SimTK: FEATURE: [#1367] incorrect processing of pdb paths

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Date:
2010-09-27 01:17

Priority:
3

State:
Closed

Submitted by:
Gurgen Tumanyan (tumanian)

Assigned to:
Teague Sterling (teague)

Summary:
incorrect processing of pdb paths

Detailed description
revision: 740 description:featurize fails with segmentation fault when run with -P(pointfile) parameter and PDB_DIR and DSSP_DIR environment variables. how to repeat: set PDB_DIR and DSSP_DIR to a directory with PDB and DSSP files, run featurize -P pointfile. fails with segmentation fault. workaround: run without set PDB_DIR and DSSP_DIR from directory which contains both PDB and DSSP files bug location: Utilities.cc, findProteinFile platform: ubuntu i686, kernel 2.6.28-13
revision: 740 description:featurize fails with segmentation fault when run with -P(pointfile) parameter and PDB_DIR and DSSP_DIR environment variables. how to repeat: set PDB_DIR and DSSP_DIR to a directory with PDB and DSSP files, run featurize -P pointfile. fails with segmentation fault. workaround: run without set PDB_DIR and DSSP_DIR from directory which contains both PDB and DSSP files bug location: Utilities.cc, findProteinFile platform: ubuntu i686, kernel 2.6.28-13

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Date: 2010-09-29 00:08 Sender: Teague Sterling It appears this bug has been resolved. Test cases do show that there could be a number of missing PDB files. Please make sure to check error output for notifications of any missing PDB files.
Date: 2010-09-28 20:46 Sender: Teague Sterling Patch for being tested right now. I've rewritten the findProteinFile function to be a lot cleaner as well as more robust. It is worth noting that this error have been occurring if a particular PDB or DSSP file is missing. FEATURE will now throw a warning and continue running if it cannot find a file. As this type of error will almost certainly cause incorrect results, we may want to consider having it exit with a fatal error.
Date: 2010-09-28 18:28 Sender: Teague Sterling I've found the cause of this. It seems to appear in protein names which consist entirely of digits. Working on patch now.
Date: 2010-09-28 05:20 Sender: Teague Sterling I'm running an almost identical system (Ubuntu x86_64, kernel 2.6.32-25) and cannot reproduce this error. I will look at the suspect areas and see if I can see any causes. Can you send me any output that occurs before the segfault?

Field	Old Value	Date	By
status_id	Open	2010-09-29 00:08	teague
resolution_id	100	2010-09-29 00:08	teague
close_date	2010-09-29 00:08	2010-09-29 00:08	teague
assigned_to	none	2010-09-28 18:28	teague

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