Make python 3 compatible

Author: lvduyfhu

quickff/context.py

@@ -37,7 +37,7 @@
    error is raised.
 '''
 
-
+from __future__ import absolute_import
 import os
 from glob import glob
 

quickff/cost.py

@@ -22,6 +22,9 @@
 # along with this program; if not, see <http://www.gnu.org/licenses/>
 #
 #--
+
+from __future__ import absolute_import
+
 from molmod.units import *
 
 from quickff.tools import boxqp

quickff/io.py

@@ -23,6 +23,8 @@
 #
 #--
 
+from __future__ import print_function, absolute_import
+
 '''Readers ab initio vibrational calculations.
 '''
 
@@ -84,20 +86,20 @@ def __init__(self, filename, field_labels=[]):
         # Read atomic masses for atomtype
         masses = np.asarray([float(atom.findall('c')[2].text) for atom in self.root.findall(".//*[@name='atomtypes']/set")[0]])*amu
         self.fields['masses'] = np.zeros(self.fields['numbers'].shape)
-        for iatype in xrange(masses.shape[0]):
+        for iatype in range(masses.shape[0]):
             self.fields['masses'][atomtypes==iatype] = masses[iatype]
         # Read SCF energies
         self.fields['energies'] = np.array([float(step.find('energy/i[@name="e_fr_energy"]').text)*electronvolt\
                  for step in self.root.findall('.//calculation')])
         # Read all requested arrays
         for label in field_labels:
-            if not label in tag_dictionary.keys():
-                raise NotImplementedError, "Failed to read %s from xml file" % label
+            if not label in list(tag_dictionary.keys()):
+                raise NotImplementedError("Failed to read %s from xml file" % label)
             self.fields[label] = self.read_array(tag_dictionary[label][0], unit=tag_dictionary[label][1])
         # Convert fractional to Cartesian coordinates
         self.fields['pos_init'] = np.dot(self.fields['pos_init'], self.fields['rvecs_init'])
         # Hessian is mass-weighted, we want the pure second derivatives
-        if 'hessian' in self.fields.keys():
+        if 'hessian' in list(self.fields.keys()):
             m3 = np.sqrt(np.array(sum([[m,m,m] for m in self.fields['masses']],[])))
             self.fields['hessian'] = m3.reshape((-1,1))*self.fields['hessian']*m3
 
@@ -154,39 +156,39 @@ def read_abinitio(fn, do_hess=True):
 def make_yaff_ei(fn, charges, bcis=None, radii=None):
     assert charges is not None or bcis is not None, 'Either charges or bcis should be parsed'
     f = open(fn, 'w')
-    print >> f, '#Fixed charges'
-    print >> f, '#---------------'
-    print >> f, ''
-    print >> f, 'FIXQ:UNIT Q0 e'
-    print >> f, 'FIXQ:UNIT P e'
-    print >> f, 'FIXQ:UNIT R angstrom'
-    print >> f, 'FIXQ:SCALE 1 1.0'
-    print >> f, 'FIXQ:SCALE 2 1.0'
-    print >> f, 'FIXQ:SCALE 3 1.0'
-    print >> f, 'FIXQ:DIELECTRIC 1.0'
-    print >> f, ''
+    print('#Fixed charges', file=f)
+    print('#---------------', file=f)
+    print('', file=f)
+    print('FIXQ:UNIT Q0 e', file=f)
+    print('FIXQ:UNIT P e', file=f)
+    print('FIXQ:UNIT R angstrom', file=f)
+    print('FIXQ:SCALE 1 1.0', file=f)
+    print('FIXQ:SCALE 2 1.0', file=f)
+    print('FIXQ:SCALE 3 1.0', file=f)
+    print('FIXQ:DIELECTRIC 1.0', file=f)
+    print('', file=f)
     if charges is not None or radii is not None:
-        print >> f, '# Atomic parameters'
-        print >> f, '# ----------------------------------------------------'
-        print >> f, '# KEY        label  Q_0A              R_A'
-        print >> f, '# ----------------------------------------------------'
+        print('# Atomic parameters', file=f)
+        print('# ----------------------------------------------------', file=f)
+        print('# KEY        label  Q_0A              R_A', file=f)
+        print('# ----------------------------------------------------', file=f)
         if charges is not None:
-            ffatypes = charges.keys()
+            ffatypes = list(charges.keys())
         else:
-            ffatypes = radii.keys()
+            ffatypes = list(radii.keys())
         for ffatype in ffatypes:
             charge, radius = 0.0, 0.0
             if charges is not None: charge = charges[ffatype]
             if radii is not None: radius = radii[ffatype]
-            print >> f, 'FIXQ:ATOM %8s % 13.10f  %12.10f' %(ffatype, charge, radius/angstrom)
+            print('FIXQ:ATOM %8s % 13.10f  %12.10f' %(ffatype, charge, radius/angstrom), file=f)
     if bcis is not None:
-        print >> f, '# Bond parameters'
-        print >> f, '# ----------------------------------------------------'
-        print >> f, '# KEY         label0   label1           P_AB          '
-        print >> f, '# ----------------------------------------------------'
-        for key, bci in bcis.iteritems():
+        print('# Bond parameters', file=f)
+        print('# ----------------------------------------------------', file=f)
+        print('# KEY         label0   label1           P_AB          ', file=f)
+        print('# ----------------------------------------------------', file=f)
+        for key, bci in bcis.items():
             ffatype1, ffatype2 = key.split('.')
-            print >> f, 'FIXQ:BOND  %8s  %8s  % 12.10f' %(ffatype1, ffatype2, bci)
+            print('FIXQ:BOND  %8s  %8s  % 12.10f' %(ffatype1, ffatype2, bci), file=f)
     f.close()
 
 
@@ -211,7 +213,7 @@ def read_bci_constraints(fn):
             master, suffix, sign = line.split(':')
             slaves = [(slave.strip(), float(sign)) for slave in suffix.split(',')]
             label = master.strip()
-            if label in constraints.keys():
+            if label in list(constraints.keys()):
                 for slave in slaves: constraints[label].append(slave)
             else:
                 constraints[label] = slaves
@@ -413,7 +415,7 @@ def dump_charmm22_prm(valence, fn):
 
 def _atoms_to_charmm22_psf(system):
     result = ['{:8d} !NATOM'.format(system.natom)]
-    for iatom in xrange(system.natom):
+    for iatom in range(system.natom):
         ffatype = system.get_ffatype(iatom)
         if len(ffatype) > 4:
             log.warning('Atom type too long for CHARMM PSF file: {}'.format(ffatype))
@@ -977,13 +979,13 @@ def dump_yaff(valence, fn):
     f = open(fn, 'w')
     for section in sections:
         if len(section['PARS'].lines)==0: continue
-        print >> f, '# %s' %section.prefix
-        print >> f, '#-%s' %('-'*len(section.prefix))
+        print('# %s' %section.prefix, file=f)
+        print('#-%s' %('-'*len(section.prefix)), file=f)
         for line in section['UNIT'].lines:
-            print >> f, '%s:UNIT  %s' %(section.prefix, line)
-        print >> f, ''
+            print('%s:UNIT  %s' %(section.prefix, line), file=f)
+        print('', file=f)
         for line in section['PARS'].lines:
-            print >> f, '%s:PARS  %s' %(section.prefix, line)
-        print >> f, ''
-        print >> f, ''
+            print('%s:PARS  %s' %(section.prefix, line), file=f)
+        print('', file=f)
+        print('', file=f)
     f.close()

quickff/log.py

@@ -23,6 +23,8 @@
 #
 #--
 
+from __future__ import print_function, absolute_import, unicode_literals
+from io import IOBase
 import os, sys, datetime, getpass, atexit
 import numpy, scipy, matplotlib
 
@@ -132,7 +134,7 @@ def set_level(self, level):
     def write_to_file(self, f):
         if isinstance(f, str):
             self._f = open(f, 'w')
-        elif isinstance(f, file):
+        elif isinstance(f, IOBase):
             self._f = f
         else:
             raise ValueError('File argument f should be a string representing a filename or a File instance')
@@ -151,16 +153,16 @@ def dump(self, message, new_line=True):
                 self.print_header()
             assert self.label is not None
             if new_line and self.add_blank_line:
-                print >> self._f , ''
+                print('', file=self._f)
                 self.add_blank_line = False
             line = ''
             for piece in splitstring(message, self.ll-self.mll):
                 line += ' ' + self.label[:self.mll-2] + ' '
                 line += ' '*(self.mll-2 - len(self.label[:self.mll-2]))
-                line += piece.encode('utf-8')
+                line += piece
                 line += '\n'
             line = line.rstrip('\n')
-            print >> self._f, line
+            print(line, file=self._f)
 
     def warning(self, message, new_line=True):
         '''
@@ -173,7 +175,7 @@ def warning(self, message, new_line=True):
                 self.print_header()
             assert self.label is not None
             if new_line and self.add_blank_line:
-                print >> self._f , ''
+                print('', file=self._f)
                 self.add_blank_line = False
             line = ''
             for piece in splitstring('WARNING: '+message, self.ll-self.mll):
@@ -182,12 +184,12 @@ def warning(self, message, new_line=True):
                 line += piece.encode('utf-8')
                 line += '\n'
             line = line.rstrip('\n')
-            print >> self._f, line
+            print(line, file=self._f)
 
     def print_header(self):
         if self.log_level>0:
-            print >> self._f, header
-            print >> self._f, ''
+            print(header, file=self._f)
+            print('', file=self._f)
         mll = self.mll
         self.mll = 20
         with self.section('USER', 1): self.dump(getpass.getuser(), new_line=False)
@@ -202,8 +204,8 @@ def print_header(self):
         with self.section('COMMAND LINE', 1): self.dump(' '.join(sys.argv), new_line=False)
         self.mll = mll
         if self.log_level>0:
-            print >> self._f, ''
-            print >> self._f, '~'*80
+            print('', file=self._f)
+            print('~'*80, file=self._f)
 
     def exit(self):
         if self._active:
@@ -213,20 +215,20 @@ def exit(self):
 
     def print_footer(self):
         if self.log_level>0:
-            print >> self._f, footer
+            print(footer, file=self._f)
 
     def print_timetable(self):
         if self.log_level>0:
-            print >> self._f, '~'*80
-            print >> self._f, ''
+            print('~'*80, file=self._f)
+            print('', file=self._f)
         with self.section('TIMING', 1):
             for label, time in self.timetable:
                 line = '%30s  ' %(label+' '*(30-len(label)))
                 line += str(time)
                 self.dump(line)
 
     def close(self):
-        if isinstance(self._f, file):
+        if isinstance(self._f, IOBase):
             self._f.close()
 
 

quickff/paracontext.py

@@ -23,6 +23,8 @@
 #
 #--
 
+from __future__ import print_function, absolute_import
+
 '''
     Convenience functions to enable using scoop.
 '''
@@ -51,7 +53,7 @@ def my_wait_first(fs):
             return fs[:1], fs[1:]
         def debug_log(*args):
             with open('debug.log', 'a') as f:
-                print >> f, ' '.join(str(arg) for arg in args)
+                print(' '.join(str(arg) for arg in args), file=f)
             return 0
         self.map = my_map
         self.wait_first = my_wait_first
@@ -67,7 +69,7 @@ def my_wait_first(fs):
             return futures.wait(fs, return_when=futures.FIRST_COMPLETED)
         def debug_log(*args):
             with open('debug_%s.log' % WORKER_NAME, 'a') as f:
-                print >> f, ' '.join(str(arg) for arg in args)
+                print(' '.join(str(arg) for arg in args), file=f)
             return 0
         self.map = my_map
         self.wait_first = my_wait_first

quickff/perturbation.py

@@ -23,6 +23,8 @@
 #
 #--
 
+from __future__ import absolute_import
+
 from molmod.io.xyz import XYZWriter
 from molmod.units import *
 from molmod.periodic import periodic as pt
@@ -78,7 +80,7 @@ def __init__(self, term, start, end, numbers, nsteps=11):
         self.qunit = term.units[1]
         self.kunit = term.units[0]
         self.step = (end-start)/(nsteps-1)
-        self.targets = start + (end-start)/(nsteps-1)*np.array(range(nsteps), float)
+        self.targets = start + (end-start)/(nsteps-1)*np.array(list(range(nsteps)), float)
         self.values = np.zeros(nsteps, float)
         self.coords = np.zeros([nsteps, len(numbers), 3], float)
         self.active = True
@@ -122,7 +124,7 @@ def plot(self, ai, ffrefs=[], valence=None, fn=None, eunit='kjmol', suffix=''):
                 when fn is specified.
         '''
         import matplotlib.pyplot as pp
-        if 'active' in self.__dict__.keys() and not self.active: return
+        if 'active' in list(self.__dict__.keys()) and not self.active: return
         fig, ax = pp.subplots()
         def add_plot(xs, ys, prefix, kwargs):
             pars = fitpar(xs, ys, rcond=1e-6)
@@ -188,7 +190,7 @@ def to_xyz(self, fn=None):
             fn
                 a string defining the name of the output file
         '''
-        if 'active' in self.__dict__.keys() and not self.active: return
+        if 'active' in list(self.__dict__.keys()) and not self.active: return
         if fn is None:
             fn = 'trajectory-%s-%i.xyz' %(self.term.basename.replace('/', '-'),self.term.index)
         f = open(fn, 'w')
@@ -331,7 +333,7 @@ def generate(self, trajectory, remove_com=True):
                 log.dump('    Converged (value=%.3f, lagmult=%.3e)' %(strain.constrain_value,sol[3*natom]))
                 if remove_com:
                     com = (x.T*self.system0.masses.copy()).sum(axis=1)/self.system0.masses.sum()
-                    for i in xrange(natom):
+                    for i in range(natom):
                         x[i,:] -= com
                 trajectory.coords[iq,:,:] = x
             #delete flagged frames
@@ -377,7 +379,7 @@ def estimate(self, trajectory, ai, ffrefs=[], do_valence=False):
             term = trajectory.term
             index = term.index
             basename = term.basename
-            if 'active' in trajectory.__dict__.keys() and not trajectory.active:
+            if 'active' in list(trajectory.__dict__.keys()) and not trajectory.active:
                 log.dump('Trajectory of %s was deactivated: skipping' %(basename))
                 return
             qs = trajectory.values.copy()
@@ -403,7 +405,7 @@ def estimate(self, trajectory, ai, ffrefs=[], do_valence=False):
                 trajectory.rv = -pars[1]/(2.0*pars[0])
             else:
                 trajectory.fc = 0.0
-                trajectory.rv = qs[len(qs)/2]
+                trajectory.rv = qs[len(qs)//2]
                 log.dump('force constant of %s is zero: rest value set to middle value' %basename)
             #no negative rest values for all ics except dihedrals and bendcos
             if term.ics[0].kind not in [1,3,4,11]:
@@ -456,7 +458,7 @@ def __init__(self, system, term, other_terms, cart_penalty=1e-3*angstrom):
         #set the rest values to the equilibrium values
         strain.dlist.forward()
         strain.iclist.forward()
-        for iterm in xrange(strain.vlist.nv):
+        for iterm in range(strain.vlist.nv):
             vterm = strain.vlist.vtab[iterm]
             ic = strain.iclist.ictab[vterm['ic0']]
             vterm['par1'] = ic['value']
@@ -490,7 +492,7 @@ def gradient(self, X):
         grad[:self.ndof] = gstrain.reshape((-1,)) + X[self.ndof]*gconstraint.reshape((-1,))
         grad[self.ndof] = self.constrain_value - self.constrain_target
         #cartesian penalty, i.e. extra penalty for deviation w.r.t. cartesian equilibrium coords
-        indices = np.array([[3*i,3*i+1,3*i+2] for i in xrange(self.ndof/3) if i not in self.cons_ic_atindexes]).ravel()
+        indices = np.array([[3*i,3*i+1,3*i+2] for i in range(self.ndof//3) if i not in self.cons_ic_atindexes]).ravel()
         if len(indices)>0:
             grad[indices] += X[indices]/(self.ndof*self.cart_penalty**2)
         with log.section('PTGEN', 4, timer='PT Generate'):