Output performed with loggers. Adds options --no-print.

Tests/pdb/1HPX-warn.pdb

@@ -0,0 +1,18 @@
+ATOM      1  N   PRO A   1      12.435  14.677  30.369  1.00 35.93           N
+ATOM      2  CA  PRO A   1      11.739  15.379  29.269  1.00 34.94           C  
+ATOM      2  CA  PRO A   1      11.739  15.379  29.269  1.00 34.94           C
+ATOM      3  C   PRO A   1      10.309  14.853  29.143  1.00 32.24           C
+ATOM      4  O   PRO A   1      10.035  13.743  29.578  1.00 32.11           O  
+ATOM      5  CB  PRO A   1      12.566  15.121  27.988  1.00 34.34           C  
+ATOM      6  CG  PRO A   1      13.973  14.970  28.518  1.00 35.36           C  
+ATOM      7  CD  PRO A   1      13.768  14.261  29.859  1.00 35.14           C  
+ATOM      8  N   GLN A   2       9.436  15.666  28.552  1.00 29.85           N  
+ATOM      9  CA  GLN A   2       8.117  15.184  28.193  1.00 29.27           C  
+ATOM     10  C   GLN A   2       7.939  15.392  26.711  1.00 28.61           C  
+ATOM     11  O   GLN A   2       8.147  16.506  26.246  1.00 31.02           O  
+ATOM     12  CB  GLN A   2       7.108  15.981  28.932  1.00 28.24           C  
+ATOM     13  CG  GLN A   2       5.789  15.599  28.365  1.00 32.41           C  
+ATOM     14  CD  GLN A   2       4.735  16.247  29.153  1.00 37.59           C  
+ATOM     15  OE1 GLN A   2       4.403  15.796  30.243  1.00 39.05           O  
+ATOM     16  NE2 GLN A   2       4.210  17.303  28.540  1.00 39.28           N  
+END

Tests/results/1HPX-warn.dat

@@ -0,0 +1 @@
+ 7.95

Tests/results/3SGB-subset.dat

@@ -0,0 +1,2 @@
+    3.51 
+   12.80

Tests/results/3SGB.dat

@@ -0,0 +1,57 @@
+    3.21
+    4.29
+    3.47
+    3.85
+    4.22
+    4.59
+    3.55
+    2.61
+    4.48
+    5.27
+    4.26
+    5.11
+    4.60
+    3.63
+    3.24
+    8.04
+    6.15
+    7.14
+   99.99
+   99.99
+   99.99
+   99.99
+   99.99
+   99.99
+   99.99
+   99.99
+   99.99
+   99.99
+   10.27
+   10.00
+   10.33
+   10.82
+   13.96
+   13.90
+   10.28
+   10.96
+   12.23
+   12.62
+   10.25
+   10.52
+   12.31
+    9.50
+   10.92
+   10.35
+   10.44
+   10.67
+   11.74
+   12.84
+   11.95
+   12.36
+   11.05
+   12.89
+   12.19
+   12.17
+   12.16
+    7.38
+    7.56

Tests/runtest.py

@@ -17,6 +17,7 @@
             ('4DFR', []),
             ('3SGB', []),
             ('3SGB-subset', ['--titrate_only', 'E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139']),
+            ('1HPX-warn', ['--quiet']),
            ]
 
     for pdb, args in pdbs:

propka/bonds.py

@@ -5,6 +5,7 @@
 import pickle,sys,os,math,propka.calculations
 
 import pkg_resources
+from propka.lib import info, warning
 
 class bondmaker:
     def __init__(self):
@@ -111,14 +112,14 @@ def find_bonds_for_protein(self, protein):
         """ Finds bonds proteins based on the way atoms
         normally bond in proteins"""
 
-        print('++++ Side chains ++++')
+        info('++++ Side chains ++++')
         # side chains
         for chain in protein.chains:
             for residue in chain.residues:
                 if residue.resName.replace(' ','') not in ['N+','C-']:
                     self.find_bonds_for_side_chain(residue.atoms)
 
-        print('++++ Backbones ++++')
+        info('++++ Backbones ++++')
         # backbone
         last_residues = []
         for chain in protein.chains:
@@ -128,12 +129,12 @@ def find_bonds_for_protein(self, protein):
                         self.connect_backbone(chain.residues[i-1], chain.residues[i])
                         last_residues.append(chain.residues[i])
 
-        print('++++ terminal oxygen ++++')
+        info('++++ terminal oxygen ++++')
         # terminal OXT
         for last_residue in last_residues:
             self.find_bonds_for_terminal_oxygen(last_residue)
 
-        print('++++ cysteines ++++')
+        info('++++ cysteines ++++')
         # Cysteines
         for chain in protein.chains:
             for i in range(0,len(chain.residues)):
@@ -349,9 +350,9 @@ def find_bonds_for_atoms_using_boxes(self, atoms):
         ylen = ymax-ymin
         zlen = zmax-zmin
 
-        #print('x range: [%6.2f;%6.2f] %6.2f'%(xmin,xmax,xlen))
-        #print('y range: [%6.2f;%6.2f] %6.2f'%(ymin,ymax,ylen))
-        #print('z range: [%6.2f;%6.2f] %6.2f'%(zmin,zmax,zlen))
+        #info('x range: [%6.2f;%6.2f] %6.2f'%(xmin,xmax,xlen))
+        #info('y range: [%6.2f;%6.2f] %6.2f'%(ymin,ymax,ylen))
+        #info('z range: [%6.2f;%6.2f] %6.2f'%(zmin,zmax,zlen))
 
         # how many boxes do we need in each dimension?
         # NOTE: math.ceil() returns an int in python3 and a float in
@@ -361,9 +362,9 @@ def find_bonds_for_atoms_using_boxes(self, atoms):
         self.no_box_y = max(1, int(math.ceil(ylen/box_size)))
         self.no_box_z = max(1, int(math.ceil(zlen/box_size)))
 
-        #print('No. box x: %6.2f'%self.no_box_x)
-        #print('No. box y: %6.2f'%self.no_box_y)
-        #print('No. box z: %6.2f'%self.no_box_z)
+        #info('No. box x: %6.2f'%self.no_box_x)
+        #info('No. box y: %6.2f'%self.no_box_y)
+        #info('No. box z: %6.2f'%self.no_box_z)
 
         # initialize boxes
         self.boxes = {}
@@ -400,7 +401,7 @@ def put_atom_in_box(self,x,y,z,atom):
                         # No box exists for this coordinate
                         pass
 
-                        #print(atom,'->',key,':',len(self.boxes[key]))
+                        #info(atom,'->',key,':',len(self.boxes[key]))
 
         return
 
@@ -415,7 +416,7 @@ def make_bond(self, atom1, atom2):
         if atom1 == atom2:
             return
 
-        #print('making bond for',atom1,atom2)
+        #info('making bond for',atom1,atom2)
         if not atom1 in atom2.bonded_atoms:
             atom2.bonded_atoms.append(atom1)
 
@@ -465,12 +466,12 @@ def generate_protein_bond_dictionary(self, atoms):
     import protein, pdb, sys,os
     arguments = sys.argv
     if len(arguments) != 2:
-        print('Usage: bonds.py <pdb_file>')
+        info('Usage: bonds.py <pdb_file>')
         sys.exit(0)
 
     filename = arguments[1]
     if not os.path.isfile(filename):
-        print('Error: Could not find \"%s\"'%filename)
+        info('Error: Could not find \"%s\"' % filename)
         sys.exit(1)
 
     pdblist = pdb.readPDB(filename)

propka/calculations.py

@@ -3,6 +3,7 @@
 from __future__ import print_function
 
 import math, propka.protonate, propka.bonds,copy, sys
+from propka.lib import info, warning
 
 
 #
@@ -60,7 +61,7 @@ def setup_bonding_and_protonation_30_style(parameters, molecular_container):
 
 def protonate_30_style(molecular_container):
     for name in molecular_container.conformation_names:
-        print('Now protonating',name)
+        info('Now protonating', name)
         # split atom into residues
         curres = -1000000
         residue = []
@@ -96,7 +97,7 @@ def addArgHydrogen(residue):
     """
     Adds Arg hydrogen atoms to residues according to the 'old way'.
     """
-    #print('Adding arg H',residue)
+    #info('Adding arg H',residue)
     for atom in residue:
         if   atom.name == "CD":
             CD  = atom
@@ -159,7 +160,7 @@ def addTrpHydrogen(residue):
             CE  = atom
     if CD == None or NE == None or CE == None:
         str = "Did not find all atoms in %s%4d - in %s" % (self.resName, self.resNumb, "addTrpHydrogen()")
-        print(str)
+        info(str)
         sys.exit(0)
 
     HE = protonateSP2([CD, NE, CE])
@@ -184,7 +185,7 @@ def addAmdHydrogen(residue):
 
     if C == None or O == None or N == None:
         str = "Did not find N, C and/or O in %s%4d - in %s" % (atom.resName, atom.resNumb, "addAmdHydrogen()")
-        print(str)
+        info(str)
         sys.exit(0)
 
     H1 = protonateDirection([N, O, C])
@@ -387,7 +388,7 @@ def radial_volume_desolvation(parameters, group):
 
 
 
-    #print('%s %5.2f %5.2f %4d'%(group, group.buried, group.Emass, group.Nmass))
+    #info('%s %5.2f %5.2f %4d'%(group, group.buried, group.Emass, group.Nmass))
     return
 
 
@@ -573,7 +574,7 @@ def hydrogen_bond_interaction(group1, group2, version):
     [closest_atom1, distance, closest_atom2] = propka.calculations.get_smallest_distance(atoms1, atoms2)
 
     if None in [closest_atom1, closest_atom2]:
-        print('Warning: Side chain interaction failed for %s and %s'%(group1.label, group2.label))
+        warning('Side chain interaction failed for %s and %s' % (group1.label, group2.label))
         return None
 
     # get the parameters
@@ -627,17 +628,17 @@ def hydrogen_bond_interaction(group1, group2, version):
     #exception = False # circumventing exception
     if exception == True:
         """ do nothing, value should have been assigned """
-            #print(" exception for %s %s %6.2lf" % (group1.label, group2.label, value))
+            #info(" exception for %s %s %6.2lf" % (group1.label, group2.label, value))
     else:
         value = version.calculateSideChainEnergy(distance, dpka_max, cutoff, weight, f_angle)
 
-    # print('distance',distance)
-    # print('dpka_max',dpka_max)
-    # print('cutoff',cutoff)
-    # print('f_angle',f_angle)
-    # print('weight',weight)
-    # print('value',value)
-    # print('===============================================')
+    # info('distance',distance)
+    # info('dpka_max',dpka_max)
+    # info('cutoff',cutoff)
+    # info('f_angle',f_angle)
+    # info('weight',weight)
+    # info('value',value)
+    # info('===============================================')
 
     return value
 
@@ -786,7 +787,7 @@ def checkCooArgException(group_coo, group_arg, version):
     #cutoff   = parameters.sidechain_cutoffs.get_value(group_coo.type,group_arg.type)
 
     # needs to be this way since you want to find shortest distance first
-    #print("--- exception for %s %s ---" % (group_coo.label, group_arg.label))
+    #info("--- exception for %s %s ---" % (group_coo.label, group_arg.label))
     atoms_coo = []
     atoms_coo.extend(group_coo.get_interaction_atoms(group_arg))
     atoms_arg = []
@@ -804,7 +805,7 @@ def checkCooArgException(group_coo, group_arg, version):
             distance, f_angle, nada = AngleFactorX(closest_coo_atom, closest_arg_atom, atom3)
 
         value = HydrogenBondEnergy(distance, dpka_max, cutoff, f_angle)
-        #print(iter, closest_coo_atom, closest_arg_atom,distance,value)
+        #info(iter, closest_coo_atom, closest_arg_atom,distance,value)
         value_tot += value
         # remove closest atoms before we attemp to find the runner-up pair
         atoms_coo.remove(closest_coo_atom)

propka/conformation_container.py

@@ -6,6 +6,7 @@
 from __future__ import print_function
 
 import propka.group, propka.determinants, propka.determinant, propka.ligand, propka.output, propka.coupled_groups, functools
+from propka.lib import info, warning
 
 class Conformation_container:
     def __init__(self, name='', parameters=None, molecular_container=None):
@@ -50,7 +51,7 @@ def additional_setup_when_reading_input_file(self):
         map = propka.output.make_interaction_map('Covalent coupling map for %s'%self,
                                                  self.get_covalently_coupled_groups(),
                                                  lambda g1,g2: g1 in g2.covalently_coupled_groups)
-        print(map)
+        info(map)
 
         # check if we should set a common charge centre as well
         if self.parameters.common_charge_centre:
@@ -96,7 +97,7 @@ def find_covalently_coupled_groups(self):
                                                  #self.get_titratable_groups(),
                                                  self.get_covalently_coupled_groups(),
                                                  lambda g1,g2: g1 in g2.covalently_coupled_groups)
-        print(map)
+        info(map)
 
 
         return
@@ -168,7 +169,7 @@ def init_group(self, group):
     #
 
     def calculate_pka(self, version, options):
-        print('\nCalculating pKas for',self)
+        info('\nCalculating pKas for', self)
 
         # calculate desolvation
         for group in self.get_titratable_groups()+self.get_ions():
@@ -193,7 +194,7 @@ def calculate_pka(self, version, options):
         penalised_labels = self.coupling_effects()
 
         if self.parameters.remove_penalised_group and len(penalised_labels)>0:
-            print('Removing penalised groups!!!')
+            info('Removing penalised groups!!!')
 
             for g in self.get_titratable_groups():
                 g.remove_determinants(penalised_labels)
@@ -297,7 +298,7 @@ def get_a_coupled_system_of_groups(self, new_group, coupled_groups, get_coupled_
     def calculate_folding_energy(self, pH=None, reference=None):
         ddg = 0.0
         for group in self.groups:
-            #print('Folding energy for %s at pH %f: %f'%(group,pH,group.calculate_folding_energy(self.parameters, pH=pH, reference=reference)))
+            #info('Folding energy for %s at pH %f: %f'%(group,pH,group.calculate_folding_energy(self.parameters, pH=pH, reference=reference)))
             ddg += group.calculate_folding_energy(self.parameters, pH=pH, reference=reference)
 
         return ddg
@@ -379,7 +380,7 @@ def get_chain(self,chain):
 
 
     def add_atom(self, atom):
-        #print(self,'adding',atom)
+        #info(self,'adding',atom)
         self.atoms.append(atom)
         if not atom.conformation_container:
             atom.conformation_container = self
@@ -446,5 +447,5 @@ def sort_atoms_key(self, atom):
         key += atom.resNumb*1000
         if len(atom.name) > len(atom.element):
             key += ord(atom.name[len(atom.element)])
-            #print(atom,ord(atom.name[len(atom.element)]), '|%s||%s|'%(atom.name,atom.element))
+            #info(atom,ord(atom.name[len(atom.element)]), '|%s||%s|'%(atom.name,atom.element))
         return key