Author: bugman
Date: Mon Mar 18 13:51:56 2013
New Revision: 18851
URL: http://svn.gna.org/viewcvs/relax?rev=18851&view=rev
Log:
The merge flag for the structure.read_pdb user function is now propaged to
the pack_structs() method.
This structure API method calls the ModelList.merge_item() method which is
yet to be implemented.
Modified:
trunk/generic_fns/structure/api_base.py
trunk/generic_fns/structure/internal.py
trunk/generic_fns/structure/main.py
trunk/generic_fns/structure/scientific.py
Modified: trunk/generic_fns/structure/api_base.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/generic_fns/structure/api_base.py?rev=18851&r1=18850&r2=18851&view=diff
==============================================================================
--- trunk/generic_fns/structure/api_base.py (original)
+++ trunk/generic_fns/structure/api_base.py Mon Mar 18 13:51:56 2013
@@ -351,7 +351,7 @@
raise RelaxImplementError
- def load_pdb(self, file_path, read_mol=None, set_mol_name=None,
read_model=None, set_model_num=None, alt_loc=None, verbosity=False):
+ def load_pdb(self, file_path, read_mol=None, set_mol_name=None,
read_model=None, set_model_num=None, alt_loc=None, verbosity=False,
merge=False):
"""Prototype method stub for loading structures from a PDB file.
This inherited prototype method is a stub which, if the
functionality is desired, should be overwritten by the derived class.
@@ -371,6 +371,8 @@
@type alt_loc: str or None
@keyword verbosity: A flag which if True will cause messages to
be printed.
@type verbosity: bool
+ @keyword merge: A flag which if set to True will try to
merge the PDB structure into the currently loaded structures.
+ @type merge: bool
@return: The status of the loading of the PDB file.
@rtype: bool
"""
@@ -477,7 +479,7 @@
return len(self.structural_data[0].mol)
- def pack_structs(self, data_matrix, orig_model_num=None,
set_model_num=None, orig_mol_num=None, set_mol_name=None, file_name=None,
file_path=None):
+ def pack_structs(self, data_matrix, orig_model_num=None,
set_model_num=None, orig_mol_num=None, set_mol_name=None, file_name=None,
file_path=None, merge=False):
"""From the given structural data, expand the structural data data
structure.
@param data_matrix: A matrix of structural objects.
@@ -490,11 +492,12 @@
@type orig_mol_num: list of int
@keyword set_mol_name: The new molecule names.
@type set_mol_name: list of str
- @keyword file_name: The name of the file from which the
molecular data has been
- extracted.
+ @keyword file_name: The name of the file from which the
molecular data has been extracted.
@type file_name: None or str
@keyword file_path: The full path to the file specified by
'file_name'.
@type file_path: None or str
+ @keyword merge: A flag which if set to True will try to
merge the structure into the currently loaded structures.
+ @type merge: bool
"""
# Test the number of models.
@@ -525,7 +528,7 @@
# Loop over the structures.
for j in range(len(self.structural_data[i].mol)):
- if self.structural_data[i].num in set_model_num and
self.structural_data[i].mol[j].mol_name in set_mol_name:
+ if not merge and self.structural_data[i].num in
set_model_num and self.structural_data[i].mol[j].mol_name in set_mol_name:
raise RelaxError("The molecule '%s' of model %s already
exists." % (self.structural_data[i].mol[j].mol_name,
self.structural_data[i].num))
# Loop over the models.
@@ -556,7 +559,10 @@
raise RelaxError("The new molecule name of '%s' in model
%s does not match the corresponding molecule's name of '%s' in model %s." %
(set_mol_name[j], set_model_num[i],
self.structural_data[0].mol[index].mol_name, self.structural_data[0].num))
# Pack the structures.
- model.mol.add_item(mol_name=set_mol_name[j],
mol_cont=data_matrix[i][j])
+ if merge:
+ mol = model.mol.merge_item(mol_name=set_mol_name[j],
mol_cont=data_matrix[i][j])
+ else:
+ model.mol.add_item(mol_name=set_mol_name[j],
mol_cont=data_matrix[i][j])
# Set the molecule name and store the structure file info.
model.mol[-1].mol_name = set_mol_name[j]
Modified: trunk/generic_fns/structure/internal.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/generic_fns/structure/internal.py?rev=18851&r1=18850&r2=18851&view=diff
==============================================================================
--- trunk/generic_fns/structure/internal.py (original)
+++ trunk/generic_fns/structure/internal.py Mon Mar 18 13:51:56 2013
@@ -1232,7 +1232,7 @@
return mol
- def load_pdb(self, file_path, read_mol=None, set_mol_name=None,
read_model=None, set_model_num=None, alt_loc=None, verbosity=False):
+ def load_pdb(self, file_path, read_mol=None, set_mol_name=None,
read_model=None, set_model_num=None, alt_loc=None, verbosity=False,
merge=False):
"""Method for loading structures from a PDB file.
@param file_path: The full path of the PDB file.
@@ -1249,6 +1249,8 @@
@type alt_loc: str or None
@keyword verbosity: A flag which if True will cause messages to
be printed.
@type verbosity: bool
+ @keyword merge: A flag which if set to True will try to
merge the PDB structure into the currently loaded structures.
+ @type merge: bool
@return: The status of the loading of the PDB file.
@rtype: bool
"""
@@ -1352,7 +1354,7 @@
return False
# Create the structural data data structures.
- self.pack_structs(mol_conts, orig_model_num=orig_model_num,
set_model_num=set_model_num, orig_mol_num=orig_mol_num,
set_mol_name=new_mol_name, file_name=file, file_path=path)
+ self.pack_structs(mol_conts, orig_model_num=orig_model_num,
set_model_num=set_model_num, orig_mol_num=orig_mol_num,
set_mol_name=new_mol_name, file_name=file, file_path=path, merge=merge)
# Loading worked.
return True
Modified: trunk/generic_fns/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/generic_fns/structure/main.py?rev=18851&r1=18850&r2=18851&view=diff
==============================================================================
--- trunk/generic_fns/structure/main.py (original)
+++ trunk/generic_fns/structure/main.py Mon Mar 18 13:51:56 2013
@@ -559,7 +559,7 @@
cdp.structure = Internal()
# Load the structures.
- cdp.structure.load_pdb(file_path, read_mol=read_mol,
set_mol_name=set_mol_name, read_model=read_model,
set_model_num=set_model_num, alt_loc=alt_loc, verbosity=verbosity)
+ cdp.structure.load_pdb(file_path, read_mol=read_mol,
set_mol_name=set_mol_name, read_model=read_model,
set_model_num=set_model_num, alt_loc=alt_loc, verbosity=verbosity,
merge=merge)
# Load into Molmol (if running).
molmol.molmol_obj.open_pdb()
Modified: trunk/generic_fns/structure/scientific.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/generic_fns/structure/scientific.py?rev=18851&r1=18850&r2=18851&view=diff
==============================================================================
--- trunk/generic_fns/structure/scientific.py (original)
+++ trunk/generic_fns/structure/scientific.py Mon Mar 18 13:51:56 2013
@@ -529,7 +529,7 @@
return mol
- def load_pdb(self, file_path, read_mol=None, set_mol_name=None,
read_model=None, set_model_num=None, alt_loc=None, verbosity=False):
+ def load_pdb(self, file_path, read_mol=None, set_mol_name=None,
read_model=None, set_model_num=None, alt_loc=None, verbosity=False,
merge=False):
"""Function for loading the structures from the PDB file.
@param file_path: The full path of the file.
@@ -546,6 +546,8 @@
@type alt_loc: str or None
@keyword verbosity: A flag which if True will cause messages to
be printed.
@type verbosity: bool
+ @keyword merge: A flag which if set to True will try to
merge the PDB structure into the currently loaded structures.
+ @type merge: bool
@return: The status of the loading of the PDB file.
@rtype: bool
"""
@@ -693,7 +695,7 @@
model_load_num = model_load_num + 1
# Create the structural data data structures.
- self.pack_structs(mol_conts, orig_model_num=orig_model_num,
set_model_num=set_model_num, orig_mol_num=list(range(1,
len(mol_conts[0])+1)), set_mol_name=new_mol_name, file_name=file,
file_path=path)
+ self.pack_structs(mol_conts, orig_model_num=orig_model_num,
set_model_num=set_model_num, orig_mol_num=list(range(1,
len(mol_conts[0])+1)), set_mol_name=new_mol_name, file_name=file,
file_path=path, merge=merge)
# Loading worked.
return True
r18851 - in /trunk/generic_fns/structure: api_base.py internal.py main.py scientific.py