python3 fixes

Author: dkoes

Diff for: bootstrap.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 import predict
 import sklearn.metrics

Diff for: calctop.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 import numpy as np
 import os, sys

Diff for: clustering.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 
 from Bio.PDB.PDBParser import PDBParser

Diff for: combine_fold_results.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 import numpy as np
 import matplotlib

Diff for: combine_rows.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 '''Combine the output of compute_rows.py into a pickle file for clustering.py'''
 

Diff for: compute_row.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 '''Compute a single row of a distance matrix from a pdbinfo file.  
 This allows for distributed processing'''

Diff for: compute_seqs.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 '''Given a pdbinfo file output sequence information for each chain'''
 

Diff for: create_caches.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 '''Takes a bunch of types training files. First argument is what index the receptor starts on
 (ligand is assumed to be right after).  Reads in the gninatypes files specified in these types 

Diff for: create_caches2.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 '''Takes a bunch of types training files. First argument is what index the receptor starts on
 (ligands are assumed to be right after).  Reads in the gninatypes files specified in these types 
@@ -9,7 +9,7 @@
 '''
 
 import os, sys
-import struct, argparse
+import struct, argparse, traceback
 
 
 def writemol(fname, out):
@@ -18,12 +18,13 @@ def writemol(fname, out):
         with open(fname,'rb') as gninatype:
             data = gninatype.read()
             assert(len(data) % 16 == 0)
-            natoms = len(data)/16
+            natoms = len(data)//16
             out.write(struct.pack('i',natoms))
             out.write(data)            
     except Exception as e:
         print(fname)
         print(e)
+        traceback.print_exc()
 
 def create_cache2(molfiles, data_root, outfile):
     '''Create an outfile molcache2 file from the list molfiles stored at data_root.'''
@@ -46,7 +47,7 @@ def create_cache2(molfiles, data_root, outfile):
         if len(mol) > 255:
             print("Skipping",mol,"since filename is too long")
             continue
-        s = bytes(mol)
+        s = bytes(mol, encoding='UTF-8')
         out.write(struct.pack('B',len(s)))
         out.write(s)
         out.write(struct.pack('L',offsets[mol]))

Diff for: predict.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 import numpy as np
 import matplotlib

Diff for: pymol_arrows.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 
 import sys

Diff for: show_xyz_arrows.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 '''Adds show_arrows command to pymol, which takes an xyz file'''
 
 import sys

Diff for: timemodel.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 '''quick script for generating a real model and caffe time command'''
 import argparse,sys

Diff for: train.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 import numpy as np
 import matplotlib