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Output performed with loggers. Adds options --no-print. (#12)

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Output performed with loggers.  Adds --quiet and --verbose options.
This commit is contained in:
Toni G
2016-04-29 08:21:35 +02:00
committed by Matvey Adzhigirey
parent ca6224433a
commit 5fbbdd4868
23 changed files with 4987 additions and 217 deletions
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18
Tests/pdb/1HPX-warn.pdb Normal file
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@@ -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

2327
Tests/pdb/3SGB-subset.pdb Normal file
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2327
Tests/pdb/3SGB.pdb Normal file
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1
Tests/results/1HPX-warn.dat Normal file
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@@ -0,0 +1 @@
7.95

2
Tests/results/3SGB-subset.dat Normal file
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@@ -0,0 +1,2 @@
3.51
12.80

57
Tests/results/3SGB.dat Normal file
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@@ -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

1
Tests/runtest.py
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@@ -17,6 +17,7 @@ if __name__ == "__main__":
('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:

29
propka/bonds.py
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@@ -5,6 +5,7 @@ from __future__ import print_function
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 @@ class bondmaker:
""" 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 @@ class bondmaker:
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 @@ class bondmaker:
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 @@ class bondmaker:
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 @@ class bondmaker:
# 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 @@ class bondmaker:
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 @@ if __name__ == '__main__':
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)

33
propka/calculations.py
View File

@@ -3,6 +3,7 @@ from __future__ import division
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)

15
propka/conformation_container.py
View File

@@ -6,6 +6,7 @@ from __future__ import division
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 @@ class Conformation_container:
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 @@ class Conformation_container:
#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 @@ class Conformation_container:
#
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 @@ class Conformation_container:
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 @@ class Conformation_container:
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 @@ class Conformation_container:
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 @@ class Conformation_container:
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

45
propka/coupled_groups.py
View File

@@ -3,6 +3,7 @@ from __future__ import division
from __future__ import print_function
import math, propka.output, propka.group, propka.lib, itertools
from propka.lib import info, warning
class non_covalently_couple_groups:
@@ -129,22 +130,22 @@ class non_covalently_couple_groups:
self.parameters = conformation.parameters
if verbose:
print('')
print(' Warning: When using the -d option, pKa values based on \'swapped\' interactions')
print(' will be writting to the output .pka file')
print('')
print('-'*103)
print(' Detecting non-covalently coupled residues')
print('-'*103)
print(' Maximum pKa difference: %4.2f pKa units'%self.parameters.max_intrinsic_pKa_diff)
print(' Minimum interaction energy: %4.2f pKa units'%self.parameters.min_interaction_energy)
print(' Maximum free energy diff.: %4.2f pKa units'%self.parameters.max_free_energy_diff)
print(' Minimum swap pKa shift: %4.2f pKa units'%self.parameters.min_swap_pka_shift)
print(' pH: %6s ' %str(self.parameters.pH))
print(' Reference: %s' %self.parameters.reference)
print(' Min pKa: %4.2f'%self.parameters.min_pka)
print(' Max pKa: %4.2f'%self.parameters.max_pka)
print('')
info('')
info(' Warning: When using the -d option, pKa values based on \'swapped\' interactions')
info(' will be writting to the output .pka file')
info('')
info('-' * 103)
info(' Detecting non-covalently coupled residues')
info('-' * 103)
info(' Maximum pKa difference: %4.2f pKa units' % self.parameters.max_intrinsic_pKa_diff)
info(' Minimum interaction energy: %4.2f pKa units' % self.parameters.min_interaction_energy)
info(' Maximum free energy diff.: %4.2f pKa units' % self.parameters.max_free_energy_diff)
info(' Minimum swap pKa shift: %4.2f pKa units' % self.parameters.min_swap_pka_shift)
info(' pH: %6s ' % str(self.parameters.pH))
info(' Reference: %s' % self.parameters.reference)
info(' Min pKa: %4.2f' % self.parameters.min_pka)
info(' Max pKa: %4.2f' % self.parameters.max_pka)
info('')
# find coupled residues
titratable_groups = conformation.get_titratable_groups()
@@ -169,7 +170,7 @@ class non_covalently_couple_groups:
map = propka.output.make_interaction_map('Non-covalent coupling map for %s'%conformation,
conformation.get_non_covalently_coupled_groups(),
lambda g1,g2: g1 in g2.non_covalently_coupled_groups)
print(map)
info(map)
for system in conformation.get_coupled_systems(conformation.get_non_covalently_coupled_groups(),propka.group.Group.get_non_covalently_coupled_groups):
self.print_system(conformation, list(system))
@@ -177,7 +178,7 @@ class non_covalently_couple_groups:
def print_system(self, conformation, system):
print('System containing %d groups:'%len(system))
info('System containing %d groups:' % len(system))
# make list of interactions withi this system
interactions = list(itertools.combinations(system,2))
@@ -187,7 +188,7 @@ class non_covalently_couple_groups:
for interaction in interactions:
data = self.is_coupled_protonation_state_probability(interaction[0], interaction[1],conformation.calculate_folding_energy, return_on_fail=False)
coup_info += self.make_data_to_string(data,interaction[0],interaction[1])+'\n\n'
print(coup_info)
info(coup_info)
# make list of possible combinations of swap to try out
combinations = propka.lib.generate_combinations(interactions)
@@ -211,7 +212,7 @@ class non_covalently_couple_groups:
#for interaction in combination:
# self.swap_interactions([interaction[0]], [interaction[1]])
print(swap_info)
info(swap_info)
return
#
@@ -236,7 +237,7 @@ class non_covalently_couple_groups:
all_labels = [g.label for g in system]
s = ' '+'-'*113+'\n'
for group in system:
s += self.tagged_print(' %-8s|'%tag,group.getDeterminantString(), all_labels)
s += self.tagged_format(' %-8s|' % tag, group.getDeterminantString(), all_labels)
return s+'\n'
@@ -287,7 +288,7 @@ class non_covalently_couple_groups:
# Output methods
#
def tagged_print(self, tag, s, labels):
def tagged_format(self, tag, s, labels):
s = "%s %s"%(tag,s)
s = s.replace('\n','\n%s '%tag)
for label in labels:

61
propka/group.py
View File

@@ -6,6 +6,7 @@ from __future__ import division
from __future__ import print_function
import propka.ligand, propka.determinant, propka.ligand_pka_values, math, propka.protonate
from propka.lib import info, warning
my_protonator = propka.protonate.Protonate(verbose=False)
@@ -80,7 +81,7 @@ expected_atoms_base_interactions = {
class Group:
def __init__(self, atom):
#print('Made new %s group from %s'%(type,atom))
#info('Made new %s group from %s'%(type,atom))
self.atom = atom
self.type = ''
atom.group = self
@@ -349,7 +350,7 @@ class Group:
if self.residue_type in self.parameters.ions.keys():
self.charge = self.parameters.ions[self.residue_type]
#print('ION setup',self,self.residue_type, self.charge)
#info('ION setup',self,self.residue_type, self.charge)
# find the center and the interaction atoms
self.setup_atoms()
@@ -396,18 +397,18 @@ class Group:
ok = False
if not ok:
print('Warning: Missing atoms or failed protonation for %s (%s) -- please check the structure'%(self.label, self.type))
print(' %s'%self)
warning('Missing atoms or failed protonation for %s (%s) -- please check the structure' % (self.label, self.type))
warning('%s' % self)
Na = sum([expected_atoms_acid_interactions[self.type][e] for e in expected_atoms_acid_interactions[self.type].keys()])
Nb = sum([expected_atoms_base_interactions[self.type][e] for e in expected_atoms_base_interactions[self.type].keys()])
print(' Expected %d interaction atoms for acids, found:'%Na)
warning('Expected %d interaction atoms for acids, found:' % Na)
for i in range(len(self.interaction_atoms_for_acids)):
print(' %s'%self.interaction_atoms_for_acids[i])
warning(' %s' % self.interaction_atoms_for_acids[i])
print(' Expected %d interaction atoms for bases, found:'%Nb)
warning('Expected %d interaction atoms for bases, found:' % Nb)
for i in range(len(self.interaction_atoms_for_bases)):
print(' %s'%self.interaction_atoms_for_bases[i])
warning(' %s' % self.interaction_atoms_for_bases[i])
#return
@@ -648,7 +649,7 @@ class HIS_group(Group):
# Find the atoms in the histidine ring
ring_atoms = propka.ligand.is_ring_member(self.atom)
if len(ring_atoms) != 5:
print('Warning: His group does not seem to contain a ring',self)
warning('His group does not seem to contain a ring', self)
# protonate ring
for r in ring_atoms:
@@ -832,7 +833,7 @@ class NAR_group(Group):
Group.__init__(self,atom)
self.type = 'NAR'
self.residue_type = 'NAR'
print('Found NAR group:',atom)
info('Found NAR group:', atom)
return
@@ -855,7 +856,7 @@ class NAM_group(Group):
Group.__init__(self,atom)
self.type = 'NAM'
self.residue_type = 'NAM'
print('Found NAM group:',atom)
info('Found NAM group:', atom)
return
@@ -876,7 +877,7 @@ class F_group(Group):
Group.__init__(self,atom)
self.type = 'F'
self.residue_type = 'F'
print('Found F group:',atom)
info('Found F group:', atom)
return
class Cl_group(Group):
@@ -884,7 +885,7 @@ class Cl_group(Group):
Group.__init__(self,atom)
self.type = 'Cl'
self.residue_type = 'Cl'
print('Found Cl group:',atom)
info('Found Cl group:', atom)
return
class OH_group(Group):
@@ -892,7 +893,7 @@ class OH_group(Group):
Group.__init__(self,atom)
self.type = 'OH'
self.residue_type = 'OH'
print('Found OH group:',atom)
info('Found OH group:', atom)
return
@@ -911,7 +912,7 @@ class OP_group(Group):
Group.__init__(self,atom)
self.type = 'OP'
self.residue_type = 'OP'
print('Found OP group:',atom)
info('Found OP group:', atom)
return
@@ -932,7 +933,7 @@ class O3_group(Group):
Group.__init__(self,atom)
self.type = 'O3'
self.residue_type = 'O3'
print('Found O3 group:',atom)
info('Found O3 group:', atom)
return
@@ -941,7 +942,7 @@ class O2_group(Group):
Group.__init__(self,atom)
self.type = 'O2'
self.residue_type = 'O2'
print('Found O2 group:',atom)
info('Found O2 group:', atom)
return
class SH_group(Group):
@@ -949,7 +950,7 @@ class SH_group(Group):
Group.__init__(self,atom)
self.type = 'SH'
self.residue_type = 'SH'
print('Found SH group:',atom)
info('Found SH group:', atom)
return
@@ -959,7 +960,7 @@ class CG_group(Group):
Group.__init__(self,atom)
self.type = 'CG'
self.residue_type = 'CG'
print('Found CG group:',atom)
info('Found CG group:', atom)
return
def setup_atoms(self):
@@ -983,7 +984,7 @@ class C2N_group(Group):
Group.__init__(self,atom)
self.type = 'C2N'
self.residue_type = 'C2N'
print('Found C2N group:',atom)
info('Found C2N group:', atom)
return
def setup_atoms(self):
@@ -1007,7 +1008,7 @@ class OCO_group(Group):
Group.__init__(self,atom)
self.type = 'OCO'
self.residue_type = 'OCO'
print('Found OCO group:',atom)
info('Found OCO group:', atom)
return
def setup_atoms(self):
@@ -1026,7 +1027,7 @@ class N30_group(Group):
Group.__init__(self,atom)
self.type = 'N30'
self.residue_type = 'N30'
print('Found N30 group:',atom)
info('Found N30 group:', atom)
return
def setup_atoms(self):
@@ -1043,7 +1044,7 @@ class N31_group(Group):
Group.__init__(self,atom)
self.type = 'N31'
self.residue_type = 'N31'
print('Found N31 group:',atom)
info('Found N31 group:', atom)
return
def setup_atoms(self):
@@ -1060,7 +1061,7 @@ class N32_group(Group):
Group.__init__(self,atom)
self.type = 'N32'
self.residue_type = 'N32'
print('Found N32 group:',atom)
info('Found N32 group:', atom)
return
def setup_atoms(self):
@@ -1077,7 +1078,7 @@ class N33_group(Group):
Group.__init__(self,atom)
self.type = 'N33'
self.residue_type = 'N33'
print('Found N33 group:',atom)
info('Found N33 group:', atom)
return
def setup_atoms(self):
@@ -1094,7 +1095,7 @@ class NP1_group(Group):
Group.__init__(self,atom)
self.type = 'NP1'
self.residue_type = 'NP1'
print('Found NP1 group:',atom)
info('Found NP1 group:', atom)
return
@@ -1112,7 +1113,7 @@ class N1_group(Group):
Group.__init__(self,atom)
self.type = 'N1'
self.residue_type = 'N1'
print('Found N1 group:',atom)
info('Found N1 group:', atom)
return
@@ -1122,7 +1123,7 @@ class Ion_group(Group):
Group.__init__(self,atom)
self.type = 'ION'
self.residue_type = atom.resName.strip()
print('Found ion group:',atom)
info('Found ion group:', atom)
return
@@ -1131,7 +1132,7 @@ class non_titratable_ligand_group(Group):
Group.__init__(self, atom)
self.type = 'LG'
self.residue_type = 'LG'
# print('Non-titratable ligand group',atom)
# info('Non-titratable ligand group',atom)
return
class titratable_ligand_group(Group):
@@ -1153,7 +1154,7 @@ class titratable_ligand_group(Group):
# this is not true if we are reading an input file
if atom.marvin_pka:
self.model_pka = atom.marvin_pka
print('Titratable ligand group ',atom, self.model_pka, self.charge)
info('Titratable ligand group ', atom, self.model_pka, self.charge)
self.model_pka_set = True
return

15
propka/iterative.py
View File

@@ -7,6 +7,7 @@ import math, time
import propka.lib as lib
from propka.determinant import Determinant
import propka.calculations
from propka.lib import info, warning, debug
# Some library functions for the interative pKa determinants
@@ -186,8 +187,8 @@ def addDeterminants(iterative_interactions, version, options=None):
done_group.append(group)
# Initialize iterative scheme
if options.verbose == True:
print("\n --- pKa iterations (%d groups, %d interactions) ---" % ( len(iteratives), len(iterative_interactions) ))
debug("\n --- pKa iterations (%d groups, %d interactions) ---" %
(len(iteratives), len(iterative_interactions)))
converged = False
iteration = 0
# set non-iterative pka values as first step
@@ -246,30 +247,30 @@ def addDeterminants(iterative_interactions, version, options=None):
itres.pKa_iter.append(itres.pKa_new)
if iteration == 10:
print("did not converge in %d iterations" % (iteration))
info("did not converge in %d iterations" % (iteration))
break
# --- Iterations finished ---
# printing pKa iterations
if options.verbose == True:
# formerly was conditioned on if options.verbosity >= 2 - now unnecessary
str = "%12s" % (" ")
for index in range(0, iteration+1 ):
str += "%8d" % (index)
print(str)
debug(str)
for itres in iteratives:
str = "%s " % (itres.label)
for pKa in itres.pKa_iter:
str += "%8.2lf" % (pKa)
if itres.converged == False:
str += " *"
print(str)
debug(str)
# creating real determinants and adding them to group object
for itres in iteratives:
for type in ['sidechain','backbone','coulomb']:
for interaction in itres.determinants[type]:
#print('done',itres.group.label,interaction[0],interaction[1])
#info('done',itres.group.label,interaction[0],interaction[1])
value = interaction[1]
if value > 0.005 or value < -0.005:
g = interaction[0]

57
propka/lib.py
View File

@@ -1,9 +1,14 @@
from __future__ import division
from __future__ import print_function
import string, sys, copy, math, os
import sys
import pkg_resources
import logging
logger = logging.getLogger("propka")
stdout_handler = logging.StreamHandler(sys.stdout)
stdout_handler.setFormatter(logging.Formatter("%(message)s"))
logger.addHandler(stdout_handler)
#
# file I/O
@@ -132,7 +137,7 @@ def parse_res_string(res_str):
def loadOptions(*args):
"""
load the arguments parser with options
Load the arguments parser with options. Note that verbosity is set as soon as this function is invoked.
"""
from optparse import OptionParser
@@ -163,14 +168,10 @@ def loadOptions(*args):
help="specifying the sub-version of propka [Jan15/Dec19]")
parser.add_option("-p", "--parameters",dest="parameters", default=pkg_resources.resource_filename(__name__, "propka.cfg"),
help="set the parameter file [%default]")
parser.add_option("-z", "--verbose", dest="verbose", action="store_true", default=True,
help="sleep during calculations")
parser.add_option("-q", "--quiet", dest="verbose", action="store_false",
help="sleep during calculations")
parser.add_option("-s", "--silent", dest="verbose", action="store_false",
help="not activated yet")
parser.add_option("--verbosity", dest="verbosity", action="store_const",
help="level of printout - not activated yet")
parser.add_option("-z", "--verbose", dest="verbosity", action="store_const", const=2,
help="output debugging information")
parser.add_option("-q", "--quiet", dest="verbosity", action="store_const", const=0, default=1,
help="inhibit printing to stdout")
parser.add_option("-o", "--pH", dest="pH", type="float", default=7.0,
help="setting pH-value used in e.g. stability calculations [7.0]")
parser.add_option("-w", "--window", dest="window", nargs=3, type="float", default=(0.0, 14.0, 1.0),
@@ -204,9 +205,10 @@ def loadOptions(*args):
for filename in options.filenames:
args.append(filename)
# checking at early stage that there is at least one pdbfile to work with
# checking at early stage that there is at least one pdbfile to work with. The error message is misleading
# if one is using the python interface via Molecular_container.
if len(args) == 0:
print("Warning: no pdbfile provided")
info("No pdbfile provided")
#sys.exit(9)
# Convert titrate_only string to a list of (chain, resnum) items:
@@ -216,11 +218,22 @@ def loadOptions(*args):
try:
chain, resnum, inscode = parse_res_string(res_str)
except ValueError:
print('Invalid residue string: "%s"' % res_str)
logger.critical('Invalid residue string: "%s"' % res_str)
sys.exit(1)
res_list.append((chain, resnum, inscode))
options.titrate_only = res_list
# Set the no-print variable
if options.verbosity == 0:
logger.setLevel(logging.CRITICAL)
elif options.verbosity == 1:
logger.setLevel(logging.INFO)
elif options.verbosity == 2:
logger.setLevel(logging.DEBUG)
else:
logger.warning("Invalid verbosity level, using default")
# done!
return options, args
@@ -272,3 +285,19 @@ def writeFile(filename, lines):
f.close()
def _args_to_str(arg_list):
return " ".join(map(str, arg_list))
def info(*args):
"""Log a message. Level defaults to INFO unless overridden."""
logger.info(_args_to_str(args))
def debug(*args):
"""Log a message on the DEBUG level."""
logger.debug(_args_to_str(args))
def warning(*args):
"""Log a WARN message"""
logger.warning(_args_to_str(args))

9
propka/ligand.py
View File

@@ -7,6 +7,7 @@ import sys
import propka.calculations
from propka.vector_algebra import *
from propka.lib import info, warning
all_sybyl_types = [
@@ -150,7 +151,7 @@ max_C_triple_bond_squared = max_C_triple_bond*max_C_triple_bond
def assign_sybyl_type(atom):
# check if we already have assigned a name to this atom
if atom.sybyl_assigned:
#print(atom.name,'already assigned')
#info(atom.name,'already assigned')
return
# find some properties of the atom
@@ -331,7 +332,7 @@ def assign_sybyl_type(atom):
element = atom.element.capitalize()
set_type(atom,element)
# print('Using element as type for %s'%atom.element)
# info('Using element as type for %s'%atom.element)
return
@@ -362,7 +363,7 @@ def identify_ring(this_atom, original_atom, number, past_atoms):
def set_type(atom,type):
#print(atom, '->',type)
#info(atom, '->',type)
atom.sybyl_type = type
atom.sybyl_assigned=True
return
@@ -387,7 +388,7 @@ def are_atoms_planar(atoms):
margin = 0.20
for b in atoms[3:]:
v = vector(atom1=atoms[0], atom2=b).rescale(1.0)
#print(atoms[0],abs(v*n) )
#info(atoms[0],abs(v*n) )
if abs(v*n)>margin:
return False

29
propka/ligand_pka_values.py
View File

@@ -2,6 +2,7 @@
from __future__ import division
from __future__ import print_function
from propka.lib import info, warning
import propka.molecular_container, propka.calculations, propka.calculations, propka.parameters, propka.pdb, propka.lib, os, subprocess, sys
@@ -12,9 +13,9 @@ class ligand_pka_values:
# attempt to find Marvin executables in the path
self.molconvert = self.find_in_path('molconvert')
self.cxcalc = self.find_in_path('cxcalc')
print('Found Marvin executables:')
print(self.cxcalc)
print(self.molconvert)
info('Found Marvin executables:')
info(self.cxcalc)
info(self.molconvert)
return
@@ -26,7 +27,7 @@ class ligand_pka_values:
map(lambda dir: os.path.join(dir, program),path))]
if len(l) == 0:
print('Error: Could not find %s. Please make sure that it is found in the path.'%program)
info('Error: Could not find %s. Please make sure that it is found in the path.' % program)
sys.exit(-1)
return l[0]
@@ -67,7 +68,7 @@ class ligand_pka_values:
propka.pdb.write_mol2_for_atoms(atoms, filename)
# check that we actually have a file to work with
if not os.path.isfile(filename):
print('Warning: Didn\'t find a user-modified file \'%s\' - generating one'%filename)
warning('Didn\'t find a user-modified file \'%s\' - generating one' % filename)
propka.pdb.write_mol2_for_atoms(atoms, filename)
@@ -79,12 +80,12 @@ class ligand_pka_values:
stdout=subprocess.PIPE, stderr=subprocess.PIPE).communicate()
if len(errors)>0:
print('********************************************************************************************************')
print('* Warning: Marvin execution failed: *')
print('* %-100s *'%errors)
print('* *')
print('* Please edit the ligand mol2 file and re-run PropKa with the -l option: %29s *'%filename)
print('********************************************************************************************************')
info('********************************************************************************************************')
info('* Warning: Marvin execution failed: *')
info('* %-100s *' % errors)
info('* *')
info('* Please edit the ligand mol2 file and re-run PropKa with the -l option: %29s *' % filename)
info('********************************************************************************************************')
sys.exit(-1)
# extract calculated pkas
@@ -94,15 +95,15 @@ class ligand_pka_values:
for i in range(len(indices)):
atoms[indices[i]].marvin_pka = pkas[i]
atoms[indices[i]].charge = {'a':-1,'b':+1}[types[i]]
print('%s model pKa: %.2f'%(atoms[indices[i]],pkas[i]))
info('%s model pKa: %.2f' % (atoms[indices[i]], pkas[i]))
return
def extract_pkas(self, output):
# split output
[tags, values,empty_line] = output.decode().split('\n')
#print(tags)
#print(values)
#info(tags)
#info(values)
tags = tags.split('\t')
values = values.split('\t')

15
propka/molecular_container.py
View File

@@ -9,6 +9,7 @@ from __future__ import print_function
import os, sys
import propka.pdb, propka.version, propka.output, propka.conformation_container, propka.group, propka.lib
from propka.lib import info, warning
class Molecular_container:
def __init__(self, input_file, options=None):
@@ -39,7 +40,7 @@ class Molecular_container:
# read in atoms and top up containers to make sure that all atoms are present in all conformations
[self.conformations, self.conformation_names] = propka.pdb.read_pdb(input_file, self.version.parameters,self)
if len(self.conformations)==0:
print('Error: The pdb file does not seems to contain any molecular conformations')
info('Error: The pdb file does not seems to contain any molecular conformations')
sys.exit(-1)
self.top_up_conformations()
@@ -76,7 +77,7 @@ class Molecular_container:
self.additional_setup_when_reading_input_file()
else:
print('Unrecognized input file:%s'%input_file)
info('Unrecognized input file:%s' % input_file)
sys.exit(-1)
@@ -90,14 +91,14 @@ class Molecular_container:
return
def find_covalently_coupled_groups(self):
print('-'*103)
info('-' * 103)
for name in self.conformation_names:
self.conformations[name].find_covalently_coupled_groups()
return
def find_non_covalently_coupled_groups(self):
print('-'*103)
info('-' * 103)
for name in self.conformation_names:
self.conformations[name].find_non_covalently_coupled_groups(verbose=self.options.display_coupled_residues)
@@ -149,7 +150,7 @@ class Molecular_container:
if group_to_add:
avr_group += group_to_add
else:
print('Warning: Group %s could not be found in conformation %s.'%(group.atom.residue_label, name))
warning('Group %s could not be found in conformation %s.' % (group.atom.residue_label, name))
# ... and store the average value
avr_group = avr_group / len(self.conformation_names)
avr_conformation.groups.append(avr_group)
@@ -192,7 +193,7 @@ class Molecular_container:
profile = []
for ph in propka.lib.make_grid(*grid):
ddg = self.conformations[conformation].calculate_folding_energy( pH=ph, reference=reference)
#print(ph,ddg)
#info(ph,ddg)
profile.append([ph, ddg])
# find optimum
@@ -225,7 +226,7 @@ class Molecular_container:
return charge_profile
def getPI(self, conformation='AVR', grid=[0., 14., 1], iteration=0):
#print('staring',grid, iteration)
#info('staring',grid, iteration)
# search
charge_profile = self.getChargeProfile(conformation=conformation, grid=grid)
pi = []

13
propka/output.py
View File

@@ -5,6 +5,7 @@ from __future__ import print_function
import sys
import propka.lib
from propka.lib import info, warning
def printHeader():
@@ -15,7 +16,7 @@ def printHeader():
str += "%s\n" % ( getReferencesHeader() )
str += "%s\n" % ( getWarningHeader() )
print(str)
info(str)
def writePDB(protein, file=None, filename=None, include_hydrogens=False, options=None):
@@ -28,7 +29,7 @@ def writePDB(protein, file=None, filename=None, include_hydrogens=False, options
if filename == None:
filename = "%s.pdb" % (protein.name)
file = open(filename, 'w')
print("writing pdbfile %s" % (filename))
info("writing pdbfile %s" % (filename))
close_file = True
else:
# don't close the file, it was opened in a different place
@@ -60,7 +61,7 @@ def writePKA(protein, parameters, filename=None, conformation ='1A',reference="n
filename = "%s.pka" % (protein.name)
file = open(filename, 'w')
if verbose == True:
print("Writing %s" % (filename))
info("Writing %s" % (filename))
# writing propka header
str = "%s\n" % ( getPropkaHeader() )
@@ -98,7 +99,7 @@ def printTmProfile(protein, reference="neutral", window=[0., 14., 1.], Tm=[0.,0.
for (pH, Tm) in profile:
if pH >= window[0] and pH <= window[1] and (pH%window[2] < 0.01 or pH%window[2] > 0.99*window[2]):
str += "%6.2lf%10.2lf\n" % (pH, Tm)
print(str)
info(str)
def printResult(protein, conformation, parameters):
@@ -114,10 +115,10 @@ def printPKASection(protein, conformation, parameters):
"""
# geting the determinants section
str = getDeterminantSection(protein, conformation, parameters)
print(str)
info(str)
str = getSummarySection(protein,conformation,parameters)
print(str)
info(str)
def getDeterminantSection(protein, conformation, parameters):

47
propka/parameters.py
View File

@@ -5,6 +5,7 @@ from __future__ import print_function
import math
import propka.lib as lib
import sys, os
from propka.lib import info, warning
import pkg_resources
@@ -99,7 +100,7 @@ class Parameters:
self.parse_to_string_dictionary(words)
#print(words)
#info(words)
return
@@ -138,7 +139,7 @@ class Parameters:
return
def parse_string(self, words):
#print('self.%s = \'%s\''%tuple(words))
#info('self.%s = \'%s\''%tuple(words))
exec('self.%s = \'%s\''%tuple(words))
return
@@ -158,12 +159,12 @@ class Parameters:
return
def print_interaction_parameters(self):
print('--------------- Model pKa values ----------------------')
info('--------------- Model pKa values ----------------------')
for k in self.model_pkas.keys():
print('%3s %8.2f'%(k,self.model_pkas[k]))
info('%3s %8.2f' % (k, self.model_pkas[k]))
print('')
print('--------------- Interactions --------------------------')
info('')
info('--------------- Interactions --------------------------')
agroups = ['COO', 'HIS', 'CYS', 'TYR', 'SER', 'N+', 'LYS', 'AMD', 'ARG', 'TRP', 'ROH', 'CG', 'C2N', 'N30', 'N31', 'N32', 'N33', 'NAR', 'OCO', 'NP1', 'OH', 'O3', 'CL', 'F', 'NAM', 'N1', 'O2', 'OP', 'SH']
lgroups = ['CG', 'C2N', 'N30', 'N31', 'N32', 'N33', 'NAR', 'OCO', 'NP1', 'OH', 'O3', 'CL', 'F', 'NAM', 'N1', 'O2', 'OP', 'SH']
@@ -213,21 +214,21 @@ class Parameters:
if len(map[g2])==0 and (self.sidechain_cutoffs.get_value(g1,g2)[0] !=3 or self.sidechain_cutoffs.get_value(g1,g2)[1] != 4):
map_interaction += '? '
print(interaction,map_interaction )
info(interaction, map_interaction)
if g1==g2:
break
print('-')
info('-')
print('--------------- Exceptions ----------------------------')
print('COO-HIS',self.COO_HIS_exception)
print('OCO-HIS',self.OCO_HIS_exception)
print('CYS-HIS',self.CYS_HIS_exception)
print('CYS-CYS',self.CYS_CYS_exception)
info('--------------- Exceptions ----------------------------')
info('COO-HIS', self.COO_HIS_exception)
info('OCO-HIS', self.OCO_HIS_exception)
info('CYS-HIS', self.CYS_HIS_exception)
info('CYS-CYS', self.CYS_CYS_exception)
print('--------------- Mapping -------------------------------')
print("""
info('--------------- Mapping -------------------------------')
info("""
Titratable:
CG ARG
C2N ARG
@@ -258,12 +259,12 @@ O2
def print_interaction_parameters_latex(self):
# print('--------------- Model pKa values ----------------------')
# info('--------------- Model pKa values ----------------------')
# for k in self.model_pkas.keys():
# print('%3s %8.2f'%(k,self.model_pkas[k]))
# info('%3s %8.2f'%(k,self.model_pkas[k]))
# print('')
# print('--------------- Interactions --------------------------')
# info('')
# info('--------------- Interactions --------------------------')
agroups = ['COO', 'HIS', 'CYS', 'TYR', 'SER', 'N+', 'LYS', 'AMD', 'ARG', 'TRP', 'ROH', 'CG', 'C2N', 'N30', 'N31', 'N32', 'N33', 'NAR', 'OCO', 'NP1', 'OH', 'O3', 'CL', 'F', 'NAM', 'N1', 'O2', 'OP', 'SH']
lgroups = ['CG', 'C2N', 'N30', 'N31', 'N32', 'N33', 'NAR', 'OCO', 'NP1', 'OH', 'O3', 'CL', 'F', 'NAM', 'N1', 'O2', 'OP', 'SH']
@@ -329,7 +330,7 @@ Group1 & Group2 & Interaction & c1 &c2 \\\\
break
s += ' \\end{longtable}\n'
print(s)
info(s)
return
def print_interactions_latex(self):
@@ -373,7 +374,7 @@ Group1 & Group2 & Interaction & c1 &c2 \\\\
break
s += ' \\end{longtable}\n'
print(s)
info(s)
return
@@ -444,7 +445,7 @@ class Interaction_matrix:
# p+='sidechain_cutoff %3s %3s %s\n'%(ks[i],ks[j],self[ks[i]][ks[j]])
# n+=1
# print('total',n,len(ks))
# info('total',n,len(ks))
# return p
@@ -476,7 +477,7 @@ class Pair_wise_matrix:
if k1 in self.dictionary.keys() and k2 in self.dictionary[k1].keys():
if k1!=k2:
print ('Warning: Paramter value for %s, %s defined more than once'%(k1,k2))
warning('Parameter value for %s, %s defined more than once' % (k1, k2))
if not k1 in self.dictionary:
self.dictionary[k1] = {}

6
propka/pdb.py
View File

@@ -5,6 +5,8 @@ from __future__ import print_function
import string, sys, copy
import propka.lib
from propka.lib import info, warning
from propka.atom import Atom
from propka.conformation_container import Conformation_container
@@ -71,12 +73,12 @@ def protein_precheck(conformations, names):
# check for c-terminal
if 'C-' in [a.terminal for a in res_atoms]:
if len(res_atoms) != expected_atom_numbers[resname]+1:
print('Warning: Unexpected number (%d) of atoms in residue %s in conformation %s'%(len(res_atoms),residue_label, name))
warning('Unexpected number (%d) of atoms in residue %s in conformation %s' % (len(res_atoms), residue_label, name))
continue
# check number of atoms in residue
if len(res_atoms) != expected_atom_numbers[resname]:
print('Warning: Unexpected number (%d) of atoms in residue %s in conformation %s'%(len(res_atoms),residue_label, name))
warning('Unexpected number (%d) of atoms in residue %s in conformation %s' % (len(res_atoms), residue_label, name))
return

73
propka/protonate.py
View File

@@ -5,6 +5,7 @@ from __future__ import print_function
from propka.vector_algebra import *
import propka.bonds, propka.pdb, propka.atom
from propka.lib import info, warning, debug
class Protonate:
""" Protonates atoms using VSEPR theory """
@@ -94,7 +95,7 @@ class Protonate:
def protonate(self, molecules):
""" Will protonate all atoms in the molecular container """
self.display('----- Protonation started -----')
debug('----- Protonation started -----')
# Remove all currently present hydrogen atoms
self.remove_all_hydrogen_atoms(molecules)
@@ -122,11 +123,11 @@ class Protonate:
if atom.type=='atom':
key = '%3s-%s'%(atom.resName, atom.name)
if atom.terminal:
self.display(atom.terminal)
debug(atom.terminal)
key=atom.terminal
if key in list(self.standard_charges.keys()):
atom.charge = self.standard_charges[key]
self.display('Charge', atom, atom.charge)
debug('Charge', atom, atom.charge)
atom.charge_set = True
# atom is a ligand atom
elif atom.type=='hetatm':
@@ -163,21 +164,21 @@ class Protonate:
def set_number_of_protons_to_add(self, atom):
self.display('*'*10)
self.display('Setting number of protons to add for',atom)
debug('*'*10)
debug('Setting number of protons to add for',atom)
atom.number_of_protons_to_add = 8
self.display(' %4d'%8)
debug(' %4d'%8)
atom.number_of_protons_to_add -= self.valence_electrons[atom.element]
self.display('Valence eletrons: %4d'%-self.valence_electrons[atom.element])
debug('Valence eletrons: %4d'%-self.valence_electrons[atom.element])
atom.number_of_protons_to_add -= len(atom.bonded_atoms)
self.display('Number of bonds: %4d'%- len(atom.bonded_atoms))
debug('Number of bonds: %4d'%- len(atom.bonded_atoms))
atom.number_of_protons_to_add -= atom.number_of_pi_electrons_in_double_and_triple_bonds
self.display('Pi electrons: %4d'%-atom.number_of_pi_electrons_in_double_and_triple_bonds)
debug('Pi electrons: %4d'%-atom.number_of_pi_electrons_in_double_and_triple_bonds)
atom.number_of_protons_to_add += int(atom.charge)
self.display('Charge: %4.1f'%atom.charge)
debug('Charge: %4.1f'%atom.charge)
self.display('-'*10)
self.display(atom.number_of_protons_to_add)
debug('-'*10)
debug(atom.number_of_protons_to_add)
return
@@ -187,8 +188,8 @@ class Protonate:
if atom.steric_number_and_lone_pairs_set:
return
self.display('='*10)
self.display('Setting steric number and lone pairs for',atom)
debug('='*10)
debug('Setting steric number and lone pairs for',atom)
# costumly set the N backbone atoms up for peptide bond trigonal planer shape
#if atom.name == 'N' and len(atom.bonded_atoms) == 2:
@@ -201,34 +202,34 @@ class Protonate:
atom.steric_number = 0
self.display('%65s: %4d'%('Valence electrons',self.valence_electrons[atom.element]))
debug('%65s: %4d'%('Valence electrons',self.valence_electrons[atom.element]))
atom.steric_number += self.valence_electrons[atom.element]
self.display('%65s: %4d'%('Number of bonds',len(atom.bonded_atoms)))
debug('%65s: %4d'%('Number of bonds',len(atom.bonded_atoms)))
atom.steric_number += len(atom.bonded_atoms)
self.display('%65s: %4d'%('Number of hydrogen atoms to add',atom.number_of_protons_to_add))
debug('%65s: %4d'%('Number of hydrogen atoms to add',atom.number_of_protons_to_add))
atom.steric_number += atom.number_of_protons_to_add
self.display('%65s: %4d'%('Number of pi-electrons in double and triple bonds(-)',atom.number_of_pi_electrons_in_double_and_triple_bonds))
debug('%65s: %4d'%('Number of pi-electrons in double and triple bonds(-)',atom.number_of_pi_electrons_in_double_and_triple_bonds))
atom.steric_number -= atom.number_of_pi_electrons_in_double_and_triple_bonds
self.display('%65s: %4d'%('Number of pi-electrons in conjugated double and triple bonds(-)',atom.number_of_pi_electrons_in_conjugate_double_and_triple_bonds))
debug('%65s: %4d'%('Number of pi-electrons in conjugated double and triple bonds(-)',atom.number_of_pi_electrons_in_conjugate_double_and_triple_bonds))
atom.steric_number -= atom.number_of_pi_electrons_in_conjugate_double_and_triple_bonds
self.display('%65s: %4d'%('Number of donated co-ordinated bonds',0))
debug('%65s: %4d'%('Number of donated co-ordinated bonds',0))
atom.steric_number += 0
self.display('%65s: %4.1f'%('Charge(-)',atom.charge))
debug('%65s: %4.1f'%('Charge(-)',atom.charge))
atom.steric_number -= atom.charge
atom.steric_number = math.floor(atom.steric_number/2.0)
atom.number_of_lone_pairs = atom.steric_number - len(atom.bonded_atoms) - atom.number_of_protons_to_add
self.display('-'*70)
self.display('%65s: %4d'%('Steric number',atom.steric_number))
self.display('%65s: %4d'%('Number of lone pairs',atom.number_of_lone_pairs))
debug('-'*70)
debug('%65s: %4d'%('Steric number',atom.steric_number))
debug('%65s: %4d'%('Number of lone pairs',atom.number_of_lone_pairs))
atom.steric_number_and_lone_pairs_set = True
@@ -237,17 +238,17 @@ class Protonate:
def add_protons(self, atom):
# decide which method to use
self.display('PROTONATING',atom)
debug('PROTONATING',atom)
if atom.steric_number in list(self.protonation_methods.keys()):
self.protonation_methods[atom.steric_number](atom)
else:
print('Warning: Do not have a method for protonating',atom,'(steric number: %d)'%atom.steric_number)
warning('Do not have a method for protonating', atom, '(steric number: %d)' % atom.steric_number)
return
def trigonal(self, atom):
self.display('TRIGONAL - %d bonded atoms'%(len(atom.bonded_atoms)))
debug('TRIGONAL - %d bonded atoms'%(len(atom.bonded_atoms)))
rot_angle = math.radians(120.0)
c = vector(atom1 = atom)
@@ -312,7 +313,7 @@ class Protonate:
def tetrahedral(self, atom):
self.display('TETRAHEDRAL - %d bonded atoms'%(len(atom.bonded_atoms)))
debug('TETRAHEDRAL - %d bonded atoms'%(len(atom.bonded_atoms)))
rot_angle = math.radians(109.5)
# sanity check
@@ -399,7 +400,7 @@ class Protonate:
i+=1
self.display('added',new_H, 'to',atom)
debug('added',new_H, 'to',atom)
return
def set_bond_distance(self, a, element):
@@ -407,31 +408,23 @@ class Protonate:
if element in list(self.bond_lengths.keys()):
d = self.bond_lengths[element]
else:
print('WARNING: Bond length for %s not found, using the standard value of %f'%(element, d))
warning('Bond length for %s not found, using the standard value of %f' % (element, d))
a = a.rescale(d)
return a
def display(self,*text):
if self.verbose:
s = ''
for t in text:
s+='%s '%t
print(s)
return
if __name__ == '__main__':
import protein, pdb, sys,os
arguments = sys.argv
if len(arguments) != 2:
print('Usage: protonate.py <pdb_file>')
info('Usage: protonate.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)

7
propka/vector_algebra.py
View File

@@ -1,6 +1,7 @@
from __future__ import division
from __future__ import print_function
import math
from propka.lib import info
class vector:
""" Vector """
@@ -47,7 +48,7 @@ class vector:
elif type(other) in [int, float]:
return vector(self.x * other, self.y * other, self.z * other)
else:
print('%s not supported'%type(other))
info('%s not supported' % type(other))
raise TypeError
def __rmul__(self,other):
@@ -235,7 +236,7 @@ class multi_vector:
atom2.setConfiguration(key)
v = vector(atom1=atom1, atom2=atom2)
self.vectors.append(v)
#print(key,v)
#info(key,v)
return
def __getattribute__(self,name):
@@ -252,7 +253,7 @@ class multi_vector:
def do_job(self, job):
#print(job)
#info(job)
self.res = multi_vector()
for i in range(len(self.vectors)):
self.res.vectors.append(eval('self.vectors[%d].%s()'%(i,job)))

7
propka/version.py
View File

@@ -4,6 +4,7 @@ import math
import sys, os
import propka.lib as lib
from propka.lib import info, warning
import propka.calculations as calculations
import propka.parameters
@@ -109,7 +110,7 @@ class simple_hb(version_A):
def __init__(self, parameters):
# set the calculation rutines used in this version
version_A.__init__(self, parameters)
print('Using simple hb model')
info('Using simple hb model')
return
def get_hydrogen_bond_parameters(self, atom1, atom2):
@@ -126,7 +127,7 @@ class element_based_ligand_interactions(version_A):
def __init__(self, parameters):
# set the calculation rutines used in this version
version_A.__init__(self, parameters)
print('Using detailed SC model!')
info('Using detailed SC model!')
return
def get_hydrogen_bond_parameters(self, atom1, atom2):
@@ -168,7 +169,7 @@ class element_based_ligand_interactions(version_A):
res = self.parameters.hydrogen_bonds.get_value(elements[0], elements[1])
if not res:
print('Could not determine backbone interaction parameters for:',
info('Could not determine backbone interaction parameters for:',
backbone_atom, atom)
return