Python3 support

Signed-off-by: Justin Lecher <[email protected]>

Author: jlec

ccp4_ncont.py

@@ -3,27 +3,27 @@
 
     ccp4_ncont -- parses CCP4/NCONT log file and selects residues and atoms.
     http://www.ccp4.ac.uk/html/ncont.html
- 
+
     PARAMS
         contactsfile
             filename of the CCP4/NCONT contacts log file
- 
+
         selName1
             the name prefix for the _res and _atom selections returned for the
             source set of chain
- 
+
         selName2
-            the name prefix for the _res and _atom selections returned for the 
+            the name prefix for the _res and _atom selections returned for the
             target set of chain
- 
+
     RETURNS
         4 selections of interface residues and atoms are created and named
         depending on what you passed into selName1 and selName2
-  
+
     AUTHOR
         Gerhard Reitmayr and Dalia Daujotyte, 2009.
 '''
-
+from __future__ import print_function
 from pymol import cmd
 import re
 
@@ -53,7 +53,7 @@ def parseNCONTContacts(f):
                 s2.append(matches[0])
             pairs.append((len(s1) - 1, len(s2) - 1))
         else:
-            print "Unknown mode", mode
+            print("Unknown mode", mode)
 
 
 def ccp4_ncont(contactsfile, selName1="source", selName2="target"):

ccp4_pisa.py

@@ -2,32 +2,32 @@
 See more here: http://www.pymolwiki.org/index.php/ccp4_pisa
 
         parse a PISA contact file and create atoms selections for all interfaces
- 
-        For each interface, two selections are created containing the atoms of 
-        the interface on each chain. The selection names follow the convention 
-        bondtype_#Id_Chain1Chain2. If Chain1 equals Chain2 then the two selections are 
-        numbered. 
- 
+
+        For each interface, two selections are created containing the atoms of
+        the interface on each chain. The selection names follow the convention
+        bondtype_#Id_Chain1Chain2. If Chain1 equals Chain2 then the two selections are
+        numbered.
+
         bondtype corresponds to h-bonds, salt-bridges, ss-bonds and cov-bonds and
         are marked with the prefixes hb, sb, ss and cov.
- 
+
         For example, all h-bonds in interface 3 between chain A and D create the selections
         hb_3_AD and hb_3_DA.
- 
+
         Salt-bridges in interface 4 between chain A and a symmetry copy of A creates the selections
         sb_4_AA1 and sb_4_AA2.
- 
+
     PARAMS
-        filename 
+        filename
             filename of the PISA contacts file
- 
+
     RETURNS
-        a set of selections in PYMOL. 
-  
+        a set of selections in PYMOL.
+
     AUTHOR
         Gerhard Reitmayr and Dalia Daujotyte, 2011.
 '''
-
+from __future__ import print_function
 from pymol import cmd
 from xml.etree import ElementTree
 
@@ -47,7 +47,7 @@ def parseBond(elementDir):
 
 
 def parseInterface(interface, bondname):
-    """ parses a single interface into the interface id, the two chain names connected 
+    """ parses a single interface into the interface id, the two chain names connected
         and two lists of atoms for each chain"""
     bonds = interface.findall(bondname)
     id = interface.find('id').text.strip()
@@ -86,8 +86,8 @@ def createInterfaceSelection(interface, prefix):
         cmd.select(leftname, leftlist)
         cmd.select(rightname, rightlist)
     except:
-        print leftname, '\t', leftlist
-        print rightname, '\t', rightlist
+        print(leftname, '\t', leftlist)
+        print(rightname, '\t', rightlist)
     return leftname, rightname
 
 
@@ -115,11 +115,11 @@ def ccp4_pisa(filename):
             try:
                 cmd.select(name, " or ".join(allselections))
             except:
-                print name, '\t', " or ".join(allselections)
+                print(name, '\t', " or ".join(allselections))
 
-    print 'selectPISAContacts found interfaces with',
+    print('selectPISAContacts found interfaces with', end=' ')
     for number, type in zip(result, bond_types):
-        print number, type[0], ",",
+        print(number, type[0], ",", end=' ')
 
 try:
     cmd.extend("ccp4_pisa", ccp4_pisa)

center_of_mass.py

@@ -2,19 +2,19 @@
 See more here: http://www.pymolwiki.org/index.php/center_of_mass
 
 DESCRIPTION
- 
+
    Places a pseudoatom at the center of mass
- 
+
    Author: Sean Law
    Michigan State University
    slaw (at) msu . edu
- 
+
 SEE ALSO
- 
+
    pseudoatom, get_com
 '''
 
-
+from __future__ import print_function
 from pymol import cmd
 
 
@@ -31,14 +31,14 @@ def com(selection, state=None, mass=None, object=None, quiet=1, **kwargs):
     if (state != None):
         x, y, z = get_com(selection, mass=mass, quiet=quiet)
         if not quiet:
-            print "%f %f %f" % (x, y, z)
+            print("%f %f %f" % (x, y, z))
         cmd.pseudoatom(object, pos=[x, y, z], **kwargs)
         cmd.show("spheres", object)
     else:
         for i in range(cmd.count_states()):
             x, y, z = get_com(selection, mass=mass, state=i + 1, quiet=quiet)
             if not quiet:
-                print "State %d:%f %f %f" % (i + 1, x, y, z)
+                print("State %d:%f %f %f" % (i + 1, x, y, z))
             cmd.pseudoatom(object, pos=[x, y, z], state=i + 1, **kwargs)
             cmd.show("spheres", 'last ' + object)
 
@@ -59,7 +59,7 @@ def get_com(selection, state=1, mass=None, quiet=1):
 
     totmass = 0.0
     if mass != None and not quiet:
-        print "Calculating mass-weighted COM"
+        print("Calculating mass-weighted COM")
 
     state = int(state)
     model = cmd.get_model(selection, state)

centroid.py

@@ -3,12 +3,12 @@
 
 DESCRIPTION
         get the centroid (geometric center) of a selection or move selection to the origin.
- 
+
 ARGUMENTS
         selection = string: a valid PyMOL selection {default: all}
         center = 0 or 1: if center=1 center the selection {default: 0}
         returns: centroid: [ x, y, z ]
- 
+
 SEE ALSO
         get_extent, get_position, http://pymolwiki.org/index.php/Center_Of_Mass
 
@@ -37,6 +37,7 @@
 # REV   : 1
 
 '''
+from __future__ import print_function
 from pymol import cmd
 from pymol import stored
 from chempy import cpv
@@ -54,7 +55,7 @@ def centroid(selection='all', center=0, quiet=1):
     centroid = cpv.scale(centroid, 1. / nAtom)
 
     if not int(quiet):
-        print ' centroid: [%8.3f,%8.3f,%8.3f]' % tuple(centroid)
+        print(' centroid: [%8.3f,%8.3f,%8.3f]' % tuple(centroid))
 
     if int(center):
         cmd.alter_state(1, selection, "(x,y,z)=sub((x,y,z), centroid)",

cgo_arrow.py

@@ -6,6 +6,7 @@
 License: BSD-2-Clause
 '''
 
+from __future__ import print_function
 from pymol import cmd, cgo, CmdException
 
 

cgo_grid.py

@@ -18,7 +18,7 @@
 
 ################################################################################
 '''
-
+from __future__ import print_function
 from pymol import cmd
 from pymol import stored
 from pymol.cgo import *
@@ -167,7 +167,7 @@ def get_coord(v):
                 # more than one atom --> use "center"
                 # alt check!
                 if cmd.count_atoms('(alt *) and not (alt "")')!=0:
-                    print "cgo_grid: warning! alternative coordinates found for origin, using center!"
+                    print("cgo_grid: warning! alternative coordinates found for origin, using center!")
                 view_temp=cmd.get_view()
                 cmd.zoom(v)
                 v=cmd.get_position()
@@ -180,8 +180,8 @@ def eval_color(v):
         try:
             if not v:
                 v=eval(cmd.get('bg_rgb'))
-                v=map(sum, zip(v,[-1,-1,-1]))
-                v=map(abs, v)
+                v=list(map(sum, list(zip(v,[-1,-1,-1]))))
+                v=list(map(abs, v))
                 if v[0]==v[1]==v[2]==0.5: # grey
                     v=[0,0,0]
                 return v
@@ -209,7 +209,7 @@ def eval_color(v):
         nstates=int(nstates)
         if nstates<1:
             nstates=1
-            print "NB! nstates set to 1 (automatic minimum)"
+            print("NB! nstates set to 1 (automatic minimum)")
         length_x=float(length_x)
         if length_z=='':
             length_z=length_x
@@ -221,14 +221,14 @@ def eval_color(v):
             npoints_x=int(npoints_x)
         if npoints_x<1:
             npoints_x=1
-            print "NB! npoints_x set to 1 (automatic minimum)"
+            print("NB! npoints_x set to 1 (automatic minimum)")
         if npoints_z =='':
             npoints_z=int(length_z)+1
         else:
             npoints_z=int(npoints_z)
         if npoints_z<1:
             npoints_z=1
-            print "NB! npoints_x set to 1 (automatic minimum)"
+            print("NB! npoints_x set to 1 (automatic minimum)")
 
         nwaves_x=abs(float(nwaves_x))
         if nwaves_z=='':
@@ -314,11 +314,11 @@ def eval_color(v):
         raise Exception("Unexpected error!")
 
     if (nstates==1):
-        if not quiet: print "Creating one state object!"
+        if not quiet: print("Creating one state object!")
 
     if startframe > endframe:
         startframe, endframe = endframe, startframe
-        if not quiet: print "Inverted start and end frames!"
+        if not quiet: print("Inverted start and end frames!")
 
 
     ########## BEGIN OF FUNCTIONAL SCRIPT ##########
@@ -464,36 +464,36 @@ def eval_color(v):
                     framecount=0
             # count up from first state
             if framecount==1: countvar=1
-        if not quiet: print "object loaded and animated with frames!"
+        if not quiet: print("object loaded and animated with frames!")
     else:
-        if not quiet: print "object loaded!"
+        if not quiet: print("object loaded!")
 
     #OUTPUT
     if not quiet:
-        print "Grid variables for:",name
-        print "corner:", xyz1
-        print "vector 1:", xyz2
-        print "vector 2:", xyz3
+        print("Grid variables for:",name)
+        print("corner:", xyz1)
+        print("vector 1:", xyz2)
+        print("vector 2:", xyz3)
 
-        print "length_x:",length_x
-        print "length_z:",length_z
-        print "npoints_x:", npoints_x
-        print "npoints_z:", npoints_z
+        print("length_x:",length_x)
+        print("length_z:",length_z)
+        print("npoints_x:", npoints_x)
+        print("npoints_z:", npoints_z)
 
-        print "nwaves_x:", nwaves_x
-        print "nwaves_z:", nwaves_z
+        print("nwaves_x:", nwaves_x)
+        print("nwaves_z:", nwaves_z)
 
-        print "offset_x:",offset_x
-        print "offset_z:",offset_z
+        print("offset_x:",offset_x)
+        print("offset_z:",offset_z)
 
-        print "gain_x:",gain_x
-        print "gain_z:",gain_z
+        print("gain_x:",gain_x)
+        print("gain_z:",gain_z)
 
-        print "thickness:",thickness
+        print("thickness:",thickness)
 
-        print "states", nstates
+        print("states", nstates)
         if (not endframe==startframe):
-            print "frames: start:",startframe,"end:",endframe
+            print("frames: start:",startframe,"end:",endframe)
 
     return grid_xyz
 

color_by_conservation.py

@@ -10,31 +10,32 @@
                from the alignment object
     color
         (string) valid PyMOL spectrum name
- 
+
     as_putty
         (0 or 1) if 0 display is not changed, else participating objects are shown
                  as cartoon putty, colored by the 'color' field
 '''
 
+from __future__ import print_function
 from pymol import cmd
 
 
 def color_by_conservation(aln, names=(), color="rainbow", as_putty=0, _self=cmd):
     # PyMOL doesn't yet know about object:alignment
     # but we need to check that this exists or we might crash
     if _self.get_type(aln) not in ("object:", "object:alignment"):
-        print "Error: Bad or incorrectly specified alignment object."
+        print("Error: Bad or incorrectly specified alignment object.")
         return None
 
     r = cmd.get_raw_alignment(aln)
 
     if names == ():
         known_objs = []
-        map(known_objs.extend, map(lambda x: map(lambda y: y[0], x), r))
+        list(map(known_objs.extend, [[y[0] for y in x] for x in r]))
         known_objs = set(known_objs)
 
         # highest number of matches seen
-        M = max(map(len, r)) + 1
+        M = max(list(map(len, r))) + 1
     else:
         known_objs = set(names)
         M = len(known_objs) + 1