade
 in the near future. First step is to get rdkit
working in Python 2.4 on
 that server.

  
  For a start, you can make your life easier by adding the
  EPEL
  repository and pulling python26 package from there.



Yeah, I am pretty sure that there is python code that
  is not going to work with 2.4


  IIRC the only real blocker that prevented me from building
  RDKit
  against CentOS5 + EPEL was flex



Fortunately, flex is no longer required, so that one is
  gone.


-greg

  

  


Thanks, Gianluca and Greg. The EPEL repository looks like it could
save the day, giving me a tool chain so I can build rdkit. I'll give
it a try!

Cheers
-- Jan

-- 
  

  
  


  

   Biochemfusion ApS
 CVR(VAT) No. DK 32 05 74 46 
  
  


  by Jan Holst Jensen
  e-mail: j...@biochemfusion.com


  Lindegrdsvej 44, 2. TV
  Web: http://biochemfusion.com


  DK-2920 Charlottenlund, Copenhagen
  Phone: +45 30 48 00 50

  

.
  

  

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Re: [Rdkit-discuss] Insert mol objects directly into postgres rdkit cartridge column?

2014-02-26 Thread Greg Landrum

Hi Hari,

You can use mol_from_pkl(). Here's a quick demo:
In [20]: m = Chem.MolFromSmiles('c1cnccc1')

In [21]: pkl = buffer(m.ToBinary())

In [22]: curs.execute('select mol_from_pkl(%s)',(pkl,))

In [23]: curs.fetchone()
Out[23]: ('c1ccncc1',)

Is that enough to get you started?
-greg



On Tue, Feb 25, 2014 at 8:28 PM, hari jayaram hari...@gmail.com wrote:

 Hi ,
 I am a newbie to postgres and the rdkit postgres database cartridge.

 I have gotten the cartridge installed and can query sub-structure
 similarity and do other things as documented in the cartridge documentation
 page.

 To create a molecule from the cartridge the documentation
 http://www.rdkit.org/docs/Cartridge.htmlrecommends something like:


  curs.execute('select molregno,mol_send(m) from rdk.mols where m@
 %s',('c12c1nncc2',))
  row = curs.fetchone()
  row
 (9830, read-only buffer for 0x...)

 Then the pickled output of mol_send will be used to create a new molecule

  from rdkit import Chem
  m = Chem.Mol(str(row[1]))
  Chem.MolToSmiles(m,True)
 'CC(C)Sc1ccc(CC2CCN(C3CCN(C(=O)c4cnnc5c54)CC3)CC2)cc1'


 My question is : how about the other way .Is the only way to use the
 smiles and do an sql insert with the smiles and the mol_from_smiles
 function as in :

  insert into compounds (smiles,rdkit_mol,internal,external) VALUES
 ('C',mol_from_smiles('C);'ID-111','EI-222');

 Is there a way to insert the python rdkit mol object into the database
 rdkit mol column directly.

 This is in some ways connected to a question I just asked ( django
 related) on stack 
 overflow.http://stackoverflow.com/questions/22022163/how-to-handle-map-custom-postgresql-type-to-django-model

 Thanks a tonne for your help in advance
 Hari




 --
 Flow-based real-time traffic analytics software. Cisco certified tool.
 Monitor traffic, SLAs, QoS, Medianet, WAAS etc. with NetFlow Analyzer
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 https://lists.sourceforge.net/lists/listinfo/rdkit-discuss


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[Rdkit-discuss] Fwd: Error in installation of RDkit from source on Mac OSx 10.9.1

2014-02-26 Thread Abhik Seal

 Hi All,

I tried to install via homebrew but after running it cannot move to stage
of rdkit installation on Mac 10.9.1

brew install --HEAD rdkit

==* Installing rdkit dependency: *boost

*==** Downloading
http://downloads.sourceforge.net/project/boost/boost/1.49.0/boos
http://downloads.sourceforge.net/project/boost/boost/1.49.0/boos*

Already downloaded: /Library/Caches/Homebrew/boost-1.49.0.tar.bz2

*==** ./bootstrap.sh --prefix=/usr/local/Cellar/boost/1.49.0
--libdir=/usr/local/C*

*==** ./bjam --prefix=/usr/local/Cellar/boost/1.49.0
--libdir=/usr/local/Cellar/bo*
When i was trying to build from source then i am having some types.cpp
error .Attached is the log of error msg.

Then i tried to install RDkit from source with Boost and all dependencies.I
was able to install Boost1.49 but the problem with rdkit cmake  is that it
is throwing an error at

make[2]: *** [Code/RDGeneral/CMakeFiles/RDGeneral.dir/types.cpp.o] Error 1

make[1]: *** [Code/RDGeneral/CMakeFiles/RDGeneral.dir/all] Error


My command was cmake -D
PYTHON_LIBRARY=/usr/lib/python2.7/config/libpython2.7.a -D
PYTHON_INCLUDE_DIR=/usr/include/python2.7 -D
PYTHON_EXECUTABLE=/usr/bin/python -DBOOST_ROOT=/usr/local/boost_1_49_0

Then i also changed the boost version to 1.55 again i found the same error

Anyone came across this type of error ?
Attached is my error log.

Can anyone guide me through whats going wrong.

Abhik Seal
Indiana University Bloomington
Department of Chemical Informatics
abs...@indiana.edu
*OSDD CHEMINFORMATICS*
+18123699097
http://mypage.iu.edu/~abseal/index.htm


-- Forwarded message --
From: Abhik Seal abhik1...@gmail.com
Date: Mon, Feb 24, 2014 at 11:25 PM
Subject: Error in installation of RDkit from source on Mac OSx 10.9.1
To: Rdkit-discuss@lists.sourceforge.net 
rdkit-discuss@lists.sourceforge.net



Hi All,

I tried to install via homebrew but after running it cannot move to stage
of rdkit installation on Mac 10.9.1

brew install --HEAD rdkit

==* Installing rdkit dependency: *boost

*==** Downloading
http://downloads.sourceforge.net/project/boost/boost/1.49.0/boos
http://downloads.sourceforge.net/project/boost/boost/1.49.0/boos*

Already downloaded: /Library/Caches/Homebrew/boost-1.49.0.tar.bz2

*==** ./bootstrap.sh --prefix=/usr/local/Cellar/boost/1.49.0
--libdir=/usr/local/C*

*==** ./bjam --prefix=/usr/local/Cellar/boost/1.49.0
--libdir=/usr/local/Cellar/bo*
When i was trying to build from source then i am having some types.cpp
error .Attached is the log of error msg.

Then i tried to install RDkit from source with Boost and all dependencies.I
was able to install Boost1.49 but the problem with rdkit cmake  is that it
is throwing an error at

make[2]: *** [Code/RDGeneral/CMakeFiles/RDGeneral.dir/types.cpp.o] Error 1

make[1]: *** [Code/RDGeneral/CMakeFiles/RDGeneral.dir/all] Error


My command was cmake -D
PYTHON_LIBRARY=/usr/lib/python2.7/config/libpython2.7.a -D
PYTHON_INCLUDE_DIR=/usr/include/python2.7 -D
PYTHON_EXECUTABLE=/usr/bin/python -DBOOST_ROOT=/usr/local/boost_1_49_0

Then i also changed the boost version to 1.55 again i found the same error

Anyone came across this type of error ?
Attached is my error log.

Can anyone guide me through whats going wrong.

Thanks
Abhik

Abhik Seal
Indiana University Bloomington
Department of Chemical Informatics
abs...@indiana.edu
*OSDD CHEMINFORMATICS*
+18123699097
http://mypage.iu.edu/~abseal/index.htm
abhikseal/usr/local/src/RDKit_2013_09_1/build$cmake ..
-- Boost version: 1.55.0
-- Found the following Boost libraries:
--   python
-- Boost version: 1.55.0
-- Found the following Boost libraries:
--   regex
-- Configuring done
-- Generating done
-- Build files have been written to: /usr/local/src/RDKit_2013_09_1/build
abhikseal/usr/local/src/RDKit_2013_09_1/build$make
[  1%] Built target fastentropy
[  1%] Built target inchi_support
Scanning dependencies of target RDGeneral
[  2%] Building CXX object 
Code/RDGeneral/CMakeFiles/RDGeneral.dir/Invariant.cpp.o
[  2%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/types.cpp.o
In file included from 
/usr/local/src/RDKit_2013_09_1/Code/RDGeneral/types.cpp:15:
In file included from /usr/local/src/RDKit_2013_09_1/Code/RDGeneral/types.h:20:
In file included from 
/usr/local/src/RDKit_2013_09_1/Code/RDGeneral/Invariant.h:15:
In file included from 
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/string:434:
In file included from 
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/algorithm:593:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/utility:255:15:
 error: 
  no viable overloaded '='
first = __p.first;
~ ^ ~
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__tree:1246:35:
 note: 
  in instantiation of member function 'std::__1::pairconst

[Rdkit-discuss] Error in installation of RDkit from source on Mac OSx 10.9.1

2014-02-26 Thread Abhik Seal

Hi All,

Apologies for multiple postings, ignore my last posting.

I tried to install rdkit via homebrew but after running it cannot move to
stage of rdkit installation on Mac 10.9.1

brew install --HEAD rdkit

==* Installing rdkit dependency: *boost

*==** Downloading
http://downloads.sourceforge.net/project/boost/boost/1.49.0/boos
http://downloads.sourceforge.net/project/boost/boost/1.49.0/boos*

Already downloaded: /Library/Caches/Homebrew/boost-1.49.0.tar.bz2

*==** ./bootstrap.sh --prefix=/usr/local/Cellar/boost/1.49.0
--libdir=/usr/local/C*

*==** ./bjam --prefix=/usr/local/Cellar/boost/1.49.0
--libdir=/usr/local/Cellar/bo*
When i was trying to build from source then i am having some types.cpp
error .Attached is the log of error msg.

Then i tried to install RDkit from source with Boost and all dependencies.I
was able to install Boost1.49 but the problem with rdkit cmake  is that it
is throwing an error at

make[2]: *** [Code/RDGeneral/CMakeFiles/RDGeneral.dir/types.cpp.o] Error 1

make[1]: *** [Code/RDGeneral/CMakeFiles/RDGeneral.dir/all] Error


My command was cmake -D
PYTHON_LIBRARY=/usr/lib/python2.7/config/libpython2.7.a -D
PYTHON_INCLUDE_DIR=/usr/include/python2.7 -D
PYTHON_EXECUTABLE=/usr/bin/python -DBOOST_ROOT=/usr/local/boost_1_49_0

Then i also changed the boost version to 1.55 again i found the same error

Anyone came across this type of error ?
Attached is my error log.

Can anyone guide me through what's going wrong ?

Thanks
Abhik



Abhik Seal
Indiana University Bloomington
Department of Chemical Informatics
abs...@indiana.edu
*OSDD CHEMINFORMATICS*
+18123699097
http://mypage.iu.edu/~abseal/index.htm
abhikseal/usr/local/src/RDKit_2013_09_1/build$cmake ..
-- Boost version: 1.55.0
-- Found the following Boost libraries:
--   python
-- Boost version: 1.55.0
-- Found the following Boost libraries:
--   regex
-- Configuring done
-- Generating done
-- Build files have been written to: /usr/local/src/RDKit_2013_09_1/build
abhikseal/usr/local/src/RDKit_2013_09_1/build$make
[  1%] Built target fastentropy
[  1%] Built target inchi_support
Scanning dependencies of target RDGeneral
[  2%] Building CXX object 
Code/RDGeneral/CMakeFiles/RDGeneral.dir/Invariant.cpp.o
[  2%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/types.cpp.o
In file included from 
/usr/local/src/RDKit_2013_09_1/Code/RDGeneral/types.cpp:15:
In file included from /usr/local/src/RDKit_2013_09_1/Code/RDGeneral/types.h:20:
In file included from 
/usr/local/src/RDKit_2013_09_1/Code/RDGeneral/Invariant.h:15:
In file included from 
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/string:434:
In file included from 
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/algorithm:593:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/utility:255:15:
 error: 
  no viable overloaded '='
first = __p.first;
~ ^ ~
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__tree:1246:35:
 note: 
  in instantiation of member function 'std::__1::pairconst 
std::__1::basic_stringchar,
  boost::any::operator=' requested here
__cache-__value_ = *__first;
  ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__tree:1187:9:
 note: 
  in instantiation of function template specialization 
'std::__1::__treestd::__1::pairconst
  std::__1::basic_stringchar, boost::any, 
std::__1::__map_value_compareconst
  std::__1::basic_stringchar, boost::any, std::__1::lessconst 
std::__1::basic_stringchar , true,
  std::__1::allocatorstd::__1::pairconst std::__1::basic_stringchar, 
boost::any 
  ::__assign_multistd::__1::__tree_const_iteratorstd::__1::pairconst 
std::__1::basic_stringchar,
  boost::any, const std::__1::__tree_nodestd::__1::pairconst 
std::__1::basic_stringchar, boost::any,
  void * *, long ' requested here
__assign_multi(__t.begin(), __t.end());
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/map:766:21:
 note: 
  in instantiation of member function 
'std::__1::__treestd::__1::pairconst std::__1::basic_stringchar,
  boost::any, std::__1::__map_value_compareconst 
std::__1::basic_stringchar, boost::any,
  std::__1::lessconst std::__1::basic_stringchar , true, 
std::__1::allocatorstd::__1::pairconst
  std::__1::basic_stringchar, boost::any  ::operator=' requested here
__tree_ = __m.__tree_;
^
/usr/local/src/RDKit_2013_09_1/Code/RDGeneral/Dict.h:41:13: note: in 
instantiation of member function
  'std::__1::mapconst std::__1::basic_stringchar, boost::any, 
std::__1::lessconst
  std::__1::basic_stringchar , std::__1::allocatorstd::__1::pairconst

Re: [Rdkit-discuss] Insert mol objects directly into postgres rdkit cartridge column?

2014-02-26 Thread Adrian Jasiński

you can try use razi:

http://razi.readthedocs.org/en/latest/database_creation_tutorial.html

pozdrawiam
Adrian


2014-02-26 18:34 GMT+01:00 Greg Landrum greg.land...@gmail.com:

 Hi Hari,

 You can use mol_from_pkl(). Here's a quick demo:
 In [20]: m = Chem.MolFromSmiles('c1cnccc1')

 In [21]: pkl = buffer(m.ToBinary())

 In [22]: curs.execute('select mol_from_pkl(%s)',(pkl,))

 In [23]: curs.fetchone()
 Out[23]: ('c1ccncc1',)

 Is that enough to get you started?
 -greg



 On Tue, Feb 25, 2014 at 8:28 PM, hari jayaram hari...@gmail.com wrote:

 Hi ,
 I am a newbie to postgres and the rdkit postgres database cartridge.

 I have gotten the cartridge installed and can query sub-structure
 similarity and do other things as documented in the cartridge documentation
 page.

 To create a molecule from the cartridge the documentation
 http://www.rdkit.org/docs/Cartridge.htmlrecommends something like:


  curs.execute('select molregno,mol_send(m) from rdk.mols where m@
 %s',('c12c1nncc2',))
  row = curs.fetchone()
  row
 (9830, read-only buffer for 0x...)

 Then the pickled output of mol_send will be used to create a new molecule

  from rdkit import Chem
  m = Chem.Mol(str(row[1]))
  Chem.MolToSmiles(m,True)
 'CC(C)Sc1ccc(CC2CCN(C3CCN(C(=O)c4cnnc5c54)CC3)CC2)cc1'


 My question is : how about the other way .Is the only way to use the
 smiles and do an sql insert with the smiles and the mol_from_smiles
 function as in :

  insert into compounds (smiles,rdkit_mol,internal,external) VALUES
 ('C',mol_from_smiles('C);'ID-111','EI-222');

 Is there a way to insert the python rdkit mol object into the database
 rdkit mol column directly.

 This is in some ways connected to a question I just asked ( django
 related) on stack 
 overflow.http://stackoverflow.com/questions/22022163/how-to-handle-map-custom-postgresql-type-to-django-model

 Thanks a tonne for your help in advance
 Hari




 --
 Flow-based real-time traffic analytics software. Cisco certified tool.
 Monitor traffic, SLAs, QoS, Medianet, WAAS etc. with NetFlow Analyzer
 Customize your own dashboards, set traffic alerts and generate reports.
 Network behavioral analysis  security monitoring. All-in-one tool.

 http://pubads.g.doubleclick.net/gampad/clk?id=126839071iu=/4140/ostg.clktrk
 ___
 Rdkit-discuss mailing list
 Rdkit-discuss@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/rdkit-discuss




 --
 Flow-based real-time traffic analytics software. Cisco certified tool.
 Monitor traffic, SLAs, QoS, Medianet, WAAS etc. with NetFlow Analyzer
 Customize your own dashboards, set traffic alerts and generate reports.
 Network behavioral analysis  security monitoring. All-in-one tool.

 http://pubads.g.doubleclick.net/gampad/clk?id=126839071iu=/4140/ostg.clktrk
 ___
 Rdkit-discuss mailing list
 Rdkit-discuss@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/rdkit-discuss


--
Flow-based real-time traffic analytics software. Cisco certified tool.
Monitor traffic, SLAs, QoS, Medianet, WAAS etc. with NetFlow Analyzer
Customize your own dashboards, set traffic alerts and generate reports.
Network behavioral analysis  security monitoring. All-in-one tool.
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Re: [Rdkit-discuss] rdkit RPM for CentOS 5.3 ?

Re: [Rdkit-discuss] rdkit RPM for CentOS 5.3 ?

Re: [Rdkit-discuss] rdkit RPM for CentOS 5.3 ?

Re: [Rdkit-discuss] Insert mol objects directly into postgres rdkit cartridge column?

[Rdkit-discuss] Fwd: Error in installation of RDkit from source on Mac OSx 10.9.1

[Rdkit-discuss] Error in installation of RDkit from source on Mac OSx 10.9.1

Re: [Rdkit-discuss] Insert mol objects directly into postgres rdkit cartridge column?

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