downloaded from propka.ki.ku.dk

Source/lib.py

@@ -0,0 +1,198 @@
+#!/usr/bin/python
+
+import string, sys, copy, math, os
+
+
+#
+# file I/O
+#
+def open_file_for_reading(filename):
+    if not os.path.isfile(filename):
+        raise Exception('Cannot find file %s' %filename)
+    
+    return open(filename,'r')
+
+def open_file_for_writing(filename):
+    res = open(filename,'w')
+    if not res:
+        raise Exception('Could not open %s'%filename)
+    return res
+    
+#
+# bookkeeping etc.
+#
+def conformation_sorter(conf):
+    model = int(conf[:-1])
+    altloc = conf[-1:]
+    return model*100+ord(altloc)
+
+def split_atoms_into_molecules(atoms):
+    molecules = []
+
+    while len(atoms)>0:
+        initial_atom = atoms.pop()
+        molecules.append( make_molecule(initial_atom,atoms))
+
+    return molecules
+
+def make_molecule(atom, atoms):
+    bonded_atoms = [a for a in atoms if atom in a.bonded_atoms]
+    res_atoms = [atom,]
+
+    for ba in bonded_atoms:
+        if ba in atoms:
+            atoms.remove(ba)
+            res_atoms.extend(make_molecule(ba, atoms))
+         
+    return res_atoms
+
+
+def make_grid(min,max,step):
+    x = min
+    while x <= max:
+        yield x
+        x += step
+    return
+
+def generate_combinations(interactions):
+    res = [[]]
+    for interaction in interactions:
+        res = make_combination(res, interaction)
+    res.remove([])
+
+    return res
+    
+
+def make_combination(combis, interaction):
+    res = []
+    for combi in combis:
+        res.append(combi+[interaction])
+        res.append(combi)
+    return res
+
+
+
+def loadOptions():
+    """
+    load the arguments parser with options
+    """
+    from optparse import OptionParser
+
+    # defining a 'usage' message
+    usage = "usage: %prog [options] filename"
+
+    # creating a parser
+    parser = OptionParser(usage)
+
+    # loading the parser
+    parser.add_option("-f", "--file", action="append", dest="filenames", 
+           help="read data from <filename>, i.e. <filename> is added to arguments")
+    parser.add_option("-r", "--reference", dest="reference", default="neutral", 
+           help="setting which reference to use for stability calculations [neutral/low-pH]")
+    parser.add_option("-c", "--chain", action="append", dest="chains", 
+           help="creating the protein with only a specified chain, note, chains without ID are labeled 'A' [all]")
+    parser.add_option("-t", "--thermophile", action="append", dest="thermophiles", 
+           help="defining a thermophile filename; usually used in 'alignment-mutations'")
+    parser.add_option("-a", "--alignment", action="append", dest="alignment", 
+           help="alignment file connecting <filename> and <thermophile> [<thermophile>.pir]")
+    parser.add_option("-m", "--mutation", action="append", dest="mutations", 
+           help="specifying mutation labels which is used to modify <filename> according to, e.g. N25R/N181D")
+    parser.add_option("-v", "--version", dest="version_label", default="Jan15", 
+           help="specifying the sub-version of propka [Jan15/Dec19]")
+    parser.add_option("-p", "--parameters",dest="parameters", default="propka.cfg",
+                      help="set the parameter file")
+    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("-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),
+           help="setting the pH-window to show e.g. stability profiles [0.0, 14.0, 1.0]")
+    parser.add_option("-g", "--grid",   dest="grid",   nargs=3, type="float", default=(0.0, 14.0, 0.1),
+           help="setting the pH-grid to calculate e.g. stability related properties [0.0, 14.0, 0.1]")
+    parser.add_option("--mutator", dest="mutator", 
+           help="setting approach for mutating <filename> [alignment/scwrl/jackal]")
+    parser.add_option("--mutator-option", dest="mutator_options", action="append",
+           help="setting property for mutator [e.g. type=\"side-chain\"]")
+
+    parser.add_option("-d","--display-coupled-residues", dest="display_coupled_residues", action="store_true",
+           help="Displays alternative pKa values due to coupling of titratable groups")
+    parser.add_option("-l","--reuse-ligand-mol2-files", dest="reuse_ligand_mol2_file", action="store_true",
+           help="Reuses the ligand mol2 files allowing the user to alter ligand bond orders", default=False)
+    parser.add_option("-k","--keep-protons", dest="keep_protons", action="store_true",
+           help="Keep protons in input file", default=False)
+    parser.add_option("--protonate-all", dest="protonate_all", action="store_true",
+           help="Protonate all atoms (will not influence pKa calculation)", default=False)
+
+
+    # parsing and returning options and arguments
+    options, args = parser.parse_args()
+
+    # adding specified filenames to arguments
+    if options.filenames:
+      for filename in options.filenames:
+        args.append(filename)
+
+    # checking at early stage that there is at least one pdbfile to work with
+    if len(args) == 0:
+      print("Warning: no pdbfile provided")
+      #sys.exit(9)
+
+
+
+    # done!
+    return options, args
+
+
+
+
+
+def makeTidyAtomLabel(name,element):
+    """
+    Returns a 'tidier' atom label for printing the new pdbfile
+    """
+    
+    if len(name)>4:# if longer than 4, just truncate the name
+        label=name[0:4]
+    elif len(name)==4:# if lenght is 4, otherwise use the name as it is
+        label = name
+    else: # if less than 4 characters long, insert white space as needed
+        if len(element)==1:
+            label = ' %-3s'%name
+        else: # The element shoul occupy the two first chars
+            label = '%-4s'%name
+
+    return label
+
+
+
+def get_sorted_configurations(configuration_keys):
+    """
+    extract and sort configurations
+    """
+    configurations = list(configuration_keys)
+    configurations.sort(key=configuration_compare)
+    return configurations
+
+def configuration_compare(conf):
+    return 100*int(conf[1:-2]) + ord(conf[-1])
+
+
+
+
+def writeFile(filename, lines):
+    """
+    Writes a new file
+    """
+    file = open(filename, 'w')
+
+    for line in lines:
+        file.write( "%s\n" % (line) )
+    file.close()
+
+