199 lines
6.5 KiB
Python
Executable File
199 lines
6.5 KiB
Python
Executable File
#!/usr/bin/python
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import string, sys, copy, math, os
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#
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# file I/O
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#
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def open_file_for_reading(filename):
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if not os.path.isfile(filename):
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raise Exception('Cannot find file %s' %filename)
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return open(filename,'r')
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def open_file_for_writing(filename):
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res = open(filename,'w')
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if not res:
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raise Exception('Could not open %s'%filename)
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return res
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#
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# bookkeeping etc.
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#
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def conformation_sorter(conf):
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model = int(conf[:-1])
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altloc = conf[-1:]
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return model*100+ord(altloc)
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def split_atoms_into_molecules(atoms):
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molecules = []
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while len(atoms)>0:
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initial_atom = atoms.pop()
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molecules.append( make_molecule(initial_atom,atoms))
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return molecules
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def make_molecule(atom, atoms):
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bonded_atoms = [a for a in atoms if atom in a.bonded_atoms]
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res_atoms = [atom,]
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for ba in bonded_atoms:
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if ba in atoms:
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atoms.remove(ba)
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res_atoms.extend(make_molecule(ba, atoms))
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return res_atoms
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def make_grid(min,max,step):
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x = min
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while x <= max:
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yield x
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x += step
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return
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def generate_combinations(interactions):
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res = [[]]
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for interaction in interactions:
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res = make_combination(res, interaction)
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res.remove([])
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return res
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def make_combination(combis, interaction):
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res = []
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for combi in combis:
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res.append(combi+[interaction])
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res.append(combi)
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return res
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def loadOptions():
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"""
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load the arguments parser with options
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"""
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from optparse import OptionParser
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# defining a 'usage' message
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usage = "usage: %prog [options] filename"
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# creating a parser
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parser = OptionParser(usage)
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# loading the parser
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parser.add_option("-f", "--file", action="append", dest="filenames",
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help="read data from <filename>, i.e. <filename> is added to arguments")
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parser.add_option("-r", "--reference", dest="reference", default="neutral",
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help="setting which reference to use for stability calculations [neutral/low-pH]")
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parser.add_option("-c", "--chain", action="append", dest="chains",
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help="creating the protein with only a specified chain, note, chains without ID are labeled 'A' [all]")
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parser.add_option("-t", "--thermophile", action="append", dest="thermophiles",
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help="defining a thermophile filename; usually used in 'alignment-mutations'")
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parser.add_option("-a", "--alignment", action="append", dest="alignment",
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help="alignment file connecting <filename> and <thermophile> [<thermophile>.pir]")
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parser.add_option("-m", "--mutation", action="append", dest="mutations",
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help="specifying mutation labels which is used to modify <filename> according to, e.g. N25R/N181D")
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parser.add_option("-v", "--version", dest="version_label", default="Jan15",
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help="specifying the sub-version of propka [Jan15/Dec19]")
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parser.add_option("-p", "--parameters",dest="parameters", default="propka.cfg",
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help="set the parameter file")
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parser.add_option("-z", "--verbose", dest="verbose", action="store_true", default=True,
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help="sleep during calculations")
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parser.add_option("-q", "--quiet", dest="verbose", action="store_false",
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help="sleep during calculations")
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parser.add_option("-s", "--silent", dest="verbose", action="store_false",
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help="not activated yet")
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parser.add_option("--verbosity", dest="verbosity", action="store_const",
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help="level of printout - not activated yet")
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parser.add_option("-o", "--pH", dest="pH", type="float", default=7.0,
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help="setting pH-value used in e.g. stability calculations [7.0]")
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parser.add_option("-w", "--window", dest="window", nargs=3, type="float", default=(0.0, 14.0, 1.0),
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help="setting the pH-window to show e.g. stability profiles [0.0, 14.0, 1.0]")
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parser.add_option("-g", "--grid", dest="grid", nargs=3, type="float", default=(0.0, 14.0, 0.1),
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help="setting the pH-grid to calculate e.g. stability related properties [0.0, 14.0, 0.1]")
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parser.add_option("--mutator", dest="mutator",
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help="setting approach for mutating <filename> [alignment/scwrl/jackal]")
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parser.add_option("--mutator-option", dest="mutator_options", action="append",
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help="setting property for mutator [e.g. type=\"side-chain\"]")
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parser.add_option("-d","--display-coupled-residues", dest="display_coupled_residues", action="store_true",
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help="Displays alternative pKa values due to coupling of titratable groups")
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parser.add_option("-l","--reuse-ligand-mol2-files", dest="reuse_ligand_mol2_file", action="store_true",
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help="Reuses the ligand mol2 files allowing the user to alter ligand bond orders", default=False)
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parser.add_option("-k","--keep-protons", dest="keep_protons", action="store_true",
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help="Keep protons in input file", default=False)
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parser.add_option("--protonate-all", dest="protonate_all", action="store_true",
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help="Protonate all atoms (will not influence pKa calculation)", default=False)
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# parsing and returning options and arguments
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options, args = parser.parse_args()
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# adding specified filenames to arguments
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if options.filenames:
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for filename in options.filenames:
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args.append(filename)
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# checking at early stage that there is at least one pdbfile to work with
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if len(args) == 0:
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print("Warning: no pdbfile provided")
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#sys.exit(9)
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# done!
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return options, args
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def makeTidyAtomLabel(name,element):
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"""
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Returns a 'tidier' atom label for printing the new pdbfile
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"""
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if len(name)>4:# if longer than 4, just truncate the name
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label=name[0:4]
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elif len(name)==4:# if lenght is 4, otherwise use the name as it is
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label = name
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else: # if less than 4 characters long, insert white space as needed
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if len(element)==1:
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label = ' %-3s'%name
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else: # The element shoul occupy the two first chars
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label = '%-4s'%name
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return label
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def get_sorted_configurations(configuration_keys):
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"""
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extract and sort configurations
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"""
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configurations = list(configuration_keys)
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configurations.sort(key=configuration_compare)
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return configurations
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def configuration_compare(conf):
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return 100*int(conf[1:-2]) + ord(conf[-1])
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def writeFile(filename, lines):
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"""
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Writes a new file
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"""
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file = open(filename, 'w')
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for line in lines:
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file.write( "%s\n" % (line) )
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file.close()
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