In [1]:

    

from seamless.highlevel import Context, Transformer, Cell

ctx = Context()
ctx.auto_translate = True


    

In [2]:

    

ctx.pdb1 = open("1AKE-flanks.pdb").read()
ctx.pdb2 = open("1AKE-B-hit.pdb").read()
ctx.load_pdb1 = Transformer()
ctx.load_pdb1.pdb = ctx.pdb1
ctx.load_pdb_code >> ctx.load_pdb1.code
ctx.load_pdb_code.mount("load_pdb.py")
ctx.coor1 = ctx.load_pdb1
ctx.load_pdb2 = Transformer()
ctx.load_pdb2.pdb = ctx.pdb2
ctx.load_pdb2.code = ctx.load_pdb_code
ctx.coor2 = ctx.load_pdb2


    

In [3]:

    

def bcscore(coor1, coor2, flanksize, gapsize):
    print("BCSCORE", flanksize, gapsize)
    return 0.5

ctx.bcscore = bcscore
ctx.bcscore.coor1 = ctx.coor1
ctx.bcscore.coor2 = ctx.coor2
ctx.bcscore.flanksize = 4
ctx.bcscore.gapsize = 7

ctx.bc_result = ctx.bcscore
await ctx.computation()
print(ctx.bc_result.value)


    

    




<Silk: 0.5 >

In [4]:

    

ctx.bcscore.language = "c"

ctx.bcscore_schema = Cell()
ctx.bcscore_schema.celltype = "plain"
ctx.bcscore_schema.mount("bcscore-schema.json", "r", authority="file")
await ctx.translation()
ctx.bcscore.result.example.set(1.0)
ctx.bcscore.result.schema["form"] = {"bytesize": 8}
await ctx.translation()
ctx.link(ctx.bcscore_schema, ctx.bcscore.inp.schema)
ctx.header = ctx.bcscore.header
ctx.header.mimetype = "h"
await ctx.translation()


    

In [5]:

    

ctx.bcscore.header.mount("bcscore.h", "w")
ctx.header.output()


    

    






 
 










    




ctx.auto_translate is currently unstable and has been disabled
You must run regularly "ctx.translate()" (IPython)
or "await ctx.translation()" (Jupyter) after modifying the graph.
Translation is not required after modifying only cell values

In [6]:

    

ctx.bcscore.code.mount("bcscore.c", authority="file")
ctx.bcscore.result.example.set(1.0)
ctx.bcscore.result.schema["form"] = {"bytesize": 4}
ctx.bcscore.main_module.bclib.language = "c"
ctx.bclib_code >> ctx.bcscore.main_module.bclib.code 
ctx.bclib_code.mount("BClib.c")
await ctx.translation()


    

    




9a4e8473b01700800d0424e3d5ea2a575213c1aa785e2dd25429e62ff8c1d10f
Warning: File path 'bcscore.c' has a different value, overwriting cell

gcc -c bclib.c -O3 -ffast-math -march=native -fPIC -p -g -o bclib.o

gcc -c main.c -O3 -ffast-math -march=native -fPIC -p -g -o main.o



gcc -c bclib.c -O3 -ffast-math -march=native -fPIC -p -g -o bclib.o

gcc -c main.c -O3 -ffast-math -march=native -fPIC -p -g -o main.o

In [7]:

    

await ctx.computation()
print(ctx.bcscore.inp.exception)
print(ctx.bcscore.exception)


    

    




None
None

In [8]:

    

import numpy as np

def validate_shape(self):
    assert self.coor1.shape[0] == 2 * self.flanksize, self.coor1.shape
    assert self.coor2.shape[0] == 2 * self.flanksize + self.gapsize, self.coor2.shape

example = ctx.bcscore.example
example.coor1 = np.zeros((10, 3))
example.coor2 = np.zeros((14, 3))
example.flanksize = 5
example.gapsize = 4
example.add_validator(validate_shape, name="validate_shape")


    

In [9]:

    

await ctx.computation()
print(ctx.bcscore.schema)
print(ctx.bcscore.result.schema)


    

    




{'properties': {'coor1': {'form': {'contiguous': True, 'ndim': 2, 'shape': [-1, 3]}, 'items': {'form': {'bytesize': 8, 'type': 'number'}}, 'storage': 'binary', 'type': 'array'}, 'coor2': {'form': {'contiguous': True, 'ndim': 2, 'shape': [-1, 3]}, 'items': {'form': {'bytesize': 8, 'type': 'number'}}, 'storage': 'binary', 'type': 'array'}, 'flanksize': {'type': 'integer'}, 'gapsize': {'type': 'integer'}}, 'type': 'object', 'validators': [{'code': 'def validate_shape(self):\n    assert self.coor1.shape[0] == 2 * self.flanksize, self.coor1.shape\n    assert self.coor2.shape[0] == 2 * self.flanksize + self.gapsize, self.coor2.shape\n', 'language': 'python', 'name': 'validate_shape'}]}
{'form': {'bytesize': 4}, 'type': 'number'}

In [10]:

    

await ctx.computation()
print(ctx.bc_result.value)


    

    




<Silk: 0.9981744289398193 >

In [11]:

    

ctx.save_graph("bcscore.seamless")
ctx.save_zip("bcscore.zip")