From: Rajarshi G. <rg...@in...> - 2008-01-22 19:54:02
|
Hi, does OB currently support InChI key generation? The wiki page at http://openbabel.sourceforge.net/wiki/InChI does not seem to indicate what version of InChI is used. Though I could use the InChI code directly, I'd rather do conversions from SMILES than have to generate SDF's from my SMILES first ------------------------------------------------------------------- Rajarshi Guha <rg...@in...> GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- The only perfect science is hindsight. |
From: Chris M. <c.m...@ds...> - 2008-01-22 22:44:26
|
Rajarshi Guha wrote: > Hi, does OB currently support InChI key generation? The wiki page at > http://openbabel.sourceforge.net/wiki/InChI does not seem to indicate > what version of InChI is used. > The development code and the v2.2 snapshots do. Use the -xK option to output the key rather than the normal InChI. Chris |
From: Rajarshi G. <rg...@in...> - 2008-01-23 00:53:35
|
On Jan 22, 2008, at 5:44 PM, Chris Morley wrote: > Rajarshi Guha wrote: >> Hi, does OB currently support InChI key generation? The wiki page at >> http://openbabel.sourceforge.net/wiki/InChI does not seem to indicate >> what version of InChI is used. >> > > The development code and the v2.2 snapshots do. Use the -xK option to > output the key rather than the normal InChI. Thanks. Also, is it the case that the sources in trunk require g++ 4 to compile? I have 3.4.6 but I get a lot of errors ------------------------------------------------------------------- Rajarshi Guha <rg...@in...> GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- All laws are simulations of reality. -- John C. Lilly |
From: Geoffrey H. <ge...@ge...> - 2008-01-23 01:08:39
|
On Jan 22, 2008, at 7:53 PM, Rajarshi Guha wrote: > Thanks. Also, is it the case that the sources in trunk require g++ 4 > to compile? I have 3.4.6 but I get a lot of errors I'd be interested to know the errors. There are known problems with GCC 3.x because it does not have the std::tr1 headers (i.e., shared_ptr). If you would be so kind, please file a bug report to remind me to enable a configure test for shared_ptr. Thanks, -Geoff |
From: Rajarshi G. <rg...@in...> - 2008-01-23 01:21:47
|
On Jan 22, 2008, at 8:08 PM, Geoffrey Hutchison wrote: > > On Jan 22, 2008, at 7:53 PM, Rajarshi Guha wrote: > >> Thanks. Also, is it the case that the sources in trunk require g++ 4 >> to compile? I have 3.4.6 but I get a lot of errors > > I'd be interested to know the errors. There are known problems with > GCC 3.x because it does not have the std::tr1 headers (i.e., > shared_ptr). Yes, that's what's happening > If you would be so kind, please file a bug report to remind me to > enable a configure test for shared_ptr. I've filed a bug report with the output of make attached ------------------------------------------------------------------- Rajarshi Guha <rg...@in...> GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- Enzymes are things invented by biologists that explain things which otherwise require harder thinking. -- Jerome Lettvin |
From: Rajarshi G. <rg...@in...> - 2008-01-24 16:15:08
|
On Jan 22, 2008, at 8:21 PM, Rajarshi Guha wrote: > > On Jan 22, 2008, at 8:08 PM, Geoffrey Hutchison wrote: > >> >> On Jan 22, 2008, at 7:53 PM, Rajarshi Guha wrote: >> >>> Thanks. Also, is it the case that the sources in trunk require g++ 4 >>> to compile? I have 3.4.6 but I get a lot of errors >> >> I'd be interested to know the errors. There are known problems with >> GCC 3.x because it does not have the std::tr1 headers (i.e., >> shared_ptr). > > Yes, that's what's happening > >> If you would be so kind, please file a bug report to remind me to >> enable a configure test for shared_ptr. Is it possible to disable shared_ptr by hand? For this task I just need SMILES to InChI key conversion - could I get by without the reaction stuff? ------------------------------------------------------------------- Rajarshi Guha <rg...@in...> GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- Mathematics consists of proving the most obvious thing in the least obvious way. -- George Polya |
From: Chris M. <c.m...@ds...> - 2008-01-24 17:34:28
|
Rajarshi Guha wrote: > On Jan 22, 2008, at 8:21 PM, Rajarshi Guha wrote: > >> On Jan 22, 2008, at 8:08 PM, Geoffrey Hutchison wrote: >> >>> On Jan 22, 2008, at 7:53 PM, Rajarshi Guha wrote: >>> >>>> Thanks. Also, is it the case that the sources in trunk require g++ 4 >>>> to compile? I have 3.4.6 but I get a lot of errors >>> I'd be interested to know the errors. There are known problems with >>> GCC 3.x because it does not have the std::tr1 headers (i.e., >>> shared_ptr). >> Yes, that's what's happening >> >>> If you would be so kind, please file a bug report to remind me to >>> enable a configure test for shared_ptr. > > Is it possible to disable shared_ptr by hand? For this task I just > need SMILES to InChI key conversion - could I get by without the > reaction stuff? Yes. I think the are the files that depend on shared_ptr are reaction.h, chemkinformat.cpp, rxnformat.cpp, cmlreactformat.cpp and, in the trunk, rsmiformat.cpp and cmlformat.cpp. The last is a bit unfortunate and maybe I should add some conditional compiling somehow. Alternatively: download Boost, http://Boost.org, make sure that the Boost include directory is on the include path and compile with USE_BOOST defined. That is how it is done in Windows builds. Chris |
From: Rajarshi G. <rg...@in...> - 2008-01-24 18:40:04
|
On Jan 24, 2008, at 12:34 PM, Chris Morley wrote: > Alternatively: download Boost, http://Boost.org, make sure that the > Boost include directory is on the include path and compile with > USE_BOOST defined. That is how it is done in Windows builds. Aah, thanks. That works fine ------------------------------------------------------------------- Rajarshi Guha <rg...@in...> GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- A committee is a group that keeps the minutes and loses hours. -- Milton Berle |
From: Rajarshi G. <rg...@in...> - 2008-01-24 18:51:32
|
On Jan 22, 2008, at 5:44 PM, Chris Morley wrote: > Rajarshi Guha wrote: >> Hi, does OB currently support InChI key generation? The wiki page at >> http://openbabel.sourceforge.net/wiki/InChI does not seem to indicate >> what version of InChI is used. >> > > The development code and the v2.2 snapshots do. Use the -xK option to > output the key rather than the normal InChI. With the trunk version of OB compiled on RHEL 4 (64 bit, gcc 3.4.6) I'm doing the following bash-3.00$ echo "c1ccccc1CCC mymol" | bin/babel -ismi -oinchi -xt InChI=1/C9H12/c1-2-6-9-7-4-3-5-8-9/h3-5,7-8H,2,6H2,1H3 mymol 1 molecule converted 18 audit log messages bash-3.00$ echo "c1ccccc1CCC mymol" | bin/babel -ismi -oinchi -xKt InChI=1/C9H12/c1-2-6-9-7-4-3-5-8-9/h3-5,7-8H,2,6H2,1H3 mymol 1 molecule converted 18 audit log messages It looks like InChI keys are not being generated. Is this a bug or am I mising something obvious? ------------------------------------------------------------------- Rajarshi Guha <rg...@in...> GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- Bus error -- driver executed. |
From: Chris M. <c.m...@ds...> - 2008-01-24 20:37:39
|
Rajarshi Guha wrote: > On Jan 22, 2008, at 5:44 PM, Chris Morley wrote: > >> Rajarshi Guha wrote: >>> Hi, does OB currently support InChI key generation? The wiki page at >>> http://openbabel.sourceforge.net/wiki/InChI does not seem to indicate >>> what version of InChI is used. >>> >> The development code and the v2.2 snapshots do. Use the -xK option to >> output the key rather than the normal InChI. > > With the trunk version of OB compiled on RHEL 4 (64 bit, gcc 3.4.6) > I'm doing the following > > bash-3.00$ echo "c1ccccc1CCC mymol" | bin/babel -ismi -oinchi -xt > InChI=1/C9H12/c1-2-6-9-7-4-3-5-8-9/h3-5,7-8H,2,6H2,1H3 mymol > 1 molecule converted > 18 audit log messages > bash-3.00$ echo "c1ccccc1CCC mymol" | bin/babel -ismi -oinchi -xKt > InChI=1/C9H12/c1-2-6-9-7-4-3-5-8-9/h3-5,7-8H,2,6H2,1H3 mymol > 1 molecule converted > 18 audit log messages > > It looks like InChI keys are not being generated. Is this a bug or am > I mising something obvious? It works for me on Windows: >echo c1ccccc1CCC mymol | babel -ismi -oinchi -xKt ODLMAHJVESYWTB-UHFFFAOYAK mymol 1 molecule converted 18 audit log messages At the risk of being insulting, the result you see is what would happen with the binary of v2.1.1... Chris |
From: Geoffrey H. <ge...@ge...> - 2008-01-24 20:44:35
|
On Jan 24, 2008, at 3:37 PM, Chris Morley wrote: >> It looks like InChI keys are not being generated. Is this a bug or am >> I mising something obvious? ... > At the risk of being insulting, the result you see is what would > happen > with the binary of v2.1.1... Ah, I think I might know the problem. On UNIX at the moment, libinchi will not be built or installed if Open Babel's configure script finds an existing version. I suspect you may have an older libinchi (i.e., before the keys were introduced). That's my guess. Cheers, -Geoff |
From: Chris M. <c.m...@ds...> - 2008-01-24 21:31:45
|
Rajarshi Guha wrote: > On Jan 24, 2008, at 3:37 PM, Chris Morley wrote: > >> It works for me on Windows: >> >>> echo c1ccccc1CCC mymol | babel -ismi -oinchi -xKt >> ODLMAHJVESYWTB-UHFFFAOYAK mymol >> 1 molecule converted >> 18 audit log messages >> >> At the risk of being insulting, the result you see is what would >> happen with the binary of v2.1.1... > > I have made dopey mistakes before ... Me too... I have now removed the #ifdef WIN32 from the InChIKey code in InChIFormat, which was added pending the InChI source files used by the UNIX build being dated. Sorry to waste your time. Chris |
From: Rajarshi G. <rg...@in...> - 2008-01-24 21:37:50
|
On Jan 24, 2008, at 4:31 PM, Chris Morley wrote: > Rajarshi Guha wrote: >> On Jan 24, 2008, at 3:37 PM, Chris Morley wrote: >>> It works for me on Windows: >>> >>>> echo c1ccccc1CCC mymol | babel -ismi -oinchi -xKt >>> ODLMAHJVESYWTB-UHFFFAOYAK mymol >>> 1 molecule converted >>> 18 audit log messages >>> >>> At the risk of being insulting, the result you see is what would >>> happen with the binary of v2.1.1... >> I have made dopey mistakes before ... > > Me too... > I have now removed the #ifdef WIN32 from the InChIKey code in > InChIFormat, which was added pending the InChI source files used by > the UNIX build being dated. Aah, thanks. It all works fine now ------------------------------------------------------------------- Rajarshi Guha <rg...@in...> GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- Q: What's purple and commutes? A: An abelian grape. |
From: Rajarshi G. <rg...@in...> - 2008-01-24 21:09:04
|
On Jan 24, 2008, at 3:37 PM, Chris Morley wrote: > It works for me on Windows: > > >echo c1ccccc1CCC mymol | babel -ismi -oinchi -xKt > ODLMAHJVESYWTB-UHFFFAOYAK mymol > 1 molecule converted > 18 audit log messages > > At the risk of being insulting, the result you see is what would > happen with the binary of v2.1.1... I have made dopey mistakes before ... I thought I might be using a wrong binary, but the machine I compiled does not have a previous OB installation: bash-3.00$ bin/babel No output file or format spec! Open Babel 2.2.0b2 -- Jan 24 2008 -- 13:37:58 Usage: babel [-i<input-type>] <name> [-o<output-type>] <name> Try -H option for more information. I went to another machine (FC 5, g++ 4.1.1), wiped out all the previous InChI and OpenBabel installations and recompiled and installed trunk. Same result as above. On both machines, config.log indicates it did not find an installed version of InChI, so it must be using it's own version: configure:21241: checking for GetINCHI in -linchi configure:21276: g++ -o conftest -I/usr/include/boost -DUSE_BOOST -I/ usr/include /boost -DUSE_BOOST conftest.cpp -linchi -lm >&5 /usr/bin/ld: cannot find -linchi collect2: ld returned 1 exit status ------------------------------------------------------------------- Rajarshi Guha <rg...@in...> GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- If you believe in telekinesis, raise my hand. |
From: Noel O'B. <bao...@gm...> - 2008-02-01 11:27:21
|
On 24/01/2008, Rajarshi Guha <rg...@in...> wrote: > > On Jan 24, 2008, at 3:37 PM, Chris Morley wrote: > > > It works for me on Windows: > > > > >echo c1ccccc1CCC mymol | babel -ismi -oinchi -xKt > > ODLMAHJVESYWTB-UHFFFAOYAK mymol > > 1 molecule converted > > 18 audit log messages > > > > At the risk of being insulting, the result you see is what would > > happen with the binary of v2.1.1... > > I have made dopey mistakes before ... > > I thought I might be using a wrong binary, but the machine I compiled > does not have a previous OB installation: > > bash-3.00$ bin/babel > No output file or format spec! > Open Babel 2.2.0b2 -- Jan 24 2008 -- 13:37:58 > Usage: babel [-i<input-type>] <name> [-o<output-type>] <name> > Try -H option for more information. > > I went to another machine (FC 5, g++ 4.1.1), wiped out all the > previous InChI and OpenBabel installations and recompiled and > installed trunk. Same result as above. > > On both machines, config.log indicates it did not find an installed > version of InChI, so it must be using it's own version: > > configure:21241: checking for GetINCHI in -linchi > configure:21276: g++ -o conftest -I/usr/include/boost -DUSE_BOOST -I/ > usr/include > /boost -DUSE_BOOST conftest.cpp -linchi -lm >&5 > /usr/bin/ld: cannot find -linchi > collect2: ld returned 1 exit status How did you get g++ to define USE_BOOST and add the extra include directory for boost? Did you hand edit the Makefile? > > > > ------------------------------------------------------------------- > Rajarshi Guha <rg...@in...> > GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE > ------------------------------------------------------------------- > > If you believe in telekinesis, raise my hand. > > > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > OpenBabel-discuss mailing list > Ope...@li... > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > |
From: Rajarshi G. <rg...@in...> - 2008-02-01 20:15:45
|
On Feb 1, 2008, at 6:27 AM, Noel O'Boyle wrote: > On 24/01/2008, Rajarshi Guha <rg...@in...> wrote: >> >> How did you get g++ to define USE_BOOST and add the extra include > directory for boost? Did you hand edit the Makefile? Yes, I edited the Makefile to define USE_BOOST ------------------------------------------------------------------- Rajarshi Guha <rg...@in...> GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- All life evolves by the differential survival of replicating entities. -- Dawkins |