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authorBruce Smith <bruce@nanorex.com>2008-04-14 07:49:50 +0000
committerBruce Smith <bruce@nanorex.com>2008-04-14 07:49:50 +0000
commit4e98f29fbacea78f0bb2963846ad0edc9500aa86 (patch)
treef83980515962d368808a064baee7c250d4973c97
parent274c933b2316bdd4e65ac5047f68a9d44a2b2006 (diff)
downloadnanoengineer-4e98f29fbacea78f0bb2963846ad0edc9500aa86.tar.gz
nanoengineer-4e98f29fbacea78f0bb2963846ad0edc9500aa86.zip
remove hyphens from PAM-5 and PAM-3 to uniformize names as PAM5 and PAM3
Diffstat
-rw-r--r--cad/src/PM/PM_PAM5_AtomChooser.py2
-rw-r--r--cad/src/dna/commands/BuildDuplex/DnaDuplex.py14
-rw-r--r--cad/src/dna/commands/BuildDuplex/DnaDuplexPropertyManager.py2
-rw-r--r--cad/src/dna/commands/BuildDuplex/DnaDuplex_EditCommand.py4
-rwxr-xr-xcad/src/dna/commands/BuildDuplex_old/DnaGenHelper.py12
-rw-r--r--cad/src/dna/commands/DnaSegment/DnaSegment_EditCommand.py6
-rw-r--r--cad/src/dna/commands/DnaSegment/DnaSegment_PropertyManager.py2
-rw-r--r--cad/src/dna/commands/DnaStrand/DnaStrand_PropertyManager.py4
-rwxr-xr-xcad/src/files/pdb/files_pdb.py6
-rwxr-xr-xcad/src/graphics/rendering/qutemol/qutemol.py6
-rwxr-xr-xcad/src/ne1_ui/MWsemantics.py2
11 files changed, 30 insertions, 30 deletions
diff --git a/cad/src/PM/PM_PAM5_AtomChooser.py b/cad/src/PM/PM_PAM5_AtomChooser.py
index 040e3e990..6e9a402d6 100644
--- a/cad/src/PM/PM_PAM5_AtomChooser.py
+++ b/cad/src/PM/PM_PAM5_AtomChooser.py
@@ -57,7 +57,7 @@ class PM_PAM5_AtomChooser( PM_MolecularModelingKit ):
@see: B{elements.py}
@see: B{L{PM_MolecularModelingKit}}
- @see: U{B{PAM-5}<http://www.nanoengineer-1.net/mediawiki/index.php?title=PAM-5>}
+ @see: U{B{PAM5}<http://www.nanoengineer-1.net/mediawiki/index.php?title=PAM5>}
"""
viewerDisplay = diBALL
diff --git a/cad/src/dna/commands/BuildDuplex/DnaDuplex.py b/cad/src/dna/commands/BuildDuplex/DnaDuplex.py
index 91a7331cf..9d9f0b29d 100644
--- a/cad/src/dna/commands/BuildDuplex/DnaDuplex.py
+++ b/cad/src/dna/commands/BuildDuplex/DnaDuplex.py
@@ -74,8 +74,8 @@ class Dna:
@type handedness: int
@ivar model: The model representation, where:
- - "PAM3" = PAM-3 reduced model.
- - "PAM5" = PAM-5 reduced model.
+ - "PAM3" = PAM3 reduced model.
+ - "PAM5" = PAM5 reduced model.
@type model: str
@@ -1082,7 +1082,7 @@ class A_Dna(Dna):
class A_Dna_PAM5(A_Dna):
"""
- Provides a PAM-5 reduced model of the B form of DNA.
+ Provides a PAM5 reduced model of the B form of DNA.
@attention: This class is not implemented yet.
"""
@@ -1091,7 +1091,7 @@ class A_Dna_PAM5(A_Dna):
class A_Dna_PAM3(A_Dna):
"""
- Provides a PAM-5 reduced model of the B form of DNA.
+ Provides a PAM5 reduced model of the B form of DNA.
@attention: This class is not implemented yet.
"""
@@ -1112,7 +1112,7 @@ class B_Dna(Dna):
class B_Dna_PAM5(B_Dna):
"""
- Provides a PAM-5 reduced model of the B form of DNA.
+ Provides a PAM5 reduced model of the B form of DNA.
"""
model = "PAM5"
@@ -1278,7 +1278,7 @@ class B_Dna_PAM5(B_Dna):
class B_Dna_PAM3(B_Dna_PAM5):
"""
- Provides a PAM-3 reduced model of the B form of DNA.
+ Provides a PAM3 reduced model of the B form of DNA.
"""
model = "PAM3"
@@ -1653,7 +1653,7 @@ class Z_Dna_Atomistic(Z_Dna):
class Z_Dna_PAM5(Z_Dna):
"""
- Provides a PAM-5 reduced model of the Z form of DNA.
+ Provides a PAM5 reduced model of the Z form of DNA.
@attention: This class is not implemented yet.
"""
diff --git a/cad/src/dna/commands/BuildDuplex/DnaDuplexPropertyManager.py b/cad/src/dna/commands/BuildDuplex/DnaDuplexPropertyManager.py
index d3afcc68b..c938b51de 100644
--- a/cad/src/dna/commands/BuildDuplex/DnaDuplexPropertyManager.py
+++ b/cad/src/dna/commands/BuildDuplex/DnaDuplexPropertyManager.py
@@ -262,7 +262,7 @@ class DnaDuplexPropertyManager( EditCommand_PM, DebugMenuMixin ):
choices = ["B-DNA"],
setAsDefault = True)
- dnaModelChoices = ['PAM-3', 'PAM-5']
+ dnaModelChoices = ['PAM3', 'PAM5']
self.dnaModelComboBox = \
PM_ComboBox( pmGroupBox,
label = "Model:",
diff --git a/cad/src/dna/commands/BuildDuplex/DnaDuplex_EditCommand.py b/cad/src/dna/commands/BuildDuplex/DnaDuplex_EditCommand.py
index 8b62c62a0..9f43bd586 100644
--- a/cad/src/dna/commands/BuildDuplex/DnaDuplex_EditCommand.py
+++ b/cad/src/dna/commands/BuildDuplex/DnaDuplex_EditCommand.py
@@ -573,9 +573,9 @@ class DnaDuplex_EditCommand(EditCommand):
getDuplexLength('B-DNA', numberOfBases)
if dnaForm == 'B-DNA':
- if dnaModel == 'PAM-3':
+ if dnaModel == 'PAM3':
dna = B_Dna_PAM3()
- elif dnaModel == 'PAM-5':
+ elif dnaModel == 'PAM5':
dna = B_Dna_PAM5()
else:
print "bug: unknown dnaModel type: ", dnaModel
diff --git a/cad/src/dna/commands/BuildDuplex_old/DnaGenHelper.py b/cad/src/dna/commands/BuildDuplex_old/DnaGenHelper.py
index e03bbb351..743cbd5a4 100755
--- a/cad/src/dna/commands/BuildDuplex_old/DnaGenHelper.py
+++ b/cad/src/dna/commands/BuildDuplex_old/DnaGenHelper.py
@@ -36,7 +36,7 @@ Bruce 2008-1-1:
# To do:
#
-# 1) Atomistic and PAM-5 generated models should have exact orientation
+# 1) Atomistic and PAM5 generated models should have exact orientation
# (i.e. rotational origin).
import foundation.env as env
@@ -79,7 +79,7 @@ class Dna:
@ivar model: The model representation, where:
- "Atomistic" = atomistic model
- - "PAM5" = PAM-5 reduced model.
+ - "PAM5" = PAM5 reduced model.
@type model: str
@ivar sequence: The sequence (of strand A of the duplex).
@@ -313,7 +313,7 @@ class A_Dna_Atomistic(A_Dna):
class A_Dna_PAM5(A_Dna):
"""
- Provides a PAM-5 reduced model of the B form of DNA.
+ Provides a PAM5 reduced model of the B form of DNA.
@attention: This class is not implemented yet.
"""
@@ -370,7 +370,7 @@ class B_Dna_Atomistic(B_Dna):
class B_Dna_PAM5(B_Dna):
"""
- Provides a PAM-5 reduced model of the B form of DNA.
+ Provides a PAM5 reduced model of the B form of DNA.
"""
model = "PAM5"
@@ -488,7 +488,7 @@ class B_Dna_PAM5(B_Dna):
class B_Dna_PAM3(B_Dna_PAM5):
"""
- Provides a PAM-3 reduced model of the B form of DNA.
+ Provides a PAM3 reduced model of the B form of DNA.
"""
model = "PAM3"
@@ -617,7 +617,7 @@ class Z_Dna_PAM5(Z_Dna):
class Z_Dna_PAM5(Z_Dna):
"""
- Provides a PAM-5 reduced model of the Z form of DNA.
+ Provides a PAM5 reduced model of the Z form of DNA.
@attention: This class is not implemented yet.
"""
diff --git a/cad/src/dna/commands/DnaSegment/DnaSegment_EditCommand.py b/cad/src/dna/commands/DnaSegment/DnaSegment_EditCommand.py
index 0da553648..91de41fd0 100644
--- a/cad/src/dna/commands/DnaSegment/DnaSegment_EditCommand.py
+++ b/cad/src/dna/commands/DnaSegment/DnaSegment_EditCommand.py
@@ -530,9 +530,9 @@ class DnaSegment_EditCommand(State_preMixin, EditCommand):
return None
if dnaForm == 'B-DNA':
- if dnaModel == 'PAM-3':
+ if dnaModel == 'PAM3':
dna = B_Dna_PAM3()
- elif dnaModel == 'PAM-5':
+ elif dnaModel == 'PAM5':
dna = B_Dna_PAM5()
else:
print "bug: unknown dnaModel type: ", dnaModel
@@ -1000,7 +1000,7 @@ class DnaSegment_EditCommand(State_preMixin, EditCommand):
##########################################
##dnaForm = 'B-DNA'
- ##dnaModel = 'PAM-3'
+ ##dnaModel = 'PAM3'
##basesPerTurn, duplexRise = self.struct.getProps()
##params_to_set_in_propMgr = (None,
diff --git a/cad/src/dna/commands/DnaSegment/DnaSegment_PropertyManager.py b/cad/src/dna/commands/DnaSegment/DnaSegment_PropertyManager.py
index c479fc23b..a8fa226ee 100644
--- a/cad/src/dna/commands/DnaSegment/DnaSegment_PropertyManager.py
+++ b/cad/src/dna/commands/DnaSegment/DnaSegment_PropertyManager.py
@@ -65,7 +65,7 @@ class DnaSegment_PropertyManager( EditCommand_PM, DebugMenuMixin ):
self._conformation = 'B-DNA'
self.duplexRise = 3.18
self.basesPerTurn = 10
- self.dnaModel = 'PAM-3'
+ self.dnaModel = 'PAM3'
EditCommand_PM.__init__( self,
win,
diff --git a/cad/src/dna/commands/DnaStrand/DnaStrand_PropertyManager.py b/cad/src/dna/commands/DnaStrand/DnaStrand_PropertyManager.py
index 94a9ca5c8..ee78be0ca 100644
--- a/cad/src/dna/commands/DnaStrand/DnaStrand_PropertyManager.py
+++ b/cad/src/dna/commands/DnaStrand/DnaStrand_PropertyManager.py
@@ -70,7 +70,7 @@ class DnaStrand_PropertyManager( EditCommand_PM, DebugMenuMixin ):
self._conformation = 'B-DNA'
self.duplexRise = 3.18
self.basesPerTurn = 10
- self.dnaModel = 'PAM-3'
+ self.dnaModel = 'PAM3'
EditCommand_PM.__init__( self,
@@ -367,4 +367,4 @@ class DnaStrand_PropertyManager( EditCommand_PM, DebugMenuMixin ):
Abstract method.
"""
pass
- \ No newline at end of file
+
diff --git a/cad/src/files/pdb/files_pdb.py b/cad/src/files/pdb/files_pdb.py
index 46d1eb469..a7c92d5f9 100755
--- a/cad/src/files/pdb/files_pdb.py
+++ b/cad/src/files/pdb/files_pdb.py
@@ -279,9 +279,9 @@ def writepdb(part,
WRITE_ALL_ATOMS = 0 (even writes hidden and invisble atoms)
EXCLUDE_BONDPOINTS = 1 (excludes bondpoints)
EXCLUDE_HIDDEN_ATOMS = 2 (excludes invisible atoms)
- EXCLUDE_DNA_ATOMS = 4 (excludes PAM-3 and PAM-5 pseudo atoms)
- EXCLUDE_DNA_AXIS_ATOMS = 8 (excludes PAM-3 axis atoms)
- EXCLUDE_DNA_AXIS_BONDS = 16 (supresses PAM-3 axis bonds)
+ EXCLUDE_DNA_ATOMS = 4 (excludes PAM3 and PAM5 pseudo atoms)
+ EXCLUDE_DNA_AXIS_ATOMS = 8 (excludes PAM3 axis atoms)
+ EXCLUDE_DNA_AXIS_BONDS = 16 (supresses PAM3 axis bonds)
@type excludeFlags: integer
@note: Atoms and bonds of hidden chunks are never written.
diff --git a/cad/src/graphics/rendering/qutemol/qutemol.py b/cad/src/graphics/rendering/qutemol/qutemol.py
index f6a1e7216..f750186d0 100755
--- a/cad/src/graphics/rendering/qutemol/qutemol.py
+++ b/cad/src/graphics/rendering/qutemol/qutemol.py
@@ -286,9 +286,9 @@ def write_qutemol_files(part, excludeFlags = EXCLUDE_HIDDEN_ATOMS):
WRITE_ALL_ATOMS = 0 (even writes hidden and invisble atoms)
EXCLUDE_BONDPOINTS = 1 (excludes bondpoints)
EXCLUDE_HIDDEN_ATOMS = 2 (excludes both hidden and invisible atoms)
- EXCLUDE_DNA_ATOMS = 4 (excludes PAM-3 and PAM-5 pseudo atoms)
- EXCLUDE_DNA_AXIS_ATOMS = 8 (excludes PAM-3 axis atoms)
- EXCLUDE_DNA_AXIS_BONDS = 16 (supresses PAM-3 axis bonds)
+ EXCLUDE_DNA_ATOMS = 4 (excludes PAM3 and PAM5 pseudo atoms)
+ EXCLUDE_DNA_AXIS_ATOMS = 8 (excludes PAM3 axis atoms)
+ EXCLUDE_DNA_AXIS_BONDS = 16 (supresses PAM3 axis bonds)
@type excludeFlags: int
@return: the name of the temp PDB file, or None if no atoms are in I{part}.
diff --git a/cad/src/ne1_ui/MWsemantics.py b/cad/src/ne1_ui/MWsemantics.py
index 018f30332..3e27e3e0e 100755
--- a/cad/src/ne1_ui/MWsemantics.py
+++ b/cad/src/ne1_ui/MWsemantics.py
@@ -343,7 +343,7 @@ class MWsemantics(QMainWindow,
non_debug = True,
prefs_key = "A9 devel/DNA Duplex"):
- print "Using original DNA generator (supports PAM-5)."
+ print "Using original DNA generator (supports PAM5)."
from dna.commands.BuildDuplex_old.DnaGenerator import DnaGenerator
self.dnacntl = DnaGenerator(self)
else:
generated by cgit v1.2.3 (git 2.39.1) at 2025-07-26 16:12:59 +0000