De-lint output.py.
Public methods/members changed; dependencies checked via Google.
This commit is contained in:
Nathan Baker
@@ -184,8 +184,7 @@ class Molecular_container:
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filename = os.path.join('%s_%s.pka' % (self.name,
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self.version.parameters.output_file_tag))
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propka.output.write_pka(self, self.version.parameters, filename=filename,
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conformation='AVR', reference=reference,
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direction=direction, options=options)
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conformation='AVR', reference=reference)
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def get_folding_profile(self, conformation='AVR', reference="neutral",
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grid=[0., 14., 0.1]):
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670
propka/output.py
670
propka/output.py
@@ -1,397 +1,451 @@
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from __future__ import division
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from __future__ import print_function
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import sys
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import propka.lib
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from propka.lib import info, warning
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"""Output routines."""
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from datetime import date
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from propka.lib import info
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def printHeader():
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def print_header():
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"""Print header section of output."""
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str_ = "%s\n" % get_propka_header()
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str_ += "%s\n" % get_references_header()
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str_ += "%s\n" % get_warning_header()
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info(str_)
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def write_pdb(protein, pdbfile=None, filename=None, include_hydrogens=False,
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_=None):
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"""Write a residue to the new PDB file.
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Args:
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protein: protein object
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pdbfile: PDB file
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filename: file to write to
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include_hydrogens: Boolean indicating whether to include hydrogens
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options: options object
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"""
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prints the header section
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"""
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str = "%s\n" % ( getPropkaHeader() )
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str += "%s\n" % ( getReferencesHeader() )
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str += "%s\n" % ( getWarningHeader() )
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info(str)
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def writePDB(protein, file=None, filename=None, include_hydrogens=False, options=None):
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"""
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Write the residue to the new pdbfile
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"""
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if file == None:
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# opening file if not given
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if filename == None:
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filename = "%s.pdb" % (protein.name)
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file = open(filename, 'w')
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info("writing pdbfile %s" % (filename))
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close_file = True
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if pdbfile is None:
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# opening file if not given
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if filename is None:
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filename = "%s.pdb" % (protein.name)
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# TODO - this would be better as a context manager
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pdbfile = open(filename, 'w')
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info("writing pdbfile %s" % (filename))
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close_file = True
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else:
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# don't close the file, it was opened in a different place
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close_file = False
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# don't close the file, it was opened in a different place
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close_file = False
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numb = 0
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for chain in protein.chains:
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for residue in chain.residues:
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if residue.res_name not in ["N+ ", "C- "]:
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for atom in residue.atoms:
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if include_hydrogens == False and atom.name[0] == "H":
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""" don't print """
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else:
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numb += 1
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line = atom.make_pdb_line2(numb=numb)
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line += "\n"
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file.write(line)
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if close_file == True:
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file.close()
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for residue in chain.residues:
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if residue.res_name not in ["N+ ", "C- "]:
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for atom in residue.atoms:
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if (not include_hydrogens) and atom.name[0] == "H":
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# don't print
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pass
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else:
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numb += 1
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line = atom.make_pdb_line2(numb=numb)
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line += "\n"
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pdbfile.write(line)
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if close_file:
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pdbfile.close()
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def writePKA(protein, parameters, filename=None, conformation ='1A',reference="neutral", direction="folding", verbose=False, options=None):
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"""
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Write the pka-file based on the given protein
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def write_pka(protein, parameters, filename=None, conformation='1A',
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reference="neutral", _="folding", verbose=False,
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__=None):
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"""Write the pKa-file based on the given protein.
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Args:
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protein: protein object
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filename: output file name
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conformation: TODO - figure this out
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reference: reference state
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_: "folding" or other
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verbose: Boolean flag for verbosity
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__: options object
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"""
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# TODO - the code immediately overrides the verbose argument; why?
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verbose = True
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if filename == None:
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filename = "%s.pka" % (protein.name)
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file = open(filename, 'w')
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if verbose == True:
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info("Writing %s" % (filename))
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if filename is None:
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filename = "%s.pka" % (protein.name)
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# TODO - this would be much better with a context manager
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file_ = open(filename, 'w')
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if verbose:
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info("Writing %s" % (filename))
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# writing propka header
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str = "%s\n" % ( getPropkaHeader() )
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str += "%s\n" % ( getReferencesHeader() )
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str += "%s\n" % ( getWarningHeader() )
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str_ = "%s\n" % get_propka_header()
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str_ += "%s\n" % get_references_header()
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str_ += "%s\n" % get_warning_header()
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# writing pKa determinant section
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str += getDeterminantSection(protein,conformation, parameters)
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str_ += get_determinant_section(protein, conformation, parameters)
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# writing pKa summary section
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str += getSummarySection(protein,conformation,parameters)
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str += "%s\n" % ( getTheLine() )
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str_ += get_summary_section(protein, conformation, parameters)
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str_ += "%s\n" % get_the_line()
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# printing Folding Profile
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str += get_folding_profileSection(protein, conformation=conformation, reference=reference, window=[0., 14., 1.0])
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str_ += get_folding_profile_section(protein, conformation=conformation,
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reference=reference,
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window=[0., 14., 1.0])
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# printing Protein Charge Profile
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str += get_charge_profileSection(protein, conformation=conformation)
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str_ += get_charge_profile_section(protein, conformation=conformation)
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# now, writing the pka text to file
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file.write(str)
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file.close()
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file_.write(str_)
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file_.close()
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def printTmProfile(protein, reference="neutral", window=[0., 14., 1.], Tm=[0.,0.], Tms=None, ref=None, verbose=False, options=None):
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def print_tm_profile(protein, reference="neutral", window=[0., 14., 1.],
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__=[0., 0.], tms=None, ref=None, _=False,
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options=None):
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"""Print Tm profile.
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I think Tm refers to the denaturation temperature.
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Args:
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protein: protein object
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reference: reference state
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window: pH window [min, max, step]
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__: temperature range [min, max]
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tms: TODO - figure this out
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ref: TODO - figure this out (probably reference state?)
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_: Boolean for verbosity
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options: options object
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"""
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prints Tm profile
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"""
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profile = protein.getTmProfile(reference=reference, grid=[0., 14., 0.1], Tms=Tms, ref=ref, options=options)
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if profile == None:
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str = "Could not determine Tm-profile\n"
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profile = protein.getTmProfile(reference=reference, grid=[0., 14., 0.1],
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tms=tms, ref=ref, options=options)
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if profile is None:
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str_ = "Could not determine Tm-profile\n"
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else:
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str = " suggested Tm-profile for %s\n" % (protein.name)
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for (pH, Tm) in profile:
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if pH >= window[0] and pH <= window[1] and (pH%window[2] < 0.01 or pH%window[2] > 0.99*window[2]):
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str += "%6.2lf%10.2lf\n" % (pH, Tm)
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info(str)
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str_ = " suggested Tm-profile for %s\n" % (protein.name)
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for (ph, tm_) in profile:
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if ph >= window[0] and ph <= window[1] and (ph%window[2] < 0.01 \
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or ph%window[2] > 0.99*window[2]):
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str_ += "%6.2lf%10.2lf\n" % (ph, tm_)
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info(str_)
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def printResult(protein, conformation, parameters):
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def print_result(protein, conformation, parameters):
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"""Prints all resulting output from determinants and down.
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Args:
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protein: protein object
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conformation: specific conformation
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parameters: parameters
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"""
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prints all resulting output from determinants and down
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"""
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printPKASection(protein, conformation, parameters)
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print_pka_section(protein, conformation, parameters)
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def printPKASection(protein, conformation, parameters):
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"""
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prints out the pka-section of the result
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def print_pka_section(protein, conformation, parameters):
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"""Prints out pKa section of results.
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Args:
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protein: protein object
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conformation: specific conformation
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parameters: parameters
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"""
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# geting the determinants section
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str = getDeterminantSection(protein, conformation, parameters)
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info(str)
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str = getSummarySection(protein,conformation,parameters)
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info(str)
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str_ = get_determinant_section(protein, conformation, parameters)
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info(str_)
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str_ = get_summary_section(protein, conformation, parameters)
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info(str_)
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def getDeterminantSection(protein, conformation, parameters):
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"""
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prints out the pka-section of the result
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def get_determinant_section(protein, conformation, parameters):
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"""Returns string with determinant section of results.
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Args:
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protein: protein object
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conformation: specific conformation
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parameters: parameters
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Returns:
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string
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"""
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# getting the same order as in propka2.0
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str = "%s\n" % ( getDeterminantsHeader() )
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str_ = "%s\n" % get_determinants_header()
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# printing determinants
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for chain in protein.conformations[conformation].chains:
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for residue_type in parameters.write_out_order:
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groups = [g for g in protein.conformations[conformation].groups if g.atom.chain_id == chain]
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groups = [g for g in protein.conformations[conformation].groups \
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if g.atom.chain_id == chain]
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for group in groups:
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if group.residue_type == residue_type:
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str += "%s" % ( group.get_determinant_string(parameters.remove_penalised_group) )
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str_ += "%s" \
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% group.get_determinant_string(parameters.remove_penalised_group)
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# Add a warning in case of coupled residues
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if protein.conformations[conformation].non_covalently_coupled_groups and not protein.options.display_coupled_residues:
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str += 'Coupled residues (marked *) were detected. Please rerun PropKa with the --display-coupled-residues \nor -d option for detailed information.\n'
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return str
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if protein.conformations[conformation].non_covalently_coupled_groups \
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and not protein.options.display_coupled_residues:
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str_ += 'Coupled residues (marked *) were detected.'
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str_ += 'Please rerun PropKa with the --display-coupled-residues \n'
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str_ += 'or -d option for detailed information.\n'
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return str_
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def getSummarySection(protein, conformation, parameters):
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def get_summary_section(protein, conformation, parameters):
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"""Returns string with summary section of the results.
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Args:
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protein: protein object
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conformation: specific conformation
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parameters: parameters
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Returns:
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string
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"""
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prints out the pka-section of the result
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"""
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str = "%s\n" % ( getSummaryHeader() )
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str_ = "%s\n" % get_summary_header()
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# printing pKa summary
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for residue_type in parameters.write_out_order:
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for group in protein.conformations[conformation].groups:
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if group.residue_type == residue_type:
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str += "%s" % ( group.get_summary_string(parameters.remove_penalised_group) )
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return str
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if group.residue_type == residue_type:
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str_ += "%s" \
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% group.get_summary_string(parameters.remove_penalised_group)
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return str_
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def get_folding_profileSection(protein, conformation='AVR', direction="folding", reference="neutral", window=[0., 14., 1.0], verbose=False, options=None):
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def get_folding_profile_section(protein, conformation='AVR',
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direction="folding", reference="neutral",
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window=[0., 14., 1.0], _=False,
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__=None):
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"""Returns string with the folding profile section of the results.
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Args:
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protein: protein object
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conformation: specific conformation
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direction: 'folding' or other
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reference: reference state
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window: pH window [min, max, step]
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_: Boolean for verbose output
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__: options object
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Returns:
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string
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"""
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returns the protein-folding-profile section
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"""
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str = getTheLine()
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str += "\n"
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str += "Free energy of %9s (kcal/mol) as a function of pH (using %s reference)\n" % (direction, reference)
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profile, [pH_opt, dG_opt], [dG_min, dG_max], [pH_min, pH_max] = protein.get_folding_profile(conformation=conformation,
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reference=reference,
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grid=[0., 14., 0.1])
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if profile == None:
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str += "Could not determine folding profile\n"
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str_ = get_the_line()
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str_ += "\n"
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str_ += "Free energy of %9s (kcal/mol) as a function" % direction
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str_ += " of pH (using %s reference)\n" % reference
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profile, [ph_opt, dg_opt], [dg_min, dg_max], [ph_min, ph_max] \
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= protein.get_folding_profile(conformation=conformation,
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reference=reference, grid=[0., 14., 0.1])
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if profile is None:
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str_ += "Could not determine folding profile\n"
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else:
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for (pH, dG) in profile:
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if pH >= window[0] and pH <= window[1] and (pH%window[2] < 0.05 or pH%window[2] > 0.95):
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str += "%6.2lf%10.2lf\n" % (pH, dG)
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str += "\n"
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if pH_opt == None or dG_opt == None:
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str += "Could not determine pH optimum\n"
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for (ph, dg) in profile:
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if ph >= window[0] and ph <= window[1]:
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if ph%window[2] < 0.05 or ph%window[2] > 0.95:
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str_ += "%6.2lf%10.2lf\n" % (ph, dg)
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str_ += "\n"
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if ph_opt is None or dg_opt is None:
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str_ += "Could not determine pH optimum\n"
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else:
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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)
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if dG_min == None or dG_max == None:
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str += "Could not determine pH values where the free energy is within 80 %s of minimum\n" % ("%")
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str_ += "The pH of optimum stability is %4.1lf" % ph_opt
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str_ += " for which the free energy is %6.1lf kcal/mol at 298K\n" % dg_opt
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if dg_min is None or dg_max is None:
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str_ += "Could not determine pH values where the free energy"
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str_ += " is within 80 %s of minimum\n" % ("%")
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else:
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str += "The free energy is within 80 %s of maximum at pH %4.1lf to %4.1lf\n" % ("%", dG_min, dG_max)
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if pH_min == None or pH_max == None:
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str += "Could not determine the pH-range where the free energy is negative\n\n"
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str_ += "The free energy is within 80 \% of maximum"
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str_ += " at pH %4.1lf to %4.1lf\n" % (dg_min, dg_max)
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if ph_min is None or ph_max is None:
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str_ += "Could not determine the pH-range where the free"
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str_ += " energy is negative\n\n"
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else:
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str += "The free energy is negative in the range %4.1lf - %4.1lf\n\n" % (pH_min, pH_max)
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str_ += "The free energy is negative in the range"
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str_ += " %4.1lf - %4.1lf\n\n" % (ph_min, ph_max)
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return str_
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return str
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def get_charge_profile_section(protein, conformation='AVR', _=None):
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"""Returns string with the charge profile section of the results.
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def get_charge_profileSection(protein, conformation='AVR', options=None):
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Args:
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protein: protein object
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conformation: specific conformation
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_: options object
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Returns:
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string
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"""
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returns the protein-folding-profile section
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"""
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str = "Protein charge of folded and unfolded state as a function of pH\n"
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profile = protein.get_charge_profile(conformation=conformation,grid=[0., 14., 1.])
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if profile == None:
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str += "Could not determine charge profile\n"
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str_ = "Protein charge of folded and unfolded state as a function of pH\n"
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profile = protein.get_charge_profile(conformation=conformation,
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grid=[0., 14., 1.])
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if profile is None:
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str_ += "Could not determine charge profile\n"
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else:
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str += "%6s%10s%8s\n" % ("pH", "unfolded", "folded")
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for (pH, Q_mod, Q_pro) in profile:
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str += "%6.2lf%10.2lf%8.2lf\n" % (pH, Q_mod, Q_pro)
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pI_pro, pI_mod = protein.get_pi(conformation=conformation)
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if pI_pro == None or pI_mod == None:
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str += "Could not determine the pI\n\n"
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str_ += "%6s%10s%8s\n" % ("pH", "unfolded", "folded")
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for (ph, q_mod, q_pro) in profile:
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str_ += "%6.2lf%10.2lf%8.2lf\n" % (ph, q_mod, q_pro)
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pi_pro, pi_mod = protein.get_pi(conformation=conformation)
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||||
if pi_pro is None or pi_mod is None:
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str_ += "Could not determine the pI\n\n"
|
||||
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
|
||||
|
||||
|
||||
def writeJackalScapFile(mutationData=None, filename="1xxx_scap.list", options=None):
|
||||
TODO - figure out what this is
|
||||
"""
|
||||
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')
|
||||
|
||||
for chain_id, code1, res_num, code2 in mutationData:
|
||||
str = "%s, %d, %s\n" % (chain_id, res_num, code2)
|
||||
file.write(str)
|
||||
file.close()
|
||||
with open(filename, 'w') as file_:
|
||||
start = 0
|
||||
while len(sequence[start:]) > 60:
|
||||
file_.write("%s\n" % (sequence[start:start+60]))
|
||||
start += 60
|
||||
file_.write("%s\n" % (sequence[start:]))
|
||||
|
||||
|
||||
def writeScwrlSequenceFile(sequence, filename="x-ray.seq", options=None):
|
||||
def get_propka_header():
|
||||
"""Create the header.
|
||||
|
||||
Returns:
|
||||
string
|
||||
"""
|
||||
writing a scwrl sequence file for, e.g., generating a mutated protein
|
||||
"""
|
||||
file = open(filename, 'w')
|
||||
|
||||
start = 0
|
||||
while len(sequence[start:]) > 60:
|
||||
file.write( "%s\n" % (sequence[start:start+60]) )
|
||||
start += 60
|
||||
file.write( "%s\n" % (sequence[start:]) )
|
||||
|
||||
file.close()
|
||||
|
||||
|
||||
|
||||
# --- various header text --- #
|
||||
|
||||
|
||||
def getPropkaHeader():
|
||||
"""
|
||||
Creates the header
|
||||
"""
|
||||
from datetime import date
|
||||
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)
|
||||
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 getReferencesHeader():
|
||||
Returns:
|
||||
string
|
||||
"""
|
||||
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 += "-------------------------------------------------------------------------------------------------------\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
|
||||
str_ = ""
|
||||
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 = ""
|
||||
|
||||
return str
|
||||
str_ = get_the_line()
|
||||
str_ += "\n"
|
||||
str_ += "SUMMARY OF THIS PREDICTION\n"
|
||||
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
|
||||
if len(list)==0:
|
||||
if len(list_) == 0:
|
||||
return ''
|
||||
|
||||
# for long list, use condensed formatting
|
||||
if len(list)>10:
|
||||
if len(list_) > 10:
|
||||
res = 'Condensed form:\n'
|
||||
for i in range(len(list)):
|
||||
for j in range(i,len(list)):
|
||||
if interaction(list[i],list[j]):
|
||||
res += 'Coupling: %9s - %9s\n'%(list[i].label,list[j].label)
|
||||
for i, group1 in enumerate(list_):
|
||||
for group2 in list_[i:]:
|
||||
if interaction(group1, group2):
|
||||
res += 'Coupling: %9s - %9s\n' % (group1.label,
|
||||
group2.label)
|
||||
return res
|
||||
|
||||
# Name and map header
|
||||
res = '%s\n%12s'%(name,'')
|
||||
for g in list:
|
||||
res += '%9s | '%g.label
|
||||
|
||||
res = '%s\n%12s' % (name, '')
|
||||
for group in list_:
|
||||
res += '%9s | ' % group.label
|
||||
# do the map
|
||||
for g1 in list:
|
||||
res += '\n%-12s'%(g1.label)
|
||||
for g2 in list:
|
||||
for group1 in list_:
|
||||
res += '\n%-12s' % (group1.label)
|
||||
for group2 in list_:
|
||||
tag = ''
|
||||
if interaction(g1, g2):
|
||||
if interaction(group1, group2):
|
||||
tag = ' X '
|
||||
res += '%10s| '%tag
|
||||
|
||||
return res
|
||||
|
||||
|
||||
@@ -433,9 +433,9 @@ if __name__ == '__main__':
|
||||
my_protein = protein.Protein(pdblist,'test.pdb')
|
||||
|
||||
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)
|
||||
|
||||
## write out protonated file
|
||||
my_protein.writePDB('protonated.pdb')
|
||||
my_protein.write_pdb('protonated.pdb')
|
||||
|
||||
Reference in New Issue
Block a user