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De-lint output.py.

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Public methods/members changed; dependencies checked via Google.
This commit is contained in:
Nathan Baker
2020-05-25 08:24:54 -07:00
parent 3342d3418c
commit f38faaed97
3 changed files with 365 additions and 312 deletions
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propka/molecular_container.py
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@@ -184,8 +184,7 @@ class Molecular_container:
filename = os.path.join('%s_%s.pka' % (self.name, filename = os.path.join('%s_%s.pka' % (self.name,
self.version.parameters.output_file_tag)) self.version.parameters.output_file_tag))
propka.output.write_pka(self, self.version.parameters, filename=filename, propka.output.write_pka(self, self.version.parameters, filename=filename,
conformation='AVR', reference=reference, conformation='AVR', reference=reference)
direction=direction, options=options)
def get_folding_profile(self, conformation='AVR', reference="neutral", def get_folding_profile(self, conformation='AVR', reference="neutral",
grid=[0., 14., 0.1]): grid=[0., 14., 0.1]):

630
propka/output.py
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@@ -1,397 +1,451 @@
"""Output routines."""
from __future__ import division from datetime import date
from __future__ import print_function from propka.lib import info
import sys
import propka.lib
from propka.lib import info, warning
def printHeader(): def print_header():
"""Print header section of output."""
str_ = "%s\n" % get_propka_header()
str_ += "%s\n" % get_references_header()
str_ += "%s\n" % get_warning_header()
info(str_)
def write_pdb(protein, pdbfile=None, filename=None, include_hydrogens=False,
_=None):
"""Write a residue to the new PDB file.
Args:
protein: protein object
pdbfile: PDB file
filename: file to write to
include_hydrogens: Boolean indicating whether to include hydrogens
options: options object
""" """
prints the header section if pdbfile is None:
"""
str = "%s\n" % ( getPropkaHeader() )
str += "%s\n" % ( getReferencesHeader() )
str += "%s\n" % ( getWarningHeader() )
info(str)
def writePDB(protein, file=None, filename=None, include_hydrogens=False, options=None):
"""
Write the residue to the new pdbfile
"""
if file == None:
# opening file if not given # opening file if not given
if filename == None: if filename is None:
filename = "%s.pdb" % (protein.name) filename = "%s.pdb" % (protein.name)
file = open(filename, 'w') # TODO - this would be better as a context manager
pdbfile = open(filename, 'w')
info("writing pdbfile %s" % (filename)) info("writing pdbfile %s" % (filename))
close_file = True close_file = True
else: else:
# don't close the file, it was opened in a different place # don't close the file, it was opened in a different place
close_file = False close_file = False
numb = 0 numb = 0
for chain in protein.chains: for chain in protein.chains:
for residue in chain.residues: for residue in chain.residues:
if residue.res_name not in ["N+ ", "C- "]: if residue.res_name not in ["N+ ", "C- "]:
for atom in residue.atoms: for atom in residue.atoms:
if include_hydrogens == False and atom.name[0] == "H": if (not include_hydrogens) and atom.name[0] == "H":
""" don't print """ # don't print
pass
else: else:
numb += 1 numb += 1
line = atom.make_pdb_line2(numb=numb) line = atom.make_pdb_line2(numb=numb)
line += "\n" line += "\n"
file.write(line) pdbfile.write(line)
if close_file:
if close_file == True: pdbfile.close()
file.close()
def writePKA(protein, parameters, filename=None, conformation ='1A',reference="neutral", direction="folding", verbose=False, options=None): def write_pka(protein, parameters, filename=None, conformation='1A',
""" reference="neutral", _="folding", verbose=False,
Write the pka-file based on the given protein __=None):
"""Write the pKa-file based on the given protein.
Args:
protein: protein object
filename: output file name
conformation: TODO - figure this out
reference: reference state
_: "folding" or other
verbose: Boolean flag for verbosity
__: options object
""" """
# TODO - the code immediately overrides the verbose argument; why?
verbose = True verbose = True
if filename == None: if filename is None:
filename = "%s.pka" % (protein.name) filename = "%s.pka" % (protein.name)
file = open(filename, 'w') # TODO - this would be much better with a context manager
if verbose == True: file_ = open(filename, 'w')
if verbose:
info("Writing %s" % (filename)) info("Writing %s" % (filename))
# writing propka header # writing propka header
str = "%s\n" % ( getPropkaHeader() ) str_ = "%s\n" % get_propka_header()
str += "%s\n" % ( getReferencesHeader() ) str_ += "%s\n" % get_references_header()
str += "%s\n" % ( getWarningHeader() ) str_ += "%s\n" % get_warning_header()
# writing pKa determinant section # writing pKa determinant section
str += getDeterminantSection(protein,conformation, parameters) str_ += get_determinant_section(protein, conformation, parameters)
# writing pKa summary section # writing pKa summary section
str += getSummarySection(protein,conformation,parameters) str_ += get_summary_section(protein, conformation, parameters)
str += "%s\n" % ( getTheLine() ) str_ += "%s\n" % get_the_line()
# printing Folding Profile # printing Folding Profile
str += get_folding_profileSection(protein, conformation=conformation, reference=reference, window=[0., 14., 1.0]) str_ += get_folding_profile_section(protein, conformation=conformation,
reference=reference,
window=[0., 14., 1.0])
# printing Protein Charge Profile # printing Protein Charge Profile
str += get_charge_profileSection(protein, conformation=conformation) str_ += get_charge_profile_section(protein, conformation=conformation)
# now, writing the pka text to file # now, writing the pka text to file
file.write(str) file_.write(str_)
file_.close()
file.close()
def printTmProfile(protein, reference="neutral", window=[0., 14., 1.], Tm=[0.,0.], Tms=None, ref=None, verbose=False, options=None): def print_tm_profile(protein, reference="neutral", window=[0., 14., 1.],
__=[0., 0.], tms=None, ref=None, _=False,
options=None):
"""Print Tm profile.
I think Tm refers to the denaturation temperature.
Args:
protein: protein object
reference: reference state
window: pH window [min, max, step]
__: temperature range [min, max]
tms: TODO - figure this out
ref: TODO - figure this out (probably reference state?)
_: Boolean for verbosity
options: options object
""" """
prints Tm profile profile = protein.getTmProfile(reference=reference, grid=[0., 14., 0.1],
""" tms=tms, ref=ref, options=options)
profile = protein.getTmProfile(reference=reference, grid=[0., 14., 0.1], Tms=Tms, ref=ref, options=options) if profile is None:
if profile == None: str_ = "Could not determine Tm-profile\n"
str = "Could not determine Tm-profile\n"
else: else:
str = " suggested Tm-profile for %s\n" % (protein.name) str_ = " suggested Tm-profile for %s\n" % (protein.name)
for (pH, Tm) in profile: 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]): if ph >= window[0] and ph <= window[1] and (ph%window[2] < 0.01 \
str += "%6.2lf%10.2lf\n" % (pH, Tm) or ph%window[2] > 0.99*window[2]):
info(str) str_ += "%6.2lf%10.2lf\n" % (ph, tm_)
info(str_)
def printResult(protein, conformation, parameters): def print_result(protein, conformation, parameters):
"""Prints all resulting output from determinants and down.
Args:
protein: protein object
conformation: specific conformation
parameters: parameters
""" """
prints all resulting output from determinants and down print_pka_section(protein, conformation, parameters)
"""
printPKASection(protein, conformation, parameters)
def printPKASection(protein, conformation, parameters): def print_pka_section(protein, conformation, parameters):
""" """Prints out pKa section of results.
prints out the pka-section of the result
Args:
protein: protein object
conformation: specific conformation
parameters: parameters
""" """
# geting the determinants section # geting the determinants section
str = getDeterminantSection(protein, conformation, parameters) str_ = get_determinant_section(protein, conformation, parameters)
info(str) info(str_)
str_ = get_summary_section(protein, conformation, parameters)
str = getSummarySection(protein,conformation,parameters) info(str_)
info(str)
def getDeterminantSection(protein, conformation, parameters): def get_determinant_section(protein, conformation, parameters):
""" """Returns string with determinant section of results.
prints out the pka-section of the result
Args:
protein: protein object
conformation: specific conformation
parameters: parameters
Returns:
string
""" """
# getting the same order as in propka2.0 # getting the same order as in propka2.0
str = "%s\n" % ( getDeterminantsHeader() ) str_ = "%s\n" % get_determinants_header()
# printing determinants # printing determinants
for chain in protein.conformations[conformation].chains: for chain in protein.conformations[conformation].chains:
for residue_type in parameters.write_out_order: for residue_type in parameters.write_out_order:
groups = [g for g in protein.conformations[conformation].groups if g.atom.chain_id == chain] groups = [g for g in protein.conformations[conformation].groups \
if g.atom.chain_id == chain]
for group in groups: for group in groups:
if group.residue_type == residue_type: if group.residue_type == residue_type:
str += "%s" % ( group.get_determinant_string(parameters.remove_penalised_group) ) str_ += "%s" \
% group.get_determinant_string(parameters.remove_penalised_group)
# Add a warning in case of coupled residues # Add a warning in case of coupled residues
if protein.conformations[conformation].non_covalently_coupled_groups and not protein.options.display_coupled_residues: if protein.conformations[conformation].non_covalently_coupled_groups \
str += 'Coupled residues (marked *) were detected. Please rerun PropKa with the --display-coupled-residues \nor -d option for detailed information.\n' and not protein.options.display_coupled_residues:
str_ += 'Coupled residues (marked *) were detected.'
return str str_ += 'Please rerun PropKa with the --display-coupled-residues \n'
str_ += 'or -d option for detailed information.\n'
return str_
def getSummarySection(protein, conformation, parameters): def get_summary_section(protein, conformation, parameters):
"""Returns string with summary section of the results.
Args:
protein: protein object
conformation: specific conformation
parameters: parameters
Returns:
string
""" """
prints out the pka-section of the result str_ = "%s\n" % get_summary_header()
"""
str = "%s\n" % ( getSummaryHeader() )
# printing pKa summary # printing pKa summary
for residue_type in parameters.write_out_order: for residue_type in parameters.write_out_order:
for group in protein.conformations[conformation].groups: for group in protein.conformations[conformation].groups:
if group.residue_type == residue_type: if group.residue_type == residue_type:
str += "%s" % ( group.get_summary_string(parameters.remove_penalised_group) ) str_ += "%s" \
% group.get_summary_string(parameters.remove_penalised_group)
return str return str_
def get_folding_profileSection(protein, conformation='AVR', direction="folding", reference="neutral", window=[0., 14., 1.0], verbose=False, options=None): def get_folding_profile_section(protein, conformation='AVR',
direction="folding", reference="neutral",
window=[0., 14., 1.0], _=False,
__=None):
"""Returns string with the folding profile section of the results.
Args:
protein: protein object
conformation: specific conformation
direction: 'folding' or other
reference: reference state
window: pH window [min, max, step]
_: Boolean for verbose output
__: options object
Returns:
string
""" """
returns the protein-folding-profile section str_ = get_the_line()
""" str_ += "\n"
str = getTheLine() str_ += "Free energy of %9s (kcal/mol) as a function" % direction
str += "\n" str_ += " of pH (using %s reference)\n" % reference
str += "Free energy of %9s (kcal/mol) as a function of pH (using %s reference)\n" % (direction, reference) profile, [ph_opt, dg_opt], [dg_min, dg_max], [ph_min, ph_max] \
= protein.get_folding_profile(conformation=conformation,
profile, [pH_opt, dG_opt], [dG_min, dG_max], [pH_min, pH_max] = protein.get_folding_profile(conformation=conformation, reference=reference, grid=[0., 14., 0.1])
reference=reference, if profile is None:
grid=[0., 14., 0.1]) str_ += "Could not determine folding profile\n"
if profile == None:
str += "Could not determine folding profile\n"
else: else:
for (pH, dG) in profile: for (ph, dg) in profile:
if pH >= window[0] and pH <= window[1] and (pH%window[2] < 0.05 or pH%window[2] > 0.95): if ph >= window[0] and ph <= window[1]:
str += "%6.2lf%10.2lf\n" % (pH, dG) if ph%window[2] < 0.05 or ph%window[2] > 0.95:
str += "\n" str_ += "%6.2lf%10.2lf\n" % (ph, dg)
str_ += "\n"
if pH_opt == None or dG_opt == None: if ph_opt is None or dg_opt is None:
str += "Could not determine pH optimum\n" str_ += "Could not determine pH optimum\n"
else: else:
str += "The pH of optimum stability is %4.1lf for which the free energy is%6.1lf kcal/mol at 298K\n" % (pH_opt, dG_opt) str_ += "The pH of optimum stability is %4.1lf" % ph_opt
str_ += " for which the free energy is %6.1lf kcal/mol at 298K\n" % dg_opt
if dG_min == None or dG_max == None: if dg_min is None or dg_max is None:
str += "Could not determine pH values where the free energy is within 80 %s of minimum\n" % ("%") str_ += "Could not determine pH values where the free energy"
str_ += " is within 80 %s of minimum\n" % ("%")
else: else:
str += "The free energy is within 80 %s of maximum at pH %4.1lf to %4.1lf\n" % ("%", dG_min, dG_max) str_ += "The free energy is within 80 \% of maximum"
str_ += " at pH %4.1lf to %4.1lf\n" % (dg_min, dg_max)
if pH_min == None or pH_max == None: if ph_min is None or ph_max is None:
str += "Could not determine the pH-range where the free energy is negative\n\n" str_ += "Could not determine the pH-range where the free"
str_ += " energy is negative\n\n"
else: else:
str += "The free energy is negative in the range %4.1lf - %4.1lf\n\n" % (pH_min, pH_max) str_ += "The free energy is negative in the range"
str_ += " %4.1lf - %4.1lf\n\n" % (ph_min, ph_max)
return str_
return str def get_charge_profile_section(protein, conformation='AVR', _=None):
"""Returns string with the charge profile section of the results.
Args:
protein: protein object
def get_charge_profileSection(protein, conformation='AVR', options=None): conformation: specific conformation
_: options object
Returns:
string
""" """
returns the protein-folding-profile section str_ = "Protein charge of folded and unfolded state as a function of pH\n"
""" profile = protein.get_charge_profile(conformation=conformation,
str = "Protein charge of folded and unfolded state as a function of pH\n" grid=[0., 14., 1.])
if profile is None:
profile = protein.get_charge_profile(conformation=conformation,grid=[0., 14., 1.]) str_ += "Could not determine charge profile\n"
if profile == None:
str += "Could not determine charge profile\n"
else: else:
str += "%6s%10s%8s\n" % ("pH", "unfolded", "folded") str_ += "%6s%10s%8s\n" % ("pH", "unfolded", "folded")
for (pH, Q_mod, Q_pro) in profile: for (ph, q_mod, q_pro) in profile:
str += "%6.2lf%10.2lf%8.2lf\n" % (pH, Q_mod, Q_pro) str_ += "%6.2lf%10.2lf%8.2lf\n" % (ph, q_mod, q_pro)
pi_pro, pi_mod = protein.get_pi(conformation=conformation)
if pi_pro is None or pi_mod is None:
pI_pro, pI_mod = protein.get_pi(conformation=conformation) str_ += "Could not determine the pI\n\n"
if pI_pro == None or pI_mod == None:
str += "Could not determine the pI\n\n"
else: else:
str += "The pI is %5.2lf (folded) and %5.2lf (unfolded)\n" % (pI_pro, pI_mod) str_ += "The pI is %5.2lf (folded) and %5.2lf (unfolded)\n" % (pi_pro,
pi_mod)
return str_
return str def write_jackal_scap_file(mutation_data=None, filename="1xxx_scap.list",
_=None):
"""Write a scap file for, i.e., generating a mutated protein
TODO - figure out what this is
def writeJackalScapFile(mutationData=None, filename="1xxx_scap.list", options=None):
""" """
writing a scap file for, i.e., generating a mutated protein with open(filename, 'w') as file_:
for chain_id, _, res_num, code2 in mutation_data:
str_ = "%s, %d, %s\n" % (chain_id, res_num, code2)
file_.write(str_)
def write_scwrl_sequence_file(sequence, filename="x-ray.seq", _=None):
"""Write a scwrl sequence file for, e.g., generating a mutated protein
TODO - figure out what this is
""" """
file = open(filename, 'w') with open(filename, 'w') as file_:
for chain_id, code1, res_num, code2 in mutationData:
str = "%s, %d, %s\n" % (chain_id, res_num, code2)
file.write(str)
file.close()
def writeScwrlSequenceFile(sequence, filename="x-ray.seq", options=None):
"""
writing a scwrl sequence file for, e.g., generating a mutated protein
"""
file = open(filename, 'w')
start = 0 start = 0
while len(sequence[start:]) > 60: while len(sequence[start:]) > 60:
file.write( "%s\n" % (sequence[start:start+60]) ) file_.write("%s\n" % (sequence[start:start+60]))
start += 60 start += 60
file.write( "%s\n" % (sequence[start:]) ) file_.write("%s\n" % (sequence[start:]))
file.close()
def get_propka_header():
"""Create the header.
# --- various header text --- # Returns:
string
def getPropkaHeader():
""" """
Creates the header
"""
from datetime import date
today = date.today() today = date.today()
str_ = "propka3.1 %93s\n" % (today)
str_ += "-------------------------------------------------------------------------------------------------------\n"
str_ += "-- --\n"
str_ += "-- PROPKA: A PROTEIN PKA PREDICTOR --\n"
str_ += "-- --\n"
str_ += "-- VERSION 1.0, 04/25/2004, IOWA CITY --\n"
str_ += "-- BY HUI LI --\n"
str_ += "-- --\n"
str_ += "-- VERSION 2.0, 11/05/2007, IOWA CITY/COPENHAGEN --\n"
str_ += "-- BY DELPHINE C. BAS AND DAVID M. ROGERS --\n"
str_ += "-- --\n"
str_ += "-- VERSION 3.0, 01/06/2011, COPENHAGEN --\n"
str_ += "-- BY MATS H.M. OLSSON AND CHRESTEN R. SONDERGARD --\n"
str_ += "-- --\n"
str_ += "-- VERSION 3.1, 07/01/2011, COPENHAGEN --\n"
str_ += "-- BY CHRESTEN R. SONDERGARD AND MATS H.M. OLSSON --\n"
str_ += "-------------------------------------------------------------------------------------------------------\n"
str_ += "\n"
return str_
def get_references_header():
"""Create the 'references' part of output file.
str = "propka3.1 %93s\n" % (today) Returns:
str += "-------------------------------------------------------------------------------------------------------\n" string
str += "-- --\n"
str += "-- PROPKA: A PROTEIN PKA PREDICTOR --\n"
str += "-- --\n"
str += "-- VERSION 1.0, 04/25/2004, IOWA CITY --\n"
str += "-- BY HUI LI --\n"
str += "-- --\n"
str += "-- VERSION 2.0, 11/05/2007, IOWA CITY/COPENHAGEN --\n"
str += "-- BY DELPHINE C. BAS AND DAVID M. ROGERS --\n"
str += "-- --\n"
str += "-- VERSION 3.0, 01/06/2011, COPENHAGEN --\n"
str += "-- BY MATS H.M. OLSSON AND CHRESTEN R. SONDERGARD --\n"
str += "-- --\n"
str += "-- VERSION 3.1, 07/01/2011, COPENHAGEN --\n"
str += "-- BY CHRESTEN R. SONDERGARD AND MATS H.M. OLSSON --\n"
str += "-------------------------------------------------------------------------------------------------------\n"
str += "\n"
return str
def getReferencesHeader():
""" """
Returns the 'references' part in output file str_ = ""
str_ += "-------------------------------------------------------------------------------------------------------\n"
str_ += " References:\n"
str_ += "\n"
str_ += " Very Fast Empirical Prediction and Rationalization of Protein pKa Values\n"
str_ += " Hui Li, Andrew D. Robertson and Jan H. Jensen\n"
str_ += " PROTEINS: Structure, Function, and Bioinformatics 61:704-721 (2005)\n"
str_ += " \n"
str_ += " Very Fast Prediction and Rationalization of pKa Values for Protein-Ligand Complexes\n"
str_ += " Delphine C. Bas, David M. Rogers and Jan H. Jensen\n"
str_ += " PROTEINS: Structure, Function, and Bioinformatics 73:765-783 (2008)\n"
str_ += " \n"
str_ += " PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKa predictions\n"
str_ += " Mats H.M. Olsson, Chresten R. Sondergard, Michal Rostkowski, and Jan H. Jensen\n"
str_ += " Journal of Chemical Theory and Computation, 7(2):525-537 (2011)\n"
str_ += " \n"
str_ += " Improved Treatment of Ligands and Coupling Effects in Empirical Calculation\n"
str_ += " and Rationalization of pKa Values\n"
str_ += " Chresten R. Sondergaard, Mats H.M. Olsson, Michal Rostkowski, and Jan H. Jensen\n"
str_ += " Journal of Chemical Theory and Computation, (2011)\n"
str_ += " \n"
str_ += "-------------------------------------------------------------------------------------------------------\n"
return str_
def get_warning_header():
"""Create the 'warning' part of the output file.
TODO - this function is essentially a no-op.
Returns:
string
""" """
str_ = ""
str = "" return str_
str += "-------------------------------------------------------------------------------------------------------\n"
str += " References:\n"
str += "\n"
str += " Very Fast Empirical Prediction and Rationalization of Protein pKa Values\n"
str += " Hui Li, Andrew D. Robertson and Jan H. Jensen\n"
str += " PROTEINS: Structure, Function, and Bioinformatics 61:704-721 (2005)\n"
str += " \n"
str += " Very Fast Prediction and Rationalization of pKa Values for Protein-Ligand Complexes\n"
str += " Delphine C. Bas, David M. Rogers and Jan H. Jensen\n"
str += " PROTEINS: Structure, Function, and Bioinformatics 73:765-783 (2008)\n"
str += " \n"
str += " PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKa predictions\n"
str += " Mats H.M. Olsson, Chresten R. Sondergard, Michal Rostkowski, and Jan H. Jensen\n"
str += " Journal of Chemical Theory and Computation, 7(2):525-537 (2011)\n"
str += " \n"
str += " Improved Treatment of Ligands and Coupling Effects in Empirical Calculation\n"
str += " and Rationalization of pKa Values\n"
str += " Chresten R. Sondergaard, Mats H.M. Olsson, Michal Rostkowski, and Jan H. Jensen\n"
str += " Journal of Chemical Theory and Computation, (2011)\n"
str += " \n"
str += "-------------------------------------------------------------------------------------------------------\n"
return str
def getWarningHeader(): def get_determinants_header():
"""Create the Determinant header.
Returns:
string
""" """
Returns the 'warning' part in output file str_ = ""
str_ += "--------- ----- ------ --------------------- -------------- -------------- --------------\n"
str_ += " DESOLVATION EFFECTS SIDECHAIN BACKBONE COULOMBIC \n"
str_ += " RESIDUE pKa BURIED REGULAR RE HYDROGEN BOND HYDROGEN BOND INTERACTION \n"
str_ += "--------- ----- ------ --------- --------- -------------- -------------- --------------\n"
return str_
def get_summary_header():
"""Create the summary header.
Returns:
string
""" """
str_ = get_the_line()
str = "" str_ += "\n"
str_ += "SUMMARY OF THIS PREDICTION\n"
return str str_ += " Group pKa model-pKa ligand atom-type"
return str_
def getDeterminantsHeader(): def get_the_line():
"""Draw the line - Johnny Cash would have been proud - or actually Aerosmith!
NOTE - Johnny Cash walked the line.
Returns:
string
""" """
Creates the Determinant header str_ = ""
str_ += ("-" * 104)
return str_
def make_interaction_map(name, list_, interaction):
"""Print out an interaction map named 'name' of the groups in 'list'
based on the function 'interaction'
Args:
list_: list of groups
interaction: some sort of function
Returns:
string
""" """
str = ""
str += "--------- ----- ------ --------------------- -------------- -------------- --------------\n"
str += " DESOLVATION EFFECTS SIDECHAIN BACKBONE COULOMBIC \n"
str += " RESIDUE pKa BURIED REGULAR RE HYDROGEN BOND HYDROGEN BOND INTERACTION \n"
str += "--------- ----- ------ --------- --------- -------------- -------------- --------------\n"
return str
def getSummaryHeader():
"""
returns the summary header
"""
str = getTheLine()
str += "\n"
str += "SUMMARY OF THIS PREDICTION\n"
str += " Group pKa model-pKa ligand atom-type"
return str
def getTheLine():
"""
draw the line - Johnny Cash would have been proud - or actually Aerosmith!
"""
str = ""
for i in range(0, 104):
str += "-"
return str
# Interaction maps
def make_interaction_map(name, list, interaction):
""" Print out an interaction map named 'name' of the groups in 'list'
based on the function 'interaction' """
# return an empty string, if the list is empty # return an empty string, if the list is empty
if len(list)==0: if len(list_) == 0:
return '' return ''
# for long list, use condensed formatting # for long list, use condensed formatting
if len(list)>10: if len(list_) > 10:
res = 'Condensed form:\n' res = 'Condensed form:\n'
for i in range(len(list)): for i, group1 in enumerate(list_):
for j in range(i,len(list)): for group2 in list_[i:]:
if interaction(list[i],list[j]): if interaction(group1, group2):
res += 'Coupling: %9s - %9s\n'%(list[i].label,list[j].label) res += 'Coupling: %9s - %9s\n' % (group1.label,
group2.label)
return res return res
# Name and map header # Name and map header
res = '%s\n%12s'%(name,'') res = '%s\n%12s' % (name, '')
for g in list: for group in list_:
res += '%9s | '%g.label res += '%9s | ' % group.label
# do the map # do the map
for g1 in list: for group1 in list_:
res += '\n%-12s'%(g1.label) res += '\n%-12s' % (group1.label)
for g2 in list: for group2 in list_:
tag = '' tag = ''
if interaction(g1, g2): if interaction(group1, group2):
tag = ' X ' tag = ' X '
res += '%10s| '%tag res += '%10s| '%tag
return res return res

4
propka/protonate.py
View File

@@ -433,9 +433,9 @@ if __name__ == '__main__':
my_protein = protein.Protein(pdblist,'test.pdb') my_protein = protein.Protein(pdblist,'test.pdb')
p.remove_all_hydrogen_atoms_from_protein(my_protein) p.remove_all_hydrogen_atoms_from_protein(my_protein)
my_protein.writePDB('before_protonation.pdb') my_protein.write_pdb('before_protonation.pdb')
p.protonate_protein(my_protein) p.protonate_protein(my_protein)
## write out protonated file ## write out protonated file
my_protein.writePDB('protonated.pdb') my_protein.write_pdb('protonated.pdb')