running 2-to-3

pdbtools/addH.py

@@ -69,8 +69,8 @@ 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 +181,7 @@ 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

@@ -20,8 +20,8 @@
 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 +46,7 @@ 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

@@ -17,7 +17,7 @@
 __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):
     """
@@ -73,9 +73,9 @@ 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)
@@ -100,7 +100,7 @@ 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

@@ -13,7 +13,7 @@
 __date__ = "080418"
 
 import math, os
-import gen_input
+from . import gen_input
 
 # Set up charmm binary
 try:
@@ -66,7 +66,7 @@ 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 +90,7 @@ 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

@@ -56,7 +56,7 @@ 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 +72,7 @@ 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 +87,7 @@ 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 +120,7 @@ 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 +197,8 @@ 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 +266,7 @@ 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 +279,13 @@ 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 +294,7 @@ 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 +304,14 @@ 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 +320,17 @@ 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/contact.py

@@ -42,7 +42,7 @@ 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/coulomb.py

@@ -33,7 +33,7 @@ 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

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/download.py

@@ -43,7 +43,7 @@ def pdbDownload(file_list,hostname=HOSTNAME,directory=DIRECTORY,prefix=PREFIX,
     success = True
 
     # Log into server
-    print "Connecting..."
+    print("Connecting...")
     ftp = ftplib.FTP()
     ftp.connect(hostname)
     ftp.login()
@@ -63,10 +63,10 @@ def pdbDownload(file_list,hostname=HOSTNAME,directory=DIRECTORY,prefix=PREFIX,
             ftp.retrbinary("RETR %s" % to_get[i],open(to_write[i],"wb").write)
             final_name = "%s.pdb" % to_write[i][:to_write[i].index(".")]
             unZip(to_write[i],final_name)
-            print "%s retrieved successfully." % final_name
+            print("%s retrieved successfully." % final_name)
         except ftplib.error_perm:
             os.remove(to_write[i])
-            print "ERROR!  %s could not be retrieved!" % file_list[i]
+            print("ERROR!  %s could not be retrieved!" % file_list[i])
             success = False
 
     # Log out

pdbtools/helper/cmdline.py

@@ -138,7 +138,7 @@ def parseCommandLine():
 
     # Remove duplicates from file_list by placing in dictionary
     file_dict = dict([(f,"") for f in file_list])
-    file_list = file_dict.keys()
+    file_list = list(file_dict.keys())
     file_list.sort()
 
     return file_list, options

pdbtools/helper/geometry.py

@@ -36,9 +36,9 @@ def calcDistances(coord):
 
     num_points = len(coord)
     d = [[0. for j in range(num_points)] for i in range(num_points)]
-    for i in xrange(num_points):
+    for i in range(num_points):
         d[i][i] = 0.
-        for j in xrange(i+1,num_points):
+        for j in range(i+1,num_points):
             d[i][j] = dist(coord[i],coord[j])
             d[j][i] = d[i][j]
 

pdbtools/iondist.py

@@ -30,11 +30,11 @@ def pdbIonDist(pdb,hist_step,remove_resid="TYR"):
     pdb = [l for l in pdb if l[0:4] == "ATOM"]
     titr_atom = [l for l in pdb
                  if l[17:20] not in remove_resid 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]]]
 
     # Extract coordinates and charges for each titratable atom
-    coord = [[float(l[30+8*i:38+8*i]) for i in xrange(3)] for l in titr_atom]
+    coord = [[float(l[30+8*i:38+8*i]) for i in range(3)] for l in titr_atom]
     charge = [CHARGE_DICT[l[17:20]] for l in titr_atom]
 
     # Calculate all ij distances
@@ -46,15 +46,15 @@ def pdbIonDist(pdb,hist_step,remove_resid="TYR"):
     max_dist_bin = max([max([dist[i][j] for j in range(N)])
                         for i in range(N)])
     max_dist_bin = int(round(max_dist_bin/hist_step)) + 1
-    histogram = [[0 for j in xrange(max_dist_bin)] for i in xrange(3)]
+    histogram = [[0 for j in range(max_dist_bin)] for i in range(3)]
 
     # Populate histogram
     #   Interaction types:
     #   acid/acid            --> 0 (-1 + -1)/2 + 1
     #   acid/base, base/acid --> 1 (-1 +  1)/2 + 1
     #   base/base            --> 2 ( 1 +  1)/2 + 2
-    for i in xrange(N):
-        for j in xrange(i+1,N):
+    for i in range(N):
+        for j in range(i+1,N):
             interaction_type = int((charge[i] + charge[j])/2 + 1)
             dist_bin = int(round(dist[i][j]/hist_step))
             histogram[interaction_type][dist_bin] += 1

pdbtools/ligand.py

@@ -22,6 +22,6 @@ def pdbLigand(pdb,skip_boring=False):
     """
 
     ligands = [l[7:10].strip() for l in pdb if l.startswith("HET   ")]
-    ligands = dict([(l,[]) for l in ligands if l not in BORING_LIGANDS]).keys()
+    ligands = list(dict([(l,[]) for l in ligands if l not in BORING_LIGANDS]).keys())
 
     return ";".join(ligands)

pdbtools/mutator.py

@@ -16,9 +16,11 @@
 __description__ = "Mutates a residue in a pdb file"
 
 import sys, time, string, os
-import .atom_renumber
-import .clean
+from . import atom_renumber
+from . import clean
+from . import helper
 from .helper import container
+from . import data
 from .data.common import *
 
 class MutatorError(Exception):
@@ -89,20 +91,20 @@ def pdbMutator(pdb,residue,mutation,chain=None,run_charmm=True):
 
     # Add missing atoms using CHARMM
     if run_charmm:
-        print log_fmt % "Adding mutated side chain using CHARMM",
+        print(log_fmt % "Adding mutated side chain using CHARMM", end=' ')
         seqres = [l for l in header if l[0:6] == "SEQRES"]
         coord = pdb_clean.addMissingAtoms(coord,seqres)
         log.append(log_fmt % "Mutated sidechain built with CHARMM")
 
     # 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 pdb_clean.pdbCheck(coord):

pdbtools/oligomer.py

@@ -109,10 +109,10 @@ def findAllChains(pdb):
 
     # grab chains from HETATM entries (if they were not listed in the COMPND
     # section)
-    known_chains = chain_dict.keys()
+    known_chains = list(chain_dict.keys())
     hetatm = [l for l in pdb if l[0:6] == "HETATM"]
     hetatm_chains = dict([(l[21],l[17:20]) for l in hetatm])
-    for k in hetatm_chains.keys():
+    for k in list(hetatm_chains.keys()):
         if k not in known_chains:
             chain_dict[k] = hetatm_chains[k]
 
@@ -138,7 +138,7 @@ def pdbOligomer(pdb,collapse_repeat=True):
     # the system as non wysiwg, but will allow chains, etc. to be parsed for
     # output
     if biomat == ():
-        keys = chain_dict.keys()
+        keys = list(chain_dict.keys())
         keys.sort()
         biomat = [[keys,(False,False)]]