Commit 4c991e2d authored by Bharath Ramsundar's avatar Bharath Ramsundar
Browse files

Continuing tf integration

parent 9da2664b

deepchem/models/tensorflow_models/.model.py.swp

deleted100644 → 0
−16 KiB

File deleted.

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deepchem/models/tensorflow_models/model_config.proto

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@@ -15,7 +15,7 @@ 
////////////////////////////////////////////////////////////////////////////////

syntax = "proto2";



package biology;

package deepchem.models.tensorflow_models;



// Neural network model configuration, used mostly for

// de/serializing model parameters for a given execution from/to disk.

deepchem/models/tensorflow_models/model_config.py

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Original line number Diff line number Diff line
@@ -20,7 +20,7 @@ import re 
from google.protobuf import text_format

from tensorflow.python.platform import gfile



from biology import model_config_pb2

from deepchem.models.tensorflow_models import model_config_pb2





class ModelConfig(object):

deepchem/models/tensorflow_models/model_config_pb2.py

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# Generated by the protocol buffer compiler.  DO NOT EDIT!

# source: model_config.proto



import sys

_b=sys.version_info[0]<3 and (lambda x:x) or (lambda x:x.encode('latin1'))

from google.protobuf import descriptor as _descriptor

from google.protobuf import message as _message

from google.protobuf import reflection as _reflection

from google.protobuf import symbol_database as _symbol_database

from google.protobuf import descriptor_pb2

# @@protoc_insertion_point(imports)



_sym_db = _symbol_database.Default()









DESCRIPTOR = _descriptor.FileDescriptor(

  name='model_config.proto',

  package='deepchem.models.tensorflow_models',

  syntax='proto2',

  serialized_pb=_b('\n\x12model_config.proto\x12!deepchem.models.tensorflow_models\"\xd1\x02\n\x0bModelConfig\x12K\n\tparameter\x18\x01 \x03(\x0b\x32\x38.deepchem.models.tensorflow_models.ModelConfig.Parameter\x12\x13\n\x0b\x64\x65scription\x18\x02 \x01(\t\x1a\xdf\x01\n\tParameter\x12\x0c\n\x04name\x18\x01 \x01(\t\x12\x13\n\x0b\x64\x65scription\x18\n \x01(\t\x12\x15\n\x0b\x66loat_value\x18\x02 \x01(\x02H\x00\x12\x13\n\tint_value\x18\x03 \x01(\x05H\x00\x12\x16\n\x0cstring_value\x18\x04 \x01(\tH\x00\x12\x14\n\nbool_value\x18\x05 \x01(\x08H\x00\x12\x12\n\nfloat_list\x18\x06 \x03(\x02\x12\x10\n\x08int_list\x18\x07 \x03(\x05\x12\x13\n\x0bstring_list\x18\x08 \x03(\t\x12\x11\n\tbool_list\x18\t \x03(\x08\x42\x07\n\x05value')

)

_sym_db.RegisterFileDescriptor(DESCRIPTOR)









_MODELCONFIG_PARAMETER = _descriptor.Descriptor(

  name='Parameter',

  full_name='deepchem.models.tensorflow_models.ModelConfig.Parameter',

  filename=None,

  file=DESCRIPTOR,

  containing_type=None,

  fields=[

    _descriptor.FieldDescriptor(

      name='name', full_name='deepchem.models.tensorflow_models.ModelConfig.Parameter.name', index=0,

      number=1, type=9, cpp_type=9, label=1,

      has_default_value=False, default_value=_b("").decode('utf-8'),

      message_type=None, enum_type=None, containing_type=None,

      is_extension=False, extension_scope=None,

      options=None),

    _descriptor.FieldDescriptor(

      name='description', full_name='deepchem.models.tensorflow_models.ModelConfig.Parameter.description', index=1,

      number=10, type=9, cpp_type=9, label=1,

      has_default_value=False, default_value=_b("").decode('utf-8'),

      message_type=None, enum_type=None, containing_type=None,

      is_extension=False, extension_scope=None,

      options=None),

    _descriptor.FieldDescriptor(

      name='float_value', full_name='deepchem.models.tensorflow_models.ModelConfig.Parameter.float_value', index=2,

      number=2, type=2, cpp_type=6, label=1,

      has_default_value=False, default_value=0,

      message_type=None, enum_type=None, containing_type=None,

      is_extension=False, extension_scope=None,

      options=None),

    _descriptor.FieldDescriptor(

      name='int_value', full_name='deepchem.models.tensorflow_models.ModelConfig.Parameter.int_value', index=3,

      number=3, type=5, cpp_type=1, label=1,

      has_default_value=False, default_value=0,

      message_type=None, enum_type=None, containing_type=None,

      is_extension=False, extension_scope=None,

      options=None),

    _descriptor.FieldDescriptor(

      name='string_value', full_name='deepchem.models.tensorflow_models.ModelConfig.Parameter.string_value', index=4,

      number=4, type=9, cpp_type=9, label=1,

      has_default_value=False, default_value=_b("").decode('utf-8'),

      message_type=None, enum_type=None, containing_type=None,

      is_extension=False, extension_scope=None,

      options=None),

    _descriptor.FieldDescriptor(

      name='bool_value', full_name='deepchem.models.tensorflow_models.ModelConfig.Parameter.bool_value', index=5,

      number=5, type=8, cpp_type=7, label=1,

      has_default_value=False, default_value=False,

      message_type=None, enum_type=None, containing_type=None,

      is_extension=False, extension_scope=None,

      options=None),

    _descriptor.FieldDescriptor(

      name='float_list', full_name='deepchem.models.tensorflow_models.ModelConfig.Parameter.float_list', index=6,

      number=6, type=2, cpp_type=6, label=3,

      has_default_value=False, default_value=[],

      message_type=None, enum_type=None, containing_type=None,

      is_extension=False, extension_scope=None,

      options=None),

    _descriptor.FieldDescriptor(

      name='int_list', full_name='deepchem.models.tensorflow_models.ModelConfig.Parameter.int_list', index=7,

      number=7, type=5, cpp_type=1, label=3,

      has_default_value=False, default_value=[],

      message_type=None, enum_type=None, containing_type=None,

      is_extension=False, extension_scope=None,

      options=None),

    _descriptor.FieldDescriptor(

      name='string_list', full_name='deepchem.models.tensorflow_models.ModelConfig.Parameter.string_list', index=8,

      number=8, type=9, cpp_type=9, label=3,

      has_default_value=False, default_value=[],

      message_type=None, enum_type=None, containing_type=None,

      is_extension=False, extension_scope=None,

      options=None),

    _descriptor.FieldDescriptor(

      name='bool_list', full_name='deepchem.models.tensorflow_models.ModelConfig.Parameter.bool_list', index=9,

      number=9, type=8, cpp_type=7, label=3,

      has_default_value=False, default_value=[],

      message_type=None, enum_type=None, containing_type=None,

      is_extension=False, extension_scope=None,

      options=None),

  ],

  extensions=[

  ],

  nested_types=[],

  enum_types=[

  ],

  options=None,

  is_extendable=False,

  syntax='proto2',

  extension_ranges=[],

  oneofs=[

    _descriptor.OneofDescriptor(

      name='value', full_name='deepchem.models.tensorflow_models.ModelConfig.Parameter.value',

      index=0, containing_type=None, fields=[]),

  ],

  serialized_start=172,

  serialized_end=395,

)



_MODELCONFIG = _descriptor.Descriptor(

  name='ModelConfig',

  full_name='deepchem.models.tensorflow_models.ModelConfig',

  filename=None,

  file=DESCRIPTOR,

  containing_type=None,

  fields=[

    _descriptor.FieldDescriptor(

      name='parameter', full_name='deepchem.models.tensorflow_models.ModelConfig.parameter', index=0,

      number=1, type=11, cpp_type=10, label=3,

      has_default_value=False, default_value=[],

      message_type=None, enum_type=None, containing_type=None,

      is_extension=False, extension_scope=None,

      options=None),

    _descriptor.FieldDescriptor(

      name='description', full_name='deepchem.models.tensorflow_models.ModelConfig.description', index=1,

      number=2, type=9, cpp_type=9, label=1,

      has_default_value=False, default_value=_b("").decode('utf-8'),

      message_type=None, enum_type=None, containing_type=None,

      is_extension=False, extension_scope=None,

      options=None),

  ],

  extensions=[

  ],

  nested_types=[_MODELCONFIG_PARAMETER, ],

  enum_types=[

  ],

  options=None,

  is_extendable=False,

  syntax='proto2',

  extension_ranges=[],

  oneofs=[

  ],

  serialized_start=58,

  serialized_end=395,

)



_MODELCONFIG_PARAMETER.containing_type = _MODELCONFIG

_MODELCONFIG_PARAMETER.oneofs_by_name['value'].fields.append(

  _MODELCONFIG_PARAMETER.fields_by_name['float_value'])

_MODELCONFIG_PARAMETER.fields_by_name['float_value'].containing_oneof = _MODELCONFIG_PARAMETER.oneofs_by_name['value']

_MODELCONFIG_PARAMETER.oneofs_by_name['value'].fields.append(

  _MODELCONFIG_PARAMETER.fields_by_name['int_value'])

_MODELCONFIG_PARAMETER.fields_by_name['int_value'].containing_oneof = _MODELCONFIG_PARAMETER.oneofs_by_name['value']

_MODELCONFIG_PARAMETER.oneofs_by_name['value'].fields.append(

  _MODELCONFIG_PARAMETER.fields_by_name['string_value'])

_MODELCONFIG_PARAMETER.fields_by_name['string_value'].containing_oneof = _MODELCONFIG_PARAMETER.oneofs_by_name['value']

_MODELCONFIG_PARAMETER.oneofs_by_name['value'].fields.append(

  _MODELCONFIG_PARAMETER.fields_by_name['bool_value'])

_MODELCONFIG_PARAMETER.fields_by_name['bool_value'].containing_oneof = _MODELCONFIG_PARAMETER.oneofs_by_name['value']

_MODELCONFIG.fields_by_name['parameter'].message_type = _MODELCONFIG_PARAMETER

DESCRIPTOR.message_types_by_name['ModelConfig'] = _MODELCONFIG



ModelConfig = _reflection.GeneratedProtocolMessageType('ModelConfig', (_message.Message,), dict(



  Parameter = _reflection.GeneratedProtocolMessageType('Parameter', (_message.Message,), dict(

    DESCRIPTOR = _MODELCONFIG_PARAMETER,

    __module__ = 'model_config_pb2'

    # @@protoc_insertion_point(class_scope:deepchem.models.tensorflow_models.ModelConfig.Parameter)

    ))

  ,

  DESCRIPTOR = _MODELCONFIG,

  __module__ = 'model_config_pb2'

  # @@protoc_insertion_point(class_scope:deepchem.models.tensorflow_models.ModelConfig)

  ))

_sym_db.RegisterMessage(ModelConfig)

_sym_db.RegisterMessage(ModelConfig.Parameter)





# @@protoc_insertion_point(module_scope)

deepchem/models/tensorflow_models/model_ops.py

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@@ -23,7 +23,7 @@ from google.protobuf import text_format 
from tensorflow.python.platform import gfile

from tensorflow.python.platform import logging



from biology import utils as model_utils

from deepchem.models.tensorflow_models import utils as model_utils





def AddBias(tensor, init=None, name=None):

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