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

 
 

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

Submitted by:  Nupur Bansal <nupur>
Submitted on:  Mon 03 Feb 2014 12:00:45 AM UTC  
 
Category: Octave Forge PackageSeverity: 3 - Normal
Priority: 5 - NormalItem Group: Incorrect Result
Status: FixedAssigned to: None
Originator Name: NupurOpen/Closed: Closed
Release: otherOperating System: Any

Add a New Comment(Rich Markup)
   

You are not logged in

Please log in, so followups can be emailed to you.

 

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:

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>
Project Administrator
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>
Project Administrator
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>
Project Administrator
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 File(s):
   
   
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

 

Carbon-Copy List
  • -unavailable- added by mtmiller (Posted a comment)
  • -unavailable- added by nupur (Submitted the item)
  •  

    Do you think this task is very important?
    If so, you can click here to add your encouragement to it.
    This task has 0 encouragements so far.

    Only project members can vote.

     

    Please enter the title of George Orwell's famous dystopian book (it's a date):

     

     

    Follow 8 latest changes.

    Date Changed By Updated Field Previous Value => Replaced By
    Thu 06 Feb 2014 05:25:45 AM UTCmtmillerStatusNeed Info=>Fixed
      Open/ClosedOpen=>Closed
      Release3.8.0=>other
      Operating SystemMac OS=>Any
    Mon 03 Feb 2014 02:06:24 PM UTCnupurAttached File-=>Added 2zo3_pocket.pdb, #30445
    Mon 03 Feb 2014 01:53:41 PM UTCmtmillerItem GroupNone=>Incorrect Result
      StatusNone=>Need Info
      Summaryread_pdb(name of pdb) giving syntax error=>pdb package: read_pdb(name of pdb) giving syntax error

    Back to the top


    Powered by Savane 3.1-cleanup1