Re: [Joelib-help] Mol2 file read error

[Joerg K. W. <we...@in...>]

Dear Koyama_Takahiko,

yes, i know, here is the bug fix. Please replace the ScanfReader.java

http://sourceforge.net/tracker/index.php?func=detail&aid=1075208&group_id=39708&atid=425969

Kind regards, Joerg

> Hello,
> 
> I am having a trouble with reading a mol2 file using JOElib. 
> The error seems occur when the coordinate entry is negative. For instance,
> 
> @<TRIPOS>ATOM
> 1	C1	1.207	2.091	0.000	C.ar	1	BENZENE	0.000
> 2	C2	2.414	1.394	0.000	C.ar	1	BENZENE	0.000
> 3	C3	2.414	0.000	0.000	C.ar	1	BENZENE	0.000
> 4	C4	1.207 -0.697	0.000	C.ar	1	BENZENE	0.000
> 
> upto 3rd atom is successfully read yet, 4th atom which has minus in y-coordinate causes throwing an exception (cformat.ScanfMatchException: Malformed floating point number: no digits). 
> 
> This is the (simplified) code I am using.
> 
> String inputFile="benzene.mol2";
> SimpleReader reader = null;
>  IOType inType = IOTypeHolder.instance().filenameToType(inputFile);
>  reader = new SimpleReader(input, inType);
>  JOEMol mol = new JOEMol(inType, inType);    
>  reader.readNext(mol));
> 
> I will appreciate for your help on this matter.
> 
> Takahiko Koyama
> 
> 
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-- 
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW:    http://www-ra.informatik.uni-tuebingen.de
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