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| from ctypes import *
|
| TS_SUCCESS=0
| TS_FAIL=1
|
| TS_ID_FILAMENT=1
|
| TS_COORD_CARTESIAN=0
| TS_COORD_SPHERICAL=1
| TS_COORD_CYLINDRICAL=2
|
|
| class ts_coord(Structure):
| _fields_=[
| ("e1", c_double),
| ("e2", c_double),
| ("e3", c_double),
| ("coord_type", c_uint)
| ]
| class ts_vertex(Structure):
| pass
| class ts_bond(Structure):
| pass
| class ts_triangle(Structure):
| pass
| class ts_cell(Structure):
| pass
| class ts_poly(Structure):
| pass
| class ts_cluster(Structure):
| pass
| ts_vertex._fields_=[
| ('idx',c_uint),
| ('x',c_double),
| ('y',c_double),
| ('z',c_double),
| ('neigh_no',c_uint),
| ('neigh', POINTER(POINTER(ts_vertex))),
| ('bond_length', POINTER(c_double)),
| ('bond_length_dual',POINTER(c_double)),
| ('curvature', c_double),
| ('energy', c_double),
| ('energy_h',c_double),
| ('tristar_no', c_uint),
| ('tristar', POINTER(POINTER(ts_triangle))),
| ('bond_no',c_uint),
| ('bond',POINTER(POINTER(ts_bond))),
| ('cell',POINTER(ts_cell)),
| ('xk',c_double),
| ('c',c_double),
| ('id', c_uint),
| ('projArea',c_double),
| ('relR', c_double),
| ('solAngle', c_double),
| ('grafted_poly', POINTER(ts_poly)),
| ('cluster',POINTER(ts_cluster)),
| ]
| class ts_vertex_list(Structure):
| _fields_=[('n',c_uint), ('vtx',POINTER(POINTER(ts_vertex)))]
|
| ts_bond._fields_=[('idx',c_uint),
| ('vtx1', POINTER(ts_vertex)),
| ('vtx2', POINTER(ts_vertex)),
| ('bond_length',c_double),
| ('bond_length_dual',c_double),
| ('tainted', c_char),
| ('energy',c_double),
| ('x',c_double),
| ('y',c_double),
| ('z',c_double),
| ]
| class ts_bond_list(Structure):
| _fields_=[('n', c_uint),('bond',POINTER(POINTER(ts_bond)))]
|
| ts_triangle._fields_=[
| ('idx',c_uint),
| ('vertex', POINTER(ts_vertex)*3),
| ('neigh_no',c_uint),
| ('neigh', POINTER(POINTER(ts_triangle))),
| ('xnorm', c_double),
| ('ynorm', c_double),
| ('znorm', c_double),
| ('area', c_double),
| ('volume', c_double),
| ('energy', c_double),
| ]
|
| class ts_triangle_list(Structure):
| _fields_=[('n',c_uint),('a0',c_double),('tria', POINTER(POINTER(ts_triangle))),]
|
|
| ts_cell._fields_=[
| ('idx', c_uint),
| ('vertex', POINTER(POINTER(ts_vertex))),
| ('nvertex', c_uint),
| ]
|
| class ts_cell_list(Structure):
| _fields_=[
| ('ncmax', c_uint*3),
| ('cellno', c_uint),
| ('cell',POINTER(POINTER(ts_cell))),
| ('dcell', c_double),
| ('shift', c_double),
| ('max_occupancy', c_double),
| ('dmin_interspecies', c_double)
| ]
|
| class ts_spharm(Structure):
| _fields_=[
| ('l',c_uint),
| ('ulm', POINTER(POINTER(c_double))),
| # ('ulmComplex', POINTER(POINTER(gsl_complex))), #poisci!!!!
| ('ulmComplex', POINTER(POINTER(c_double))), #temporary solution
| ('sumUlm2', POINTER(POINTER(c_double))),
| ('N', c_uint),
| ('co',POINTER(POINTER(c_double))),
| ('Ylmi', POINTER(POINTER(c_double))),
| ]
|
| ts_poly._fields_=[
| ('vlist', POINTER(ts_vertex_list)),
| ('blist', POINTER(ts_bond_list)),
| ('grafted_vtx',POINTER(ts_vertex)),
| ('k', c_double),
| ]
|
| class ts_poly_list(Structure):
| _fields_=[('n',c_uint),('poly',POINTER(POINTER(ts_poly)))]
|
| class ts_tape(Structure):
| _fields_=[
| ('nshell',c_long),
| ('ncxmax',c_long),
| ('ncymax',c_long),
| ('nczmax',c_long),
| ('npoly',c_long),
| ('nmono',c_long),
| ('internal_poly',c_long),
| ('nfil',c_long),
| ('nfono', c_long),
| ('R_nucleus',c_long),
| ('R_nucleusX',c_double),
| ('R_nucleusY',c_double),
| ('R_nucleusZ',c_double),
| ('pswitch',c_long),
| ('constvolswitch',c_long),
| ('constareaswitch',c_long),
| ('stretchswitch',c_long),
| ('xkA0',c_double),
| ('constvolprecision',c_double),
| ('multiprocessing',c_char_p),
| ('brezveze0',c_long),
| ('brezveze1',c_long),
| ('brezveze2',c_long),
| ('xk0',c_double),
| ('dmax',c_double),
| ('dmin_interspecies',c_double),
| ('stepsize',c_double),
| ('kspring',c_double),
| ('xi',c_double),
| ('pressure',c_double),
| ('iterations',c_long),
| ('inititer',c_long),
| ('mcsweeps',c_long),
| ('quiet',c_long),
| ('shc',c_long),
| ('number_of_vertice_with_c0',c_long),
| ('c0', c_double),
| ('w', c_double),
| ('F', c_double),
| ]
|
|
| class ts_vesicle(Structure):
| _fields_=[
| ('vlist', POINTER(ts_vertex_list)),
| ('blist', POINTER(ts_bond_list)),
| ('tlist', POINTER(ts_triangle_list)),
| ('clist', POINTER(ts_cell_list)),
| ('nshell', c_uint),
| ('bending_rigidity',c_double),
| ('dmax',c_double),
| ('stepsize',c_double),
| ('cm', c_double*3),
| ('volume', c_double),
| ('sphHarmonics',POINTER(ts_spharm)),
| ('poly_list', POINTER(ts_poly_list)),
| ('filament_list', POINTER(ts_poly_list)),
| ('spring_constant', c_double),
| ('pressure', c_double),
| ('pswitch', c_int),
| ('tape', POINTER(ts_tape)),
| ('R_nucleus', c_double),
| ('R_nucleusX', c_double),
| ('R_nucleusY', c_double),
| ('R_nucleusZ', c_double),
| ('nucleus_center', c_double *3 ),
| ('area', c_double),
| ]
|
| ts_cluster._fields_=[('nvtx',c_uint),('idx',c_uint),('vtx', POINTER(POINTER(ts_vertex)))]
|
| class ts_cluster_list(Structure):
| _fields_=[('n',c_uint),('cluster',POINTER(POINTER(ts_cluster)))]
|
|
|
|
| ts=CDLL('libtrisurf.so')
|
|
|
| #function call wrappers
| def create_vesicle_from_tape(tape):
| """Using pointer for tape, it creates a vesicle, returning pointer to it."""
| ts.create_vesicle_from_tape.argtype=POINTER(ts_tape)
| ts.create_vesicle_from_tape.restype=POINTER(ts_vesicle)
| return ts.create_vesicle_from_tape(tape)
|
| def parsetape(filename='tape'):
| """Loads tape with filename (if not given it defaults to 'tape'). It returns a pointer to structure for tape"""
| ts.parsetape.restype=POINTER(ts_tape)
| ts.parsetape.argtype=[c_char_p]
| return ts.parsetape(filename.encode('ascii'))
|
| def parseDump(filename):
| """Loads a vtu file with 'filename' and creates a vesicle returning pointer to it"""
| ts.parseDump.argtype=[c_char_p]
| ts.parseDump.restype=POINTER(ts_vesicle)
| vesicle=ts.parseDump(filename.encode('ascii'))
| return vesicle
|
| def single_timestep(vesicle):
| """Makes a single timestep in simulations. Returns a tuple of vmsrt and bfrt (vertex move success rate and bond flip success rate)"""
| ts.single_timestep.argtype=[POINTER(ts_vesicle),POINTER(c_double),POINTER(c_double)]
| vmsrt=c_double(0.0)
| bfsrt=c_double(0.0)
| ts.single_timestep(vesicle,byref(vmsrt),byref(bfsrt))
| return (vmsrt.value, bfsrt.value)
|
| def write_vertex_xml_file(vesicle,timestep_no=0):
| """Writes a vesicle into file with filename 'timestep_XXXXXX.vtu', where XXXXXX is a leading zeroed number given with timestep_no parameter (defaults to 0 if not given"""
| ts.write_vertex_xml_file.argtypes=[POINTER(ts_vesicle),c_int]
| ts.write_vertex_xml_file(vesicle,c_int(timestep_no))
|
|
| def vesicle_free(vesicle):
| """Free memory of the whole vesicle"""
| ts.vesicle_free.argtype=[POINTER(ts_vesicle)]
| ts.vesicle_free(vesicle)
|
| def vesicle_volume(vesicle):
| ts.vesicle_volume.argtype=[POINTER(ts_vesicle)]
| ts.vesicle_volume(vesicle)
|
| def vesicle_area(vesicle):
| ts.vesicle_area.argtype=[POINTER(ts_vesicle)]
| ts.vesicle_area(vesicle)
|
| def gyration_eigen(vesicle):
| ts.gyration_eigen.argtype=[POINTER(ts_vesicle), POINTER(c_double), POINTER(c_double), POINTER(c_double)]
| l1=c_double(0.0)
| l2=c_double(0.0)
| l3=c_double(0.0)
| ts.gyration_eigen(vesicle , byref(l1), byref(l2), byref(l3))
| return (l1.value, l2.value, l3.value)
|
| def vesicle_meancurvature(vesicle):
| ts.vesicle_meancurvature.argtype=[POINTER(ts_vesicle)]
| ts.vesicle_meancurvature.restype=c_double
| return ts.vesicle_meancurvature(vesicle)
|
| def init_cluster_list():
| ts.init_cluster_list.restype=POINTER(ts_cluster_list)
| ret=ts.init_cluster_list()
| return ret
|
| def clusterize_vesicle(vesicle, cluster_list):
| ts.clusterize_vesicle.argtype=[POINTER(ts_vesicle), POINTER(ts_cluster_list)]
| ts.clusterize_vesicle(vesicle, cluster_list)
|
| def cluster_list_free(cluster_list):
| """Free memory of cluster list"""
| ts.cluster_list_free.argtype=[POINTER(ts_cluster_list)]
| ts.cluster_list_free(cluster_list)
|
| def stretchenergy(vesicle, triangle):
| ts.stretchenergy.argtype=[POINTER(ts_vesicle), POINTER(ts_triangle)]
| ts.stretchenergy(vesicle,triangle)
|
| def get_absolute_ulm2(vesicle,l,m):
| ts.get_absolute_ulm2.argtype=[POINTER(ts_vesicle), c_double, c_double]
| ts.get_absolute_ulm2.restype=c_double
| ret=ts.get_absolute_ulm2(vesicle,l,m)
| return ret
|
| def getR0(vesicle):
| ts.getR0.argtype=[POINTER(ts_vesicle)]
| ts.getR0.restype=c_double
| r0=ts.getR0(vesicle)
| return r0
|
| def preparationSh(vesicle,r0):
| ts.preparationSh.argtype=[POINTER(ts_vesicle), c_double]
| ts.preparationSh(vesicle,float(r0))
|
| def calculateUlmComplex(vesicle):
| ts.calculateUlmComplex.argtype=[POINTER(ts_vesicle)]
| ts.calculateUlmComplex(vesicle)
|
| def solve_for_ulm2(vesicle):
| ts.solve_for_ulm2.argtype=[POINTER(ts_vesicle)]
| ts.solve_for_ulm2(vesicle)
|
| def mean_curvature_and_energy(vesicle):
| ts.mean_curvature_and_energy.argtype=[POINTER(ts_vesicle)]
| ts.mean_curvature_and_energy(vesicle)
|
|
