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authorPiotr Rotkiewicz <piotr@pirx.com>2008-04-09 16:02:40 +0000
committerPiotr Rotkiewicz <piotr@pirx.com>2008-04-09 16:02:40 +0000
commit1a4d6f222c8a645022ccf2e3be4a24091506ca6a (patch)
tree963397459b90abe4459619320ba167cd34002b29
parentc02aebf839f502cfe42daa626d738a0a6b18b3aa (diff)
downloadnanoengineer-theirix-1a4d6f222c8a645022ccf2e3be4a24091506ca6a.tar.gz
nanoengineer-theirix-1a4d6f222c8a645022ccf2e3be4a24091506ca6a.zip
=Enables Peptide Generator by default.
Diffstat
-rwxr-xr-xcad/src/commands/InsertPeptide/PeptideGenerator.py45
-rwxr-xr-xcad/src/commands/InsertPeptide/PeptideGeneratorPropertyManager.py14
-rwxr-xr-xcad/src/ne1_startup/startup_misc.py59
-rwxr-xr-xcad/src/ui/actions/Tools/Build Structures/Peptide.pngbin328 -> 333 bytes
4 files changed, 72 insertions, 46 deletions
diff --git a/cad/src/commands/InsertPeptide/PeptideGenerator.py b/cad/src/commands/InsertPeptide/PeptideGenerator.py
index 55aaeddd9..7b6ca8b0c 100755
--- a/cad/src/commands/InsertPeptide/PeptideGenerator.py
+++ b/cad/src/commands/InsertPeptide/PeptideGenerator.py
@@ -292,20 +292,20 @@ TRP_ZMATRIX = [
( 4, "H ", "H", "", 3, 2, 1, 1.010, 119.800, 0.000 ),
( 5, "CA ", "C", "sp3", 3, 2, 1, 1.449, 121.900, 180.000 ),
( 6, "HA ", "H", "", 5, 3, 2, 1.090, 109.500, 300.000 ),
- ( 7, "CB ", "C", "sp2", 5, 3, 2, 1.525, 111.100, 60.000 ),
+ ( 7, "CB ", "C", "sp3", 5, 3, 2, 1.525, 111.100, 60.000 ),
( 8, "HB2", "H", "", 7, 5, 3, 1.090, 109.500, 300.000 ),
( 9, "HB3", "H", "", 7, 5, 3, 1.090, 109.500, 60.000 ),
- ( 10, "CG ", "C", "sp2", 7, 5, 3, 1.510, 115.000, 180.000 ),
- ( 11, "CD1", "C", "sp2", 10, 7, 5, 1.340, 127.000, 180.000 ),
+ ( 10, "CG ", "C", "sp3", 7, 5, 3, 1.510, 115.000, 180.000 ),
+ ( 11, "CD1", "C", "sp3", 10, 7, 5, 1.340, 127.000, 180.000 ),
( 12, "HD1", "H", "", 11, 10, 7, 1.090, 120.000, 0.000 ),
- ( 13, "NE1", "N", "sp2", 11, 10, 7, 1.430, 107.000, 180.000 ),
+ ( 13, "NE1", "N", "sp3", 11, 10, 7, 1.430, 107.000, 180.000 ),
( 14, "HE1", "H", "", 13, 11, 10, 1.010, 125.500, 180.000 ),
- ( 15, "CE2", "C", "", 13, 11, 10, 1.310, 109.000, 0.000 ),
- ( 16, "CZ2", "C", "", 15, 13, 11, 1.400, 128.000, 180.000 ),
+ ( 15, "CE2", "C", "sp2", 13, 11, 10, 1.310, 109.000, 0.000 ),
+ ( 16, "CZ2", "C", "sp2", 15, 13, 11, 1.400, 128.000, 180.000 ),
( 17, "HZ2", "H", "", 16, 15, 13, 1.090, 120.000, 0.000 ),
( 18, "CH2", "C", "sp2", 16, 15, 13, 1.390, 116.000, 180.000 ),
- ( 19, "HH2", "H", "", 18, 16, 15, 1.090, 120.000, 180.000 ),
- ( 20, "CZ3", "C", "sp2", 18, 16, 15, 1.350, 121.000, 0.000 ),
+ ( 19, "HH2", "H", "", 18, 16, 15, 1.090, 120.000, 180.000 ),
+ ( 20, "CZ3", "C", "sp2", 18, 16, 15, 1.350, 121.000, 0.000 ),
( 21, "HZ3", "H", "", 20, 18, 16, 1.090, 120.000, 180.000 ),
( 22, "CE3", "C", "sp2", 20, 18, 16, 1.410, 122.000, 0.000 ),
( 23, "HE3", "H", "", 22, 20, 18, 1.090, 120.000, 180.000 ),
@@ -322,7 +322,7 @@ TYR_ZMATRIX = [
( 4, "H ", "H", "", 3, 2, 1, 1.010, 119.800, 0.000 ),
( 5, "CA ", "C", "sp3", 3, 2, 1, 1.449, 121.900, 180.000 ),
( 6, "HA ", "H", "", 5, 3, 2, 1.090, 109.500, 300.000 ),
- ( 7, "CB ", "C", "sp2", 5, 3, 2, 1.525, 111.100, 60.000 ),
+ ( 7, "CB ", "C", "sp3", 5, 3, 2, 1.525, 111.100, 60.000 ),
( 8, "HB2", "H", "", 7, 5, 3, 1.090, 109.500, 300.000 ),
( 9, "HB3", "H", "", 7, 5, 3, 1.090, 109.500, 60.000 ),
( 10, "CG ", "C", "sp2", 7, 5, 3, 1.510, 109.470, 180.000 ),
@@ -334,9 +334,9 @@ TYR_ZMATRIX = [
( 16, "OH ", "O", "sp3", 15, 13, 11, 1.360, 120.000, 180.000 ),
( 17, "HH ", "H", "", 16, 15, 13, 0.960, 113.000, 0.000 ),
( 18, "CE2", "C", "sp2", 15, 13, 11, 1.400, 120.000, 0.000 ),
- ( 19, "HE2", "H", "", 18, 15, 13, 1.090, 120.000, 180.000 ),
- ( 20, "CD2", "C", "sp2", 18, 15, 13, 1.400, 120.000, 0.000 ),
- ( 21, "HD2", "H", "", 20, 18, 15, 1.090, 120.000, 180.000 ),
+ ( 19, "HE2", "H", "", 18, 15, 13, 1.090, 120.000, 180.000 ),
+ ( 20, "CD2", "C", "sp2", 18, 15, 13, 1.400, 120.000, 0.000 ),
+ ( 21, "HD2", "H", "", 20, 18, 15, 1.090, 120.000, 180.000 ),
( 22, "C ", "C", "sp2", 5, 3, 2, 1.522, 111.100, 180.000 ),
( 23, "O ", "O", "sp2", 22, 5, 3, 1.229, 120.500, 0.000 ),
]
@@ -407,7 +407,7 @@ HIS_ZMATRIX = [
( 4, "H ", "H", "", 3, 2, 1, 1.010, 119.800, 0.000 ),
( 5, "CA ", "C", "sp3", 3, 2, 1, 1.449, 121.900, 180.000 ),
( 6, "HA ", "H", "", 5, 3, 2, 1.090, 109.500, 300.000 ),
- ( 7, "CB ", "C", "sp2", 5, 3, 2, 1.525, 111.100, 60.000 ),
+ ( 7, "CB ", "C", "sp3", 5, 3, 2, 1.525, 111.100, 60.000 ),
( 8, "HB2", "H", "", 7, 5, 3, 1.090, 109.500, 300.000 ),
( 9, "HB3", "H", "", 7, 5, 3, 1.090, 109.500, 60.000 ),
( 10, "CG ", "C", "sp2", 7, 5, 3, 1.510, 115.000, 180.000 ),
@@ -689,6 +689,7 @@ class PeptideGenerator(PeptideGeneratorPropertyManager, GeneratorBaseClass):
# add a new atom to the molecule
atom = Atom(atom_name, V(self.coords[n][0], self.coords[n][1], self.coords[n][2]), mol)
atom.set_atomtype_but_dont_revise_singlets(atom_type)
+
if name=="CA ": # set c-alpha flag for visualization
atom.is_calpha = True
else:
@@ -725,15 +726,29 @@ class PeptideGenerator(PeptideGeneratorPropertyManager, GeneratorBaseClass):
self.prev_coords[2][1] = position[1]
self.prev_coords[2][2] = position[2]
- # generate the chain
+ # Generate the peptide chain.
self.length = 1
for index, phi, psi in self.peptide_cache:
name, short_name, symbol, zmatrix, size = AMINO_ACIDS[index]
self._buildResiduum(mol, zmatrix, size, phi, psi)
- # Compute bonds. This should be replaced by a proper bond assignment.
+ # Compute bonds (slow!)
+ # This should be replaced by a proper bond assignment.
inferBonds(mol)
+ # Assign proper bond orders.
+ for atom in mol.atoms.itervalues():
+ if atom.bonds:
+ for bond in atom.bonds:
+ if bond.atom1.getAtomTypeName()=="sp2" and \
+ bond.atom2.getAtomTypeName()=="sp2":
+ if ((bond.atom1.element.symbol=="C" and
+ bond.atom2.element.symbol=="C")):
+ bond.set_v6(V_AROMATIC)
+ else:
+ bond.set_v6(V_DOUBLE)
+
+
return mol
def addAminoAcid(self, index):
diff --git a/cad/src/commands/InsertPeptide/PeptideGeneratorPropertyManager.py b/cad/src/commands/InsertPeptide/PeptideGeneratorPropertyManager.py
index 502bc016f..631edd8e3 100755
--- a/cad/src/commands/InsertPeptide/PeptideGeneratorPropertyManager.py
+++ b/cad/src/commands/InsertPeptide/PeptideGeneratorPropertyManager.py
@@ -196,7 +196,19 @@ class PeptideGeneratorPropertyManager(PM_Dialog):
Adds a new amino acid to the peptide molecule.
"""
button, idx, short_name, dum, name, symbol, x, y = AA_BUTTON_LIST[aaTypeIndex]
- self.sequenceEditor.insertHtml(symbol, False, 4, 10, False)
+ if self.ss_idx==0:
+ aa_txt = "<font color=red>"
+ elif self.ss_idx==1:
+ aa_txt = "<font color=orange>"
+ elif self.ss_idx==2:
+ aa_txt = "<font color=green>"
+ elif self.ss_idx==3:
+ aa_txt = "<font color=blue>"
+ else:
+ aa_txt = "<font color=black>"
+
+ aa_txt += symbol+"</font>"
+ self.sequenceEditor.insertHtml(aa_txt, False, 4, 10, False)
self.addAminoAcid(aaTypeIndex)
def _startOverClicked(self):
diff --git a/cad/src/ne1_startup/startup_misc.py b/cad/src/ne1_startup/startup_misc.py
index 52fd5809e..96a83380d 100755
--- a/cad/src/ne1_startup/startup_misc.py
+++ b/cad/src/ne1_startup/startup_misc.py
@@ -38,13 +38,13 @@ def call_module_init_functions(): #bruce 071005 split this out of main_startup.s
# as a clarification. Likely desirable change (###TODO): register a model updater in assy,
# which calls the bond updater presently registered by bond_updater.initialize.)
# [bruce 070925 comment]
-
+
import model_updater.master_model_updater as master_model_updater
master_model_updater.initialize()
-
+
import model.assembly
model.assembly.Assembly.initialize()
-
+
import PM.GroupButtonMixin as GroupButtonMixin
GroupButtonMixin.GroupButtonMixin.initialize()
@@ -72,9 +72,9 @@ def register_MMP_RecordParsers(): #bruce 071019
pass
# TODO: add more of these.
-
+
return
-
+
# (MWsemantics.__init__ is presumably run after the above functions and before the following ones.)
def pre_main_show( win):
@@ -91,13 +91,13 @@ def pre_main_show( win):
from platform.PlatformDependent import screen_pos_size
((x0, y0), (screen_w, screen_h)) = screen_pos_size()
# note: y0 is nonzero on mac, due to menubar at top of screen.
-
+
# use 85% of screen width and 90% of screen height, or more if that would be
# less than 780 by 560 pixels, but never more than the available space.
norm_w = int( min(screen_w - 2, max(780, screen_w * 0.85)))
norm_h = int( min(screen_h - 2, max(560, screen_h * 0.90)))
#bruce 050118 reduced max norm_h to never overlap mac menubar (bugfix?)
-
+
# determine normal window origin
# [bruce 041230 changed this to center it, but feel free to change this back
# by changing the next line to center_it = 0]
@@ -113,7 +113,7 @@ def pre_main_show( win):
want_y = 36 # Top (36 pixels)
norm_x = min( want_x, (screen_w - norm_w)) + x0
norm_y = min( want_y, (screen_h - norm_h)) + y0
-
+
# Set the main window geometry, hopefully before the caller shows the window
from PyQt4.Qt import QRect
win.setGeometry(QRect(norm_x, norm_y, norm_w, norm_h))
@@ -140,7 +140,7 @@ def pre_main_show( win):
# provided they are fully supported (not experimental, unlikely to cause bugs when added)
# and won't take a lot of runtime to add. Otherwise they can be added after the
# main window is shown. [bruce 071005 comment] ###@@@
-
+
return # from pre_main_show
# This is debugging code used to find out the origin and size of the fullscreen window
@@ -155,23 +155,23 @@ def _initialize_custom_display_modes(win):
# They must match the order of related display style list-index definitions
# in constants.py.
# [bruce 080212 comment; related code has comments with same signature]
-
+
# diDNACYLINDER
import graphics.display_styles.DnaCylinderChunks as DnaCylinderChunks #mark 2008-02-11
-
+
# diCYLINDER
import graphics.display_styles.CylinderChunks as CylinderChunks #bruce 060609
from utilities.debug_prefs import debug_pref, Choice_boolean_False
enable_CylinderChunks = debug_pref("enable CylinderChunks next session?",
- Choice_boolean_False,
- non_debug = True,
- prefs_key = True)
+ Choice_boolean_False,
+ non_debug = True,
+ prefs_key = True)
win.dispCylinderAction.setText("Cylinder (experimental)")
win.dispCylinderAction.setEnabled(enable_CylinderChunks)
win.dispCylinderAction.setVisible(enable_CylinderChunks)
if enable_CylinderChunks:
win.displayStylesToolBar.addAction(win.dispCylinderAction)
-
+
# diSURFACE
import graphics.display_styles.SurfaceChunks as SurfaceChunks #mark 060610
enable_SurfaceChunks = debug_pref("enable SurfaceChunks next session?",
@@ -183,7 +183,7 @@ def _initialize_custom_display_modes(win):
win.dispSurfaceAction.setVisible(enable_SurfaceChunks)
if enable_SurfaceChunks:
win.displayStylesToolBar.addAction(win.dispSurfaceAction)
-
+
return
# ==
@@ -199,7 +199,7 @@ def post_main_show( win):
# NOTE: if possible, new code should be added into one of the following
# functions, or into a new function called by this one, rather than
# directly into this function.
-
+
# TODO: rebuild pyx modules if necessary and safe -- but only for
# developers, not end-users
# TODO: initialize Python extensions: ## import experimental/pyrex_test/extensions.py
@@ -234,24 +234,23 @@ def _init_command_Atom_Generator():
from utilities.debug_prefs import debug_pref, Choice_boolean_False
from commands.BuildAtom.AtomGenerator import enableAtomGenerator
_atomGeneratorIsEnabled = \
- debug_pref("Atom Generator example code: enabled?",
- Choice_boolean_False,
- non_debug = True,
- prefs_key = "A9/Atom Generator Visible",
- call_with_new_value = enableAtomGenerator )
+ debug_pref("Atom Generator example code: enabled?",
+ Choice_boolean_False,
+ non_debug = True,
+ prefs_key = "A9/Atom Generator Visible",
+ call_with_new_value = enableAtomGenerator )
enableAtomGenerator(_atomGeneratorIsEnabled)
return
def _init_command_Peptide_Generator(): # piotr 080304
# This function enables an experimental peptide generator.
- from utilities.debug_prefs import debug_pref, Choice_boolean_False
+ from utilities.debug_prefs import debug_pref, Choice_boolean_True
from commands.InsertPeptide.PeptideGenerator import enablePeptideGenerator
_peptideGeneratorIsEnabled = \
- debug_pref("Peptide Generator: enabled?",
- Choice_boolean_False,
- non_debug = True,
- prefs_key = "A9/Peptide Generator Visible",
- call_with_new_value = enablePeptideGenerator )
+ debug_pref("Peptide Generator: enabled?",
+ Choice_boolean_True,
+ prefs_key = "A10/Peptide Generator Visible",
+ call_with_new_value = enablePeptideGenerator )
enablePeptideGenerator(_peptideGeneratorIsEnabled)
return
@@ -281,7 +280,7 @@ def _set_mainwindow_splitter_position( win):
pixels.
This should be called after all visible changes to the main window.
-
+
@param win: the single Main Window object.
@type win: L{MWsemantics}
"""
@@ -310,7 +309,7 @@ def _set_mainwindow_splitter_position( win):
# Since we want the default width of the PropMgr to be <pmDefaultWidth>,
# I compute the new glpane width = magic_combined_width - pmDefaultWidth.
# Note: the resize is visible at startup.
-
+
pw = win.activePartWindow()
from PM.PropMgr_Constants import pmDefaultWidth
w1, w2 = pw.pwSplitter.sizes()
diff --git a/cad/src/ui/actions/Tools/Build Structures/Peptide.png b/cad/src/ui/actions/Tools/Build Structures/Peptide.png
index 79e7b899c..ab62409b9 100755
--- a/cad/src/ui/actions/Tools/Build Structures/Peptide.png
+++ b/cad/src/ui/actions/Tools/Build Structures/Peptide.png
Binary files differ
generated by cgit v1.2.3 (git 2.39.1) at 2025-05-05 04:41:20 +0000