[Biopython-dev] [Bug 3100] New: Bio.PDB.ResidueDepth distance calculation error
bugzilla-daemon at portal.open-bio.org
bugzilla-daemon at portal.open-bio.org
Wed Jun 16 12:43:07 UTC 2010
http://bugzilla.open-bio.org/show_bug.cgi?id=3100
Summary: Bio.PDB.ResidueDepth distance calculation error
Product: Biopython
Version: 1.54b
Platform: All
OS/Version: All
Status: NEW
Severity: normal
Priority: P2
Component: Main Distribution
AssignedTo: biopython-dev at biopython.org
ReportedBy: andres.colubri at gmail.com
ResidueDepth.py in Bio.PDB contains an error at line 100:
d2=sum(d*d, 1)
This uses the built-in sum() function, which just sums all the elements of d*d,
starting at 1. But it should use numpy's sum instead:
d2=numpy.sum(d*d, 1)
To check the error, try the following code:
from Bio.PDB import
from Bio.PDB.ResidueDepth import
parser = PDBParser()
str = parser.get_structure('test', '3M38.pdb')
surf = get_surface('3M38.pdb', PDB_TO_XYZR='./pdb_to_xyzr', MSMS='./msms')
print min_dist(surf[10], surf)
3M38.pdb could be replaced by any other pdb file. The result of this
calculation printed to the console should be zero, since we are calculating the
minimum distance to the surface of a point belonging to the surface. But this
gives a value greater than zero.
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