orange, purple, deeppink, lightcoral, \
blue, cyan, mediumslateblue, steelblue, darkcyan, \
limegreen, darkorchid, tomato, khaki, gold, magenta, green
MSca = 18.0
# Surface:
rSurf1 = Recipe()
# outside
ingrOut = MultiSphereIngr( MSca*.001, color=gold, name='out outside',
sphereFile=wrkDir+'/recipes/anchor.sph',
packingPriority=1,
jitterMax=(0.2,1,1),
#perturbAxisAmplitude=.9,
principalVector=(1,0,0))
rSurf1.addIngredient(ingrOut)
#inside
ingrIn = MultiSphereIngr( MSca*.001, color=chartreuse, name='in inside',
sphereFile=wrkDir+'/recipes/anchor.sph',
packingPriority=1,
jitterMax=(0.2,1,1),
nbJitter=20,
principalVector=(-1,0,0),)
# packingMode='close')
rSurf1.addIngredient(ingrIn)
#Cytoplasm:
rCyto1 = Recipe()
principalVector=(0,0,-1))#,
#packingMode='close')
#Surf1.addIngredient(ingr1qo1)
## cyl test 1
cyl1Ingr = MultiCylindersIngr(MSca*0.1, color=coral, pdb='1CYL',
name='SingleCylinder', radii=[[8.]],
positions=[[[0,0,0]]], positions2=[[[20,0,0]]],
packingPriority=1,
jitterMax=(1,1,0.2),
principalVector=(1,0,0),
meshFile=plgDir+'/extension/testAF/Lip',
#packingMode='close',
rejectionThreshold=30
)
rSurf1.addIngredient(cyl1Ingr)
# 1qo1
##
## Matrix
##
rMatrix1 = Recipe()
##
## Cytoplasm:
##
rCyto = Recipe()
# 1TWT
ingr1TWT = MultiSphereIngr( MSca*.000005, name='30S RIBOSOME', pdb='1TWT',
ViewerType='c4d'
MSca = 1.0
# Surface:
rSurf1 = Recipe()
## cyl test 1
cyl1Ingr = MultiCylindersIngr(MSca*.001, color=coral, pdb='1CYL',
name='SingleCylinder', radii=[[23]],
positions=[[[-35,0,0]]], positions2=[[[45,0,0]]],
packingPriority=1,
principalVector=(1,0,0)
)
rSurf1.addIngredient(cyl1Ingr)
cylCoord1 = [ (-35,0,0), (45,0,0), (45,0,0), (85, 40, 0),]
cylCoord2 = [ (45,0,0), (85,40,0), (105, -40,0), (135, 40, 30)]
cylRadii = [25, 20, 16, 16]
cyl4Ingr = MultiCylindersIngr(MSca*.001, color=aquamarine, pdb='1CYL',
name='4Cylinders', radii=[cylRadii],
positions=[cylCoord1], positions2=[cylCoord2],
packingPriority=1,
principalVector=(1,0,0)
)
rSurf1.addIngredient(cyl4Ingr)
## # 1h6i
#define the viewer type dejavu,c4d,blender
ViewerType='c4d'
MSca = 1.0
## Surface:
rSurf1 = Recipe()
## cyl test 1
cyl1Ingr = MultiCylindersIngr(2, color=coral, pdb='1CYL',
name='SingleCylinder', radii=[[23]],
positions=[[[-35,0,0]]], positions2=[[[45,0,0]]],
packingPriority=1,
principalVector=(1,0,0)
)
rSurf1.addIngredient(cyl1Ingr)
cylCoord1 = [ (-35,0,0), (45,0,0), (45,0,0), (85, 40, 0),]
cylCoord2 = [ (45,0,0), (85,40,0), (105, -40,0), (135, 40, 30)]
cylRadii = [25, 20, 16, 16]
cyl4Ingr = MultiCylindersIngr(3, color=aquamarine, pdb='1CYL',
name='4Cylinders', radii=[cylRadii],
positions=[cylCoord1], positions2=[cylCoord2],
packingPriority=1,
principalVector=(1,0,0)
)
rSurf1.addIngredient(cyl4Ingr)
##
## Matrix
#define the viewer type dejavu,c4d,blender
ViewerType='c4d'
MSca = 1.0
## Surface:
rSurf1 = Recipe()
## cyl test 1
cyl1Ingr = MultiCylindersIngr(2, color=coral, pdb='1CYL',
name='SingleCylinder', radii=[[23]],
positions=[[[-35,0,0]]], positions2=[[[45,0,0]]],
packingPriority=1,
principalVector=(1,0,0)
)
rSurf1.addIngredient(cyl1Ingr)
cylCoord1 = [ (-35,0,0), (45,0,0), (45,0,0), (85, 40, 0),]
cylCoord2 = [ (45,0,0), (85,40,0), (105, -40,0), (135, 40, 30)]
cylRadii = [25, 20, 16, 16]
cyl4Ingr = MultiCylindersIngr(3, color=aquamarine, pdb='1CYL',
name='4Cylinders', radii=[cylRadii],
positions=[cylCoord1], positions2=[cylCoord2],
packingPriority=1,
principalVector=(1,0,0)
)
rSurf1.addIngredient(cyl4Ingr)
##
## Matrix
## cyl test 1
cyl1Ingr = MultiCylindersIngr(
MSca * 0.1,
color=coral,
pdb='1CYL',
name='SingleCylinder',
radii=[[8.]],
positions=[[[0, 0, 0]]],
positions2=[[[20, 0, 0]]],
packingPriority=1,
jitterMax=(1, 1, 0.2),
principalVector=(1, 0, 0),
meshFile=plgDir + '/extension/testAF/Lip',
#packingMode='close',
rejectionThreshold=30)
rSurf1.addIngredient(cyl1Ingr)
# 1qo1
##
## Matrix
##
rMatrix1 = Recipe()
##
## Cytoplasm:
##
rCyto = Recipe()
# 1TWT
ingr1TWT = MultiSphereIngr(MSca * .000005,
name='30S RIBOSOME',
MSca = 1.0
# Surface:
rSurf1 = Recipe()
## cyl test 1
cyl1Ingr = MultiCylindersIngr(MSca * .001,
color=coral,
pdb='1CYL',
name='SingleCylinder',
radii=[[23]],
positions=[[[-35, 0, 0]]],
positions2=[[[45, 0, 0]]],
packingPriority=1,
principalVector=(1, 0, 0))
rSurf1.addIngredient(cyl1Ingr)
cylCoord1 = [
(-35, 0, 0),
(45, 0, 0),
(45, 0, 0),
(85, 40, 0),
]
cylCoord2 = [(45, 0, 0), (85, 40, 0), (105, -40, 0), (135, 40, 30)]
cylRadii = [25, 20, 16, 16]
cyl4Ingr = MultiCylindersIngr(MSca * .001,
color=aquamarine,
pdb='1CYL',
name='4Cylinders',
radii=[cylRadii],
orange, purple, deeppink, lightcoral, \
blue, cyan, mediumslateblue, steelblue, darkcyan, \
limegreen, darkorchid, tomato, khaki, gold, magenta, green
MSca = 18.0
# Surface:
rSurf1 = Recipe()
# outside
ingrOut = MultiSphereIngr( MSca*.001, color=gold, name='out outside',
sphereFile=wrkDir+'/recipes/anchor.sph',
packingPriority=1,
jitterMax=(0.2,1,1),
#perturbAxisAmplitude=.9,
principalVector=(1,0,0))
rSurf1.addIngredient(ingrOut)
#inside
ingrIn = MultiSphereIngr( MSca*.001, color=chartreuse, name='in inside',
sphereFile=wrkDir+'/recipes/anchor.sph',
packingPriority=1,
jitterMax=(0.2,1,1),
nbJitter=20,
principalVector=(-1,0,0),)
# packingMode='close')
rSurf1.addIngredient(ingrIn)
#Cytoplasm:
rCyto1 = Recipe()
