Re: [OpenBabel-scripting] [openbabel-scripting] Using Fingerprinter with perl

[Noel O'B. <bao...@gm...>]

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.
>>>
>>>
>>>
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>
> --
> 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 &#45; New Free Runtime and 30 Day Trial
> Check out the new simplified licensign option that enables unlimited
> royalty&#45;free distribution of the report engine for externally facing
> server and web deployment.
> http://p.sf.net/sfu/businessobjects
> _______________________________________________
> OpenBabel-scripting mailing list
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> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>