py2 and py3 compatibility

README.md

@@ -15,8 +15,6 @@ pdbTools is a set of command line [python](http://www.python.org) scripts that m
 
 Most of the scripts will run "out of the box" using a python interpreter.  The command line parser is designed to be flexible.  It will take an arbitrarily long list of pdb files, pdb ids, text files with pdb ids, or some mixture of all three.  If the pdb file or id is not in the working directory, scripts will attempt to download the pdb file from [RCSB](http://www.rcsb.org/).  Depending on the type of operation being done, a program will either write output files in the working directory or will print to stdout.  All structure outputs are written in standard pdb format.  All data outputs are in fixed-width column format.  They were designed to be read by the statistics package [R](http://cran.r-project.org/); however, they should be easily parsed by other graphing programs.
 
-*Note:* These scripts are only compatible with Python version 2.4-2.7.
-
 ## Installation
 
 Install the development version by cloning this repo and running `pip`:

pdbtools/addH.py

@@ -4,6 +4,7 @@
 # This program is distributed under General Public License v. 3.  See the file
 # COPYING for a copy of the license.
 
+from builtins import range
 __description__ = "Adds polar hydrogens to a pdb file for a UHBD calculation."
 __author__ = "Michael J. Harms"
 __date__ = "070727"
@@ -69,8 +70,8 @@ def convertResidues(pdb,atom_conv={},resid_conv={},atom_skip=[],resid_skip=[]):
     states and give every group a charge.
     """
 
-    atom_to_convert = atom_conv.keys()
-    res_to_convert = resid_conv.keys()
+    atom_to_convert = list(atom_conv.keys())
+    res_to_convert = list(resid_conv.keys())
 
     new_pdb = []
     for line in pdb:
@@ -181,7 +182,7 @@ def flipAtoms(pdb):
 
     flip = {"ASP":("OD1","OD2"),
             "GLU":("OE1","OE2")}
-    flip_keys = flip.keys()
+    flip_keys = list(flip.keys())
 
     for index, line in enumerate(pdb):
         res = line[17:30]

pdbtools/bfactor.py

@@ -63,7 +63,7 @@ def pdbBfactor(pdb,data_dict):
     for line in pdb:
         if line[0:6] == "ATOM  ":
             resnum = line[23:26].strip()
-            if resnum in data_dict.keys():
+            if resnum in list(data_dict.keys()):
                 out.append("%s%6.2F%s" % (line[:60],data_dict[resnum],
                                           line[66:]))
             else:

pdbtools/centerasu.py

@@ -5,6 +5,9 @@
 # This program is distributed under General Public License v. 3.  See the file
 # COPYING for a copy of the license.
 
+from __future__ import print_function
+from builtins import map
+from builtins import range
 __description__ = \
 """
 pdb_centerasu.py
@@ -20,8 +23,8 @@
 try:
     from numpy import array, linalg, dot, mean, squeeze
 except ImportError:
-    print "numpy package is required for this program!"
-    print "(http://numpy.scipy.org/)"
+    print("numpy package is required for this program!")
+    print("(http://numpy.scipy.org/)")
     sys.exit()
 
 class PdbCenterAsuError(Exception):
@@ -46,7 +49,7 @@ def pdbCenterasu(pdb, write_coord =False):
     fmx = []
     for line in pdb:
         if line.startswith('SCALE'):
-            data = map(float, line[6:].split()[:-1])
+            data = list(map(float, line[6:].split()[:-1]))
             fmx.append(data)
 
     if len(fmx) == 0:

pdbtools/centermass.py

@@ -4,6 +4,11 @@
 # This program is distributed under General Public License v. 3.  See the file
 # COPYING for a copy of the license.
 
+from __future__ import division
+from __future__ import print_function
+from __future__ import absolute_import
+from builtins import range
+from past.utils import old_div
 __description__ = \
 """
 pdb_centermass.py
@@ -17,7 +22,7 @@
 __date__ = "061109"
 
 import sys, re
-from data import common
+from .data import common
 
 def pdbCentermass(pdb,write_coord=False,include_hetatm=False,include_mass=True):
     """
@@ -73,15 +78,15 @@ def pdbCentermass(pdb,write_coord=False,include_hetatm=False,include_mass=True):
         try:
             masses.append(common.ATOM_WEIGHTS[atom_type])
         except:
-            print "File contains atoms of unknown type (%s)" % atom_type
-            print "Will assign them mass of carbon (12.011 g/mol)"
-            print "To fix, edit ATOM_WEIGHTS dictionary in pdb_data/common.py"
+            print("File contains atoms of unknown type (%s)" % atom_type)
+            print("Will assign them mass of carbon (12.011 g/mol)")
+            print("To fix, edit ATOM_WEIGHTS dictionary in pdb_data/common.py")
             masses.append(12.011)
 
     num_atoms = len(coord)
 
     total_mass = sum(masses)
-    weights = [m/total_mass for m in masses]
+    weights = [old_div(m,total_mass) for m in masses]
     center = [sum([coord[i][j]*weights[i] for i in range(num_atoms)])
               for j in range(3)]
 
@@ -100,7 +105,7 @@ def pdbCentermass(pdb,write_coord=False,include_hetatm=False,include_mass=True):
     center_out = ["%10.4F" % c for c in center]
 
     if warn:
-        print "Warning.  No element entries in file.  Attempting to extract"
-        print "from the atom names.  Not always reliable..."
+        print("Warning.  No element entries in file.  Attempting to extract")
+        print("from the atom names.  Not always reliable...")
 
     return center_out, out

pdbtools/charmm/interface.py

@@ -1,3 +1,5 @@
+from __future__ import print_function
+from __future__ import absolute_import
 # Copyright 2007, Michael J. Harms
 # This program is distributed under General Public License v. 3.  See the file
 # COPYING for a copy of the license.  
@@ -13,7 +15,7 @@
 __date__ = "080418"
 
 import math, os
-import gen_input
+from . import gen_input
 
 # Set up charmm binary
 try:
@@ -66,7 +68,7 @@ def runCharmm(input):
         err = "charmm binary \"%s\" does not exist!" % charmm_bin
         raise CharmmInterfaceError(err)
 
-    print "Running: %s" % (charmm_bin)
+    print("Running: %s" % (charmm_bin))
 
     cin, cout = os.popen2(charmm_bin)
     cin.write(input)
@@ -90,7 +92,7 @@ def charmm2pdb(charmm_output):
 
     # Rename oddball residues
     rename_dict = {"OCT1":" O  ","OCT2":" OXT"}
-    rename_lines = [l for l in pdb if l[12:16] in rename_dict.keys()]
+    rename_lines = [l for l in pdb if l[12:16] in list(rename_dict.keys())]
     for line in rename_lines:
         index = pdb.index(line)
         new_atom = rename_dict[line[12:16]]

pdbtools/clean.py

@@ -4,6 +4,7 @@
 # This program is distributed under General Public License v. 3.  See the file
 # COPYING for a copy of the license.
 
+from __future__ import print_function
 __description__ = \
 """
 pdb_clean.py
@@ -56,7 +57,7 @@ def convertModifiedAA(coord,header):
     backbone_atoms = ["N  ","CA ","C  ","O  "]
     new_coord = []
     for line in coord:
-        if line[17:20] in mod_dict.keys():
+        if line[17:20] in list(mod_dict.keys()):
             new = mod_dict[line[17:20]]
             if line[13:16] in backbone_atoms:
                 new_line = "ATOM  %s%s%s" % (line[6:17],new,line[20:])
@@ -72,7 +73,7 @@ def convertModifiedAA(coord,header):
             old_seq = line[19:70].split()
             new_seq = []
             for aa in old_seq:
-                if aa in mod_dict.keys():
+                if aa in list(mod_dict.keys()):
                     new_seq.append(mod_dict[aa])
                 else:
                     new_seq.append(aa)
@@ -87,7 +88,7 @@ def convertModifiedAA(coord,header):
 
     # Create output remarks
     conv = ["REMARK       converted %s to %s\n" % (k,mod_dict[k])
-            for k in mod_dict.keys()]
+            for k in list(mod_dict.keys())]
 
     return new_coord, new_header, conv
 
@@ -120,7 +121,7 @@ def removeLetters(line):
 
         # If the residue is not known, update known_atom_dict and append line
         # to coordinate file
-        if residue not in known_atom_dict.keys():
+        if residue not in list(known_atom_dict.keys()):
             out = removeLetters(c)
             coord_out.append(out)
             known_atom_dict.update([(residue,[c[13:16]])])
@@ -197,7 +198,8 @@ def addMissingAtoms(coord,seqres,keep_temp=False,renumber_residues=False,
     try:
         new_coord = charmm.interface.charmmWash(structure_list,
             keep_temp=keep_temp,fix_atoms=fix_atoms,num_steps=num_steps)
-    except charmm.interface.CharmmInterfaceError, (strerror):
+    except charmm.interface.CharmmInterfaceError as xxx_todo_changeme:
+        (strerror) = xxx_todo_changeme
         err = "CharmmInterfaceError\n%s\n" % strerror
         raise PdbCleanError(err)
 
@@ -265,7 +267,7 @@ def pdbClean(pdb,pdb_id="temp",chains="all",renumber_residues=False,
     coord, header, converted = convertModifiedAA(coord,header)
     if len(converted) != 0:
         log.append(log_fmt % "Modified amino acids converted.")
-        print log[-1],
+        print(log[-1], end=' ')
         log.extend(converted)
     if pdbCheck(coord):
         err = "Modified amino acid converter removed all atoms!  Mangled pdb!"
@@ -278,13 +280,13 @@ def pdbClean(pdb,pdb_id="temp",chains="all",renumber_residues=False,
         raise PdbCleanError(err)
     else:
         log.append(log_fmt % "HETATM entries removed.")
-        print log[-1],
+        print(log[-1], end=' ')
 
     # Grab only the chain we want, if specified
     if chains != "all":
         coord = [l for l in coord if l[21] in chains]
         log.append(log_fmt % ("Took only chain %r." % chains))
-        print log[-1],
+        print(log[-1], end=' ')
         if pdbCheck(coord):
             err = "Chain filter (%r) removed all atoms in pdb file!" % chains
             raise PdbCleanError(err)
@@ -293,7 +295,7 @@ def pdbClean(pdb,pdb_id="temp",chains="all",renumber_residues=False,
     coord, skipped = stripACS(coord)
     if len(skipped) != 0:
         log.append(log_fmt % "Alternate conformations were removed.")
-        print log[-1],
+        print(log[-1], end=' ')
         log.extend(skipped)
     if pdbCheck(coord):
         err = "ACS stripper removed all atoms!  Mangled pdb file."
@@ -303,14 +305,14 @@ def pdbClean(pdb,pdb_id="temp",chains="all",renumber_residues=False,
     coord, removed = backboneCheck(coord)
     if len(removed) != 0:
         log.append(log_fmt % "Residues with missing backbone atoms removed.")
-        print log[-1],
+        print(log[-1], end=' ')
         log.extend(removed)
     if pdbCheck(coord):
         err = "Backbone checker removed all atoms!  Mangled pdb file."
         raise PdbCleanError(err)
 
     # Add missing atoms using CHARMM
-    print log_fmt % "Adding heavy atoms using CHARMM.",
+    print(log_fmt % "Adding heavy atoms using CHARMM.", end=' ')
     seqres = [l for l in header if l[0:6] == "SEQRES"]
     coord = addMissingAtoms(coord,seqres,keep_temp,renumber_residues,pdb_id,
                             fix_atoms,num_steps)
@@ -319,17 +321,17 @@ def pdbClean(pdb,pdb_id="temp",chains="all",renumber_residues=False,
     # Renumber residues if requested
     if renumber_residues:
         log.append(log_fmt % "Residues renumbered from one.")
-        print log[-1],
+        print(log[-1], end=' ')
 
     # Renumber atoms from 1
     coord = pdb_atom_renumber.pdbAtomRenumber(coord)
     log.append(log_fmt % "Renumbered atoms from 1")
-    print log[-1],
+    print(log[-1], end=' ')
 
     # Standardize atom-type on far right pdb column
     coord = ["%s           %s  \n" % (c[:66],c[13]) for c in coord]
     log.append(log_fmt % "Atom types were standardized.")
-    print log[-1],
+    print(log[-1], end=' ')
 
     # Final check
     if pdbCheck(coord):

pdbtools/closecontacts.py

@@ -4,6 +4,7 @@
 # This program is distributed under General Public License v. 3.  See the file
 # COPYING for a copy of the license.
 
+from builtins import range
 __description__ = \
 """
 pdb_close-contacts.py

pdbtools/contact.py

@@ -4,6 +4,7 @@
 # This program is distributed under General Public License v. 3.  See the file
 # COPYING for a copy of the license.
 
+from builtins import range
 __description__ = \
 """
 pdb_contacting-residues.py
@@ -42,7 +43,7 @@ def pdbContacting(pdb,target,cutoff,target_type="resname"):
                 contacts.append(a[0][5:].strip())
 
         # Grab only unique contacts
-        contacts = dict([(c,()) for c in contacts]).keys()
+        contacts = list(dict([(c,()) for c in contacts]).keys())
         out.append("%s\t%s\n" % (t[0],("\t".join(contacts))))
 
     return out 

pdbtools/contactplot.py

@@ -4,6 +4,7 @@
 # This program is distributed under General Public License v. 3.  See the file
 # COPYING for a copy of the license.
 
+from builtins import range
 __description__ = \
 """
 pdb_contact.py

pdbtools/coulomb.py

@@ -4,6 +4,9 @@
 # This program is distributed under General Public License v. 3.  See the file
 # COPYING for a copy of the license.
 
+from __future__ import division
+from builtins import range
+from past.utils import old_div
 __description__ = \
 """
 pdb_coulomb.py
@@ -33,7 +36,7 @@ def readPDB(pdb_file):
 
     # Grab only ATOM entries that are titratable
     pdb = [l for l in pdb if l[0:4] == "ATOM" and
-                             l[17:20] in TITR_ATOM.keys() and
+                             l[17:20] in list(TITR_ATOM.keys()) and
                              l[13:16] == TITR_ATOM[l[17:20]]]
 
     # Initalize lists to hold coordinates, pkas, and charge
@@ -60,7 +63,7 @@ def hendersonHasselbach(pKa,charge,pH):
     pH value.
     """
 
-    return charge/(1 + 10**(charge*(pH-pKa)))
+    return old_div(charge,(1 + 10**(charge*(pH-pKa))))
 
 
 def pdbCoulomb(coord,pKa,charge,dielec_const,ionic_str,pH,temperature):
@@ -70,10 +73,10 @@ def pdbCoulomb(coord,pKa,charge,dielec_const,ionic_str,pH,temperature):
     ionic strength.
     """
 
-    ionic_str = ionic_str/1000
+    ionic_str = old_div(ionic_str,1000)
 
     # Initialize variables
-    kappa = 50.29*sqrt(ionic_str/(dielec_const*temperature))
+    kappa = 50.29*sqrt(old_div(ionic_str,(dielec_const*temperature)))
     num_groups = len(coord)
     energy = 0.
 

pdbtools/data/polar.py

@@ -34,7 +34,7 @@ def _readParam(param_file):
     # Fill charge and radii dictionaries keyed to aa, then atom type
     charge = dict([(x[0],[]) for x in param])
     radii  = dict([(x[0],[]) for x in param])
-    for k in charge.keys():
+    for k in list(charge.keys()):
         charge[k] = dict([(x[1],x[2]) for x in param if x[0] == k])
         radii[k]  = dict([(x[1],x[3]) for x in param if x[0] == k])
 

pdbtools/dist_filter.py

@@ -4,6 +4,7 @@
 # This program is distributed under General Public License v. 3.  See the file
 # COPYING for a copy of the license.
 
+from builtins import range
 __author__ = "Michael J. Harms"
 __date__ = "070709"
 __description__ = \

pdbtools/disulfide.py

@@ -4,6 +4,7 @@
 # This program is distributed under General Public License v. 3.  See the file
 # COPYING for a copy of the license.
 
+from builtins import range
 __description__ = \
 """
 pdb_disulfide.py