Re: [Rdkit-discuss] Error when building RdKit 2013_09_1

2016-09-05 Thread Menaka Jayawardena 
Hi,

The above issue was fixed but it hangs when running 'make install'.
Nothing is printed and after some time machine freezes.

On 6 September 2016 at 00:11, Menaka Jayawardena 
wrote:

> Hi Paul, Hongbin Yang,
>
> Thank you very much for helping me.
> I think now it's becoming alright.
>
> Best Regards,
> Menaka
>
> On 5 September 2016 at 22:41, Paul Emsley 
> wrote:
>
>> On 05/09/16 17:27, 杨弘宾 wrote:
>>
>> Hi, Menaka,
>> An easy way I suggest is to install boost via package manager, for
>> example:
>> $ sudo apt-get install libboost-dev libboost-system-dev libboost-
>> thread-dev libboost-serialization-dev libboost-python-dev libboost-regex-
>> dev
>>
>>
>>
>> and if you're on fedora you can now do:
>>
>> $ sudo dnf install rdkit
>>
>> and that's easier than working out where boost::python has been installed.
>>
>>
>> 
>> --
>>
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>>
>>
>
>
> --
> *Menaka Madushanka Jayawardena*
> Faculty of Engineering, 
> University of Peradeniyaya.
> LinkedIn 
> TP:- 071 885 1183/ 071 350 5470
>



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Re: [Rdkit-discuss] Error when building RdKit 2013_09_1

2016-09-05 Thread Menaka Jayawardena 
Hi Paul, Hongbin Yang,

Thank you very much for helping me.
I think now it's becoming alright.

Best Regards,
Menaka

On 5 September 2016 at 22:41, Paul Emsley  wrote:

> On 05/09/16 17:27, 杨弘宾 wrote:
>
> Hi, Menaka,
> An easy way I suggest is to install boost via package manager, for
> example:
> $ sudo apt-get install libboost-dev libboost-system-dev libboost-
> thread-dev libboost-serialization-dev libboost-python-dev libboost-regex-
> dev
>
>
>
> and if you're on fedora you can now do:
>
> $ sudo dnf install rdkit
>
> and that's easier than working out where boost::python has been installed.
>
>
> 
> --
>
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>
>


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LinkedIn 
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Re: [Rdkit-discuss] Error when building RdKit 2013_09_1

2016-09-05 Thread Paul Emsley 

On 05/09/16 17:27, ??? wrote:

Hi, Menaka,
An easy way I suggest is to install boost via package manager, for 
example:
$ sudo apt-get install 
libboost-devlibboost-system-devlibboost-thread-devlibboost-serialization-devlibboost-python-devlibboost-regex-dev




and if you're on fedora you can now do:

$ sudo dnf install rdkit

and that's easier than working out where boost::python has been installed.

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Re: [Rdkit-discuss] Error when building RdKit 2013_09_1

2016-09-05 Thread 杨弘宾 






Hi, Menaka,    An easy way I suggest is to install boost via package manager, 
for example:    $ sudo apt-get install libboost-dev libboost-system-dev 
libboost-thread-dev libboost-serialization-dev libboost-python-dev 
libboost-regex-dev     When installing boost from source, remember to add 
python-library    $ ./bootstrap.sh --with-libraries=python,regex; ./b2; ./b2 
install
reference: http://www.rdkit.org/docs/Install.html#ubuntu-12-04-and-later  hope 
it is helpful
PS  Other troubles may cause the error,  for example:Problem:Your system has a 
version of boost installed in /usr/lib, but you would like to force the RDKit 
to use a more recent one.Solution:This can be solved by using cmake version 
2.8.3 (or more recent) and providing the -D Boost_NO_SYSTEM_PATHS=ON 
argument:cmake -D BOOST_ROOT=/usr/local -D Boost_NO_SYSTEM_PATHS=ON ..
reference: 
http://www.rdkit.org/docs/Install.html#frequently-encountered-problems 
Hope it is helpful.

Hongbin Yang 杨弘宾

Research: Toxicophore and Chemoinformatics
Pharmaceutical Science, School of Pharmacy

East China University of Science and Technology 

 From: Menaka JayawardenaDate: 2016-09-06 00:05To: rdkit-discussSubject: 
[Rdkit-discuss] Error when building RdKit 2013_09_1Hello,
When I try to build the above version of RDKit, I got the following error.
CMake Error at /usr/share/cmake-2.8/Modules/FindBoost.cmake:1131 (message):  
Unable to find the requested Boost libraries.
  Boost version: 1.55.0
  Boost include path: /home/menaka/Downloads/boost_1_55_0/include
  Could not find the following Boost libraries:
          boost_python
  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):  CMakeLists.txt:113 (find_package)
I'd be very grateful if someone could help me in solving this issue. 
Best regardsMenaka
-- 
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Peradeniyaya.LinkedIn
TP:- 071 885 1183/ 071 350 5470


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[Rdkit-discuss] Error when building RdKit 2013_09_1

2016-09-05 Thread Menaka Jayawardena 
Hello,

When I try to build the above version of RDKit, I got the following error.

CMake Error at /usr/share/cmake-2.8/Modules/FindBoost.cmake:1131 (message):
  Unable to find the requested Boost libraries.

  Boost version: 1.55.0

  Boost include path: /home/menaka/Downloads/boost_1_55_0/include

  Could not find the following Boost libraries:

  boost_python

  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):
  CMakeLists.txt:113 (find_package)

I'd be very grateful if someone could help me in solving this issue.

Best regards
Menaka

-- 
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Re: [Rdkit-discuss] HashedMorgan Fingerprint function for RDKit database cartridge

2016-09-05 Thread Greg Landrum 
Hi,

A (mostly complete) list of functions available in the cartridge is here:
http://rdkit.org/docs/Cartridge.html#functions

There isn't a particularly good match for GetHashedMorganFingerprint(),
which returns a count-based fingerprint of a particular length. The best
you can do is morgan_fp(), which gives you a count-based sparse fingerprint
(i.e. not of a particular length).

If you are primarily interested in similarity scores, then using a
bit-vector based morgan fingerprint: morganbv_fp() is probably your best
bet. Search performance with the bit vector fingerprints is much better
than with the count-based fingerprints.

-greg



On Mon, Sep 5, 2016 at 11:00 AM, Antonio Peón López 
wrote:

> Hi,
> I have no idea how to run the function for hashedMorganfingenprint
> (AllChem.GetHashedMorganFingerprint(ml, radius=2, nBits = 2048)) with
> RDKit database cartridge. Thanks in advance.
> Best,
> Smith
>
>
> 
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[Rdkit-discuss] HashedMorgan Fingerprint function for RDKit database cartridge

2016-09-05 Thread Antonio Peón López 
Hi,
I have no idea how to run the function for hashedMorganfingenprint 
(AllChem.GetHashedMorganFingerprint(ml, radius=2, nBits = 2048)) with RDKit 
database cartridge. Thanks in advance.
Best,
Smith

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Re: [Rdkit-discuss] rdMolDraw2D drawing code

2016-09-05 Thread Greg Landrum 
Dave's right about the font size: it's expressed in whatever coordinates
the molecule is being drawn in.
Cross-platform font handling is tough. Cross-platform, cross-toolkit font
handling is even tougher. What's currently there seems to be an
quasi-workable solution.

I suspect the other part of Dmitri's question is about the way bonds are
shortened so that they don't draw all the way through the atom labels. This
is handled by a function in MolDraw2D that attempts to take into account
the font size. It doesn't always succeed (see the comments above about font
handling). It's easy enough to add an option that allows you to adjust the
amount of padding that's used in that code.
Here's the github issue:
https://github.com/rdkit/rdkit/issues/1056

-greg



On Mon, Sep 5, 2016 at 9:57 AM, David Cosgrove 
wrote:

> HI Dmitri,
>
> Sorry for the delay replying. I assume that by 'add padding' you mean that
> the code that generates the 2D drawing coordinates should take account of
> the size of the labels and would, from your example, maybe open out the
> C9-O23-C14 bond a bit so that O21 and O24 are further apart?  If so, then I
> can duck that one cheerfully as it's not part of the MolDraw2D code. The 2D
> coordinates are generated in RDDepictor - MolDraw2D just uses the results
> from that.  Having just had a peer at $RDBASE/GraphMol/Depictor/Depictor.h,
> it would seem as though adding a padding as you suggest might not be
> straightforward, but I guess it might be possible to alter the distance
> matrix that is being embedded in 2D to take account of atom label sizes.
> The joy of open source projects is of course that you have the opportunity
> to change things if you don't like how they're done at present.  Maybe
> something to think about at the UGM hackathon day?
>
> As you say, your best bet in the short term is probably to adjust the font
> size in the drawing.  MolDraw2D.h says that the font sizes are given "in
> molecule coordinate units. That's probably Angstrom for RDKit" which in
> reality means it's relative to a C-C bond in benzene of 1.5 units. This is
> then changed internally to a value appropriate for the drawing engine that
> is being used in a particular instance.  If you can see a sensible place to
> put this information in the documentation, feel free to send a changed
> version to Greg for inclusion in the next release.  I am struggling to find
> any such documentation myself, and maybe that was your point ;-).
>
> Cheers,
> Dave
>
>
> On Fri, Sep 2, 2016 at 9:07 PM, Dimitri Maziuk 
> wrote:
>
>> Hi all,
>>
>> I finally got a round tuit for playing with the drawing code and I like
>> it -- great job, thank you Greg and Dave and everyone who contributed.
>>
>> One question though: is it possible to add padding around atom labels?
>> Or use some other trick to make the attached look less crowded? (Yes, I
>> do want all Hs and all atom labels with numbers.)
>>
>> The best I can come up with is reduce the font size a little, that works
>> fine. I think it'd be nice if the fine manual for MolDraw2D said what
>> the units used by FontSize()/SetFontSize() are.
>>
>> So, any better ideas than just slightly smaller labels?
>>
>> TIA
>> --
>> Dimitri Maziuk
>> Programmer/sysadmin
>> BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
>>
>> 
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>>
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Re: [Rdkit-discuss] rdMolDraw2D drawing code

2016-09-05 Thread David Cosgrove 
HI Dmitri,

Sorry for the delay replying. I assume that by 'add padding' you mean that
the code that generates the 2D drawing coordinates should take account of
the size of the labels and would, from your example, maybe open out the
C9-O23-C14 bond a bit so that O21 and O24 are further apart?  If so, then I
can duck that one cheerfully as it's not part of the MolDraw2D code. The 2D
coordinates are generated in RDDepictor - MolDraw2D just uses the results
from that.  Having just had a peer at $RDBASE/GraphMol/Depictor/Depictor.h,
it would seem as though adding a padding as you suggest might not be
straightforward, but I guess it might be possible to alter the distance
matrix that is being embedded in 2D to take account of atom label sizes.
The joy of open source projects is of course that you have the opportunity
to change things if you don't like how they're done at present.  Maybe
something to think about at the UGM hackathon day?

As you say, your best bet in the short term is probably to adjust the font
size in the drawing.  MolDraw2D.h says that the font sizes are given "in
molecule coordinate units. That's probably Angstrom for RDKit" which in
reality means it's relative to a C-C bond in benzene of 1.5 units. This is
then changed internally to a value appropriate for the drawing engine that
is being used in a particular instance.  If you can see a sensible place to
put this information in the documentation, feel free to send a changed
version to Greg for inclusion in the next release.  I am struggling to find
any such documentation myself, and maybe that was your point ;-).

Cheers,
Dave


On Fri, Sep 2, 2016 at 9:07 PM, Dimitri Maziuk 
wrote:

> Hi all,
>
> I finally got a round tuit for playing with the drawing code and I like
> it -- great job, thank you Greg and Dave and everyone who contributed.
>
> One question though: is it possible to add padding around atom labels?
> Or use some other trick to make the attached look less crowded? (Yes, I
> do want all Hs and all atom labels with numbers.)
>
> The best I can come up with is reduce the font size a little, that works
> fine. I think it'd be nice if the fine manual for MolDraw2D said what
> the units used by FontSize()/SetFontSize() are.
>
> So, any better ideas than just slightly smaller labels?
>
> TIA
> --
> Dimitri Maziuk
> Programmer/sysadmin
> BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
>
> 
> --
>
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