Author: bugman
Date: Wed Nov 15 09:20:34 2006
New Revision: 2848
URL: http://svn.gna.org/viewcvs/relax?rev=2848&view=rev
Log:
Renamed the 'pdb' user function class to 'structure'.
For full details, see the post at
https://mail.gna.org/public/relax-devel/2006-11/msg00081.html
(Message-id: <7f080ed10611062354i6c4c8601y825585c2c021b9ab@xxxxxxxxxxxxxx>).
Added:
1.3/generic_fns/structure.py
- copied, changed from r2847, 1.3/generic_fns/pdb.py
1.3/prompt/structure.py
- copied, changed from r2847, 1.3/prompt/pdb.py
Removed:
1.3/generic_fns/pdb.py
1.3/prompt/pdb.py
Modified:
1.3/generic_fns/main.py
1.3/prompt/interpreter.py
Modified: 1.3/generic_fns/main.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/main.py?rev=2848&r1=2847&r2=2848&view=diff
==============================================================================
--- 1.3/generic_fns/main.py (original)
+++ 1.3/generic_fns/main.py Wed Nov 15 09:20:34 2006
@@ -34,7 +34,7 @@
from monte_carlo import Monte_carlo
from nuclei import Nuclei
from palmer import Palmer
-from pdb import PDB
+from structure import Structure
from pymol import Pymol
from results import Results
from runs import Runs
@@ -67,7 +67,7 @@
self.nuclei = Nuclei(self.relax)
self.opendx = OpenDX(self.relax)
self.palmer = Palmer(self.relax)
- self.pdb = PDB(self.relax)
+ self.structure = Structure(self.relax)
self.pymol = Pymol(self.relax)
self.results = Results(self.relax)
self.runs = Runs(self.relax)
Copied: 1.3/generic_fns/structure.py (from r2847, 1.3/generic_fns/pdb.py)
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure.py?p2=1.3/generic_fns/structure.py&p1=1.3/generic_fns/pdb.py&r1=2847&r2=2848&rev=2848&view=diff
==============================================================================
--- 1.3/generic_fns/pdb.py (original)
+++ 1.3/generic_fns/structure.py Wed Nov 15 09:20:34 2006
@@ -28,7 +28,7 @@
from string import ascii_uppercase
-class PDB:
+class Structure:
def __init__(self, relax):
"""Class containing the PDB related functions."""
@@ -725,7 +725,7 @@
i = i + 1
- def read(self, run=None, file=None, dir=None, model=None, load_seq=1,
fail=1, print_flag=1):
+ def read_pdb(self, run=None, file=None, dir=None, model=None,
load_seq=1, fail=1, print_flag=1):
"""The pdb loading function."""
# Arguments.
Modified: 1.3/prompt/interpreter.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/interpreter.py?rev=2848&r1=2847&r2=2848&view=diff
==============================================================================
--- 1.3/prompt/interpreter.py (original)
+++ 1.3/prompt/interpreter.py Wed Nov 15 09:20:34 2006
@@ -58,7 +58,7 @@
from monte_carlo import Monte_carlo
from noe import Noe
from palmer import Palmer
-from pdb import PDB
+from structure import Structure
from pymol import Pymol
from relax_data import Relax_data
from relax_fit import Relax_fit
@@ -116,7 +116,7 @@
self._Monte_carlo = Monte_carlo(relax)
self._Noe = Noe(relax)
self._Palmer = Palmer(relax)
- self._PDB = PDB(relax)
+ self._Structure = Structure(relax)
self._Pymol = Pymol(relax)
self._Relax_data = Relax_data(relax)
self._Relax_fit = Relax_fit(relax)
@@ -174,7 +174,7 @@
monte_carlo = self._Monte_carlo
noe = self._Noe
palmer = self._Palmer
- pdb = self._PDB
+ structure = self._Structure
pymol = self._Pymol
relax_data = self._Relax_data
relax_fit = self._Relax_fit
Copied: 1.3/prompt/structure.py (from r2847, 1.3/prompt/pdb.py)
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/structure.py?p2=1.3/prompt/structure.py&p1=1.3/prompt/pdb.py&r1=2847&r2=2848&rev=2848&view=diff
==============================================================================
--- 1.3/prompt/pdb.py (original)
+++ 1.3/prompt/structure.py Wed Nov 15 09:20:34 2006
@@ -25,11 +25,11 @@
import help
-class PDB:
+class Structure:
def __init__(self, relax):
# Help.
self.__relax_help__ = \
- """Class containing the PDB related functions."""
+ """Class containing the structural related functions."""
# Add the generic help string.
self.__relax_help__ = self.__relax_help__ + "\n" +
help.relax_class_help
@@ -166,10 +166,10 @@
raise RelaxBinError, ('force flag', force)
# Execute the functional code.
- self.__relax__.generic.pdb.create_tensor_pdb(run=run, scale=scale,
file=file, dir=dir, force=force)
-
-
- def read(self, run=None, file=None, dir=None, model=None, load_seq=1):
+ self.__relax__.generic.structure.create_tensor_pdb(run=run,
scale=scale, file=file, dir=dir, force=force)
+
+
+ def read_pdb(self, run=None, file=None, dir=None, model=None,
load_seq=1):
"""The pdb loading function.
Keyword Arguments
@@ -216,7 +216,7 @@
# Function intro text.
if self.__relax__.interpreter.intro:
- text = sys.ps3 + "pdb.read("
+ text = sys.ps3 + "pdb.read_pdb("
text = text + "run=" + `run`
text = text + ", file=" + `file`
text = text + ", dir=" + `dir`
@@ -245,7 +245,7 @@
raise RelaxBinError, ('load sequence flag', load_seq)
# Execute the functional code.
- self.__relax__.generic.pdb.read(run=run, file=file, dir=dir,
model=model, load_seq=load_seq)
+ self.__relax__.generic.structure.read_pdb(run=run, file=file,
dir=dir, model=model, load_seq=load_seq)
def vectors(self, run=None, heteronuc='N', proton='H', res_num=None,
res_name=None):
@@ -330,4 +330,4 @@
raise RelaxNoneStrError, ('residue name', res_name)
# Execute the functional code.
- self.__relax__.generic.pdb.vectors(run=run, heteronuc=heteronuc,
proton=proton, res_num=res_num, res_name=res_name)
+ self.__relax__.generic.structure.vectors(run=run,
heteronuc=heteronuc, proton=proton, res_num=res_num, res_name=res_name)
r2848 - in /1.3: generic_fns/ prompt/