Source code for procutil

"""Module with utility functions used by several Python functions."""
import os
import pickle
import PsiMod
import input
from psiexceptions import *

[docs]def kwargs_lower(kwargs): """Function to rebuild and return *kwargs* dictionary with all keys made lowercase. Should be called by every function that could be called directly by the user. """ caseless_kwargs = {} for key, value in kwargs.iteritems(): caseless_kwargs[key.lower()] = value return caseless_kwargs
[docs]def get_psifile(fileno, pidspace=str(os.getpid())): """Function to return the full path and filename for psi file *fileno* (e.g., psi.32) in current namespace *pidspace*. """ psioh = PsiMod.IOManager.shared_object() psio = PsiMod.IO.shared_object() filepath = psioh.get_file_path(fileno) namespace = psio.get_default_namespace() targetfile = filepath + 'psi' + '.' + pidspace + '.' + namespace + '.' + str(fileno) return targetfile
[docs]def format_molecule_for_input(mol): """Function to return a string of the output of :py:func:`input.process_input` applied to the XYZ format of molecule *mol*. Used to capture molecule information for distributed (sow/reap) input files. """ commands = '' commands += 'input.process_input("""\nmolecule %s {\n' % ( commands += mol.save_string_xyz() commands += 'units angstrom\n}\n""", 0)\n' return eval(commands)
[docs]def format_options_for_input(): """Function to return a string of commands to replicate the current state of user-modified options. Used to capture C++ options information for distributed (sow/reap) input files. .. caution:: Some features are not yet implemented. Buy a developer a coffee. - Does not cover local (as opposed to global) options. - Does not work with array-type options. """ commands = '' commands += """\nPsiMod.set_memory(%s)\n\n""" % (PsiMod.get_memory()) for chgdopt in PsiMod.get_global_option_list(): if PsiMod.has_option_changed(chgdopt): chgdoptval = PsiMod.get_global_option(chgdopt) if isinstance(chgdoptval, basestring): commands += """PsiMod.set_global_option('%s', '%s')\n""" % (chgdopt, chgdoptval) elif isinstance(chgdoptval, int) or isinstance(chgdoptval, float): commands += """PsiMod.set_global_option('%s', %s)\n""" % (chgdopt, chgdoptval) else: raise ValidationError('Option \'%s\' is not of a type (string, int, float, bool) that can be processed.' % (chgdopt)) return commands
[docs]def format_kwargs_for_input(filename, lmode=1, **kwargs): """Function to pickle to file *filename* the options dictionary *kwargs*. Mode *lmode* =2 pickles appropriate settings for reap mode. Used to capture Python options information for distributed (sow/reap) input files. """ if lmode == 2: kwargs['mode'] = 'reap' kwargs['linkage'] = os.getpid() filename.write('''\npickle_kw = ("""''') pickle.dump(kwargs, filename) filename.write('''""")\n''') filename.write("""\nkwargs = pickle.loads(pickle_kw)\n""") if lmode == 2: kwargs['mode'] = 'sow' del kwargs['linkage']
[docs]def drop_duplicates(seq): """Function that given an array *seq*, returns an array without any duplicate entries. There is no guarantee of which duplicate entry is dropped. """ noDupes = [] [noDupes.append(i) for i in seq if not noDupes.count(i)] return noDupes