move data files into project directory

MANIFEST.in

@@ -1,4 +1,4 @@
-include cgdms/cgdms_params_ep45.pt
-include protein_data/results/*
-include protein_data/train_val/*
-include datasets/*
+inlude cgdms/cgdms_params_ep45.pt
+inlude cgdms/protein_data/results/*
+inlude cgdms/protein_data/train_val/*
+inlude cgdms/datasets/*

README.md

@@ -27,7 +27,7 @@ The modes are described below but there are other options outlined in the help t
 ### Generating protein data files
 
 To simulate or calculate the energy of proteins you need to generate files of a certain format.
-If you want to use the proteins presented in the paper, the data files are [here](protein_data/results).
+If you want to use the proteins presented in the paper, the data files are [here](cgdms/protein_data/results).
 Otherwise you will need to generate these files:
 
 ```bash
@@ -158,7 +158,7 @@ See `cgdms.interactions` for the interaction described by each potential, which
 Running a simulation takes less than 1 GB of GPU memory for any number of steps.
 Training a model takes up to 32 GB of GPU memory once the number of steps is fully scaled up to 2,000.
 
-The lists of training and validation PDB chains are available [here](datasets) and the protein data files [here](protein_data/train_val).
+The lists of training and validation PDB chains are available [here](cgdms/datasets) and the protein data files [here](cgdms/protein_data/train_val).
 
 The code in this package is set up to run specific coarse-grained simulations of proteins.
 However, the package contains code that could be useful to others wishing to carry out general differentiable simulations with PyTorch.

cgdms/cgdms.py

@@ -12,10 +12,10 @@
 import os
 from random import gauss, random, shuffle
 
-cgdms_dir = os.path.dirname(os.path.dirname(os.path.realpath(__file__)))
+cgdms_dir = os.path.dirname(os.path.realpath(__file__))
 dataset_dir = os.path.join(cgdms_dir, "datasets")
 train_val_dir = os.path.join(cgdms_dir, "protein_data", "train_val")
-trained_model_file = os.path.join(cgdms_dir, "cgdms", "cgdms_params_ep45.pt")
+trained_model_file = os.path.join(cgdms_dir, "cgdms_params_ep45.pt")
 
 n_bins_pot = 140
 n_bins_force = n_bins_pot - 2

setup.py

@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="cgdms",
-    version="0.1",
+    version="0.1.1",
     author="Joe G Greener",
     author_email="j.greener@ucl.ac.uk",
     description="Differentiable molecular simulation of proteins with a coarse-grained potential",