Author: bugman
Date: Tue Mar 19 13:48:34 2013
New Revision: 18874
URL: http://svn.gna.org/viewcvs/relax?rev=18874&view=rev
Log:
HELIX PDB records are now read, stored, and written out by the internal
structural object.
This affects the structure.read_pdb and structure.write_pdb user functions.
The helix is stored as
a metadata type object - its elements do not correspond to the atoms in the
structural object.
Modified:
trunk/generic_fns/structure/internal.py
trunk/generic_fns/structure/pdb_write.py
Modified: trunk/generic_fns/structure/internal.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/generic_fns/structure/internal.py?rev=18874&r1=18873&r2=18874&view=diff
==============================================================================
--- trunk/generic_fns/structure/internal.py (original)
+++ trunk/generic_fns/structure/internal.py Tue Mar 19 13:48:34 2013
@@ -444,6 +444,16 @@
# No match, therefore assume to be out of the secondary
structure section.
if lines[i][:6] not in records:
break
+
+ # A helix.
+ if lines[i][:5] == 'HELIX':
+ # Parse the record.
+ record_type, ser_num, helix_id, init_res_name,
init_chain_id, init_seq_num, init_icode, end_res_name, end_chain_id,
end_seq_num, end_icode, helix_class, comment, length =
pdb_read.helix(lines[i])
+
+ # Store the data.
+ if not hasattr(self, 'helices'):
+ self.helices = []
+ self.helices.append([helix_id, init_chain_id, init_res_name,
init_seq_num, end_chain_id, end_res_name, end_seq_num, helix_class, length])
# Return the remaining lines.
return lines[i:]
@@ -1851,6 +1861,23 @@
pdb_write.formul(file, comp_num=i+1, het_id=het[1], text=formula)
+ ###############################
+ # Secondary structure section #
+ ###############################
+
+ # The HELIX records.
+ ####################
+
+ # Printout.
+ print("HELIX")
+
+ # Loop over and unpack the helix data.
+ index = 1
+ for helix_id, init_chain_id, init_res_name, init_seq_num,
end_chain_id, end_res_name, end_seq_num, helix_class, length in self.helices:
+ pdb_write.helix(file, ser_num=index, helix_id=helix_id,
init_chain_id=init_chain_id, init_res_name=init_res_name,
init_seq_num=init_seq_num, end_chain_id=end_chain_id,
end_res_name=end_res_name, end_seq_num=end_seq_num, helix_class=helix_class,
length=length)
+ index += 1
+
+
######################
# Coordinate section #
######################
Modified: trunk/generic_fns/structure/pdb_write.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/generic_fns/structure/pdb_write.py?rev=18874&r1=18873&r2=18874&view=diff
==============================================================================
--- trunk/generic_fns/structure/pdb_write.py (original)
+++ trunk/generic_fns/structure/pdb_write.py Tue Mar 19 13:48:34 2013
@@ -686,7 +686,7 @@
file.write('\n')
-def helix(file, ser_num='', helix_id='', init_res_name='', init_chain_id='',
init_seq_id='', init_icode='', end_res_name='', end_chain_id='',
end_seq_num='', end_icode='', helix_class='', comment='', length=''):
+def helix(file, ser_num='', helix_id='', init_res_name='', init_chain_id='',
init_seq_num='', init_icode='', end_res_name='', end_chain_id='',
end_seq_num='', end_icode='', helix_class='', comment='', length=''):
"""Generate the HELIX record.
The following is the PDB v3.3 documentation
U{http://www.wwpdb.org/documentation/format33/sect5.html#HELIX}.
@@ -788,8 +788,8 @@
@type init_res_name: str
@keyword init_chain_id: The chain identifier
@type init_chain_id: str
- @keyword init_seq_id: The sequence number of the initial residue
- @type init_seq_id: int
+ @keyword init_seq_num: The sequence number of the initial residue
+ @type init_seq_num: int
@keyword init_icode: The insertion code of the initial residue
@type init_icode: str
@keyword end_res_name: The name of the terminal residue
@@ -815,7 +815,7 @@
_handle_none(helix_id),
_handle_none(init_res_name),
_handle_none(init_chain_id),
- _handle_none(init_seq_id),
+ _handle_none(init_seq_num),
_handle_none(init_icode),
_handle_none(end_res_name),
_handle_none(end_chain_id),
r18874 - in /trunk/generic_fns/structure: internal.py pdb_write.py