YML

README.md

@@ -29,8 +29,12 @@ See README in each folder for details on how to use each component.
 * tqdm
 * networkx >= 2.1
 
-See `requirements.txt` for detailed list of versions.
 
+You can automatically install all the dependencies with Anaconda using the following command:
+
+```
+conda env create -f environment.yml
+```
 
 ## Usage
 

environment.yml

+name: rnamigos_minimal
+channels:
+  - pytorch
+  - dglteam
+  - conda-forge
+  - defaults
+dependencies:
+  - absl-py=0.9.0=py36_0
+  - biopython=1.76=py36h0b31af3_0
+  - blas=1.0=mkl
+  - blinker=1.4=py_1
+  - brotlipy=0.7.0=py36h37b9a7d_1000
+  - c-ares=1.15.0=h01d97ff_1001
+  - ca-certificates=2020.1.1=0
+  - cachetools=4.1.0=py_1
+  - cairo=1.16.0=ha8983da_1004
+  - certifi=2020.6.20=py36_0
+  - cffi=1.14.0=py36h356ff06_0
+  - chardet=3.0.4=py36h9f0ad1d_1006
+  - click=7.1.2=pyh9f0ad1d_0
+  - cryptography=2.9.2=py36hc9d8292_0
+  - cycler=0.10.0=py36hfc81398_0
+  - decorator=4.4.2=py_0
+  - dgl=0.4.3post2=py36_0
+  - fontconfig=2.13.1=h79c0d67_1002
+  - freetype=2.10.2=h8da9a1a_0
+  - gettext=0.19.8.1=h46ab8bc_1002
+  - glib=2.64.3=h577aef8_0
+  - google-auth=1.17.2=py_0
+  - google-auth-oauthlib=0.4.1=py_2
+  - grpcio=1.27.2=py36h7c1f37e_0
+  - icu=67.1=h4a8c4bd_0
+  - idna=2.9=py_1
+  - importlib-metadata=1.6.1=py36h9f0ad1d_0
+  - intel-openmp=2019.4=233
+  - kiwisolver=1.2.0=py36h04f5b5a_0
+  - libcxx=10.0.0=1
+  - libedit=3.1.20191231=haf1e3a3_0
+  - libffi=3.2.1=h4a8c4bd_1007
+  - libgfortran=3.0.1=h93005f0_2
+  - libiconv=1.15=h0b31af3_1006
+  - libpng=1.6.37=hbbe82c9_1
+  - libprotobuf=3.12.3=hd174df1_0
+  - libxml2=2.9.10=hc06c4ae_1
+  - markdown=3.2.2=py_0
+  - matplotlib=3.2.1=0
+  - matplotlib-base=3.2.1=py36h5670ca0_0
+  - mkl=2019.4=233
+  - mkl-service=2.3.0=py36hfbe908c_0
+  - mkl_fft=1.1.0=py36hc64f4ea_0
+  - mkl_random=1.1.1=py36h959d312_0
+  - ncurses=6.2=h0a44026_1
+  - networkx=2.4=py_0
+  - ninja=1.9.0=py36h04f5b5a_0
+  - numpy=1.18.5=py36h1da2735_0
+  - numpy-base=1.18.5=py36h3304bdc_0
+  - oauthlib=3.0.1=py_0
+  - openbabel=3.1.1=py36h715b1f7_0
+  - openssl=1.1.1g=h1de35cc_0
+  - pandas=1.0.5=py36h959d312_0
+  - pcre=8.44=h4a8c4bd_0
+  - pip=20.1.1=py36_1
+  - pixman=0.38.0=h01d97ff_1003
+  - protobuf=3.12.3=py36h0130604_0
+  - pyasn1=0.4.8=py_0
+  - pyasn1-modules=0.2.7=py_0
+  - pycparser=2.20=py_0
+  - pyjwt=1.7.1=py_0
+  - pyopenssl=19.1.0=py_1
+  - pyparsing=2.4.7=py_0
+  - pysocks=1.7.1=py36h9f0ad1d_1
+  - python=3.6.10=hc70fcce_1
+  - python-dateutil=2.8.1=py_0
+  - python_abi=3.6=1_cp36m
+  - pytorch=1.5.1=py3.6_0
+  - pytz=2020.1=py_0
+  - readline=8.0=h1de35cc_0
+  - requests=2.24.0=pyh9f0ad1d_0
+  - requests-oauthlib=1.2.0=py_0
+  - rsa=4.6=pyh9f0ad1d_0
+  - scipy=1.4.1=py36h9fa6033_0
+  - seaborn=0.10.1=py_0
+  - setuptools=47.3.1=py36_0
+  - six=1.15.0=py_0
+  - sqlite=3.32.2=hffcf06c_0
+  - tensorboard=2.2.2=py_0
+  - tensorboard-plugin-wit=1.6.0=pyh9f0ad1d_0
+  - tk=8.6.10=hb0a8c7a_0
+  - tornado=6.0.4=py36h1de35cc_1
+  - tqdm=4.46.1=py_0
+  - urllib3=1.25.9=py_0
+  - werkzeug=1.0.1=pyh9f0ad1d_0
+  - wheel=0.34.2=py36_0
+  - xz=5.2.5=h1de35cc_0
+  - zipp=3.1.0=py_0
+  - zlib=1.2.11=h1de35cc_3

learning/loader.py

@@ -161,7 +161,7 @@ class Loader():
                  sim_function="R_1",
                  shuffle=False,
                  seed=0,
-                 get_sim_mat=False,
+                 get_sim_mat=True,
                  nucs=True,
                  depth=3):
         """
@@ -191,7 +191,7 @@ class Loader():
     def get_data(self, k_fold=0):
         n = len(self.dataset)
         indices = list(range(n))
-        collate_block = collate_wrapper(self.dataset.node_sim_func)
+        collate_block = collate_wrapper(self.dataset.node_sim_func, self.dataset.get_sim_mat)
 
         if k_fold > 1:
             from sklearn.model_selection import KFold