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# @BEGIN LICENSE
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# Psi4: an open-source quantum chemistry software package
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"""Module with utility classes and functions related
to data tables and text.
"""
import sys
import warnings
from psi4 import core
from psi4.driver import constants
[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):
warnings.warn(
"Using `psi4.driver.p4util.Table` is deprecated, and in 1.4 it will stop working\n",
category=FutureWarning,
stacklevel=2)
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:
max_length = max(len(line), max_length)
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."""
warnings.warn(
"Using `psi4.driver.p4util.print_stdout` instead of `print` is deprecated, and in 1.4 it will stop working\n",
category=FutureWarning,
stacklevel=2)
print(stuff, file=sys.stdout)
[docs]def print_stderr(stuff):
"""Function to print *stuff* to standard error stream."""
warnings.warn(
"Using `psi4.driver.p4util.print_stderr` instead of `print(..., file=sys.stderr)` is deprecated, and in 1.4 it will stop working\n",
category=FutureWarning,
stacklevel=2)
print(stuff, file=sys.stderr)
[docs]def levenshtein(seq1, seq2):
"""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):
"""Find list of approximate (within `max_distance`) matches to string `seq1` among `options`."""
return [seq2 for seq2 in options if (levenshtein(seq1, seq2) <= max_distance)]
