Author: bugman
Date: Mon Jan 12 14:14:46 2009
New Revision: 8407
URL: http://svn.gna.org/viewcvs/relax?rev=8407&view=rev
Log:
Shifted atom_add() and atom_connect() from the Internal class to the
MolContainer.
Modified:
branches/multi_structure/generic_fns/structure/internal.py
Modified: branches/multi_structure/generic_fns/structure/internal.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_structure/generic_fns/structure/internal.py?rev=8407&r1=8406&r2=8407&view=diff
==============================================================================
--- branches/multi_structure/generic_fns/structure/internal.py (original)
+++ branches/multi_structure/generic_fns/structure/internal.py Mon Jan 12
14:14:46 2009
@@ -544,86 +544,6 @@
# Check the other lengths.
if len(struct.bonded) != num and len(struct.chain_id) != num and
len(struct.element) != num and len(struct.pdb_record) != num and
len(struct.res_name) != num and len(struct.res_num) != num and
len(struct.seg_id) != num and len(struct.x) != num and len(struct.y) != num and
len(struct.z) != num:
raise RelaxError, "The structural data is invalid."
-
-
- def atom_add(self, pdb_record=None, atom_num=None, atom_name=None,
res_name=None, chain_id=None, res_num=None, pos=[None, None, None],
segment_id=None, element=None, struct_index=None):
- """Method for adding an atom to the structural data object.
-
- This method will create the key-value pair for the given atom.
-
-
- @keyword pdb_record: The optional PDB record name, e.g. 'ATOM' or
'HETATM'.
- @type pdb_record: str or None
- @keyword atom_num: The atom number.
- @type atom_num: int or None
- @keyword atom_name: The atom name, e.g. 'H1'.
- @type atom_name: str or None
- @keyword res_name: The residue name.
- @type res_name: str or None
- @keyword chain_id: The chain identifier.
- @type chain_id: str or None
- @keyword res_num: The residue number.
- @type res_num: int or None
- @keyword pos: The position vector of coordinates.
- @type pos: list (length = 3)
- @keyword segment_id: The segment identifier.
- @type segment_id: str or None
- @keyword element: The element symbol.
- @type element: str or None
- @keyword struct_index: The index of the structure to add the atom to.
If not supplied and
- multiple structures or models are loaded, then
the atom will be
- added to all structures.
- @type struct_index: None or int
- """
-
- # Loop over the structures.
- for i in xrange(self.num):
- # Skip non-matching structures.
- if struct_index != None and struct_index != i:
- continue
-
- # Append to all the arrays.
- self.structural_data[i].atom_num.append(atom_num)
- self.structural_data[i].atom_name.append(atom_name)
- self.structural_data[i].bonded.append([])
- self.structural_data[i].chain_id.append(chain_id)
- self.structural_data[i].element.append(element)
- self.structural_data[i].pdb_record.append(pdb_record)
- self.structural_data[i].res_name.append(res_name)
- self.structural_data[i].res_num.append(res_num)
- self.structural_data[i].seg_id.append(segment_id)
- self.structural_data[i].x.append(pos[0])
- self.structural_data[i].y.append(pos[1])
- self.structural_data[i].z.append(pos[2])
-
-
- def atom_connect(self, index1=None, index2=None, struct_index=None):
- """Method for connecting two atoms within the data structure object.
-
- This method will append index2 to the array at bonded[index1] and vice
versa.
-
-
- @keyword index1: The index of the first atom.
- @type index1: int
- @keyword index2: The index of the second atom.
- @type index2: int
- @keyword struct_index: The index of the structure to connect the
atoms of. If not supplied
- and multiple structures or models are loaded,
then the atoms will be
- connected within all structures.
- @type struct_index: None or int
- """
-
- # Loop over the structures.
- for i in xrange(self.num):
- # Skip non-matching structures.
- if struct_index != None and struct_index != i:
- continue
-
- # Update the bonded array structure, if necessary.
- if index2 not in self.structural_data[i].bonded[index1]:
- self.structural_data[i].bonded[index1].append(index2)
- if index1 not in self.structural_data[i].bonded[index2]:
- self.structural_data[i].bonded[index2].append(index1)
def atom_loop(self, atom_id=None, str_id=None, model_num_flag=False,
mol_name_flag=False, res_num_flag=False, res_name_flag=False,
atom_num_flag=False, atom_name_flag=False, element_flag=False, pos_flag=False,
ave=False):
@@ -1446,3 +1366,75 @@
# Make the connection.
self.atom_connect(index1=self.__atom_index(record[1],
struct_index), index2=self.__atom_index(record[i+2], struct_index))
+
+
+ def atom_add(self, pdb_record=None, atom_num=None, atom_name=None,
res_name=None, chain_id=None, res_num=None, pos=[None, None, None],
segment_id=None, element=None):
+ """Method for adding an atom to the structural data object.
+
+ This method will create the key-value pair for the given atom.
+
+
+ @keyword pdb_record: The optional PDB record name, e.g. 'ATOM' or
'HETATM'.
+ @type pdb_record: str or None
+ @keyword atom_num: The atom number.
+ @type atom_num: int or None
+ @keyword atom_name: The atom name, e.g. 'H1'.
+ @type atom_name: str or None
+ @keyword res_name: The residue name.
+ @type res_name: str or None
+ @keyword chain_id: The chain identifier.
+ @type chain_id: str or None
+ @keyword res_num: The residue number.
+ @type res_num: int or None
+ @keyword pos: The position vector of coordinates.
+ @type pos: list (length = 3)
+ @keyword segment_id: The segment identifier.
+ @type segment_id: str or None
+ @keyword element: The element symbol.
+ @type element: str or None
+ """
+
+ # Loop over the structures.
+ for i in xrange(self.num):
+ # Skip non-matching structures.
+ if struct_index != None and struct_index != i:
+ continue
+
+ # Append to all the arrays.
+ self.structural_data[i].atom_num.append(atom_num)
+ self.structural_data[i].atom_name.append(atom_name)
+ self.structural_data[i].bonded.append([])
+ self.structural_data[i].chain_id.append(chain_id)
+ self.structural_data[i].element.append(element)
+ self.structural_data[i].pdb_record.append(pdb_record)
+ self.structural_data[i].res_name.append(res_name)
+ self.structural_data[i].res_num.append(res_num)
+ self.structural_data[i].seg_id.append(segment_id)
+ self.structural_data[i].x.append(pos[0])
+ self.structural_data[i].y.append(pos[1])
+ self.structural_data[i].z.append(pos[2])
+
+
+ def atom_connect(self, index1=None, index2=None):
+ """Method for connecting two atoms within the data structure object.
+
+ This method will append index2 to the array at bonded[index1] and vice
versa.
+
+
+ @keyword index1: The index of the first atom.
+ @type index1: int
+ @keyword index2: The index of the second atom.
+ @type index2: int
+ """
+
+ # Loop over the structures.
+ for i in xrange(self.num):
+ # Skip non-matching structures.
+ if struct_index != None and struct_index != i:
+ continue
+
+ # Update the bonded array structure, if necessary.
+ if index2 not in self.structural_data[i].bonded[index1]:
+ self.structural_data[i].bonded[index1].append(index2)
+ if index1 not in self.structural_data[i].bonded[index2]:
+ self.structural_data[i].bonded[index2].append(index1)
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