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debian/patches/2to3.patch
View file @ 382cbb2c
......@@ -8632,6 +8632,17 @@ Last-Update: Thu, 12 Dec 2019 15:41:47 +0100
sys.exit(2)
# Print the PQR file
@@ -765,8 +765,8 @@ Please cite your use of PDB2PQR as:
size = psize.Psize()
size.parseInput(outpath)
size.runPsize(outpath)
- async = 0 # No async files here!
- input = inputgen.Input(outpath, size, method, async, potdx=True)
+ async_files = 0 # No async files here!
+ input = inputgen.Input(outpath, size, method, async_files, potdx=True)
input.printInputFiles()
input.dumpPickle()
--- a/main_cgi.py
+++ b/main_cgi.py
@@ -53,7 +53,7 @@ import time
......@@ -8876,6 +8887,17 @@ Last-Update: Thu, 12 Dec 2019 15:41:47 +0100
sys.exit()
else:
currentdir = os.getcwd()
@@ -620,8 +620,8 @@ def handleNonOpal(weboptions):
size = psize.Psize()
size.parseInput(pqrpath)
size.runPsize(pqrpath)
- async = 0 # No async files here!
- myinput = inputgen.Input(pqrpath, size, method, async, potdx=True)
+ async_files = 0 # No async files here!
+ myinput = inputgen.Input(pqrpath, size, method, async_files, potdx=True)
myinput.printInputFiles()
myinput.dumpPickle()
@@ -646,10 +646,10 @@ def handleNonOpal(weboptions):
#TODO: Better error reporting.
......@@ -8899,6 +8921,13 @@ Last-Update: Thu, 12 Dec 2019 15:41:47 +0100
import cgi
import cgitb
@@ -676,4 +676,4 @@ def mainCGI():
handleNonOpal(weboptions)
return
-
\ No newline at end of file
+
--- a/pdb2pka/NEWligand_topology.py
+++ b/pdb2pka/NEWligand_topology.py
@@ -7,13 +7,13 @@
......@@ -9618,6 +9647,15 @@ Last-Update: Thu, 12 Dec 2019 15:41:47 +0100
extent[axis]=minmax[axis][1]-minmax[axis][0]
center[axis]=extent[axis]/2.0+minmax[axis][0]
return center,extent
@@ -138,7 +138,7 @@ class inputGen:
#
# Not a known type
#
- raise 'unknown type',type
+ raise Exception('unknown type')
return
def getText_sub(self):
--- a/pdb2pka/ligand_topology.py
+++ b/pdb2pka/ligand_topology.py
@@ -9,7 +9,7 @@ except:
......@@ -10013,7 +10051,7 @@ Last-Update: Thu, 12 Dec 2019 15:41:47 +0100
else:
# Yes - nothing to do
pass
@@ -378,7 +378,7 @@ class ligand_charge_handler(MOL2MOLECULE
@@ -378,10 +378,10 @@ class ligand_charge_handler(MOL2MOLECULE
for at in residue.atoms: # WAS: self.lAtoms:
ele = at.sybylType.split('.')[0]
charge = at.charge
......@@ -10021,7 +10059,11 @@ Last-Update: Thu, 12 Dec 2019 15:41:47 +0100
+ if ele in ParseRadiiDict:
radius = ParseRadiiDict[ele]
else:
raise 'Please check ParseRadiiDict in ligff.py -- radius data not found for',ele
- raise 'Please check ParseRadiiDict in ligff.py -- radius data not found for',ele
+ raise Exception('Please check ParseRadiiDict in ligff.py -- radius data not found for %s' % ele)
#
# Store the radii and charges
#
--- a/pdb2pka/ligandclean/peoe_PDB2PQR.py
+++ b/pdb2pka/ligandclean/peoe_PDB2PQR.py
@@ -67,7 +67,7 @@ Chargeterms = {
......@@ -10033,12 +10075,14 @@ Last-Update: Thu, 12 Dec 2019 15:41:47 +0100
Chargeterms.update(ChargetermsLower)
def PEOE( atoms, damp=0.778, k=1.56):
@@ -88,8 +88,8 @@ def PEOE( atoms, damp=0.778, k=1.56):
@@ -87,9 +87,9 @@ def PEOE( atoms, damp=0.778, k=1.56):
abs_qges = 0.0
counter = 0
for a in atoms.atoms:
sybylType = a.sybylType.lower()
- sybylType = a.sybylType.lower()
- if not Chargeterms.has_key(sybylType):
- raise KeyError, 'PEOE Error: Atomtype <%s> not known, treating atom %s as dummy' % (a.sybylType, a.name)
+ sybylType = a.sybylType.lower()
+ if sybylType not in Chargeterms:
+ raise KeyError('PEOE Error: Atomtype <%s> not known, treating atom %s as dummy' % (a.sybylType, a.name))
if a.sybylType == 'O.3':
......@@ -10055,7 +10099,7 @@ Last-Update: Thu, 12 Dec 2019 15:41:47 +0100
class pKaIO:
@@ -95,7 +95,7 @@ class pKaIO:
@@ -95,10 +95,10 @@ class pKaIO:
filename=self.pkafile
import string
if not filename:
......@@ -10063,7 +10107,20 @@ Last-Update: Thu, 12 Dec 2019 15:41:47 +0100
+ print(filename,'is not a filename')
os._exit(0)
if not os.path.isfile(filename):
raise 'File does not exist:',filename
- raise 'File does not exist:',filename
+ raise Exception('File does not exist: %s' % filename)
fd=open(filename)
lines=fd.readlines()
fd.close()
@@ -112,7 +112,7 @@ class pKaIO:
else:
raise ValueError('Unknown format')
if string.lower(string.strip(lines[1]))!=string.lower('Format 1.0'):
- raise 'unknown format: ',lines[1]
+ raise Exception('unknown format: %s' % lines[1])
# Next line is text
linenumber=3
pKa={}
@@ -246,13 +246,13 @@ class pKaIO:
fd.write('%s pKa File\n' %format)
fd.write('Format 1.0\n')
......@@ -10089,6 +10146,27 @@ Last-Update: Thu, 12 Dec 2019 15:41:47 +0100
this_data=data[group]
fd.write('%15s %7.4f %7.4f %7.4f %7.4f %7.4f %7.4f \n' %(self.WI_res_text(group,format),
this_data['pKa'],
@@ -295,7 +295,7 @@ class pKaIO:
filename=self.titcurvfile
import string
if not os.path.isfile(filename):
- raise 'File does not exist:',filename
+ raise Exception('File does not exist: %s' % filename)
fd=open(filename)
lines=fd.readlines()
fd.close()
@@ -307,9 +307,9 @@ class pKaIO:
elif string.lower(string.strip(lines[0]))==string.lower('pdb2pka Titration Curve File'):
format='pdb2pka'
else:
- raise 'Unknown format'
+ raise Exception('Unknown format')
if string.lower(string.strip(lines[1]))!=string.lower('Format 1.0'):
- raise 'unknown format: ',lines[1]
+ raise Exception('unknown format: %s' % lines[1])
phvals=string.split(lines[2])
phstart=string.atof(phvals[0])
phend=string.atof(phvals[1])
@@ -361,27 +361,27 @@ class pKaIO:
#
# Extract some data from the dictionary
......@@ -10105,9 +10183,10 @@ Last-Update: Thu, 12 Dec 2019 15:41:47 +0100
if newpHvals!=phvals:
- print phvals
- print newpHvals
- raise 'Dictionary does not contain identical pH values'
+ print(phvals)
+ print(newpHvals)
raise 'Dictionary does not contain identical pH values'
+ raise Exception('Dictionary does not contain identical pH values')
#
# Check that a pKa value is in the pH values
#
......@@ -10140,6 +10219,41 @@ Last-Update: Thu, 12 Dec 2019 15:41:47 +0100
newresiduekeys.sort()
residues = []
for k in newresiduekeys:
@@ -439,11 +439,11 @@ class pKaIO:
if self.matrix_file:
filename=self.matrix_file
else:
- raise 'No matrix filename given'
+ raise Exception('No matrix filename given')
#
import os, string
if not os.path.isfile(filename):
- raise "File not found",filename
+ raise Exception("File not found %s" % filename)
fd=open(filename)
lines=fd.readlines()
fd.close()
@@ -459,9 +459,9 @@ class pKaIO:
elif string.lower(string.strip(lines[0]))==string.lower('pdb2pka Interaction Matrix File'):
format='WHAT IF'
else:
- raise 'Unknown format'
+ raise Exception('Unknown format')
if not string.strip(lines[1])=='Format 1.0':
- raise 'Wrong format',lines[1]
+ raise Exception('Wrong format %s' % lines[1])
x=1
done=None
partners=None
@@ -500,7 +500,7 @@ class pKaIO:
partners=np
else:
if partners!=np:
- raise 'Number of partners changes:',np
+ raise Exception('Number of partners changes: %s' % np)
self.matrix[resid]={}
#
# Now read all the interactions with the partners
@@ -577,7 +577,7 @@ class pKaIO:
fd=open(filename,'w')
fd.write('%s Interaction Matrix File\n' %format)
......@@ -10251,6 +10365,23 @@ Last-Update: Thu, 12 Dec 2019 15:41:47 +0100
fd.write('%s %7.4f\n' %(self.WI_res_text('T'+group2,format),self.matrix[group]['T'+group2][0]))
fd.write('%7.4f\n%7.4f\n%7.4f\n'%(self.matrix[group]['T'+group2][1],self.matrix[group]['T'+group2][2],self.matrix[group]['T'+group2][3]))
written['T'+group2]=1
@@ -706,14 +706,14 @@ class pKaIO:
if self.desolv_file:
filename=self.desolv_file
else:
- raise 'No desolv filename given'
+ raise Exception('No desolv filename given')
#
#
# This subroutine reads a DESOLV file
#
import os, string
if not os.path.isfile(filename):
- raise "File not found",filename
+ raise Exception("File not found %s" % filename)
fd=open(filename)
lines=fd.readlines()
fd.close()
@@ -729,7 +729,7 @@ class pKaIO:
elif string.strip(lines[0])=='pdb2pka Desolvation Energy File':
format='pdb2pka'
......@@ -10260,6 +10391,20 @@ Last-Update: Thu, 12 Dec 2019 15:41:47 +0100
#
# Call the generic read routine
#
@@ -748,11 +748,11 @@ class pKaIO:
if self.backgr_file:
filename=self.backgr_file
else:
- raise 'No matrix filename given'
+ raise Exception('No matrix filename given')
#
import os, string
if not os.path.isfile(filename):
- raise "File not found",filename
+ raise Exception("File not found %s" % filename)
fd=open(filename)
lines=fd.readlines()
fd.close()
@@ -768,7 +768,7 @@ class pKaIO:
elif string.strip(lines[0])=='pdb2pka Background Energy File':
format='pdb2pka'
......@@ -10558,9 +10703,12 @@ Last-Update: Thu, 12 Dec 2019 15:41:47 +0100
#
# Create the APBS input file
#
@@ -504,17 +504,17 @@ def pre_init(pdbfilename=None,
@@ -502,19 +502,19 @@ def pre_init(pdbfilename=None,
size=src.psize.Psize()
method=""
async=0
- async=0
+ #async=0
split=0
- import inputgen_pKa
+ from . import inputgen_pKa
......@@ -11433,6 +11581,15 @@ Last-Update: Thu, 12 Dec 2019 15:41:47 +0100
#
# Create the APBS input file
#
@@ -420,7 +420,7 @@ def pre_init(original_pdb_list=None,
size=src.psize.Psize()
method=""
- async=0
+ #async=0
split=0
igen = inputgen_pKa.inputGen(working_pdb_filename)
@@ -428,11 +428,11 @@ def pre_init(original_pdb_list=None,
# For convenience
#
......@@ -12853,7 +13010,7 @@ Last-Update: Thu, 12 Dec 2019 15:41:47 +0100
-import Source.lib as lib
-from Source.protein import Protein
+from . import Source.lib as lib
+from .Source import lib
+from .Source.protein import Protein
......@@ -12874,8 +13031,8 @@ Last-Update: Thu, 12 Dec 2019 15:41:47 +0100
-import Source.lib as lib
-from Source.protein import Protein
-from Source.mutate import makeCompositeAtomsDictionary
+from . import Source.version as propka
+from . import Source.lib as lib
+from .Source import version as propka
+from .Source import lib
+from .Source.protein import Protein
+from .Source.mutate import makeCompositeAtomsDictionary
......@@ -12897,8 +13054,8 @@ Last-Update: Thu, 12 Dec 2019 15:41:47 +0100
-import Source.lib as lib
-from Source.protein import Protein
-from Source.mutate import makeCompositeAtomsDictionary
+from . import Source.version as propka
+from . import Source.lib as lib
+from .Source import version as propka
+from .Source import lib
+from .Source.protein import Protein
+from .Source.mutate import makeCompositeAtomsDictionary
pka_print = lib.pka_print
......@@ -12921,11 +13078,11 @@ Last-Update: Thu, 12 Dec 2019 15:41:47 +0100
-from Source.protein import Protein
-from Source.pdb import readPDB
-import Source.version as propka
+from . import Source.lib as lib
+from . import Source.mutate as mutate
+from .Source import lib
+from .Source import mutate
+from .Source.protein import Protein
+from .Source.pdb import readPDB
+from . import Source.version as propka
+from .Source import version as propka
pka_print = lib.pka_print
......@@ -12943,7 +13100,7 @@ Last-Update: Thu, 12 Dec 2019 15:41:47 +0100
-import Source.lib as lib
-from Source.protein import Protein
+from . import Source.lib as lib
+from .Source import lib
+from .Source.protein import Protein
......@@ -14023,6 +14180,33 @@ Last-Update: Thu, 12 Dec 2019 15:41:47 +0100
class Elec:
"""
@@ -102,7 +102,7 @@ class Elec:
self.label = ""
self.nlev = 4
self.ofrac = 0.1
- self.async = 0
+ self.async_files = 0
self.asyncflag = asyncflag
self.cgcent = "mol 1"
self.fgcent = "mol 1"
@@ -152,7 +152,7 @@ class Elec:
text += " cgcent %s\n" % self.cgcent
text += " fgcent %s\n" % self.fgcent
if self.asyncflag == 1:
- text += " async %i\n" % self.async
+ text += " async %i\n" % self.async_files
text += " mol %i\n" % self.mol
if self.lpbe: text += " lpbe\n"
else: text += " npbe\n"
@@ -261,7 +261,7 @@ class Input:
outname = base_pqr_name + "-PE%i.in" % i
for elec in self.elecs:
elec.asyncflag = 1
- elec.async = i
+ elec.async_files = i
file = open(outname, "w")
file.write(str(self))
file.close()
@@ -368,7 +368,7 @@ def main():
try:
......@@ -14032,6 +14216,33 @@ Last-Update: Thu, 12 Dec 2019 15:41:47 +0100
sys.stderr.write("Option error (%s)!\n" % details)
usage()
@@ -380,7 +380,7 @@ def main():
method = ""
size = psize.Psize()
- async = 0
+ async_files = 0
split = 0
istrng = 0
potdx = 0
@@ -400,7 +400,7 @@ def main():
elif a == "async":
sys.stdout.write("Forcing an asynchronous calculation\n")
method = "mg-para"
- async = 1
+ async_files = 1
elif a == "manual":
sys.stdout.write("Forcing a manual calculation\n")
method = "mg-manual"
@@ -426,7 +426,7 @@ def main():
splitInput(filename)
else:
size.runPsize(filename)
- input = Input(filename, size, method, async, istrng, potdx)
+ input = Input(filename, size, method, async_files, istrng, potdx)
input.printInputFiles()
if __name__ == "__main__": main()
--- a/src/na.py
+++ b/src/na.py
@@ -49,7 +49,7 @@ __date__ = "28 February 2006"
......
debian/pdb2pqr.install
View file @ 382cbb2c
......@@ -11,5 +11,5 @@ pdb2pka/substruct/*.py usr/share/pdb2pqr/pdb2pka/substruct
pdb2pka/graph_cut/*.py usr/share/pdb2pqr/pdb2pka/graph_cut
propka30/* usr/share/pdb2pqr/propka30/
# Binary parts
pdb2pka/_pMC_mult.so usr/lib/pdb2pqr/pdb2pka
pdb2pka/substruct/Algorithms.so usr/lib/pdb2pqr/pdb2pka/substruct
pdb2pka/_pMC_mult*.so usr/lib/pdb2pqr/pdb2pka
pdb2pka/substruct/Algorithms*.so usr/lib/pdb2pqr/pdb2pka/substruct
debian/pdb2pqr.links
View file @ 382cbb2c
usr/lib/pdb2pqr/pdb2pka/_pMC_mult.so usr/share/pdb2pqr/pdb2pka/_pMC_mult.so
usr/lib/pdb2pqr/pdb2pka/substruct/Algorithms.so usr/share/pdb2pqr/pdb2pka/substruct/Algorithms.so
#usr/lib/pdb2pqr/pdb2pka/_pMC_mult.so usr/share/pdb2pqr/pdb2pka/_pMC_mult.so
#usr/lib/pdb2pqr/pdb2pka/substruct/Algorithms.so usr/share/pdb2pqr/pdb2pka/substruct/Algorithms.so
usr/share/pdb2pqr/pdb2pqr.py usr/bin/pdb2pqr
usr/share/pdb2pqr/propka30/propka.py usr/bin/propka
usr/share/pdb2pqr/src/psize.py usr/bin/psize
debian/rules
View file @ 382cbb2c
......@@ -46,6 +46,11 @@ override_dh_install-arch:
dos2unix debian/pdb2pqr/usr/share/pdb2pqr/propka30/propka.py
dos2unix debian/pdb2pqr/usr/share/pdb2pqr/src/psize.py
override_dh_link-arch:
dh_link -a
dh_link -a usr/lib/pdb2pqr/pdb2pka/$(shell basename `find . -name "_pMC_mult*.so"`) usr/share/pdb2pqr/pdb2pka/_pMC_mult.so
dh_link -a usr/lib/pdb2pqr/pdb2pka/substruct/$(shell basename `find . -name "Algorithms*.so"`) usr/share/pdb2pqr/pdb2pka/substruct/Algorithms.so
override_dh_fixperms-arch:
dh_fixperms -a
chmod 0644 debian/pdb2pqr/usr/share/pdb2pqr/main.py
......