def color_op(surfaces, color = None):
from Commands import parse_surfaces, parse_color
surfs = parse_surfaces(surfaces)
if color == 'byatom':
from chimera import MSMSModel
if [s for s in surfs if not isinstance(s, MSMSModel)]:
raise CommandError, 'Cannot color byatom non-molecular surfaces'
elif not color is None:
color = parse_color(color)
for surf in surfs:
import SurfaceColor as sc
sc.stop_coloring_surface(surf)
if color == 'byatom':
surf.colorMode = surf.ByAtom
elif not color is None:
import Surface
Surface.set_coloring_method('static', surf)
from chimera import MSMSModel
if isinstance(surf, MSMSModel):
surf.customRGBA = [color] * surf.vertexCount
else:
for p in surf.surfacePieces:
p.color = color
def color_op(surfaces, color=None):
from Commands import parse_surfaces, parse_color
surfs = parse_surfaces(surfaces)
if color == 'byatom':
from chimera import MSMSModel
if [s for s in surfs if not isinstance(s, MSMSModel)]:
raise CommandError, 'Cannot color byatom non-molecular surfaces'
elif not color is None:
color = parse_color(color)
for surf in surfs:
import SurfaceColor as sc
sc.stop_coloring_surface(surf)
if color == 'byatom':
surf.colorMode = surf.ByAtom
elif not color is None:
import Surface
Surface.set_coloring_method('static', surf)
from chimera import MSMSModel
if isinstance(surf, MSMSModel):
surf.customRGBA = [color] * surf.vertexCount
else:
for p in surf.surfacePieces:
p.color = color
def add_Surface(self, surf):
if type(surf) == str:
surf = Surface(surf)
if self.reference_surface_name is None:
self.reference_surface_name = surf.name
surf.parent = self
self.surfaces[surf.name] = surf
def __init__(self):
pygame.init()
self.s = Surface((0, 0), "Ball Fall", black)
self.s.draw_surface()
self.run_game = True
self.score = 0
self.d = database()
def __init__(self,
molecule,
category,
probeRadius=1.4,
allComponents=True,
vertexDensity=2.0):
SurfaceModel.__init__(self)
name = 'MSMS %s surface of %s' % (category, molecule.name)
SurfaceModel.__setattr__(self, 'name', name)
SurfaceModel.__setattr__(self, 'piecesAreSelectable', True)
SurfaceModel.__setattr__(self, 'oneTransparentLayer', True)
init = {
'molecule': molecule,
'colorMode': self.ByAtom,
'visibilityMode': self.ByAtom,
'density': vertexDensity,
'probeRadius': probeRadius,
'category': category,
'allComponents': allComponents,
'atomMap': None, # vertex number to Atom
'surface_piece': None,
'srf': None, # MSMS surface object
'triData': None, # MSMS triangle data
'areaSES': 0.0,
'areaSAS': 0.0,
'calculationFailed': False,
}
self.__dict__.update(init)
from _surface import SurfacePiece
self.surface_piece_defaults = {
'drawMode': self.Filled,
'lineWidth': 1.0,
'pointSize': 1.0,
'useLighting': True,
'twoSidedLighting': True,
'smoothLines': False,
'transparencyBlendMode': SurfacePiece.SRC_ALPHA_DST_1_MINUS_ALPHA,
}
self.update_surface()
# Detect changes in atom color, atom surfaceColor, atom surfaceOpacity,
# molecule color, atom surfaceDisplay.
from chimera import triggers as t
self.molecule_handler = t.addHandler('Molecule', self.molecule_cb,
None)
# Detect when surface or molecule deleted.
from chimera import addModelClosedCallback
addModelClosedCallback(self, self.surface_closed_cb)
addModelClosedCallback(self.molecule, self.molecule_closed_cb)
import Surface
Surface.set_coloring_method('msms', self, self.custom_coloring)
Surface.set_visibility_method('msms', self, self.custom_visibility)
class GFXEngine :
"""
This class draws the gfx
"""
def __init__ (self, lll, viewspace, mymap):
self.lll = lll
self.display = Display ()
self.viewspace = viewspace
self.mymap = mymap
self.terrainset = TerrainSet ()
# Test
self.settsurf = Surface ()
self.settsurf.loadFromFile ("gfx/protosettler.png")
self.settsurf.cols = 16
self.settsurf.rows = 16
self.sprites = []
def create_settler(self, x, y):
""" Adds a settler to be drawn on the screen at position x, y and returns a reference to this settler. """
sprite = Sprite (self.viewspace, self.settsurf)
sprite.x = x
sprite.y = y
sprite.configAnimation (True, 0, 24, 25)
self.sprites.append(sprite)
return sprite
def tick (self):
"""
tick() executes all actions which must be done by the GFX-Engine in one Game-Loop-cycle
This is: clearing the screen, drawing all objects, showing the new game-frame
"""
self.display.clear ()
self.draw ()
for sprite in self.sprites:
sprite.drawToDisplay (self.display)
self.display.showFrame ()
def draw (self):
self.drawLandscape ()
def drawLandscape (self):
self.drawTerrain ()
def drawTerrain (self):
self.lll.view.DrawTerrain (self.mymap.terra.asCArray (), self.mymap.mapsize, TRIA_W, TRIA_H,
TEX_FACTOR, self.terrainset.asCArray(), self.mymap.getVertarray().asCArray())
def __init__ (self): self.tcount = len(TERRAIN_TEXTURE_FILES) self.data = [] for terrafilename in TERRAIN_TEXTURE_FILES : newsurf = Surface () newsurf.loadFromFile (TERRAIN_PNG_DIR +"/"+ terrafilename, True) self.data.append (newsurf) self.carr = None
def colorMSMSSurface(s, color):
if s.colorMode == s.Custom or s.molecule is None:
import Surface
Surface.set_coloring_method('static', s, None)
s.customColors = s.vertexCount * [color]
elif s.colorMode == s.ByMolecule:
s.molecule.surfaceColor = color
elif s.colorMode == s.ByAtom:
for a in s.atoms:
a.surfaceColor = color
def colorMSMSSurface(s, color):
if s.colorMode == s.Custom or s.molecule is None:
import Surface
Surface.set_coloring_method('static', s, None)
s.customColors = s.vertexCount * [color]
elif s.colorMode == s.ByMolecule:
s.molecule.surfaceColor = color
elif s.colorMode == s.ByAtom:
for a in s.atoms:
a.surfaceColor = color
def __setattr__(self, attrname, value):
if attrname in ('drawMode', 'lineWidth', 'pointSize', 'useLighting',
'twoSidedLighting', 'smoothLines',
'transparencyBlendMode'):
# SurfacePiece attributes
if value == getattr(self, attrname):
return
elif attrname in ('colorMode', 'visibilityMode', 'density',
'probeRadius', 'category', 'allComponents'):
if value == getattr(self, attrname):
return
self.__dict__[attrname] = value
elif attrname not in ('customColors', 'customRGBA'):
SurfaceModel.__setattr__(self, attrname, value)
return
if attrname in ('density', 'probeRadius', 'category', 'allComponents'):
self.update_surface()
else:
p = self.surface_piece
if p is None or p.__destroyed__:
return
if attrname == 'drawMode':
style = {
self.Filled: p.Solid,
self.Mesh: p.Mesh,
self.Dot: p.Dot,
}[value]
p.displayStyle = style
elif attrname == 'lineWidth':
p.lineThickness = value
elif attrname == 'pointSize':
p.dotSize = value
elif attrname in ('useLighting', 'twoSidedLighting', 'smoothLines',
'transparencyBlendMode'):
setattr(p, attrname, value)
elif attrname == 'colorMode':
if value != self.Custom:
import Surface
Surface.set_coloring_method('msms', self,
self.custom_coloring)
self.update_coloring()
elif attrname == 'visibilityMode':
if value == self.ByAtom:
import Surface
Surface.set_visibility_method('msms', self,
self.custom_visibility)
self.update_visibility()
elif attrname == 'customColors':
self.set_custom_colors(value)
elif attrname == 'customRGBA':
self.set_custom_rgba(value)
self.report_change(self.change_reason[attrname])
def __setattr__(self, attrname, value):
if attrname in ('drawMode', 'lineWidth', 'pointSize', 'useLighting',
'twoSidedLighting', 'smoothLines',
'transparencyBlendMode'):
# SurfacePiece attributes
if value == getattr(self, attrname):
return
elif attrname in ('colorMode', 'visibilityMode',
'density', 'probeRadius',
'category', 'allComponents'):
if value == getattr(self, attrname):
return
self.__dict__[attrname] = value
elif attrname not in ('customColors', 'customRGBA'):
SurfaceModel.__setattr__(self, attrname, value)
return
if attrname in ('density', 'probeRadius', 'category', 'allComponents'):
self.update_surface()
else:
p = self.surface_piece
if p is None or p.__destroyed__:
return
if attrname == 'drawMode':
style = {self.Filled: p.Solid,
self.Mesh: p.Mesh,
self.Dot: p.Dot,
}[value]
p.displayStyle = style
elif attrname == 'lineWidth':
p.lineThickness = value
elif attrname == 'pointSize':
p.dotSize = value
elif attrname in ('useLighting', 'twoSidedLighting', 'smoothLines',
'transparencyBlendMode'):
setattr(p, attrname, value)
elif attrname == 'colorMode':
if value != self.Custom:
import Surface
Surface.set_coloring_method('msms', self,
self.custom_coloring)
self.update_coloring()
elif attrname == 'visibilityMode':
if value == self.ByAtom:
import Surface
Surface.set_visibility_method('msms', self,
self.custom_visibility)
self.update_visibility()
elif attrname == 'customColors':
self.set_custom_colors(value)
elif attrname == 'customRGBA':
self.set_custom_rgba(value)
self.report_change(self.change_reason[attrname])
def __init__(self, molecule, category, probeRadius = 1.4,
allComponents = True, vertexDensity = 2.0):
SurfaceModel.__init__(self)
name = 'MSMS %s surface of %s' % (category, molecule.name)
SurfaceModel.__setattr__(self, 'name', name)
SurfaceModel.__setattr__(self, 'piecesAreSelectable', True)
SurfaceModel.__setattr__(self, 'oneTransparentLayer', True)
init = {
'molecule': molecule,
'colorMode': self.ByAtom,
'visibilityMode': self.ByAtom,
'density': vertexDensity,
'probeRadius': probeRadius,
'category': category,
'allComponents': allComponents,
'atomMap': None, # vertex number to Atom
'surface_piece': None,
'srf': None, # MSMS surface object
'triData': None, # MSMS triangle data
'areaSES': 0.0,
'areaSAS': 0.0,
'calculationFailed': False,
}
self.__dict__.update(init)
from _surface import SurfacePiece
self.surface_piece_defaults = {
'drawMode': self.Filled,
'lineWidth': 1.0,
'pointSize': 1.0,
'useLighting': True,
'twoSidedLighting': True,
'smoothLines': False,
'transparencyBlendMode': SurfacePiece.SRC_ALPHA_DST_1_MINUS_ALPHA,
}
self.update_surface()
# Detect changes in atom color, atom surfaceColor, atom surfaceOpacity,
# molecule color, atom surfaceDisplay.
from chimera import triggers as t
self.molecule_handler = t.addHandler('Molecule', self.molecule_cb, None)
# Detect when surface or molecule deleted.
from chimera import addModelClosedCallback
addModelClosedCallback(self, self.surface_closed_cb)
addModelClosedCallback(self.molecule, self.molecule_closed_cb)
import Surface
Surface.set_coloring_method('msms', self, self.custom_coloring)
Surface.set_visibility_method('msms', self, self.custom_visibility)
def adjustSurfacePieceTransparency(p, opacity, frac=1):
rgba = list(p.color)
rgba[3] = frac * opacity + (1 - frac) * rgba[3]
p.color = tuple(rgba)
vrgba = p.vertexColors
if not vrgba is None:
import Surface
Surface.set_coloring_method('static', p.model, None)
vrgba[:, 3] *= 1 - frac
vrgba[:, 3] += frac * opacity
p.vertexColors = vrgba
def adjustSurfacePieceTransparency(p, opacity, frac = 1):
rgba = list(p.color)
rgba[3] = frac*opacity + (1-frac)*rgba[3]
p.color = tuple(rgba)
vrgba = p.vertexColors
if not vrgba is None:
import Surface
Surface.set_coloring_method('static', p.model, None)
vrgba[:,3] *= 1-frac
vrgba[:,3] += frac*opacity
p.vertexColors = vrgba
def distance(operation,
object1,
object2,
multiple=False,
show=False,
color=(0, 1, 1, 1)):
a1 = object1.atoms()
import Surface as s
s1 = s.selected_surface_pieces(object1, include_outline_boxes=False)
if len(a1) == 0 and len(s1) == 0:
raise CommandError('No atoms or surfaces specified')
a2 = object2.atoms()
s2 = s.selected_surface_pieces(object2, include_outline_boxes=False)
if len(a2) == 0 and len(s2) == 0:
raise CommandError('No target atoms or surfaces')
# Remove near stuff.
if a1:
a2 = list(set(a2).difference(a1))
if s1:
s2 = list(set(s2).difference(s1))
name2 = object_name(a2, s2)
xyz2 = point_array(a2, s2)
if show:
from Commands import parse_color
color = parse_color(color)
from _surface import SurfaceModel
surf = SurfaceModel()
surf.name = 'Distance measurement'
from chimera import openModels
openModels.add([surf])
else:
surf = None
if multiple:
pairs = [([a], []) for a in a1] + [([], [s]) for s in s1]
else:
pairs = [(a1, s1)]
for a, s in pairs:
name = object_name(a, s)
xyz = point_array(a, s)
report_distance(xyz, xyz2, name, name2, surf, color)
def spine(operation,
regions,
spacing=None,
tipLength=None,
color=None,
showDiameter=False):
sel = parse_object_specifier(regions, 'segmentation region')
import Surface
plist = Surface.selected_surface_pieces(sel, include_outline_boxes=False)
from Segger.regions import Segmentation
rlist = [
p.region for p in plist
if (hasattr(p, 'region') and isinstance(p.model, Segmentation))
]
if len(rlist) == 0:
raise CommandError('No segmentation regions specified: "%s"' % regions)
if not (spacing is None or isinstance(spacing,
(int, float)) and spacing > 0):
raise CommandError('spacing must be positive numeric value')
if not (tipLength is None or isinstance(tipLength,
(int, float)) and tipLength > 0):
raise CommandError('tipLength must be positive numeric value')
if not color is None:
from Commands import parse_color
color = parse_color(color)
if showDiameter:
from _surface import SurfaceModel
diam_model = SurfaceModel()
diam_model.name = 'Diameters'
from chimera import openModels
openModels.add([diam_model], sameAs=rlist[0].segmentation)
else:
diam_model = None
import spine
from chimera import replyobj
from PathLength import path_length
for r in rlist:
mset = spine.trace_spine(r, spacing, tipLength, color)
slen = path_length([l.bond for l in mset.links()])
r.set_attribute('spine length', slen)
msg = 'Spine length for region %d is %.4g' % (r.rid, slen)
dmax, dmin = spine.measure_diameter(r, mset, diam_model)
if not dmax is None:
r.set_attribute('diameter1', dmax)
r.set_attribute('diameter2', dmin)
msg += ', diameters %.4g, %.4g' % (dmax, dmin)
kave, kmin, kmax = spine.measure_curvature(mset)
if not kmax is None:
r.set_attribute('curvature average', kave)
r.set_attribute('curvature minimum', kmin)
r.set_attribute('curvature maximum', kmax)
msg += ', curvature %.4g (ave), %.4g (max), %.4g (min)' % (
kave, kmax, kmin)
replyobj.info(msg + '\n')
def runAll(mol, surface, molClass):
resultPath(mol, molClass)
au_a = 4.06 # Lattice constant of gold
relative_coverage = 1.0
Density = 21.6 * relative_coverage # Angstroms^2/chain
GOLD_Obj = Surface.Surface(
data.getSurface(surface)) # Make gold "Surface Object"
Mol_Obj = Molecule.Molecule(mol, data.getMol(
mol, molClass)) # Make Molecular objects
Mol_Obj.UnConverged = True
Box_Length = GOLD_Obj.Box_Length
Area = Box_Length[0] * Box_Length[1]
Num_SAMs = int(np.sqrt(Area / Density))
Mol_Obj.Set_Up_FF(run_orca=True,
local=True) # Parameterize Molecule Object
OPLS.Assign_OPLS(Mol_Obj, ChelpG=False) # Parameterize Molecule Object
OPLS.Assign_OPLS(GOLD_Obj, ChelpG=False) # Parametrize Au slab
SAM_System = SAM.SAM(Mol_Obj, GOLD_Obj, Num_SAMs, Box_Length, mol)
SAM_System.Gen_SAM()
SAM_System.Write_LAMMPS_Data()
SAM_System.Run_Lammps_Init()
SAM_System.Run_Lammps_NPT(Temp_Out=400, time_steps=5000000)
SAM_System.Run_Lammps_NPT(Temp_Out=400, time_steps=5000000)
SAM_System.Run_Lammps_NPT(Temp_Out=300, time_steps=5000000)
SAM_System.Run_Lammps_NPT(Temp_Out=300, time_steps=5000000)
SAM_System.Run_Lammps_NPT(Temp_Out=300, time_steps=5000000)
print "Aromodel.py complete for: " + mol + " molecule on " + surface + " surface!"
def parse_surface_pieces(spec):
from chimera.specifier import evalSpec
sel = evalSpec(spec)
import Surface
plist = Surface.selected_surface_pieces(sel)
return plist
def parse_surface_pieces(spec):
from chimera.specifier import evalSpec
sel = evalSpec(spec)
import Surface
plist = Surface.selected_surface_pieces(sel)
return plist
def mouse_drag_cb(self, v, e):
if self.last_xy is None:
self.last_xy = (e.x, e.y)
return
import Surface
plist = Surface.selected_surface_pieces()
if len(plist) == 0:
from chimera.replyobj import status
status('No surfaces selected for resizing')
return
dx, dy = (e.x - self.last_xy[0], self.last_xy[1] - e.y)
delta = dx + dy
self.last_xy = (e.x, e.y)
shift_mask = 1
shift = (e.state & shift_mask)
if shift:
factor_per_pixel = 1.001 # shift key held so scale by smaller amount
else:
factor_per_pixel = 1.01
factor = factor_per_pixel ** delta
for p in plist:
scale_surface_piece(p, factor)
def inertia(operation, objects, showEllipsoid = True, color = None,
perChain = False):
from chimera import specifier
try:
sel = specifier.evalSpec(objects)
except:
raise CommandError, 'Bad object specifier "%s"' % objects
if not color is None:
from Commands import parse_color
color = parse_color(color)
atoms = sel.atoms()
if atoms:
import inertia
if perChain:
xf = atoms[0].molecule.openState.xform
mname = molecules_name(list(set([a.molecule for a in atoms])))
s = inertia.surface_model(None, xf, 'ellipsoids ' + mname)
for achain in atoms_by_chain(atoms):
p = inertia.atoms_inertia_ellipsoid(achain, showEllipsoid,
color, s)
if p:
p.oslName = achain[0].residue.id.chainId
else:
inertia.atoms_inertia_ellipsoid(atoms, showEllipsoid, color)
import Surface
plist = Surface.selected_surface_pieces(sel, include_outline_boxes = False)
if plist:
import inertia
inertia.surface_inertia_ellipsoid(plist, showEllipsoid, color)
def __init__(self, lll, viewspace, mymap):
self.lll = lll
self.display = Display()
self.viewspace = viewspace
self.mymap = mymap
self.terrainset = TerrainSet()
self.units = []
# Test
self.settsurf = Surface()
self.settsurf.loadFromFile("gfx/protosettler.png")
self.settsurf.cols = 16
self.settsurf.rows = 16
"""self.sett = Unit (self.viewspace, self.settsurf)
def afunc(fname = function_name, sel = on_selection):
import Surface
f = getattr(Surface, fname)
if sel:
f(Surface.selected_surface_pieces())
else:
f()
def afunc(fname=function_name, sel=on_selection):
import Surface
f = getattr(Surface, fname)
if sel:
f(Surface.selected_surface_pieces())
else:
f()
def selected_surface_pieces(self):
plist = Surface.selected_surface_pieces()
if len(plist) > 0:
return plist
plist = []
for m in openModels.list(modelTypes = [SurfaceModel]):
plist.extend(m.surfacePieces)
return plist
def split_selected_surfaces(session, in_place=True):
import Surface
plist = Surface.selected_surface_pieces()
if plist:
pplist = split_surfaces(plist, session, in_place)
from chimera.replyobj import status
status('%d surface pieces' % len(pplist))
def selectedSurfacePieces(excludeMSMS = False, noneReturnsAll = True, implied = False): import Surface if noneReturnsAll and selection.currentEmpty(): plist = Surface.all_surface_pieces() else: plist = Surface.selected_surface_pieces() if implied and surfacesWithAtomsAndBonds(): atoms = selAtoms(noneReturnsAll) bonds = selBonds(noneReturnsAll) pset = set(plist) pab = atomAndBondSurfacePieces(atoms, bonds) plist.extend([p for p in pab if p not in pset]) if excludeMSMS: plist = [p for p in plist if (not isinstance(p.model, chimera.MSMSModel) or p.model.molecule is None)] return plist
def main():
Script, Mult = sys.argv
Density = 0.01
Mult = int(Mult)
File_List = glob.glob('*.data')
print len(File_List)
print File_List
Mol_Temp_List = []
Mol_Temp_List.append(Surface.Surface('alkane-monolayer_2.lammps'))
i = 0
Total_Mass = 0.0
MW = 0.0
for File in File_List:
Mol_Temp_List.append(DA_Polymer.DA_Polymer(File))
Total_Mass += Mol_Temp_List[i].MW
MW = Mol_Temp_List[i].MW
i += 1
print i
Avogadro = 6.0221413e23
Comp_List = np.ones(i + 2, dtype=int)
Comp_List = Comp_List * Mult
Comp_List[0] = 1
Total_Mols = float(i * Mult + 1) / Avogadro
Molar_Volume = MW / Density
Volume = Molar_Volume * Total_Mols
#Name = File_List[0].split('.')[1].split('_')[0] + "_%s" % i*Mult
Name = os.getcwd().split('/')[-1] + "_%s" % int(i * Mult)
print Name
DA_System = System.System(Mol_Temp_List, Comp_List, Box_Length, Name)
DA_System.Gen_Rand()
DA_System.Write_LAMMPS_Data()
DA_System.Run_Lammps_Init()
DA_System.Temperature = 800
DA_System.Run_Lammps_NPT(GPU=True)
DA_System.Run_Lammps_NPT(GPU=True)
#System.Run_Glass_Transition(DA_System, -100, Ramp_Steps = 1000000, Equil_Steps = 1000000, T_End = 600)
DA_System.Run_Lammps_NPT(GPU=True)
DA_System.Run_Lammps_NPT(GPU=True)
DA_System.Run_Lammps_NPT(GPU=True)
DA_System.Temperature = 600
DA_System.Run_Lammps_NPT(GPU=True)
DA_System.Run_Lammps_NPT(GPU=True)
DA_System.Run_Lammps_NPT(GPU=True)
DA_System.Run_Lammps_NPT(GPU=True)
DA_System.Run_Lammps_NPT(GPU=True)
DA_System.Run_Lammps_NPT(GPU=True)
System.Run_Glass_Transition(DA_System,
20,
Ramp_Steps=100000,
Equil_Steps=100000,
T_End=100)
def selectedSurfacePieces(excludeMSMS=False,
noneReturnsAll=True,
implied=False):
import Surface
if noneReturnsAll and selection.currentEmpty():
plist = Surface.all_surface_pieces()
else:
plist = Surface.selected_surface_pieces()
if implied and surfacesWithAtomsAndBonds():
atoms = selAtoms(noneReturnsAll)
bonds = selBonds(noneReturnsAll)
pset = set(plist)
pab = atomAndBondSurfacePieces(atoms, bonds)
plist.extend([p for p in pab if p not in pset])
if excludeMSMS:
plist = [
p for p in plist if (not isinstance(p.model, chimera.MSMSModel)
or p.model.molecule is None)
]
return plist
def adjustMSMSTransparency(s, atoms, opacity, aopacity):
if s.colorMode == s.Custom:
# Change transparency of just the atom vertices.
vrgba = s.customRGBA
if vrgba is None:
return
if s.atomMap is None:
vrgba[:,3] = opacity
else:
aset = set(atoms)
av = [i for i,a in enumerate(s.atomMap) if a in aset]
vrgba[av,3] = opacity
import Surface
Surface.set_coloring_method('static', s, None)
s.customRGBA = vrgba
elif s.colorMode == s.ByMolecule:
s.molecule.surfaceOpacity = aopacity
else:
for a in atoms:
a.surfaceOpacity = aopacity
def adjustMSMSTransparency(s, atoms, opacity, aopacity):
if s.colorMode == s.Custom:
# Change transparency of just the atom vertices.
vrgba = s.customRGBA
if vrgba is None:
return
if s.atomMap is None:
vrgba[:, 3] = opacity
else:
aset = set(atoms)
av = [i for i, a in enumerate(s.atomMap) if a in aset]
vrgba[av, 3] = opacity
import Surface
Surface.set_coloring_method('static', s, None)
s.customRGBA = vrgba
elif s.colorMode == s.ByMolecule:
s.molecule.surfaceOpacity = aopacity
else:
for a in atoms:
a.surfaceOpacity = aopacity
def test_blend_curve(self):
# Create C0 BlendPoint at origin
b1 = Surface.BlendPoint()
# Create G1 BlendPoint
b2 = Surface.BlendPoint([vec(10, 3, 6), vec(2, 5, 6)])
# BlendCurve between the two BlendPoints
bc = Surface.BlendCurve(b1, b2)
# Compute the interpolating BezierCurve
curve1 = bc.compute()
# Create G2 BlendPoint at the end of previous BlendCurve
b1 = Surface.BlendPoint(curve1.toShape(), 1, 2)
# Create G1 BlendPoint
b2 = Surface.BlendPoint([vec(5, 6, 2), vec(2, 5, 6)])
bc = Surface.BlendCurve(b1, b2)
# Compute the interpolating BezierCurve
curve2 = bc.compute()
d1 = curve1.getD2(1)
d2 = curve2.getD2(0)
self.assertEqual(len(d1), len(d2))
self.assertAlmostCoincide(d1[0], d2[0])
self.assertAlmostCoincide(d1[1], d2[1])
self.assertAlmostCoincide(d1[2], d2[2])
def setupUi(self):
self.view = QGraphicsView(self)
self.view.setMouseTracking(True)
self.vl = QVBoxLayout(self)
self.vl.addWidget(self.view)
self.surface = Surface.Surface(QRectF(0, 0, 800, 800), self)
self.surface.dragStarted.connect(self.onDragStarted)
self.surface.dragging.connect(self.onDragging)
self.surface.dragEnded.connect(self.onDragEnded)
self.surface.scaled.connect(self.onScaled)
self.view.setScene(self.surface)
self.surface.setScale(10)
def regions_arg(s):
from chimera.specifier import evalSpec
sel = evalSpec(s)
import Surface
plist = Surface.selected_surface_pieces(sel)
from Segger import Region
rlist = [
p.region for p in plist
if hasattr(p, 'region') and isinstance(p.region, Region)
]
if len(rlist) == 0:
raise CommandError, 'No segmentation regions specified'
return rlist
def volume_area(operation, surface):
from _surface import SurfaceModel
slist = [s for s in surface if isinstance(s, SurfaceModel)]
if len(slist) == 0:
raise CommandError, 'No surfaces specified'
import Surface
plist = Surface.surface_pieces(slist)
import MeasureVolume as m
op = operation[0]
m.report_volume_and_area(plist,
report_volume=(op == 'v'),
report_area=(op == 'a'))
def volume_area(operation, surface):
from _surface import SurfaceModel
slist = [s for s in surface if isinstance(s, SurfaceModel)]
if len(slist) == 0:
raise CommandError, 'No surfaces specified'
import Surface
plist = Surface.surface_pieces(slist)
import MeasureVolume as m
op = operation[0]
m.report_volume_and_area(plist,
report_volume = (op == 'v'),
report_area = (op == 'a'))
def __init__ (self, lll, viewspace, mymap):
self.lll = lll
self.display = Display ()
self.viewspace = viewspace
self.mymap = mymap
self.terrainset = TerrainSet ()
# Test
self.settsurf = Surface ()
self.settsurf.loadFromFile ("gfx/protosettler.png")
self.settsurf.cols = 16
self.settsurf.rows = 16
self.sprites = []
def contact_area(operation,
surf1,
surf2,
distance,
show=True,
color=(1, 0, 0, 1),
offset=1,
slab=None,
smooth=False,
optimize=True):
plist = []
import Surface
for spec in (surf1, surf2):
s = parse_object_specifier(spec, 'surface')
p = Surface.selected_surface_pieces(s, include_outline_boxes=False)
if len(p) == 0:
raise CommandError('%s has no surface pieces' % spec)
elif len(p) > 1:
raise CommandError('%s has %d surface pieces, require 1' %
(spec, len(p)))
plist.append(p[0])
p1, p2 = plist
from Commands import parse_color
color = parse_color(color)
if not show:
color = None
from Commands import check_number
check_number(offset, 'offset')
if not slab is None:
if isinstance(slab, (float, int)):
slab = (-0.5 * slab, 0.5 * slab)
else:
from Commands import parse_floats
slab = parse_floats(slab, 'slab', 2)
offset = None
import contactarea as c
area = c.contact_area(p1, p2, distance, color, offset, slab, smooth,
optimize)
from chimera import replyobj
replyobj.info('Contact area on %s within distance %.4g\nof %s = %.4g\n' %
(p1.model.name, distance, p2.model.name, area))
replyobj.status('Contact area = %.4g' % area)
def generateSurfaces(self, n):
self.mesh.compute_triangle_normals()
self.triangleNormals = np.asarray(self.mesh.triangle_normals)
self.isTriangleFree = [True for i in self.triangles]
p = len(self.triangles)
randomSeeds = [randint(0, p - 1)]
for i in range(n - 1):
q = randint(0, p - 1)
while q in randomSeeds:
q = randint(0, p - 1)
randomSeeds.append(q)
for t in randomSeeds:
self.isTriangleFree[t] = False
self.surfaces = [Surface(self, q) for q in randomSeeds]
def inertia(operation,
objects,
showEllipsoid=True,
color=None,
perChain=False):
from chimera import specifier
try:
sel = specifier.evalSpec(objects)
except:
raise CommandError, 'Bad object specifier "%s"' % objects
if not color is None:
from Commands import parse_color
color = parse_color(color)
atoms = sel.atoms()
if atoms:
import inertia
if perChain:
xf = atoms[0].molecule.openState.xform
mname = molecules_name(list(set([a.molecule for a in atoms])))
s = inertia.surface_model(None, xf, 'ellipsoids ' + mname)
for achain in atoms_by_chain(atoms):
p = inertia.atoms_inertia_ellipsoid(achain, showEllipsoid,
color, s)
if p:
p.oslName = achain[0].residue.id.chainId
else:
inertia.atoms_inertia_ellipsoid(atoms, showEllipsoid, color)
import Surface
plist = Surface.selected_surface_pieces(sel, include_outline_boxes=False)
if plist:
import inertia
inertia.surface_inertia_ellipsoid(plist, showEllipsoid, color)
bdo = bd.BarrelData() # Set True for inter-lines: bdo.loadAnalysisData = False bdo.loadDivisions = False # If loadGuidance is True, then expt id map will be plotted: bdo.loadGuidance = False bdo.loadHexFlags = True bdo.loadSimData = True bdo.loadTimeStep = ti bdo.load(logdirname) #maxa = np.max (bdo.a, axis=0) # Plot a surface import Surface as surf sf = surf.Surface(12, 11) sf.associate(bdo) # Plot a single field using a colour map sf.z = 2.0 * bdo.a[0, :, 0] # 13 is barrel/barreloid C4, 0 is barrel alpha sf.showScalebar = False sf.showAxes = False sf.sb1 = [-1.3, -0.8] sf.sb2 = [-0.3, -0.8] sf.sbtext = '1 mm' sf.sbtpos = [-1.1, -1.1] sf.sblw = 5 sf.sbfs = 48 sf.showNames = False sf.showBoundaries = False sf.cmap = plt.cm.Greys
class GFXEngine:
"""
This class draws the gfx
"""
def __init__(self, lll, viewspace, mymap):
self.lll = lll
self.display = Display()
self.viewspace = viewspace
self.mymap = mymap
self.terrainset = TerrainSet()
self.units = []
# Test
self.settsurf = Surface()
self.settsurf.loadFromFile("gfx/protosettler.png")
self.settsurf.cols = 16
self.settsurf.rows = 16
"""self.sett = Unit (self.viewspace, self.settsurf)
self.sett.x = 100
self.sett.y = 100
self.sett.configAnimation (True, 0, 24, 25)"""
def tick(self):
"""
tick() executes all actions which must be done by the GFX-Engine in one Game-Loop-cycle
This is: clearing the screen, drawing all objects, showing the new game-frame
"""
self.display.clear()
self.draw()
for sprite in self.units:
sprite.drawToDisplay(self.display)
#self.sett.drawToDisplay (self.display)
self.display.showFrame()
def createSettler(self, x, y):
"""
Adds a settler to be drawn on the screen at position x, y and returns a reference to this settler.
"""
unit = Unit(self.viewspace, self.settsurf, x, y)
#unit.x = x
#unit.y = y
unit.configAnimation(True, 0, 24, 25)
self.units.append(unit)
return unit
def draw(self):
self.drawLandscape()
def drawLandscape(self):
self.drawTerrain()
def drawTerrain(self):
self.lll.view.DrawTerrain(self.mymap.terra.asCArray(),
self.mymap.mapsize, TRIA_W, TRIA_H,
TEX_FACTOR, self.terrainset.asCArray(),
self.mymap.getVertarray().asCArray())
screen.blit(text, textpos)
textbox.draw(screen)
textbox1.draw(screen)
pygame.display.update()
pygame.time.delay(2000)
stop2=False
while not stop2:
screen.fill(color1)
events2 = pygame.event.get()
textbox2.draw(screen)
textbox2.update(events2)
pygame.display.update()
if(textbox2.value.lower()=='w'):
stop2=True
pygame.quit()
Surface.mainfunction()
elif(textbox2.value.lower()=='r'):
stop2=True
pygame.quit()
Render.mainfunction()
screen.fill(color1)
textbox.update(events)
textbox.draw(screen)
screen.blit(text1, textpos1)
screen.blit(text2, textpos2)
pygame.display.update()
pygame.quit()
quit()
def content():
# Get target x/y hex to show trace for and the time step to show the
# map for from the arguments:
if len(sys.argv) < 3:
print('Provide logdirname and time index (in sim steps) on cmd line.')
exit(1)
logdirname = sys.argv[1].rstrip('/')
print('basename: {0}'.format(os.path.basename(logdirname)))
# time index
ti = int(sys.argv[2])
# Read the data
rdo = rd.RettecData()
rdo.debug = True
# Set True for inter-lines:
rdo.loadAnalysisData = False
rdo.loadDivisions = False
# If loadGuidance is True, then expt barrel adjacency measure can be calculated in computeAdjacencyMeasure()
rdo.loadGuidance = True
rdo.loadSimData = True
rdo.loadTimeStep = ti
rdo.loadHexFlags = True
rdo.load(logdirname)
##rdo.computeAdjacencyMeasure()
# Compute max of c
maxc = np.max(rdo.c, axis=0)
# Either use the precomputed ID map: ONLY GOOD IF dr was computed!!
#c_id = rdo.id_c[:,0]
# or compute it here:
c_id_int = np.argmax(rdo.c, axis=0)
c_id = c_id_int[:, 0].astype(np.float32) / np.float32(rdo.N)
# Compute the colour map
colmap = np.zeros([rdo.nhex, 3], dtype=float)
ii = 0
for oneid in c_id:
colmap[ii] = rdo.gammaColour_byid[oneid]
ii = ii + 1
# Plot a surface
import Surface as surf
sf = surf.Surface(12, 11)
sf.associate(rdo)
sf.c = colmap # assign the colour map computed above
if ti < 5000:
sf.showScalebar = True
else:
sf.showScalebar = False
sf.showAxes = False
sf.sb1 = [-1.3, -0.9]
sf.sb2 = [-0.3, -0.9]
sf.sbtext = ''
sf.sbtpos = [-1.1, -1.1]
sf.sblw = 5
sf.sbfs = 48
if ti > 12000:
sf.showNames = True
else:
sf.showNames = False
##sf.domcentres = rdo.domcentres[0]
col = sc.Colour()
sf.boundarylw = 1.0
sf.boundaryColour = col.black
sf.boundaryOuterHexColour = col.gray50
sf.showBoundaries = False
if sf.showBoundaries == True:
sf.domdivision = rdo.domdivision
sf.textid = False
sf.plotPoly()
# Add two contours, for different levels of localization
#sf.addContour (maxc[:,0], 0.8, 'white', 1.0);
#sf.addContour (maxc[:,0], 0.4, 'grey', 1.6);
# Or single contour for each field
do_contour = 0
if do_contour:
for ii in range(0, rdo.N):
c = rdo.c[ii, :, 0]
sf.addContour(c, 0.5, 'white', 1.0, ii, False)
sf.addOuterBoundary()
mapname = 'plots/{0}_c_id_{1:06d}.png'.format(os.path.basename(logdirname),
ti)
plt.savefig(mapname, dpi=300, transparent=True)
plt.show()
spacing=10,
colour=(255, 255, 0),
size=keypad_lane_1.size,
elements=(keypad_button_3, keypad_button_6, keypad_button_9),
)
housing_frame = Frame(
position=((current_res[0] / 2) - 100, (current_res[1] / 2) - 100),
direction="right",
stacked=True,
spacing=10,
size=(keypad_lane_1.width * 3 + 20, keypad_lane_1.height),
elements=(keypad_lane_1, keypad_lane_2, keypad_lane_3),
)
main_surface = Surface([housing_frame], current_res)
# ----Main Loop---- #
count = 0
while running:
main_surface.fill([0, 0, 0])
count += 1
if count < 3:
for frame in Frame.all_frames:
frame.reassign_element_positions()
def zonable_surface_models():
import Surface as s
return s.surface_models()
def loadFile(self):
fileName = QtGui.QFileDialog.getOpenFileName(self, 'Open file', './',
'Surface Template(*.nv)')
self.surface = Surface()
self.surface.LoadIn(fileName)
self.sceneManager.rootNode.localObjectDict['Surface'] = self.surface
