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| author | Mark Sims <mark@nanorex.com> | 2008-12-12 18:33:24 +0000 |
|---|---|---|
| committer | Mark Sims <mark@nanorex.com> | 2008-12-12 18:33:24 +0000 |
| commit | 39393f0e83ac7de97a4e45cf6a072485f5b68db6 (patch) | |
| tree | dc2267432b41ba8fb701733f1cd1f55cb4e5e2d2 | |
| parent | abb841c13c9569f1c30bbebbaa3e97e505b55974 (diff) | |
| download | nanoengineer-39393f0e83ac7de97a4e45cf6a072485f5b68db6.tar.gz nanoengineer-39393f0e83ac7de97a4e45cf6a072485f5b68db6.zip | |
Renamed "BuildPeptide" to "InsertPeptide".
Renamed "Peptide_EditCommand" to "InsertPeptide_EditCommand"
| -rw-r--r-- | cad/src/commandSequencer/builtin_command_loaders.py | 4 | ||||
| -rw-r--r-- | cad/src/graphics/drawing/drawPeptideTrace.py | 2 | ||||
| -rwxr-xr-x | cad/src/ne1_startup/startup_misc.py | 2 | ||||
| -rw-r--r-- | cad/src/protein/commands/InsertPeptide/InsertPeptide_EditCommand.py (renamed from cad/src/protein/commands/BuildPeptide/Peptide_EditCommand.py) | 10 | ||||
| -rwxr-xr-x | cad/src/protein/commands/InsertPeptide/InsertPeptide_PropertyManager.py (renamed from cad/src/protein/commands/BuildPeptide/InsertPeptide_PropertyManager.py) | 2 | ||||
| -rwxr-xr-x | cad/src/protein/commands/InsertPeptide/PeptideGenerator.py (renamed from cad/src/protein/commands/BuildPeptide/PeptideGenerator.py) | 2 | ||||
| -rw-r--r-- | cad/src/protein/commands/InsertPeptide/__init__.py (renamed from cad/src/protein/commands/BuildPeptide/__init__.py) | 0 | ||||
| -rw-r--r-- | cad/src/protein/model/PeptideGroup.py | 2 | ||||
| -rw-r--r-- | cad/src/protein/model/PeptideSegment.py | 2 | ||||
| -rw-r--r-- | cad/src/protein/temporary_commands/PeptideLineMode.py | 4 |
10 files changed, 15 insertions, 15 deletions
diff --git a/cad/src/commandSequencer/builtin_command_loaders.py b/cad/src/commandSequencer/builtin_command_loaders.py index f27d6a90f..3826495fe 100644 --- a/cad/src/commandSequencer/builtin_command_loaders.py +++ b/cad/src/commandSequencer/builtin_command_loaders.py @@ -80,7 +80,7 @@ from dna.commands.JoinStrands.JoinStrands_By_DND_RequestCommand import JoinStran from dna.commands.ConvertDna.ConvertDna_Command import ConvertDna_Command # Protein commands -from protein.commands.BuildPeptide.Peptide_EditCommand import Peptide_EditCommand +from protein.commands.InsertPeptide.InsertPeptide_EditCommand import InsertPeptide_EditCommand from protein.commands.BuildProtein.BuildProtein_EditCommand import BuildProtein_EditCommand from protein.commands.ProteinDisplayStyle.ProteinDisplayStyle_Command import ProteinDisplayStyle_Command from protein.commands.EditRotamers.EditRotamers_Command import EditRotamers_Command @@ -169,7 +169,7 @@ def preloaded_command_classes(): TestGraphics_Command, QuteMol_Command, ColorScheme_Command, - Peptide_EditCommand, + InsertPeptide_EditCommand, BuildProtein_EditCommand, ProteinDisplayStyle_Command, LightingScheme_Command, diff --git a/cad/src/graphics/drawing/drawPeptideTrace.py b/cad/src/graphics/drawing/drawPeptideTrace.py index baab3f615..188f62f9e 100644 --- a/cad/src/graphics/drawing/drawPeptideTrace.py +++ b/cad/src/graphics/drawing/drawPeptideTrace.py @@ -26,7 +26,7 @@ from geometry.VQT import norm, vlen, V, cross from utilities.prefs_constants import DarkBackgroundContrastColor_prefs_key from utilities.constants import blue, gray -from protein.commands.BuildPeptide.PeptideGenerator import get_unit_length +from protein.commands.InsertPeptide.PeptideGenerator import get_unit_length def drawPeptideTrace_new(mol): diff --git a/cad/src/ne1_startup/startup_misc.py b/cad/src/ne1_startup/startup_misc.py index 327e93b69..d4fdbf4cc 100755 --- a/cad/src/ne1_startup/startup_misc.py +++ b/cad/src/ne1_startup/startup_misc.py @@ -257,7 +257,7 @@ def _init_command_Atom_Generator(): def _init_command_Peptide_Generator(): # piotr 080304 # This function enables an experimental peptide generator. from utilities.debug_prefs import debug_pref, Choice_boolean_True - from protein.commands.BuildPeptide.PeptideGenerator import enablePeptideGenerator + from protein.commands.InsertPeptide.PeptideGenerator import enablePeptideGenerator _peptideGeneratorIsEnabled = \ debug_pref("Peptide Generator: enabled?", Choice_boolean_True, diff --git a/cad/src/protein/commands/BuildPeptide/Peptide_EditCommand.py b/cad/src/protein/commands/InsertPeptide/InsertPeptide_EditCommand.py index 761286b60..f0ef2ee25 100644 --- a/cad/src/protein/commands/BuildPeptide/Peptide_EditCommand.py +++ b/cad/src/protein/commands/InsertPeptide/InsertPeptide_EditCommand.py @@ -12,7 +12,7 @@ History: from utilities.Log import greenmsg from command_support.EditCommand import EditCommand -from protein.commands.BuildPeptide.PeptideGenerator import PeptideGenerator +from protein.commands.InsertPeptide.PeptideGenerator import PeptideGenerator from utilities.constants import gensym from commands.SelectChunks.SelectChunks_GraphicsMode import SelectChunks_GraphicsMode from protein.temporary_commands.PeptideLineMode import PeptideLine_GM @@ -23,12 +23,12 @@ import foundation.env as env from utilities.prefs_constants import cursorTextColor_prefs_key from protein.commands.ModelAndSimulateProtein.ModelAndSimulateProtein_Command import ModelAndSimulateProtein_Command -from protein.commands.BuildPeptide.InsertPeptide_PropertyManager import InsertPeptide_PropertyManager +from protein.commands.InsertPeptide.InsertPeptide_PropertyManager import InsertPeptide_PropertyManager #_superclass = ModelAndSimulateProtein_Command _superclass = EditCommand -class Peptide_EditCommand(EditCommand): -#class Peptide_EditCommand(ModelAndSimulateProtein_Command): +class InsertPeptide_EditCommand(EditCommand): +#class InsertPeptide_EditCommand(ModelAndSimulateProtein_Command): PM_class = InsertPeptide_PropertyManager @@ -60,7 +60,7 @@ class Peptide_EditCommand(EditCommand): def __init__(self, commandSequencer): """ - Constructor for Peptide_EditCommand + Constructor for InsertPeptide_EditCommand """ _superclass.__init__(self, commandSequencer) diff --git a/cad/src/protein/commands/BuildPeptide/InsertPeptide_PropertyManager.py b/cad/src/protein/commands/InsertPeptide/InsertPeptide_PropertyManager.py index c1ff953ca..a5bf33a1c 100755 --- a/cad/src/protein/commands/BuildPeptide/InsertPeptide_PropertyManager.py +++ b/cad/src/protein/commands/InsertPeptide/InsertPeptide_PropertyManager.py @@ -125,7 +125,7 @@ class InsertPeptide_PropertyManager(EditCommand_PM): to be used to create the peptide. @return: A tuple containing the parameters @rtype: tuple - @see: L{Peptide_EditCommand._gatherParameters()} where this is used + @see: L{InsertPeptide_EditCommand._gatherParameters()} where this is used """ return (self.secondary, self.phi, self.psi, self.current_amino_acid) diff --git a/cad/src/protein/commands/BuildPeptide/PeptideGenerator.py b/cad/src/protein/commands/InsertPeptide/PeptideGenerator.py index 553cde14a..90641b84b 100755 --- a/cad/src/protein/commands/BuildPeptide/PeptideGenerator.py +++ b/cad/src/protein/commands/InsertPeptide/PeptideGenerator.py @@ -15,7 +15,7 @@ for notes about what's going on here. History: Ninad 2008-07-24: Refactoring / cleanup to port PeptideGenerator to the - EditCommand API. (see Peptide_EditCommand) + EditCommand API. (see InsertPeptide_EditCommand) """ import foundation.env as env diff --git a/cad/src/protein/commands/BuildPeptide/__init__.py b/cad/src/protein/commands/InsertPeptide/__init__.py index e69de29bb..e69de29bb 100644 --- a/cad/src/protein/commands/BuildPeptide/__init__.py +++ b/cad/src/protein/commands/InsertPeptide/__init__.py diff --git a/cad/src/protein/model/PeptideGroup.py b/cad/src/protein/model/PeptideGroup.py index 2489066a2..60f3c33d7 100644 --- a/cad/src/protein/model/PeptideGroup.py +++ b/cad/src/protein/model/PeptideGroup.py @@ -84,7 +84,7 @@ class PeptideGroup(Group): Returns True if there are no Peptide chunks as its members (Returns True even when there are empty PeptideSegment objects inside) - @see: Peptide_EditCommand._finalizeStructure where this test is used. + @see: InsertPeptide_EditCommand._finalizeStructure where this test is used. """ #May be for the short term, we can use self.getAtomList()? But that #doesn't ensure if the DnaGroup always has atom of type either diff --git a/cad/src/protein/model/PeptideSegment.py b/cad/src/protein/model/PeptideSegment.py index bd0fa46c3..688e56f3a 100644 --- a/cad/src/protein/model/PeptideSegment.py +++ b/cad/src/protein/model/PeptideSegment.py @@ -172,7 +172,7 @@ class PeptideSegment(Group): Sets some properties. These will be used while editing the structure. (but if the structure is read from an mmp file, this won't work. As a fall back, it returns some constant values) - @see: Peptide_EditCommand.createStructure which calls this method. + @see: InsertPeptide_EditCommand.createStructure which calls this method. @see: self.getProps, PeptideSegment_EditCommand.editStructure """ (_n, _m), _type, _endings, (_endPoint1, _endPoint2) = props diff --git a/cad/src/protein/temporary_commands/PeptideLineMode.py b/cad/src/protein/temporary_commands/PeptideLineMode.py index 1340f92dd..7d4fe6062 100644 --- a/cad/src/protein/temporary_commands/PeptideLineMode.py +++ b/cad/src/protein/temporary_commands/PeptideLineMode.py @@ -16,7 +16,7 @@ from graphics.drawing.drawPeptideTrace import drawPeptideTrace, drawPeptideTrace from utilities.constants import gray, black, darkred, blue, white -from protein.commands.BuildPeptide.PeptideGenerator import PeptideGenerator, get_unit_length +from protein.commands.InsertPeptide.PeptideGenerator import PeptideGenerator, get_unit_length # == GraphicsMode part @@ -24,7 +24,7 @@ class PeptideLine_GM( Line_GraphicsMode ): """ Custom GraphicsMode for use as a component of PeptideLineMode. @see: L{PeptideLineMode} for more comments. - @see: Peptide_EditCommand where this is used as a GraphicsMode class. + @see: InsertPeptide_EditCommand where this is used as a GraphicsMode class. """ # The following valuse are used in drawing the 'sphere' that represent the |