Re: [Rdkit-discuss] Using the RDKit with Dask

[Peter Schmidtke]

Hi,

did you try to do something along these lines already?:
https://stackoverflow.com/questions/7089386/pickling-boost-python-functions

Peter
[https://cdn.sstatic.net/Sites/stackoverflow/Img/apple-touch-i...@2.png?v=73d79a89bded]
pickle - Pickling boost python functions - Stack 
Overflow
For the use with joblib.Parallel, I need to be able to pickle a boost::python 
function. When I try to do so, I get a TypeError: can't pickle 
builtin_function_or_method objects As far as I underst...
stackoverflow.com



From: Patrick Walters 
Sent: Monday, March 22, 2021 13:49
To: rdkit-discuss 
Subject: Re: [Rdkit-discuss] Using the RDKit with Dask

Apologies, there was a bug in the code I sent in my previous message.  The 
problem is the same.  Here is the corrected code in a gist.

https://gist.github.com/PatWalters/ca41289a6990ebf7af1e5c44e188fccd



On Mon, Mar 22, 2021 at 8:16 AM Patrick Walters 
mailto:wpwalt...@gmail.com>> wrote:
Hi All,

I've been trying to calculate BCUT2D descriptors in parallel with Dask and get 
this error with the code below.
TypeError: cannot pickle 'Boost.Python.function' object

Everything works if I call mw_df, which calculates molecular weight, but I get 
the error above if I call bcut_df.  Does anyone have a workaround?

Thanks,

Pat

#!/usr/bin/env python

import sys
import dask.dataframe as dd
import pandas as pd
from rdkit import Chem
from rdkit.Chem.Descriptors import MolWt
from rdkit.Chem.rdMolDescriptors import BCUT2D
import time

# --  molecular weight functions
def calc_mw(smi):
mol = Chem.MolFromSmiles(smi)
return MolWt(mol)

def mw_df(df):
return df.SMILES.apply(calc_mw)

# -- bcut functions
def bcut_df(df):
return df.apply(calc_bcut)

def calc_bcut(smi):
mol = Chem.MolFromSmiles(smi)
return BCUT2D(mol)

def main():
start = time.time()
df = pd.read_csv(sys.argv[1],sep=" ",names=["SMILES","Name"])
ddf = dd.from_pandas(df,npartitions=16)
ddf['MW'] = 
ddf.map_partitions(mw_df,meta='float').compute(scheduler='processes')
ddf['BCUT'] = 
ddf.map_partitions(bcut_df,meta='float').compute(scheduler='processes')
print(time.time()-start)
print(ddf.head())


if __name__ == "__main__":
main()
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Re: [Rdkit-discuss] reduced graphs fingerprints in postgresql cartridge

[Peter Schmidtke]

Hi Maciek,

I tried this today, and the trouble is that the erg fingerprints are neither 
sparse nor explicit rdkit bitvectors, but are represented as numpy arrays. As 
such they cannot even be used by current similarity functions in RDkit like 
Tanimoto similarity or other.

The only example I found on how to compare two erg fingerprints is the post by 
iwatobipen here:
https://iwatobipen.wordpress.com/2016/01/16/ergfingerprint-in-rdkit/
[https://iwatobipen.files.wordpress.com/2016/01/screen-shot-2016-01-16-at-10-19-47-pm.png]<https://iwatobipen.wordpress.com/2016/01/16/ergfingerprint-in-rdkit/>
ErGFingerprint in RDKit | Is life worth 
living?<https://iwatobipen.wordpress.com/2016/01/16/ergfingerprint-in-rdkit/>
Sometime, medicinal Chemists think about scaffold hopping approach in drug 
discovery project to overcome their issue. When I think about scaffold hopping, 
I consider about what's key interaction of molecule and protein. It's called 
pharmacophore. And also hopping approach is used me too approach to find 
another IP space. BTW, In 2006, researchers in Lilly…
iwatobipen.wordpress.com


Is there any documentation along those lines somewhere? The way I understand it 
 right now my options are:

  *   serialize numpy arrays to register them as binary to a postgresql database
 *   how to compare them in pgsql then?
  *   find a way / means to transform the numpy array into a sparse or explicit 
bitvector (would that make sense at all?)
  *   or just consider exact matches for erg fp's and do not integrate any 
similarity metric

Thanks in advance for ideas 

Peter






From: Maciek Wójcikowski 
Sent: Tuesday, December 17, 2019 20:18
To: Peter Schmidtke 
Cc: RDKit Discuss 
Subject: Re: [Rdkit-discuss] reduced graphs fingerprints in postgresql cartridge

While creating more detailed answer for you I stumbled upon very useful 
blogpost by Greg 
https://rdkit.blogspot.com/2017/04/using-custom-fingerprint-in-postgresql.html 
which explains in detail how custom fingerprints can be handled.

Both Tanimoto and Dice are supported for any sfp/bfp.

Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl<mailto:mac...@wojcikowski.pl>


wt., 17 gru 2019 o 18:38 Maciek Wójcikowski 
mailto:mac...@wojcikowski.pl>> napisał(a):
Hi Peter,

You can index any binary fingerprint (both sparse and explicit). Also, you can 
create any custom fp in python and pass it over to postgresql. That said, I 
have not managed to transfer a sparse one from python to postgres, only the 
explicit.

Best,
Maciek

wt., 17 gru 2019, 13:00 użytkownik Peter Schmidtke 
mailto:peter.schmid...@discngine.com>> napisał:
Hi all,

is it possible to index the reduced graphs fingerprints in the pgsql cartridge 
as well? From my understanding the fingerprint provided by rdkit isn’t exactly 
in the same format as for standard morgan fingerprints.
Would this work anyhow? if yes with which similarity functions in pgsql? 
Anybody ever tried this and has a bit of documentation?

Thanks in advance

Peter
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Re: [Rdkit-discuss] reduced graphs fingerprints in postgresql cartridge

[Peter Schmidtke]

Thanks Maciek,

will check that out just wasn’t sure if this applies correctly to the reduced 
graph fingerprints which seemed a bit different:
ie: https://iwatobipen.wordpress.com/2016/01/16/ergfingerprint-in-rdkit

Anyway, we’ll try that out and write something up in case it’s working ;)

Cheers

Peter

On 17 Dec 2019, at 20:18, Maciek Wójcikowski 
mailto:mac...@wojcikowski.pl>> wrote:

While creating more detailed answer for you I stumbled upon very useful 
blogpost by Greg 
https://rdkit.blogspot.com/2017/04/using-custom-fingerprint-in-postgresql.html 
which explains in detail how custom fingerprints can be handled.

Both Tanimoto and Dice are supported for any sfp/bfp.

Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl<mailto:mac...@wojcikowski.pl>


wt., 17 gru 2019 o 18:38 Maciek Wójcikowski 
mailto:mac...@wojcikowski.pl>> napisał(a):
Hi Peter,

You can index any binary fingerprint (both sparse and explicit). Also, you can 
create any custom fp in python and pass it over to postgresql. That said, I 
have not managed to transfer a sparse one from python to postgres, only the 
explicit.

Best,
Maciek

wt., 17 gru 2019, 13:00 użytkownik Peter Schmidtke 
mailto:peter.schmid...@discngine.com>> napisał:
Hi all,

is it possible to index the reduced graphs fingerprints in the pgsql cartridge 
as well? From my understanding the fingerprint provided by rdkit isn’t exactly 
in the same format as for standard morgan fingerprints.
Would this work anyhow? if yes with which similarity functions in pgsql? 
Anybody ever tried this and has a bit of documentation?

Thanks in advance

Peter
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[Rdkit-discuss] reduced graphs fingerprints in postgresql cartridge

[Peter Schmidtke]

Hi all,

is it possible to index the reduced graphs fingerprints in the pgsql cartridge 
as well? From my understanding the fingerprint provided by rdkit isn’t exactly 
in the same format as for standard morgan fingerprints. 
Would this work anyhow? if yes with which similarity functions in pgsql? 
Anybody ever tried this and has a bit of documentation?

Thanks in advance

Peter
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Re: [Rdkit-discuss] decomposing products to reactants from an rxn

[Peter Schmidtke]

Yep started to use the GitHub wiki also recently, but not sure how well this is 
indexed.
There’s also quite a lot of useful content on several things on various blogs 
(yours, iwatobipen, Pat’s etc … ) but when you have to dive into a whole new 
area you haven’t used before in rdkit (reaction management for me), then it’s 
really complicated to deduce how to do things and actually also understand what 
is possible, what is not yet implemented.

Would be good to find an indexed way to put all of these examples and where the 
community could also easily contribute (so that you don’t have to do all of 
them yourself). Github wiki seems like a good place to try, but I find mixed 
returns on the fact it’s indexed on google or not, but it appears like it is 
now. Happy to contribute once I’m a proficient rdkit expert ;)

Cheers

Peter

On 4 Dec 2019, at 16:05, Greg Landrum 
mailto:greg.land...@gmail.com>> wrote:



On Wed, Dec 4, 2019 at 3:45 PM Peter Schmidtke 
mailto:peter.schmid...@discngine.com>> wrote:

Would be cool to have these examples somewhere findable via google 

That's an interesting meta-point. I agree, but I wonder what an effective way 
to do this is.
Using jupyter to answer questions and then sticking the results into a gist 
makes my life a lot easier. I also think it makes the answers easier to read 
and understand than pasting python code and output into an email. But it does 
make the list archives (which tend to show up pretty high in google searches) 
less useful.

Gists do end up being indexed by google, which is nice, but without links to 
them they won't ever show up high in search results. So that's suboptimal.

I guess I could start collecting particularly useful items (based on 
feedback/my gut feeling) into a wiki on github... that probably wouldn't be 
completely useless.

Ideas/suggestions are welcome.

-greg


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Re: [Rdkit-discuss] decomposing products to reactants from an rxn

[Peter Schmidtke]

Indeed that seems to work rather well. I forgot to use Initialize during my 
naive initial tests, that's probably why nothing worked back at the time.

Would be cool to have these examples somewhere findable via google 

Thanks a lot for the helpwe'll check a bit further on larger sets of 
reactions what works and what doesn't.

Cheers

Peter



From: Greg Landrum 
Sent: Wednesday, December 4, 2019 09:59
To: Peter Schmidtke 
Cc: rdkit-discuss@lists.sourceforge.net 
Subject: Re: [Rdkit-discuss] decomposing products to reactants from an rxn



On Tue, Dec 3, 2019 at 8:37 PM Peter Schmidtke 
mailto:peter.schmid...@discngine.com>> wrote:

We’re currently working on an algorithm to make that work in a purely pythonic 
way (for now). Let’s see if we can come up with something sensible and good to 
have your simple example. It is exactly the type of use case we have in mind.
For instance, take these reactions here (maybe they’d need a bit of adaptation 
& refinement for rdkit) : https://pubs.acs.org/doi/abs/10.1021/ci200379p (SI : 
https://pubs.acs.org/doi/suppl/10.1021/ci200379p/suppl_file/ci200379p_si_002.pdf)
 .

Side remark: the Hartenfeller reactions ought to work without modification. 
Markus was using the RDKit when he did that work and I have certainly used the 
reaction smarts in the xls file that's also in the SI without problems in the  
past.
FWIW, I just picked the first one of those (Pictet Spengler) and it reverses 
without problems. I updated the gist:
https://gist.github.com/greglandrum/5ca4eebbe78f4d6d9b8cb03f401ad9cd

-greg

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Re: [Rdkit-discuss] decomposing products to reactants from an rxn

[Peter Schmidtke]

On 2 Dec 2019, at 11:32, Greg Landrum 
mailto:greg.land...@gmail.com>> wrote:

HI Peter,

On Mon, Dec 2, 2019 at 10:11 AM Peter Schmidtke 
mailto:peter.schmid...@discngine.com>> wrote:

I wanted to know whether there was an easy way in rdkit to decompose a product 
to its reactants using an  rdkit smarts-based reaction?
Basically I’m looking for the runReactants function but the other way around.
Is there any chance this would work with a reverted reaction or is this just 
wishful thinking?

Nice question. And, as with any good question, the answer is: "It depends".

It's pretty straightforward to reverse a reaction by creating a new one and 
copying the reactants/products from your example in as products/reactants in 
the new reaction. This will work as long as you don't use query features in the 
specification of the reaction.


Yep I saw I could easily redefine a reversed reaction. What I couldn’t find was 
that this also sort of works for reaction smarts.

Unfortunately it stops working sensibly pretty quickly once you introduce query 
features.

Here's a gist showing some of this.
https://gist.github.com/greglandrum/5ca4eebbe78f4d6d9b8cb03f401ad9cd

I'm having a hard time coming up with even a hack solution that isn't a ton of 
work, but I'll think about it a bit more. There may be a way to make this work 
on the C++ side.

To help with this, can you give a specific example of the kind of reaction 
you'd like to reverse?



We’re currently working on an algorithm to make that work in a purely pythonic 
way (for now). Let’s see if we can come up with something sensible and good to 
have your simple example. It is exactly the type of use case we have in mind.
For instance, take these reactions here (maybe they’d need a bit of adaptation 
& refinement for rdkit) : https://pubs.acs.org/doi/abs/10.1021/ci200379p (SI : 
https://pubs.acs.org/doi/suppl/10.1021/ci200379p/suppl_file/ci200379p_si_002.pdf)
 .

thanks a lot for the gist, didn’t know it was possible this way already :)

Peter



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[Rdkit-discuss] decomposing products to reactants from an rxn

[Peter Schmidtke]

Hi,

I wanted to know whether there was an easy way in rdkit to decompose a product 
to its reactants using an  rdkit smarts-based reaction? 
Basically I’m looking for the runReactants function but the other way around. 
Is there any chance this would work with a reverted reaction or is this just 
wishful thinking?

Thanks in advance for your reply.

Peter Schmidtke
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[Rdkit-discuss] label properties on 2D depiction

[Peter Schmidtke]

Dear all,

I wondered if it was possible and easy to show some numerical properties
or strings or whatever for each atom on a 2d representation of a molecule.

Is something like that implemented (didn't really see it right now)?

Thanks in advance.
-- 

Peter Schmidtke
PhD Student
Dept. Physical Chemistry
Faculty of Pharmacy
University of Barcelona


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Re: [Rdkit-discuss] label properties on 2D depiction

[Peter Schmidtke]

Thanks Greg,

I'll give it a try ;)

++

Peter

On 07/11/2011 06:47 PM, Greg Landrum wrote:
 Hi Peter,

 On Mon, Jul 11, 2011 at 1:35 PM, Peter Schmidtke pschmid...@ub.edu wrote:
   
 I wondered if it was possible and easy to show some numerical properties
 or strings or whatever for each atom on a 2d representation of a molecule.

 Is something like that implemented (didn't really see it right now)?
 
 There's nothing like that built in, but pretty much everything you
 need to be able to annotate the drawing yourself after the molecule
 has been drawn is already there.

 Take a look at the code in $RDBASE/rdkit/Chem/Draw/__init__.py:MolToImage
 After line 70 executes, you have a canvas (either cairo, aggdraw, or
 sping, depending on which system you have installed) that contains the
 molecule drawing as well as MolDrawing instance named drawer. drawer
 has a data element atomPs that can be used to get the position of
 atoms in canvas coordinates : drawer.atomPs[mol][atomIdx]. The code
 for the individual canvases shows how to do something with these
 coordinates.

  -greg
   


-- 

Peter Schmidtke
PhD Student
Dept. Physical Chemistry
Faculty of Pharmacy
University of Barcelona


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Re: [Rdkit-discuss] Building RDKit on CentOS 5

[Peter Schmidtke]

/python2.7/ -D 
PYTHON_EXECUTABLE=/usr/local/bin/python -D BOOST_ROOT=/usr/local/ 
-DBoost_USE_STATIC_LIBS=OFF  ..

make

make install

Next you should install the test databases for rdkit, like said in the 
documentation.



On 15/11/2010, at 21:45, Robert DeLisle wrote:

 I've been working to build RDKit on Centos 5, and I'm hitting a very common 
 error.  Unfortunately, none of the standard fixes have helped.
 
 Details:
 
 The error that I'm seeing is this:
 
 [ 82%] Building CXX object 
 Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNParse.cpp.o
 [ 83%] Building CXX object 
 Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o
 [ 83%] Building CXX object 
 Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/sln.tab.cpp.o
 [ 84%] Building CXX object 
 Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/lex.yysln.cpp.o
 Linking CXX shared library libSLNParse.so
 /usr/bin/ld: /usr/lib/../lib64/libboost_regex.a(instances.o): relocation 
 R_X86_64_32 against 
 `boost::object_cacheboost::re_detail::cpp_regex_traits_basechar, 
 boost::re_detail::cpp_regex_traits_implementationchar 
 ::do_get(boost::re_detail::cpp_regex_traits_basechar const, unsigned 
 long)::s_data' can not be used when making a shared object; recompile with 
 -fPIC
 /usr/lib/../lib64/libboost_regex.a: could not read symbols: Bad value
 collect2: ld returned 1 exit status
 make[2]: *** [Code/GraphMol/SLNParse/libSLNParse.so] Error 1
 make[1]: *** [Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/all] Error 2
 make: *** [all] Error 2
 
 
 I've taken the standard steps of building Python (v2.7) with the -fPIC flag.  
 Specficially, I attached CFLAGS=-fPIC to configure in the Python build.  This 
 solved the first instance of this type of error occuring at about 3%.
 
 I've also tried the two fixes for Boost with the following command line to 
 build RDKit:
 
 cmake -DBOOST_ROOT=/usr/local -DBoost_USE_STATIC_LIBS=OFF ..  
   
 
 I still get this error, and I notice that the Boost libraries that are being 
 referred to are actually the system installation in usr/lib64 and not those 
 that I've build in /usr/local/lib.  It would seem that I can't seem to force 
 make to look in the right location.
 
 Any tips are greatly apprciated.
 
 -Kirk
 
 
 
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-
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School of Pharmacy
University of Barcelona
Barcelona, Spain

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Re: [Rdkit-discuss] Building RDKit on CentOS 5

[Peter Schmidtke]

Hey Greg,

yep that would be great, as right now they are only on a group internal blog ;) 
I saw that you recently changed you linux build instructions (concerning 
database things, boost numerical bindings etc...), but I did this before this 
came out ;) 

First lets see if Robert comes through the install process without major 
problems and then you can post it on your wiki (I might have forgotten some 
stuff). 
Some things are based on installing pycuda on those machines, this is why 
signals and things like that are compiled with boost (might be worth to mention 
somehow in case people need both).

++

Peter

On 17/11/2010, at 14:25, Greg Landrum wrote:

 Dear Peter,
 
 Thanks for posting these very detailed instructions. Do you mind if I
 post them to the wiki (with credit of course) to make them easier to
 find?
 
 I made a few comments and suggestions below:
 
 On Wed, Nov 17, 2010 at 11:19 AM, Peter Schmidtke pschmid...@ub.edu wrote:
 Dear Robert,
 I recently ran also into several problems while installing rdkit on a fresh
 Centos 5.3. It's a real headache. Anyway, this time I've written up a guide
 of how to do it step by step, I hope I didn't forget anything in the end.
 However, now it works just fine on our Centos machines. Here's the step by
 step installing guide :
 
 Centos is a stable but not very userfriendly OS. This becomes obvious when
 one wants to install python packages like pycuda etc...Centos comes with a
 very old python version, 2.4, but lots of newer features, like pycuda
 require a newer python version. Lets start the lengthy install process under
 Centos :
 
 Installing Python 2.6 or newer
 
 If you already have python2.7 installed, please check that it was installed
 with --enabled-shared. If this is the case you should have libpython2.7.so
 in /usr/local/lib. If not, you should have libpython2.7.a. If the second is
 the case, you have to install python2.7 with the following way :
 
 Download the current version from python (source code). Like with 2.6 or 2.7
 (don't grab the 3.x for now) :
 
 wget http://www.python.org/ftp/python/2.7/Python-2.7.tgz
 
 Next untar and unzip the file, go to Python-2.7 directory and issue :
 
 ./configure --enable-shared; make; sudo make install
 
 This installs python in the /usr/local/ directory.
 
 Add the RPMForge repo to yum :
 
 wget
 http://packages.sw.be/rpmforge-release/rpmforge-release-0.5.1-1.el5.rf.x86_64.rpm
 
 su -c 'rpm -Uvh rpmforge-release-0.5.1-1.el5.rf.x86_64.rpm'
 
 Then install atlas, lapack, blas :
 
 yum install atlas-c++.x86_64 atlas-c++-devel.x86_64 lapack.x86_64
 lapack-devel.x86_64 blas.x86_64 blas-devel.x86_64
 
 Now we can install fftw3 :
 
 yum install fftw3.x86_64 fftw3-devel.x86_64
 
 
 
 Now we could potentially install numpy 1.3 or 1.4, but as python2.7 is brand
 new there are some problems. I downloaded :
 
 wget 
 http://sourceforge.net/projects/numpy/files/NumPy/1.3.0/numpy-1.3.0.tar.gz/download
 
 then untar and unzip this whole thing and go to the numpy directory
 
 Download the following patch :
 
 wget 
 http://sources.gentoo.org/cgi-bin/viewvc.cgi/gentoo-x86/dev-python/numpy/files/numpy-1.4.0-python-2.7.patch
 
 and apply it in this directory using :
 
 patch -p0  numpy-1.4.0-python-2.7.patch
 
 Now build numpy using python setup.py build; python setup.py install
 
 Numpy should now be accessible from python2.7, simply try a import numpy
 after launching python to check.
 
 First we need to install the boost libraries and their python bindings.
 Download boost to your downloads directory using, here I use the version
 1.41 of boost. :
 
 wget
 http://sourceforge.net/projects/boost/files/boost/1.41.0/boost_1_41_0.tar.gz/download
 
 untar and unzip this file and go to the directory.
 
 Then issue the following commands :
 
 ./bootstrap.sh --with-libraries=python,regex,signals,thread
 
 signals should not be necessary for the rdkit.
 
 
 Then you can issue the boost build command :
 
 ./bjam -j24 variant=release address-model=64 cflags=-fPIC cxxflags=-fPIC
 link=shared install
 
 Then add the line export LD_LIBRARY_PATH=/usr/local/lib:${LD_LIBRARY_PATH}
 to your .bashrc file and source it.
 
 If you have the default flex and bison packages installed from the yum
 repositories erase them using yum erase flex and yum erase bison. Those are
 extremely old and Rdkit needs newer ones, we have to build them by hand now.
 
 wget http://prdownloads.sourceforge.net/flex/flex-2.5.35.tar.gz?download
 
 untar and unzip, cd flex-2.5.35 and then do a classic :
 
 ./configure; make; make install
 
 Now grab and install bison using the same procedure as for flex :
 
 wget http://ftp.gnu.org/gnu/bison/bison-2.4.2.tar.gz
 
 ...
 
 Now we have to upgrade cmake, because Centos uses, as usual an old and a bit
 buggy on. Download cmake 2.8 from here and untar and unzip it and go to the
 directory. Previously uninstall the existing (if existing) cmake version on
 your Centos platform using yum erase cmake.
 
  The installation

Re: [Rdkit-discuss] read SD file with hydrogens

[Peter Schmidtke]

Hey Greg,

thanks for the reply. Mea culpa, indeed, I have to get used to the C++
oriented API doc (I'm more used into Pythonic docs, the reason why I did
not look into the constructor arguments).

Cheers.

Peter

Greg Landrum wrote:
 Dear Peter,

 On Tue, Sep 28, 2010 at 1:32 AM, Peter Schmidtke pschmid...@ub.edu wrote:
   
 I'd like to read several molecules from a SD file (created with MOE).
 These molecules have already added H's and I'd like to keep them as they
 are (so not readd them in rdkit after reading). How can I do this with
 the SDMolSupplier...right now I get the impression that he reads
 everything but H's.
 

 By default the RDKit removes Hs from molecules. To keep them you need
 to use the optional removeHs argument when constructing your
 SDMolSupplier:
 In [11]: suppl = Chem.SDMolSupplier('blah.sdf',removeHs=False)
 In [12]: ms = [x for x in suppl]
 In [13]: ms[0].Debug()
 Atoms:
 0 6 C chg: 0  deg: 4 exp: 4 imp: 0 hyb: 4 arom?: 0 chi: 0
 1 6 C chg: 0  deg: 4 exp: 4 imp: 0 hyb: 4 arom?: 0 chi: 0
 2 1 H chg: 0  deg: 1 exp: 1 imp: 0 hyb: 1 arom?: 0 chi: 0
 3 1 H chg: 0  deg: 1 exp: 1 imp: 0 hyb: 1 arom?: 0 chi: 0
 4 1 H chg: 0  deg: 1 exp: 1 imp: 0 hyb: 1 arom?: 0 chi: 0
 5 1 H chg: 0  deg: 1 exp: 1 imp: 0 hyb: 1 arom?: 0 chi: 0
 6 1 H chg: 0  deg: 1 exp: 1 imp: 0 hyb: 1 arom?: 0 chi: 0
 7 1 H chg: 0  deg: 1 exp: 1 imp: 0 hyb: 1 arom?: 0 chi: 0
 Bonds:
 0 0-1 order: 1 conj?: 0 aromatic?: 0
 1 0-2 order: 1 conj?: 0 aromatic?: 0
 2 0-3 order: 1 conj?: 0 aromatic?: 0
 3 0-4 order: 1 conj?: 0 aromatic?: 0
 4 1-5 order: 1 conj?: 0 aromatic?: 0
 5 1-6 order: 1 conj?: 0 aromatic?: 0
 6 1-7 order: 1 conj?: 0 aromatic?: 0

 Best Regards,
 -greg
   


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University of Barcelona


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[Rdkit-discuss] read SD file with hydrogens

[Peter Schmidtke]

Dear rdkit mailing list readers,

I'd like to read several molecules from a SD file (created with MOE).
These molecules have already added H's and I'd like to keep them as they
are (so not readd them in rdkit after reading). How can I do this with
the SDMolSupplier...right now I get the impression that he reads
everything but H's.

Thanks for a hint.

Cheers

Peter Schmidtke

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Re: [Rdkit-discuss] Build on Windows

[Peter Schmidtke]

 BOOST_ROOT=/pathToBoost

where pathToBoost is the directory containing the include and lib directory of 
your boost install...

what cmake version are you using? If it's the 2.6, go for the 2.8 instead!

On 28/07/2010, at 16:20, Evgueni Kolossov wrote:

 Done but it still cannot find libraries
 
 On 28 July 2010 15:17, Peter Schmidtke pschmid...@ub.edu wrote:
 did you erase all content in the build directory before running cmake again?
 
 I sometimes noticed some strange behaviour when some old cmake stuff was 
 still in the dir. 
 
 On 28/07/2010, at 16:14, Evgueni Kolossov wrote:
 
 Tried Run cmake with -DBoost_LIBRARYDIR=whatever
 but it still cannot find regex
 
 On 28 July 2010 15:07, Noel O'Boyle baoille...@gmail.com wrote:
 On 28 July 2010 15:04, Evgueni Kolossov ekolos...@gmail.com wrote:
  Dear Greg,
 
  I am trying to rebuild RDKit on Windows using boost 1_43 and cannot go
  through the configuration stage with CMake:
 
  CMake Error at C:/Program Files/CMake
  2.8/share/cmake-2.8/Modules/FindBoost.cmake:910 (message):
Unable to find the requested Boost libraries.
 
Boost version: 1.43.0
 
Boost include path: C:/boost/boost_1_43_0
 
The following Boost libraries could not be found:
 
boost_regex
 
No Boost libraries were found.  You may need to set Boost_LIBRARYDIR to
  the
directory containing Boost libraries or BOOST_ROOT to the location of
Boost.
  Call Stack (most recent call first):
Code/GraphMol/SLNParse/CMakeLists.txt:4 (find_package)
 
 
  CMake Error: The following variables are used in this project, but they are
  set to NOTFOUND.
  Please set them or make sure they are set and tested correctly in the CMake
  files:
  Boost_REGEX_LIBRARY (ADVANCED)
  linked by target testSLNParse in directory
  C:/RDKit/Code/GraphMol/SLNParse
 
  Configuring incomplete, errors occurred!
 
  I have tried to set environmental variable Boost_LIBRARYDIR to
  .\boost_1_43_0\bin.v2\libs or to \boost_1_43_0\boost where regex directory
  is but it still cannot find it.
 
 Run cmake with -DBoost_LIBRARYDIR=whatever
 
  Please help.
 
  Regards,
  Evgueni
 
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 ekolos...@gmail.com
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Peter Schmidtke

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University of Barcelona
Barcelona, Spain

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Re: [Rdkit-discuss] Build on Windows

[Peter Schmidtke]

Ah sorry mea culpa this was for unix based systems. 
However, on windows you should use :

.\bjam.exe --toolset=msvc --with-python --with-regex release install


instead I think to build boost. I'm not 100% sure about this as the rkdit build 
documentation for windows says something different.

Try to build boost with this and build rdkit again.
 

On 28/07/2010, at 16:34, Evgueni Kolossov wrote:

 No, what is this for?
 
 On 28 July 2010 15:31, Peter Schmidtke pschmid...@ub.edu wrote:
 Did you ./boostrap boost with regex using   :
 
 ./bootstrap.sh --prefix=$HOME/pool --libdir=$HOME/pool/lib 
 --with-libraries=python,regex
 
 
 ?
 
 On 28/07/2010, at 16:28, Evgueni Kolossov wrote:
 
 Yes this is set in environmental variables and I am using CMake 2.8
 
 On 28 July 2010 15:24, Peter Schmidtke pschmid...@ub.edu wrote:
  BOOST_ROOT=/pathToBoost
 
 where pathToBoost is the directory containing the include and lib directory 
 of your boost install...
 
 what cmake version are you using? If it's the 2.6, go for the 2.8 instead!
 
 On 28/07/2010, at 16:20, Evgueni Kolossov wrote:
 
 Done but it still cannot find libraries
 
 On 28 July 2010 15:17, Peter Schmidtke pschmid...@ub.edu wrote:
 did you erase all content in the build directory before running cmake again?
 
 I sometimes noticed some strange behaviour when some old cmake stuff was 
 still in the dir. 
 
 On 28/07/2010, at 16:14, Evgueni Kolossov wrote:
 
 Tried Run cmake with -DBoost_LIBRARYDIR=whatever
 but it still cannot find regex
 
 On 28 July 2010 15:07, Noel O'Boyle baoille...@gmail.com wrote:
 On 28 July 2010 15:04, Evgueni Kolossov ekolos...@gmail.com wrote:
  Dear Greg,
 
  I am trying to rebuild RDKit on Windows using boost 1_43 and cannot go
  through the configuration stage with CMake:
 
  CMake Error at C:/Program Files/CMake
  2.8/share/cmake-2.8/Modules/FindBoost.cmake:910 (message):
Unable to find the requested Boost libraries.
 
Boost version: 1.43.0
 
Boost include path: C:/boost/boost_1_43_0
 
The following Boost libraries could not be found:
 
boost_regex
 
No Boost libraries were found.  You may need to set Boost_LIBRARYDIR to
  the
directory containing Boost libraries or BOOST_ROOT to the location of
Boost.
  Call Stack (most recent call first):
Code/GraphMol/SLNParse/CMakeLists.txt:4 (find_package)
 
 
  CMake Error: The following variables are used in this project, but they 
  are
  set to NOTFOUND.
  Please set them or make sure they are set and tested correctly in the 
  CMake
  files:
  Boost_REGEX_LIBRARY (ADVANCED)
  linked by target testSLNParse in directory
  C:/RDKit/Code/GraphMol/SLNParse
 
  Configuring incomplete, errors occurred!
 
  I have tried to set environmental variable Boost_LIBRARYDIR to
  .\boost_1_43_0\bin.v2\libs or to \boost_1_43_0\boost where regex 
  directory
  is but it still cannot find it.
 
 Run cmake with -DBoost_LIBRARYDIR=whatever
 
  Please help.
 
  Regards,
  Evgueni
 
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 Peter Schmidtke
 
 -
 PhD Student
 Department of Physical Chemistry
 School of Pharmacy
 University of Barcelona
 Barcelona, Spain
 
 
 
 
 -- 
 
 Peter Schmidtke
 
 -
 PhD Student
 Department of Physical Chemistry
 School of Pharmacy
 University of Barcelona
 Barcelona, Spain
 
 
 
 Mob. +44(0)7812070446
 
 Peter Schmidtke
 
 -
 PhD Student
 Department of Physical Chemistry
 School of Pharmacy
 University of Barcelona
 Barcelona, Spain
 
 
 

Peter Schmidtke

-
PhD Student
Department of Physical Chemistry
School of Pharmacy
University of Barcelona
Barcelona, Spain

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Re: [Rdkit-discuss] install problems on Centos 5.3

[Peter Schmidtke]

Hey Greg,

I already compiled boost using the instructions from the rdkit wiki. Anyway, 
recompiling rdkit completely solves this problem.

But that wasn't easy enough. Next error : 

[ 84%] Built target rdSLNParse
[ 85%] Building CXX object 
Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/EditableMol.cpp.o
/root/pool/include/boost/type_traits/detail/cv_traits_impl.hpp: In 
instantiation of ‘const bool 
boost::detail::cv_traits_impRDKit::unnamed::EditableMol*::is_const’:
/root/pool/include/boost/type_traits/is_const.hpp:57:   instantiated from 
‘boost::is_constRDKit::unnamed::EditableMol’
/root/pool/include/boost/python/detail/cv_category.hpp:31:   instantiated from 
‘boost::python::detail::cv_categoryRDKit::unnamed::EditableMol’
/root/pool/include/boost/python/detail/unwind_type.hpp:58:   instantiated from 
‘typename Generator::result_type boost::python::detail::unwind_ptr_type(U*, 
Generator*) [with Generator = 
boost::python::converter::detail::unwind_type_id_helper, U = 
RDKit::unnamed::EditableMol]’
/root/pool/include/boost/python/detail/unwind_type.hpp:127:   instantiated from 
‘static typename Generator::result_type 
boost::python::detail::unwind_helper22::execute(U (*)(), Generator*) [with 
Generator = boost::python::converter::detail::unwind_type_id_helper, U = 
RDKit::unnamed::EditableMol]’
/root/pool/include/boost/python/detail/unwind_type.hpp:165:   instantiated from 
‘typename Generator::result_type 
boost::python::detail::unwind_type(boost::typeU*, Generator*) [with Generator 
= boost::python::converter::detail::unwind_type_id_helper, U = 
RDKit::unnamed::EditableMol]’
/root/pool/include/boost/python/converter/pytype_function.hpp:45:   
instantiated from ‘boost::python::type_info 
boost::python::converter::detail::unwind_type_id_(boost::typeTarget*, 
mpl_::false_*) [with T = RDKit::unnamed::EditableMol]’
/root/pool/include/boost/python/converter/pytype_function.hpp:68:   
instantiated from ‘static const PyTypeObject* 
boost::python::converter::expected_pytype_for_argT::get_pytype() [with T = 
RDKit::unnamed::EditableMol]’
/root/pool/include/boost/python/detail/signature.hpp:98:   instantiated from 
‘static const boost::python::detail::signature_element* 
boost::python::detail::signature_arity3u::implSig::elements() [with Sig = 
boost::mpl::vector4void, RDKit::unnamed::EditableMol, unsigned int, 
unsigned int]’
/root/pool/include/boost/python/detail/caller.hpp:232:   instantiated from 
‘static boost::python::detail::py_func_sig_info 
boost::python::detail::caller_arity3u::implF, Policies, Sig::signature() 
[with F = void (RDKit::unnamed::EditableMol::*)(unsigned int, unsigned int), 
Policies = boost::python::default_call_policies, Sig = 
boost::mpl::vector4void, RDKit::unnamed::EditableMol, unsigned int, 
unsigned int]’
/root/pool/include/boost/python/object/py_function.hpp:48:   instantiated from 
‘boost::python::detail::py_func_sig_info 
boost::python::objects::caller_py_function_implCaller::signature() const 
[with Caller = boost::python::detail::callervoid 
(RDKit::unnamed::EditableMol::*)(unsigned int, unsigned int), 
boost::python::default_call_policies, boost::mpl::vector4void, 
RDKit::unnamed::EditableMol, unsigned int, unsigned int ]’
/usr/local/RDKit_Q22010_1/Code/GraphMol/Wrap/EditableMol.cpp:114:   
instantiated from here
/root/pool/include/boost/type_traits/detail/cv_traits_impl.hpp:37: internal 
compiler error: in make_rtl_for_nonlocal_decl, at cp/decl.c:5067
Please submit a full bug report,
with preprocessed source if appropriate.
See URL:http://bugzilla.redhat.com/bugzilla for instructions.
Preprocessed source stored into /tmp/ccgSaXge.out file, please attach this to 
your bugreport.
make[2]: *** [Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/EditableMol.cpp.o] Error 
1
make[1]: *** [Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/all] Error 2
make: *** [all] Error 2



I saw this error online also, and people suggested to add the 
BOOST_PYTHON_NO_PY_SIGNATURES
 flag, and recompile boost, which is what I did, but no effect on this error.

Someone has an idea? Are there plans to come around these boost dependencies in 
rdkit...it's a real showstopper on older systems...real pain to get it 
installed :(

Cheers.

Peter


On 24/07/2010, at 05:39, Greg Landrum wrote:

 On Sat, Jul 24, 2010 at 5:31 AM, Greg Landrum greg.land...@gmail.com wrote:
 On Fri, Jul 23, 2010 at 11:20 PM, Peter Schmidtke pschmid...@ub.edu wrote:
 Dear Greg,
 
 thanks for the hint, but this one changes absolutely nothing to the 
 compilation for me...unfortunately (I completely redid the whole 
 compilation and ended up with the same error)
 
 Any ideas of how to debug this?
 
 
 Did you re-run cmake? That change should have made it so that you
 don't need the static regex library at all (which is the source of the
 problems).
 
 
 One last suggestion before I leave for the weekend. If re-running
 cmake and then rebuilding doesn't work, you might want to try
 re-building boost following the instructions on the wiki
 (http

Re: [Rdkit-discuss] install problems on Centos 5.3

[Peter Schmidtke]

Dear Greg and Gianluca,

indeed this solved the compilation problem. 
Now I am testing a little, let's see. 

Concerning the boost dependencies...I understand your point of view. The fact 
is, that I like projects like rdkit and I am trying to promote them myself. The 
problem is only then people coming back to me saying, ah finally I didn't 
install because it was too complicated, especially on production environments 
like the 64 bit centos machines I am working with...the accumulation of gcc 
bugs, boost static library problems and libraries etc to update to make 
everything run was a bit heavy. 

In the contrary, installing it on a opensuse 11.1 64 bit was rather 
straightforward. 

Thanks for putting the issues I encountered in the wiki, searching mailing 
lists is also rather cumbersome.

Cheers.

Peter

On 26/07/2010, at 15:47, Greg Landrum wrote:

 Dear Peter,
 
 On Mon, Jul 26, 2010 at 3:19 PM, Peter Schmidtke pschmid...@ub.edu wrote:
 Hey Greg,
 I already compiled boost using the instructions from the rdkit wiki. Anyway,
 recompiling rdkit completely solves this problem.
 But that wasn't easy enough. Next error :
 [ 84%] Built target rdSLNParse
 [ 85%] Building CXX object
  ... snip ...
 /root/pool/include/boost/type_traits/detail/cv_traits_impl.hpp:37: internal
 compiler error: in make_rtl_for_nonlocal_decl, at cp/decl.c:5067
 Please submit a full bug report,
 with preprocessed source if appropriate.
 See URL:http://bugzilla.redhat.com/bugzilla for instructions.
 Preprocessed source stored into /tmp/ccgSaXge.out file, please attach this
 to your bugreport.
 make[2]: *** [Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/EditableMol.cpp.o]
 Error 1
 make[1]: *** [Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/all] Error 2
 make: *** [all] Error 2
 
 
 I saw this error online also, and people suggested to add
 the BOOST_PYTHON_NO_PY_SIGNATURES
  flag, and recompile boost, which is what I did, but no effect on this
 error.
 
 Ah... it's not boost that you need to recompile. Add the following to
 the top of $RDBASE/Code/GraphMol/Wrap/EditableMol.cpp:
 #define BOOST_PYTHON_NO_PY_SIGNATURES
 
 (related post: 
 http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg01178.html)
 
 Someone has an idea? Are there plans to come around these boost dependencies
 in rdkit...it's a real showstopper on older systems...real pain to get it
 installed :(
 
 No plans to stop using boost, sorry. The fact that the RDKit uses such
 a high-quality, well-documented library (that is maintained by someone
 else) is actually one of the strengths of the project. The problem you
 describe above is a bug in gcc, not a problem with boost.
 
 -greg

Peter Schmidtke

-
PhD Student
Department of Physical Chemistry
School of Pharmacy
University of Barcelona
Barcelona, Spain


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[Rdkit-discuss] install problems on Centos 5.3

[Peter Schmidtke]

Dear Rdkit ML readers,

I am trying to install rdkit on a Centos 5.3 64 bit machine and this now for 
some time but I don't stop to run into trouble. 

Right now I get the following error message : 

[ 80%] Built target rdMolCatalog
Linking CXX shared library libSLNParse.so
/usr/bin/ld: /root/pool/lib/libboost_regex.a(cpp_regex_traits.o): relocation 
R_X86_64_32S against `std::basic_stringchar, std::char_traitschar, 
std::allocatorchar ::_Rep::_S_empty_rep_storage' can not be used when making 
a shared object; recompile with -fPIC
/root/pool/lib/libboost_regex.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
make[2]: *** [Code/GraphMol/SLNParse/libSLNParse.so] Error 1
make[1]: *** [Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/all] Error 2
make: *** [all] Error 2

I needed basically to install lots of deps manually, including Python 2.7 (I 
used --enabled-shared for the installation), numpy and deps and boost using : 
./bootstrap.sh --prefix=$HOME/pool --libdir=$HOME/pool/lib 
--with-libraries=python,regex

and ./bjam address-model=64 cflags=-fPIC cxxflags=-fPIC install

I don't understand the compilation error here, is it boost that I have to 
recompile using 32  64 bit as address model?

The rdkit version I try to install is the RDKit_Q22010_1 using boost 1.41. 


Thanks for your help.



Peter Schmidtke

-
PhD Student
Department of Physical Chemistry
School of Pharmacy
University of Barcelona
Barcelona, Spain

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Re: [Rdkit-discuss] install problems on Centos 5.3

[Peter Schmidtke]

Dear Greg, 

thanks for the hint, but this one changes absolutely nothing to the compilation 
for me...unfortunately (I completely redid the whole compilation and ended up 
with the same error)

Any ideas of how to debug this?

Ciao

Peter


On 23/07/2010, at 21:48, Greg Landrum wrote:

 Dear Peter,
 
 On Fri, Jul 23, 2010 at 12:48 PM, Peter Schmidtke pschmid...@ub.edu wrote:
 Dear Rdkit ML readers,
 I am trying to install rdkit on a Centos 5.3 64 bit machine and this now for
 some time but I don't stop to run into trouble.
 Right now I get the following error message :
 [ 80%] Built target rdMolCatalog
 Linking CXX shared library libSLNParse.so
 /usr/bin/ld: /root/pool/lib/libboost_regex.a(cpp_regex_traits.o): relocation
 R_X86_64_32S against `std::basic_stringchar, std::char_traitschar,
 std::allocatorchar ::_Rep::_S_empty_rep_storage' can not be used when
 making a shared object; recompile with -fPIC
 /root/pool/lib/libboost_regex.a: could not read symbols: Bad value
 collect2: ld returned 1 exit status
 make[2]: *** [Code/GraphMol/SLNParse/libSLNParse.so] Error 1
 make[1]: *** [Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/all] Error 2
 make: *** [all] Error 2
 
 Noel posted a good (and simple) solution to this one:
 http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg01119.html
 
 I needed basically to install lots of deps manually, including Python 2.7 (I
 used --enabled-shared for the installation), numpy and deps and boost using
 
 A word of warning: I have not tested the code with Python2.7 yet, so
 I'm not sure how things work there.
 
 Best regards,
 -greg

Peter Schmidtke

-
PhD Student
Department of Physical Chemistry
School of Pharmacy
University of Barcelona
Barcelona, Spain


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