Author: bugman
Date: Wed Oct 8 09:22:04 2014
New Revision: 26205
URL: http://svn.gna.org/viewcvs/relax?rev=26205&view=rev
Log:
Improvements for PDB creation in the relax library for out of bounds structural
coordinates.
The lib.structure.pdb_write module atom() and hetatm() functions will now more
gracefully handle
atomic coordinates which are outside of the PDB limits of [-999.999, 9999.999].
When such
coordinates are encountered, instead of producing a too long PDB line which
does not pass the
validation step, the functions will set the coordinates to the boundary value.
This will at least
allow a valid PDB file to be created, despite the warping of the coordinates.
Modified:
trunk/lib/structure/pdb_write.py
Modified: trunk/lib/structure/pdb_write.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/structure/pdb_write.py?rev=26205&r1=26204&r2=26205&view=diff
==============================================================================
--- trunk/lib/structure/pdb_write.py (original)
+++ trunk/lib/structure/pdb_write.py Wed Oct 8 09:22:04 2014
@@ -269,6 +269,16 @@
@type charge: int
"""
+ # Coordinate bounds.
+ pdb_min = -999.999
+ pdb_max = 9999.999
+ coord = [x, y, z]
+ for i in range(3):
+ if coord[i] != '' and coord[i] < pdb_min:
+ coord[i] = pdb_min
+ if coord[i] != '' and coord[i] > pdb_max:
+ coord[i] = pdb_max
+
# The formatted record.
text = "%-6s%5s %-4s%1s%3s %1s%4s%1s %8.3f%8.3f%8.3f%6.2f%6.2f
%2s%2s" % (
'ATOM',
@@ -279,9 +289,9 @@
_handle_none(chain_id),
_handle_none(res_seq),
_handle_none(icode),
- _handle_none(x),
- _handle_none(y),
- _handle_none(z),
+ _handle_none(coord[0]),
+ _handle_none(coord[1]),
+ _handle_none(coord[2]),
_handle_none(occupancy),
_handle_none(temp_factor),
_handle_none(element),
@@ -1082,6 +1092,16 @@
@type charge: int
"""
+ # Coordinate bounds.
+ pdb_min = -999.999
+ pdb_max = 9999.999
+ coord = [x, y, z]
+ for i in range(3):
+ if coord[i] != '' and coord[i] < pdb_min:
+ coord[i] = pdb_min
+ if coord[i] != '' and coord[i] > pdb_max:
+ coord[i] = pdb_max
+
# The formatted record.
text = "%-6s%5s %4s%1s%3s %1s%4s%1s %8.3f%8.3f%8.3f%6.2f%6.2f
%2s%2s" % (
'HETATM',
@@ -1092,9 +1112,9 @@
_handle_none(chain_id),
_handle_none(res_seq),
_handle_none(icode),
- _handle_none(x),
- _handle_none(y),
- _handle_none(z),
+ _handle_none(coord[0]),
+ _handle_none(coord[1]),
+ _handle_none(coord[2]),
_handle_none(occupancy),
_handle_none(temp_factor),
_handle_none(element),
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