Renamed chemlab.data -> chemlab.db

chemlab · Apr 17, 2013 · 951cde4 · 951cde4
1 parent 16eb2a9
commit 951cde4
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Showing 34 changed files with 21 additions and 21 deletions.
diff --git a/chemlab/core/molecule.py b/chemlab/core/molecule.py
@@ -3,8 +3,8 @@
 import numpy as np
 from copy import copy
 
-from ..data import symbols
-from ..data import masses
+from ..db import symbols
+from ..db import masses
 
 
 class Atom(object):

diff --git a/chemlab/core/system.py b/chemlab/core/system.py
@@ -1,6 +1,6 @@
 import numpy as np
 from .molecule import Atom, Molecule
-from ..data import units, masses
+from ..db import units, masses
 from ..utils import overlapping_points
 
 from collections import namedtuple

diff --git a/chemlab/data/__init__.py → chemlab/db/__init__.py b/chemlab/data/__init__.py → chemlab/db/__init__.py
diff --git a/chemlab/data/base.py → chemlab/db/base.py b/chemlab/data/base.py → chemlab/db/base.py
diff --git a/chemlab/data/cirdb.py → chemlab/db/cirdb.py b/chemlab/data/cirdb.py → chemlab/db/cirdb.py
diff --git a/chemlab/data/covalent_radii.dat → chemlab/db/covalent_radii.dat b/chemlab/data/covalent_radii.dat → chemlab/db/covalent_radii.dat
diff --git a/chemlab/data/lj.py → chemlab/db/lj.py b/chemlab/data/lj.py → chemlab/db/lj.py
diff --git a/chemlab/data/local.py → chemlab/db/local.py b/chemlab/data/local.py → chemlab/db/local.py
diff --git a/chemlab/data/localdb/data/element.txt → chemlab/db/localdb/data/element.txt b/chemlab/data/localdb/data/element.txt → chemlab/db/localdb/data/element.txt
diff --git a/chemlab/data/localdb/molecule/gromacs.cl- → chemlab/db/localdb/molecule/gromacs.cl- b/chemlab/data/localdb/molecule/gromacs.cl- → chemlab/db/localdb/molecule/gromacs.cl-
diff --git a/chemlab/data/localdb/molecule/gromacs.li+ → chemlab/db/localdb/molecule/gromacs.li+ b/chemlab/data/localdb/molecule/gromacs.li+ → chemlab/db/localdb/molecule/gromacs.li+
diff --git a/chemlab/data/localdb/molecule/gromacs.na+ → chemlab/db/localdb/molecule/gromacs.na+ b/chemlab/data/localdb/molecule/gromacs.na+ → chemlab/db/localdb/molecule/gromacs.na+
diff --git a/chemlab/data/localdb/molecule/gromacs.spc → chemlab/db/localdb/molecule/gromacs.spc b/chemlab/data/localdb/molecule/gromacs.spc → chemlab/db/localdb/molecule/gromacs.spc
diff --git a/chemlab/data/localdb/molecule/gromacs.spce → chemlab/db/localdb/molecule/gromacs.spce b/chemlab/data/localdb/molecule/gromacs.spce → chemlab/db/localdb/molecule/gromacs.spce
diff --git a/chemlab/data/masses.py → chemlab/db/masses.py b/chemlab/data/masses.py → chemlab/db/masses.py
diff --git a/chemlab/data/moldb.py → chemlab/db/moldb.py b/chemlab/data/moldb.py → chemlab/db/moldb.py
diff --git a/chemlab/data/symbols.py → chemlab/db/symbols.py b/chemlab/data/symbols.py → chemlab/db/symbols.py
diff --git a/chemlab/data/units.py → chemlab/db/units.py b/chemlab/data/units.py → chemlab/db/units.py
diff --git a/chemlab/data/utils.py → chemlab/db/utils.py b/chemlab/data/utils.py → chemlab/db/utils.py
diff --git a/chemlab/data/vdw.py → chemlab/db/vdw.py b/chemlab/data/vdw.py → chemlab/db/vdw.py
diff --git a/chemlab/graphics/renderers/atom.py b/chemlab/graphics/renderers/atom.py
@@ -1,6 +1,6 @@
 import numpy as np
 from .. import colors
-from ...data.vdw import vdw_dict
+from ...db.vdw import vdw_dict
 from .base import AbstractRenderer
 from .sphere import SphereRenderer
 from .sphere_imp import SphereImpostorRenderer
@@ -33,7 +33,7 @@ class AtomRenderer(AbstractRenderer):
     
     radii_map: dict, should contain the 'Xx' key,value pair.
        A dictionary mapping atom types to radii. The default is the
-       mapping contained in `chemlab.data.vdw.vdw_dict`
+       mapping contained in `chemlab.db.vdw.vdw_dict`
     
     """
 

diff --git a/chemlab/graphics/renderers/ballandstick.py b/chemlab/graphics/renderers/ballandstick.py
@@ -2,7 +2,7 @@
 from .atom import AtomRenderer
 from .bond import BondRenderer
 
-from ...data import cdb
+from ...db import cdb
 
 class BallAndStickRenderer(AbstractRenderer):
     def __init__(self, widget, r_array, type_array, bonds):

diff --git a/chemlab/graphics/renderers/wireframe.py b/chemlab/graphics/renderers/wireframe.py
@@ -2,7 +2,7 @@
 from .atom import AtomRenderer
 from .bond import BondRenderer
 
-from ...data import cdb
+from ...db import cdb
 
 class WireframeRenderer(AbstractRenderer):
     def __init__(self, widget, r_array, type_array, bonds):

diff --git a/chemlab/io/handlers/gro.py b/chemlab/io/handlers/gro.py
@@ -6,7 +6,7 @@
 
 from ...core.system import System
 from ...core.molecule import Atom
-from ...data.symbols import symbol_list
+from ...db.symbols import symbol_list
 
 
 symbol_list = [s.lower() for s in symbol_list]

diff --git a/chemlab/io/handlers/pdb.py b/chemlab/io/handlers/pdb.py
@@ -2,7 +2,7 @@
 from .base import IOHandler
 from itertools import groupby
 import numpy as np
-from ...data import cdb
+from ...db import cdb
 
 symbols = cdb.get("symbols", "data")
 u_symbols = [s.upper() for s in symbols]

diff --git a/chemlab/molsim/integrators.py b/chemlab/molsim/integrators.py
@@ -1,4 +1,4 @@
-from chemlab.data import masses
+from chemlab.db import masses
 from chemlab.molsim import cforces2 as cforces
 
 def euler(r0, v0, a0, dt):

diff --git a/setup.py b/setup.py
@@ -27,7 +27,7 @@
     package_data = {'': ['distribute_setup.py', '*.rst', '*.txt'],
                     'chemlab.graphics.renderers.shaders': ['*.vert', '*.frag'],
                     'chemlab.resources' : ["*"],
-                    'chemlab.data' : ['*'],
+                    'chemlab.db' : ['*'],
                     'chemlab.core.spacegroup': ['*']},
 
     author = "Gabriele Lanaro",

diff --git a/tests/test_analysis.py b/tests/test_analysis.py
@@ -5,7 +5,7 @@
 import numpy as np
 from chemlab.core.spacegroup.crystal import crystal
 from chemlab.molsim.analysis import rdf, rdf_multi
-from chemlab.data import moldb
+from chemlab.db import moldb
 from chemlab.io import datafile
 from chemlab.graphics import display_system
 

diff --git a/tests/test_conservation.py b/tests/test_conservation.py
@@ -4,7 +4,7 @@
 from chemlab.graphics import display_system
 from chemlab.molsim.integrators import evolve_generator
 from chemlab.molsim import cenergy
-from chemlab.data.masses import typetomass
+from chemlab.db.masses import typetomass
 import pylab as pl
 import pyglet; pyglet.options['vsync'] = False
 

diff --git a/tests/test_core.py b/tests/test_core.py
@@ -89,7 +89,7 @@ def test_system():
 def test_merge_system():
     # take a protein
     from chemlab.io import datafile
-    from chemlab.data import moldb
+    from chemlab.db import moldb
     from chemlab.graphics import display_system
     from chemlab.core import merge_systems
 

diff --git a/tests/test_data.py b/tests/test_data.py
@@ -1,5 +1,5 @@
-from chemlab.data.cirdb import CirDB
-from chemlab.data.local import LocalDB
+from chemlab.db.cirdb import CirDB
+from chemlab.db.local import LocalDB
 from chemlab.graphics import display_molecule
 
 def test_cir():

diff --git a/tests/test_forces.py b/tests/test_forces.py
@@ -101,7 +101,7 @@ def update_pos():
     v.schedule(update_pos)
     v.run()
 
-from chemlab.data import lj
+from chemlab.db import lj
 
 def test_energy():
     '''This is made as a test to verify is the potential produced is

diff --git a/tests/test_graphics.py b/tests/test_graphics.py
@@ -147,7 +147,7 @@ def test_cylinder_renderer():
 
 def test_bond_renderer():
 
-    from chemlab.data.cirdb import CirDB
+    from chemlab.db.cirdb import CirDB
     from collections import defaultdict
 
     v = QtViewer()
@@ -173,7 +173,7 @@ def test_bond_renderer():
 
 def test_ball_and_stick_renderer():
     from collections import defaultdict
-    from chemlab.data.cirdb import CirDB
+    from chemlab.db.cirdb import CirDB
 
     v = QtViewer()
     v.widget.background_color = black
@@ -193,7 +193,7 @@ def test_ball_and_stick_renderer():
 
 def test_wireframe_renderer():
     from collections import defaultdict
-    from chemlab.data.cirdb import CirDB
+    from chemlab.db.cirdb import CirDB
 
     v = QtViewer()
     v.widget.background_color = black

diff --git a/tools/parse_forcefield.py b/tools/parse_forcefield.py
@@ -49,7 +49,7 @@ def parse(FILE):
             else:
                 print fields
 
-from chemlab.data import masses
+from chemlab.db import masses
 opls_to_type = {}
 # Parse atp file
 def parse_atp(file):