diff options
| author | Eric Messick <ericm@nanorex.com> | 2008-03-11 04:37:52 +0000 |
|---|---|---|
| committer | Eric Messick <ericm@nanorex.com> | 2008-03-11 04:37:52 +0000 |
| commit | 2b4377c7b0499c5d056541e6429dc02b972196da (patch) | |
| tree | 42c2e0061d8afcc6b626ef57b565726951a9c0d5 /cad | |
| parent | e8d1e252aacc540b3abcac66bef174136a4bff70 (diff) | |
| download | nanoengineer-theirix-2b4377c7b0499c5d056541e6429dc02b972196da.tar.gz nanoengineer-theirix-2b4377c7b0499c5d056541e6429dc02b972196da.zip | |
move files into history, model, model_updater, modelTree, ne1_startup, ne1_ui
Diffstat (limited to 'cad')
199 files changed, 425 insertions, 422 deletions
diff --git a/cad/src/DebugMenuMixin.py b/cad/src/DebugMenuMixin.py index 25a418383..795705a75 100644 --- a/cad/src/DebugMenuMixin.py +++ b/cad/src/DebugMenuMixin.py @@ -36,7 +36,7 @@ from utilities import debug_flags import debug import debug_prefs -from UserPrefs import save_window_pos_size, load_window_pos_size +from ne1_ui.UserPrefs import save_window_pos_size, load_window_pos_size from prefs_constants import mainwindow_geometry_prefs_key_prefix from debug import registered_commands_menuspec from debug import print_compact_traceback diff --git a/cad/src/PM/PM_MolecularModelingKit.py b/cad/src/PM/PM_MolecularModelingKit.py index a3c44e964..57e705e77 100644 --- a/cad/src/PM/PM_MolecularModelingKit.py +++ b/cad/src/PM/PM_MolecularModelingKit.py @@ -7,7 +7,7 @@ PM_MolecularModelingKit.py """
-from elements import PeriodicTable
+from model.elements import PeriodicTable
from PyQt4.Qt import SIGNAL
from PM.PM_GroupBox import PM_GroupBox
diff --git a/cad/src/analysis/ESP/ESPImage.py b/cad/src/analysis/ESP/ESPImage.py index 806d5b497..12166898d 100755 --- a/cad/src/analysis/ESP/ESPImage.py +++ b/cad/src/analysis/ESP/ESPImage.py @@ -63,8 +63,8 @@ import foundation.env as env from utilities import debug_flags from foundation.state_utils import DataMixin -from chunk import Chunk -from chem import Atom +from model.chunk import Chunk +from model.chem import Atom from graphics.drawing.drawer import drawPlane from graphics.drawing.drawer import drawwirecube @@ -77,7 +77,7 @@ from geometry.Slab import Slab from utilities.Log import redmsg, greenmsg from debug_prefs import debug_pref, Choice_boolean_False -from jigs import Jig # REVIEW: all uses of this are suspicious! +from model.jigs import Jig # REVIEW: all uses of this are suspicious! from graphics.images.ImageUtils import nEImageOps from constants import black @@ -86,8 +86,8 @@ from constants import green from constants import START_NEW_SELECTION from constants import SUBTRACT_FROM_SELECTION -from jigs_planes import RectGadget -from jigs_planes import povStrVec +from model.jigs_planes import RectGadget +from model.jigs_planes import povStrVec from analysis.ESP.ESPImageProp import ESPImageProp from PlatformDependent import find_or_make_Nanorex_subdir diff --git a/cad/src/analysis/ESP/NanoHive.py b/cad/src/analysis/ESP/NanoHive.py index 87df49579..d1060f1f0 100755 --- a/cad/src/analysis/ESP/NanoHive.py +++ b/cad/src/analysis/ESP/NanoHive.py @@ -73,7 +73,7 @@ class NanoHive(QWidget, Ui_NanoHiveDialog): # This is where What's This descriptions should go for the Nano-Hive dialog. # Mark 050831. - from gui.WhatsThisText_for_MainWindow import create_whats_this_descriptions_for_NanoHive_dialog + from ne1_ui.WhatsThisText_for_MainWindow import create_whats_this_descriptions_for_NanoHive_dialog create_whats_this_descriptions_for_NanoHive_dialog(self) return diff --git a/cad/src/analysis/GAMESS/GamessJob.py b/cad/src/analysis/GAMESS/GamessJob.py index d2ce650b7..2640856d3 100755 --- a/cad/src/analysis/GAMESS/GamessJob.py +++ b/cad/src/analysis/GAMESS/GamessJob.py @@ -43,7 +43,7 @@ from icon_utilities import geticon from ServerManager import ServerManager ## from PlatformDependent import open_file_in_editor from debug import print_compact_traceback -from UserPrefs import get_filename_and_save_in_prefs +from ne1_ui.UserPrefs import get_filename_and_save_in_prefs from PlatformDependent import hhmmss_str from prefs_constants import gmspath_prefs_key diff --git a/cad/src/analysis/GAMESS/files_gms.py b/cad/src/analysis/GAMESS/files_gms.py index b6ff21d82..e1a03f7a9 100755 --- a/cad/src/analysis/GAMESS/files_gms.py +++ b/cad/src/analysis/GAMESS/files_gms.py @@ -13,10 +13,10 @@ to make it more modular and consistent. """ import os, re, time -from chunk import Chunk -from chem import Atom +from model.chunk import Chunk +from model.chem import Atom from string import capitalize -from elements import PeriodicTable +from model.elements import PeriodicTable from PlatformDependent import get_gms_name from utilities.Log import redmsg, orangemsg from geometry.VQT import A diff --git a/cad/src/analysis/GAMESS/jig_Gamess.py b/cad/src/analysis/GAMESS/jig_Gamess.py index b0b8729be..17f22d8b8 100755 --- a/cad/src/analysis/GAMESS/jig_Gamess.py +++ b/cad/src/analysis/GAMESS/jig_Gamess.py @@ -9,14 +9,14 @@ jig_Gamess.py import sys -from jigs import Jig +from model.jigs import Jig from graphics.drawing.drawer import drawwirecube from graphics.rendering.povray.povheader import povpoint # Fix for bug 692 Mark 050628 from analysis.GAMESS.files_gms import get_energy_from_gms_outfile, get_atompos_from_gms_outfile from utilities.Log import redmsg, greenmsg import foundation.env as env from utilities.Log import redmsg -from chem import move_alist_and_snuggle +from model.chem import move_alist_and_snuggle import foundation.state_utils as state_utils from debug import print_compact_traceback diff --git a/cad/src/bond_chains.py b/cad/src/bond_chains.py index 209109d1e..0f8465f9b 100644 --- a/cad/src/bond_chains.py +++ b/cad/src/bond_chains.py @@ -9,12 +9,12 @@ bond_chains.py -- helper functions related to chains of bonds @copyright: 2007-2008 Nanorex, Inc. See LICENSE file for details. """ -from bond_constants import DIRBOND_CHAIN_MIDDLE -from bond_constants import DIRBOND_CHAIN_END -from bond_constants import DIRBOND_NONE -from bond_constants import DIRBOND_ERROR +from model.bond_constants import DIRBOND_CHAIN_MIDDLE +from model.bond_constants import DIRBOND_CHAIN_END +from model.bond_constants import DIRBOND_NONE +from model.bond_constants import DIRBOND_ERROR -from bond_constants import find_bond +from model.bond_constants import find_bond def grow_bond_chain(bond, atom, next_bond_in_chain): #bruce 070415; generalized from grow_pi_sp_chain """ diff --git a/cad/src/bond_utils.py b/cad/src/bond_utils.py index 5914a8152..cc2e07d06 100755 --- a/cad/src/bond_utils.py +++ b/cad/src/bond_utils.py @@ -19,10 +19,10 @@ import foundation.env as env from utilities.Log import greenmsg, redmsg, orangemsg, quote_html from debug import print_compact_stack -from bond_constants import bonded_atoms_summary -from bond_constants import btype_from_v6 -from bond_constants import v6_from_btype -from bond_constants import bond_left_atom +from model.bond_constants import bonded_atoms_summary +from model.bond_constants import btype_from_v6 +from model.bond_constants import v6_from_btype +from model.bond_constants import bond_left_atom def intersect_sequences(s1, s2): """ diff --git a/cad/src/bonds_from_atoms.py b/cad/src/bonds_from_atoms.py index 13e2414db..a9114430d 100755 --- a/cad/src/bonds_from_atoms.py +++ b/cad/src/bonds_from_atoms.py @@ -38,11 +38,11 @@ from geometry.VQT import atom_angle_radians import foundation.env as env -from bonds import bond_atoms_faster, NeighborhoodGenerator +from model.bonds import bond_atoms_faster, NeighborhoodGenerator -from bond_constants import atoms_are_bonded # was: from bonds import bonded -from bond_constants import V_SINGLE -from bond_constants import bond_params +from model.bond_constants import atoms_are_bonded # was: from bonds import bonded +from model.bond_constants import V_SINGLE +from model.bond_constants import bond_params # constants; angles are in radians diff --git a/cad/src/cnt/commands/BuildCnt/BuildCnt_EditCommand.py b/cad/src/cnt/commands/BuildCnt/BuildCnt_EditCommand.py index be09f149d..968f984db 100644 --- a/cad/src/cnt/commands/BuildCnt/BuildCnt_EditCommand.py +++ b/cad/src/cnt/commands/BuildCnt/BuildCnt_EditCommand.py @@ -28,11 +28,11 @@ from command_support.GeneratorBaseClass import PluginBug, UserError from constants import gensym -from Ui_CntFlyout import CntFlyout +from ne1_ui.toolbars.Ui_CntFlyout import CntFlyout -from chem import Atom -from chunk import Chunk -from bonds import Bond +from model.chem import Atom +from model.chunk import Chunk +from model.bonds import Bond ##from SelectChunks_GraphicsMode import SelectChunks_GraphicsMode diff --git a/cad/src/cnt/commands/CntSegment/CntSegment_EditCommand.py b/cad/src/cnt/commands/CntSegment/CntSegment_EditCommand.py index d11f336e4..0a1f66ede 100644 --- a/cad/src/cnt/commands/CntSegment/CntSegment_EditCommand.py +++ b/cad/src/cnt/commands/CntSegment/CntSegment_EditCommand.py @@ -60,9 +60,9 @@ from exprs.Exprs import norm_Expr from prefs_widgets import ObjAttr_StateRef from exprs.ExprsConstants import Width, Point -from chunk import Chunk -from chem import Atom -from bonds import Bond +from model.chunk import Chunk +from model.chem import Atom +from model.bonds import Bond from cnt.commands.CntSegment.CntSegment_ResizeHandle import CntSegment_ResizeHandle diff --git a/cad/src/cnt/commands/CntSegment/CntSegment_GraphicsMode.py b/cad/src/cnt/commands/CntSegment/CntSegment_GraphicsMode.py index 6f3dc3931..7ada4feed 100644 --- a/cad/src/cnt/commands/CntSegment/CntSegment_GraphicsMode.py +++ b/cad/src/cnt/commands/CntSegment/CntSegment_GraphicsMode.py @@ -14,7 +14,7 @@ While in this command, user can @author: Ninad, Mark @copyright: 2008 Nanorex, Inc. See LICENSE file for details. -@version:$Id:$ +@version:$Id$ History: Created 2008-03-10 from copy of DnaSegment_GraphicsMode.py @@ -52,8 +52,8 @@ from debug import print_compact_traceback from commands.Select.Select_GraphicsMode import DRAG_STICKINESS_LIMIT -from chem import Atom -from bonds import Bond +from model.chem import Atom +from model.bonds import Bond SPHERE_RADIUS = 2.0 SPHERE_DRAWLEVEL = 2 diff --git a/cad/src/cnt/commands/InsertCnt/InsertCnt_PropertyManager.py b/cad/src/cnt/commands/InsertCnt/InsertCnt_PropertyManager.py index bc05ca602..6a83f3e00 100644 --- a/cad/src/cnt/commands/InsertCnt/InsertCnt_PropertyManager.py +++ b/cad/src/cnt/commands/InsertCnt/InsertCnt_PropertyManager.py @@ -40,7 +40,7 @@ from PM.PM_Constants import pmWhatsThisButton from PM.PM_Constants import pmCancelButton from PM.PM_Constants import pmPreviewButton -from bonds import CC_GRAPHITIC_BONDLENGTH, BN_GRAPHITIC_BONDLENGTH +from model.bonds import CC_GRAPHITIC_BONDLENGTH, BN_GRAPHITIC_BONDLENGTH #@from gui.WhatsThisText_for_PropertyManagers import whatsThis_InsertCnt_PropertyManager diff --git a/cad/src/cnt/model/CntGroup.py b/cad/src/cnt/model/CntGroup.py index 7626e9784..9c9e82d2b 100644 --- a/cad/src/cnt/model/CntGroup.py +++ b/cad/src/cnt/model/CntGroup.py @@ -8,7 +8,7 @@ CntGroup.py - ... """ from dna.model.Block import Block -from chunk import Chunk +from model.chunk import Chunk from constants import gensym diff --git a/cad/src/cnt/model/CntLadderRailChunk.py b/cad/src/cnt/model/CntLadderRailChunk.py index 6e17c47f6..193cc1ce7 100644 --- a/cad/src/cnt/model/CntLadderRailChunk.py +++ b/cad/src/cnt/model/CntLadderRailChunk.py @@ -7,7 +7,7 @@ CntLadderRailChunk.py - @copyright: 2007-2008 Nanorex, Inc. See LICENSE file for details. """ -from chunk import Chunk +from model.chunk import Chunk from constants import gensym from constants import black @@ -22,7 +22,7 @@ def _DEBUG_REUSE_CHUNKS(): import foundation.env as env from utilities.Log import orangemsg, graymsg -from elements import Singlet +from model.elements import Singlet # see also: ## from cnt_model.CntLadder import _rail_end_atom_to_ladder diff --git a/cad/src/cnt/model/CntSegment.py b/cad/src/cnt/model/CntSegment.py index 1e4816db0..d49ae8c9a 100644 --- a/cad/src/cnt/model/CntSegment.py +++ b/cad/src/cnt/model/CntSegment.py @@ -11,9 +11,9 @@ from cnt.model.CntStrandOrSegment import CntStrandOrSegment from cnt.model.CntLadderRailChunk import CntAxisChunk from debug import print_compact_stack, print_compact_traceback -from chunk import Chunk -from chem import Atom -from bonds import Bond +from model.chunk import Chunk +from model.chem import Atom +from model.bonds import Bond from geometry.VQT import V, norm, vlen from cnt.model.Cnt_Constants import getCntRiseFromNumberOfCells diff --git a/cad/src/cnt/updater/cnt_updater_globals.py b/cad/src/cnt/updater/cnt_updater_globals.py index bf65a967d..6b433837a 100644 --- a/cad/src/cnt/updater/cnt_updater_globals.py +++ b/cad/src/cnt/updater/cnt_updater_globals.py @@ -13,7 +13,7 @@ from utilities import debug_flags from foundation.changedicts import refreshing_changedict_subscription from foundation.changedicts import _cdproc_for_dictid # but it's private! -from chem import _changed_structure_Atoms, _changed_parent_Atoms # but they're private! refactor sometime +from model.chem import _changed_structure_Atoms, _changed_parent_Atoms # but they're private! refactor sometime from debug import print_compact_stack diff --git a/cad/src/commandSequencer/CommandSequencer.py b/cad/src/commandSequencer/CommandSequencer.py index d4ff44684..879ec2635 100644 --- a/cad/src/commandSequencer/CommandSequencer.py +++ b/cad/src/commandSequencer/CommandSequencer.py @@ -310,7 +310,7 @@ class modeMixin(object): Exception if requested mode object is not found -- unlike pre-050911 code, never return some other mode than asked for -- let caller do that if desired. """ - import UserPrefs #bruce 060403 + import ne1_ui.UserPrefs as UserPrefs #bruce 060403 assert commandName_or_obj, "mode arg should be a mode object or mode name, not None or whatever it is here: %r" % (commandName_or_obj,) if type(commandName_or_obj) == type(''): # usual case - internal or symbolic commandName string diff --git a/cad/src/commandToolbar/CommandToolbar.py b/cad/src/commandToolbar/CommandToolbar.py index d6ac8d20b..d1383c5ad 100755 --- a/cad/src/commandToolbar/CommandToolbar.py +++ b/cad/src/commandToolbar/CommandToolbar.py @@ -81,7 +81,7 @@ from PyQt4.Qt import Qt from PyQt4.Qt import SIGNAL from PyQt4.Qt import QToolButton -from Ui_CommandToolbar import Ui_CommandToolbar +from ne1_ui.toolbars.Ui_CommandToolbar import Ui_CommandToolbar from debug import print_compact_traceback class CommandToolbar(Ui_CommandToolbar): diff --git a/cad/src/command_support/Command.py b/cad/src/command_support/Command.py index 2cf25a79a..cc7a8d7b9 100755 --- a/cad/src/command_support/Command.py +++ b/cad/src/command_support/Command.py @@ -41,7 +41,7 @@ from foundation.state_utils import StateMixin from constants import noop, GLPANE_IS_COMMAND_SEQUENCER -from jigs import Jig +from model.jigs import Jig # this is used only for cmenu making # TODO: probably it should be factored into a method on the object being tested @@ -949,7 +949,7 @@ class basicCommand(anyCommand): # This shows the Done button on the dashboard unless the current command is the # Default command. Resolves bug #958 and #959. Mark 050922. - import UserPrefs + import ne1_ui.UserPrefs as UserPrefs if self.commandName == UserPrefs.default_commandName(): #bruce 060403 revised this self.w.toolsDoneAction.setVisible(0) else: diff --git a/cad/src/command_support/GraphicsMode.py b/cad/src/command_support/GraphicsMode.py index f834835bc..d0a992e60 100755 --- a/cad/src/command_support/GraphicsMode.py +++ b/cad/src/command_support/GraphicsMode.py @@ -46,8 +46,8 @@ from prefs_constants import displayOriginAxis_prefs_key from prefs_constants import displayOriginAsSmallAxis_prefs_key from prefs_constants import displayPOVAxis_prefs_key -from chem import Atom -from bonds import Bond +from model.chem import Atom +from model.bonds import Bond from foundation.Utility import Node from foundation.Group import Group diff --git a/cad/src/commands/BuildAtom/AtomGenerator.py b/cad/src/commands/BuildAtom/AtomGenerator.py index ea91fa2c2..ebd224529 100755 --- a/cad/src/commands/BuildAtom/AtomGenerator.py +++ b/cad/src/commands/BuildAtom/AtomGenerator.py @@ -23,10 +23,10 @@ Mark 2007-07-25: Uses new PM module. from utilities import debug_flags import foundation.env as env -from chem import Atom -from chunk import Chunk +from model.chem import Atom +from model.chunk import Chunk from geometry.VQT import V -from elements import PeriodicTable +from model.elements import PeriodicTable from utilities.Log import greenmsg from commands.BuildAtom.AtomGeneratorPropertyManager import AtomGeneratorPropertyManager diff --git a/cad/src/commands/BuildAtoms/BuildAtomsPropertyManager.py b/cad/src/commands/BuildAtoms/BuildAtomsPropertyManager.py index 0cbbba8e4..69a083e75 100644 --- a/cad/src/commands/BuildAtoms/BuildAtomsPropertyManager.py +++ b/cad/src/commands/BuildAtoms/BuildAtomsPropertyManager.py @@ -24,7 +24,7 @@ import foundation.env as env from PyQt4.Qt import SIGNAL from commands.BuildAtoms.Ui_BuildAtomsPropertyManager import Ui_BuildAtomsPropertyManager -from bond_constants import btype_from_v6 +from model.bond_constants import btype_from_v6 from geometry.VQT import V from utilities.Comparison import same_vals diff --git a/cad/src/commands/BuildAtoms/BuildAtoms_Command.py b/cad/src/commands/BuildAtoms/BuildAtoms_Command.py index 717ce62ab..1e6bc0ae6 100755 --- a/cad/src/commands/BuildAtoms/BuildAtoms_Command.py +++ b/cad/src/commands/BuildAtoms/BuildAtoms_Command.py @@ -1006,7 +1006,7 @@ class BuildAtoms_basicCommand(SelectAtoms_basicCommand): return self.propMgr.elementChooser.getElement() else: # we're presumably a subclass with no propMgr or a different one - from elements import Carbon + from model.elements import Carbon return Carbon def pastable_atomtype(self): diff --git a/cad/src/commands/BuildAtoms/BuildAtoms_GraphicsMode.py b/cad/src/commands/BuildAtoms/BuildAtoms_GraphicsMode.py index 7cae4f80e..8da6ac18c 100755 --- a/cad/src/commands/BuildAtoms/BuildAtoms_GraphicsMode.py +++ b/cad/src/commands/BuildAtoms/BuildAtoms_GraphicsMode.py @@ -61,10 +61,10 @@ from utilities import debug_flags from PlatformDependent import fix_plurals -from chunk import Chunk -from chem import Atom -from chem import oneUnbonded -from elements import Singlet +from model.chunk import Chunk +from model.chem import Atom +from model.chem import oneUnbonded +from model.elements import Singlet from geometry.VQT import Q, A, norm, twistor from graphics.drawing.drawer import drawline @@ -74,8 +74,8 @@ from foundation.Utility import Node from commands.Select.Select_GraphicsMode import DRAG_STICKINESS_LIMIT from graphics.behaviors.shape import get_selCurve_color -from bonds import bond_atoms, bond_at_singlets -from bond_constants import V_SINGLE +from model.bonds import bond_atoms, bond_at_singlets +from model.bond_constants import V_SINGLE from debug import print_compact_stack @@ -83,11 +83,11 @@ from constants import elemKeyTab from constants import diINVISIBLE from constants import diTUBES -from bond_constants import btype_from_v6 -from bond_constants import V_DOUBLE -from bond_constants import V_GRAPHITE -from bond_constants import V_TRIPLE -from bond_constants import V_AROMATIC +from model.bond_constants import btype_from_v6 +from model.bond_constants import V_DOUBLE +from model.bond_constants import V_GRAPHITE +from model.bond_constants import V_TRIPLE +from model.bond_constants import V_AROMATIC from prefs_constants import buildModeSelectAtomsOfDepositedObjEnabled_prefs_key from prefs_constants import buildModeWaterEnabled_prefs_key diff --git a/cad/src/commands/BuildAtoms/Ui_BuildAtomsPropertyManager.py b/cad/src/commands/BuildAtoms/Ui_BuildAtomsPropertyManager.py index cf66fe7d0..99721fff3 100644 --- a/cad/src/commands/BuildAtoms/Ui_BuildAtomsPropertyManager.py +++ b/cad/src/commands/BuildAtoms/Ui_BuildAtomsPropertyManager.py @@ -368,14 +368,14 @@ class Ui_BuildAtomsPropertyManager(PM_Dialog): """ "What's This" text for widgets in this Property Manager. """ - from gui.WhatsThisText_for_PropertyManagers import whatsThis_BuildAtomsPropertyManager + from ne1_ui.WhatsThisText_for_PropertyManagers import whatsThis_BuildAtomsPropertyManager whatsThis_BuildAtomsPropertyManager(self) def _addToolTipText(self): """ Tool Tip text for widgets in this Property Manager. """ - from gui.ToolTipText_for_PropertyManagers import ToolTip_BuildAtomsPropertyManager + from ne1_ui.ToolTipText_for_PropertyManagers import ToolTip_BuildAtomsPropertyManager ToolTip_BuildAtomsPropertyManager(self) def toggle_selectedAtomPosGroupBox(self, show = 0): diff --git a/cad/src/commands/BuildAtoms/build_utils.py b/cad/src/commands/BuildAtoms/build_utils.py index a8795c808..59a2a3093 100755 --- a/cad/src/commands/BuildAtoms/build_utils.py +++ b/cad/src/commands/BuildAtoms/build_utils.py @@ -17,7 +17,7 @@ with new bonding patterns. And did some of that extension, 050511. """ from geometry.VQT import norm -from chem import Atom +from model.chem import Atom from debug import print_compact_traceback diff --git a/cad/src/commands/BuildCrystal/CookieShape.py b/cad/src/commands/BuildCrystal/CookieShape.py index 4f8aa69a2..6262a8d5c 100755 --- a/cad/src/commands/BuildCrystal/CookieShape.py +++ b/cad/src/commands/BuildCrystal/CookieShape.py @@ -848,8 +848,8 @@ class CookieShape(shape): Build Chunk for the cookies. First, combine bonds from all layers together, which may fuse some half bonds to full bonds. """ - from chunk import Chunk - from chem import Atom + from model.chunk import Chunk + from model.chem import Atom from constants import gensym numLayers = len(self.bondLayers) diff --git a/cad/src/commands/BuildCrystal/Ui_CookiePropertyManager.py b/cad/src/commands/BuildCrystal/Ui_CookiePropertyManager.py index 18cdd43dc..a5d3e1489 100755 --- a/cad/src/commands/BuildCrystal/Ui_CookiePropertyManager.py +++ b/cad/src/commands/BuildCrystal/Ui_CookiePropertyManager.py @@ -328,14 +328,14 @@ class Ui_CookiePropertyManager(PM_Dialog): @note: Many PM widgets are still missing their "What's This" text. """ - from gui.WhatsThisText_for_PropertyManagers import whatsThis_CookiePropertyManager + from ne1_ui.WhatsThisText_for_PropertyManagers import whatsThis_CookiePropertyManager whatsThis_CookiePropertyManager(self) def _addToolTipText(self): """ What's Tool Tip text for widgets in this Property Manager. """ - from gui.ToolTipText_for_PropertyManagers import ToolTip_CookiePropertyManager + from ne1_ui.ToolTipText_for_PropertyManagers import ToolTip_CookiePropertyManager ToolTip_CookiePropertyManager(self)
\ No newline at end of file diff --git a/cad/src/commands/BuildCrystal/cookieMode.py b/cad/src/commands/BuildCrystal/cookieMode.py index 9764627e6..bfdf7c8f6 100755 --- a/cad/src/commands/BuildCrystal/cookieMode.py +++ b/cad/src/commands/BuildCrystal/cookieMode.py @@ -45,8 +45,8 @@ from commands.BuildCrystal.CookieShape import CookieShape import graphics.drawing.drawer as drawer from graphics.drawing.drawer import DiGridSp from graphics.drawing.drawer import genDiam -from chunk import Chunk -from chem import Atom +from model.chunk import Chunk +from model.chem import Atom from constants import gensym from constants import diTUBES diff --git a/cad/src/commands/CommentProperties/CommentProp.py b/cad/src/commands/CommentProperties/CommentProp.py index 6a02d0088..99ca76fda 100755 --- a/cad/src/commands/CommentProperties/CommentProp.py +++ b/cad/src/commands/CommentProperties/CommentProp.py @@ -13,7 +13,7 @@ History: __author__ = "Mark" from PyQt4.Qt import QDialog, QTextEdit, SIGNAL -from Comment import Comment +from model.Comment import Comment from commands.CommentProperties.CommentPropDialog import Ui_CommentPropDialog import time import foundation.env as env diff --git a/cad/src/commands/ElementColors/elementColors.py b/cad/src/commands/ElementColors/elementColors.py index 3ed3413be..a649f476a 100755 --- a/cad/src/commands/ElementColors/elementColors.py +++ b/cad/src/commands/ElementColors/elementColors.py @@ -15,7 +15,7 @@ from PyQt4.Qt import QApplication from PyQt4.Qt import QGLFormat from commands.ElementColors.ElementColorsDialog import Ui_ElementColorsDialog -from elements import PeriodicTable +from model.elements import PeriodicTable from constants import diTrueCPK, diBALL, diTUBES from graphics.widgets.ThumbView import ElementView from qt4transition import qt4todo diff --git a/cad/src/commands/ElementSelector/elementSelector.py b/cad/src/commands/ElementSelector/elementSelector.py index c6adc1660..8246e1b42 100755 --- a/cad/src/commands/ElementSelector/elementSelector.py +++ b/cad/src/commands/ElementSelector/elementSelector.py @@ -11,7 +11,7 @@ from PyQt4.Qt import QVBoxLayout from commands.ElementSelector.ElementSelectorDialog import Ui_ElementSelectorDialog from graphics.widgets.ThumbView import ElementView -from elements import PeriodicTable +from model.elements import PeriodicTable from constants import diTUBES class elementSelector(QDialog, Ui_ElementSelectorDialog): diff --git a/cad/src/commands/Extrude/Ui_ExtrudePropertyManager.py b/cad/src/commands/Extrude/Ui_ExtrudePropertyManager.py index 9fca9e329..5c41d23da 100755 --- a/cad/src/commands/Extrude/Ui_ExtrudePropertyManager.py +++ b/cad/src/commands/Extrude/Ui_ExtrudePropertyManager.py @@ -301,7 +301,7 @@ class Ui_ExtrudePropertyManager(PM_Dialog): @note: Many PM widgets are still missing their "What's This" text. """ - from gui.WhatsThisText_for_PropertyManagers import whatsThis_ExtrudePropertyManager + from ne1_ui.WhatsThisText_for_PropertyManagers import whatsThis_ExtrudePropertyManager whatsThis_ExtrudePropertyManager(self) return diff --git a/cad/src/commands/Extrude/extrudeMode.py b/cad/src/commands/Extrude/extrudeMode.py index 67296fefa..97069a899 100755 --- a/cad/src/commands/Extrude/extrudeMode.py +++ b/cad/src/commands/Extrude/extrudeMode.py @@ -52,7 +52,7 @@ from debug_prefs import debug_pref, Choice, Choice_boolean_False ##, Choice_bool from command_support.modes import basicMode from debug import print_compact_traceback, print_compact_stack -from bonds import bond_at_singlets +from model.bonds import bond_at_singlets from icon_utilities import geticon from utilities.Log import redmsg @@ -63,7 +63,7 @@ from geometry.VQT import V, Q, norm, vlen, cross from commands.Extrude.ExtrudePropertyManager import ExtrudePropertyManager from graphics.drawing.drawer import drawline -from chunk import Chunk +from model.chunk import Chunk from graphics.behaviors.shape import get_selCurve_color from graphics.drawables.handles import repunitHandleSet @@ -2122,7 +2122,7 @@ class fake_merged_mol( virtual_group_of_Chunks): #e rename? 'extrude_unit_holder assy = oldnodes[0].assy for newMol in newnodes: if newMol is not None: #bruce 070525 precaution - from chunk import mol_copy_name + from model.chunk import mol_copy_name newMol.name = mol_copy_name(newMol.name) # this should work for any kind of node, unless it has an update bug for some of them, # but since the node doesn't yet have a dad, that's very unlikely. diff --git a/cad/src/commands/Fuse/FuseChunks_Command.py b/cad/src/commands/Fuse/FuseChunks_Command.py index f22dc19f7..c5d50f64d 100755 --- a/cad/src/commands/Fuse/FuseChunks_Command.py +++ b/cad/src/commands/Fuse/FuseChunks_Command.py @@ -22,7 +22,7 @@ import foundation.env as env import foundation.changes as changes from geometry.VQT import vlen -from elements import Singlet +from model.elements import Singlet from utilities.Log import redmsg, orangemsg from PlatformDependent import fix_plurals from commands.Fuse.FusePropertyManager import FusePropertyManager diff --git a/cad/src/commands/Fuse/fusechunksMode.py b/cad/src/commands/Fuse/fusechunksMode.py index 845b38fe2..a0b6fc695 100755 --- a/cad/src/commands/Fuse/fusechunksMode.py +++ b/cad/src/commands/Fuse/fusechunksMode.py @@ -16,9 +16,9 @@ import foundation.changes as changes from geometry.VQT import vlen from graphics.drawing.drawer import drawline -from elements import Singlet +from model.elements import Singlet from commands.Move.modifyMode import modifyMode -from bonds import bond_at_singlets +from model.bonds import bond_at_singlets from utilities.Log import redmsg, orangemsg from PlatformDependent import fix_plurals from commands.Fuse.FusePropertyManager import FusePropertyManager diff --git a/cad/src/commands/InsertGraphene/GrapheneGenerator.py b/cad/src/commands/InsertGraphene/GrapheneGenerator.py index d8ec459f0..2633f6877 100755 --- a/cad/src/commands/InsertGraphene/GrapheneGenerator.py +++ b/cad/src/commands/InsertGraphene/GrapheneGenerator.py @@ -16,15 +16,15 @@ Mark 2007-08-06: Renamed GrapheneGeneratorDialog to GrapheneGeneratorPropertyMan from math import atan2, pi from geometry.VQT import V -from chem import Atom +from model.chem import Atom -import bonds # for bond_atoms -import bond_constants +import model.bonds as bonds # for bond_atoms +import model.bond_constants as bond_constants -from chunk import Chunk +from model.chunk import Chunk import foundation.env as env from debug import Stopwatch -from elements import PeriodicTable +from model.elements import PeriodicTable from utilities.Log import greenmsg from commands.InsertGraphene.GrapheneGeneratorPropertyManager import GrapheneGeneratorPropertyManager diff --git a/cad/src/commands/InsertGraphene/GrapheneGeneratorPropertyManager.py b/cad/src/commands/InsertGraphene/GrapheneGeneratorPropertyManager.py index 1874f545c..9e0179b89 100755 --- a/cad/src/commands/InsertGraphene/GrapheneGeneratorPropertyManager.py +++ b/cad/src/commands/InsertGraphene/GrapheneGeneratorPropertyManager.py @@ -14,7 +14,7 @@ Mark 2007-08-06: Renamed GrapheneGeneratorDialog to GrapheneGeneratorPropertyMan __author__ = "Mark" -from bonds import CC_GRAPHITIC_BONDLENGTH +from model.bonds import CC_GRAPHITIC_BONDLENGTH from PM.PM_Dialog import PM_Dialog from PM.PM_GroupBox import PM_GroupBox @@ -112,13 +112,13 @@ class GrapheneGeneratorPropertyManager(PM_Dialog): """ What's This text for widgets in this Property Manager. """ - from gui.WhatsThisText_for_PropertyManagers import whatsThis_GrapheneGeneratorPropertyManager + from ne1_ui.WhatsThisText_for_PropertyManagers import whatsThis_GrapheneGeneratorPropertyManager whatsThis_GrapheneGeneratorPropertyManager(self) def _addToolTipText(self): """ Tool Tip text for widgets in this Property Manager. """ - from gui.ToolTipText_for_PropertyManagers import ToolTip_GrapheneGeneratorPropertyManager + from ne1_ui.ToolTipText_for_PropertyManagers import ToolTip_GrapheneGeneratorPropertyManager ToolTip_GrapheneGeneratorPropertyManager(self) diff --git a/cad/src/commands/InsertHeterojunction/CoNTubGenerator.py b/cad/src/commands/InsertHeterojunction/CoNTubGenerator.py index 46ed5711f..c2a5d6b9f 100755 --- a/cad/src/commands/InsertHeterojunction/CoNTubGenerator.py +++ b/cad/src/commands/InsertHeterojunction/CoNTubGenerator.py @@ -594,8 +594,8 @@ class PluginlikeGenerator: print "create_methane_test" assy = self.win.assy from geometry.VQT import V - from chunk import Chunk - from chem import Atom + from model.chunk import Chunk + from model.chem import Atom mol = Chunk(assy, 'bug') # name is reset below! n = max(params[0],1) for x in range(n): diff --git a/cad/src/commands/InsertNanotube/NanotubeGenerator.py b/cad/src/commands/InsertNanotube/NanotubeGenerator.py index 962dbdee1..e23ce309e 100755 --- a/cad/src/commands/InsertNanotube/NanotubeGenerator.py +++ b/cad/src/commands/InsertNanotube/NanotubeGenerator.py @@ -18,19 +18,19 @@ import foundation.env as env from utilities import debug_flags from debug import Stopwatch -from chem import Atom +from model.chem import Atom -from chunk import Chunk +from model.chunk import Chunk -from elements import PeriodicTable +from model.elements import PeriodicTable -from bonds import bond_atoms -from bonds import NeighborhoodGenerator +from model.bonds import bond_atoms +from model.bonds import NeighborhoodGenerator -from bond_constants import V_GRAPHITE, V_SINGLE +from model.bond_constants import V_GRAPHITE, V_SINGLE ##from bonds_from_atoms import make_bonds ##from buckyball import BuckyBall -from bond_constants import atoms_are_bonded +from model.bond_constants import atoms_are_bonded from commands.InsertNanotube.NanotubeGeneratorPropertyManager import NanotubeGeneratorPropertyManager from command_support.GeneratorBaseClass import GeneratorBaseClass diff --git a/cad/src/commands/InsertNanotube/NanotubeGeneratorPropertyManager.py b/cad/src/commands/InsertNanotube/NanotubeGeneratorPropertyManager.py index 3bda5cc8b..26728ad7c 100755 --- a/cad/src/commands/InsertNanotube/NanotubeGeneratorPropertyManager.py +++ b/cad/src/commands/InsertNanotube/NanotubeGeneratorPropertyManager.py @@ -19,7 +19,7 @@ from PM.PM_ComboBox import PM_ComboBox from PM.PM_DoubleSpinBox import PM_DoubleSpinBox from PM.PM_SpinBox import PM_SpinBox -from bonds import CC_GRAPHITIC_BONDLENGTH, BN_GRAPHITIC_BONDLENGTH +from model.bonds import CC_GRAPHITIC_BONDLENGTH, BN_GRAPHITIC_BONDLENGTH from debug import print_compact_traceback ntBondLengths = [CC_GRAPHITIC_BONDLENGTH, BN_GRAPHITIC_BONDLENGTH] @@ -240,14 +240,14 @@ class NanotubeGeneratorPropertyManager(PM_Dialog): """ What's This text for widgets in this Property Manager. """ - from gui.WhatsThisText_for_PropertyManagers import whatsThis_NanotubeGeneratorPropertyManager + from ne1_ui.WhatsThisText_for_PropertyManagers import whatsThis_NanotubeGeneratorPropertyManager whatsThis_NanotubeGeneratorPropertyManager(self) def _addToolTipText(self): """ Tool Tip text for widgets in this Property Manager. """ - from gui.ToolTipText_for_PropertyManagers import ToolTip_NanotubeGeneratorPropertyManager + from ne1_ui.ToolTipText_for_PropertyManagers import ToolTip_NanotubeGeneratorPropertyManager ToolTip_NanotubeGeneratorPropertyManager(self) def chirality_fixup(self, spinBoxValueJunk = None): diff --git a/cad/src/commands/InsertPeptide/PeptideGenerator.py b/cad/src/commands/InsertPeptide/PeptideGenerator.py index c1acaa8f8..339e27a11 100755 --- a/cad/src/commands/InsertPeptide/PeptideGenerator.py +++ b/cad/src/commands/InsertPeptide/PeptideGenerator.py @@ -21,13 +21,13 @@ from command_support.GeneratorBaseClass import GeneratorBaseClass from utilities.Log import greenmsg -from chem import Atom -from chunk import Chunk +from model.chem import Atom +from model.chunk import Chunk -from bonds import bond_atoms -from bonds import NeighborhoodGenerator -from bond_constants import atoms_are_bonded -from bond_constants import V_SINGLE, V_DOUBLE, V_AROMATIC +from model.bonds import bond_atoms +from model.bonds import NeighborhoodGenerator +from model.bond_constants import atoms_are_bonded +from model.bond_constants import V_SINGLE, V_DOUBLE, V_AROMATIC from bonds_from_atoms import inferBonds from Numeric import zeros, array, sqrt, pi, sin, cos, dot, Float diff --git a/cad/src/commands/InsertPeptide/PeptideGeneratorPropertyManager.py b/cad/src/commands/InsertPeptide/PeptideGeneratorPropertyManager.py index 4b9314535..ec48faa6c 100755 --- a/cad/src/commands/InsertPeptide/PeptideGeneratorPropertyManager.py +++ b/cad/src/commands/InsertPeptide/PeptideGeneratorPropertyManager.py @@ -160,14 +160,14 @@ class PeptideGeneratorPropertyManager(PM_Dialog): """ What's This text for widgets in this Property Manager. """ - from gui.WhatsThisText_for_PropertyManagers import whatsThis_PeptideGeneratorPropertyManager + from ne1_ui.WhatsThisText_for_PropertyManagers import whatsThis_PeptideGeneratorPropertyManager whatsThis_PeptideGeneratorPropertyManager(self) def _addToolTipText(self): """ Tool Tip text for widgets in this Property Manager. """ - from gui.ToolTipText_for_PropertyManagers import ToolTip_PeptideGeneratorPropertyManager + from ne1_ui.ToolTipText_for_PropertyManagers import ToolTip_PeptideGeneratorPropertyManager ToolTip_PeptideGeneratorPropertyManager(self) def _aaTypeChanged(self, idx): diff --git a/cad/src/commands/LinearMotorProperties/LinearMotorPropertyManager.py b/cad/src/commands/LinearMotorProperties/LinearMotorPropertyManager.py index ca5156430..cdd6753f4 100644 --- a/cad/src/commands/LinearMotorProperties/LinearMotorPropertyManager.py +++ b/cad/src/commands/LinearMotorProperties/LinearMotorPropertyManager.py @@ -239,7 +239,7 @@ class LinearMotorPropertyManager(MotorPropertyManager): """
What's This text for widgets in this Property Manager.
"""
- from gui.WhatsThisText_for_PropertyManagers import whatsThis_LinearMotorPropertyManager
+ from ne1_ui.WhatsThisText_for_PropertyManagers import whatsThis_LinearMotorPropertyManager
whatsThis_LinearMotorPropertyManager(self)
@@ -247,5 +247,5 @@ class LinearMotorPropertyManager(MotorPropertyManager): """
What's Tool Tip text for widgets in this Property Manager.
"""
- from gui.ToolTipText_for_PropertyManagers import ToolTip_LinearMotorPropertyManager
+ from ne1_ui.ToolTipText_for_PropertyManagers import ToolTip_LinearMotorPropertyManager
ToolTip_LinearMotorPropertyManager(self)
diff --git a/cad/src/commands/LinearMotorProperties/LinearMotor_EditCommand.py b/cad/src/commands/LinearMotorProperties/LinearMotor_EditCommand.py index 5c7f33d98..1fc3a3e15 100644 --- a/cad/src/commands/LinearMotorProperties/LinearMotor_EditCommand.py +++ b/cad/src/commands/LinearMotorProperties/LinearMotor_EditCommand.py @@ -12,7 +12,7 @@ ninad 2007-10-09: Created. import foundation.env as env from utilities.Log import redmsg, greenmsg, orangemsg -from jigs_motors import LinearMotor +from model.jigs_motors import LinearMotor from jigmakers_Mixin import atom_limit_exceeded_and_confirmed from command_support.EditCommand import EditCommand diff --git a/cad/src/commands/MinimizeEnergy/MinimizeEnergyProp.py b/cad/src/commands/MinimizeEnergy/MinimizeEnergyProp.py index 924567aa3..d2d32f9a7 100755 --- a/cad/src/commands/MinimizeEnergy/MinimizeEnergyProp.py +++ b/cad/src/commands/MinimizeEnergy/MinimizeEnergyProp.py @@ -34,7 +34,7 @@ from prefs_constants import electrostaticsForDnaDuringMinimize_prefs_key from debug import print_compact_traceback import foundation.env as env from utilities import debug_flags -from UserPrefs import get_pref_or_optval +from ne1_ui.UserPrefs import get_pref_or_optval from widgets.widget_helpers import double_fixup from debug_prefs import debug_pref, Choice_boolean_False from prefs_widgets import connect_checkbox_with_boolean_pref diff --git a/cad/src/commands/Move/Ui_MovePropertyManager.py b/cad/src/commands/Move/Ui_MovePropertyManager.py index 57f322c14..5b5beb6c4 100755 --- a/cad/src/commands/Move/Ui_MovePropertyManager.py +++ b/cad/src/commands/Move/Ui_MovePropertyManager.py @@ -558,13 +558,13 @@ class Ui_MovePropertyManager( PM_Dialog ): What's This text for some of the widgets in this Property Manager. """ - from gui.WhatsThisText_for_PropertyManagers import whatsThis_MovePropertyManager + from ne1_ui.WhatsThisText_for_PropertyManagers import whatsThis_MovePropertyManager whatsThis_MovePropertyManager(self) def _addToolTipText(self): """ Tool Tip text for widgets in this Property Manager. """ - from gui.ToolTipText_for_PropertyManagers import ToolTip_MovePropertyManager + from ne1_ui.ToolTipText_for_PropertyManagers import ToolTip_MovePropertyManager ToolTip_MovePropertyManager(self)
\ No newline at end of file diff --git a/cad/src/commands/PartLibrary/PartLibPropertyManager.py b/cad/src/commands/PartLibrary/PartLibPropertyManager.py index 4cd2a6a9b..49b3f658c 100644 --- a/cad/src/commands/PartLibrary/PartLibPropertyManager.py +++ b/cad/src/commands/PartLibrary/PartLibPropertyManager.py @@ -21,7 +21,7 @@ in popular cad softwares. (it probably shouldn't be in a Property manager). from commands.Paste.PastePropertyManager import PastePropertyManager from PM.PM_PartLib import PM_PartLib -from gui.WhatsThisText_for_PropertyManagers import whatsThis_PartLibPropertyManager +from ne1_ui.WhatsThisText_for_PropertyManagers import whatsThis_PartLibPropertyManager class PartLibPropertyManager(PastePropertyManager): """ @@ -123,6 +123,6 @@ class PartLibPropertyManager(PastePropertyManager): """ Tool Tip text for widgets in this Property Manager. """ - from gui.ToolTipText_for_PropertyManagers import ToolTip_PartLibPropertyManager + from ne1_ui.ToolTipText_for_PropertyManagers import ToolTip_PartLibPropertyManager ToolTip_PartLibPropertyManager(self) diff --git a/cad/src/commands/PartLibrary/PartLibraryMode.py b/cad/src/commands/PartLibrary/PartLibraryMode.py index a2c514086..2335ce09f 100644 --- a/cad/src/commands/PartLibrary/PartLibraryMode.py +++ b/cad/src/commands/PartLibrary/PartLibraryMode.py @@ -27,8 +27,8 @@ import os from utilities.Log import orangemsg, greenmsg, quote_html, redmsg -from chem import Atom -from elements import Singlet +from model.chem import Atom +from model.elements import Singlet from geometry.VQT import Q from ops_copy import copied_nodes_for_DND diff --git a/cad/src/commands/Paste/PasteMode.py b/cad/src/commands/Paste/PasteMode.py index a72dd7653..4703cadd2 100644 --- a/cad/src/commands/Paste/PasteMode.py +++ b/cad/src/commands/Paste/PasteMode.py @@ -25,14 +25,14 @@ import foundation.changes as changes from utilities.Log import orangemsg, redmsg from foundation.Group import Group -from chem import Atom -from chunk import Chunk -from elements import Singlet +from model.chem import Atom +from model.chunk import Chunk +from model.elements import Singlet from pastables import is_pastable from commands.BuildAtoms.depositMode import depositMode from pastables import find_hotspot_for_pasting -from bonds import bond_at_singlets +from model.bonds import bond_at_singlets from commands.Paste.PastePropertyManager import PastePropertyManager diff --git a/cad/src/commands/Paste/PastePropertyManager.py b/cad/src/commands/Paste/PastePropertyManager.py index 9e9028cbf..9edc362a5 100644 --- a/cad/src/commands/Paste/PastePropertyManager.py +++ b/cad/src/commands/Paste/PastePropertyManager.py @@ -140,13 +140,13 @@ class PastePropertyManager(BuildAtomsPropertyManager): """ What's This text for widgets in this Property Manager. """ - from gui.WhatsThisText_for_PropertyManagers import whatsThis_PasteItemsPropertyManager + from ne1_ui.WhatsThisText_for_PropertyManagers import whatsThis_PasteItemsPropertyManager whatsThis_PasteItemsPropertyManager(self) def _addToolTipText(self): """ Tool Tip text for widgets in this Property Manager. """ - from gui.ToolTipText_for_PropertyManagers import ToolTip_PasteItemPropertyManager + from ne1_ui.ToolTipText_for_PropertyManagers import ToolTip_PasteItemPropertyManager ToolTip_PasteItemPropertyManager(self)
\ No newline at end of file diff --git a/cad/src/commands/PlaneProperties/PlanePropertyManager.py b/cad/src/commands/PlaneProperties/PlanePropertyManager.py index 95f27d1c4..13d2c6dd9 100755 --- a/cad/src/commands/PlaneProperties/PlanePropertyManager.py +++ b/cad/src/commands/PlaneProperties/PlanePropertyManager.py @@ -158,7 +158,7 @@ class PlanePropertyManager(EditCommand_PM): @note: Many PM widgets are still missing their "What's This" text. """ - from gui.WhatsThisText_for_PropertyManagers import whatsThis_PlanePropertyManager + from ne1_ui.WhatsThisText_for_PropertyManagers import whatsThis_PlanePropertyManager whatsThis_PlanePropertyManager(self) def show(self): diff --git a/cad/src/commands/PlaneProperties/Plane_EditCommand.py b/cad/src/commands/PlaneProperties/Plane_EditCommand.py index 79e740018..83e6b71a1 100755 --- a/cad/src/commands/PlaneProperties/Plane_EditCommand.py +++ b/cad/src/commands/PlaneProperties/Plane_EditCommand.py @@ -16,7 +16,7 @@ ninad 2007-12-26: Changes to make Plane_EditCommand a command on command stack from utilities.Log import greenmsg from command_support.EditCommand import EditCommand from commands.PlaneProperties.PlanePropertyManager import PlanePropertyManager -from Plane import Plane +from model.Plane import Plane from commands.SelectAtoms.SelectAtoms_GraphicsMode import SelectAtoms_GraphicsMode diff --git a/cad/src/commands/PlayMovie/Ui_MoviePropertyManager.py b/cad/src/commands/PlayMovie/Ui_MoviePropertyManager.py index 7e4a611d2..9aa276e5d 100755 --- a/cad/src/commands/PlayMovie/Ui_MoviePropertyManager.py +++ b/cad/src/commands/PlayMovie/Ui_MoviePropertyManager.py @@ -281,12 +281,12 @@ class Ui_MoviePropertyManager(PM_Dialog): What's This text for widgets in this Property Manager. """ - from gui.WhatsThisText_for_PropertyManagers import whatsThis_MoviePropertyManager + from ne1_ui.WhatsThisText_for_PropertyManagers import whatsThis_MoviePropertyManager whatsThis_MoviePropertyManager(self) def _addToolTipText(self): """ Tool Tip text for widgets in this Property Manager. """ - from gui.ToolTipText_for_PropertyManagers import ToolTip_MoviePropertyManager + from ne1_ui.ToolTipText_for_PropertyManagers import ToolTip_MoviePropertyManager ToolTip_MoviePropertyManager(self)
\ No newline at end of file diff --git a/cad/src/commands/PovraySceneProperties/PovraySceneProp.py b/cad/src/commands/PovraySceneProperties/PovraySceneProp.py index c6cdbdcff..0c16cc375 100755 --- a/cad/src/commands/PovraySceneProperties/PovraySceneProp.py +++ b/cad/src/commands/PovraySceneProperties/PovraySceneProp.py @@ -64,7 +64,7 @@ class PovraySceneProp(QDialog, SponsorableMixin, GroupButtonMixin, Ui_PovrayScen if not pov: self.node_is_new = True - from PovrayScene import PovrayScene + from model.PovrayScene import PovrayScene self.node = PovrayScene(self.win.assy, None) else: self.node_is_new = False diff --git a/cad/src/commands/QuteMol/QuteMolPropertyManager.py b/cad/src/commands/QuteMol/QuteMolPropertyManager.py index 43fe80363..8dc99a357 100644 --- a/cad/src/commands/QuteMol/QuteMolPropertyManager.py +++ b/cad/src/commands/QuteMol/QuteMolPropertyManager.py @@ -137,14 +137,14 @@ class QuteMolPropertyManager(PM_Dialog): """ "What's This" text for widgets in this Property Manager. """ - from gui.WhatsThisText_for_PropertyManagers import whatsThis_QuteMolPropertyManager + from ne1_ui.WhatsThisText_for_PropertyManagers import whatsThis_QuteMolPropertyManager whatsThis_QuteMolPropertyManager(self) def _addToolTipText(self): """ Tool Tip text for widgets in this Property Manager. """ - from gui.ToolTipText_for_PropertyManagers import ToolTip_QuteMolPropertyManager + from ne1_ui.ToolTipText_for_PropertyManagers import ToolTip_QuteMolPropertyManager ToolTip_QuteMolPropertyManager(self) def show(self): diff --git a/cad/src/commands/RotaryMotorProperties/RotaryMotorPropertyManager.py b/cad/src/commands/RotaryMotorProperties/RotaryMotorPropertyManager.py index b61f9e0de..aa7581ebf 100755 --- a/cad/src/commands/RotaryMotorProperties/RotaryMotorPropertyManager.py +++ b/cad/src/commands/RotaryMotorProperties/RotaryMotorPropertyManager.py @@ -276,14 +276,14 @@ class RotaryMotorPropertyManager(MotorPropertyManager): """ What's This text for widgets in this Property Manager. """ - from gui.WhatsThisText_for_PropertyManagers import whatsThis_RotaryMotorPropertyManager + from ne1_ui.WhatsThisText_for_PropertyManagers import whatsThis_RotaryMotorPropertyManager whatsThis_RotaryMotorPropertyManager(self) def _addToolTipText(self): """ What's Tool Tip text for widgets in this Property Manager. """ - from gui.ToolTipText_for_PropertyManagers import ToolTip_RotaryMotorPropertyManager + from ne1_ui.ToolTipText_for_PropertyManagers import ToolTip_RotaryMotorPropertyManager ToolTip_RotaryMotorPropertyManager(self) diff --git a/cad/src/commands/RotaryMotorProperties/RotaryMotor_EditCommand.py b/cad/src/commands/RotaryMotorProperties/RotaryMotor_EditCommand.py index 226b00c5f..7461d6ec3 100644 --- a/cad/src/commands/RotaryMotorProperties/RotaryMotor_EditCommand.py +++ b/cad/src/commands/RotaryMotorProperties/RotaryMotor_EditCommand.py @@ -12,7 +12,7 @@ ninad 2007-10-09: Created. This deprecates 'RotoryMotorGenerator' import foundation.env as env from utilities.Log import redmsg, greenmsg, orangemsg -from jigs_motors import RotaryMotor +from model.jigs_motors import RotaryMotor from jigmakers_Mixin import atom_limit_exceeded_and_confirmed from command_support.EditCommand import EditCommand diff --git a/cad/src/commands/Select/Select_GraphicsMode.py b/cad/src/commands/Select/Select_GraphicsMode.py index ffb52fde6..9895d7f68 100755 --- a/cad/src/commands/Select/Select_GraphicsMode.py +++ b/cad/src/commands/Select/Select_GraphicsMode.py @@ -96,9 +96,9 @@ from debug_prefs import Choice from geometry.VQT import V, A, vlen from graphics.behaviors.shape import SelectionShape -from bonds import Bond -from chem import Atom -from jigs import Jig +from model.bonds import Bond +from model.chem import Atom +from model.jigs import Jig from debug import print_compact_traceback from debug import print_compact_stack @@ -1033,7 +1033,7 @@ class Select_basicGraphicsMode(Select_GraphicsMode_DrawMethod_preMixin, continue pass # list is empty, just return a new one - from chunk import BorrowerChunk + from model.chunk import BorrowerChunk return BorrowerChunk(self.o.assy) def deallocate_borrowerchunk(self, bc): diff --git a/cad/src/commands/Select/Select_GraphicsMode_MouseHelpers_preMixin.py b/cad/src/commands/Select/Select_GraphicsMode_MouseHelpers_preMixin.py index 46b8d6185..74873008c 100755 --- a/cad/src/commands/Select/Select_GraphicsMode_MouseHelpers_preMixin.py +++ b/cad/src/commands/Select/Select_GraphicsMode_MouseHelpers_preMixin.py @@ -20,9 +20,9 @@ To be used as a Mixin class only for Select_basicGraphicsMode. """ import foundation.env as env -from bonds import Bond -from chem import Atom -from jigs import Jig +from model.bonds import Bond +from model.chem import Atom +from model.jigs import Jig from debug import print_compact_stack debug_update_selobj_calls = False # do not commit with true diff --git a/cad/src/commands/SelectAtoms/SelectAtoms_GraphicsMode.py b/cad/src/commands/SelectAtoms/SelectAtoms_GraphicsMode.py index 221a2aee8..b0752c11e 100755 --- a/cad/src/commands/SelectAtoms/SelectAtoms_GraphicsMode.py +++ b/cad/src/commands/SelectAtoms/SelectAtoms_GraphicsMode.py @@ -35,10 +35,10 @@ import foundation.env as env from utilities import debug_flags from geometry.VQT import V, Q, norm, vlen, ptonline -from chem import Atom -from jigs import Jig -from bonds import Bond -from elements import Singlet +from model.chem import Atom +from model.jigs import Jig +from model.bonds import Bond +from model.elements import Singlet from debug import print_compact_traceback, print_compact_stack diff --git a/cad/src/commands/SelectChunks/SelectChunks_Command.py b/cad/src/commands/SelectChunks/SelectChunks_Command.py index 756b95096..779e0a7f9 100755 --- a/cad/src/commands/SelectChunks/SelectChunks_Command.py +++ b/cad/src/commands/SelectChunks/SelectChunks_Command.py @@ -32,9 +32,9 @@ from commands.Select.Select_Command import Select_basicCommand from commands.SelectChunks.SelectChunks_GraphicsMode import SelectChunks_GraphicsMode from command_support.GraphicsMode_API import GraphicsMode_API -from chem import Atom -from chunk import Chunk -from bonds import Bond +from model.chem import Atom +from model.chunk import Chunk +from model.bonds import Bond class SelectChunks_basicCommand(Select_basicCommand): """ diff --git a/cad/src/commands/SelectChunks/SelectChunks_GraphicsMode.py b/cad/src/commands/SelectChunks/SelectChunks_GraphicsMode.py index c8f5c112d..af4367ce8 100755 --- a/cad/src/commands/SelectChunks/SelectChunks_GraphicsMode.py +++ b/cad/src/commands/SelectChunks/SelectChunks_GraphicsMode.py @@ -32,11 +32,11 @@ from PyQt4.Qt import QMouseEvent import foundation.env as env -from bonds import Bond -from chem import Atom +from model.bonds import Bond +from model.chem import Atom from commands.Select.Select_GraphicsMode import DRAG_STICKINESS_LIMIT -from chunk import Chunk +from model.chunk import Chunk from graphics.drawing.drawer import apply_material, allow_color_sorting, use_color_sorted_dls from OpenGL.GL import glCallList from debug import print_compact_traceback, print_compact_stack diff --git a/cad/src/dna/DnaSequenceEditor/Ui_DnaSequenceEditor.py b/cad/src/dna/DnaSequenceEditor/Ui_DnaSequenceEditor.py index 219d0c365..e0fa04697 100644 --- a/cad/src/dna/DnaSequenceEditor/Ui_DnaSequenceEditor.py +++ b/cad/src/dna/DnaSequenceEditor/Ui_DnaSequenceEditor.py @@ -242,7 +242,7 @@ class Ui_DnaSequenceEditor(PM_DockWidget): """ What's Tool Tip text for widgets in this Property Manager. """ - from gui.ToolTipText_for_PropertyManagers import ToolTip_SequenceEditor + from ne1_ui.ToolTipText_for_PropertyManagers import ToolTip_SequenceEditor ToolTip_SequenceEditor(self) def _addWhatsThisText(self): @@ -250,5 +250,5 @@ class Ui_DnaSequenceEditor(PM_DockWidget): What's This text for widgets in this Property Manager. """ - from gui.WhatsThisText_for_PropertyManagers import whatsThis_SequenceEditor + from ne1_ui.WhatsThisText_for_PropertyManagers import whatsThis_SequenceEditor whatsThis_SequenceEditor(self)
\ No newline at end of file diff --git a/cad/src/dna/commands/BuildDna/BuildDna_EditCommand.py b/cad/src/dna/commands/BuildDna/BuildDna_EditCommand.py index c660c2193..65c80b677 100644 --- a/cad/src/dna/commands/BuildDna/BuildDna_EditCommand.py +++ b/cad/src/dna/commands/BuildDna/BuildDna_EditCommand.py @@ -28,11 +28,11 @@ from command_support.GeneratorBaseClass import PluginBug, UserError from constants import gensym -from Ui_DnaFlyout import DnaFlyout +from ne1_ui.toolbars.Ui_DnaFlyout import DnaFlyout -from chem import Atom -from chunk import Chunk -from bonds import Bond +from model.chem import Atom +from model.chunk import Chunk +from model.bonds import Bond ##from SelectChunks_GraphicsMode import SelectChunks_GraphicsMode diff --git a/cad/src/dna/commands/BuildDna/BuildDna_PropertyManager.py b/cad/src/dna/commands/BuildDna/BuildDna_PropertyManager.py index 946a0c153..81244a906 100644 --- a/cad/src/dna/commands/BuildDna/BuildDna_PropertyManager.py +++ b/cad/src/dna/commands/BuildDna/BuildDna_PropertyManager.py @@ -570,7 +570,7 @@ class BuildDna_PropertyManager( EditCommand_PM, DebugMenuMixin ): """ Tool Tip text for widgets in the DNA Property Manager. """ - from gui.ToolTipText_for_PropertyManagers import ToolTip_SequenceEditor + from ne1_ui.ToolTipText_for_PropertyManagers import ToolTip_SequenceEditor ToolTip_SequenceEditor(self) print "inside add tool tiptest" pass diff --git a/cad/src/dna/commands/BuildDuplex/DnaDuplex.py b/cad/src/dna/commands/BuildDuplex/DnaDuplex.py index deaeeb7f1..6845ea0b1 100644 --- a/cad/src/dna/commands/BuildDuplex/DnaDuplex.py +++ b/cad/src/dna/commands/BuildDuplex/DnaDuplex.py @@ -34,7 +34,7 @@ from dna.model.Dna_Constants import getDuplexBasesPerTurn from runSim import adjustSinglet -from elements import PeriodicTable +from model.elements import PeriodicTable Element_Ae3 = PeriodicTable.getElement('Ae3') from dna.model.Dna_Constants import basesDict, dnaDict diff --git a/cad/src/dna/commands/BuildDuplex/DnaDuplexPropertyManager.py b/cad/src/dna/commands/BuildDuplex/DnaDuplexPropertyManager.py index 9e8d1704a..8901d9a01 100644 --- a/cad/src/dna/commands/BuildDuplex/DnaDuplexPropertyManager.py +++ b/cad/src/dna/commands/BuildDuplex/DnaDuplexPropertyManager.py @@ -44,7 +44,7 @@ from PM.PM_Constants import pmWhatsThisButton from PM.PM_Constants import pmCancelButton from PM.PM_Constants import pmPreviewButton -from gui.WhatsThisText_for_PropertyManagers import whatsThis_DnaDuplexPropertyManager +from ne1_ui.WhatsThisText_for_PropertyManagers import whatsThis_DnaDuplexPropertyManager class DnaDuplexPropertyManager( EditCommand_PM, DebugMenuMixin ): """ diff --git a/cad/src/dna/commands/BuildDuplex_old/DnaGenerator.py b/cad/src/dna/commands/BuildDuplex_old/DnaGenerator.py index dc67660f9..0646415d3 100755 --- a/cad/src/dna/commands/BuildDuplex_old/DnaGenerator.py +++ b/cad/src/dna/commands/BuildDuplex_old/DnaGenerator.py @@ -35,7 +35,7 @@ from foundation.Group import Group from utilities.Log import redmsg, greenmsg ##, orangemsg from geometry.VQT import Q, V, angleBetween, cross, vlen, Veq from math import pi -from chunk import Chunk +from model.chunk import Chunk from constants import gensym from dna.model.Dna_Constants import basesDict, getReverseSequence diff --git a/cad/src/dna/commands/DnaSegment/DnaSegment_EditCommand.py b/cad/src/dna/commands/DnaSegment/DnaSegment_EditCommand.py index f2edc6936..10ab7fc1c 100644 --- a/cad/src/dna/commands/DnaSegment/DnaSegment_EditCommand.py +++ b/cad/src/dna/commands/DnaSegment/DnaSegment_EditCommand.py @@ -66,9 +66,9 @@ from exprs.Exprs import norm_Expr from prefs_widgets import ObjAttr_StateRef from exprs.ExprsConstants import Width, Point -from chunk import Chunk -from chem import Atom -from bonds import Bond +from model.chunk import Chunk +from model.chem import Atom +from model.bonds import Bond from dna.commands.DnaSegment.DnaSegment_ResizeHandle import DnaSegment_ResizeHandle diff --git a/cad/src/dna/commands/DnaSegment/DnaSegment_GraphicsMode.py b/cad/src/dna/commands/DnaSegment/DnaSegment_GraphicsMode.py index dc4518471..91e4cbb38 100644 --- a/cad/src/dna/commands/DnaSegment/DnaSegment_GraphicsMode.py +++ b/cad/src/dna/commands/DnaSegment/DnaSegment_GraphicsMode.py @@ -53,8 +53,8 @@ from debug import print_compact_traceback from commands.Select.Select_GraphicsMode import DRAG_STICKINESS_LIMIT -from chem import Atom -from bonds import Bond +from model.chem import Atom +from model.bonds import Bond SPHERE_RADIUS = 2.0 SPHERE_DRAWLEVEL = 2 diff --git a/cad/src/dna/commands/DnaStrand/DnaStrand_EditCommand.py b/cad/src/dna/commands/DnaStrand/DnaStrand_EditCommand.py index 437678548..83413d9ba 100644 --- a/cad/src/dna/commands/DnaStrand/DnaStrand_EditCommand.py +++ b/cad/src/dna/commands/DnaStrand/DnaStrand_EditCommand.py @@ -31,9 +31,9 @@ from exprs.Exprs import norm_Expr from prefs_widgets import ObjAttr_StateRef from exprs.ExprsConstants import Width, Point -from chunk import Chunk -from chem import Atom -from bonds import Bond +from model.chunk import Chunk +from model.chem import Atom +from model.bonds import Bond from dna.commands.DnaStrand.DnaStrand_GraphicsMode import DnaStrand_GraphicsMode from dna.commands.DnaStrand.DnaStrand_ResizeHandle import DnaStrand_ResizeHandle diff --git a/cad/src/dna/model/ChainAtomMarker.py b/cad/src/dna/model/ChainAtomMarker.py index ff122b5a6..c73f25d4f 100644 --- a/cad/src/dna/model/ChainAtomMarker.py +++ b/cad/src/dna/model/ChainAtomMarker.py @@ -19,7 +19,7 @@ See also: class DnaMarker, which inherits this. """ -from jigs import Jig +from model.jigs import Jig _NUMBER_OF_MARKER_ATOMS = 2 diff --git a/cad/src/dna/model/DnaChain.py b/cad/src/dna/model/DnaChain.py index 5386025cf..9cbf4d86c 100644 --- a/cad/src/dna/model/DnaChain.py +++ b/cad/src/dna/model/DnaChain.py @@ -18,7 +18,7 @@ from dna.model.dna_model_constants import LADDER_END0 import foundation.env as env from utilities.Log import redmsg -from bond_constants import find_bond +from model.bond_constants import find_bond # == diff --git a/cad/src/dna/model/DnaGroup.py b/cad/src/dna/model/DnaGroup.py index 4bdd26764..810ac82fb 100644 --- a/cad/src/dna/model/DnaGroup.py +++ b/cad/src/dna/model/DnaGroup.py @@ -8,7 +8,7 @@ DnaGroup.py - ... """ from dna.model.Block import Block -from chunk import Chunk +from model.chunk import Chunk from constants import gensym diff --git a/cad/src/dna/model/DnaLadder.py b/cad/src/dna/model/DnaLadder.py index 40af4094a..ff891a6ef 100644 --- a/cad/src/dna/model/DnaLadder.py +++ b/cad/src/dna/model/DnaLadder.py @@ -49,7 +49,7 @@ A ladder will be fully visible to copy and undo (i.e. it will contain undoable state), but will not be stored in the mmp file. """ -from bond_constants import atoms_are_bonded +from model.bond_constants import atoms_are_bonded from dna.model.DnaChain import merged_chain diff --git a/cad/src/dna/model/DnaLadderRailChunk.py b/cad/src/dna/model/DnaLadderRailChunk.py index 0db7aaa83..6b2474ee1 100644 --- a/cad/src/dna/model/DnaLadderRailChunk.py +++ b/cad/src/dna/model/DnaLadderRailChunk.py @@ -7,7 +7,7 @@ DnaLadderRailChunk.py - @copyright: 2007-2008 Nanorex, Inc. See LICENSE file for details. """ -from chunk import Chunk +from model.chunk import Chunk from constants import gensym from constants import black @@ -22,7 +22,7 @@ def _DEBUG_REUSE_CHUNKS(): import foundation.env as env from utilities.Log import orangemsg, graymsg -from elements import Singlet +from model.elements import Singlet # see also: ## from dna_model.DnaLadder import _rail_end_atom_to_ladder diff --git a/cad/src/dna/model/DnaSegment.py b/cad/src/dna/model/DnaSegment.py index 515f19b69..4c7da89e8 100644 --- a/cad/src/dna/model/DnaSegment.py +++ b/cad/src/dna/model/DnaSegment.py @@ -11,9 +11,9 @@ from dna.model.DnaStrandOrSegment import DnaStrandOrSegment from dna.model.DnaLadderRailChunk import DnaAxisChunk from debug import print_compact_stack, print_compact_traceback -from chunk import Chunk -from chem import Atom -from bonds import Bond +from model.chunk import Chunk +from model.chem import Atom +from model.bonds import Bond from geometry.VQT import V, norm, vlen from dna.model.Dna_Constants import getDuplexRiseFromNumberOfBasePairs diff --git a/cad/src/dna/model/elements_data_PAM3.py b/cad/src/dna/model/elements_data_PAM3.py index 626573651..945540690 100755 --- a/cad/src/dna/model/elements_data_PAM3.py +++ b/cad/src/dna/model/elements_data_PAM3.py @@ -12,7 +12,7 @@ Bruce 071105 revised init code, and split PAM3 and PAM5 data out of elements_data.py into separate files. """ -from elements_data import tetra4, flat, tetra2, tetra3 +from model.elements_data import tetra4, flat, tetra2, tetra3 _DIRECTIONAL_BOND_ELEMENTS_PAM3 = ('Ss3', 'Pl3', 'Sj3', 'Se3', 'Sh3', 'Hp3') diff --git a/cad/src/dna/model/elements_data_PAM5.py b/cad/src/dna/model/elements_data_PAM5.py index de8f0e13c..7ad30be89 100755 --- a/cad/src/dna/model/elements_data_PAM5.py +++ b/cad/src/dna/model/elements_data_PAM5.py @@ -14,7 +14,7 @@ out of elements_data.py into separate files. Bruce 080108 added Gv5 for use in Eric D's forthcoming PAM5 revision. """ -from elements_data import tetra4, flat, tetra2 +from model.elements_data import tetra4, flat, tetra2 _DIRECTIONAL_BOND_ELEMENTS_PAM5 = ('Ss5', 'Pl5', 'Sj5', 'Pe5', 'Sh5', 'Hp5') diff --git a/cad/src/dna/operations/crossovers.py b/cad/src/dna/operations/crossovers.py index 6e84d28a9..a3f96c2aa 100755 --- a/cad/src/dna/operations/crossovers.py +++ b/cad/src/dna/operations/crossovers.py @@ -17,14 +17,14 @@ TODO: make it work for PAM3 as well as PAM5. # - Undo and Feature Help cmdnames are wrong (not working) from constants import noop, average_value -from bond_constants import V_SINGLE -from bond_constants import atoms_are_bonded, find_bond -from bonds import bond_atoms_faster, bond_direction ##, bond_atoms +from model.bond_constants import V_SINGLE +from model.bond_constants import atoms_are_bonded, find_bond +from model.bonds import bond_atoms_faster, bond_direction ##, bond_atoms from utilities.Log import redmsg, greenmsg, quote_html ##, orangemsg ##from debug_prefs import debug_pref, Choice import foundation.env as env -from elements import PeriodicTable +from model.elements import PeriodicTable Element_Sj5 = PeriodicTable.getElement('Sj5') Element_Ss5 = PeriodicTable.getElement('Ss5') diff --git a/cad/src/dna/updater/dna_updater_commands.py b/cad/src/dna/updater/dna_updater_commands.py index 00ccc1617..14b05e253 100644 --- a/cad/src/dna/updater/dna_updater_commands.py +++ b/cad/src/dna/updater/dna_updater_commands.py @@ -9,7 +9,7 @@ dna_updater_commands.py - UI commands offered directly by the dna updater. from debug import register_debug_menu_command -from chem import _changed_structure_Atoms # but it's private! refactor sometime +from model.chem import _changed_structure_Atoms # but it's private! refactor sometime import foundation.env as env diff --git a/cad/src/dna/updater/dna_updater_debug.py b/cad/src/dna/updater/dna_updater_debug.py index f15502085..c8c9ce472 100644 --- a/cad/src/dna/updater/dna_updater_debug.py +++ b/cad/src/dna/updater/dna_updater_debug.py @@ -11,7 +11,7 @@ from utilities import debug_flags from graphics.drawing.drawer import drawline -from jigs import Jig +from model.jigs import Jig import foundation.env as env diff --git a/cad/src/dna/updater/dna_updater_globals.py b/cad/src/dna/updater/dna_updater_globals.py index 3571aed32..0f3b0585f 100644 --- a/cad/src/dna/updater/dna_updater_globals.py +++ b/cad/src/dna/updater/dna_updater_globals.py @@ -13,7 +13,7 @@ from utilities import debug_flags from foundation.changedicts import refreshing_changedict_subscription from foundation.changedicts import _cdproc_for_dictid # but it's private! -from chem import _changed_structure_Atoms, _changed_parent_Atoms # but they're private! refactor sometime +from model.chem import _changed_structure_Atoms, _changed_parent_Atoms # but they're private! refactor sometime from debug import print_compact_stack diff --git a/cad/src/dna/updater/fix_atom_classes.py b/cad/src/dna/updater/fix_atom_classes.py index 1a75f4470..d70b02345 100644 --- a/cad/src/dna/updater/fix_atom_classes.py +++ b/cad/src/dna/updater/fix_atom_classes.py @@ -9,7 +9,7 @@ fix_atom_classes.py - fix classes of PAM atoms from dna.updater.dna_updater_utils import replace_atom_class -from chem import Atom +from model.chem import Atom StrandAtom = Atom # stub AxisAtom = Atom # stub diff --git a/cad/src/dna/updater/fix_bond_directions.py b/cad/src/dna/updater/fix_bond_directions.py index ee498b326..e24236075 100644 --- a/cad/src/dna/updater/fix_bond_directions.py +++ b/cad/src/dna/updater/fix_bond_directions.py @@ -7,7 +7,7 @@ fix_bond_directions.py - dna updater helper functions @copyright: 2008 Nanorex, Inc. See LICENSE file for details. """ -from elements import Singlet +from model.elements import Singlet import foundation.env as env from utilities.Log import orangemsg diff --git a/cad/src/dna/updater/fix_deprecated_elements.py b/cad/src/dna/updater/fix_deprecated_elements.py index f84aaf596..7f7f6b09e 100644 --- a/cad/src/dna/updater/fix_deprecated_elements.py +++ b/cad/src/dna/updater/fix_deprecated_elements.py @@ -7,7 +7,7 @@ fix_deprecated_elements.py - fix deprecated PAM elements in-place in models @copyright: 2007-2008 Nanorex, Inc. See LICENSE file for details. """ -from elements import PeriodicTable +from model.elements import PeriodicTable from constants import diDEFAULT diff --git a/cad/src/exprs/dna_ribbon_view.py b/cad/src/exprs/dna_ribbon_view.py index 2c6c18247..c94e68d88 100755 --- a/cad/src/exprs/dna_ribbon_view.py +++ b/cad/src/exprs/dna_ribbon_view.py @@ -211,7 +211,7 @@ class Cylinder(Geom3D): #e super? ####IMPLEM - and answer the design Qs herein a def _C__dy_dz(self): #e if axis has a dy, use that (some lines might come with one) # otherwise get an arb perp to our dx - from pi_bond_sp_chain import arb_ortho_pair + from model.pi_bond_sp_chain import arb_ortho_pair # "Given a nonzero vector, return an arbitrary pair of unit vectors perpendicular to it and to each other." #e refile that into geometry.py in cad/src, or use smth else in there, and grab these from a more central source in exprs return arb_ortho_pair(self.dx) diff --git a/cad/src/files/mmp/files_mmp.py b/cad/src/files/mmp/files_mmp.py index 3ca39f68e..167296e8e 100755 --- a/cad/src/files/mmp/files_mmp.py +++ b/cad/src/files/mmp/files_mmp.py @@ -31,25 +31,25 @@ import re, time import foundation.env as env from utilities import debug_flags -from chem import Atom -from jigs import AtomSet -from jigs import Anchor -from jigs import Stat -from jigs import Thermo -from jigs_motors import RotaryMotor -from jigs_motors import LinearMotor -from jigs_planes import GridPlane +from model.chem import Atom +from model.jigs import AtomSet +from model.jigs import Anchor +from model.jigs import Stat +from model.jigs import Thermo +from model.jigs_motors import RotaryMotor +from model.jigs_motors import LinearMotor +from model.jigs_planes import GridPlane from analysis.ESP.ESPImage import ESPImage -from jigs_measurements import MeasureAngle -from jigs_measurements import MeasureDihedral +from model.jigs_measurements import MeasureAngle +from model.jigs_measurements import MeasureDihedral from geometry.VQT import V, Q, A from utilities.Log import redmsg, quote_html -from elements import PeriodicTable -from bonds import bond_atoms -from chunk import Chunk +from model.elements import PeriodicTable +from model.bonds import bond_atoms +from model.chunk import Chunk from foundation.Utility import Node from foundation.Group import Group -from NamedView import NamedView # for reading one, and for isinstance +from model.NamedView import NamedView # for reading one, and for isinstance from debug import print_compact_traceback from debug import print_compact_stack @@ -57,15 +57,15 @@ from debug import print_compact_stack from constants import gensym from constants import dispNames -from bond_constants import find_bond -from bond_constants import V_SINGLE -from bond_constants import V_DOUBLE -from bond_constants import V_TRIPLE -from bond_constants import V_AROMATIC -from bond_constants import V_GRAPHITE -from bond_constants import V_CARBOMERIC +from model.bond_constants import find_bond +from model.bond_constants import V_SINGLE +from model.bond_constants import V_DOUBLE +from model.bond_constants import V_TRIPLE +from model.bond_constants import V_AROMATIC +from model.bond_constants import V_GRAPHITE +from model.bond_constants import V_CARBOMERIC -from Plane import Plane +from model.Plane import Plane from files.mmp.files_mmp_registration import find_registered_parser_class @@ -795,7 +795,7 @@ class _readmmp_state: # mdistance (name) (r, g, b) (font_name) font_size a1 a2 # no longer modeled on motor, wware 051103 def _read_mdistance(self, card): - from jigs_measurements import MeasureDistance + from model.jigs_measurements import MeasureDistance m = mdistancepat.match(card) # Try to read card assert len(m.groups()) == 8 name = m.group(1) diff --git a/cad/src/files/pdb/files_pdb.py b/cad/src/files/pdb/files_pdb.py index 92eab1fe4..a5becce06 100755 --- a/cad/src/files/pdb/files_pdb.py +++ b/cad/src/files/pdb/files_pdb.py @@ -18,12 +18,12 @@ identical in both, so doing that should not cause a problem.) """ import os, time -from chunk import Chunk -from chem import Atom -from bonds import bond_atoms +from model.chunk import Chunk +from model.chem import Atom +from model.bonds import bond_atoms from bonds_from_atoms import inferBonds from string import capitalize -from elements import PeriodicTable, Singlet +from model.elements import PeriodicTable, Singlet from PlatformDependent import fix_plurals from utilities.Log import redmsg, orangemsg from geometry.VQT import A diff --git a/cad/src/graphics/display_styles/DnaCylinderChunks.py b/cad/src/graphics/display_styles/DnaCylinderChunks.py index afde43c2b..68164c428 100644 --- a/cad/src/graphics/display_styles/DnaCylinderChunks.py +++ b/cad/src/graphics/display_styles/DnaCylinderChunks.py @@ -32,7 +32,7 @@ from debug import print_compact_traceback from graphics.display_styles.displaymodes import ChunkDisplayMode from constants import ave_colors, red from prefs_constants import atomHighlightColor_prefs_key -from elements import Singlet +from model.elements import Singlet chunkHighlightColor_prefs_key = atomHighlightColor_prefs_key # initial kluge diff --git a/cad/src/graphics/drawing/bond_drawer.py b/cad/src/graphics/drawing/bond_drawer.py index 5ab604b2b..27d2fe266 100755 --- a/cad/src/graphics/drawing/bond_drawer.py +++ b/cad/src/graphics/drawing/bond_drawer.py @@ -35,7 +35,7 @@ from utilities import debug_flags from graphics.rendering.povray.povheader import povpoint from utilities.Printing import Vector3ToString -from elements import Singlet +from model.elements import Singlet from debug import print_compact_stack, print_compact_traceback @@ -60,13 +60,13 @@ from constants import black from constants import white from constants import orange -from bond_constants import V_SINGLE -from bond_constants import V_DOUBLE -from bond_constants import V_TRIPLE -from bond_constants import bond_letter_from_v6 -from bond_constants import V_AROMATIC -from bond_constants import V_GRAPHITE -from bond_constants import V_CARBOMERIC +from model.bond_constants import V_SINGLE +from model.bond_constants import V_DOUBLE +from model.bond_constants import V_TRIPLE +from model.bond_constants import bond_letter_from_v6 +from model.bond_constants import V_AROMATIC +from model.bond_constants import V_GRAPHITE +from model.bond_constants import V_CARBOMERIC from prefs_constants import _default_toolong_hicolor ## not yet in prefs db? from prefs_constants import diBALL_BondCylinderRadius_prefs_key diff --git a/cad/src/graphics/rendering/qutemol/qutemol.py b/cad/src/graphics/rendering/qutemol/qutemol.py index 55dbda4e7..112c667a4 100755 --- a/cad/src/graphics/rendering/qutemol/qutemol.py +++ b/cad/src/graphics/rendering/qutemol/qutemol.py @@ -30,7 +30,7 @@ from debug import print_compact_traceback from debug_prefs import debug_pref, Choice_boolean_True from constants import properDisplayNames, TubeRadius, diBALL_SigmaBondRadius from files.pdb.files_pdb import writePDB_Header, writepdb, EXCLUDE_HIDDEN_ATOMS -from elements import PeriodicTable +from model.elements import PeriodicTable from prefs_constants import cpkScaleFactor_prefs_key from prefs_constants import diBALL_AtomRadius_prefs_key diff --git a/cad/src/graphics/widgets/DynamicTip.py b/cad/src/graphics/widgets/DynamicTip.py index f4e2dd8a7..a34765a16 100755 --- a/cad/src/graphics/widgets/DynamicTip.py +++ b/cad/src/graphics/widgets/DynamicTip.py @@ -35,10 +35,10 @@ import time from PyQt4.Qt import QToolTip, QRect import foundation.env as env -from chem import Atom -from elements import Singlet -from bonds import Bond -from jigs import Jig +from model.chem import Atom +from model.elements import Singlet +from model.bonds import Bond +from model.jigs import Jig from geometry.VQT import vlen from geometry.VQT import atom_angle_radians diff --git a/cad/src/graphics/widgets/GLPane.py b/cad/src/graphics/widgets/GLPane.py index dc193bafb..69251bc87 100755 --- a/cad/src/graphics/widgets/GLPane.py +++ b/cad/src/graphics/widgets/GLPane.py @@ -140,7 +140,7 @@ from debug import print_compact_traceback, print_compact_stack import foundation.preferences as preferences import foundation.env as env from foundation.changes import SubUsageTrackingMixin -from cursors import createCompositeCursor +from ne1_ui.cursors import createCompositeCursor from graphics.widgets.DynamicTip import DynamicTip from graphics.drawing.Guides import Guides @@ -186,7 +186,7 @@ from graphics.widgets.GLPane_minimal import GLPane_minimal import qt4transition # suspicious imports [should not really be needed, according to bruce 070919] -from bonds import Bond # used only for selobj ordering +from model.bonds import Bond # used only for selobj ordering debug_lighting = False #bruce 050418 diff --git a/cad/src/graphics/widgets/GLPane_minimal.py b/cad/src/graphics/widgets/GLPane_minimal.py index 5093e0272..0ad45b983 100644 --- a/cad/src/graphics/widgets/GLPane_minimal.py +++ b/cad/src/graphics/widgets/GLPane_minimal.py @@ -19,7 +19,7 @@ from PyQt4.Qt import QGLWidget from geometry.VQT import V, Q from graphics.behaviors.Trackball import Trackball -from NamedView import NamedView +from model.NamedView import NamedView from prefs_constants import undoRestoreView_prefs_key diff --git a/cad/src/graphics/widgets/ThumbView.py b/cad/src/graphics/widgets/ThumbView.py index 49295618c..e2c7a771e 100755 --- a/cad/src/graphics/widgets/ThumbView.py +++ b/cad/src/graphics/widgets/ThumbView.py @@ -79,9 +79,9 @@ from constants import GL_FAR_Z from prefs_constants import bondpointHighlightColor_prefs_key from foundation.Group import Group -from chem import Atom -from elements import Singlet -from chunk import Chunk +from model.chem import Atom +from model.elements import Singlet +from model.chunk import Chunk from pastables import find_hotspot_for_pasting diff --git a/cad/src/HistoryWidget.py b/cad/src/history/HistoryWidget.py index 80472a81f..80472a81f 100755 --- a/cad/src/HistoryWidget.py +++ b/cad/src/history/HistoryWidget.py diff --git a/cad/src/history/__init__.py b/cad/src/history/__init__.py new file mode 100644 index 000000000..e69de29bb --- /dev/null +++ b/cad/src/history/__init__.py diff --git a/cad/src/jigmakers_Mixin.py b/cad/src/jigmakers_Mixin.py index 504bd2a4c..d1690a808 100644 --- a/cad/src/jigmakers_Mixin.py +++ b/cad/src/jigmakers_Mixin.py @@ -19,10 +19,10 @@ from PyQt4.Qt import QMessageBox from utilities.Log import redmsg, greenmsg, orangemsg import foundation.env as env -from jigs import Anchor -from jigs import Stat -from jigs import Thermo -from jigs import AtomSet +from model.jigs import Anchor +from model.jigs import Stat +from model.jigs import Thermo +from model.jigs import AtomSet class jigmakers_Mixin: @@ -214,7 +214,7 @@ class jigmakers_Mixin: env.history.message(cmd + redmsg(msg)) return - from jigs_planes import GridPlane + from model.jigs_planes import GridPlane m = GridPlane(self.assy, atoms) m.edit() if m.cancelled: # User hit 'Cancel' button in the jig dialog. @@ -297,7 +297,7 @@ class jigmakers_Mixin: env.history.message(cmd + redmsg(msg)) return - from jigs_measurements import MeasureDistance + from model.jigs_measurements import MeasureDistance d = MeasureDistance(self.assy, atoms) self.unpickall_in_GLPane() self.place_new_jig(d) @@ -319,7 +319,7 @@ class jigmakers_Mixin: env.history.message(cmd + redmsg(msg)) return - from jigs_measurements import MeasureAngle + from model.jigs_measurements import MeasureAngle d = MeasureAngle(self.assy, atoms) self.unpickall_in_GLPane() self.place_new_jig(d) @@ -340,7 +340,7 @@ class jigmakers_Mixin: env.history.message(cmd + redmsg(msg)) return - from jigs_measurements import MeasureDihedral + from model.jigs_measurements import MeasureDihedral d = MeasureDihedral(self.assy, atoms) self.unpickall_in_GLPane() self.place_new_jig(d) diff --git a/cad/src/main.py b/cad/src/main.py index 6616147d8..b5712e1c6 100755 --- a/cad/src/main.py +++ b/cad/src/main.py @@ -127,7 +127,7 @@ def _start_NE1(): _main_globals = globals() # needed by startup_script - from startup.main_startup import startup_script + from ne1_startup.main_startup import startup_script startup_script( _main_globals ) diff --git a/cad/src/Comment.py b/cad/src/model/Comment.py index 5d925c32d..5d925c32d 100755 --- a/cad/src/Comment.py +++ b/cad/src/model/Comment.py diff --git a/cad/src/Elem.py b/cad/src/model/Elem.py index d40457f30..7cf2afd1b 100644 --- a/cad/src/Elem.py +++ b/cad/src/model/Elem.py @@ -22,7 +22,7 @@ to help permit specialized modules and Elem/Atom subclasses for PAM3 and PAM5 (etc). (Should we define new Elem subclasses for them?) """ -from atomtypes import AtomType +from model.atomtypes import AtomType from foundation.state_utils import IdentityCopyMixin class Elem(IdentityCopyMixin): # bruce 050510 renamed this from 'elem' (not using 'Element' since too common in strings/comments) diff --git a/cad/src/Line.py b/cad/src/model/Line.py index 3ce885b40..4c23278b4 100755 --- a/cad/src/Line.py +++ b/cad/src/model/Line.py @@ -23,7 +23,7 @@ from geometry.VQT import V, Q, cross, A, planeXline, vlen, norm, angleBetween from debug import print_compact_traceback from constants import blue from graphics.drawables.ResizeHandle import ResizeHandle -from ReferenceGeometry import ReferenceGeometry +from model.ReferenceGeometry import ReferenceGeometry class Line(ReferenceGeometry): diff --git a/cad/src/NamedView.py b/cad/src/model/NamedView.py index fc1fba58c..fc1fba58c 100644 --- a/cad/src/NamedView.py +++ b/cad/src/model/NamedView.py diff --git a/cad/src/Plane.py b/cad/src/model/Plane.py index da3c16b35..0daf13caa 100755 --- a/cad/src/Plane.py +++ b/cad/src/model/Plane.py @@ -34,7 +34,7 @@ from debug import print_compact_traceback import foundation.env as env from utilities.Log import redmsg -from ReferenceGeometry import ReferenceGeometry +from model.ReferenceGeometry import ReferenceGeometry from graphics.drawables.DirectionArrow import DirectionArrow from graphics.drawables.ResizeHandle import ResizeHandle diff --git a/cad/src/PovrayScene.py b/cad/src/model/PovrayScene.py index 69713936c..69713936c 100755 --- a/cad/src/PovrayScene.py +++ b/cad/src/model/PovrayScene.py diff --git a/cad/src/ReferenceGeometry.py b/cad/src/model/ReferenceGeometry.py index 4d52901d9..5009f7ead 100755 --- a/cad/src/ReferenceGeometry.py +++ b/cad/src/model/ReferenceGeometry.py @@ -37,7 +37,7 @@ from OpenGL.GL import glPushName from OpenGL.GL import glPopName from foundation.Utility import Node -from jigs import Jig +from model.jigs import Jig from graphics.drawables.DragHandler import DragHandler_API from utilities.Log import greenmsg diff --git a/cad/src/model/assembly.py b/cad/src/model/assembly.py index cdb25a1d4..383c52f59 100755 --- a/cad/src/model/assembly.py +++ b/cad/src/model/assembly.py @@ -87,18 +87,18 @@ import foundation.undo_archive as undo_archive from constants import gensym, SELWHAT_CHUNKS, SELWHAT_ATOMS from foundation.state_constants import S_CHILD, S_DATA, S_REF -from part import Part as Part_class # use a name we can search for [bruce 071029] +from model.part import Part as Part_class # use a name we can search for [bruce 071029] ### TODO: rename the class Part itself somehow; both Part and part are too generic -from part import MainPart -from part import ClipboardItemPart +from model.part import MainPart +from model.part import ClipboardItemPart from icon_utilities import imagename_to_pixmap from commands.PartProperties.PartProp import PartProp from PyQt4 import QtGui from foundation.Assembly_API import Assembly_API -from prefsTree import MainPrefsGroupPart +from model.prefsTree import MainPrefsGroupPart import foundation.undo_manager as undo_manager from files.mmp.files_mmp_writing import writemmpfile_assy diff --git a/cad/src/atomtypes.py b/cad/src/model/atomtypes.py index ef6af0aed..7f65abb29 100755 --- a/cad/src/atomtypes.py +++ b/cad/src/model/atomtypes.py @@ -30,7 +30,7 @@ from utilities import debug_flags from foundation.state_utils import IdentityCopyMixin import foundation.env as env -from bond_constants import V_SINGLE, V_DOUBLE, V_TRIPLE, V_AROMATIC, V_GRAPHITE, V_CARBOMERIC +from model.bond_constants import V_SINGLE, V_DOUBLE, V_TRIPLE, V_AROMATIC, V_GRAPHITE, V_CARBOMERIC class AtomType(IdentityCopyMixin): """An atom type includes an element and its bonding pattern (and maybe more) -- diff --git a/cad/src/bond_constants.py b/cad/src/model/bond_constants.py index 0ccb66585..0ccb66585 100755 --- a/cad/src/bond_constants.py +++ b/cad/src/model/bond_constants.py diff --git a/cad/src/bonds.py b/cad/src/model/bonds.py index 25648b517..9785ab88d 100755 --- a/cad/src/bonds.py +++ b/cad/src/model/bonds.py @@ -40,21 +40,21 @@ from debug import reload_once_per_event from utilities import debug_flags -from elements import Singlet - -from bond_constants import V_SINGLE -from bond_constants import BOND_VALENCES -from bond_constants import BOND_MMPRECORDS -from bond_constants import BOND_VALENCES_HIGHEST_FIRST -from bond_constants import bond_params -from bond_constants import bonded_atoms_summary -from bond_constants import bond_type_names -from bond_constants import atoms_are_bonded -from bond_constants import find_bond +from model.elements import Singlet + +from model.bond_constants import V_SINGLE +from model.bond_constants import BOND_VALENCES +from model.bond_constants import BOND_MMPRECORDS +from model.bond_constants import BOND_VALENCES_HIGHEST_FIRST +from model.bond_constants import bond_params +from model.bond_constants import bonded_atoms_summary +from model.bond_constants import bond_type_names +from model.bond_constants import atoms_are_bonded +from model.bond_constants import find_bond from bond_chains import grow_directional_bond_chain -import global_model_changedicts +import model.global_model_changedicts as global_model_changedicts import foundation.env as env from GlobalPreferences import usePyrexAtomsAndBonds @@ -1548,9 +1548,9 @@ class Bond(BondBase, StateMixin, Selobj_API, IdentityCopyMixin): If computed, and if it's partly arbitrary, **kws (out/up) might be used. """ if debug_flags.atom_debug: - import pi_bond_sp_chain + import model.pi_bond_sp_chain as pi_bond_sp_chain reload_once_per_event(pi_bond_sp_chain) #bruce 050825 use reload_once_per_event to remove intolerable slowdown - from pi_bond_sp_chain import bond_get_pi_info + from model.pi_bond_sp_chain import bond_get_pi_info return bond_get_pi_info(self, **kws) # no need to pass an index -- that method can find one on self if it stored one def potential_pi_bond(self): #bruce 050718 diff --git a/cad/src/chem.py b/cad/src/model/chem.py index 903769f45..e5e38baec 100755 --- a/cad/src/chem.py +++ b/cad/src/model/chem.py @@ -60,16 +60,19 @@ from graphics.drawing.drawer import drawsphere from graphics.drawing.drawer import drawpolycone from graphics.drawing.drawer import drawwiresphere -from elements import Singlet -from elements import Hydrogen -from elements import PeriodicTable +from model.elements import Singlet +from model.elements import Hydrogen +from model.elements import PeriodicTable -from bonds import bonds_mmprecord, bond_copied_atoms, bond_atoms +from model.bonds import bonds_mmprecord, bond_copied_atoms, bond_atoms -import global_model_changedicts +import model.global_model_changedicts as global_model_changedicts # note: chunk and chem form a two element import cycle. -import chunk +# this should be: +# import model.chunk as chunk +# but that fails, so we have to do a relative import to satisfy the cycle: +import chunk # from model from geometry.VQT import V, Q, A, norm, cross, twistor, vlen, orthodist from geometry.VQT import atom_angle_radians @@ -110,14 +113,14 @@ from constants import PickedColor from GlobalPreferences import disable_do_not_draw_open_bonds from GlobalPreferences import usePyrexAtomsAndBonds -from bond_constants import V_SINGLE -from bond_constants import min_max_valences_from_v6 -from bond_constants import valence_to_v6 +from model.bond_constants import V_SINGLE +from model.bond_constants import min_max_valences_from_v6 +from model.bond_constants import valence_to_v6 -from bond_constants import DIRBOND_CHAIN_MIDDLE -from bond_constants import DIRBOND_CHAIN_END -from bond_constants import DIRBOND_NONE -from bond_constants import DIRBOND_ERROR +from model.bond_constants import DIRBOND_CHAIN_MIDDLE +from model.bond_constants import DIRBOND_CHAIN_END +from model.bond_constants import DIRBOND_NONE +from model.bond_constants import DIRBOND_ERROR from prefs_constants import arrowsOnFivePrimeEnds_prefs_key from prefs_constants import arrowsOnThreePrimeEnds_prefs_key @@ -149,7 +152,7 @@ from graphics.display_styles.displaymodes import remap_atom_dispdefs from foundation.inval import InvalMixin #bruce 050510 import foundation.Utility as Utility -from jigs import Jig +from model.jigs import Jig from dna.operations.crossovers import crossover_menu_spec @@ -2863,7 +2866,7 @@ class Atom(AtomBase, InvalMixin, StateMixin, Selobj_API, IdentityCopyMixin): # And, break_interpart_bonds can then dislike .molecule being None # and set it back to _nullMol. So test for these values too. mol = self.molecule - from chunk import _nullMol + from model.chunk import _nullMol res = self.__killed or mol is None or mol is _nullMol if debug_flags.atom_debug: # this cond is for speed better_alive_answer = mol is not None and self.key in mol.atoms and mol is not _nullMol ##e and mol is not killed?? @@ -2891,7 +2894,7 @@ class Atom(AtomBase, InvalMixin, StateMixin, Selobj_API, IdentityCopyMixin): if killed: assert self.__killed == 1 assert not self.picked - from chunk import _nullMol + from model.chunk import _nullMol assert self.molecule is _nullMol or self.molecule is None # thus don't do this: assert not self.key in self.molecule.assy.selatoms assert not self.bonds @@ -3212,7 +3215,7 @@ class Atom(AtomBase, InvalMixin, StateMixin, Selobj_API, IdentityCopyMixin): # (though it's untested, since I ended up fixing a current bug # in a different way; but it looks correct and seems useful # enough to leave). - from bond_constants import V_ZERO_VALENCE, BOND_VALENCES + from model.bond_constants import V_ZERO_VALENCE, BOND_VALENCES _debug = False ## debug_flags.atom_debug is sometimes useful here if self._modified_valence: self._modified_valence = False # do this first, so exceptions in the following only happen once diff --git a/cad/src/chunk.py b/cad/src/model/chunk.py index e586beb2a..00335511c 100755 --- a/cad/src/chunk.py +++ b/cad/src/model/chunk.py @@ -65,7 +65,7 @@ from OpenGL.GL import glCallList # chunk and chem form a two element import cycle # (chem is used here only for class Atom and one global changedict, # as of before 071113) -import chem +import model.chem as chem from geometry.VQT import V, Q, A, vlen @@ -96,9 +96,9 @@ from debug_prefs import debug_pref, Choice_boolean_True, Choice_boolean_False from icon_utilities import imagename_to_pixmap -import bonds # TODO: import specific functions, since no longer an import cycle +import model.bonds as bonds # TODO: import specific functions, since no longer an import cycle -from elements import Singlet +from model.elements import Singlet from geometry.BoundingBox import BBox from graphics.drawing.drawer import ColorSorter, ColorSortedDisplayList @@ -120,7 +120,7 @@ from constants import diDNACYLINDER from constants import ATOM_CONTENT_FOR_DISPLAY_STYLE from constants import noop -from elements import PeriodicTable +from model.elements import PeriodicTable from commands.ChunkProperties.ChunkProp import ChunkProp @@ -3115,7 +3115,7 @@ class Chunk(NodeWithAtomContents, InvalMixin, SelfUsageTrackingMixin, SubUsageTr Given some copied atoms (in a private format in pairlis and ndix), ensure their bonds and jigs will be taken care of. """ - from bonds import bond_copied_atoms # might be a recursive import if done at toplevel + from model.bonds import bond_copied_atoms # might be a recursive import if done at toplevel origid_to_copy = mapping.origid_to_copy extern_atoms_bonds = mapping.extern_atoms_bonds #e could be integrated with mapping.do_at_end, @@ -3236,7 +3236,7 @@ class Chunk(NodeWithAtomContents, InvalMixin, SelfUsageTrackingMixin, SubUsageTr # bruce 041116: note: callers seem to be mainly in model tree copy ops # and in depositMode. # [where do they call addmol? why did extrude's copies break on 041116?] - from bonds import bond_copied_atoms # might be a recursive import if done at toplevel + from model.bonds import bond_copied_atoms # might be a recursive import if done at toplevel pairlis = [] ndix = {} newname = mol_copy_name(self.name) diff --git a/cad/src/elements.py b/cad/src/model/elements.py index fed38e1e0..7d4d9e926 100755 --- a/cad/src/elements.py +++ b/cad/src/model/elements.py @@ -38,9 +38,9 @@ and then access the attribute directly. from foundation.preferences import prefs_context -from Elem import Elem +from model.Elem import Elem -from elements_data import init_chemical_elements +from model.elements_data import init_chemical_elements from dna.model.elements_data_PAM3 import init_PAM3_elements from dna.model.elements_data_PAM5 import init_PAM5_elements diff --git a/cad/src/elements_data.py b/cad/src/model/elements_data.py index 1cc541f80..1cc541f80 100755 --- a/cad/src/elements_data.py +++ b/cad/src/model/elements_data.py diff --git a/cad/src/global_model_changedicts.py b/cad/src/model/global_model_changedicts.py index 3dce7065c..3dce7065c 100644 --- a/cad/src/global_model_changedicts.py +++ b/cad/src/model/global_model_changedicts.py diff --git a/cad/src/jigs.py b/cad/src/model/jigs.py index 13f7265ba..13f7265ba 100755 --- a/cad/src/jigs.py +++ b/cad/src/model/jigs.py diff --git a/cad/src/jigs_measurements.py b/cad/src/model/jigs_measurements.py index 3948d77c2..db876cd35 100755 --- a/cad/src/jigs_measurements.py +++ b/cad/src/model/jigs_measurements.py @@ -32,7 +32,7 @@ from geometry.VQT import V, norm, cross, vlen, angleBetween from foundation.Utility import Node from utilities.Log import redmsg, greenmsg, orangemsg from debug import print_compact_stack, print_compact_traceback -from jigs import Jig +from model.jigs import Jig from graphics.drawing.dimensions import drawLinearDimension, drawAngleDimension, drawDihedralDimension from graphics.drawing.drawer import drawtext diff --git a/cad/src/jigs_motors.py b/cad/src/model/jigs_motors.py index 00f19e697..eb767108e 100755 --- a/cad/src/jigs_motors.py +++ b/cad/src/model/jigs_motors.py @@ -35,7 +35,7 @@ from utilities.Log import orangemsg from utilities.Log import redmsg, greenmsg from graphics.rendering.povray.povheader import povpoint #bruce 050413 from debug import print_compact_stack, print_compact_traceback -from jigs import Jig +from model.jigs import Jig from constants import gray diff --git a/cad/src/jigs_planes.py b/cad/src/model/jigs_planes.py index e79deb52c..db7f34f31 100755 --- a/cad/src/jigs_planes.py +++ b/cad/src/model/jigs_planes.py @@ -34,7 +34,7 @@ from graphics.drawing.draw_grid_lines import drawSiCGrid from geometry.VQT import V, Q, A, cross from graphics.rendering.povray.povheader import povpoint -from jigs import Jig +from model.jigs import Jig from constants import black from constants import gray diff --git a/cad/src/part.py b/cad/src/model/part.py index 8b98f01b5..5ec0535d9 100755 --- a/cad/src/part.py +++ b/cad/src/model/part.py @@ -52,7 +52,7 @@ from foundation.Group import Group from foundation.Assembly_API import Assembly_API -from NamedView import NamedView +from model.NamedView import NamedView from geometry.VQT import V, Q from debug import print_compact_traceback, print_compact_stack from utilities import debug_flags @@ -60,8 +60,8 @@ from utilities import debug_flags from utilities.Log import greenmsg, redmsg from geometry.BoundingBox import BBox -from chunk import Chunk -from jigs import Jig +from model.chunk import Chunk +from model.jigs import Jig from foundation.node_indices import fix_one_or_complain from constants import diINVISIBLE @@ -83,7 +83,7 @@ from constants import SELWHAT_CHUNKS, SELWHAT_ATOMS from foundation.state_constants import S_REF, S_DATA, S_PARENT, S_CHILD from prefs_constants import levelOfDetail_prefs_key -from Line import Line +from model.Line import Line # number of atoms for detail level 0 HUGE_MODEL = 40000 diff --git a/cad/src/pi_bond_sp_chain.py b/cad/src/model/pi_bond_sp_chain.py index 67069c3d4..773671633 100755 --- a/cad/src/pi_bond_sp_chain.py +++ b/cad/src/model/pi_bond_sp_chain.py @@ -27,17 +27,17 @@ import math from Numeric import dot from utilities import debug_flags -from jigs import Jig +from model.jigs import Jig from geometry.VQT import V, Q, A, cross, vlen, norm, twistor_angle from bond_chains import grow_bond_chain -from bond_constants import V_SINGLE -from bond_constants import V_DOUBLE -from bond_constants import V_TRIPLE -from bond_constants import V_AROMATIC -from bond_constants import V_GRAPHITE -from bond_constants import V_CARBOMERIC +from model.bond_constants import V_SINGLE +from model.bond_constants import V_DOUBLE +from model.bond_constants import V_TRIPLE +from model.bond_constants import V_AROMATIC +from model.bond_constants import V_GRAPHITE +from model.bond_constants import V_CARBOMERIC DFLT_OUT = V(0.0, -0.6, 0.8) # these are rotated from standard out = V(0,0,1), up = V(0,1,0) but still orthonormal DFLT_UP = V(0.0, 0.8, 0.6) diff --git a/cad/src/prefsTree.py b/cad/src/model/prefsTree.py index 68298b3e0..307b46be5 100755 --- a/cad/src/prefsTree.py +++ b/cad/src/model/prefsTree.py @@ -22,7 +22,7 @@ Perhaps ought to be split into two files? import os from foundation.Utility import Node from foundation.Group import Group -from part import Part +from model.part import Part from constants import noop, dispLabel, default_display_mode import foundation.env as env diff --git a/cad/src/modelTree/ModelTree.py b/cad/src/modelTree/ModelTree.py index 35d735895..71064c299 100755 --- a/cad/src/modelTree/ModelTree.py +++ b/cad/src/modelTree/ModelTree.py @@ -42,10 +42,10 @@ from PyQt4 import QtCore import foundation.env as env from utilities import debug_flags from PlatformDependent import fix_plurals -import modelTreeGui # defines ModelTreeGui (note case difference), Ne1Model_api +import modelTree.modelTreeGui as modelTreeGui # defines ModelTreeGui (note case difference), Ne1Model_api -from chunk import Chunk -from jigs import Jig +from model.chunk import Chunk +from model.jigs import Jig from utilities.Log import orangemsg from foundation.Group import Group from debug import print_compact_traceback @@ -329,9 +329,9 @@ class modelTree(modelTreeGui.Ne1Model_api): try: from foundation.Utility import Node ## print "reloading prefsTree" - import prefsTree as _X + import model.prefsTree as _X reload(_X) - from prefsTree import prefsTree # constructor for an object which has a tree of nodes and controls them + from model.prefsTree import prefsTree # constructor for an object which has a tree of nodes and controls them self.pt = prefsTree(self.assy) # guess; guessing it's ok to remake it each time ptnode = self.pt.topnode assert ptnode is not None @@ -478,7 +478,7 @@ class modelTree(modelTreeGui.Ne1Model_api): # this part of the menu-spec itself #e. [bruce 050421] jig = nodeset[0] - from jigs_planes import RectGadget # Try to remove this menu item. [Huaicai 10/11/05] + from model.jigs_planes import RectGadget # Try to remove this menu item. [Huaicai 10/11/05] if not isinstance(jig, RectGadget): #raise disabled_must = jig.disabled_by_atoms() # (by its atoms being in the wrong part) @@ -754,7 +754,7 @@ class modelTree(modelTreeGui.Ne1Model_api): if allstats.njigs == 1: jig = nodeset[0] - from jigs_planes import RectGadget # Try to remove this menu item. [Huaicai 10/11/05] + from model.jigs_planes import RectGadget # Try to remove this menu item. [Huaicai 10/11/05] if isinstance(jig, RectGadget): ## return res -- this 'return' was causing bug 1189 by skipping the rest of the menu, not just this item. # Try to do something less drastic. [bruce 051208] diff --git a/cad/src/Node_as_MT_DND_Target.py b/cad/src/modelTree/Node_as_MT_DND_Target.py index af6e57548..af6e57548 100644 --- a/cad/src/Node_as_MT_DND_Target.py +++ b/cad/src/modelTree/Node_as_MT_DND_Target.py diff --git a/cad/src/modelTreeGui.py b/cad/src/modelTree/modelTreeGui.py index 7a2762dd2..8acde6484 100755 --- a/cad/src/modelTreeGui.py +++ b/cad/src/modelTree/modelTreeGui.py @@ -77,7 +77,7 @@ import foundation.env as env from widgets.simple_dialogs import grab_text_line_using_dialog from icon_utilities import imagename_to_pixmap -from Node_as_MT_DND_Target import Node_as_MT_DND_Target #bruce 071025 +from modelTree.Node_as_MT_DND_Target import Node_as_MT_DND_Target #bruce 071025 from constants import AC_INVISIBLE, AC_HAS_INDIVIDUAL_DISPLAY_STYLE diff --git a/cad/src/model_updater/__init__.py b/cad/src/model_updater/__init__.py new file mode 100644 index 000000000..e69de29bb --- /dev/null +++ b/cad/src/model_updater/__init__.py diff --git a/cad/src/bond_updater.py b/cad/src/model_updater/bond_updater.py index dfd24de51..5c7728f18 100755 --- a/cad/src/bond_updater.py +++ b/cad/src/model_updater/bond_updater.py @@ -27,12 +27,12 @@ type- and atom-type- updating code in this file. from debug import print_compact_traceback -from bond_constants import V_SINGLE -from bond_constants import V_DOUBLE -from bond_constants import V_AROMATIC -from bond_constants import V_GRAPHITE -from bond_constants import V_TRIPLE -from bond_constants import V_CARBOMERIC +from model.bond_constants import V_SINGLE +from model.bond_constants import V_DOUBLE +from model.bond_constants import V_AROMATIC +from model.bond_constants import V_GRAPHITE +from model.bond_constants import V_TRIPLE +from model.bond_constants import V_CARBOMERIC # == diff --git a/cad/src/master_model_updater.py b/cad/src/model_updater/master_model_updater.py index 69550e63a..6da2037d9 100755 --- a/cad/src/master_model_updater.py +++ b/cad/src/model_updater/master_model_updater.py @@ -42,14 +42,14 @@ DNA-specific code in other specific updater modules, for this to also call. bruce 080305 added _autodelete_empty_groups. """ -from global_model_changedicts import changed_structure_atoms -from global_model_changedicts import changed_bond_types +from model.global_model_changedicts import changed_structure_atoms +from model.global_model_changedicts import changed_bond_types import foundation.env as env from utilities.Log import redmsg -from bond_updater import update_bonds_after_each_event -from bond_updater import process_changed_bond_types +from model_updater.bond_updater import update_bonds_after_each_event +from model_updater.bond_updater import process_changed_bond_types from debug import print_compact_stack, print_compact_traceback diff --git a/cad/src/movie.py b/cad/src/movie.py index 8274e4478..a22aedbac 100755 --- a/cad/src/movie.py +++ b/cad/src/movie.py @@ -18,7 +18,7 @@ from struct import unpack from PyQt4.Qt import Qt, qApp, QApplication, QCursor, SIGNAL from utilities.Log import redmsg, orangemsg, greenmsg from geometry.VQT import A -from chem import move_alist_and_snuggle +from model.chem import move_alist_and_snuggle from utilities import debug_flags from PlatformDependent import fix_plurals from debug import print_compact_stack, print_compact_traceback diff --git a/cad/src/startup/ALTERNATE_CAD_SRC_PATH-doc.txt b/cad/src/ne1_startup/ALTERNATE_CAD_SRC_PATH-doc.txt index 145d9f510..145d9f510 100644 --- a/cad/src/startup/ALTERNATE_CAD_SRC_PATH-doc.txt +++ b/cad/src/ne1_startup/ALTERNATE_CAD_SRC_PATH-doc.txt diff --git a/cad/src/startup/__init__.py b/cad/src/ne1_startup/__init__.py index 6dfef6d58..6dfef6d58 100644 --- a/cad/src/startup/__init__.py +++ b/cad/src/ne1_startup/__init__.py diff --git a/cad/src/startup/main_startup.py b/cad/src/ne1_startup/main_startup.py index 5dc13ef33..d53c43e23 100755 --- a/cad/src/startup/main_startup.py +++ b/cad/src/ne1_startup/main_startup.py @@ -17,7 +17,7 @@ by bruce 070704. import sys, time -from startup import startup_before_most_imports +from ne1_startup import startup_before_most_imports # NOTE: all other imports MUST be added inside the following function, # since they must not be done before startup_before_most_imports.before_most_imports is executed. @@ -116,12 +116,12 @@ def startup_script( main_globals): # An old comment (I don't know if it's still true -- bruce 071008): # this might have side effects other than defining things. - from MWsemantics import MWsemantics + from ne1_ui.MWsemantics import MWsemantics # initialize modules and data structures - from startup import startup_misc + from ne1_startup import startup_misc # do this here, not earlier, so it's free to do whatever toplevel imports it wants # [bruce 071008 change] diff --git a/cad/src/startup/startup_before_most_imports.py b/cad/src/ne1_startup/startup_before_most_imports.py index 1be02ee52..1be02ee52 100644 --- a/cad/src/startup/startup_before_most_imports.py +++ b/cad/src/ne1_startup/startup_before_most_imports.py diff --git a/cad/src/startup/startup_misc.py b/cad/src/ne1_startup/startup_misc.py index 70cbb4c80..01369ef7d 100755 --- a/cad/src/startup/startup_misc.py +++ b/cad/src/ne1_startup/startup_misc.py @@ -39,7 +39,7 @@ def call_module_init_functions(): #bruce 071005 split this out of main_startup.s # which calls the bond updater presently registered by bond_updater.initialize.) # [bruce 070925 comment] - import master_model_updater + import model_updater.master_model_updater as master_model_updater master_model_updater.initialize() import model.assembly @@ -55,13 +55,13 @@ def register_MMP_RecordParsers(): #bruce 071019 Register MMP_RecordParser subclasses for the model objects that can be read from mmp files, and whose parsers are not hardcoded into files_mmp.py. """ - import Comment + import model.Comment as Comment Comment.register_MMP_RecordParser_for_Comment() import analysis.GAMESS.jig_Gamess as jig_Gamess jig_Gamess.register_MMP_RecordParser_for_Gamess() - import PovrayScene + import model.PovrayScene as PovrayScene PovrayScene.register_MMP_RecordParser_for_PovrayScene() try: @@ -125,7 +125,7 @@ def pre_main_show( win): from debug import print_compact_stack try: # this code is similar to debug.py's _debug_load_window_layout - from UserPrefs import load_window_pos_size + from ne1_ui.UserPrefs import load_window_pos_size from prefs_constants import mainwindow_geometry_prefs_key_prefix keyprefix = mainwindow_geometry_prefs_key_prefix load_window_pos_size( win, keyprefix) diff --git a/cad/src/MWsemantics.py b/cad/src/ne1_ui/MWsemantics.py index e86aaaba6..d5cf58efe 100755 --- a/cad/src/MWsemantics.py +++ b/cad/src/ne1_ui/MWsemantics.py @@ -41,7 +41,7 @@ from PyQt4.Qt import QMessageBox from PyQt4.Qt import QToolBar from PyQt4.Qt import QStatusBar -from elements import PeriodicTable +from model.elements import PeriodicTable from model.assembly import assembly from graphics.drawing.drawer import get_gl_info_string ## grantham 20051201 import os, sys @@ -54,20 +54,20 @@ from PlatformDependent import find_or_make_Nanorex_directory from PlatformDependent import open_file_in_editor from PlatformDependent import find_or_make_Nanorex_subdir -from ViewOrientationWindow import ViewOrientationWindow # Ninad 061121 +from ne1_ui.ViewOrientationWindow import ViewOrientationWindow # Ninad 061121 from debug import print_compact_traceback from debug_prefs import debug_pref, Choice_boolean_False -from Ui_MainWindow import Ui_MainWindow -from Ui_PartWindow import Ui_PartWindow +from ne1_ui.Ui_MainWindow import Ui_MainWindow +from ne1_ui.Ui_PartWindow import Ui_PartWindow ##from modelTree.ModelTree import modelTree ##from GLPane import GLPane from utilities.Log import greenmsg, redmsg, orangemsg -import Ui_CntFlyout -import Ui_DnaFlyout +import ne1_ui.toolbars.Ui_CntFlyout as Ui_CntFlyout +import ne1_ui.toolbars.Ui_DnaFlyout as Ui_DnaFlyout from ops_files import fileSlotsMixin from ops_view import viewSlotsMixin @@ -202,7 +202,7 @@ class MWsemantics(QMainWindow, # self.load_icons_to_iconsets() # Uncomment this line to test if Redo button has custom icon when disabled. mark 060427 # Load all NE1 custom cursors. - from cursors import loadCursors + from ne1_ui.cursors import loadCursors loadCursors(self) # Set the main window environment variable. This sets a single @@ -300,7 +300,7 @@ class MWsemantics(QMainWindow, # Create the Preferences dialog widget. # Mark 050628 - from UserPrefs import UserPrefs + from ne1_ui.UserPrefs import UserPrefs self.userPrefs = UserPrefs(self.assy) # Enable/disable plugins. These should be moved to a central method @@ -315,7 +315,7 @@ class MWsemantics(QMainWindow, env.prefs[zoomAboutScreenCenter_prefs_key]) # Create the Help dialog. Mark 050812 - from help import Ne1HelpDialog + from ne1_ui.help.help import Ne1HelpDialog self.help = Ne1HelpDialog() from commands.InsertGraphene.GrapheneGenerator import GrapheneGenerator diff --git a/cad/src/gui/ToolTipText_for_PropertyManagers.py b/cad/src/ne1_ui/ToolTipText_for_PropertyManagers.py index 0a5f9a81b..0a5f9a81b 100644 --- a/cad/src/gui/ToolTipText_for_PropertyManagers.py +++ b/cad/src/ne1_ui/ToolTipText_for_PropertyManagers.py diff --git a/cad/src/Ui_MainWindow.py b/cad/src/ne1_ui/Ui_MainWindow.py index 91e9fa26c..2149e7f4f 100755 --- a/cad/src/Ui_MainWindow.py +++ b/cad/src/ne1_ui/Ui_MainWindow.py @@ -10,27 +10,27 @@ from PyQt4.Qt import Qt, QWidget, QVBoxLayout from icon_utilities import geticon -import Ui_MainWindowWidgets -import Ui_MainWindowWidgetConnections - -import Ui_FileMenu -import Ui_EditMenu -import Ui_ViewMenu -import Ui_InsertMenu -import Ui_ToolsMenu -import Ui_SimulationMenu -import Ui_RenderingMenu -import Ui_HelpMenu - -import Ui_StandardToolBar -import Ui_ViewToolBar -import Ui_StandardViewsToolBar -import Ui_DisplayStylesToolBar -import Ui_SelectToolBar -import Ui_SimulationToolBar -import Ui_BuildToolsToolBar -import Ui_BuildStructuresToolBar -import Ui_RenderingToolBar +import ne1_ui.Ui_MainWindowWidgets as Ui_MainWindowWidgets +import ne1_ui.Ui_MainWindowWidgetConnections as Ui_MainWindowWidgetConnections + +import ne1_ui.menus.Ui_FileMenu as Ui_FileMenu +import ne1_ui.menus.Ui_EditMenu as Ui_EditMenu +import ne1_ui.menus.Ui_ViewMenu as Ui_ViewMenu +import ne1_ui.menus.Ui_InsertMenu as Ui_InsertMenu +import ne1_ui.menus.Ui_ToolsMenu as Ui_ToolsMenu +import ne1_ui.menus.Ui_SimulationMenu as Ui_SimulationMenu +import ne1_ui.menus.Ui_RenderingMenu as Ui_RenderingMenu +import ne1_ui.help.Ui_HelpMenu as Ui_HelpMenu + +import ne1_ui.toolbars.Ui_StandardToolBar as Ui_StandardToolBar +import ne1_ui.toolbars.Ui_ViewToolBar as Ui_ViewToolBar +import ne1_ui.toolbars.Ui_StandardViewsToolBar as Ui_StandardViewsToolBar +import ne1_ui.toolbars.Ui_DisplayStylesToolBar as Ui_DisplayStylesToolBar +import ne1_ui.toolbars.Ui_SelectToolBar as Ui_SelectToolBar +import ne1_ui.toolbars.Ui_SimulationToolBar as Ui_SimulationToolBar +import ne1_ui.toolbars.Ui_BuildToolsToolBar as Ui_BuildToolsToolBar +import ne1_ui.toolbars.Ui_BuildStructuresToolBar as Ui_BuildStructuresToolBar +import ne1_ui.toolbars.Ui_RenderingToolBar as Ui_RenderingToolBar from StatusBar import StatusBar @@ -103,7 +103,7 @@ class Ui_MainWindow(object): # = # Create the "What's This?" text for all main window widgets. - from gui.WhatsThisText_for_MainWindow import createWhatsThisTextForMainWindowWidgets + from ne1_ui.WhatsThisText_for_MainWindow import createWhatsThisTextForMainWindowWidgets createWhatsThisTextForMainWindowWidgets(self) # IMPORTANT: All main window widgets and their "What's This" text should diff --git a/cad/src/Ui_MainWindowWidgetConnections.py b/cad/src/ne1_ui/Ui_MainWindowWidgetConnections.py index 28b9273ee..28b9273ee 100644 --- a/cad/src/Ui_MainWindowWidgetConnections.py +++ b/cad/src/ne1_ui/Ui_MainWindowWidgetConnections.py diff --git a/cad/src/Ui_MainWindowWidgets.py b/cad/src/ne1_ui/Ui_MainWindowWidgets.py index 6da45c0d5..124ff0a84 100644 --- a/cad/src/Ui_MainWindowWidgets.py +++ b/cad/src/ne1_ui/Ui_MainWindowWidgets.py @@ -850,7 +850,7 @@ def setupUi(win): win.toolsDoneAction.setObjectName("toolsDoneAction") # Dock widgets - from Ui_ReportsDockWidget import Ui_ReportsDockWidget + from ne1_ui.Ui_ReportsDockWidget import Ui_ReportsDockWidget win.reportsDockWidget = Ui_ReportsDockWidget(win) def retranslateUi(win): diff --git a/cad/src/Ui_PartWindow.py b/cad/src/ne1_ui/Ui_PartWindow.py index 4478bb302..4478bb302 100755 --- a/cad/src/Ui_PartWindow.py +++ b/cad/src/ne1_ui/Ui_PartWindow.py diff --git a/cad/src/Ui_ReportsDockWidget.py b/cad/src/ne1_ui/Ui_ReportsDockWidget.py index 52939af76..750cd0658 100644 --- a/cad/src/Ui_ReportsDockWidget.py +++ b/cad/src/ne1_ui/Ui_ReportsDockWidget.py @@ -12,7 +12,7 @@ To do: History: Mark 2008-01-05: Created. """ -from HistoryWidget import HistoryWidget +from history.HistoryWidget import HistoryWidget from PyQt4.Qt import Qt, QDockWidget, QWidget, QVBoxLayout, QTabWidget from PyQt4.Qt import QPalette, QSizePolicy from PM.PM_Colors import pmGrpBoxColor diff --git a/cad/src/Ui_ViewOrientation.py b/cad/src/ne1_ui/Ui_ViewOrientation.py index 284003e03..284003e03 100755 --- a/cad/src/Ui_ViewOrientation.py +++ b/cad/src/ne1_ui/Ui_ViewOrientation.py diff --git a/cad/src/UserPrefs.py b/cad/src/ne1_ui/UserPrefs.py index 4b0583481..87c3cf396 100755 --- a/cad/src/UserPrefs.py +++ b/cad/src/ne1_ui/UserPrefs.py @@ -33,7 +33,7 @@ from PyQt4.Qt import QFont from PyQt4.Qt import Qt -from UserPrefsDialog import Ui_UserPrefsDialog +from ne1_ui.UserPrefsDialog import Ui_UserPrefsDialog import foundation.preferences as preferences from debug import print_compact_traceback from debug_prefs import debug_pref, Choice_boolean_False @@ -690,7 +690,7 @@ class UserPrefs(QDialog, Ui_UserPrefsDialog): # This is where What's This descriptions should go for UserPrefs. # Mark 050831. - from gui.WhatsThisText_for_MainWindow import create_whats_this_descriptions_for_UserPrefs_dialog + from ne1_ui.WhatsThisText_for_MainWindow import create_whats_this_descriptions_for_UserPrefs_dialog create_whats_this_descriptions_for_UserPrefs_dialog(self) self.display_origin_axis_checkbox.setWhatsThis("""<p><b>Display Origin Axis</b></p>Shows/Hides the Origin Axis""") diff --git a/cad/src/UserPrefsDialog.py b/cad/src/ne1_ui/UserPrefsDialog.py index cf35f2e22..cf35f2e22 100755 --- a/cad/src/UserPrefsDialog.py +++ b/cad/src/ne1_ui/UserPrefsDialog.py diff --git a/cad/src/UserPrefsDialog.ui b/cad/src/ne1_ui/UserPrefsDialog.ui index ff7967676..ff7967676 100755 --- a/cad/src/UserPrefsDialog.ui +++ b/cad/src/ne1_ui/UserPrefsDialog.ui diff --git a/cad/src/ViewOrientationWindow.py b/cad/src/ne1_ui/ViewOrientationWindow.py index 72a1c5ca8..1502b3040 100755 --- a/cad/src/ViewOrientationWindow.py +++ b/cad/src/ne1_ui/ViewOrientationWindow.py @@ -19,7 +19,7 @@ almost all of it into "widgets" would be good to do sometime. from PyQt4 import QtCore, QtGui from PyQt4.Qt import Qt, SIGNAL, QMainWindow, QDockWidget -from Ui_ViewOrientation import Ui_ViewOrientation +from ne1_ui.Ui_ViewOrientation import Ui_ViewOrientation from icon_utilities import geticon class ViewOrientationWindow(QDockWidget, Ui_ViewOrientation): diff --git a/cad/src/gui/WhatsThisText_for_MainWindow.py b/cad/src/ne1_ui/WhatsThisText_for_MainWindow.py index 5560e847f..5560e847f 100755 --- a/cad/src/gui/WhatsThisText_for_MainWindow.py +++ b/cad/src/ne1_ui/WhatsThisText_for_MainWindow.py diff --git a/cad/src/gui/WhatsThisText_for_PropertyManagers.py b/cad/src/ne1_ui/WhatsThisText_for_PropertyManagers.py index 9b55c6ddb..9b55c6ddb 100644 --- a/cad/src/gui/WhatsThisText_for_PropertyManagers.py +++ b/cad/src/ne1_ui/WhatsThisText_for_PropertyManagers.py diff --git a/cad/src/gui/__init__.py b/cad/src/ne1_ui/__init__.py index 6b0cf38e3..6b0cf38e3 100644 --- a/cad/src/gui/__init__.py +++ b/cad/src/ne1_ui/__init__.py diff --git a/cad/src/cursors.py b/cad/src/ne1_ui/cursors.py index bdf4d4711..bdf4d4711 100755 --- a/cad/src/cursors.py +++ b/cad/src/ne1_ui/cursors.py diff --git a/cad/src/HelpDialog.py b/cad/src/ne1_ui/help/HelpDialog.py index 65e3825c1..65e3825c1 100755 --- a/cad/src/HelpDialog.py +++ b/cad/src/ne1_ui/help/HelpDialog.py diff --git a/cad/src/HelpDialog.ui b/cad/src/ne1_ui/help/HelpDialog.ui index 378633e5f..378633e5f 100755 --- a/cad/src/HelpDialog.ui +++ b/cad/src/ne1_ui/help/HelpDialog.ui diff --git a/cad/src/Ui_HelpMenu.py b/cad/src/ne1_ui/help/Ui_HelpMenu.py index 58337e5e5..58337e5e5 100755 --- a/cad/src/Ui_HelpMenu.py +++ b/cad/src/ne1_ui/help/Ui_HelpMenu.py diff --git a/cad/src/ne1_ui/help/__init__.py b/cad/src/ne1_ui/help/__init__.py new file mode 100644 index 000000000..e69de29bb --- /dev/null +++ b/cad/src/ne1_ui/help/__init__.py diff --git a/cad/src/help.py b/cad/src/ne1_ui/help/help.py index 0803debcf..cf96242ba 100755 --- a/cad/src/help.py +++ b/cad/src/ne1_ui/help/help.py @@ -26,7 +26,7 @@ import os, sys from PyQt4.Qt import QWidget from PyQt4.Qt import SIGNAL -from HelpDialog import Ui_HelpDialog +from ne1_ui.help.HelpDialog import Ui_HelpDialog from icon_utilities import geticon class Ne1HelpDialog(QWidget, Ui_HelpDialog): diff --git a/cad/src/Ui_BuildStructuresMenu.py b/cad/src/ne1_ui/menus/Ui_BuildStructuresMenu.py index d08b6e0cb..d08b6e0cb 100755 --- a/cad/src/Ui_BuildStructuresMenu.py +++ b/cad/src/ne1_ui/menus/Ui_BuildStructuresMenu.py diff --git a/cad/src/Ui_BuildToolsMenu.py b/cad/src/ne1_ui/menus/Ui_BuildToolsMenu.py index 5407db345..5407db345 100755 --- a/cad/src/Ui_BuildToolsMenu.py +++ b/cad/src/ne1_ui/menus/Ui_BuildToolsMenu.py diff --git a/cad/src/Ui_DimensionsMenu.py b/cad/src/ne1_ui/menus/Ui_DimensionsMenu.py index b2905cd6e..b2905cd6e 100755 --- a/cad/src/Ui_DimensionsMenu.py +++ b/cad/src/ne1_ui/menus/Ui_DimensionsMenu.py diff --git a/cad/src/Ui_EditMenu.py b/cad/src/ne1_ui/menus/Ui_EditMenu.py index 700937a72..700937a72 100755 --- a/cad/src/Ui_EditMenu.py +++ b/cad/src/ne1_ui/menus/Ui_EditMenu.py diff --git a/cad/src/Ui_FileMenu.py b/cad/src/ne1_ui/menus/Ui_FileMenu.py index ee077c172..ee077c172 100755 --- a/cad/src/Ui_FileMenu.py +++ b/cad/src/ne1_ui/menus/Ui_FileMenu.py diff --git a/cad/src/Ui_InsertMenu.py b/cad/src/ne1_ui/menus/Ui_InsertMenu.py index 3684814d4..3684814d4 100755 --- a/cad/src/Ui_InsertMenu.py +++ b/cad/src/ne1_ui/menus/Ui_InsertMenu.py diff --git a/cad/src/Ui_RenderingMenu.py b/cad/src/ne1_ui/menus/Ui_RenderingMenu.py index cef144034..5f2bde179 100644 --- a/cad/src/Ui_RenderingMenu.py +++ b/cad/src/ne1_ui/menus/Ui_RenderingMenu.py @@ -4,7 +4,7 @@ Ui_RenderingMenu.py - Menu for Rendering plug-ins like QuteMolX, POV-Ray and others to come (i.e. Sunflow) @author: Mark -@version: $Id:$ +@version: $Id$ @copyright: 2005-2007 Nanorex, Inc. See LICENSE file for details. """ diff --git a/cad/src/Ui_SelectMenu.py b/cad/src/ne1_ui/menus/Ui_SelectMenu.py index 83c60e5c5..83c60e5c5 100755 --- a/cad/src/Ui_SelectMenu.py +++ b/cad/src/ne1_ui/menus/Ui_SelectMenu.py diff --git a/cad/src/Ui_SimulationMenu.py b/cad/src/ne1_ui/menus/Ui_SimulationMenu.py index f72b2c214..f72b2c214 100755 --- a/cad/src/Ui_SimulationMenu.py +++ b/cad/src/ne1_ui/menus/Ui_SimulationMenu.py diff --git a/cad/src/Ui_ToolsMenu.py b/cad/src/ne1_ui/menus/Ui_ToolsMenu.py index b19ab1f15..33d1c0dce 100755 --- a/cad/src/Ui_ToolsMenu.py +++ b/cad/src/ne1_ui/menus/Ui_ToolsMenu.py @@ -5,10 +5,10 @@ $Id$ from PyQt4 import QtGui -import Ui_BuildStructuresMenu -import Ui_BuildToolsMenu -import Ui_SelectMenu -import Ui_DimensionsMenu +import ne1_ui.menus.Ui_BuildStructuresMenu as Ui_BuildStructuresMenu +import ne1_ui.menus.Ui_BuildToolsMenu as Ui_BuildToolsMenu +import ne1_ui.menus.Ui_SelectMenu as Ui_SelectMenu +import ne1_ui.menus.Ui_DimensionsMenu as Ui_DimensionsMenu def setupUi(win): """ diff --git a/cad/src/Ui_ViewMenu.py b/cad/src/ne1_ui/menus/Ui_ViewMenu.py index d9971488a..d9971488a 100755 --- a/cad/src/Ui_ViewMenu.py +++ b/cad/src/ne1_ui/menus/Ui_ViewMenu.py diff --git a/cad/src/ne1_ui/menus/__init__.py b/cad/src/ne1_ui/menus/__init__.py new file mode 100644 index 000000000..e69de29bb --- /dev/null +++ b/cad/src/ne1_ui/menus/__init__.py diff --git a/cad/src/Ui_BuildStructuresToolBar.py b/cad/src/ne1_ui/toolbars/Ui_BuildStructuresToolBar.py index 4aa5f1aef..4aa5f1aef 100755 --- a/cad/src/Ui_BuildStructuresToolBar.py +++ b/cad/src/ne1_ui/toolbars/Ui_BuildStructuresToolBar.py diff --git a/cad/src/Ui_BuildToolsToolBar.py b/cad/src/ne1_ui/toolbars/Ui_BuildToolsToolBar.py index 828ff1a71..828ff1a71 100755 --- a/cad/src/Ui_BuildToolsToolBar.py +++ b/cad/src/ne1_ui/toolbars/Ui_BuildToolsToolBar.py diff --git a/cad/src/Ui_CntFlyout.py b/cad/src/ne1_ui/toolbars/Ui_CntFlyout.py index 37a47b1c8..37a47b1c8 100644 --- a/cad/src/Ui_CntFlyout.py +++ b/cad/src/ne1_ui/toolbars/Ui_CntFlyout.py diff --git a/cad/src/Ui_CommandToolbar.py b/cad/src/ne1_ui/toolbars/Ui_CommandToolbar.py index a3c950ec1..a3c950ec1 100755 --- a/cad/src/Ui_CommandToolbar.py +++ b/cad/src/ne1_ui/toolbars/Ui_CommandToolbar.py diff --git a/cad/src/Ui_DisplayStylesToolBar.py b/cad/src/ne1_ui/toolbars/Ui_DisplayStylesToolBar.py index 3d6b49a60..3d6b49a60 100644 --- a/cad/src/Ui_DisplayStylesToolBar.py +++ b/cad/src/ne1_ui/toolbars/Ui_DisplayStylesToolBar.py diff --git a/cad/src/Ui_DnaFlyout.py b/cad/src/ne1_ui/toolbars/Ui_DnaFlyout.py index e99353380..e99353380 100644 --- a/cad/src/Ui_DnaFlyout.py +++ b/cad/src/ne1_ui/toolbars/Ui_DnaFlyout.py diff --git a/cad/src/Ui_RenderingToolBar.py b/cad/src/ne1_ui/toolbars/Ui_RenderingToolBar.py index f5db559d3..f5db559d3 100644 --- a/cad/src/Ui_RenderingToolBar.py +++ b/cad/src/ne1_ui/toolbars/Ui_RenderingToolBar.py diff --git a/cad/src/Ui_SelectToolBar.py b/cad/src/ne1_ui/toolbars/Ui_SelectToolBar.py index a6327c566..a6327c566 100755 --- a/cad/src/Ui_SelectToolBar.py +++ b/cad/src/ne1_ui/toolbars/Ui_SelectToolBar.py diff --git a/cad/src/Ui_SimulationToolBar.py b/cad/src/ne1_ui/toolbars/Ui_SimulationToolBar.py index afb0e2be0..afb0e2be0 100755 --- a/cad/src/Ui_SimulationToolBar.py +++ b/cad/src/ne1_ui/toolbars/Ui_SimulationToolBar.py diff --git a/cad/src/Ui_StandardToolBar.py b/cad/src/ne1_ui/toolbars/Ui_StandardToolBar.py index 743226688..743226688 100755 --- a/cad/src/Ui_StandardToolBar.py +++ b/cad/src/ne1_ui/toolbars/Ui_StandardToolBar.py diff --git a/cad/src/Ui_StandardViewsToolBar.py b/cad/src/ne1_ui/toolbars/Ui_StandardViewsToolBar.py index 9d08b91d6..9d08b91d6 100644 --- a/cad/src/Ui_StandardViewsToolBar.py +++ b/cad/src/ne1_ui/toolbars/Ui_StandardViewsToolBar.py diff --git a/cad/src/Ui_ViewToolBar.py b/cad/src/ne1_ui/toolbars/Ui_ViewToolBar.py index 615693a6a..615693a6a 100755 --- a/cad/src/Ui_ViewToolBar.py +++ b/cad/src/ne1_ui/toolbars/Ui_ViewToolBar.py diff --git a/cad/src/ne1_ui/toolbars/__init__.py b/cad/src/ne1_ui/toolbars/__init__.py new file mode 100644 index 000000000..e69de29bb --- /dev/null +++ b/cad/src/ne1_ui/toolbars/__init__.py diff --git a/cad/src/ops_atoms.py b/cad/src/ops_atoms.py index 01f260a5a..752a19443 100755 --- a/cad/src/ops_atoms.py +++ b/cad/src/ops_atoms.py @@ -17,7 +17,7 @@ from utilities.Log import greenmsg, redmsg from constants import SELWHAT_CHUNKS, SELWHAT_ATOMS from PlatformDependent import fix_plurals -from elements import Singlet +from model.elements import Singlet import foundation.env as env class ops_atoms_Mixin: @@ -33,7 +33,7 @@ class ops_atoms_Mixin: # now change selected atoms to the specified element # [bruce 041215: this should probably be made available for any modes # in which "selected atoms" are permitted, not just Select modes. #e] - from elements import PeriodicTable + from model.elements import PeriodicTable if self.selatoms: dstElem = PeriodicTable.getElement(elem) for atm in self.selatoms.values(): diff --git a/cad/src/ops_copy.py b/cad/src/ops_copy.py index 28b5e79f6..fb838cdf3 100755 --- a/cad/src/ops_copy.py +++ b/cad/src/ops_copy.py @@ -18,17 +18,17 @@ from debug import print_compact_stack from utilities.Log import greenmsg, redmsg, orangemsg from PlatformDependent import fix_plurals from foundation.Group import Group -from chunk import Chunk -from chunk import mol_copy_name -from chem import Atom_prekill_prep +from model.chunk import Chunk +from model.chunk import mol_copy_name +from model.chem import Atom_prekill_prep from ops_select import Selection -from bonds import bond_copied_atoms +from model.bonds import bond_copied_atoms from constants import gensym from ops_select import selection_from_part from constants import noop from geometry.VQT import V from geometry.BoundingBox import BBox -from jigs import Jig +from model.jigs import Jig class ops_copy_Mixin: """ diff --git a/cad/src/ops_motion.py b/cad/src/ops_motion.py index eeb38805c..3079ac35c 100755 --- a/cad/src/ops_motion.py +++ b/cad/src/ops_motion.py @@ -19,9 +19,9 @@ import foundation.env as env from math import pi from debug import print_compact_traceback -from chunk import Chunk -from jigs import Jig -from jigs_motors import Motor +from model.chunk import Chunk +from model.jigs import Jig +from model.jigs_motors import Motor from analysis.ESP.ESPImage import ESPImage from foundation.Group import Group diff --git a/cad/src/ops_rechunk.py b/cad/src/ops_rechunk.py index 3ee82be96..1337a4c3e 100755 --- a/cad/src/ops_rechunk.py +++ b/cad/src/ops_rechunk.py @@ -13,7 +13,7 @@ bruce 050507 made this by collecting appropriate methods from class Part. from utilities.Log import greenmsg, redmsg from PlatformDependent import fix_plurals -from chunk import Chunk +from model.chunk import Chunk from constants import gensym from dna.model.Dna_Constants import getNextStrandColor import foundation.env as env diff --git a/cad/src/ops_select.py b/cad/src/ops_select.py index ec3b71ac4..1f56e9b79 100755 --- a/cad/src/ops_select.py +++ b/cad/src/ops_select.py @@ -13,10 +13,10 @@ bruce 050507 made this by collecting appropriate methods from class Part. from constants import SELWHAT_CHUNKS, SELWHAT_ATOMS from constants import diINVISIBLE, diDEFAULT -from jigs import Jig -from chem import _changed_picked_Atoms -from chunk import Chunk -from elements import Singlet +from model.jigs import Jig +from model.chem import _changed_picked_Atoms +from model.chunk import Chunk +from model.elements import Singlet from geometry.VQT import V, A, norm, cross from Numeric import dot, transpose import foundation.env as env diff --git a/cad/src/ops_view.py b/cad/src/ops_view.py index 73c7473c7..1e51b40a0 100755 --- a/cad/src/ops_view.py +++ b/cad/src/ops_view.py @@ -22,8 +22,8 @@ from geometry.VQT import V, Q, A, norm, vlen from utilities.Log import greenmsg, redmsg, orangemsg from prefs_constants import ORTHOGRAPHIC from prefs_constants import PERSPECTIVE -from NamedView import NamedView -from PovrayScene import PovrayScene +from model.NamedView import NamedView +from model.PovrayScene import PovrayScene class viewSlotsMixin: """ diff --git a/cad/src/outtakes/BasePair.py b/cad/src/outtakes/BasePair.py index c88f01a3a..7755b9a7f 100644 --- a/cad/src/outtakes/BasePair.py +++ b/cad/src/outtakes/BasePair.py @@ -16,11 +16,11 @@ it to outtakes soon. In fact, why not now? Ok, moving it now. TODO: split into several files. """ -from chem import Atom # for isinstance +from model.chem import Atom # for isinstance ## see also crossovers.py -from bond_constants import atoms_are_bonded, find_bond +from model.bond_constants import atoms_are_bonded, find_bond # == diff --git a/cad/src/outtakes/MMKit.py b/cad/src/outtakes/MMKit.py index b9e4dc350..71b287a10 100755 --- a/cad/src/outtakes/MMKit.py +++ b/cad/src/outtakes/MMKit.py @@ -36,21 +36,21 @@ from PyQt4.Qt import QDir, QTreeView, QTreeWidgetItem, QAbstractItemDelegate, QW from MMKitDialog import Ui_MMKitDialog from graphics.widgets.ThumbView import MMKitView, ChunkView -from elements import PeriodicTable +from model.elements import PeriodicTable from constants import diTUBES ## from chem import Atom [not used i think - bruce 071113] ## from chunk import Chunk [not used i think - bruce 071113] from foundation.Utility import imagename_to_icon, geticon from assembly import assembly from files.mmp.files_mmp import readmmp -from part import Part +from model.part import Part import foundation.env as env from utilities import debug_flags from debug import print_compact_traceback from Sponsors import SponsorableMixin from PropertyManagerMixin import PropertyManagerMixin, pmSetPropMgrIcon, pmSetPropMgrTitle from PropMgr_Constants import pmMMKitPageMargin -from bond_constants import btype_from_v6 +from model.bond_constants import btype_from_v6 # PageId constants for mmkit_tab AtomsPage=0 @@ -1001,7 +1001,7 @@ class MMKit(QDialog, self.dirView.setRootPath(libDir) else: self.rootDir = None - from HistoryWidget import redmsg + from history.HistoryWidget import redmsg env.history.message(redmsg("The part library directory: %s doesn't exist." %libDir)) def browseDirectories(self): @@ -1024,7 +1024,7 @@ class MMKit(QDialog, def useDefaultPartLibDirectory(self): ''' Slot method that to reset the part lib directory path to default''' - from HistoryWidget import redmsg + from history.HistoryWidget import redmsg #ninad070503 : A future enhancement would be a preference to have # a user defined 'default dir path' for the diff --git a/cad/src/outtakes/TreeWidget.py b/cad/src/outtakes/TreeWidget.py index 4728140aa..dc0ad92ca 100755 --- a/cad/src/outtakes/TreeWidget.py +++ b/cad/src/outtakes/TreeWidget.py @@ -1379,7 +1379,7 @@ class TreeWidget(TreeView, DebugMenuMixin): def redmsg(self, errmsg): #e someday this might come from the subclass #e refile this method near statusbar_msg "put an error message into the History" - from HistoryWidget import redmsg + from history.HistoryWidget import redmsg env.history.message( redmsg(errmsg)) self.statusbar_msg(" ") # probably a good idea -- not sure! return diff --git a/cad/src/outtakes/uiPrototype.py b/cad/src/outtakes/uiPrototype.py index 63b2eaa59..98f1f654b 100755 --- a/cad/src/outtakes/uiPrototype.py +++ b/cad/src/outtakes/uiPrototype.py @@ -69,7 +69,7 @@ from PyQt4.Qt import QTimer from PyQt4.Qt import QHBoxLayout from PyQt4.Qt import QGridLayout -import modelTreeGui +import modelTree.modelTreeGui as modelTreeGui # Hunt for the icons directory icons = 'icons' diff --git a/cad/src/pastables.py b/cad/src/pastables.py index 2ffd50e85..7a94d0300 100644 --- a/cad/src/pastables.py +++ b/cad/src/pastables.py @@ -25,7 +25,7 @@ implementations on a few subclasses of Node. and paste it onto a bondpoint. """ -from chunk import Chunk # only for isinstance +from model.chunk import Chunk # only for isinstance from foundation.Group import Group # only for isinstance def is_pastable(obj): diff --git a/cad/src/reposition_baggage.py b/cad/src/reposition_baggage.py index cb5e52b68..41634292c 100755 --- a/cad/src/reposition_baggage.py +++ b/cad/src/reposition_baggage.py @@ -11,8 +11,8 @@ import math from utilities import debug_flags from geometry.VQT import V, norm, cross, vlen -from bond_constants import find_bond -from bond_constants import V_SINGLE +from model.bond_constants import find_bond +from model.bond_constants import V_SINGLE from geometry.geometryUtilities import arbitrary_perpendicular diff --git a/cad/src/runSim.py b/cad/src/runSim.py index cf0c09c61..a5e7ebcb2 100755 --- a/cad/src/runSim.py +++ b/cad/src/runSim.py @@ -50,8 +50,8 @@ import foundation.env as env from foundation.env import seen_before from geometry.VQT import A import re -from chem import AtomDict -from chunk import Chunk +from model.chem import AtomDict +from model.chunk import Chunk from debug_prefs import debug_pref, Choice, Choice_boolean_True, Choice_boolean_False from constants import filesplit from Process import Process @@ -2712,7 +2712,7 @@ def LocalMinimize_function( atomlist, nlayers ): #bruce 051207 # == helper code for Minimize Selection [by bruce, circa 050406] [also used for Minimize All, probably as of 050419, as guessed 051115] -from elements import Singlet +from model.elements import Singlet def adjustSinglet(singlet, minimize = False): # Mark 2007-10-21. """ @@ -2933,7 +2933,7 @@ class sim_aspect: # as of 051115 this is used for Min Sel and Min All but not Ru atm.writemmp( mapping) # mapping.sim means don't include any info not relevant to the sim # note: this method knows whether & how to write a Singlet as an H (repositioned)! def write_grounds(self, mapping): - from jigs import fake_Anchor_mmp_record + from model.jigs import fake_Anchor_mmp_record atoms = self.anchored_atoms_list nfixed = len(atoms) max_per_jig = 20 @@ -2955,7 +2955,7 @@ class sim_aspect: # as of 051115 this is used for Min Sel and Min All but not Ru """ assert mapping.min #bruce 051031; detected by writemmp call, below; this scheme is a slight kluge - from jigs import Jig + from model.jigs import Jig def func_write_jigs(nn): if isinstance(nn, Jig) and nn.enable_minimize: #bruce 051031 comment: should we exclude the ones written by write_grounds?? doesn't matter for now. ####@@@@ diff --git a/cad/src/scratch/buckyball.py b/cad/src/scratch/buckyball.py index 8803a801a..b10aee46d 100755 --- a/cad/src/scratch/buckyball.py +++ b/cad/src/scratch/buckyball.py @@ -38,9 +38,9 @@ __author__ = "Will" from math import sin, cos, pi, floor from geometry.VQT import V, vlen -from bonds import NeighborhoodGenerator, bond_atoms, CC_GRAPHITIC_BONDLENGTH -from bond_constants import V_GRAPHITE -from chem import Atom +from model.bonds import NeighborhoodGenerator, bond_atoms, CC_GRAPHITIC_BONDLENGTH +from model.bond_constants import V_GRAPHITE +from model.chem import Atom class BuckyBall: diff --git a/cad/src/test_command_PMs.py b/cad/src/test_command_PMs.py index c97ae8a33..170c999ba 100755 --- a/cad/src/test_command_PMs.py +++ b/cad/src/test_command_PMs.py @@ -175,7 +175,7 @@ class ExampleCommand2_PM( PM_Dialog_with_example_widgets, GeneratorBaseClass): assert self.name == name # true by test and by examining GBC code # ignoring params and position for now assy = self.win.assy - from Comment import Comment + from model.Comment import Comment return Comment(assy, name, "comment created at " + time.asctime()) #e bugs that remain: |