Re: [Open Babel] Release candidates available for testing

[Douglas Houston]

Hi,

According to this page:

http://baoilleach.webfactional.com/site_media/ob-docs/Features/Fingerprints.html#fingerprints

I can use the -s option with the name of a file, e.g.:

babel mymols.sdf -sSubstructure.sdf mymols_filtered.sdf

will write out all the compounds in mymols.sdf that contain the group  
in Substructure.sdf. However, what I'd like is the opposite, i.e. to  
write out everything that doesn't match. I tried using -v instead of  
-s but this didn't work.

It would also be nice if I could use a file that contained more than  
one entry, i.e. the file Substructure.sdf could define multiple  
fragments that I don't want  in my molecules, rather than having to  
run Babel on each one separately.

Would this be doable before the final release?

cheers,

Doug




> - Forwarded message from baoille...@gmail.com -
> Date: Sat, 21 Aug 2010 20:03:08 +0100
> From: Noel O'Boyle 
> Reply-To: Noel O'Boyle 
>  Subject: [Open Babel] Release candidates available for testing
>   To: openbabel-discuss@lists.sourceforge.net
>
> Hello all,
>
> The release of Open Babel 2.3.0 is coming up soon. There have been
> many changes so it would be great to get some feedback on whether the
> current release candidates are working.
>
> These are available at
> http://sourceforge.net/projects/openbabel/files/openbabel-snapshots/2010-08-03/openbabel-2.3.0b2-20100803-r3942.tar.gz/download
> for Linux and
> http://sourceforge.net/projects/openbabel/files/openbabel-snapshots/2010-08-18/OpenBabel2.3.0rc2_Windows_Installer.exe/download
> for Windows.
>
> I'm responsible for the new compiling documentation, currently
> available at
> http://baoilleach.webfactional.com/site_media/ob-docs/Installation/install.html#compiling-open-babel.
> If there are any problems with these, please let us know also.
>
> Regards,
>Noel
>
> --
> This SF.net email is sponsored by
>
> Make an app they can't live without
> Enter the BlackBerry Developer Challenge
> http://p.sf.net/sfu/RIM-dev2dev
> ___
> OpenBabel-discuss mailing list
> OpenBabel-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>



_
Dr. Douglas R. Houston
Scientific Programme Coordinator / Research Associate
Room 3.23
Institute of Structural and Molecular Biology
Michael Swann Building
King's Buildings
University of Edinburgh
Edinburgh, EH9 3JR, UK
Tel. 0131 650 7358

-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.



--
This SF.net Dev2Dev email is sponsored by:

Show off your parallel programming skills.
Enter the Intel(R) Threading Challenge 2010.
http://p.sf.net/sfu/intel-thread-sfd
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] Release candidates available for testing

[Douglas Houston]

Thanks Chris,

The line you gave seemed to do the trick - after I escaped out the  
tilde. Is the usage of the tilde to reverse the sense of the filter  
documented? I would have thought the -v option would be logical.

Sieve seems to do what I want - almost. It looks like it filters using  
SMARTS - but all my undesirable groups are in SDF format. How do I  
convert to SMARTS? OpenBabel doesn't seem to do it (although it can  
filter using them, strangely).

I realise I could potentially use SMILES as input but this doesn't  
work in some cases, e.g. 'C1=CC=CC=C1' is a benzene ring in SMILES  
format but according to the following link will not match benzene if  
it's used as a SMARTS string.

http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html

cheers,

Doug



Quoting Chris Morley :

> On 08/09/2010 13:17, Douglas Houston wrote:
>> Hi,
>>
>> According to this page:
>>
>> http://baoilleach.webfactional.com/site_media/ob-docs/Features/Fingerprints.html#fingerprints
>>
>> I can use the -s option with the name of a file, e.g.:
>>
>> babel mymols.sdf -sSubstructure.sdf mymols_filtered.sdf
>>
>> will write out all the compounds in mymols.sdf that contain the group
>> in Substructure.sdf. However, what I'd like is the opposite, i.e. to
>> write out everything that doesn't match. I tried using -v instead of
>> -s but this didn't work.
>
> I think the following will do what you want
> babel mymols.sdf -s ~Substructure.sdf mymols_filtered.sdf
>>
>> It would also be nice if I could use a file that contained more than
>> one entry, i.e. the file Substructure.sdf could define multiple
>> fragments that I don't want  in my molecules, rather than having to
>> run Babel on each one separately.
>
> It would have to be decided whether the combination was AND or OR.
> What you want is NOT(frag1 OR frag2 OR...)
> In the related --filter option there is an implicit AND between tests,
> but I think for both the -s filter and its inverse the OR behaviour is
> more intuitive.
>>
>> Would this be doable before the final release?
>
> It may be, but I am about to go on holiday, so don't hold your breath.
>
> Thanks for this suggestion. Other suggestions for useful features are
> very welcome.
>
> You could look at the Sieve program, http://www.silicos.be/sieve.html
> which is an industrial-strength filtering program, now using OpenBabel.
>
> Chris
>
> --
> This SF.net Dev2Dev email is sponsored by:
>
> Show off your parallel programming skills.
> Enter the Intel(R) Threading Challenge 2010.
> http://p.sf.net/sfu/intel-thread-sfd
> ___
> OpenBabel-discuss mailing list
> OpenBabel-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
>




_
Dr. Douglas R. Houston
Scientific Programme Coordinator / Research Associate
Room 3.23
Institute of Structural and Molecular Biology
Michael Swann Building
King's Buildings
University of Edinburgh
Edinburgh, EH9 3JR, UK
Tel. 0131 650 7358

-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.



--
This SF.net Dev2Dev email is sponsored by:

Show off your parallel programming skills.
Enter the Intel(R) Threading Challenge 2010.
http://p.sf.net/sfu/intel-thread-sfd
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

[Open Babel] "make test" fails

[Douglas Houston]

Hi,

I am trying to compile the new version of Openbabel. Here are the  
commands I used:

mkdir build
cd build
cmake -DCMAKE_INSTALL_PREFIX=/usr/people/douglas/programs/openbabel-2.3.0/ ../
make -j2

Everything seems to be OK up to this point.

Then I try:
make test

Everything passes right up to the near the end, when I get:

   Start 52: pytest_babel
52/56 Test #52: pytest_babel .***Failed  Error  
regular expression found in output. Regex=[FAIL]  0.16 sec
   Start 53: pytest_sym
53/56 Test #53: pytest_sym ...***Failed  Error  
regular expression found in output. Regex=[FAIL]  0.40 sec
   Start 54: pytest_fastsearch
54/56 Test #54: pytest_fastsearch ***Failed  Error  
regular expression found in output. Regex=[FAIL]  0.07 sec
   Start 55: pytest_unique
55/56 Test #55: pytest_unique ***Failed  Error  
regular expression found in output. Regex=[FAIL]  0.06 sec
   Start 56: pytest_kekule
56/56 Test #56: pytest_kekule ***Failed  Error  
regular expression found in output. Regex=[FAIL]  0.09 sec

91% tests passed, 5 tests failed out of 56

Total Test time (real) =  86.32 sec

The following tests FAILED:
  52 - pytest_babel (Failed)
  53 - pytest_sym (Failed)
  54 - pytest_fastsearch (Failed)
  55 - pytest_unique (Failed)
  56 - pytest_kekule (Failed)
Errors while running CTest
make: *** [test] Error 8


"make install" seems to go OK, but I'm worried that there will be some  
features that won't work properly.

Can anyone advise?

thanks,

Doug

_
Dr. Douglas R. Houston
Scientific Programme Coordinator / Research Associate
Room 3.23
Institute of Structural and Molecular Biology
Michael Swann Building
King's Buildings
University of Edinburgh
Edinburgh, EH9 3JR, UK
Tel. 0131 650 7358

-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.



--
Nokia and AT&T present the 2010 Calling All Innovators-North America contest
Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
$10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store 
http://p.sf.net/sfu/nokia-dev2dev
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] "make test" fails

[Douglas Houston]

Thanks Noel, it does seem to be working OK.

I'm not sure if this is the correct place to ask, but the reason I  
installed OpenBabel 2.3.0 is because it's required by the program Sieve.

I am now encountering problems trying to install version 3.0.3 of this  
software. I realise this is only OpenBabel-related, but I figure there  
might be people on this list who have tried Sieve as well.

Here is what I am trying, in /usr/local/sieve-3.0.3/:

cmake CMakeLists.txt
make
make install
make clean

There appears to be no warning or errors, but when I try to run  
/usr/local/bin/sieve I get:

/usr/local/bin/sieve: error while loading shared libraries:  
libopenbabel.so.4: cannot open shared object file: No such file or  
directory

This file is located here:

/usr/local/lib/libopenbabel.so.4

Does anyone know how to tell Sieve where it is? I've tried to edit the  
file /usr/local/sieve-3.0.3/CMakeCache.txt with various alternatives,  
to no avail.

cheers,

Doug



Quoting Noel O'Boyle :

> It's all fine. I will reply in more detail about a workaround later...
>
> On 2 November 2010 10:37, Douglas Houston  
>  wrote:
>> Hi,
>>
>> I am trying to compile the new version of Openbabel. Here are the
>> commands I used:
>>
>> mkdir build
>> cd build
>> cmake  
>> -DCMAKE_INSTALL_PREFIX=/usr/people/douglas/programs/openbabel-2.3.0/  
>> ../
>> make -j2
>>
>> Everything seems to be OK up to this point.
>>
>> Then I try:
>> make test
>>
>> Everything passes right up to the near the end, when I get:
>>
>>   Start 52: pytest_babel
>> 52/56 Test #52: pytest_babel .***Failed  Error
>> regular expression found in output. Regex=[FAIL]  0.16 sec
>>   Start 53: pytest_sym
>> 53/56 Test #53: pytest_sym ...***Failed  Error
>> regular expression found in output. Regex=[FAIL]  0.40 sec
>>   Start 54: pytest_fastsearch
>> 54/56 Test #54: pytest_fastsearch ***Failed  Error
>> regular expression found in output. Regex=[FAIL]  0.07 sec
>>   Start 55: pytest_unique
>> 55/56 Test #55: pytest_unique ***Failed  Error
>> regular expression found in output. Regex=[FAIL]  0.06 sec
>>   Start 56: pytest_kekule
>> 56/56 Test #56: pytest_kekule ***Failed  Error
>> regular expression found in output. Regex=[FAIL]  0.09 sec
>>
>> 91% tests passed, 5 tests failed out of 56
>>
>> Total Test time (real) =  86.32 sec
>>
>> The following tests FAILED:
>>  52 - pytest_babel (Failed)
>>  53 - pytest_sym (Failed)
>>  54 - pytest_fastsearch (Failed)
>>  55 - pytest_unique (Failed)
>>  56 - pytest_kekule (Failed)
>> Errors while running CTest
>> make: *** [test] Error 8
>>
>>
>> "make install" seems to go OK, but I'm worried that there will be some
>> features that won't work properly.
>>
>> Can anyone advise?
>>
>> thanks,
>>
>> Doug
>>
>> _
>> Dr. Douglas R. Houston
>> Scientific Programme Coordinator / Research Associate
>> Room 3.23
>> Institute of Structural and Molecular Biology
>> Michael Swann Building
>> King's Buildings
>> University of Edinburgh
>> Edinburgh, EH9 3JR, UK
>> Tel. 0131 650 7358
>>
>> --
>> The University of Edinburgh is a charitable body, registered in
>> Scotland, with registration number SC005336.
>>
>>
>>
>> --
>> Nokia and AT&T present the 2010 Calling All Innovators-North America contest
>> Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
>> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
>> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
>> http://p.sf.net/sfu/nokia-dev2dev
>> ___
>> OpenBabel-discuss mailing list
>> OpenBabel-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>
>
>




_
Dr. Douglas R. Houston
Scientific Programme Coordinator / Research Associate
Room 3.23
Institute of Structural and Molecular Biology
Michael Swann Building
King's Buildings
University of Edinburgh
Edinburgh, EH9 3JR, UK
Tel. 0131 650 7358

-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.



--
Nokia and AT&T present the 2010 Calling All Innovators-North America contest
Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
$10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store 
http://p.sf.net/sfu/nokia-dev2dev
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] Problem installing Sieve

[Douglas Houston]

Hi Pascal,

I tried:

setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/usr/local/lib/

and that worked a treat.

Thanks a lot!

Doug



Quoting Pascal Muller :

> Hi,
>
> /usr/local/bin/sieve: error while loading shared libraries:
>> libopenbabel.so.4: cannot open shared object file: No such file or
>> directory
>>
>> This file is located here:
>>
>> /usr/local/lib/libopenbabel.so.4
>>
>> Does anyone know how to tell Sieve where it is?
>
>
> Try putting in your e.g. ~/.bashrc
> export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib/
>
> Then restart a shell, and run Sieve again.
>
> Regards,
> Pascal
>




_
Dr. Douglas R. Houston
Scientific Programme Coordinator / Research Associate
Room 3.23
Institute of Structural and Molecular Biology
Michael Swann Building
King's Buildings
University of Edinburgh
Edinburgh, EH9 3JR, UK
Tel. 0131 650 7358


-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.



--
Nokia and AT&T present the 2010 Calling All Innovators-North America contest
Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
$10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store 
http://p.sf.net/sfu/nokia-dev2dev
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

[Open Babel] Error in DoTransformations

[Douglas Houston]

Hi,

I am trying to strip all salts from an SDF. Presumably the -r option  
should be able to do this?

However, when I try the following command:

babel -isdf test1000.sdf -osdf test1000_nofrags.sdf -r

I get 997 of the following errors, and only 3 molecules converted:

*** Open Babel Error  in DoTransformations
   Error executing an option

Any help would be appreciated,

cheers,

Doug

_
Dr. Douglas R. Houston
Scientific Programme Coordinator / Research Associate
Room 3.23
Institute of Structural and Molecular Biology
Michael Swann Building
King's Buildings
University of Edinburgh
Edinburgh, EH9 3JR, UK
Tel. 0131 650 7358

-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.



--
Achieve Improved Network Security with IP and DNS Reputation.
Defend against bad network traffic, including botnets, malware, 
phishing sites, and compromised hosts - saving your company time, 
money, and embarrassment.   Learn More! 
http://p.sf.net/sfu/hpdev2dev-nov
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] Error in DoTransformations

[Douglas Houston]

Thanks a lot for your reply Geoff,

I can wait until the release of 2.3.1 as Hans De Winter has very  
kindly provided me with a similar fix in Sieve that provides this  
functonality (v. 3.0.4),

cheers,

Doug



Quoting Geoffrey Hutchison :

>>
 babel -isdf test1000.sdf -osdf test1000_nofrags.sdf -r

 I get 997 of the following errors, and only 3 molecules converted:

 *** Open Babel Error  in DoTransformations
 Error executing an option
>
> To get back to Douglas's question, it's a non-obvious bug in the  
> transformation code. OBMol::StripSalts() will return false if there  
> is nothing to remove (e.g., there's only one component). That's  
> fine, but for a transformation, it means you don't have to do any  
> work -- just output the molecule.
>
> This is now fixed in SVN trunk and will go into v2.3.1. If you'd  
> like a source code patch, please let me know.
>
> Thanks very much,
> -Geoff
>




_
Dr. Douglas R. Houston
Scientific Programme Coordinator / Research Associate
Room 3.23
Institute of Structural and Molecular Biology
Michael Swann Building
King's Buildings
University of Edinburgh
Edinburgh, EH9 3JR, UK
Tel. 0131 650 7358


-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.



--
Increase Visibility of Your 3D Game App & Earn a Chance To Win $500!
Tap into the largest installed PC base & get more eyes on your game by
optimizing for Intel(R) Graphics Technology. Get started today with the
Intel(R) Software Partner Program. Five $500 cash prizes are up for grabs.
http://p.sf.net/sfu/intelisp-dev2dev
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

[Open Babel] Gasteiger partial charges and the -p option

[Douglas Houston]

Hi,

I have observed something curious about variations in the way  
OpenBabel assigns Gasteiger charges.


For example,

babel -isdf molecule.sdf -omol2 molecule_H.mol2 -h

produces a molecule with an overall charge that is essentially 0.  
However, the command


babel -isdf molecule.sdf -omol2 molecule_H.mol2 -p 7.4

produces a molecule that has an overall charge of -9.0. Both output  
files have had the same number of hydrogens added. Is this what's  
supposed to happen?


I have attached the input file for others to test. This seems to  
happen with both 2.2.3 and 2.3.0,


cheers,

Doug
_
Dr. Douglas R. Houston
Scientific Programme Coordinator / Research Associate
Room 3.23
Institute of Structural and Molecular Biology
Michael Swann Building
King's Buildings
University of Edinburgh
Edinburgh, EH9 3JR, UK
Tel. 0131 650 7358

--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.



molecule.sdf
Description: Binary data
--
Increase Visibility of Your 3D Game App & Earn a Chance To Win $500!
Tap into the largest installed PC base & get more eyes on your game by
optimizing for Intel(R) Graphics Technology. Get started today with the
Intel(R) Software Partner Program. Five $500 cash prizes are up for grabs.
http://p.sf.net/sfu/intelisp-dev2dev___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] Gasteiger partial charges and the -p option

[Douglas Houston]

Hi all,

Just wondering if anyone got a chance to test this molecule? I want to  
make sure it's not just my installation ...

cheers,

Doug



Quoting Douglas Houston :

> Hi,
>
> I have observed something curious about variations in the way   
> OpenBabel assigns Gasteiger charges.
>
> For example,
>
> babel -isdf molecule.sdf -omol2 molecule_H.mol2 -h
>
> produces a molecule with an overall charge that is essentially 0.   
> However, the command
>
> babel -isdf molecule.sdf -omol2 molecule_H.mol2 -p 7.4
>
> produces a molecule that has an overall charge of -9.0. Both output   
> files have had the same number of hydrogens added. Is this what's   
> supposed to happen?
>
> I have attached the input file for others to test. This seems to   
> happen with both 2.2.3 and 2.3.0,
>
> cheers,
>
> Doug
> _
> Dr. Douglas R. Houston
> Scientific Programme Coordinator / Research Associate
> Room 3.23
> Institute of Structural and Molecular Biology
> Michael Swann Building
> King's Buildings
> University of Edinburgh
> Edinburgh, EH9 3JR, UK
> Tel. 0131 650 7358
>
> -- 
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
>
>




_
Dr. Douglas R. Houston
Scientific Programme Coordinator / Research Associate
Room 3.23
Institute of Structural and Molecular Biology
Michael Swann Building
King's Buildings
University of Edinburgh
Edinburgh, EH9 3JR, UK
Tel. 0131 650 7358

-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.



--
Increase Visibility of Your 3D Game App & Earn a Chance To Win $500!
Tap into the largest installed PC base & get more eyes on your game by
optimizing for Intel(R) Graphics Technology. Get started today with the
Intel(R) Software Partner Program. Five $500 cash prizes are up for grabs.
http://p.sf.net/sfu/intelisp-dev2dev
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] Gasteiger partial charges and the -p option

[Douglas Houston]

That's strange, if I sum everything in the charge column in your  
molecule_H.mol2 file, I get -9.0 ...



Quoting "Mathias W." :

> Servus,
>
> I get both times over all charge  zero (with ob-2.2.3)
>
> (molecule_H2.mol2 was produced with -h)
>
>
> 2010/12/3 Douglas Houston :
>> Hi all,
>>
>> Just wondering if anyone got a chance to test this molecule? I want to
>> make sure it's not just my installation ...
>>
>> cheers,
>>
>> Doug
>
>
>
> --
> Mathias
>




_
Dr. Douglas R. Houston
Scientific Programme Coordinator / Research Associate
Room 3.23
Institute of Structural and Molecular Biology
Michael Swann Building
King's Buildings
University of Edinburgh
Edinburgh, EH9 3JR, UK
Tel. 0131 650 7358

-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.



--
Increase Visibility of Your 3D Game App & Earn a Chance To Win $500!
Tap into the largest installed PC base & get more eyes on your game by
optimizing for Intel(R) Graphics Technology. Get started today with the
Intel(R) Software Partner Program. Five $500 cash prizes are up for grabs.
http://p.sf.net/sfu/intelisp-dev2dev
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] Gasteiger partial charges and the -p option

[Douglas Houston]

OK, just to follow up on this, if no-one has any objections I will  
submit a bug report.


Quoting "Mathias W." :

> Yeah, thats because I'm stupid - I didn't recognize that all these
> numbers were recognized as text :-(
>
> 2010/12/3 Douglas Houston :
>> That's strange, if I sum everything in the charge column in your
>> molecule_H.mol2 file, I get -9.0 ...
>>
>>
>>
>> Quoting "Mathias W." :
>>
>>> Servus,
>>>
>>> I get both times over all charge  zero (with ob-2.2.3)
>>>
>>> (molecule_H2.mol2 was produced with -h)
>>>
>>>
>>> 2010/12/3 Douglas Houston :
>>>>
>>>> Hi all,
>>>>
>>>> Just wondering if anyone got a chance to test this molecule? I want to
>>>> make sure it's not just my installation ...
>>>>
>>>> cheers,
>>>>
>>>> Doug
>>>
>>>
>>>
>>> --
>>>Mathias
>>>
>>
>>
>>
>>
>> _
>> Dr. Douglas R. Houston
>> Scientific Programme Coordinator / Research Associate
>> Room 3.23
>> Institute of Structural and Molecular Biology
>> Michael Swann Building
>> King's Buildings
>> University of Edinburgh
>> Edinburgh, EH9 3JR, UK
>> Tel. 0131 650 7358
>>
>> --
>> The University of Edinburgh is a charitable body, registered in
>> Scotland, with registration number SC005336.
>>
>>
>
>
>
> --
> Mathias Weigt
>
> Institute of Pharmaceutical Chemistry
> University of Bonn
>
> An der Immenburg 4
> 53121 Bonn
> Germany
>
> Phone: +49/228/73-5240
>
> --
> Increase Visibility of Your 3D Game App & Earn a Chance To Win $500!
> Tap into the largest installed PC base & get more eyes on your game by
> optimizing for Intel(R) Graphics Technology. Get started today with the
> Intel(R) Software Partner Program. Five $500 cash prizes are up for grabs.
> http://p.sf.net/sfu/intelisp-dev2dev
> ___
> OpenBabel-discuss mailing list
> OpenBabel-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>




_
Dr. Douglas R. Houston
Scientific Programme Coordinator / Research Associate
Room 3.23
Institute of Structural and Molecular Biology
Michael Swann Building
King's Buildings
University of Edinburgh
Edinburgh, EH9 3JR, UK
Tel. 0131 650 7358

-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.



--
Free Software Download: Index, Search & Analyze Logs and other IT data in 
Real-Time with Splunk. Collect, index and harness all the fast moving IT data 
generated by your applications, servers and devices whether physical, virtual
or in the cloud. Deliver compliance at lower cost and gain new business 
insights. http://p.sf.net/sfu/splunk-dev2dev 
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] Gasteiger partial charges and the -p option

[Douglas Houston]

I tried to do this but I get a 500 Internal Server Error when I try to  
use the 'Add new' link here:

http://sourceforge.net/tracker/?atid=428740&group_id=40728&func=browse



Quoting Noel O'Boyle :

> Please go ahead - it's the only way to ensure that issues like this
> don't fall between the cracks...
>
> On 3 March 2011 10:50, Douglas Houston  wrote:
>> OK, just to follow up on this, if no-one has any objections I will
>> submit a bug report.
>>
>>
>> Quoting "Mathias W." :
>>
>>> Yeah, thats because I'm stupid - I didn't recognize that all these
>>> numbers were recognized as text :-(
>>>
>>> 2010/12/3 Douglas Houston :
>>>> That's strange, if I sum everything in the charge column in your
>>>> molecule_H.mol2 file, I get -9.0 ...
>>>>
>>>>
>>>>
>>>> Quoting "Mathias W." :
>>>>
>>>>> Servus,
>>>>>
>>>>> I get both times over all charge  zero (with ob-2.2.3)
>>>>>
>>>>> (molecule_H2.mol2 was produced with -h)
>>>>>
>>>>>
>>>>> 2010/12/3 Douglas Houston :
>>>>>>
>>>>>> Hi all,
>>>>>>
>>>>>> Just wondering if anyone got a chance to test this molecule? I want to
>>>>>> make sure it's not just my installation ...
>>>>>>
>>>>>> cheers,
>>>>>>
>>>>>> Doug
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>>Mathias
>>>>>
>>>>
>>>>
>>>>
>>>>
>>>> _
>>>> Dr. Douglas R. Houston
>>>> Scientific Programme Coordinator / Research Associate
>>>> Room 3.23
>>>> Institute of Structural and Molecular Biology
>>>> Michael Swann Building
>>>> King's Buildings
>>>> University of Edinburgh
>>>> Edinburgh, EH9 3JR, UK
>>>> Tel. 0131 650 7358
>>>>
>>>> --
>>>> The University of Edinburgh is a charitable body, registered in
>>>> Scotland, with registration number SC005336.
>>>>
>>>>
>>>
>>>
>>>
>>> --
>>> Mathias Weigt
>>>
>>> Institute of Pharmaceutical Chemistry
>>> University of Bonn
>>>
>>> An der Immenburg 4
>>> 53121 Bonn
>>> Germany
>>>
>>> Phone: +49/228/73-5240
>>>
>>> --
>>> Increase Visibility of Your 3D Game App & Earn a Chance To Win $500!
>>> Tap into the largest installed PC base & get more eyes on your game by
>>> optimizing for Intel(R) Graphics Technology. Get started today with the
>>> Intel(R) Software Partner Program. Five $500 cash prizes are up for grabs.
>>> http://p.sf.net/sfu/intelisp-dev2dev
>>> ___
>>> OpenBabel-discuss mailing list
>>> OpenBabel-discuss@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>>
>>
>>
>>
>>
>> _
>> Dr. Douglas R. Houston
>> Scientific Programme Coordinator / Research Associate
>> Room 3.23
>> Institute of Structural and Molecular Biology
>> Michael Swann Building
>> King's Buildings
>> University of Edinburgh
>> Edinburgh, EH9 3JR, UK
>> Tel. 0131 650 7358
>>
>> --
>> The University of Edinburgh is a charitable body, registered in
>> Scotland, with registration number SC005336.
>>
>>
>>
>> --
>> Free Software Download: Index, Search & Analyze Logs and other IT data in
>> Real-Time with Splunk. Collect, index and harness all the fast  
>> moving IT data
>> generated by your applications, servers and devices whether  
>> physical, virtual
>> or in the cloud. Deliver compliance at lower cost and gain new business
>> insights. http://p.sf.net/sfu/splunk-dev2dev
>> ___
>> OpenBabel-discuss mailing list
>> OpenBabel-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>
>
>




_
Dr. Douglas R. Houston
Scientific Programme Coordinator / Research Associate
Room 3.23
Institute of Structural and Molecular Biology
Michael Swann Building
King's Buildings
University of Edinburgh
Edinburgh, EH9 3JR, UK
Tel. 0131 650 7358

-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.



--
What You Don't Know About Data Connectivity CAN Hurt You
This paper provides an overview of data connectivity, details
its effect on application quality, and explores various alternative
solutions. http://p.sf.net/sfu/progress-d2d
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

[Open Babel] explicit hydrogens in smiles

[Douglas Houston]

Hi,

Can anyone tell if if there's a way to get OpenBabel to output  
explicit hydrogens in smiles strings?

I'm trying to define a hydroxymate group, which has a hydroxyl group,  
but the smiles I'm getting from OB at the moment doesn't seem to  
differentiate between a hydroxyl and an ether, i.e. it gives ONC=O  
when I need [OH]NC=O. I thought using -h might do it but no luck.

Regards,

Doug

_
Dr. Douglas R. Houston
Scientific Programme Coordinator / Research Associate
Room 3.23
Institute of Structural and Molecular Biology
Michael Swann Building
King's Buildings
University of Edinburgh
Edinburgh, EH9 3JR, UK
Tel. 0131 650 7358

-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.



--
Enable your software for Intel(R) Active Management Technology to meet the
growing manageability and security demands of your customers. Businesses
are taking advantage of Intel(R) vPro (TM) technology - will your software 
be a part of the solution? Download the Intel(R) Manageability Checker 
today! http://p.sf.net/sfu/intel-dev2devmar
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] explicit hydrogens in smiles

[Douglas Houston]

I must be missing something really obvious. I tried the -h option but  
there are no hydrogens in the output.

This is the command I'm using:

babel -ipdb hydroxymate.pdb -osmi -h

The help page says:
Write Options e.g. -xt
   h  Output explicit hydrogens as such

How else do you use the h option?





Quoting Noel O'Boyle :

> babel -H smi gives the "h" output option. See the docs for more info.
>
> - Noel
>
> On 24 March 2011 16:10, Douglas Houston  wrote:
>> Hi,
>>
>> Can anyone tell if if there's a way to get OpenBabel to output
>> explicit hydrogens in smiles strings?
>>
>> I'm trying to define a hydroxymate group, which has a hydroxyl group,
>> but the smiles I'm getting from OB at the moment doesn't seem to
>> differentiate between a hydroxyl and an ether, i.e. it gives ONC=O
>> when I need [OH]NC=O. I thought using -h might do it but no luck.
>>
>> Regards,
>>
>> Doug
>>
>> _
>> Dr. Douglas R. Houston
>> Scientific Programme Coordinator / Research Associate
>> Room 3.23
>> Institute of Structural and Molecular Biology
>> Michael Swann Building
>> King's Buildings
>> University of Edinburgh
>> Edinburgh, EH9 3JR, UK
>> Tel. 0131 650 7358
>>
>> --
>> The University of Edinburgh is a charitable body, registered in
>> Scotland, with registration number SC005336.
>>
>>
>>
>> --
>> Enable your software for Intel(R) Active Management Technology to meet the
>> growing manageability and security demands of your customers. Businesses
>> are taking advantage of Intel(R) vPro (TM) technology - will your software
>> be a part of the solution? Download the Intel(R) Manageability Checker
>> today! http://p.sf.net/sfu/intel-dev2devmar
>> ___
>> OpenBabel-discuss mailing list
>> OpenBabel-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>
>
>




_
Dr. Douglas R. Houston
Scientific Programme Coordinator / Research Associate
Room 3.23
Institute of Structural and Molecular Biology
Michael Swann Building
King's Buildings
University of Edinburgh
Edinburgh, EH9 3JR, UK
Tel. 0131 650 7358

-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.



--
Enable your software for Intel(R) Active Management Technology to meet the
growing manageability and security demands of your customers. Businesses
are taking advantage of Intel(R) vPro (TM) technology - will your software 
be a part of the solution? Download the Intel(R) Manageability Checker 
today! http://p.sf.net/sfu/intel-dev2devmar
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] Gasteiger partial charges and the -p option

[Douglas Houston]

Sorry, I meant to cc the list in.

Quoting Noel O'Boyle  on Wed, 23 Nov 2011  
20:06:40 +0100:

> There seems to be a series of related issues. By the way, you should
> really email the list, so that people are aware you want something
> done about it.
>
> - Noel
>
> On 23 November 2011 19:33, Douglas Houston  
>  wrote:
>> I just checked and it is. Do you think this bug is related to this post?:
>>
>> http://forums.openbabel.org/Wrong-gasteiger-atomic-partial-charges-BUG-tp4096059p4096059.html
>>
>>
>>
>>
>> Quoting Noel O'Boyle  on Mon, 21 Nov 2011 18:47:36
>> +0100:
>>
>>> I don't know. Is the bug report still open?
>>>
>>> On 21 November 2011 17:21, Douglas Houston 
>>> wrote:
>>>>
>>>> Can I just check whether this bug was fixed for new 2.3.1 release? I
>>>> don't
>>>> see a mention of it in the release notes ...
>>>>
>>>>
>>>>
>>>> Quoting Noel O'Boyle  on Mon, 7 Mar 2011 17:23:07
>>>> +:
>>>>
>>>>> Please go ahead - it's the only way to ensure that issues like this
>>>>> don't fall between the cracks...
>>>>>
>>>>> On 3 March 2011 10:50, Douglas Houston 
>>>>> wrote:
>>>>>>
>>>>>>
>>>>>> OK, just to follow up on this, if no-one has any objections I will
>>>>>> submit a bug report.
>>>>>>
>>>>>>
>>>>>> Quoting "Mathias W." :
>>>>>>
>>>>>>> Yeah, thats because I'm stupid - I didn't recognize that all these
>>>>>>> numbers were recognized as text :-(
>>>>>>>
>>>>>>> 2010/12/3 Douglas Houston :
>>>>>>>>
>>>>>>>>
>>>>>>>> That's strange, if I sum everything in the charge column in your
>>>>>>>> molecule_H.mol2 file, I get -9.0 ...
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> Quoting "Mathias W." :
>>>>>>>>
>>>>>>>>> Servus,
>>>>>>>>>
>>>>>>>>> I get both times over all charge  zero (with ob-2.2.3)
>>>>>>>>>
>>>>>>>>> (molecule_H2.mol2 was produced with -h)
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> 2010/12/3 Douglas Houston :
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Hi all,
>>>>>>>>>>
>>>>>>>>>> Just wondering if anyone got a chance to test this molecule? I want
>>>>>>>>>> to
>>>>>>>>>> make sure it's not just my installation ...
>>>>>>>>>>
>>>>>>>>>> cheers,
>>>>>>>>>>
>>>>>>>>>> Doug
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>>  Mathias
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> _
>>>>>>>> Dr. Douglas R. Houston
>>>>>>>> Scientific Programme Coordinator / Research Associate
>>>>>>>> Room 3.23
>>>>>>>> Institute of Structural and Molecular Biology
>>>>>>>> Michael Swann Building
>>>>>>>> King's Buildings
>>>>>>>> University of Edinburgh
>>>>>>>> Edinburgh, EH9 3JR, UK
>>>>>>>> Tel. 0131 650 7358
>>>>>>>>
>>>>>>>> --
>>>>>>>> The University of Edinburgh is a charitable body, registered in
>>>>>>>> Scotland, with registration number SC005336.
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>&

Re: [Open Babel] problems with make test on centos 5.5

[Douglas Houston]

Thankyou Peter and Noel, I was having the exact same problem.


Quoting Peter Schmidtke  on Thu, 15 Dec 2011  
08:12:11 +0100:

> Ah ok, I'll try that then.
>
> Thanks.
>
> Peter
>
> On Wed, 14 Dec 2011 23:50:58 +0100, "Noel O'Boyle" 
> wrote:
>> I'm sure it's fine. If you really want "make test" to work, you should
>> set LD_LIIBRARY_PATH and/or BABEL_LIBDIR to point to the build/lib
>> folder.
>>
>> - Noel
>>
>> On 14 December 2011 21:50, Peter Schmidtke 
>> wrote:
>>> Dear OpenBabel community,
>>>
>>> I'm trying to install openbabel (version 2.3.1) on a Centos 5.5 64bit
>>> machine with perl bindings.
>>>
>>> I manage to compile with cmake and install with make install...but
>>> running make test yields tons of errors like segfaults, double free or
>>> corruption etc...and I don't understand why. The obabel standalone
>>> works, the perl bindings don't seem to work.
>>>
>>> How can check what is wrong? Somebody had similar issues on such a
>>> system?
>>>
>>> Attached here only the beginning of the log of make test.
>>>
>>>
>>> Thanks in advance for every help-
>>>
>>> Peter Schmidtke
>>>
>>>
>>> Test project /usr/local/openbabel-2.3.1/build
>>>  1/ 58 Testing align_Test                    ***Exception:
>>> SegFault
>>>  2/ 58 Testing automorphism_Test             *** glibc detected
>>> ***
>>> /usr/local/openbabel-2.3.1/build/bin/test_automorphism: double free or
>>> corruption (!prev): 0x158ff800 ***
>>> === Backtrace: =
>>> /lib64/libc.so.6[0x33da07230f]
>>> /lib64/libc.so.6(cfree+0x4b)[0x33da07276b]
>>>
> /usr/local/lib/libopenbabel.so.4(_ZN9OpenBabel14OBElementTableD1Ev+0x4a)[0x2b56f1059c5a]
>>> /lib64/libc.so.6(__cxa_finalize+0x8e)[0x33da03368e]
>>> /usr/local/lib/libopenbabel.so.4[0x2b56f1020cd6]
>>>
>>>
>>>
>>>
> --
>>> Cloud Computing - Latest Buzzword or a Glimpse of the Future?
>>> This paper surveys cloud computing today: What are the benefits?
>>> Why are businesses embracing it? What are its payoffs and pitfalls?
>>> http://www.accelacomm.com/jaw/sdnl/114/51425149/
>>> ___
>>> OpenBabel-discuss mailing list
>>> OpenBabel-discuss@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
> --
>
> Peter Schmidtke
>
> --
> PhD Student at the Molecular Modeling and Bioinformatics Group
> Dep. Physical Chemistry
> Faculty of Pharmacy
> University of Barcelona
>
>
> --
> 10 Tips for Better Server Consolidation
> Server virtualization is being driven by many needs.
> But none more important than the need to reduce IT complexity
> while improving strategic productivity.  Learn More!
> http://www.accelacomm.com/jaw/sdnl/114/51507609/
> ___
> OpenBabel-discuss mailing list
> OpenBabel-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>




_
Dr. Douglas R. Houston
Lecturer
Room 3.23
Institute of Structural and Molecular Biology
Michael Swann Building
King's Buildings
University of Edinburgh
Edinburgh, EH9 3JR, UK
Tel. 0131 650 7358

-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.



--
10 Tips for Better Server Consolidation
Server virtualization is being driven by many needs.  
But none more important than the need to reduce IT complexity 
while improving strategic productivity.  Learn More! 
http://www.accelacomm.com/jaw/sdnl/114/51507609/
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

[Open Babel] Open Babel Warning in ReadMolecule Open Babel Warning in ReadMolecule: This Mol2 file is non-standard. Cannot interpret atom types correctly

[Douglas Houston]

Hi all,

I wonder if anyone can help me work out what's going on here. I'm  
trying to convert a PDB file of ADP (from structure 3ATV) to mol2  
format and add hydrogens. The first step seems to work fine:


babel -ipdb 3ATV_ADP.pdb -omol2 3ATV_ADP1.mol2 -p 7.4

however as a check I thought I'd try to convert back from mol2 to PDB,  
but when I do I get lots of errors:


babel -imol2 3ATV_ADP1.mol2 -opdb tmp.pdb

==
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
==
*** Open Babel Warning  in ReadMolecule
  This Mol2 file is non-standard. Cannot interpret atom types  
correctly, instead attempting to interpret as elements instead.

==
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
==
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
==
*** Open Babel Warning  in ReadMolecule
  This Mol2 file is non-standard. Cannot interpret atom types  
correctly, instead attempting to interpret as elements instead.

==
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
==
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
==
*** Open Babel Warning  in ReadMolecule
  This Mol2 file is non-standard. Cannot interpret atom types  
correctly, instead attempting to interpret as elements instead.

==
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
==
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
==
*** Open Babel Warning  in ReadMolecule
  This Mol2 file is non-standard. Cannot interpret atom types  
correctly, instead attempting to interpret as elements instead.

==
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
1 molecule converted
12 warnings 11 audit log messages

This seems to happen with versions 2.2.3, 2.3.0 and 2.3.1. Can anyone  
try to replicate this error? I have attached the PDB file. One  
interesting point is that if I leave out the -p option in the initial  
conversion I get 3 errors instead of 12. AutodockTools also chokes on  
the mol2 file created by OpenBabel. Presumably there is something  
wrong with the mol2 file, but I can't see what.


thanks a lot,

Doug

_
Dr. Douglas R. Houston
Lecturer
Room 3.23
Institute of Structural and Molecular Biology
Michael Swann Building
King's Buildings
University of Edinburgh
Edinburgh, EH9 3JR, UK
Tel. 0131 650 7358

--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.



3ATV_ADP.pdb
Description: Protein Databank data
--
Try before you buy = See our experts in action!
The most comprehensive online learning library for Microsoft developers
is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
Metro Style Apps, more. Free future releases when you subscribe now!
http://p.sf.net/sfu/learndevnow-dev2___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] chemdraw bond lenghts

[Douglas Houston]

Yes, this is a serious problem in Chemdraw. I found that using  
OpenBabel to convert to 3D then back to 2D adjusted the bonds to the  
correct dimensions.


Quoting cadeddu  on Tue, 6 Mar 2012 03:06:02 -0800 (PST):

> seems that files converted from the cdx or cdxml have wrong bond lenght (I've
> the feeling that is related to the document properties in chemoffice);
> benzene bond lenght --> 70Angstrom
> anyone has already find a solution? I'm thinking to something like a
> "feed2babel" style, or something similar.
> thanks anyone
>
>
>
> --
> View this message in context:  
> http://forums.openbabel.org/chemdraw-bond-lenghts-tp4449415p4449415.html
> Sent from the General discussion mailing list archive at Nabble.com.
>
> --
> Keep Your Developer Skills Current with LearnDevNow!
> The most comprehensive online learning library for Microsoft developers
> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
> Metro Style Apps, more. Free future releases when you subscribe now!
> http://p.sf.net/sfu/learndevnow-d2d
> ___
> OpenBabel-discuss mailing list
> OpenBabel-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
>




_
Dr. Douglas R. Houston
Lecturer
Room 3.23
Institute of Structural and Molecular Biology
Michael Swann Building
King's Buildings
University of Edinburgh
Edinburgh, EH9 3JR, UK
Tel. 0131 650 7358

-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.



--
Keep Your Developer Skills Current with LearnDevNow!
The most comprehensive online learning library for Microsoft developers
is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
Metro Style Apps, more. Free future releases when you subscribe now!
http://p.sf.net/sfu/learndevnow-d2d
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] chemdraw bond lenghts

[Douglas Houston]

Hi,

I used the --gen3D option, so something like

babel -isdf chemdraw.sdf -osdf chemdraw3d.sdf --gen3D
babel -isdf chemdraw3D.sdf -osdf chemdraw.sdf --gen2D

cheers,

Doug


Quoting cadeddu  on Tue, 06 Mar 2012 13:39:28 +0100:

> can you specify which 3D format? I've tested this series
>
> babel -h -i cdxml benzeneACS.cdxml -o c3d1 benzeneACSvi.c3d
> babel -h -i c3d1 benzeneACSvi.c3d -o pdb benzeneACSviac3d.pdb
>
> and I still have 14.9 angstrom for a benzene double bond.
>
> Did someone has already produced a stylefile (.chm?), and want to share
> it? that will be of tremendous help, and eventually be a fast patch
>
>
> On 6/3/12 12:52 PM, Douglas Houston wrote:
>> Yes, this is a serious problem in Chemdraw. I found that using
>> OpenBabel to convert to 3D then back to 2D adjusted the bonds to the
>> correct dimensions.
>>
>>
>> Quoting cadeddu  on Tue, 6 Mar 2012 03:06:02  
>> -0800 (PST):
>>
>>> seems that files converted from the cdx or cdxml have wrong bond  
>>> lenght (I've
>>> the feeling that is related to the document properties in chemoffice);
>>> benzene bond lenght -->  70Angstrom
>>> anyone has already find a solution? I'm thinking to something like a
>>> "feed2babel" style, or something similar.
>>> thanks anyone
>>>
>>>
>>>
>>> --
>>> View this message in context:
>>> http://forums.openbabel.org/chemdraw-bond-lenghts-tp4449415p4449415.html
>>> Sent from the General discussion mailing list archive at Nabble.com.
>>>
>>> --
>>> Keep Your Developer Skills Current with LearnDevNow!
>>> The most comprehensive online learning library for Microsoft developers
>>> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
>>> Metro Style Apps, more. Free future releases when you subscribe now!
>>> http://p.sf.net/sfu/learndevnow-d2d
>>> ___
>>> OpenBabel-discuss mailing list
>>> OpenBabel-discuss@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>>
>>>
>>
>>
>>
>>
>> _
>> Dr. Douglas R. Houston
>> Lecturer
>> Room 3.23
>> Institute of Structural and Molecular Biology
>> Michael Swann Building
>> King's Buildings
>> University of Edinburgh
>> Edinburgh, EH9 3JR, UK
>> Tel. 0131 650 7358
>>
>
>
> --
> Andrea Cadeddu
>
> --
> Nanochemistry Laboratory
> Institut de Science et d'Ingénierie Supramoléculaires (I.S.I.S.)
> Université de Strasbourg
> 8, allée Gaspard Monge
> F-67000 Strasbourg (France)
> Tel: +33-(0)3-68855185
> Fax: +33-(0)3-68855161
> cade...@unistra.fr
>
> --
> Keep Your Developer Skills Current with LearnDevNow!
> The most comprehensive online learning library for Microsoft developers
> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
> Metro Style Apps, more. Free future releases when you subscribe now!
> http://p.sf.net/sfu/learndevnow-d2d
> ___
> OpenBabel-discuss mailing list
> OpenBabel-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
>




_
Dr. Douglas R. Houston
Lecturer
Room 3.23
Institute of Structural and Molecular Biology
Michael Swann Building
King's Buildings
University of Edinburgh
Edinburgh, EH9 3JR, UK
Tel. 0131 650 7358

-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.



--
Keep Your Developer Skills Current with LearnDevNow!
The most comprehensive online learning library for Microsoft developers
is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
Metro Style Apps, more. Free future releases when you subscribe now!
http://p.sf.net/sfu/learndevnow-d2d
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] erroneous structures when the option "-p" is activated

[Douglas Houston]

This may be related to a longstanding bug that has yet to be fixed. See:

http://sourceforge.net/tracker/index.php?func=detail&aid=3203137&group_id=40728&atid=428740

This essentially makes the -p option unusable if you are expecting  
charges in the output format.



Quoting green69  on Fri, 15 Jun 2012 03:53:36  
-0700 (PDT):

> Hi guys!
> I'm using Open Babel 2.3.1 in a GNU/Linux (2.6.32-5-amd64) machine with
> debian OS.
> openbabel generate erroneous structures when the option "-p" to add
> hydrogens appropriate for a certain pH is activated and the output is SMILES
> or canonical SMILES. An example is provided with 3 files:
> http://forums.openbabel.org/file/n4655151/test.zip test.zip
>
> *test1_2D.sdf* file contains an exemple input molecule. If I execute:
>
> /obabel -isdf test1_2D.sdf -osmi -O test1.smi/
>
> The *test1.smi* output is correct.
>
> But if I execute:
>
> /obabel -isdf test1_2D.sdf -p 7 -osmi -O test1_obcharged.smi/
>
> The output *test1_obcharged.smi*contains a wrong positive charge in a carbon
> atom.
>
> The same problem appears with similar molecules. Please, does anybody know
> why is this happens and how can we solve this issue?
>
> Many thanks!
>
> --
> View this message in context:  
> http://forums.openbabel.org/erroneous-structures-when-the-option-p-is-activated-tp4655151.html
> Sent from the General discussion mailing list archive at Nabble.com.
>
> --
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> ___
> OpenBabel-discuss mailing list
> OpenBabel-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
>




_
Dr. Douglas R. Houston
Lecturer
Room 3.23
Institute of Structural and Molecular Biology
Michael Swann Building
King's Buildings
University of Edinburgh
Edinburgh, EH9 3JR, UK
Tel. 0131 650 7358

-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.



--
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and 
threat landscape has changed and how IT managers can respond. Discussions 
will include endpoint security, mobile security and the latest in malware 
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

[Open Babel] Cleaning up structures

[Douglas Houston]

Hi all,

I'm having problems "cleaning up" the structure of a small molecule. I
was hoping to use obminimize to fix the distorted bond lengths/angles
in the nitro group of the attached file obmin_in.mol. However, the
program does not appear to be paying attention to the bond order
information in the .mol file - the output has lost the delocalisation
on both the nitro and carboxylate groups (see attached obmin_out.pdb).

The following command was used:
~/programs/openbabel-2.3.1/build/bin/obminimize -n 100 -imol
obmin_in.mol -opdb > obmin_out.pdb

This led me to try other input formats to obminimize in case it was a
problem with the way it reads .mol files. However, using babel to
convert the obmin_in.mol to say .mol2 format also loses the
delocalisation on the nitro and carboxylate groups; the corresponding
lines in obmin_in.mol for the nitro group (note bond type 4 which  
denotes aromatic):


6  4  4  0  0  0  0
6  7  4  0  0  0  0

are changed to the following lines in the output (babel_out.mol2):

5 6 41
6 6 71

when in fact they should be:

5 6 4   ar
6 6 7   ar

or at the very least:

5 6 41
6 6 72

The command used was:

babel -imol obmin_in.mol -omol2 babel_out.mol2

Is there a problem with the way babel interprets .mol bond blocks?

cheers,

Doug
_
Dr. Douglas R. Houston
Lecturer
Room 3.23
Institute of Structural and Molecular Biology
Michael Swann Building
King's Buildings
University of Edinburgh
Edinburgh, EH9 3JR, UK
Tel. 0131 650 7358

--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.



obmin_in.mol
Description: Binary data


obmin_out.pdb
Description: Protein Databank data


babel_out.mol2
Description: Binary data
--
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and 
threat landscape has changed and how IT managers can respond. Discussions 
will include endpoint security, mobile security and the latest in malware 
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

[Open Babel] OB writing non-standard atom types?

[Douglas Houston]

Hi all,

I've been trying to convert the attached in.pdb file to .mol2 format.  
I happened to be using the -p option:


babel -ipdb in.pdb -omol2 out_p.mol2 -p 7.4

This produces a file that babel chokes on if used as input:

babel -imol2 out_p.mol2 -opdb

==
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
==
*** Open Babel Warning  in ReadMolecule
  This Mol2 file is non-standard. Problem with molecule: in.pdb  
Cannot interpret atom types correctly, instead attempting to interpret  
atom type: C.cat1490 as elements instead.

==
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.

Atom 1 in the mol2 file has been assigned as type C.cat, which  
presumably is causing the problem.


This atom is assigned type C.2 if I use the following command:

babel -ipdb in.pdb -omol2 out_h.mol2 -h

Is it that babel expects a space between the C.cat and the 1490?

If so, that still doesn't explain why I get different atom type  
assignments using -p vs. -h.  I know I can't use -p if I want the  
charges in the output to be sensible (I assign them separately later),  
but it's now looking like the -p option will also change atom types ...


Is it simply that the -p option is fully broken and I should just stop  
using it?


cheers,

Doug


_
Dr. Douglas R. Houston
Lecturer
Room 3.23
Institute of Structural and Molecular Biology
Michael Swann Building
King's Buildings
University of Edinburgh
Edinburgh, EH9 3JR, UK
Tel. 0131 650 7358

--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.



in.pdb
Description: Protein Databank data


out_p.mol2
Description: Binary data


out_h.mol2
Description: Binary data
--
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and 
threat landscape has changed and how IT managers can respond. Discussions 
will include endpoint security, mobile security and the latest in malware 
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] OpenCL

[Douglas Houston]

This seems like a good compromise to me, especially if it means we see  
it sooner ...


Quoting JP  on Thu, 12 Jul 2012 19:07:06 +0100:

> A sidepoint from GPU development - and directly related to Geoff's
> earlier point.
>
> Perhaps multicore awareness is the way to go...
>
> In the most reductionist of approaches -- you could launch n threads
> (instead of one) and have each generate a conformer each since these
> are really independent processes.  This way the time enhancement would
> be close (but not quite) 1/n.  I'd imagine you would still do some
> aggregation at the end of conformer generation (e.g. cluster results
> and remove very similar conformers)...
>
> My rationale for this is that everyone has a multi core processor (and
> if you don't, throw away that piece of historical junk), but not
> everyone has a CUDA/OpenCL enabled video card.
>
> Even in the terms of re architecture needed -- it is ""easier"" to
> move the code into threads than having to rewrite it as a kernel for
> the GPU.
>
> Just a thought.
>
> -
> Jean-Paul Ebejer
> Early Stage Researcher
>
>
> On 12 July 2012 18:29, ovalerio  wrote:
>> Hi Chris,
>>
>>
>> On 12.07.2012 13:16, Geoff Hutchison wrote:

 I've just seen a demo of the impact of running applications on the GPU
 and it does seem for some operations you can get striking  
 performance gains.
 Would it be worth considering porting openbabel to OpenCL?
>>>
>>>
>>> Much like muti-threading, it's not clear how some operations in Open
>>> Babel would work in OpenCL.
>>
>>
>> As Geoff points out they are couple of factors to consider in this regard.
>> Sometimes making algorithmic changes can boost performance even more than
>> going the GPU way. In my case however, I'm interested in optimization
>> through parallel approaches. That's why I'm researching on GPU and I will be
>> very glad to hear whatever ideas you might have.
>>
>>
>>>
>>> That said, there are certain types of code which make clear sense as
>>> multi-threaded and/or OpenCL, for example the force fields and
>>> conformer generation code, or the charge assignment. There's actually
>>> a student in Ireland sponsored by Noel who's investigating this as we
>>> speak. (You may have seen some posts from Omar already.)
>>>
>>
>> I have look at force fields and conformer generation codes since they are
>> both related. When you are doing conformational search you also need to
>> asses the energy of the conformer to decide if you are going to keep it.
>> Improving forcefields calculation should also improve performance for
>> conformer generation.
>>
>> Conformer generation also looks promising, Attached you can find a plot of
>> the time spent generating conformers for several different drug like
>> molecules using Confab [1]. I used the optimized Borodina set that you can
>> get from Confab's article [2].  As you can appreciate from the plot as the
>> number of conformers involved increases, execution times for conformational
>> search increases noticeably. I will be happy if I can shave those numbers by
>> a half factor offloading some operations to the GPU.
>>
>> Cheers,
>> --
>> Omar
>>
>> [1] Confab -  http://confab.googlecode.com/
>> [2] Confab Article (Borodina Optimized Set) -
>> http://www.jcheminf.com/content/3/1/8
>>
>> --
>> Live Security Virtual Conference
>> Exclusive live event will cover all the ways today's security and
>> threat landscape has changed and how IT managers can respond. Discussions
>> will include endpoint security, mobile security and the latest in malware
>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>> ___
>> OpenBabel-discuss mailing list
>> OpenBabel-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>
>
> --
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> ___
> OpenBabel-discuss mailing list
> OpenBabel-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
>




_
Dr. Douglas R. Houston
Lecturer
Room 3.23
Institute of Structural and Molecular Biology
Michael Swann Building
King's Buildings
University of Edinburgh
Edinburgh, EH9 3JR, UK
Tel. 0131 650 7358

-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.



--
Live Security Virtual Conference
Exclusive

[Open Babel] Fwd: OB writing non-standard atom types?

[Douglas Houston]

Just to follow up on this, can someone please try to replicate the  
problem for me using the attached files?



- Forwarded message from dhous...@staffmail.ed.ac.uk -
Date: Fri, 29 Jun 2012 16:50:03 +0100
From: Douglas Houston 
 Subject: [Open Babel] OB writing non-standard atom types?
  To: openbabel-discuss@lists.sourceforge.net

Hi all,

I've been trying to convert the attached in.pdb file to .mol2 format.   
I happened to be using the -p option:


babel -ipdb in.pdb -omol2 out_p.mol2 -p 7.4

This produces a file that babel chokes on if used as input:

babel -imol2 out_p.mol2 -opdb

==
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.
==
*** Open Babel Warning  in ReadMolecule
  This Mol2 file is non-standard. Problem with molecule: in.pdb   
Cannot interpret atom types correctly, instead attempting to interpret  
 atom type: C.cat1490 as elements instead.

==
*** Open Babel Warning  in Translate
  Cannot perform atom type translation: table cannot find requested types.

Atom 1 in the mol2 file has been assigned as type C.cat, which   
presumably is causing the problem.


This atom is assigned type C.2 if I use the following command:

babel -ipdb in.pdb -omol2 out_h.mol2 -h

Is it that babel expects a space between the C.cat and the 1490?

If so, that still doesn't explain why I get different atom type   
assignments using -p vs. -h.  I know I can't use -p if I want the   
charges in the output to be sensible (I assign them separately later),  
 but it's now looking like the -p option will also change atom types  
...


Is it simply that the -p option is fully broken and I should just stop  
 using it?


cheers,

Doug


_
Dr. Douglas R. Houston
Lecturer
Room 3.23
Institute of Structural and Molecular Biology
Michael Swann Building
King's Buildings
University of Edinburgh
Edinburgh, EH9 3JR, UK
Tel. 0131 650 7358

--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.



- End forwarded message -



_
Dr. Douglas R. Houston
Lecturer
Room 3.23
Institute of Structural and Molecular Biology
Michael Swann Building
King's Buildings
University of Edinburgh
Edinburgh, EH9 3JR, UK
Tel. 0131 650 7358

--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.



in.pdb
Description: x-unknown/pdb


out_p.mol2
Description: Binary data


out_h.mol2
Description: Binary data
--
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and 
threat landscape has changed and how IT managers can respond. Discussions 
will include endpoint security, mobile security and the latest in malware 
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] erroneous structures when the option "-p" is activated

[Douglas Houston]

Hi,

I don't know if this is related, but I've found another example of  
what appears to be an "erroneous structure" with the -p option in  
2.3.1. I noticed it when converting to PDBQT format, but there's also  
a problem when I convert to PDB. The files in question are attached.


babel -isdf input.sdf -opdbqt nop.pdbqt
#works fine (also works OK with -h option)

babel -isdf input.sdf -opdbqt p.pdbqt -p 7.4
#produces a nonstandard PDBQT file with multiple header sections.  
Converting to PDB with -p also produces an erroneous structure but at  
least the file format is complied with (I think).


I've noticed this problem with a number of molecules, all of which  
contain azide groups.


cheers,

Doug


Quoting Noel O'Boyle  on Wed, 22 Aug 2012  
15:28:11 +0100:



Just following up on this as Chris just fixed the issue reported by
Douglas. The problem in your case is different, if it is actually an
error by Open Babel. If you look in phmodel.txt, you can see all of
the protonation rules. The one being applied in your case is:

#guanidine or amidine
TRANSFORM [#6^2+0:1](~[N^2])(~[N^2])* >> [#6+:1](~N)(~N)* 12.5

If you don't like this, just comment it out by putting a # at the
start. Should we adjust the rule somehow as you think it is incorrect?

Regards,
   Noel

On 18 June 2012 05:43, green69  wrote:

Hey Douglas, thank you for your help and for the information provided. I'll
take this into account.

I hope somebody could fix this bug soon. The '-p' option seems so useful to
me.

Cheers!

--
View this message in context:  
http://forums.openbabel.org/erroneous-structures-when-the-option-p-is-activated-tp4655151p4655158.html

Sent from the General discussion mailing list archive at Nabble.com.

--
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss


--
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss







_
Dr. Douglas R. Houston
Lecturer
Room 3.23
Institute of Structural and Molecular Biology
Michael Swann Building
King's Buildings
University of Edinburgh
Edinburgh, EH9 3JR, UK
Tel. 0131 650 7358

--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.



p.pdbqt
Description: Binary data


nop.pdbqt
Description: Binary data


input.sdf
Description: Binary data
--
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and 
threat landscape has changed and how IT managers can respond. Discussions 
will include endpoint security, mobile security and the latest in malware 
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] erroneous structures when the option "-p" is activated

[Douglas Houston]

Thanks Paolo,

Unfortunately the behaviour I described persists with SVN 4995.

cheers,

Doug



Quoting Paolo Tosco  on Thu, 30 Aug 2012 11:48:51 +0200:

> Dear Douglas,
>
> did you try to use the SVN version? I myself submitted a number of  
> fixes to the pdbqt format module which might solve your header  
> issues (not the protonation problems, though).
>
> Cheers,
> Paolo
>
> --
> ==
> Paolo Tosco, Ph.D.
> Department of Drug Science and Technology
> Via Pietro Giuria, 9 - 10125 Torino (Italy)
> Tel: +39 011 670 7680 | Mob: +39 348 5537206
> Fax: +39 011 670 7687 | E-mail: paolo.to...@unito.it
> http://open3dqsar.org | http://open3dalign.org
> ==========
>
>
>
> On 30 Aug 2012, at 11:33, Douglas Houston  
>  wrote:
>
>> Hi,
>>
>> I don't know if this is related, but I've found another example of  
>> what appears to be an "erroneous structure" with the -p option in  
>> 2.3.1. I noticed it when converting to PDBQT format, but there's  
>> also a problem when I convert to PDB. The files in question are  
>> attached.
>>
>> babel -isdf input.sdf -opdbqt nop.pdbqt
>> #works fine (also works OK with -h option)
>>
>> babel -isdf input.sdf -opdbqt p.pdbqt -p 7.4
>> #produces a nonstandard PDBQT file with multiple header sections.  
>> Converting to PDB with -p also produces an erroneous structure but  
>> at least the file format is complied with (I think).
>>
>> I've noticed this problem with a number of molecules, all of which  
>> contain azide groups.
>>
>> cheers,
>>
>> Doug
>>
>>
>> Quoting Noel O'Boyle  on Wed, 22 Aug 2012  
>> 15:28:11 +0100:
>>
>>> Just following up on this as Chris just fixed the issue reported by
>>> Douglas. The problem in your case is different, if it is actually an
>>> error by Open Babel. If you look in phmodel.txt, you can see all of
>>> the protonation rules. The one being applied in your case is:
>>>
>>> #guanidine or amidine
>>> TRANSFORM [#6^2+0:1](~[N^2])(~[N^2])* >> [#6+:1](~N)(~N)*12.5
>>>
>>> If you don't like this, just comment it out by putting a # at the
>>> start. Should we adjust the rule somehow as you think it is incorrect?
>>>
>>> Regards,
>>>   Noel
>>>
>>> On 18 June 2012 05:43, green69  wrote:
>>>> Hey Douglas, thank you for your help and for the information  
>>>> provided. I'll
>>>> take this into account.
>>>>
>>>> I hope somebody could fix this bug soon. The '-p' option seems so  
>>>> useful to
>>>> me.
>>>>
>>>> Cheers!
>>>>
>>>> --
>>>> View this message in context:  
>>>> http://forums.openbabel.org/erroneous-structures-when-the-option-p-is-activated-tp4655151p4655158.html
>>>> Sent from the General discussion mailing list archive at Nabble.com.
>>>>
>>>> --
>>>> Live Security Virtual Conference
>>>> Exclusive live event will cover all the ways today's security and
>>>> threat landscape has changed and how IT managers can respond. Discussions
>>>> will include endpoint security, mobile security and the latest in malware
>>>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>>>> ___
>>>> OpenBabel-discuss mailing list
>>>> OpenBabel-discuss@lists.sourceforge.net
>>>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>>
>>> --
>>> Live Security Virtual Conference
>>> Exclusive live event will cover all the ways today's security and
>>> threat landscape has changed and how IT managers can respond. Discussions
>>> will include endpoint security, mobile security and the latest in malware
>>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>>> ___
>>> OpenBabel-discuss mailing list
>>> OpenBabel-discuss@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>>
>>>
>>
>>
>>
>>
>> _
>> Dr. Douglas

Re: [Open Babel] chemdraw bond lenghts

[Douglas Houston]

I should point out that the --gen3D workaround doesn't work in all  
cases. See the attached 2D SDF for an example - converting it to 3D  
results in 'nan' coordinates.


What is the official stance on this? On the one hand Babel can't be  
expected to fix files that other software has screwed up. On the other  
hand, is there really such a thing as "incorrect" bond lengths in a 2D  
SDF?




Quoting cadeddu  on Mon, 06 Aug 2012 16:25:11 +0200:


To conclude:
this small workaround works  - but great care must be taken into
checking the structures:
--
import pybel, openbabel
mol=pybel.readfile("cdx", "benzene_acs.cdx").next()
factor=1.39/1.89  # this is the error of the bond length: real
value/wrong one
for each in mol.atoms:
  x=each.coords[0]*factor
  y=each.coords[1]*factor
  z=each.coords[2]*factor
  each.OBAtom.SetVector(x,y,z)
mol.addh()
output = pybel.Outputfile("mol2", "benzene_acs.mol2","overwrite=True")
output.write(mol)
output.close()
--

hope this will help
thank you guys for this wonderful software and those lovely python
libraries! :)
andrea



--
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss







_
Dr. Douglas R. Houston
Lecturer
Room 3.23
Institute of Structural and Molecular Biology
Michael Swann Building
King's Buildings
University of Edinburgh
Edinburgh, EH9 3JR, UK
Tel. 0131 650 7358


--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.



2Dtonan.sdf
Description: Binary data
--
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and 
threat landscape has changed and how IT managers can respond. Discussions 
will include endpoint security, mobile security and the latest in malware 
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] Generating a diverse set of conformers

[Douglas Houston]

This doesn't work either:

 /usr/people/douglas/programs/openbabel-2.3.2/build/bin/obabel
crystal_ligand.sdf  -oconfbareport -xf tmp.sdf -xr 1.0


I get:

obabel: cannot write output format!
Open Babel 2.3.2 -- Mar 20 2013 -- 08:59:03
Usage:
obabel [-i]  [-o] -O
[Options]
Try  -H option for more information.




--
View this message in context: 
http://forums.openbabel.org/Generating-a-diverse-set-of-conformers-tp4656011p4657394.html
Sent from the General discussion mailing list archive at Nabble.com.

--
Is your legacy SCM system holding you back? Join Perforce May 7 to find out:
• 3 signs your SCM is hindering your productivity
• Requirements for releasing software faster
• Expert tips and advice for migrating your SCM now
http://p.sf.net/sfu/perforce
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] Generating a diverse set of conformers

[Douglas Houston]

Anyone have any comment on this? I am observing the same problem as OP. I am 
using the following:

/usr/people/douglas/programs/openbabel-2.3.2/build/bin/obabel
crystal_ligand.sdf -O tmp.sdf --conformer --nconf 50  --writeconformers

I only get 1 conformer in the 1 output file.

I have also tried the following:

 /usr/people/douglas/programs/openbabel-2.3.2/build/bin/obabel
crystal_ligand.sdf -O tmp.sdf --confab -rcutoff 0.1 -ecutoff 10 --original
--verbose

Still get 1 conformer in the 1 output file. 

The verbose option seems to have no effect, neither do the rcutoff and
ecutoff options. I believe there may be something wrong with the way obabel
is handling the options, it's like they aren't being used at all.

Can anyone honestly state that they have observed this feature actually
working?




--
View this message in context: 
http://forums.openbabel.org/Generating-a-diverse-set-of-conformers-tp4656011p4657393.html
Sent from the General discussion mailing list archive at Nabble.com.

--
Is your legacy SCM system holding you back? Join Perforce May 7 to find out:
• 3 signs your SCM is hindering your productivity
• Requirements for releasing software faster
• Expert tips and advice for migrating your SCM now
http://p.sf.net/sfu/perforce
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] Generating a diverse set of conformers

[Douglas Houston]

/usr/people/douglas/programs/openbabel-2.3.2/build/bin/obabel -L

outputs:

charges
descriptors
fingerprints
forcefields
formats
loaders
ops

How do I tell?



--
View this message in context: 
http://forums.openbabel.org/Generating-a-diverse-set-of-conformers-tp4656011p4657397.html
Sent from the General discussion mailing list archive at Nabble.com.

--
Is your legacy SCM system holding you back? Join Perforce May 7 to find out:
• 3 signs your SCM is hindering your productivity
• Requirements for releasing software faster
• Expert tips and advice for migrating your SCM now
http://p.sf.net/sfu/perforce
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] Generating a diverse set of conformers

[Douglas Houston]

itiwks-> /usr/people/douglas/programs/openbabel-2.3.2/build/bin/obabel -L ops
0xout Additional file output
addfilenameAppend input filename to title
AddInIndexAppend input index to title
AddPolarHAdds hydrogen to polar atoms only
canonicalCanonicalize the atom order
energyForceField Energy Evaluation (not displayed in GUI)
fillUC Fill the unit cell (strict or keepconnect)
gen2DGenerate 2D coordinates
gen3DGenerate 3D coordinates
largest#  Output # mols with largest values
minimizeForceField Energy Minimization (not displayed in GUI)
partialcharge Calculate partial charges by specified method
readconformerAdjacent conformers combined into a single molecule
sIsomorphism filter(-s, -v options replacement)(not displayed in GUI)
smallest#  Output # mols with smallest values of descriptor(not
displayed in GUI)
sort Sort by descriptor(~desc for reverse)
unique[param] remove duplicates by descriptor;default inchi
vIsomorphism filter(-s, -v options replacement)(not displayed in GUI)

I see no mention of conformers right enough ... 

However obabel -H output includes the line:

--writeconformers Output multiple conformers separately






--
View this message in context: 
http://forums.openbabel.org/Generating-a-diverse-set-of-conformers-tp4656011p4657399.html
Sent from the General discussion mailing list archive at Nabble.com.

--
Is your legacy SCM system holding you back? Join Perforce May 7 to find out:
• 3 signs your SCM is hindering your productivity
• Requirements for releasing software faster
• Expert tips and advice for migrating your SCM now
http://p.sf.net/sfu/perforce
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] Generating a diverse set of conformers

[Douglas Houston]

OK will do.

Just out of curiosity, what is my install of Babel doing when I specify
those options? Just ignoring them, without informing the user?



--
View this message in context: 
http://forums.openbabel.org/Generating-a-diverse-set-of-conformers-tp4656011p4657402.html
Sent from the General discussion mailing list archive at Nabble.com.

--
Is your legacy SCM system holding you back? Join Perforce May 7 to find out:
• 3 signs your SCM is hindering your productivity
• Requirements for releasing software faster
• Expert tips and advice for migrating your SCM now
http://p.sf.net/sfu/perforce
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] Generating a diverse set of conformers

[Douglas Houston]

So I've recompiled obabel with eigen, but the output of obabel -L ops has not
changed:

0xout Additional file output
addfilenameAppend input filename to title
AddInIndexAppend input index to title
AddPolarHAdds hydrogen to polar atoms only
canonicalCanonicalize the atom order
energyForceField Energy Evaluation (not displayed in GUI)
fillUC Fill the unit cell (strict or keepconnect)
gen2DGenerate 2D coordinates
gen3DGenerate 3D coordinates
largest#  Output # mols with largest values
minimizeForceField Energy Minimization (not displayed in GUI)
partialcharge Calculate partial charges by specified method
readconformerAdjacent conformers combined into a single molecule
sIsomorphism filter(-s, -v options replacement)(not displayed in GUI)
smallest#  Output # mols with smallest values of descriptor(not
displayed in GUI)
sort Sort by descriptor(~desc for reverse)
unique[param] remove duplicates by descriptor;default inchi
vIsomorphism filter(-s, -v options replacement)(not displayed in GUI)

obabel still writes only 1 conformer (with no error messages) no matter the
options I use.




--
View this message in context: 
http://forums.openbabel.org/Generating-a-diverse-set-of-conformers-tp4656011p4657403.html
Sent from the General discussion mailing list archive at Nabble.com.

--
Is your legacy SCM system holding you back? Join Perforce May 7 to find out:
• 3 signs your SCM is hindering your productivity
• Requirements for releasing software faster
• Expert tips and advice for migrating your SCM now
http://p.sf.net/sfu/perforce
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] Generating a diverse set of conformers

[Douglas Houston]

obconformer when run outputs:

Usage: obconformer NSteps GeomSteps 




--
View this message in context: 
http://forums.openbabel.org/Generating-a-diverse-set-of-conformers-tp4656011p4657404.html
Sent from the General discussion mailing list archive at Nabble.com.

--
Is your legacy SCM system holding you back? Join Perforce May 7 to find out:
• 3 signs your SCM is hindering your productivity
• Requirements for releasing software faster
• Expert tips and advice for migrating your SCM now
http://p.sf.net/sfu/perforce
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] Generating a diverse set of conformers

[Douglas Houston]

obconformer with arguments:  /usr/local/bin/obconformer 10 10
crystal_ligand.sdf


outputs:




The conformers appear to be generated - how do I get them written out? The
input structure is in 3D by the way.



--
View this message in context: 
http://forums.openbabel.org/Generating-a-diverse-set-of-conformers-tp4656011p4657405.html
Sent from the General discussion mailing list archive at Nabble.com.

--
Is your legacy SCM system holding you back? Join Perforce May 7 to find out:
• 3 signs your SCM is hindering your productivity
• Requirements for releasing software faster
• Expert tips and advice for migrating your SCM now
http://p.sf.net/sfu/perforce
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] Generating a diverse set of conformers

[Douglas Houston]

It's gone worryingly quiet ...



--
View this message in context: 
http://forums.openbabel.org/Generating-a-diverse-set-of-conformers-tp4656011p4657420.html
Sent from the General discussion mailing list archive at Nabble.com.

--
Is your legacy SCM system holding you back? Join Perforce May 7 to find out:
• 3 signs your SCM is hindering your productivity
• Requirements for releasing software faster
• Expert tips and advice for migrating your SCM now
http://p.sf.net/sfu/perforce
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] Generating a diverse set of conformers

[Douglas Houston]

The only message I got during the recompilation was:

CMake Error at cmake_install.cmake:88 (FILE):
  file Internal CMake error when trying to open file:
 
/usr/people/douglas/programs/openbabel-2.3.2_witheigen/openbabel-2.3.2/build/install_manifest.txt
  for writing.


make: *** [install] Error 1


"touch 
/usr/people/douglas/programs/openbabel-2.3.2_witheigen/openbabel-2.3.2/build/install_manifest.txt
chmod 777
/usr/people/douglas/programs/openbabel-2.3.2_witheigen/openbabel-2.3.2/build/install_manifest.txt"
 then rerunning the compilation fixed it. 



--
View this message in context: 
http://forums.openbabel.org/Generating-a-diverse-set-of-conformers-tp4656011p4657428.html
Sent from the General discussion mailing list archive at Nabble.com.

--
"Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
Instantly run your Selenium tests across 300+ browser/OS combos.
Get unparalleled scalability from the best Selenium testing platform available
Simple to use. Nothing to install. Get started now for free."
http://p.sf.net/sfu/SauceLabs
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] Generating a diverse set of conformers

[Douglas Houston]

Sorry, I missed the request for the input file (still can't see it to be
honest). Anyway, I have attached the file.

obabel -V gives "Open Babel 2.3.2 -- May  7 2014 -- 09:05:30" i.e. the
expected compilation date

crystal_ligand.sdf
  

My problem is not piping output to a file, but getting obabel, obconformer,
or any program at all to output more than one conformer. 

How do I get more than one conformer in the output?



--
View this message in context: 
http://forums.openbabel.org/Generating-a-diverse-set-of-conformers-tp4656011p4657426.html
Sent from the General discussion mailing list archive at Nabble.com.

--
"Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
Instantly run your Selenium tests across 300+ browser/OS combos.
Get unparalleled scalability from the best Selenium testing platform available
Simple to use. Nothing to install. Get started now for free."
http://p.sf.net/sfu/SauceLabs
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] Generating a diverse set of conformers

[Douglas Houston]

Actually that input file isn't the most flexible, here is a different one
that is more flexible and also only generates one conformer.

crystal_ligand_flex.sdf
  



--
View this message in context: 
http://forums.openbabel.org/Generating-a-diverse-set-of-conformers-tp4656011p4657427.html
Sent from the General discussion mailing list archive at Nabble.com.

--
"Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
Instantly run your Selenium tests across 300+ browser/OS combos.
Get unparalleled scalability from the best Selenium testing platform available
Simple to use. Nothing to install. Get started now for free."
http://p.sf.net/sfu/SauceLabs
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] Generating a diverse set of conformers

[Douglas Houston]

Can I just check people received the input file? I used the Nabble forum to
attach it ...



--
View this message in context: 
http://forums.openbabel.org/Generating-a-diverse-set-of-conformers-tp4656011p4657429.html
Sent from the General discussion mailing list archive at Nabble.com.

--
"Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
Instantly run your Selenium tests across 300+ browser/OS combos.
Get unparalleled scalability from the best Selenium testing platform available
Simple to use. Nothing to install. Get started now for free."
http://p.sf.net/sfu/SauceLabs
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] [openbabel:bugs] #710 Gasteiger partial charges and the -p option

[Douglas Houston]

Should the -p option be removed from Open Babel? I dread to think how  
many people are blithely using it, unaware that it could be screwing  
up their results.


Quoting Stefano Forli  on Wed, 13 Aug 2014  
20:27:46 +:

> I bumped in this bug report while trying to understand why I  
> couldn't generate the proper protonation state even for simple  
> molecules. I've tried to identify the source of the problem with the  
> version I'm using, v2.3.2 (Ubuntu).
> I hope I'm not missing something trivial in my tests...
> Hopefully it can be useful to debugging, I apologize for the long  
> post (and the horrible formatting... blame Markdown).
> I've tried the test case Noel reported, and while the charge issue  
> seems to be fixed, protonation state and atom typing are still  
> wrong. Besides, I found the following behavior to be rather puzzling:
> obabel -:"OC(=O)c1c1" -omol2 --gen3D -p 7.4 -O  
> obabel_firstpass.mol2
> obabel -imol2 obabel_firstpass.mol2 -omol2  -p 7.4 -O obabel_secondpass.mol2
> The molecule obabel_secondpass.mol2 has correct typing  
> and charge (~-1).
> The following code replicates the behavior of obabel commands above,  
> generating the proper molecule only at the second pass:
> 
> # Python Obabel/Pybel test
> import pybel
> ob = pybel.ob
> from sys import argv
> fp = open('benzoicAcid.smi', 'w')
> fp.write('OC(=O)c1c1  benzoicAcid\n')
> fp.close()
> """read SMI and generate Mol2 (first pass)"""
> obc = ob.OBConversion()
> obc.SetInAndOutFormats('smi', 'mol2')
> obc.OpenInAndOutFiles('benzoicAcid.smi', 'wrong.mol2')
> mol = ob.OBMol()
> notatend = obc.Read(mol)
> while notatend:
>"""pybel shortcut"""
>pmol = pybel.Molecule(mol)
>pmol.make3D()
>mol = pmol.OBMol
>mol.CorrectForPH()
>mol.AddHydrogens()
>obc.Write(mol)
>"""XXX write molecule with wrong carboxylic atom typing: O.3 and O.2"""
>print "Atoms count (first pass):", mol.NumAtoms()
>mol = ob.OBMol()
>notatend = obc.Read(mol)
> """ re-read the wrong molecule"""
> obc = ob.OBConversion()
> obc.SetInAndOutFormats('mol2', 'mol2')
> obc.OpenInAndOutFiles('op.mol2', 'right.mol2')
> mol = ob.OBMol()
> notatend = obc.Read(mol)
> while notatend:
>"""pybel shortcut"""
>pmol = pybel.Molecule(mol)
>#pmol.make3D()
>mol = pmol.OBMol
>mol.CorrectForPH()
>mol.AddHydrogens()
>obc.Write(mol)
>"""XXX write molecule with correct carboxylic atom typing: O.co2 """
>print "Atoms count (second pass):", mol.NumAtoms()
>mol = ob.OBMol()
>notatend = obc.Read(mol)
> 
> I've tried to dig into the problem a bit more, using the patterns  
> from the phmodel.txt, and they seem to fail to identify the 'COO-'  
> pattern in the mol2 files generated with the previous code.
> 
> # pH model test
> import pybel
> from sys import argv
> """patterns from phmodel.txt"""
> pre = 'O=C[OD1-0:1]'
> post = 'O=C[O-:1]'
> transform = pybel.ob.OBChemTsfm()
> success = transform.Init(pre, post)
> mol = pybel.readfile('mol2', argv[1]).next()
> smart = pybel.Smarts(pre)
> print "PATTERN FOUND", smart.findall(mol)
> transform.Apply(mol.OBMol)
> mol.write('mol2', 'obpython.mol2', overwrite=1)
> .
>
>
> ---
>
> ** [bugs:#710] Gasteiger partial charges and the -p option**
>
> **Status:** open
> **Group:** 2.3.x
> **Labels:** Command-line Tools
> **Created:** Tue Mar 08, 2011 04:41 PM UTC by Douglas Houston
> **Last Updated:** Thu Feb 20, 2014 03:35 PM UTC
> **Owner:** Noel O'Boyle
>
> I have observed something curious about variations in the way  
> OpenBabel assigns Gasteiger charges.
>
> For example,
>
> babel -isdf molecule.sdf -omol2 molecule_H.mol2 -h
>
> produces a molecule with an overall charge that is essentially 0.  
> However, the command
>
> babel -isdf molecule.sdf -omol2 molecule_H.mol2 -p 7.4
>
> produces a molecule that has an overall charge of -9.0. Both output  
> files have had the same number of hydrogens added. Is this what's  
> supposed to happen?
>
> I have attached the input file for others to test. This seems to  
> happen with both 2.2.3 and 2.3.0,
>
>
>
>
> ---
>
> Sent from sourceforge.net because you indicated interest in  
> <https://sourcefo

[Open Babel] Open Babel compilation to add Python bindings fails

[Douglas Houston]

Hi all,

I am trying to install a Pymol plugin and it requires my Open Babel to  
be re-installed, this time including the Python bindings:

Python 2.5.1 (r251:54863, Sep 21 2007, 11:20:07)
[GCC 3.2.3 20030502 (Red Hat Linux 3.2.3-56)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
import openbabel
Traceback (most recent call last):   File "", line 1, in 
ImportError: No module named openbabel


I have tried recompiling Open Babel as root with the Python bindings using:

tar -xvf openbabel-2.3.2.tar.gz
cd openbabel-2.3.2
mkdir build
cd build/
~douglas/programs/cmake-2.8.7/bin/cmake  ~/openbabel-2.3.2  
-DPYTHON_BINDINGS=ON
make -j2


but it fails with the following errors; can anyone help?:


[100%] Building CXX object  
scripts/CMakeFiles/bindings_python.dir/python/openbabel-python.cpp.o
Linking CXX executable ../bin/test_unitcell
[100%] Built target test_unitcell
Linking CXX shared module ../lib/_openbabel.so
/usr/local/lib/libpython2.7.a(thread.o): In function  
`_pythread_pthread_set_stacksize':
/usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:497: undefined  
reference to `pthread_attr_setstacksize'
/usr/local/lib/libpython2.7.a(thread.o): In function `PyThread_release_lock':
/usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:350: undefined  
reference to `sem_post'
/usr/local/lib/libpython2.7.a(thread.o): In function `PyThread_free_lock':
/usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:294: undefined  
reference to `sem_destroy'
/usr/local/lib/libpython2.7.a(thread.o): In function `PyThread_allocate_lock':
/usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:269: undefined  
reference to `sem_init'
/usr/local/lib/libpython2.7.a(thread.o): In function `PyThread_acquire_lock':
/usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:326: undefined  
reference to `sem_trywait'
/usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:324: undefined  
reference to `sem_wait'
/usr/local/lib/libpython2.7.a(thread.o): In function  
`PyThread_start_new_thread':
/usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:184: undefined  
reference to `pthread_attr_setstacksize'
/usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:194: undefined  
reference to `pthread_create'
/usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:210: undefined  
reference to `pthread_detach'
/usr/local/lib/libpython2.7.a(thread.o): In function `PyThread_release_lock':
/usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:350: undefined  
reference to `sem_post'
/usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:350: undefined  
reference to `sem_post'
/usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:350: undefined  
reference to `sem_post'
/usr/local/lib/libpython2.7.a(thread.o): In function `PyThread_allocate_lock':
/usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:269: undefined  
reference to `sem_init'
/usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:269: undefined  
reference to `sem_init'
/usr/local/lib/libpython2.7.a(posixmodule.o): In function `posix_forkpty':
/usr/bin/tmp/Python-2.7.6/./Modules/posixmodule.c:3958: undefined  
reference to `forkpty'
/usr/local/lib/libpython2.7.a(posixmodule.o): In function `posix_openpty':
/usr/bin/tmp/Python-2.7.6/./Modules/posixmodule.c:3898: undefined  
reference to `openpty'
collect2: ld returned 1 exit status
make[2]: *** [lib/_openbabel.so] Error 1
make[1]: *** [scripts/CMakeFiles/bindings_python.dir/all] Error 2
make: *** [all] Error 2



-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.



--
Comprehensive Server Monitoring with Site24x7.
Monitor 10 servers for $9/Month.
Get alerted through email, SMS, voice calls or mobile push notifications.
Take corrective actions from your mobile device.
http://pubads.g.doubleclick.net/gampad/clk?id=154624111&iu=/4140/ostg.clktrk
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

[Open Babel] Open Babel compilation to add Python bindings fails

[Douglas Houston]

Hi all,

I am trying to install a Pymol plugin and it requires my Open Babel to  
be re-installed, this time including the Python bindings:

Python 2.5.1 (r251:54863, Sep 21 2007, 11:20:07)
[GCC 3.2.3 20030502 (Red Hat Linux 3.2.3-56)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
import openbabel
Traceback (most recent call last):   File "", line 1, in 
ImportError: No module named openbabel


I have tried recompiling Open Babel as root with the Python bindings using:

tar -xvf openbabel-2.3.2.tar.gz
cd openbabel-2.3.2
mkdir build
cd build/
~douglas/programs/cmake-2.8.7/bin/cmake  ~/openbabel-2.3.2  
-DPYTHON_BINDINGS=ON
make -j2


but it fails with the following errors; can anyone help?:


[100%] Building CXX object  
scripts/CMakeFiles/bindings_python.dir/python/openbabel-python.cpp.o
Linking CXX executable ../bin/test_unitcell
[100%] Built target test_unitcell
Linking CXX shared module ../lib/_openbabel.so
/usr/local/lib/libpython2.7.a(thread.o): In function  
`_pythread_pthread_set_stacksize':
/usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:497: undefined  
reference to `pthread_attr_setstacksize'
/usr/local/lib/libpython2.7.a(thread.o): In function `PyThread_release_lock':
/usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:350: undefined  
reference to `sem_post'
/usr/local/lib/libpython2.7.a(thread.o): In function `PyThread_free_lock':
/usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:294: undefined  
reference to `sem_destroy'
/usr/local/lib/libpython2.7.a(thread.o): In function `PyThread_allocate_lock':
/usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:269: undefined  
reference to `sem_init'
/usr/local/lib/libpython2.7.a(thread.o): In function `PyThread_acquire_lock':
/usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:326: undefined  
reference to `sem_trywait'
/usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:324: undefined  
reference to `sem_wait'
/usr/local/lib/libpython2.7.a(thread.o): In function  
`PyThread_start_new_thread':
/usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:184: undefined  
reference to `pthread_attr_setstacksize'
/usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:194: undefined  
reference to `pthread_create'
/usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:210: undefined  
reference to `pthread_detach'
/usr/local/lib/libpython2.7.a(thread.o): In function `PyThread_release_lock':
/usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:350: undefined  
reference to `sem_post'
/usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:350: undefined  
reference to `sem_post'
/usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:350: undefined  
reference to `sem_post'
/usr/local/lib/libpython2.7.a(thread.o): In function `PyThread_allocate_lock':
/usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:269: undefined  
reference to `sem_init'
/usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:269: undefined  
reference to `sem_init'
/usr/local/lib/libpython2.7.a(posixmodule.o): In function `posix_forkpty':
/usr/bin/tmp/Python-2.7.6/./Modules/posixmodule.c:3958: undefined  
reference to `forkpty'
/usr/local/lib/libpython2.7.a(posixmodule.o): In function `posix_openpty':
/usr/bin/tmp/Python-2.7.6/./Modules/posixmodule.c:3898: undefined  
reference to `openpty'
collect2: ld returned 1 exit status
make[2]: *** [lib/_openbabel.so] Error 1
make[1]: *** [scripts/CMakeFiles/bindings_python.dir/all] Error 2
make: *** [all] Error 2





_
Dr. Douglas R. Houston
Lecturer
Institute of Structural and Molecular Biology
Room 3.23, Michael Swann Building
King's Buildings
University of Edinburgh
Edinburgh, EH9 3JR, UK
Tel. 0131 650 7358
http://tinyurl.com/douglasrhouston

-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.



--
Comprehensive Server Monitoring with Site24x7.
Monitor 10 servers for $9/Month.
Get alerted through email, SMS, voice calls or mobile push notifications.
Take corrective actions from your mobile device.
http://pubads.g.doubleclick.net/gampad/clk?id=154624111&iu=/4140/ostg.clktrk
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

Re: [Open Babel] Open Babel compilation to add Python bindings fails

[Douglas Houston]

.h:350: undefined  
reference to `sem_post'
/usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:350: undefined  
reference to `sem_post'
/usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:350: undefined  
reference to `sem_post'
/usr/local/lib/libpython2.7.a(thread.o): In function `PyThread_allocate_lock':
/usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:269: undefined  
reference to `sem_init'
/usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:269: undefined  
reference to `sem_init'
/usr/local/lib/libpython2.7.a(posixmodule.o): In function `posix_forkpty':
/usr/bin/tmp/Python-2.7.6/./Modules/posixmodule.c:3958: undefined  
reference to `forkpty'
/usr/local/lib/libpython2.7.a(posixmodule.o): In function `posix_openpty':
/usr/bin/tmp/Python-2.7.6/./Modules/posixmodule.c:3898: undefined  
reference to `openpty'
collect2: ld returned 1 exit status
make[2]: *** [lib/_openbabel.so] Error 1
make[1]: *** [scripts/CMakeFiles/bindings_python.dir/all] Error 2
make: *** [all] Error 2

In the latter case the errors mention /usr/bin/tmp/Python-2.7.6/ ...  
but I have not specified any location with 'tmp' in the path ... ?

The output from 'grep PYTHON CMakeCache.txt' (below) also does not  
mention any pathname with 'tmp' in it ... so where is this coming from?

PYTHON_BINDINGS:BOOL=ON
PYTHON_EXECUTABLE:FILEPATH=/usr/local/bin/python2.7
PYTHON_INCLUDE_DIR:PATH=/usr/local/include/python2.7
PYTHON_LIBRARY:FILEPATH=/usr/local/lib/libpython2.7.a
//ADVANCED property for variable: PYTHON_EXECUTABLE
PYTHON_EXECUTABLE-ADVANCED:INTERNAL=1
//ADVANCED property for variable: PYTHON_INCLUDE_DIR
PYTHON_INCLUDE_DIR-ADVANCED:INTERNAL=1
PYTHON_INCLUDE_PATH:INTERNAL=/usr/local/include/python2.7
//ADVANCED property for variable: PYTHON_LIBRARY
PYTHON_LIBRARY-ADVANCED:INTERNAL=1

cheers,
Doug




Quoting Noel O'Boyle  on Fri, 14 Nov 2014  
13:05:04 +:

> Hi Douglas,
>
> Your system appears to have at least two, and possibly more, competing
> installations of Python. Is the Python 2.7 in /usr/local the same as
> the one in /usr/bin/tmp? Either way you need to pick a Python
> installation and stick with it - I would try the system Python first
> of all, which appears to be Python 2.5 in your case. Does your PyMol
> use a specific Python installation? - if so, try that one next.
>
> If you "grep PYTHON CMakeCache.txt" you will see which Python has been
> found and what the variable names are. Something like "cmake ..
> -DPYTHON_INCLUDE_DIR=whatever -DPYTHON_LIBRARY=whatever
> -DPYTHON_EXECUTABLE=whatever" (check the variable names) will cover
> all of the bases. If this is not clear, let us know.
>
> And as I always say on this list, as a general rule you should not
> compile anything as root. This may lead to permissions problems down
> the line which will be difficult to diagnose.
>
> Regards,
>  Noel
>
> On 14 November 2014 10:05, Douglas Houston  
>  wrote:
>> Hi all,
>>
>> I am trying to install a Pymol plugin and it requires my Open Babel to
>> be re-installed, this time including the Python bindings:
>>
>> Python 2.5.1 (r251:54863, Sep 21 2007, 11:20:07)
>> [GCC 3.2.3 20030502 (Red Hat Linux 3.2.3-56)] on linux2
>> Type "help", "copyright", "credits" or "license" for more information.
>> import openbabel
>> Traceback (most recent call last):   File "", line 1, in 
>> ImportError: No module named openbabel
>>
>>
>> I have tried recompiling Open Babel as root with the Python bindings using:
>>
>> tar -xvf openbabel-2.3.2.tar.gz
>> cd openbabel-2.3.2
>> mkdir build
>> cd build/
>> ~douglas/programs/cmake-2.8.7/bin/cmake  ~/openbabel-2.3.2
>> -DPYTHON_BINDINGS=ON
>> make -j2
>>
>>
>> but it fails with the following errors; can anyone help?:
>>
>>
>> [100%] Building CXX object
>> scripts/CMakeFiles/bindings_python.dir/python/openbabel-python.cpp.o
>> Linking CXX executable ../bin/test_unitcell
>> [100%] Built target test_unitcell
>> Linking CXX shared module ../lib/_openbabel.so
>> /usr/local/lib/libpython2.7.a(thread.o): In function
>> `_pythread_pthread_set_stacksize':
>> /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:497: undefined
>> reference to `pthread_attr_setstacksize'
>> /usr/local/lib/libpython2.7.a(thread.o): In function  
>> `PyThread_release_lock':
>> /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:350: undefined
>> reference to `sem_post'
>> /usr/local/lib/libpython2.7.a(thread.o): In function `PyThread_free_lock':
>> /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:294: undefined
>> reference to `sem_destroy'