Author: bugman
Date: Mon Apr 7 10:49:17 2008
New Revision: 5335
URL: http://svn.gna.org/viewcvs/relax?rev=5335&view=rev
Log:
Updated the internal PDB structural object to use the self.structural_data
object.
The atomic_data structure has been replaced by self.structural_data, and is
no longer passed into
each method. The description of this object has also shifted from the
methods into the class
docstring.
Modified:
1.3/generic_fns/structure/internal_pdb.py
Modified: 1.3/generic_fns/structure/internal_pdb.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/internal_pdb.py?rev=5335&r1=5334&r2=5335&view=diff
==============================================================================
--- 1.3/generic_fns/structure/internal_pdb.py (original)
+++ 1.3/generic_fns/structure/internal_pdb.py Mon Apr 7 10:49:17 2008
@@ -26,36 +26,35 @@
class Internal_PDB(Str_object):
- """The internal relax PDB data object."""
+ """The internal relax PDB data object.
+
+ The structural data object for this class is a dictionary of arrays.
The keys correspond to the
+ 'atom_id' strings. The elements of the array are:
+
+ 0: Atom number.
+ 1: The record name (one of ATOM, HETATM, or TER).
+ 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.
+ """
# Identification string.
id = 'internal pdb'
- def atom_add(self, atomic_data=None, atom_id=None, record_name='',
atom_name='', res_name='', chain_id='', res_num=None, pos=[None, None, None],
segment_id='', element=''):
- """Function for adding an atom to the atomic_data structure.
-
- The 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: The record name (one of ATOM, HETATM, or TER).
- 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.
+ def atom_add(self, atom_id=None, record_name='', atom_name='',
res_name='', chain_id='', res_num=None, pos=[None, None, None],
segment_id='', element=''):
+ """Function for adding an atom to the structural data object.
This function will create the key-value pair for the given atom.
- @param atomic_data: The dictionary to place the atomic data into.
- @type atomic_data: dict
@param atom_id: The atom identifier. This is used as the key
within the dictionary.
@type atom_id: str
@param record_name: The record name, e.g. 'ATOM', 'HETATM', or 'TER'.
@@ -78,40 +77,24 @@
"""
# Initialise the key-value pair.
- atomic_data[atom_id] = []
+ self.structural_data[atom_id] = []
# Fill the positions.
- atomic_data[atom_id].append(len(atomic_data))
- atomic_data[atom_id].append(record_name)
- atomic_data[atom_id].append(atom_name)
- atomic_data[atom_id].append(res_name)
- atomic_data[atom_id].append(chain_id)
- atomic_data[atom_id].append(res_num)
- atomic_data[atom_id].append(pos[0])
- atomic_data[atom_id].append(pos[1])
- atomic_data[atom_id].append(pos[2])
- atomic_data[atom_id].append(segment_id)
- atomic_data[atom_id].append(element)
-
-
- def atom_connect(self, atomic_data=None, atom_id=None, bonded_id=None):
- """Function for connecting two atoms within the atomic_data data
structure.
-
- The 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: The record name (one of ATOM, HETATM, or TER).
- 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.
+ self.structural_data[atom_id].append(len(self.structural_data))
+ self.structural_data[atom_id].append(record_name)
+ self.structural_data[atom_id].append(atom_name)
+ self.structural_data[atom_id].append(res_name)
+ self.structural_data[atom_id].append(chain_id)
+ self.structural_data[atom_id].append(res_num)
+ self.structural_data[atom_id].append(pos[0])
+ self.structural_data[atom_id].append(pos[1])
+ self.structural_data[atom_id].append(pos[2])
+ self.structural_data[atom_id].append(segment_id)
+ self.structural_data[atom_id].append(element)
+
+
+ def atom_connect(self, atom_id=None, bonded_id=None):
+ """Function for connecting two atoms within the data structure
object.
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
@@ -119,8 +102,6 @@
bonded_id atom array as well.
- @param atomic_data: The dictionary to place the atomic data into.
- @type atomic_data: dict
@param atom_id: The atom identifier. This is used as the key
within the dictionary.
@type atom_id: str
@param bonded_id: The second atom identifier. This is used as the
key within the
@@ -129,22 +110,22 @@
"""
# Find the atom number corresponding to atom_id.
- if atomic_data.has_key(atom_id):
- atom_num = atomic_data[atom_id][0]
+ if self.structural_data.has_key(atom_id):
+ atom_num = self.structural_data[atom_id][0]
else:
raise RelaxError, "The atom corresponding to the atom_id " +
`atom_id` + " doesn't exist."
# Find the atom number corresponding to bonded_id.
- if atomic_data.has_key(bonded_id):
- bonded_num = atomic_data[bonded_id][0]
+ if self.structural_data.has_key(bonded_id):
+ bonded_num = self.structural_data[bonded_id][0]
else:
raise RelaxError, "The atom corresponding to the bonded_id " +
`bonded_id` + " doesn't exist."
# Add the bonded_id to the atom_id array.
- atomic_data[atom_id].append(bonded_num)
+ self.structural_data[atom_id].append(bonded_num)
# Add the atom_id to the bonded_id array.
- atomic_data[bonded_id].append(atom_num)
+ self.structural_data[bonded_id].append(atom_num)
def get_chemical_name(self, hetID):
@@ -201,11 +182,9 @@
raise RelaxError, "The residue ID (hetID) " + `hetID` + " is not
recognised."
- def terminate(self, atomic_data=None, atom_id_ext='', res_num=None):
- """Function for terminating the chain by adding a TER record to the
atomic_data object.
-
- @param atomic_data: The dictionary to place the atomic data into.
- @type atomic_data: dict
+ def terminate(self, atom_id_ext='', res_num=None):
+ """Function for terminating the chain by adding a TER record to the
structral data object.
+
@param atom_id_ext: The atom identifier extension.
@type atom_id_ext: str
@param res_num: The residue number.
@@ -213,15 +192,15 @@
"""
# The name of the last residue.
- atomic_arrays = atomic_data.values()
+ atomic_arrays = self.structural_data.values()
atomic_arrays.sort()
last_res = atomic_arrays[-1][3]
# Add the TER 'atom'.
- atom_add(atomic_data=atomic_data, atom_id='TER' + atom_id_ext,
record_name='TER', res_name=last_res, res_num=res_num)
-
-
- def write_pdb_file(self, atomic_data, file):
+ atom_add(atom_id='TER' + atom_id_ext, record_name='TER',
res_name=last_res, res_num=res_num)
+
+
+ def write_pdb_file(self, file):
"""Function for creating a PDB file from the given data.
Introduction
@@ -451,8 +430,6 @@
- @param atomic_data: The dictionary containing the atomic data.
- @type atomic_data: dict
@param file: The PDB file object. This object must be
writable.
@type file: file object
"""
@@ -460,8 +437,8 @@
# Sort the atoms.
#################
- # Convert the atomic_data structure from a dictionary of arrays to
an array of arrays and sort it by atom number.
- atomic_arrays = atomic_data.values()
+ # Convert the self.structural_data structure from a dictionary of
arrays to an array of arrays and sort it by atom number.
+ atomic_arrays = self.structural_data.values()
atomic_arrays.sort()
@@ -659,7 +636,7 @@
print "Creating the MASTER record."
# Write the MASTER record.
- file.write("%-6s %5s%5s%5s%5s%5s%5s%5s%5s%5s%5s%5s%5s\n" %
('MASTER', 0, 0, len(het_data), 0, 0, 0, 0, 0, len(atomic_data), 1,
connect_count, 0))
+ file.write("%-6s %5s%5s%5s%5s%5s%5s%5s%5s%5s%5s%5s%5s\n" %
('MASTER', 0, 0, len(het_data), 0, 0, 0, 0, 0, len(self.structural_data), 1,
connect_count, 0))
# END.
r5335 - /1.3/generic_fns/structure/internal_pdb.py