#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, version 3.
#
# Psi4 is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Lesser General Public License for more details.
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# You should have received a copy of the GNU Lesser General Public License along
# with Psi4; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
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# @END LICENSE
#
from __future__ import print_function
"""Module with utility classes and functions related
to data tables and text.
"""
import sys
import re
from psi4 import core
from psi4.driver import constants
from .exceptions import *
[docs]class Table(object):
"""Class defining a flexible Table object for storing data."""
def __init__(self, rows=(),
row_label_width=10,
row_label_precision=4,
cols=(),
width=16, precision=10):
self.row_label_width = row_label_width
self.row_label_precision = row_label_precision
self.width = width
self.precision = precision
self.rows = rows
if isinstance(cols, str):
self.cols = (cols,)
else:
self.cols = cols
self.labels = []
self.data = []
def __getitem__(self, value):
self.labels.append(value)
return self
def __setitem__(self, name, value):
self.labels.append(name)
label = self.format_label()
self.labels = []
if isinstance(value, list):
self.data.append((label, value))
else:
self.data.append((label, [value]))
[docs] def save(self, file):
"""Function to save string of the Table object to *file*."""
import pickle
pickle_str = pickle.dumps(self)
fileobj = open(file, "w")
fileobj.write(str(self))
fileobj.close()
def __str__(self):
rowstr = lambda x: '%%%ds' % self.row_label_width % x
colstr = lambda x: '%%%ds' % self.width % x
lines = []
table_header = ""
if isinstance(self.rows, str):
table_header += "%%%ds" % self.row_label_width % self.rows
else:
table_header += " ".join(map(rowstr, self.rows))
table_header += " ".join(map(colstr, self.cols))
lines.append(table_header)
for datarow in self.data:
#print datarow
row_data = datarow[0]
row_data += self.format_values(datarow[1])
lines.append(row_data)
return "\n".join(lines) + "\n"
[docs] def copy(self):
"""Function to return a copy of the Table object."""
import copy
return copy.deepcopy(self)
[docs] def absolute_to_relative(self, Factor=constants.hartree2kcalmol):
"""Function to shift the data of each column of the Table object
such that the lowest value is zero. A scaling factor of *Factor* is applied.
"""
import copy
if len(self.data) == 0:
return
current_min = list(copy.deepcopy(self.data[0][1]))
for datarow in self.data:
for col in range(0, len(datarow[1])):
if current_min[col] > datarow[1][col]:
current_min[col] = datarow[1][col]
for datarow in self.data:
for col in range(0, len(datarow[1])):
#print datarow[1][col]
datarow[1][col] = (datarow[1][col] - current_min[col]) * Factor
[docs] def scale(self, Factor=constants.hartree2kcalmol):
"""Function to apply a scaling factor *Factor* to the
data of the Table object.
"""
if len(self.data) == 0:
return
for datarow in self.data:
for col in range(0, len(datarow[1])):
#print datarow[1][col]
datarow[1][col] = datarow[1][col] * Factor
[docs]def banner(text, type=1, width=35, strNotOutfile=False):
"""Function to print *text* to output file in a banner of
minimum width *width* and minimum three-line height for
*type* = 1 or one-line height for *type* = 2. If *strNotOutfile*
is True, function returns string rather than printing it
to output file.
"""
lines = text.split('\n')
max_length = 0
for line in lines:
if (len(line) > max_length):
max_length = len(line)
max_length = max([width, max_length])
null = ''
if type == 1:
banner = ' //' + null.center(max_length, '>') + '//\n'
for line in lines:
banner += ' //' + line.center(max_length) + '//\n'
banner += ' //' + null.center(max_length, '<') + '//\n'
if type == 2:
banner = ''
for line in lines:
banner += (' ' + line + ' ').center(max_length, '=')
if strNotOutfile:
return banner
else:
core.print_out(banner)
[docs]def print_stdout(stuff):
"""Function to print *stuff* to standard output stream."""
print(stuff, file=sys.stdout)
[docs]def print_stderr(stuff):
"""Function to print *stuff* to standard error stream."""
print(stuff, file=sys.stderr)
[docs]def levenshtein(seq1, seq2):
"""Function to compute the Levenshtein distance between two strings."""
oneago = None
thisrow = list(range(1, len(seq2) + 1)) + [0]
for x in range(len(seq1)):
twoago, oneago, thisrow = oneago, thisrow, [0] * len(seq2) + [x + 1]
for y in range(len(seq2)):
delcost = oneago[y] + 1
addcost = thisrow[y - 1] + 1
subcost = oneago[y - 1] + (seq1[x] != seq2[y])
thisrow[y] = min(delcost, addcost, subcost)
return thisrow[len(seq2) - 1]
[docs]def find_approximate_string_matches(seq1,options,max_distance):
"""Function to compute approximate string matches from a list of options."""
matches = []
for seq2 in options:
distance = levenshtein(seq1,seq2)
if distance <= max_distance:
matches.append(seq2)
return matches
