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| author | Ninad Sathaye <ninad@nanorex.com> | 2008-09-24 18:53:34 +0000 |
|---|---|---|
| committer | Ninad Sathaye <ninad@nanorex.com> | 2008-09-24 18:53:34 +0000 |
| commit | f575eda394d1b234e94e3306ddce5889825d0113 (patch) | |
| tree | e04c94d0aa2b8b07215afba07e0c66508593cb9c | |
| parent | e9f081f064150f9cf1b362cffddc75db188c7116 (diff) | |
| download | nanoengineer-f575eda394d1b234e94e3306ddce5889825d0113.tar.gz nanoengineer-f575eda394d1b234e94e3306ddce5889825d0113.zip | |
bug fixes after module renaming
5 files changed, 14 insertions, 14 deletions
diff --git a/cad/src/dna/commands/BuildDuplex/DnaDuplex_EditCommand.py b/cad/src/dna/commands/BuildDuplex/DnaDuplex_EditCommand.py index 3e390c33b..e252b90f3 100644 --- a/cad/src/dna/commands/BuildDuplex/DnaDuplex_EditCommand.py +++ b/cad/src/dna/commands/BuildDuplex/DnaDuplex_EditCommand.py @@ -557,9 +557,9 @@ class DnaDuplex_EditCommand(EditCommand): if dnaForm == 'B-DNA': if dnaModel == 'PAM3': - dna = B_Dna_PAM3() + dna = B_Dna_PAM3_Generator() elif dnaModel == 'PAM5': - dna = B_Dna_PAM5() + dna = B_Dna_PAM5_Generator() else: print "bug: unknown dnaModel type: ", dnaModel else: diff --git a/cad/src/dna/commands/DnaSegment/DnaSegment_EditCommand.py b/cad/src/dna/commands/DnaSegment/DnaSegment_EditCommand.py index b88e1d56b..1c6390076 100644 --- a/cad/src/dna/commands/DnaSegment/DnaSegment_EditCommand.py +++ b/cad/src/dna/commands/DnaSegment/DnaSegment_EditCommand.py @@ -664,9 +664,9 @@ class DnaSegment_EditCommand(State_preMixin, EditCommand): if dnaForm == 'B-DNA': if dnaModel == 'PAM3': - dna = B_Dna_PAM3() + dna = B_Dna_PAM3_Generator() elif dnaModel == 'PAM5': - dna = B_Dna_PAM5() + dna = B_Dna_PAM5_Generator() else: print "bug: unknown dnaModel type: ", dnaModel else: @@ -746,7 +746,7 @@ class DnaSegment_EditCommand(State_preMixin, EditCommand): """ assert self.struct - self.dna = B_Dna_PAM3() + self.dna = B_Dna_PAM3_Generator() number_of_basePairs_from_struct,\ numberOfBases, \ diff --git a/cad/src/dna/commands/DnaStrand/DnaStrand_EditCommand.py b/cad/src/dna/commands/DnaStrand/DnaStrand_EditCommand.py index 17a2dabdf..2171285d9 100644 --- a/cad/src/dna/commands/DnaStrand/DnaStrand_EditCommand.py +++ b/cad/src/dna/commands/DnaStrand/DnaStrand_EditCommand.py @@ -342,7 +342,7 @@ class DnaStrand_EditCommand(State_preMixin, EditCommand): # made with) name = self.name - self.dna = B_Dna_PAM3_SingleStrand() + self.dna = B_Dna_PAM3_SingleStrand_Generator() numberOfBases, \ dnaForm, \ diff --git a/cad/src/dna/commands/MakeCrossovers/MakeCrossovers_Command.py b/cad/src/dna/commands/MakeCrossovers/MakeCrossovers_Command.py index bcc78b52a..5209d80aa 100644 --- a/cad/src/dna/commands/MakeCrossovers/MakeCrossovers_Command.py +++ b/cad/src/dna/commands/MakeCrossovers/MakeCrossovers_Command.py @@ -281,7 +281,7 @@ class MakeCrossovers_Command(SelectChunks_Command, @Note: This method is copied from DnaDuplex.py """ - #Moved from B_Dna_PAM3_SingleStrand to here, to fix bugs like + #Moved from B_Dna_PAM3_SingleStrand_Generator to here, to fix bugs like #2711 in segment resizing-- Ninad 2008-04-14 assert atm1.element.role == 'strand' and atm2.element.role == 'strand' #Initialize all possible bond points to None diff --git a/cad/src/dna/generators/Dna_Generator.py b/cad/src/dna/generators/Dna_Generator.py index 4c720027c..0abc22322 100644 --- a/cad/src/dna/generators/Dna_Generator.py +++ b/cad/src/dna/generators/Dna_Generator.py @@ -124,7 +124,7 @@ class Dna_Generator: - the optional argument resizeEndStrandAtom and assignment of self.resizeEndStrand1Atom needs to be cleaned up. - refactoring cleanup and more renaming etc planned post FNANO - - See also comments in B_Dna_PAM3_SingleStrand + - See also comments in B_Dna_PAM3_SingleStrand_Generator """ self.assy = group.assy assy = group.assy @@ -325,7 +325,7 @@ class Dna_Generator: def _replace_overlapping_axisAtoms_of_new_dna(self, new_endBaseAtomList): """ - @see: B_Dna_PAM3_SingleStrand._replace_overlapping_axisAtoms_of_new_dna() + @see: B_Dna_PAM3_SingleStrand_Generator._replace_overlapping_axisAtoms_of_new_dna() """ pass @@ -347,7 +347,7 @@ class Dna_Generator: only a duplex and thats why the name 'duplex' @see: self.modify() - @see: B_Dna_PAM3_SingleStrand._fuse_new_dna_with_original_duplex() + @see: B_Dna_PAM3_SingleStrand_Generator._fuse_new_dna_with_original_duplex() """ @@ -581,7 +581,7 @@ class Dna_Generator: @see: self._fuse_new_dna_with_original_duplex() @see: self._bond_atoms_in_atomPairs() which calls this """ - #Moved from B_Dna_PAM3_SingleStrand to here, to fix bugs like + #Moved from B_Dna_PAM3_SingleStrand_Generator to here, to fix bugs like #2711 in segment resizing-- Ninad 2008-04-14 assert atm1.element.role == 'strand' and atm2.element.role == 'strand' #Initialize all possible bond points to None @@ -868,8 +868,8 @@ class Dna_Generator: needs to be deleted. The latter is the case while resizing a single strand of a Dna. @see: self._remove_bases_from_dna() where this is called. - @see: B_Dna_PAM3._strand_neighbors_to_delete() - @see: B_Dna_PAM3_SingleStrand._strand_neighbors_to_delete() + @see: B_Dna_PAM3_Generator._strand_neighbors_to_delete() + @see: B_Dna_PAM3_SingleStrand_Generator._strand_neighbors_to_delete() """ return () @@ -1037,7 +1037,7 @@ class Dna_Generator: #Perhaps computing this strand atom always be done at a later #stage. But I am unsure if this will cause any bugs. So not #changing the original implementation . - #See B_Dna_PAM3.orient_for_modify() for details. + #See B_Dna_PAM3_Generator.orient_for_modify() for details. #This NEEDS CLEANUP -- Ninad 2008-06-02 self._determine_axis_and_strandA_endAtoms_at_end_1(self.baseList[0]) |