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From: Matt K. <mke...@iu...> - 2009-04-26 02:34:48
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I am somewhat confused on how to obtain fingerprints using perl. I tried
doing a simple SetInAndOutFormats("smi","fpt") and then write the molecule
out but got a segmentation fault, while it worked for other formats such as
smiles to molfile. I am also unfamiliar with using the
OBConversion.convert() function, as it complained that input and output was
not set.
I know that pybel is available and could use that although I am already
using perl to parse pubchem data into a flat file before it goes into my
postgresql database and would like to calculate fingerprints from the smiles
of each line on the fly before it goes in.
Thanks for any help.
--
View this message in context: http://www.nabble.com/Using-Fingerprinter-with-perl-tp23238185p23238185.html
Sent from the openbabel-scripting mailing list archive at Nabble.com.
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From: Matt K. <mke...@iu...> - 2009-04-27 07:15:29
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I downloaded a fresh install and installed the wrappers and in the Perl
script I do see that it includes the header file for fingerprints but I just
wanted to know if anyone else has had trouble pulling up methods from this
class. when I do the OBFingerprint::GetDefault() or
OBFingerprint::FindFingerprint("FP2") it states that it might not be loaded.
Thx,
Matt
Matt Ketterer wrote:
>
> I am somewhat confused on how to obtain fingerprints using perl. I tried
> doing a simple SetInAndOutFormats("smi","fpt") and then write the molecule
> out but got a segmentation fault, while it worked for other formats such
> as smiles to molfile. I am also unfamiliar with using the
> OBConversion.convert() function, as it complained that input and output
> was not set.
>
> I know that pybel is available and could use that although I am already
> using perl to parse pubchem data into a flat file before it goes into my
> postgresql database and would like to calculate fingerprints from the
> smiles of each line on the fly before it goes in.
> Thanks for any help.
>
--
View this message in context: http://www.nabble.com/Using-Fingerprinter-with-perl-tp23238185p23251252.html
Sent from the openbabel-scripting mailing list archive at Nabble.com.
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From: Noel O'B. <bao...@gm...> - 2009-04-27 08:11:54
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Hello Matt, Did you download OpenBabel 2.2.1, remove any previous OpenBabel installation, and install globally or locally following the instructions at http://openbabel.org/wiki/Install_(source_code)? Does using babel work? E.g. bash-3.2$ echo "C(=O)CCl" | babel -ismi -ofpt -xfFP2 > 7 bits set 00000000 00000000 00000000 00000000 00000000 00000000 00000000 00000000 00000000 00000000 00000000 40000000 00008000 00000000 00000000 00000000 00000000 00000000 00000000 00000000 00000000 00000300 00000000 00000000 00000000 08000000 00000000 00000000 00000004 00000000 00000000 00020000 1 molecule converted 12 audit log messages OBFingerprint::FindFingerprint("FP2") should work fine if babel can find FP2. You should test your perl script in an empty directory. - Noel 2009/4/27 Matt Ketterer <mke...@iu...> > > I downloaded a fresh install and installed the wrappers and in the Perl > script I do see that it includes the header file for fingerprints but I > just > wanted to know if anyone else has had trouble pulling up methods from this > class. when I do the OBFingerprint::GetDefault() or > OBFingerprint::FindFingerprint("FP2") it states that it might not be > loaded. > Thx, > Matt > > > > Matt Ketterer wrote: > > > > I am somewhat confused on how to obtain fingerprints using perl. I tried > > doing a simple SetInAndOutFormats("smi","fpt") and then write the > molecule > > out but got a segmentation fault, while it worked for other formats such > > as smiles to molfile. I am also unfamiliar with using the > > OBConversion.convert() function, as it complained that input and output > > was not set. > > > > I know that pybel is available and could use that although I am already > > using perl to parse pubchem data into a flat file before it goes into my > > postgresql database and would like to calculate fingerprints from the > > smiles of each line on the fly before it goes in. > > Thanks for any help. > > > > -- > View this message in context: > http://www.nabble.com/Using-Fingerprinter-with-perl-tp23238185p23251252.html > Sent from the openbabel-scripting mailing list archive at Nabble.com. > > > > ------------------------------------------------------------------------------ > Crystal Reports - New Free Runtime and 30 Day Trial > Check out the new simplified licensign option that enables unlimited > royalty-free distribution of the report engine for externally facing > server and web deployment. > http://p.sf.net/sfu/businessobjects > _______________________________________________ > OpenBabel-scripting mailing list > Ope...@li... > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting > |
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From: Matt K. <mke...@iu...> - 2009-04-27 13:59:56
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Hi Noel, Yes openbabel does work. I got perl to stop barking at me by taking away the "new" in front of the fingerprint class as I see it is static. I'm still unsure of how to return or print the value. I was trying to follow the python implementation at http://www.nabble.com/Re%3A-fingerprints-from-Python-td22189375.html#a22189375 but am not sure how to manipulate the vector that was used. [matt@localhost Desktop]$ echo "C(=O)CCl" | babel -ismi -ofpt -xfFP2 > 7 bits set 00000000 00000000 00000000 00000000 00000000 00000300 00000000 00000000 00000000 08000000 00000000 40000000 00008004 00000000 00000000 00020000 1 molecule converted 19 audit log messages #!/usr/bin/perl use Chemistry::OpenBabel; my $smiles = "C(=O)CCl"; my $obMol = new Chemistry::OpenBabel::OBMol; my $obConversion = new Chemistry::OpenBabel::OBConversion; $obConversion->SetInFormat("smi"); $obConversion->ReadString($obMol,$smiles); my $fingerprinter = Chemistry::OpenBabel::OBFingerprint::FindFingerprint("FP2"); my $fp = new Chemistry::OpenBabel::vectorUnsignedInt(); my $thumb = $fingerprinter->GetFingerprint($obMol, $fp); print "$thumb\n"; #only returns 1 baoilleach wrote: > > Hello Matt, > > Did you download OpenBabel 2.2.1, remove any previous OpenBabel > installation, and install globally or locally following the instructions > at > http://openbabel.org/wiki/Install_(source_code)? > > Does using babel work? E.g. > bash-3.2$ echo "C(=O)CCl" | babel -ismi -ofpt -xfFP2 >> 7 bits set > 00000000 00000000 00000000 00000000 00000000 00000000 > 00000000 00000000 00000000 00000000 00000000 40000000 > 00008000 00000000 00000000 00000000 00000000 00000000 > 00000000 00000000 00000000 00000300 00000000 00000000 > 00000000 08000000 00000000 00000000 00000004 00000000 > 00000000 00020000 > 1 molecule converted > 12 audit log messages > > OBFingerprint::FindFingerprint("FP2") should work fine if babel can find > FP2. You should test your perl script in an empty directory. > > - Noel > > > 2009/4/27 Matt Ketterer <mke...@iu...> > >> >> I downloaded a fresh install and installed the wrappers and in the Perl >> script I do see that it includes the header file for fingerprints but I >> just >> wanted to know if anyone else has had trouble pulling up methods from >> this >> class. when I do the OBFingerprint::GetDefault() or >> OBFingerprint::FindFingerprint("FP2") it states that it might not be >> loaded. >> Thx, >> Matt >> >> >> >> Matt Ketterer wrote: >> > >> > I am somewhat confused on how to obtain fingerprints using perl. I >> tried >> > doing a simple SetInAndOutFormats("smi","fpt") and then write the >> molecule >> > out but got a segmentation fault, while it worked for other formats >> such >> > as smiles to molfile. I am also unfamiliar with using the >> > OBConversion.convert() function, as it complained that input and output >> > was not set. >> > >> > I know that pybel is available and could use that although I am already >> > using perl to parse pubchem data into a flat file before it goes into >> my >> > postgresql database and would like to calculate fingerprints from the >> > smiles of each line on the fly before it goes in. >> > Thanks for any help. >> > >> >> -- >> View this message in context: >> http://www.nabble.com/Using-Fingerprinter-with-perl-tp23238185p23251252.html >> Sent from the openbabel-scripting mailing list archive at Nabble.com. >> >> >> >> ------------------------------------------------------------------------------ >> Crystal Reports - New Free Runtime and 30 Day Trial >> Check out the new simplified licensign option that enables unlimited >> royalty-free distribution of the report engine for externally facing >> server and web deployment. >> http://p.sf.net/sfu/businessobjects >> _______________________________________________ >> OpenBabel-scripting mailing list >> Ope...@li... >> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting >> > > ------------------------------------------------------------------------------ > Crystal Reports - New Free Runtime and 30 Day Trial > Check out the new simplified licensign option that enables unlimited > royalty-free distribution of the report engine for externally facing > server and web deployment. > http://p.sf.net/sfu/businessobjects > _______________________________________________ > OpenBabel-scripting mailing list > Ope...@li... > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting > > -- View this message in context: http://www.nabble.com/Using-Fingerprinter-with-perl-tp23238185p23256721.html Sent from the openbabel-scripting mailing list archive at Nabble.com. |
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From: Noel O'B. <bao...@gm...> - 2009-04-27 14:34:57
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You're almost there. The result is in $fp. BTW, if you are interested in writing up some Perl recipes (e.g. the code below) on the wiki, it would be greatly appreciated. It would help other users avoid the same pitfalls. -- Noel 2009/4/27 Matt Ketterer <mke...@iu...>: > > Hi Noel, > Yes openbabel does work. I got perl to stop barking at me by taking away > the "new" in front of the fingerprint class as I see it is static. I'm > still unsure of how to return or print the value. I was trying to follow > the python implementation at > http://www.nabble.com/Re%3A-fingerprints-from-Python-td22189375.html#a22189375 > but am not sure how to manipulate the vector that was used. > > [matt@localhost Desktop]$ echo "C(=O)CCl" | babel -ismi -ofpt -xfFP2 >> 7 bits set > 00000000 00000000 00000000 00000000 00000000 00000300 > 00000000 00000000 00000000 08000000 00000000 40000000 > 00008004 00000000 00000000 00020000 > 1 molecule converted > 19 audit log messages > > #!/usr/bin/perl > use Chemistry::OpenBabel; > > my $smiles = "C(=O)CCl"; > my $obMol = new Chemistry::OpenBabel::OBMol; > my $obConversion = new Chemistry::OpenBabel::OBConversion; > $obConversion->SetInFormat("smi"); > $obConversion->ReadString($obMol,$smiles); > my $fingerprinter = > Chemistry::OpenBabel::OBFingerprint::FindFingerprint("FP2"); > > my $fp = new Chemistry::OpenBabel::vectorUnsignedInt(); > my $thumb = $fingerprinter->GetFingerprint($obMol, $fp); > print "$thumb\n"; #only returns 1 > > > > > > > > baoilleach wrote: >> >> Hello Matt, >> >> Did you download OpenBabel 2.2.1, remove any previous OpenBabel >> installation, and install globally or locally following the instructions >> at >> http://openbabel.org/wiki/Install_(source_code)? >> >> Does using babel work? E.g. >> bash-3.2$ echo "C(=O)CCl" | babel -ismi -ofpt -xfFP2 >>> 7 bits set >> 00000000 00000000 00000000 00000000 00000000 00000000 >> 00000000 00000000 00000000 00000000 00000000 40000000 >> 00008000 00000000 00000000 00000000 00000000 00000000 >> 00000000 00000000 00000000 00000300 00000000 00000000 >> 00000000 08000000 00000000 00000000 00000004 00000000 >> 00000000 00020000 >> 1 molecule converted >> 12 audit log messages >> >> OBFingerprint::FindFingerprint("FP2") should work fine if babel can find >> FP2. You should test your perl script in an empty directory. >> >> - Noel >> >> >> 2009/4/27 Matt Ketterer <mke...@iu...> >> >>> >>> I downloaded a fresh install and installed the wrappers and in the Perl >>> script I do see that it includes the header file for fingerprints but I >>> just >>> wanted to know if anyone else has had trouble pulling up methods from >>> this >>> class. when I do the OBFingerprint::GetDefault() or >>> OBFingerprint::FindFingerprint("FP2") it states that it might not be >>> loaded. >>> Thx, >>> Matt >>> >>> >>> >>> Matt Ketterer wrote: >>> > >>> > I am somewhat confused on how to obtain fingerprints using perl. I >>> tried >>> > doing a simple SetInAndOutFormats("smi","fpt") and then write the >>> molecule >>> > out but got a segmentation fault, while it worked for other formats >>> such >>> > as smiles to molfile. I am also unfamiliar with using the >>> > OBConversion.convert() function, as it complained that input and output >>> > was not set. >>> > >>> > I know that pybel is available and could use that although I am already >>> > using perl to parse pubchem data into a flat file before it goes into >>> my >>> > postgresql database and would like to calculate fingerprints from the >>> > smiles of each line on the fly before it goes in. >>> > Thanks for any help. >>> > >>> >>> -- >>> View this message in context: >>> http://www.nabble.com/Using-Fingerprinter-with-perl-tp23238185p23251252.html >>> Sent from the openbabel-scripting mailing list archive at Nabble.com. >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> Crystal Reports - New Free Runtime and 30 Day Trial >>> Check out the new simplified licensign option that enables unlimited >>> royalty-free distribution of the report engine for externally facing >>> server and web deployment. >>> http://p.sf.net/sfu/businessobjects >>> _______________________________________________ >>> OpenBabel-scripting mailing list >>> Ope...@li... >>> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting >>> >> >> ------------------------------------------------------------------------------ >> Crystal Reports - New Free Runtime and 30 Day Trial >> Check out the new simplified licensign option that enables unlimited >> royalty-free distribution of the report engine for externally facing >> server and web deployment. >> http://p.sf.net/sfu/businessobjects >> _______________________________________________ >> OpenBabel-scripting mailing list >> Ope...@li... >> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting >> >> > > -- > View this message in context: http://www.nabble.com/Using-Fingerprinter-with-perl-tp23238185p23256721.html > Sent from the openbabel-scripting mailing list archive at Nabble.com. > > > ------------------------------------------------------------------------------ > Crystal Reports - New Free Runtime and 30 Day Trial > Check out the new simplified licensign option that enables unlimited > royalty-free distribution of the report engine for externally facing > server and web deployment. > http://p.sf.net/sfu/businessobjects > _______________________________________________ > OpenBabel-scripting mailing list > Ope...@li... > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting > |
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