python_code stringlengths 0 992k | repo_name stringlengths 8 46 | file_path stringlengths 5 162 |
|---|---|---|
# Copyright 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
dna_updater_commands.py - UI commands offered directly by the dna updater.
@author: Bruce
@version: $Id$
@copyright: 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
from utilities.debug import register_debug_menu_command
from model.glo... | NanoCAD-master | cad/src/dna/updater/dna_updater_commands.py |
# Copyright 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
dna_updater_utils.py -- miscellaneous utilities for dna_updater
@author: Bruce
@version: $Id$
@copyright: 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
from utilities import debug_flags
from utilities.debug import print_compact_trace... | NanoCAD-master | cad/src/dna/updater/dna_updater_utils.py |
# Copyright 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
dna_updater_chunks.py - enforce rules on chunks containing changed PAM atoms
@author: Bruce
@version: $Id$
@copyright: 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
from foundation.state_utils import transclose
from dna.updater.dna_u... | NanoCAD-master | cad/src/dna/updater/dna_updater_chunks.py |
NanoCAD-master | cad/src/dna/updater/__init__.py | |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
dna_updater_debug.py -- debug code for dna_updater
@author: Bruce
@version: $Id$
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.
"""
from utilities import debug_flags
from graphics.drawing.CS_draw_primitives import drawline
from model.j... | NanoCAD-master | cad/src/dna/updater/dna_updater_debug.py |
# Copyright 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
dna_updater_find_chains.py - helper for dna_updater_chunks
@author: Bruce
@version: $Id$
@copyright: 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
from utilities import debug_flags
from operations.bond_chains import abstract_bond_cha... | NanoCAD-master | cad/src/dna/updater/dna_updater_find_chains.py |
# Copyright 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
fix_atom_classes.py - fix classes of PAM atoms
@author: Bruce
@version: $Id$
@copyright: 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
from dna.updater.dna_updater_utils import replace_atom_class
from model.chem import Atom
StrandAt... | NanoCAD-master | cad/src/dna/updater/fix_atom_classes.py |
# Copyright 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
dna_updater_ladders.py - ladder-related helpers for dna_updater_chunks
@author: Bruce
@version: $Id$
@copyright: 2007-2008 Nanorex, Inc. See LICENSE file for details.
See also: DnaLadder
"""
from utilities import debug_flags
from dna.updater.dn... | NanoCAD-master | cad/src/dna/updater/dna_updater_ladders.py |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
fix_after_readmmp.py - helpers to fix dna-related structure after readmmp
@author: Bruce
@version: $Id$
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.
"""
from dna.updater.dna_updater_prefs import pref_fix_after_readmmp_before_updaters
f... | NanoCAD-master | cad/src/dna/updater/fix_after_readmmp.py |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
fix_bond_directions.py - dna updater helper functions
@author: Bruce
@version: $Id$
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.
"""
from model.elements import Singlet
import foundation.env as env
from utilities.Log import orangemsg
f... | NanoCAD-master | cad/src/dna/updater/fix_bond_directions.py |
# Copyright 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
delete_bare_atoms.py - delete atoms lacking required neighbors
@author: Bruce
@version: $Id$
@copyright: 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
from dna.updater.dna_updater_prefs import pref_fix_bare_PAM3_atoms
from dna.updater... | NanoCAD-master | cad/src/dna/updater/delete_bare_atoms.py |
# Copyright 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
dna_updater_init.py --
@author: Bruce
@version: $Id$
@copyright: 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
from dna.updater.dna_updater_globals import initialize_globals
from dna.updater.dna_updater_prefs import initialize_prefs... | NanoCAD-master | cad/src/dna/updater/dna_updater_init.py |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
convert_from_PAM5.py - detect PAM5 atoms and convert (some of) them to PAM3+5
WARNING: THIS MODULE IS PROBABLY OBSOLETE, and is no longer called as of 080408.
Newer code does this in later stages of the dna updater after ladders are made.
However, it mi... | NanoCAD-master | cad/src/dna/updater/convert_from_PAM5.py |
# Copyright 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
dna_updater_main.py - enforce rules on newly changed DNA-related model objects,
including DnaGroups, AxisChunks, PAM atoms, etc.
@author: Bruce
@version: $Id$
@copyright: 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
from dna.updater.... | NanoCAD-master | cad/src/dna/updater/dna_updater_main.py |
# Copyright 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
dna_updater_groups.py - enforce rules on chunks containing changed PAM atoms
@author: Bruce
@version: $Id$
@copyright: 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
from dna.updater.dna_updater_globals import ignore_new_changes
_DEBU... | NanoCAD-master | cad/src/dna/updater/dna_updater_groups.py |
# find directional bond chains (or rings) covering our atoms
def func( atom1, dir1): # wrong, see below
if atom1.killed(): ###k
return ### best place to do this?
for b in atom1.bonds:
if b.is_directional():
a1, a2 = b.atom1, b.atom2
dir1[... | NanoCAD-master | cad/src/dna/updater/dna_updater_scratch.py |
# Copyright 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
fix_deprecated_elements.py - fix deprecated PAM elements in-place in models
@author: Bruce
@version: $Id$
@copyright: 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
from model.elements import PeriodicTable
from utilities.constants imp... | NanoCAD-master | cad/src/dna/updater/fix_deprecated_elements.py |
# Copyright 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
dna_updater_globals.py -- global variables or mutables for dna_updater,
and their lowest-level accessors.
@author: Bruce
@version: $Id$
@copyright: 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
from utilities import debug_flags
from ... | NanoCAD-master | cad/src/dna/updater/dna_updater_globals.py |
# Copyright 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
crossovers.py -- support for DNA crossovers, modelled at various levels
@author: Bruce
@version: $Id$
@copyright: 2007-2008 Nanorex, Inc. See LICENSE file for details.
Includes Make Crossover and Remove Crossover Pl-atom-pair context menu command... | NanoCAD-master | cad/src/dna/operations/crossovers.py |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
ops_pam.py - PAM3+5 <-> PAM5 conversion operations
@author: Bruce
@version: $Id$
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.
"""
from utilities.Log import greenmsg, redmsg, orangemsg
from platform_dependent.PlatformDependent import f... | NanoCAD-master | cad/src/dna/operations/ops_pam.py |
NanoCAD-master | cad/src/dna/operations/__init__.py | |
# Copyright 2008-2009 Nanorex, Inc. See LICENSE file for details.
"""
@author: Ninad
@version: $Id$
@copyright: 2008-2009 Nanorex, Inc. See LICENSE file for details.
History:
2008-08-07: Created.
TODO:
"""
from PyQt4.Qt import QFont, QString
import foundation.env as env
from graphics.drawing.drawDnaLabels impor... | NanoCAD-master | cad/src/dna/command_support/BreakOrJoinStrands_GraphicsMode.py |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
@author: Urmi, Ninad
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.
@version:$Id$
History:
Ninad 2008-06-05: Revised and refactored code in JoinStrands_PropertyManager,
and moved it to this class.
"""
from PyQt4.Qt import Qt
from PyQt4.... | NanoCAD-master | cad/src/dna/command_support/BreakOrJoinStrands_PropertyManager.py |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
@author: Ninad
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.
@version: $Id$
History:
2008-08-06: refactored Break and Join Strands commands to create this new class
TODO:
"""
import foundation.env as env
from commands.BuildAtoms.Buil... | NanoCAD-master | cad/src/dna/command_support/BreakOrJoinStrands_Command.py |
NanoCAD-master | cad/src/dna/command_support/__init__.py | |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
@author: Ninad
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.
@version:$Id$
History:
TODO:
- See items in EditCommand_StructureList
"""
from utilities.Comparison import same_vals
from command_support.EditCommand_StructureList import Ed... | NanoCAD-master | cad/src/dna/command_support/DnaSegmentList.py |
# Copyright 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
DnaGroup.py - ...
@author: Bruce
@version: $Id$
@copyright: 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
from foundation.Group import Group
from utilities.constants import gensym
from utilities.icon_utilities import imagename_to_pi... | NanoCAD-master | cad/src/dna/model/DnaGroup.py |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
WholeChain.py - a complete chain or ring of PAM atoms, made of one or more
smaller chains (or 1 smaller ring) often known as rails (short for ladder rails,
referring to DnaLadder), with refs to markers and a strand or segment
@author: Bruce
@version: $I... | NanoCAD-master | cad/src/dna/model/WholeChain.py |
# Copyright 2005-2008 Nanorex, Inc. See LICENSE file for details.
"""
Dna_Constants.py -- constants for Dna.
Note: these are used both by the newer DnaDuplex.py,
and the older DnaGenHelper.py which it supersedes
(and their associated files).
@author: Mark Sims
@version: $Id$
@copyright: 2005-2008 Nanorex, Inc. See ... | NanoCAD-master | cad/src/dna/model/Dna_Constants.py |
# Copyright 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
ChainAtomMarker.py - a marked atom and direction in a chain of atoms,
with help for moving it to a new atom if its old atom is killed;
has state for undo/copy/save
@author: Bruce
@version: $Id$
@copyright: 2007-2008 Nanorex, Inc. See LICENSE file ... | NanoCAD-master | cad/src/dna/model/ChainAtomMarker.py |
# Copyright 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
dna_model_constants.py -- constants for dna_model internals
(not the same as Dna_Constants.py, which is about DNA itself)
@author: Bruce
@version: $Id$
@copyright: 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
# Codes for ladder ends ... | NanoCAD-master | cad/src/dna/model/dna_model_constants.py |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
pam_conversion_mmp.py -- help dna model objects convert between PAM models during writemmp
@author: Bruce
@version: $Id$
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.
"""
# Note: this file is indirectly imported by chem.py via PAM_Atom_... | NanoCAD-master | cad/src/dna/model/pam_conversion_mmp.py |
# Copyright 2007-2009 Nanorex, Inc. See LICENSE file for details.
"""
DnaStrand.py - ...
@author: Bruce, Ninad
@version: $Id$
@copyright: 2007-2009 Nanorex, Inc. See LICENSE file for details.
TODO:
- See comments in self.getStrandSequence(), self.get_strand_atoms_in_bond_direction()
"""
import re
from dna.model.D... | NanoCAD-master | cad/src/dna/model/DnaStrand.py |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
DnaLadder_pam_conversion.py - PAM3+5 <-> PAM5 conversion methods for DnaLadder,
and (perhaps in future) related helper functions.
@author: Bruce
@version: $Id$
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.
"""
from model.elements import... | NanoCAD-master | cad/src/dna/model/DnaLadder_pam_conversion.py |
# Copyright 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
elements_data_PAM5.py -- data for PAM5 pseudoatom elements
@author: Mark, Eric D
@version: $Id$
@copyright: 2007-2008 Nanorex, Inc. See LICENSE file for details.
History:
Bruce 071105 revised init code, and split PAM3 and PAM5 data
out of elemen... | NanoCAD-master | cad/src/dna/model/elements_data_PAM5.py |
# Copyright 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
DnaMarker.py - marked positions on atom chains, moving to live atoms as needed
Used internally for base indexing in strands and segments; perhaps used in the
future to mark subsequence endpoints for relations or display styles.
@author: Bruce
@ver... | NanoCAD-master | cad/src/dna/model/DnaMarker.py |
# Copyright 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
DnaLadder.py - automatically recognized guide objects for understanding PAM DNA
duplexes, sticky end regions, and single strands.
@author: Bruce
@version: $Id$
@copyright: 2007-2008 Nanorex, Inc. See LICENSE file for details.
Context: [warning: s... | NanoCAD-master | cad/src/dna/model/DnaLadder.py |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
PAM_atom_rules.py - functions that define rules for permissible PAM structure
(note: not all such code is in this module; some of it is implicit
or hardcoded in other files)
@author: Bruce
@version: $Id$
@copyright: 2008 Nanorex, Inc. See LICENSE file... | NanoCAD-master | cad/src/dna/model/PAM_atom_rules.py |
NanoCAD-master | cad/src/dna/model/__init__.py | |
# Copyright 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
DnaSegment.py
@author: Bruce, Ninad
@version: $Id$
@copyright: 2007-2008 Nanorex, Inc. See LICENSE file for details.
Note:
*DnaSegment has the following direct members --
-- DnaAxisChunks,
-- DnaSegmentMarkers
*It can also have fol... | NanoCAD-master | cad/src/dna/model/DnaSegment.py |
# Copyright 2007-2009 Nanorex, Inc. See LICENSE file for details.
"""
DnaLadderRailChunk.py - Chunk subclasses for axis and strand rails of a DnaLadder
@author: Bruce
@version: $Id$
@copyright: 2007-2009 Nanorex, Inc. See LICENSE file for details.
"""
from dna.model.pam_conversion_mmp import DnaLadderRailChunk_writ... | NanoCAD-master | cad/src/dna/model/DnaLadderRailChunk.py |
# Copyright 2007 Nanorex, Inc. See LICENSE file for details.
"""
AtomChainOrRing.py - cache info about atom/bond chains or rings of various types
@author: Bruce
@version: $Id$
@copyright: 2007 Nanorex, Inc. See LICENSE file for details.
Note: this is not specific to DNA, so it probably doesn't belong inside the
dna... | NanoCAD-master | cad/src/dna/model/AtomChainOrRing.py |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
pam3plus5_ops.py - PAM3+5 conversion helpers that modify model objects
(but that are not writemmp-specific -- those have their own module)
@author: Bruce (based on algorithms proposed by Eric D)
@version: $Id$
@copyright: 2008 Nanorex, Inc. See LICENSE... | NanoCAD-master | cad/src/dna/model/pam3plus5_ops.py |
# Copyright 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
elements_data_PAM3.py -- data for PAM3 pseudoatom elements
@author: Mark
@version: $Id$
@copyright: 2007-2008 Nanorex, Inc. See LICENSE file for details.
History:
Bruce 071105 revised init code, and split PAM3 and PAM5 data
out of elements_data.... | NanoCAD-master | cad/src/dna/model/elements_data_PAM3.py |
# Copyright 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
DnaStrandOrSegment.py - abstract superclass for DnaStrand and DnaSegment
@author: Bruce
@version: $Id$
@copyright: 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
from foundation.LeafLikeGroup import LeafLikeGroup
_superclass = LeafLik... | NanoCAD-master | cad/src/dna/model/DnaStrandOrSegment.py |
# Copyright 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
DnaChain.py - Dna-aware AtomChainOrRing subclasses, AxisChain and StrandChain
@author: Bruce
@version: $Id$
@copyright: 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
from dna.model.DnaMarker import DnaSegmentMarker
from dna.model.DnaM... | NanoCAD-master | cad/src/dna/model/DnaChain.py |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
pam3plus5_math.py -- mathematical helper functions for PAM3+5 <-> PAM5 conversion
@author: Bruce (based on formulas developed by Eric D)
@version: $Id$
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.
Reference and explanation for PAM3+5 c... | NanoCAD-master | cad/src/dna/model/pam3plus5_math.py |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
BaseIterator.py - stub, not yet used -- probably superseded by
class PositionInWholeChain in WholeChain.py, being written now.
@author: Bruce
@version: $Id$
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.
Plan:
- write this code as proto ... | NanoCAD-master | cad/src/dna/model/outtakes/BaseIterator.py |
# Copyright 2007 Nanorex, Inc. See LICENSE file for details.
"""
BasePair.py - BasePair, StackedBasePairs flyweight objects
WARNING -- this is not yet used; it's really just a scratch file.
Furthermore, it will probably never be used, since the recognition
of base pairs by the dna updater will occur differently, but ... | NanoCAD-master | cad/src/dna/model/outtakes/BasePair.py |
from Numeric import sign
class PositionInWholeChain(object):
"""
"""
def __init__(self, wholechain, rail, index, direction):
self.wholechain = wholechain
self.rail = rail
self.index = index # base index in current rail
self.direction = direction # in current rail only
... | NanoCAD-master | cad/src/dna/model/outtakes/PositionInWholeChain-outtakes.py |
# Copyright 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
Block.py - ... DEPRECATED CLASS (as of shortly before 080331)
@author: Bruce
@version: $Id$
@copyright: 2007-2008 Nanorex, Inc. See LICENSE file for details.
Note: this is likely to not always be Dna-specific, and accordingly
might be moved into ... | NanoCAD-master | cad/src/dna/model/outtakes/Block.py |
NanoCAD-master | cad/src/dna/commands/__init__.py | |
NanoCAD-master | cad/src/dna/commands/DnaStrand/__init__.py | |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
DnaStrand_ResizeHandle.py
@author: Ninad
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.
@version: $Id$
@license: GPL
History:
Created on 2008-02-14
TODO: as of 2008-02-14
- Attributes such as height_ref need to be renamed. But th... | NanoCAD-master | cad/src/dna/commands/DnaStrand/DnaStrand_ResizeHandle.py |
# Copyright 2008-2009 Nanorex, Inc. See LICENSE file for details.
"""
@author: Ninad
@version: $Id$
@copyright: 2008-2009 Nanorex, Inc. See LICENSE file for details.
History:
Created on 2008-02-14
TODO: as of 2008-02-14
- Post dna data model implementation:
- We need to make sure that the strand doesn't form a ri... | NanoCAD-master | cad/src/dna/commands/DnaStrand/DnaStrand_EditCommand.py |
# Copyright 2008-2009 Nanorex, Inc. See LICENSE file for details.
"""
Graphics mode intended to be used while in DnaStrand_EditCommand.
@author: Ninad
@version: $Id$
@copyright: 2008-2009 Nanorex, Inc. See LICENSE file for details.
History:
Created 2008-02-14
"""
from dna.commands.BuildDna.BuildDna_GraphicsMode im... | NanoCAD-master | cad/src/dna/commands/DnaStrand/DnaStrand_GraphicsMode.py |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
DnaStrand_PropertyManager.py
@author: Ninad
@version: $Id$
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.
Special notes:
- Sequence editor is also created in BuildDna_PropertyManager (of course
its a child of that PM) . See if that cre... | NanoCAD-master | cad/src/dna/commands/DnaStrand/DnaStrand_PropertyManager.py |
# Copyright 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
InsertDna_EditCommand.py
InsertDna_EditCommand that provides an editCommand object for
generating DNA Duplex . This command should be invoked only from
BuildDna_EditCommand
@author: Mark Sims, Ninad Sathaye
@version: $Id$
@copyright: 2007-2008 Nan... | NanoCAD-master | cad/src/dna/commands/InsertDna/InsertDna_EditCommand.py |
NanoCAD-master | cad/src/dna/commands/InsertDna/__init__.py | |
# Copyright 2004-2008 Nanorex, Inc. See LICENSE file for details.
"""
InsertDna_PropertyManager.py
@author: Mark Sims
@version: $Id$
@copyright: 2004-2008 Nanorex, Inc. See LICENSE file for details.
Mark 2007-10-18:
- Created. Major rewrite of DnaGeneratorPropertyManager.py.
Ninad 2007-10-24:
- Another major rewri... | NanoCAD-master | cad/src/dna/commands/InsertDna/InsertDna_PropertyManager.py |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
InsertDna_GraphicsMode.py
Graphics mode class for creating a dna duplex by specifying two line end
points. The duplex can be created on a specified plane or parallel to screen
@author: Ninad
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.... | NanoCAD-master | cad/src/dna/commands/InsertDna/InsertDna_GraphicsMode.py |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
DnaDisplayStyle_PropertyManager.py
The DnaDisplayStyle_PropertyManager class provides a Property Manager
for the B{Display Style} command on the flyout toolbar in the
Build > Dna mode.
@author: Mark, Urmi
@version: $Id$
@copyright: 2008 Nanorex, Inc... | NanoCAD-master | cad/src/dna/commands/DnaDisplayStyle/DnaDisplayStyle_PropertyManager.py |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
@author: Mark
@version: $Id$
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.
"""
import foundation.changes as changes
from commands.SelectChunks.SelectChunks_GraphicsMode import SelectChunks_GraphicsMode
from command_support.EditComma... | NanoCAD-master | cad/src/dna/commands/DnaDisplayStyle/DnaDisplayStyle_Command.py |
NanoCAD-master | cad/src/dna/commands/DnaDisplayStyle/__init__.py | |
# Copyright 2008-2009 Nanorex, Inc. See LICENSE file for details.
"""
Graphics mode intended to be used while in DnaSegment_EditCommand.
While in this command, user can
(a) Highlight and then left drag the resize handles located at the
two 'axis endpoints' of thje segment to change its length.
(b) Highlight and th... | NanoCAD-master | cad/src/dna/commands/DnaSegment/DnaSegment_GraphicsMode.py |
# Copyright 2008-2009 Nanorex, Inc. See LICENSE file for details.
"""
DnaSegment_EditCommand provides a way to edit an existing DnaSegment.
To edit a segment, first enter BuildDna_EditCommand (accessed using Build> Dna)
then, select an axis chunk of an existing DnaSegment within the DnaGroup you
are editing. When yo... | NanoCAD-master | cad/src/dna/commands/DnaSegment/DnaSegment_EditCommand.py |
NanoCAD-master | cad/src/dna/commands/DnaSegment/__init__.py | |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
@author: Ninad
@version: $Id$
@copyright: 2007-2008 Nanorex, Inc. See LICENSE file for details.
TODO: as of 2008-01-18
See DnaSegment_EditCommand for details.
"""
from PyQt4.Qt import SIGNAL
from PM.PM_GroupBox import PM_GroupBox
from command_sup... | NanoCAD-master | cad/src/dna/commands/DnaSegment/DnaSegment_PropertyManager.py |
# Copyright 2008-2009 Nanorex, Inc. See LICENSE file for details.
"""
@author: Ninad
@version: $Id$
@copyright: 2008-2009 Nanorex, Inc. See LICENSE file for details.
@license: GPL
TODO:
Attributes such as height_ref need to be renamed. But this should really be done
in the superclass exprs.DraggableHandle_Alo... | NanoCAD-master | cad/src/dna/commands/DnaSegment/DnaSegment_ResizeHandle.py |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
@author: Ninad
@version: $Id$
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.
@license: GPL
History:
2008-10-22: Created to support single click join strand operation
Example: while in this command, if user clicks anywhere on a stra... | NanoCAD-master | cad/src/dna/commands/JoinStrands/ClickToJoinStrands_Command.py |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
@author: Ninad
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.
@version:$Id$
History:
TODO:
"""
from utilities.prefs_constants import arrowsOnThreePrimeEnds_prefs_key
from utilities.prefs_constants import arrowsOnFivePrimeEnds_prefs_key... | NanoCAD-master | cad/src/dna/commands/JoinStrands/JoinStrands_GraphicsMode.py |
NanoCAD-master | cad/src/dna/commands/JoinStrands/__init__.py | |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
@author: Ninad
@version: $Id$
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.
@license: GPL
TODOs:
Many changes planned in JoinStrands_GraphicsMode .
"""
from dna.commands.JoinStrands.JoinStrands_PropertyManager import JoinStrands_... | NanoCAD-master | cad/src/dna/commands/JoinStrands/JoinStrands_Command.py |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
JoinStrands_PropertyManager.py
The JoinStrands_PropertyManager class provides a Property Manager
for the B{Join Strands} command on the flyout toolbar in the
Build > Dna mode.
@author: Ninad
@version: $Id$
@copyright: 2008 Nanorex, Inc. See L... | NanoCAD-master | cad/src/dna/commands/JoinStrands/JoinStrands_PropertyManager.py |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
JoinStrands_By_DND_RequestCommand
This is a request command called whenever a user wants to join two strands by
drag and drop. (DND = Drag and Drop). During singletLeftDown of the current
graphicsMode, it calls this request command and then during left ... | NanoCAD-master | cad/src/dna/commands/JoinStrands/JoinStrands_By_DND_RequestCommand.py |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
@author: Ninad
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.
@version:$Id$
History:
2008-10-21 : Created
TODO:
"""
from utilities.prefs_constants import arrowsOnThreePrimeEnds_prefs_key
from utilities.prefs_constants import arrowsOnFi... | NanoCAD-master | cad/src/dna/commands/JoinStrands/ClickToJoinStrands_GraphicsMode.py |
# Copyright 2007-2009 Nanorex, Inc. See LICENSE file for details.
"""
BuildDna_EditCommand.py
@author: Ninad
@version: $Id$
@copyright: 2007-2009 Nanorex, Inc. See LICENSE file for details.
History:
Ninad 2008-01-11: Created
TODO: as of 2008-01-11
- Needs more documentation and the file is subjected to heavy revi... | NanoCAD-master | cad/src/dna/commands/BuildDna/BuildDna_EditCommand.py |
NanoCAD-master | cad/src/dna/commands/BuildDna/__init__.py | |
# Copyright 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
BuildDna_PropertyManager.py
@author: Ninad
@version: $Id$
@copyright: 2007-2008 Nanorex, Inc. See LICENSE file for details.
History:
Ninad 2008-01-11: Created
TODO: as of 2008-01-11
- Needs more documentation and the file is subjected to heavy ... | NanoCAD-master | cad/src/dna/commands/BuildDna/BuildDna_PropertyManager.py |
# Copyright 2008-2009 Nanorex, Inc. See LICENSE file for details.
"""
@author: Ninad
@version: $Id$
@copyright: 2008-2009 Nanorex, Inc. See LICENSE file for details.
History:
TODO:
"""
from commands.SelectChunks.SelectChunks_GraphicsMode import SelectChunks_GraphicsMode
from model.chem import Atom
from model.bond... | NanoCAD-master | cad/src/dna/commands/BuildDna/BuildDna_GraphicsMode.py |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
@author: Ninad
@version: $Id$
@copyright:2008 Nanorex, Inc. See LICENSE file for details.
History:
2008-05-09 Created
TODO: as of 2008-01-18
- See MultipleDnaSegmentResize_EditCommand for details.
- need to implement model_changed method
"""
from PyQt... | NanoCAD-master | cad/src/dna/commands/MultipleDnaSegmentResize/MultipleDnaSegmentResize_PropertyManager.py |
NanoCAD-master | cad/src/dna/commands/MultipleDnaSegmentResize/__init__.py | |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
MultipleDnaSegmentResize_EditCommand provides a way to edit (resize) one or more
DnaSegments. To resize segments, select the segments you want to resize,
highlight the axis of any one (in the default command), right click and select
'Resize DnaSegments'... | NanoCAD-master | cad/src/dna/commands/MultipleDnaSegmentResize/MultipleDnaSegmentResize_EditCommand.py |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
MultipleDnaSegmentResize_GraphicsMode.py
Graphics mode for resizing multiple dna segments at once
@author: Ninad
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.
@version:$Id$
History:
TODO:
see MultipleDnaSegmentResize_EditCommand
"""
f... | NanoCAD-master | cad/src/dna/commands/MultipleDnaSegmentResize/MultipleDnaSegmentResize_GraphicsMode.py |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
@author: Mark
@version: $Id$
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.
"""
import foundation.changes as changes
from commands.SelectChunks.SelectChunks_GraphicsMode import SelectChunks_GraphicsMode
from command_support.EditComma... | NanoCAD-master | cad/src/dna/commands/OrderDna/OrderDna_Command.py |
NanoCAD-master | cad/src/dna/commands/OrderDna/__init__.py | |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
OrderDna_PropertyManager.py
The OrderDna_PropertyManager class provides a Property Manager
for the B{Order Dna} command on the flyout toolbar in the
Build > Dna mode.
@author: Mark
@version: $Id$
@copyright: 2008 Nanorex, Inc. See LICENSE fil... | NanoCAD-master | cad/src/dna/commands/OrderDna/OrderDna_PropertyManager.py |
# Copyright 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
BreakStrands_GraphicsMode.py
@author: Ninad
@version: $Id$
@copyright: 2007-2008 Nanorex, Inc. See LICENSE file for details.
@license: GPL
History:
2008-07-01:
Split this out of BreakStrands_Command.py into its own module.
The class was o... | NanoCAD-master | cad/src/dna/commands/BreakStrands/BreakStrands_GraphicsMode.py |
# Copyright 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
@author: Ninad
@version: $Id$
@copyright: 2007-2008 Nanorex, Inc. See LICENSE file for details.
@license: GPL
TODOs: [ as of 2008-01-04]
- To be revised heavily . Still a stub, needs documentation.
"""
from dna.command_support.BreakOrJoinS... | NanoCAD-master | cad/src/dna/commands/BreakStrands/BreakStrands_Command.py |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
BreakStrands_PropertyManager.py
The BreakStrands_PropertyManager class provides a Property Manager
for the B{Break Strands} command on the flyout toolbar in the
Build > Dna mode.
@author: Ninad
@version: $Id$
@copyright: 2008 Nanorex, Inc. Se... | NanoCAD-master | cad/src/dna/commands/BreakStrands/BreakStrands_PropertyManager.py |
NanoCAD-master | cad/src/dna/commands/BreakStrands/__init__.py | |
# Copyright 2008-2009 Nanorex, Inc. See LICENSE file for details.
"""
BreakSite_Marker object wraps the functionality of identifying
the potential break sites within a DnaStrand.
NOTE: This class has nothing to do with DnaMarker class.
@author: Ninad
@version: $Id$
@copyright: 2008-2009 Nanorex, Inc. See LICENSE fi... | NanoCAD-master | cad/src/dna/commands/BreakStrands/BreakSite_Marker.py |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
@author: Ninad
@version: $Id$
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.
"""
from widgets.prefs_widgets import connect_checkbox_with_boolean_pref
from PyQt4.Qt import Qt
from PyQt4.Qt import SIGNAL
from PM.PM_GroupBox import PM_Gr... | NanoCAD-master | cad/src/dna/commands/ConvertDna/ConvertDna_PropertyManager.py |
NanoCAD-master | cad/src/dna/commands/ConvertDna/__init__.py | |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
@author: Ninad
@version: $Id$
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.
"""
from utilities.constants import CL_EXTERNAL_ACTION
from commands.SelectChunks.SelectChunks_Command import SelectChunks_Command
from dna.commands.Convert... | NanoCAD-master | cad/src/dna/commands/ConvertDna/ConvertDna_Command.py |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
@author: Ninad
@version: $Id$
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.
"""
from commands.SelectChunks.SelectChunks_GraphicsMode import SelectChunks_GraphicsMode
class ConvertDna_GraphicsMode(SelectChunks_GraphicsMode):
""... | NanoCAD-master | cad/src/dna/commands/ConvertDna/ConvertDna_GraphicsMode.py |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
@author: Ninad
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.
@version:$Id$
History:
2008-05-21 - 2008-06-01 Created and further refactored and modified
@See: ListWidgetItems_Command_Mixin,
ListWidgetItems_GraphicsMode_Mixin
... | NanoCAD-master | cad/src/dna/commands/MakeCrossovers/MakeCrossovers_Command.py |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
MakeCrossovers_PropertyManager.py
@author: Ninad
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.
@version:$Id$
History:
TODO:
See MakeCrossovers_Command for details.
"""
import foundation.env as env
from PM.PM_SelectionListWidget impor... | NanoCAD-master | cad/src/dna/commands/MakeCrossovers/MakeCrossovers_PropertyManager.py |
NanoCAD-master | cad/src/dna/commands/MakeCrossovers/__init__.py | |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
ListWidgetItems_Command_Mixin.py
@author: Ninad
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.
@version:$Id$
History:
2008-05-27 -2008-05-29 Created and modified.
TODO as of 2008-06-01:
- Rename this class and others like ListWidgetItem... | NanoCAD-master | cad/src/dna/commands/MakeCrossovers/ListWidgetItems_Command_Mixin.py |
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