Author: bugman
Date: Sun Nov 5 10:08:53 2006
New Revision: 2750
URL: http://svn.gna.org/viewcvs/relax?rev=2750&view=rev
Log:
Readjustment of 'self.atomic_data' and the addition of epydoc fields to
'self.atom_add()'.
The record name has been removed as this can be determined by the
'self.write_pdb_file()' function.
Modified:
branches/tensor_pdb/generic_fns/pdb.py
Modified: branches/tensor_pdb/generic_fns/pdb.py
URL:
http://svn.gna.org/viewcvs/relax/branches/tensor_pdb/generic_fns/pdb.py?rev=2750&r1=2749&r2=2750&view=diff
==============================================================================
--- branches/tensor_pdb/generic_fns/pdb.py (original)
+++ branches/tensor_pdb/generic_fns/pdb.py Sun Nov 5 10:08:53 2006
@@ -37,26 +37,44 @@
self.print_flag = 1
- def atom_add(self, atom_id='', record_name='HETATM', atom_name='',
res_name='', chain_id='', res_num='', pos=None, segment_id='', element=''):
+ def atom_add(self, atom_id=None, atom_name='', res_name='', chain_id='',
res_num=None, pos=None, segment_id='', element=''):
"""Function for adding an atom to the self.atomic_data structure.
The self.atomic_data data structure is a dictionary of arrays. The
keys correspond to the
'atom_id' strings. The elements of the array are:
0: Atom number.
- 1: Record name.
- 2: Atom name.
- 3: Residue name.
- 4: Chain ID.
- 5: Residue number.
- 6: The x coordinate of the atom.
- 7: The y coordinate of the atom.
- 8: The z coordinate of the atom.
- 9: Segment ID.
- 10: Element symbol.
- 11+: The bonded atom numbers.
+ 1: Atom name.
+ 2: Residue name.
+ 3: Chain ID.
+ 4: Residue number.
+ 5: The x coordinate of the atom.
+ 6: The y coordinate of the atom.
+ 7: The z coordinate of the atom.
+ 8: Segment ID.
+ 9: Element symbol.
+ 10+: The bonded atom numbers.
This function will create the key-value pair for the given atom.
+
+
+ @param atom_id: The atom identifier. This is used as the key
within the dictionary.
+ @type atom_id: str
+ @param atom_name: The atom name, e.g. H1.
+ @type atom_name: str
+ @param res_name: The residue name.
+ @type res_name: str
+ @param chain_id: The chain identifier.
+ @type chain_id: str
+ @param res_num: The residue number.
+ @type res_num: int
+ @param pos: The position vector of coordinates.
+ @type pos: list (length = 3)
+ @param segment_id: The segment identifier.
+ @type segment_id: str
+ @param element: The element symbol.
+ @type element: str
+ @return: None
"""
# Initialise the key-value pair.
@@ -64,7 +82,6 @@
# Fill the positions.
self.atomic_data[atom_id].append(len(self.atomic_data) + 1)
- self.atomic_data[atom_id].append(record_name)
self.atomic_data[atom_id].append(atom_name)
self.atomic_data[atom_id].append(residue_name)
self.atomic_data[atom_id].append(chain_id)
@@ -76,29 +93,28 @@
self.atomic_data[atom_id].append(element)
- def atom_connect(self, atom_id, bonded_id):
+ def atom_connect(self, atom_id=None, bonded_id=None):
"""Function for connecting two atoms within the self.atomic_data
data structure.
The self.atomic_data data structure is a dictionary of arrays. The
keys correspond to the
'atom_id' strings. The elements of the array are:
0: Atom number.
-
- 1: Element type.
-
- 2: The x coordinate of the atom.
-
- 3: The y coordinate of the atom.
-
- 4: The z coordinate of the atom.
-
- 5 onwards: The bonded atom numbers.
+ 1: Atom name.
+ 2: Residue name.
+ 3: Chain ID.
+ 4: Residue number.
+ 5: The x coordinate of the atom.
+ 6: The y coordinate of the atom.
+ 7: The z coordinate of the atom.
+ 8: Segment ID.
+ 9: Element symbol.
+ 10+: The bonded atom numbers.
This function will find the atom number corresponding to both the
atom_id and bonded_id.
The bonded_id atom number will then be appended to the atom_id
array. Because the
connections work both ways in the PDB file, the atom_id atom number
will be appended to the
bonded_id atom array as well.
-
"""
# Find the atom number corresponding to atom_id.
r2750 - /branches/tensor_pdb/generic_fns/pdb.py