bugGNU Octave - Bugs: bug #41440, pdb package: read_pdb(name of pdb)...

 
 

bug #41440: pdb package: read_pdb(name of pdb) giving syntax error

Submitter:  Nupur Bansal <nupur>
Submitted:  Mon 03 Feb 2014 12:00:45 AM UTC
   
 
Category:  Octave Package Severity:  3 - Normal
Priority:  5 - Normal Item Group:  Incorrect Result
Status:  Fixed Assigned to:  None
Originator Name:  Nupur Open/Closed:  * Closed
Release:  * other Operating System:  * Any
Fixed Release:  None Planned Release:  None
* Mandatory Fields

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Thu 06 Feb 2014 05:25:45 AM UTC, comment #4: 

I get the following error with the latest (2009) release of the pdb package:


octave:1> p = read_pdb ("2zo3_pocket.pdb")
error: 'struct_contains' undefined near line 57 column 4
error: called from:
error:   /home/mike/octave/pdb-1.0.7/read_pdb.m at line 57, column 1


However, this has apparently been fixed in svn. If I use the current read_pdb function from the Octave Forge svn repository

https://sourceforge.net/p/octave/code/HEAD/tree/trunk/octave-forge/extra/pdb/inst/read_pdb.m

it loads the attached PDB file successfully with no error. So all that is needed is for someone interested in this package to make a release, preferably someone willing to take over maintenance since it is now in the list of "unmaintained" packages.

Mike Miller <mtmiller>
Group Member
Mon 03 Feb 2014 02:07:46 PM UTC, comment #3: 

Hi, I have attached the pdb now. Any help would be appreciated.

Nupur Bansal <nupur>
Mon 03 Feb 2014 02:02:28 PM UTC, comment #2: 

Hi Nupur, please post comments to the bug tracker web interface, if you reply via email your comments are lost.

> I am using the command "p = read_pdb(name_of_pdb_file)" on the
> command line, but it is giving me syntax error. I have tried to use
> various variants to hit and try if something fits in, but I always
> ended up getting the syntax error. Please help me with this.
>
> I have never used octave before, so I am not sure if I would be able
> to do that.


Can you attach the pdb file to this bug report? If someone else is going to work on this bug, they will need the file you are using, or a similar file. I personally have no knowledge about pdb files or the pdb package, I'm just trying to help you provide the necessary information so someone can work on this.

Mike Miller <mtmiller>
Group Member
Mon 03 Feb 2014 01:53:41 PM UTC, comment #1: 

Thanks for your report, although it is very incomplete. What is the error? Please give a complete example of how to reproduce the error you are seeing.

Also note that the pdb package is currently unmaintained and hasn't seen a release in almost 5 years. Can you provide a patch to fix the error? Would you be able to help maintain this package since you find it useful?

Mike Miller <mtmiller>
Group Member
Mon 03 Feb 2014 12:00:45 AM UTC, original submission:  


Nupur Bansal <nupur>

 

(Note: upload size limit is set to 16384 kB, after insertion of the required escape characters.)

Attach Files:
   
   
Comment:
   

Attached Files
file #30445:  2zo3_pocket.pdb added by nupur (51KiB - chemical/x-pdb)

 

Depends on the following items: None found

Items that depend on this one: None found

 

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  • -email is unavailable- added by nupur (Submitted the item)
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    Follow 8 latest changes.

    Date Changed by Updated Field Previous Value => Replaced by
    2014-02-06 mtmiller StatusNeed Info Fixed
        Open/ClosedOpen Closed
        Release3.8.0 other
        Operating SystemMac OS Any
    2014-02-03 nupur Attached File- Added 2zo3_pocket.pdb, #30445
    2014-02-03 mtmiller Item GroupNone Incorrect Result
        StatusNone Need Info
        Summaryread_pdb(name of pdb) giving syntax error pdb package: read_pdb(name of pdb) giving syntax error

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