[Rdkit-discuss] Compiling issues
Hi Greg, I have tried to install the latest RDKit on a freshly installed Ubuntu 10.10. After installing python-dev, sqlite3, numpy, bison, flex AND THE BOOST LIBRARIES VIA APT (boost 1.42), I additionally installed boost 1.4.2 in /opt/boost_1_42_0. During the cmake step flex and bison were found in /usr/lib. Several Warnings were issued during the cmake -DBOOST_ROOT=/opt/boost_1_42_0 .. -step. Obviously the system built boost installation was erroneously used (?is this the problem if the versions of boost are the same?). When doing the make the following error occurs: -snip [ 34%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RingInfo.cpp.o [ 34%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Conformer.cpp.o Linking CXX shared library ../../lib/libGraphMol.so [ 34%] Built target GraphMol [ 34%] [FLEX][SmartsL] Building scanner with flex /usr/bin/flex version 2.5.4 smarts.ll, line 1: unrecognized %option: reentrant smarts.ll, line 2: unrecognized %option: bison-bridge make[2]: *** [../Code/GraphMol/SmilesParse/lex.yysmarts.cpp] Error 1 make[1]: *** [Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/all] Error 2 make: *** [all] Error 2 -snip Here are my envs: -snip --mar...@markus:/opt/RDKit/build$ echo $RDBASE --/opt/RDKit --mar...@markus:/opt/RDKit/build$ echo $LD_LIBRARY_PATH --/opt/RDKit/lib:/opt/RDKit/bin:/opt/boost_1_42_0:/opt/boost_1_42_1/boost --mar...@markus:/opt/RDKit/build$ echo $PYTHONPATH --:/opt/RDKit:/opt/RDKit/rdkit -snip Does anyone have a hint? Thanks in advance, Markus -- Centralized Desktop Delivery: Dell and VMware Reference Architecture Simplifying enterprise desktop deployment and management using Dell EqualLogic storage and VMware View: A highly scalable, end-to-end client virtualization framework. Read more! http://p.sf.net/sfu/dell-eql-dev2dev ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Compiling issues
Hi Greg, exactly that was the case. RDKit nicely installs now! Cheers, Markus On 11/15/2010 10:05 AM, Greg Landrum wrote: HI Markus, On Mon, Nov 15, 2010 at 9:51 AM, Markus Kossner m.koss...@googlemail.com wrote: Hi Greg, I have tried to install the latest RDKit on a freshly installed Ubuntu 10.10. After installing python-dev, sqlite3, numpy, bison, flex AND THE BOOST LIBRARIES VIA APT (boost 1.42), I additionally installed boost 1.4.2 in /opt/boost_1_42_0. During the cmake step flex and bison were found in /usr/lib. Several Warnings were issued during the cmake -DBOOST_ROOT=/opt/boost_1_42_0 .. -step. Obviously the system built boost installation was erroneously used (?is this the problem if the versions of boost are the same?). Should be no problem. In fact, if the system boost is the version you want, then you shouldn't need to install your own at all. When doing the make the following error occurs: -snip [ 34%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RingInfo.cpp.o [ 34%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Conformer.cpp.o Linking CXX shared library ../../lib/libGraphMol.so [ 34%] Built target GraphMol [ 34%] [FLEX][SmartsL] Building scanner with flex /usr/bin/flex version 2.5.4 smarts.ll, line 1: unrecognized %option: reentrant smarts.ll, line 2: unrecognized %option: bison-bridge make[2]: *** [../Code/GraphMol/SmilesParse/lex.yysmarts.cpp] Error 1 make[1]: *** [Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/all] Error 2 make: *** [all] Error 2 -snip This is almost definitely due to an older version of flex. There's some info here: http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg01079.html From what I can tell about Ubuntu 10.10, you should have a more recent version of flex available... did you install the flex-old package? Best Regards, -greg -- Centralized Desktop Delivery: Dell and VMware Reference Architecture Simplifying enterprise desktop deployment and management using Dell EqualLogic storage and VMware View: A highly scalable, end-to-end client virtualization framework. Read more! http://p.sf.net/sfu/dell-eql-dev2dev ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] coordinates in Conformer class are different from the original sdf file
정종영 wrote: Hi, I found that the xyz coordinates in conformer class are different from coordinates in the original input sdf file. Why does the loss of original cooridinates happen? And how can I use Conformer with original coordinates in input file? Jongyoung -- 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 ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss Dear Jongyoung, can you give us an example of how you read in the multiconformer sd-file? I routinely read and write multiconformer sd-files and they seemed O.K. for me. Which version of the RDKit are you using? Cheers, Markus -- 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 ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] 'SDWriter' object has no attribute 'close
Cedric MORETTI wrote: Hello all, I have I little problem with RDKIT( I hope :D) My program don’t arrive to close the SDwriter whereas I put the command “writer.close()” and Chem.SDWriter.close() in the end of programm I just let the part of the code that is import for understand the problem and the error. I have the error when the program has finished to read the file Tks C from sys import * #from ChemScript11 import * from cinfony import rdk from rdkit import Chem import time reader1 = Chem.SDMolSupplier(sys.argv[0]) writer = Chem.SDWriter(sys.argv[1]) z = 0 for mol in reader1: “ [Blablablablabla ( It’s to simulate a code)] writer.write(mol) writer.close() reader1.close() Chem.SDWriter.close() Traceback (most recent call last): File C:\Scripttravail\supermain.py, line 18, in module exec(file.read()) File string, line 51, in module AttributeError: 'SDWriter' object has no attribute 'close ** DISCLAIMER This email and any files transmitted with it, including replies and forwarded copies (which may contain alterations) subsequently transmitted from Firmenich, are confidential and solely for the use of the intended recipient. The contents do not represent the opinion of Firmenich except to the extent that it relates to their official business. ** -- ThinkGeek and WIRED's GeekDad team up for the Ultimate GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the lucky parental unit. See the prize list and enter to win: http://p.sf.net/sfu/thinkgeek-promo ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss Hi Cedric, the Chem.SDWriter Object does not need to be closed, does it? It is automatically closed at the end of your program. It doesn't even have a method that is named 'close()' like the ones you might know from python text file I/O objects. This is what the Traceback error complains when it says : -AttributeError: 'SDWriter' object has no attribute 'close' So you should go well with simply deleting the three lines at the end of your script that give the .close() commands. Hope this helps, Markus -- ThinkGeek and WIRED's GeekDad team up for the Ultimate GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the lucky parental unit. See the prize list and enter to win: http://p.sf.net/sfu/thinkgeek-promo ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] van der Waals Radii
Hi Greg, I just searched for a possibility to query an Atom for its van der Waals Radius, but did not find a 'pythonic way' like an Atom-Property or the like in the docu. Do you have a hint on the best way to get this information using the RDKit? Thank you in advance, Markus -- ThinkGeek and WIRED's GeekDad team up for the Ultimate GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the lucky parental unit. See the prize list and enter to win: http://p.sf.net/sfu/thinkgeek-promo ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Can't kekulize mol
bouille wrote: Dear Greg How I can raise the following error ? 291475, COc1ccc(cc1)\C=C1\[S]=C(Nc2ccc(cc2)S(N)(=O)=O)NC1=O |t:11| Traceback (most recent call last): File /home/bouille/DescriptorsCalcul/3mon3D.py, line 85, in module sdf3D = Chem.MolToMolBlock(molH) ValueError: Sanitization error: Can't kekulize mol Best Regards Christian de Bouillé -- ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss Dear Christian, I'm no expert regarding smiles strings, but the molecule has several rings (if I can read it correctly there are 3 separated rings). one of them is a five-membered ring containing a sulfur. Maybe RDKit chokes on the three bonds that the sulfur is connected with. Is that molecule really O.K. There should at least be a charge at the sulfur atom in the ring, otherwise we get an insane structure, don't we? Best regards, Markus -- ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] read a smi files
Dear Sedric,
I copied and pasted the smiles codes to a local file and used the
following python snippet:
#I don't use cynfony, so this is pure RDKit Version Q4_2009 on Ubunto 9.4
from rdkit import Chem
suppl = Chem.SmilesMolSupplier(test.smi)
for mol in suppl:
print mol.GetNumAtoms()
The output is as expected:
[17:17:35] WARNING: no name column found on line 1
10
[17:17:35] WARNING: no name column found on line 2
18
... (some output cut away!)
17
[17:17:35] WARNING: no name column found on line 18
22
[17:17:35] WARNING: no name column found on line 19
12
Are you sure, it's not a problem with the text format you use?
Might this be a problem slash ('/') and backslash ('\') in the smiles files?
Additionally your path might be corrected according from
C:\Test/testsmi.smi
to
C:\Test\testsmi.smi
Hope this helps,
Markus
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[Rdkit-discuss] Where to find the CompressedSDMolSupplier
Dear All, I read about a CompressedSDMolSupplier (assuming it is a Supplier for zipped sd files, isn't it?) in the release Notes for Q32009_1. However I could neither find a function like that in the rdkit.Chem Module nor any hint in the docs. Could anyone please give me a pointer? Cheers, Markus -- The Planet: dedicated and managed hosting, cloud storage, colocation Stay online with enterprise data centers and the best network in the business Choose flexible plans and management services without long-term contracts Personal 24x7 support from experience hosting pros just a phone call away. http://p.sf.net/sfu/theplanet-com ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Some failing tests after installation
Hi Greg, I updated to the latest RDKit installation using boost_1_41_0 and the compilation did not throw any error (boost as well as rdkit). However when I run the tests, I get some errors from two scripts as follows (The first representatives per script): ** File SplitData.py, line 206, in __main__.SplitDbData Failed example: [str(x) for x in train] Expected: ['id-7', 'id-6', 'id-2', 'id-8'] Got: ['id-6', 'id-3', 'id-9', 'id-7', 'id-11', 'id-5', 'id-1', 'id-5'] ** ** File DbFpSupplier.py, line 84, in __main__.ForwardDbFpSupplier Failed example: len(fps) Expected: 12 Got: 48 ** For database access I use the standard Ubuntu9.04 sqlite3 packages, that obviously build up the database correctly. Do you have any hints? Cheers, Markus -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
