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Red Hat Bugzilla – Attachment 1648700 Details for
Bug 1780849
Review Request: pymol - PyMOL Molecular Graphics System
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[patch]
pymol-python3.patch
pymol-python3.patch (text/plain), 12.05 KB, created by
Sergio Basto
on 2019-12-31 01:30:47 UTC
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hide
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Description:
pymol-python3.patch
Filename:
MIME Type:
Creator:
Sergio Basto
Created:
2019-12-31 01:30:47 UTC
Size:
12.05 KB
patch
obsolete
>diff -rup pymol-open-source-2.3.0.orig/test/headerTest.py pymol-open-source-2.3.0/test/headerTest.py >--- pymol-open-source-2.3.0.orig/test/headerTest.py 2019-02-11 14:08:10.000000000 +0000 >+++ pymol-open-source-2.3.0/test/headerTest.py 2019-12-31 00:58:56.747925023 +0000 >@@ -7,28 +7,28 @@ import os > if len(sys.argv)>1: > p = sys.argv[1:] > else: >- print "Usage: pymol -cq ./headerTest.py -- MTZTestDirectory" >+ print("Usage: pymol -cq ./headerTest.py -- MTZTestDirectory") > sys.exit(1) > > > for curPath in p: >- print "Processing MTZ files in path: '%s'" % curPath >+ print("Processing MTZ files in path: '%s'" % curPath) > > l = glob.glob(curPath + os.sep + "*.mtz") > > d = {} > > for mtzFile in l: >- print "Processing %s." % mtzFile >+ print("Processing %s." % mtzFile) > d[mtzFile] = headering.MTZHeader(mtzFile) > > for f in d: >- print "Columns for file '%s':" % f >+ print("Columns for file '%s':" % f) > pprint.pprint(d[f].getColumns()) >- print "" >+ print("") > > for f in d: >- print "Columns of type W ofr file '%s':" % f >+ print("Columns of type W ofr file '%s':" % f) > pprint.pprint(d[f].getColumnsOfType("W")) >- print "" >+ print("") > >diff -rup pymol-open-source-2.3.0.orig/test/inp/B01.py pymol-open-source-2.3.0/test/inp/B01.py >--- pymol-open-source-2.3.0.orig/test/inp/B01.py 2019-02-11 14:08:10.000000000 +0000 >+++ pymol-open-source-2.3.0/test/inp/B01.py 2019-12-31 01:05:14.326755274 +0000 >@@ -50,7 +50,7 @@ def load(): > try: > cmd.set("suspend_updates","1") > cmd.delete('pdb') >- print file,last1,last2,c,"of",l >+ print(file,last1,last2,c,"of",l) > last2 = last1 > last1 = file > cmd.load(file,'pdb') >diff -rup pymol-open-source-2.3.0.orig/test/inp/B02.py pymol-open-source-2.3.0/test/inp/B02.py >--- pymol-open-source-2.3.0.orig/test/inp/B02.py 2019-02-11 14:08:10.000000000 +0000 >+++ pymol-open-source-2.3.0/test/inp/B02.py 2019-12-31 01:06:50.254201459 +0000 >@@ -26,7 +26,7 @@ def load(): > # list.pop(0) > for file in list: > try: >- print file >+ print(file) > cmd.delete('pdb') > cmd.load(file,'pdb') > cmd.orient('pdb') >diff -rup pymol-open-source-2.3.0.orig/test/inp/B04.py pymol-open-source-2.3.0/test/inp/B04.py >--- pymol-open-source-2.3.0.orig/test/inp/B04.py 2019-02-11 14:08:10.000000000 +0000 >+++ pymol-open-source-2.3.0/test/inp/B04.py 2019-12-31 01:07:35.787938573 +0000 >@@ -42,15 +42,15 @@ def load(): > l=f.readlines() > f.close() > if len(l): >- print >+ print() > for a in l: >- print a, >+ print(a,) > # save it so we have something to look at... > os.system("/bin/cp -f %s %s_s"%(cmp_file,cmp_file)) > os.system("/bin/cp -f %s %s_s"%(ref_file,ref_file)) > os.system("/bin/cp -f %s %s_src"%(out_file,cmp_file)) > os.system("/bin/cp -f %s %s_src"%(file,ref_file)) >- print file >+ print(file) > else: > sys.__stdout__.write(".") > sys.__stdout__.flush() >diff -rup pymol-open-source-2.3.0.orig/test/inp/B06.py pymol-open-source-2.3.0/test/inp/B06.py >--- pymol-open-source-2.3.0.orig/test/inp/B06.py 2019-02-11 14:08:10.000000000 +0000 >+++ pymol-open-source-2.3.0/test/inp/B06.py 2019-12-31 01:00:00.870564958 +0000 >@@ -26,7 +26,7 @@ def load(): > # while list[0]!="pdb/f8/pdb1f8u": > # list.pop(0) > for file in list: >- print file >+ print(file) > cmd.delete('pdb') > cmd.load(file,'pdb') > cmd.orient('pdb') >diff -rup pymol-open-source-2.3.0.orig/test/inp/B07.py pymol-open-source-2.3.0/test/inp/B07.py >--- pymol-open-source-2.3.0.orig/test/inp/B07.py 2019-02-11 14:08:10.000000000 +0000 >+++ pymol-open-source-2.3.0/test/inp/B07.py 2019-12-31 01:08:26.179647638 +0000 >@@ -33,10 +33,10 @@ def load(): > idx = ch.insert_model(model) > > ch.pattern_orient_bonds(idx) >- print " %5d"%cmd.count_atoms(),"%5d"%len(ch.pattern_get_string(idx)), >+ print(" %5d"%cmd.count_atoms(),"%5d"%len(ch.pattern_get_string(idx)),) > ch.pattern_detect_chirality(idx) > pat = ch.pattern_get_string(idx) >- print "%5d"%len(pat),pat[0:22]+"..."+pat[-10:] >+ print("%5d"%len(pat),pat[0:22]+"..."+pat[-10:]) > > cmd.feedback('disable','symmetry objectmolecule executive','everything') > load() >diff -rup pymol-open-source-2.3.0.orig/test/inp/C1050fitting.py pymol-open-source-2.3.0/test/inp/C1050fitting.py >--- pymol-open-source-2.3.0.orig/test/inp/C1050fitting.py 2019-02-11 14:08:10.000000000 +0000 >+++ pymol-open-source-2.3.0/test/inp/C1050fitting.py 2019-12-31 01:09:57.017123219 +0000 >@@ -5,11 +5,11 @@ from pymol import cmd > > from random import random,seed > >-print "BEGIN-LOG" >+print("BEGIN-LOG") > > seed(123) > >-print "the 1st random number should be %8.3f\notherwise the rest of the test is meaningless...\n"%pymol.random() >+print("the 1st random number should be %8.3f\notherwise the rest of the test is meaningless...\n"%pymol.random()) > > pymol.random = random > >@@ -23,29 +23,29 @@ for a in xrange(1,11): > > > cmd.frame(1) >-print "%8.3f"%cmd.fit("ref","trg") >+print("%8.3f"%cmd.fit("ref","trg")) > > # asdf > > > for a in xrange(1,14): >- print a, >- print "%8.3f"%cmd.fit("ref and resi %d"%a,"trg"), >- print "%8.3f"%cmd.rms("ref","trg"), >- print "%8.3f"%cmd.rms_cur("ref","trg") >+ print(a,) >+ print("%8.3f"%cmd.fit("ref and resi %d"%a,"trg"),) >+ print("%8.3f"%cmd.rms("ref","trg"),) >+ print("%8.3f"%cmd.rms_cur("ref","trg")) > > cmd.frame(10) > >-print "%8.3f"%cmd.fit("ref","trg") >+print("%8.3f"%cmd.fit("ref","trg")) > for a in xrange(1,14): >- print a, >- print "%8.3f"%cmd.fit("ref and resi %d"%a,"trg"), >- print "%8.3f"%cmd.rms("ref","trg"), >- print "%8.3f"%cmd.rms_cur("ref","trg") >+ print(a,) >+ print("%8.3f"%cmd.fit("ref and resi %d"%a,"trg"),) >+ print("%8.3f"%cmd.rms("ref","trg"),) >+ print("%8.3f"%cmd.rms_cur("ref","trg")) > > > a = 1 >-print "%8.3f"%cmd.fit("ref","trg") >+print("%8.3f"%cmd.fit("ref","trg")) > for b in xrange(1,11): > cmd._dump_floats(cmd.intra_fit("trg and resi %d"%a,b)) > cmd._dump_floats(cmd.intra_rms("trg",b)) >@@ -56,7 +56,7 @@ cmd.do("intra_fit (trg and resi 1),10") > cmd.do("intra_rms (trg),10") > cmd.do("intra_rms_cur (trg),10") > >-print "END-LOG" >+print("END-LOG") > > > >diff -rup pymol-open-source-2.3.0.orig/test/inp/C1060controlling.py pymol-open-source-2.3.0/test/inp/C1060controlling.py >--- pymol-open-source-2.3.0.orig/test/inp/C1060controlling.py 2019-02-11 14:08:10.000000000 +0000 >+++ pymol-open-source-2.3.0/test/inp/C1060controlling.py 2019-12-31 01:12:25.376266687 +0000 >@@ -2,30 +2,30 @@ > > from pymol import cmd > >-print "BEGIN-LOG" >+print("BEGIN-LOG") > >-print cmd.set_key('F1',lambda :cmd.turn('x',10)) >-print cmd.set_key('F12',lambda :cmd.turn('x',10)) >+print(cmd.set_key('F1',lambda :cmd.turn('x',10))) >+print(cmd.set_key('F12',lambda :cmd.turn('x',10))) > >-print cmd.set_key('left',lambda :cmd.turn('x',10)) >-print cmd.set_key('right',lambda :cmd.turn('x',10)) >-print cmd.set_key('pgup',lambda :cmd.turn('x',10)) >-print cmd.set_key('pgdn',lambda :cmd.turn('x',10)) >-print cmd.set_key('home',lambda :cmd.turn('x',10)) >-print cmd.set_key('insert',lambda :cmd.turn('x',10)) >+print(cmd.set_key('left',lambda :cmd.turn('x',10))) >+print(cmd.set_key('right',lambda :cmd.turn('x',10))) >+print(cmd.set_key('pgup',lambda :cmd.turn('x',10))) >+print(cmd.set_key('pgdn',lambda :cmd.turn('x',10))) >+print(cmd.set_key('home',lambda :cmd.turn('x',10))) >+print(cmd.set_key('insert',lambda :cmd.turn('x',10))) > >-print cmd.set_key('ALT-A',lambda :cmd.turn('y',10)) >+print(cmd.set_key('ALT-A',lambda :cmd.turn('y',10))) > >-print cmd.set_key('CTRL-C',lambda :cmd.turn('z',10)) >+print(cmd.set_key('CTRL-C',lambda :cmd.turn('z',10))) > >-print cmd.set_key('SHFT-F1', lambda :cmd.turn('z',10)) >+print(cmd.set_key('SHFT-F1', lambda :cmd.turn('z',10))) > >-print cmd.set_key('ALT-F1', lambda :cmd.turn('y',10)) >+print(cmd.set_key('ALT-F1', lambda :cmd.turn('y',10))) > >-print cmd.set_key('CTRL-F8', lambda :cmd.move('x',1)) >+print(cmd.set_key('CTRL-F8', lambda :cmd.move('x',1))) > > >-print "END-LOG" >+print("END-LOG") > > > >diff -rup pymol-open-source-2.3.0.orig/test/inp/C1100do.py pymol-open-source-2.3.0/test/inp/C1100do.py >--- pymol-open-source-2.3.0.orig/test/inp/C1100do.py 2019-02-11 14:08:10.000000000 +0000 >+++ pymol-open-source-2.3.0/test/inp/C1100do.py 2019-12-31 01:12:44.051158878 +0000 >@@ -2,7 +2,7 @@ > > from pymol import cmd > >-print "BEGIN-LOG" >+print("BEGIN-LOG") > > cmd.do(""" > load dat/pept.pdb >@@ -27,16 +27,16 @@ cmd.do('ray') > > # see if when can embed Python blocks inside of PyMOL inside of Python > >-cmd.do('for a in range(1,10):\\\n print a\\\n print a+10') >+cmd.do('for a in range(1,10):\\\n print (a)\\\n print (a+10)') > > cmd.do(r""" > for a in range(11,21):\ >- print a\ >- print a+10 >+ print (a)\ >+ print (a+10) > """) > > >-print "END-LOG" >+print("END-LOG") > > > >diff -rup pymol-open-source-2.3.0.orig/test/inp/C2000returns.py pymol-open-source-2.3.0/test/inp/C2000returns.py >--- pymol-open-source-2.3.0.orig/test/inp/C2000returns.py 2019-02-11 14:08:10.000000000 +0000 >+++ pymol-open-source-2.3.0/test/inp/C2000returns.py 2019-12-31 01:14:11.048656595 +0000 >@@ -1,6 +1,6 @@ > # -c > >-print "BEGIN-LOG" >+print("BEGIN-LOG") > > import pymol > from pymol import cmd >@@ -8,18 +8,18 @@ from pymol import cmd > # need to do this for all supported file types because the load routines diverge... > > def x(st): >- print st >+ print(st) > cmd.set("raise_exceptions",0) > valu = eval(st) >- print valu >+ print(valu) > if cmd.is_error(valu): > cmd.set("raise_exceptions",1) > try: >- print eval(st) >+ print(eval(st)) > except pymol.CmdException: >- print "CmdException raised." >+ print("CmdException raised.") > except cmd.QuietException: >- print "QuietException raised." >+ print("QuietException raised.") > > map(x,[ > 'cmd.load("dat/pept.pdb")' , >@@ -55,12 +55,12 @@ map(x,[ > cmd.delete("all") > cmd.load("dat/pept.pdb") > mdl = cmd.get_model("pept") >-print mdl.__class__ >-print len(mdl.atom) >+print(mdl.__class__) >+print(len(mdl.atom)) > > mdl = cmd.get_model("none") >-print mdl.__class__ >-print len(mdl.atom) >+print(mdl.__class__) >+print(len(mdl.atom)) > > map( x, [ > 'cmd.get_model("nonexistent")', >@@ -119,7 +119,7 @@ map( x, [ > > > >-print "END-LOG" >+print("END-LOG") > > TODO=""" > >diff -rup pymol-open-source-2.3.0.orig/test/inp/T04.py pymol-open-source-2.3.0/test/inp/T04.py >--- pymol-open-source-2.3.0.orig/test/inp/T04.py 2019-02-11 14:08:10.000000000 +0000 >+++ pymol-open-source-2.3.0/test/inp/T04.py 2019-12-31 01:00:30.116396114 +0000 >@@ -34,7 +34,7 @@ def centers(): > cmd.center("(resi %d)"%resi) > time.sleep(random.random()*0.30) > except: >- print "exception" >+ print("exception") > > t = threading.Thread(target=centers) > t.setDaemon(1) >@@ -146,7 +146,7 @@ def carts(): > time.sleep(random.random()*0.03) > > except: >- print "exception" >+ print("exception") > > t = threading.Thread(target=carts) > t.setDaemon(1) >diff -rup pymol-open-source-2.3.0.orig/test/win.py pymol-open-source-2.3.0/test/win.py >--- pymol-open-source-2.3.0.orig/test/win.py 2019-02-11 14:08:10.000000000 +0000 >+++ pymol-open-source-2.3.0/test/win.py 2019-12-31 01:15:21.879273187 +0000 >@@ -58,10 +58,10 @@ for test in tests: > tst = re.sub(r".*/|.*\\","",ifil) # get exact test name without suffix > tst = re.sub(r"\..*","",tst) > >- print " run_tests: "+tst+"..." >+ print(" run_tests: "+tst+"...") > > syscmd = cmmd+" -x -d pwd "+opt+" "+ifil+" > tmp.txt 2>&1" >- print syscmd >+ print(syscmd) > #os.system("c:\\pymolws\\pymol.exe") > os.system(syscmd) > # generate log file >@@ -94,10 +94,10 @@ for test in tests: > if (not lf) and not (lg): > break > if string.strip(lf)!=string.strip(lg): >- print "<",lf >- print ">",lg >+ print("<",lf) >+ print(">",lg) > >-print "done" >+print("done") > time.sleep(360) > > #
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bug 1780849
: 1648700