updated nerf & getpy usage

README.md

@@ -1 +1,90 @@
 # pyRIF
+Using Rotamer Interaction Fields from RIFGen/Dock in python
+
+
+### Installation
+`pip install pyRIF`
+
+### Pose Example
+Moves your input pose into the region of the RIF
+```
+import glob
+import pyrosetta
+from pyrosetta.rosetta.core.select.residue_selector import ChainSelector
+
+from pyrif import RotamerInteractionField
+
+pyrosetta.init()
+
+
+# dictionary pointing to RIFGen outputs
+L_AA_RIF = {
+    'HDF5'   : '/path/to/py_rif.h5',
+    'rots'   : '/path/to/rotamer_index_spec.txt',
+    'target' : '/path/to/target.pdb.gz',
+}
+
+
+# residue selectors to select target and binder residues
+target_selector = ChainSelector('A')
+binder_selector = ChainSelector('B')
+
+
+# create RIF object outside of loop
+RIF = RotamerInteractionField(
+    L_AA_RIF_kwargs=L_AA_RIF,
+    residue_selector=binder_selector,
+    target_selector=target_selector,
+)
+
+for PDB in glob.iglob('/path/to/pdbs/*.pdb'):
+    pose = pyrosetta.io.pose_from_pdb(PDB)
+
+    # apply the RIF
+    STATUS, RIF_score, sequence_mapping = RIF.apply(pose)
+
+    if STATUS:
+        print(f'pass, {RIF_SCORE}\n{sequence_mapping}')
+        # continue with remainder of protocol
+    else:
+        print('fail')
+
+```
+
+### Numpy Example
+Assumes your XYZs are already within the region of the RIF
+```
+import glob
+import numpy as np
+import pyrosetta
+
+from pyrif import RotamerInteractionField
+pyrosetta.init()
+
+
+# dictionary pointing to RIFGen outputs
+L_AA_RIF = {
+    'HDF5'   : '/path/to/py_rif.h5',
+    'rots'   : '/path/to/rotamer_index_spec.txt',
+    'target' : '/path/to/target.pdb.gz',
+}
+
+
+# create RIF object outside of loop
+RIF = RotamerInteractionField(
+    L_AA_RIF_kwargs=L_AA_RIF,
+)
+
+binder_xyzs = np.random.rand(1000, 100, 3, 3)# [(1000 proteins), (100 residues), (N CA C), (X Y Z)]
+
+for i in range(binder_xyzs.shape[0]):
+
+    STATUS, RIF_score, sequence_mapping = RIF.search_xyzs(binder_xyzs[i, :, :, :])
+
+    if STATUS:
+        print(f'pass, {RIF_SCORE}\n{sequence_mapping}')
+        # continue with remainder of protocol
+    else:
+        print('fail')
+
+```

example/example.py

@@ -85,8 +85,6 @@
     if STATUS: print(f'rif score: {RIF_score}\n{sequence_mapping}')
 
 
-
-print('D_RIF ONLY')
 # RIF just with canonical D-AAs
 RIF = RotamerInteractionField(
     D_AA_RIF_kwargs=D_AA_RIF,