Author: bugman
Date: Mon Nov 17 11:56:50 2014
New Revision: 26595
URL: http://svn.gna.org/viewcvs/relax?rev=26595&view=rev
Log:
Set more reasonable default values for the lib.structure.pdb_write functions
atom() and hetatm().
The occupancy now defaults to 1.0 instead of '', and the temperature factor to
0.0 instead of ''.
This avoid painful errors when using these functions, as these arguments must
be floating point
numbers at all times, hence the default value of '' causes a TypeError.
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=26595&r1=26594&r2=26595&view=diff
==============================================================================
--- trunk/lib/structure/pdb_write.py (original)
+++ trunk/lib/structure/pdb_write.py Mon Nov 17 11:56:50 2014
@@ -89,7 +89,7 @@
raise RelaxError("The PDB record '%s' contains NaN values." % record)
-def atom(file, serial='', name='', alt_loc='', res_name='', chain_id='',
res_seq='', icode='', x='', y='', z='', occupancy='', temp_factor='',
element='', charge=''):
+def atom(file, serial='', name='', alt_loc='', res_name='', chain_id='',
res_seq='', icode='', x='', y='', z='', occupancy=1.0, temp_factor=0.0,
element='', charge=''):
"""Generate the ATOM record.
The following is the PDB v3.3 documentation
U{http://www.wwpdb.org/documentation/format33/sect9.html#ATOM}.
@@ -297,6 +297,7 @@
_handle_none(element),
_handle_none(charge)
)
+ print text
# Validate.
_record_validate(text)
@@ -972,7 +973,7 @@
file.write('\n')
-def hetatm(file, serial='', name='', alt_loc='', res_name='', chain_id='',
res_seq='', icode='', x='', y='', z='', occupancy='', temp_factor='',
element='', charge=''):
+def hetatm(file, serial='', name='', alt_loc='', res_name='', chain_id='',
res_seq='', icode='', x='', y='', z='', occupancy=1.0, temp_factor=0.0,
element='', charge=''):
"""Generate the HETATM record.
The following is the PDB v3.3 documentation
U{http://www.wwpdb.org/documentation/format33/sect9.html#HETATM}.
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