User: mossig89

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mossig890
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Posts by mossig89

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Comment: C: EMBOSS needle question
... I guess the post got deleted somehow, because I remembered that answer solved my problem, I didnt install EMBOSS in the first place. ...
written 3.8 years ago by mossig890
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Comment: C: Atomcache function in biojava
... aight I deleted everything concerning eclipse, redid everything from scratch, installed egit, maven and after that followed your steps that you mentioned above. after that I tested the DemoAtomCache, it worked just fine. Thanks alot. I created a new java project, in the Java settings under the proj ...
written 3.8 years ago by mossig890
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Comment: C: Atomcache function in biojava
... whenever I go to file>import>maven>existing Maven Projects and after that select the biopython folder downloaded it's not selecting and saying under the Maven projects: "project biojava already exists add a version or a custom suffix using name template in Advanced settings " it seems like ...
written 3.8 years ago by mossig890
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Comment: C: Atomcache function in biojava
... im using linux 32 bit, with netbeanse 8.0. I tried using biojava with eclipse I followed the commands provided here: http://biojava.org/wiki/BioJava3_eclipse however I couldnt do step 5 of option 1 and step 4 of option 2, because whenever I right clicked on the biojava projects within the project ex ...
written 3.8 years ago by mossig890
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Atomcache function in biojava
... Hi everyone I'm fairly new to biojava and trying to implement this piece of code:    AtomCache cache = new AtomCache(); cache.setPath("/tmp/"); FileParsingParameters params = cache.getFileParsingParams(); params.setLoadChemCompInfo(true); StructureIO.setAtomCache(cache); S ...
biojava java netbeans written 3.8 years ago by mossig890 • updated 3.8 years ago by Biostar ♦♦ 20
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Comment: C: python wrapper for Jfatcat and Jce proteins structure alignment tools
... well I tried to do something about it, writing a wrapper or using python subprocess module to make us of the functionality of that web program... however I failed, since I don't have the slightest clue of how these wrappers work, I only use them. However in BioJava there's a class that implements th ...
written 3.9 years ago by mossig890
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python subprocesses and wrappers for Jce tool
... Hi everyone, I'm fairly new to Biopython, I'm interested in the tool Jce (protein structure alignment by combinatorial extensions) provided @ http://source.rcsb.org/jfatcatserver/ . now the online application works perfectly fine, however I need to implement this tool in my code, possibly using wra ...
python alignment biopython written 3.9 years ago by mossig890 • updated 3.9 years ago by donfreed1.2k
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Comment: C: python wrapper for Jfatcat and Jce proteins structure alignment tools
... I know there are GUI web apps for them two, which work perfectly fine, that's why you make use of wrappers which is basically using the functionality of those apps inside our python code, by calling their methods with specific parameters. However I can't seem to find any documentation or any online ...
written 3.9 years ago by mossig890
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python wrapper for Jfatcat and Jce proteins structure alignment tools
... is there any documentation provided concerning the wrappers for Jfatcat and Jce (combinatorial extensions) I'm assuming it's within the PDB tools in Biopython... as in Bio.PDB.---- but I cant seem to find it. Thanks. ...
python alignment biopython written 3.9 years ago by mossig890 • updated 3.9 years ago by Peter5.6k
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Structure structure alignment using combinatorial extensions
... I am trying to find a tool that performs structure structure alignment for two sequences given their residues using combinatorial extensions (CE). I found a tool based on combinatorial extensions provided by the protein data bank: http://source.rcsb.org/jfatcatserver/ However I was wondering if ther ...
python alignment biopython written 3.9 years ago by mossig890 • updated 3.9 years ago by Ashutosh Pandey11k

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