Change organisation
This commit is contained in:
Thomas Applencourt
parent
0af5cb6fa1
commit
baebe0de19
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@ -38,11 +38,11 @@ Example of use:
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./EMSL_api.py get_basis_data --basis 3-21++G*
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"""
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version = "0.3.0"
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version = "0.8.1"
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import os
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from src.docopt import docopt
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from src.misc.docopt import docopt
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from src.EMSL_dump import EMSL_dump
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from src.EMSL_local import EMSL_local, checkSQLite3
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@ -5,7 +5,7 @@ import time
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import sqlite3
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from collections import OrderedDict
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from src.parser import format_dict
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from src.parser_handler import format_dict
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def install_with_pip(name):
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@ -233,6 +233,7 @@ class EMSL_dump:
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basis_data = self.parser(text, name, des, elts,
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self.debug)
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except:
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raise
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time.sleep(0.1)
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attemps += 1
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else:
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@ -192,7 +192,7 @@ class EMSL_local:
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dict_info = OrderedDict()
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# Description : dict_info[name] = [description, nb_mo, nb_ele]
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from src.parser import get_symmetry_function
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from src.parser_handler import get_symmetry_function
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if average_mo_number:
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f_symmetry = get_symmetry_function(self.format)
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@ -267,7 +267,7 @@ class EMSL_local:
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# h a n d l e _ f #
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# ~#~#~#~#~#~#~#~ #
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if handle_l_format:
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from src.parser import get_handle_l_function
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from src.parser_handler import get_handle_l_function
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f = get_handle_l_function(self.format)
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l_atom_basis = f(l_atom_basis)
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@ -277,8 +277,8 @@ class EMSL_local:
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if check_format:
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from src.parser import get_symmetry_function
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from src.check_validity import get_check_function
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from src.parser_handler import get_symmetry_function
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from src.parser.check_validity import get_check_function
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f = get_check_function(check_format)
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f_symmetry = get_symmetry_function(self.format)
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@ -1,52 +0,0 @@
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# _
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# / |_ _ _ | _. | o _| o _|_
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# \_ | | (/_ (_ |< \/ (_| | | (_| | |_ \/
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# /
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# Do this After the L special case traitement.
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import sys
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def check_gamess(str_type):
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"""Check is the orbital type is handle by gamess"""
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assert len(str_type) == 1
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if str_type in "S P D".split():
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return True
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elif str_type == "SP":
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raise BaseException
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else:
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return True
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def check_NWChem(str_type):
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"""Check is the orbital type is handle by gamess"""
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assert len(str_type) == 1
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if str_type in "S P D".split():
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return True
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elif str_type > "I" or str_type in "K L M".split():
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raise BaseException
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else:
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return True
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d_check = {"GAMESS-US": check_gamess,
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"NWChem": check_NWChem}
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def get_check_function(name_program):
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"""
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Tranforme SP special function (create using get_symmetry_function)
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into S and P
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"""
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try:
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f = d_check[name_program]
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except KeyError:
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str_ = "You need to add a check funtion for your program {0}"
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print >> sys.stderr, str_.format(name_program)
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print >> sys.stderr, "This one are avalaible {0}".format(d_check.keys())
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sys.exit(1)
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return f
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590
src/docopt.py
590
src/docopt.py
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@ -1,590 +0,0 @@
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"""Pythonic command-line interface parser that will make you smile.
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* http://docopt.org
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* Repository and issue-tracker: https://github.com/docopt/docopt
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* Licensed under terms of MIT license (see LICENSE-MIT)
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* Copyright (c) 2013 Vladimir Keleshev, vladimir@keleshev.com
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"""
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import sys
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import re
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__all__ = ['docopt']
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__version__ = '0.6.1'
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class DocoptLanguageError(Exception):
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"""Error in construction of usage-message by developer."""
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class DocoptExit(SystemExit):
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"""Exit in case user invoked program with incorrect arguments."""
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usage = ''
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def __init__(self, message=''):
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SystemExit.__init__(self, (message + '\n' + self.usage).strip())
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class Pattern(object):
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def __eq__(self, other):
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return repr(self) == repr(other)
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def __hash__(self):
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return hash(repr(self))
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def fix(self):
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self.fix_identities()
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self.fix_repeating_arguments()
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return self
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def fix_identities(self, uniq=None):
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"""Make pattern-tree tips point to same object if they are equal."""
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if not hasattr(self, 'children'):
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return self
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uniq = list(set(self.flat())) if uniq is None else uniq
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for i, child in enumerate(self.children):
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if not hasattr(child, 'children'):
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assert child in uniq
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self.children[i] = uniq[uniq.index(child)]
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else:
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child.fix_identities(uniq)
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def fix_repeating_arguments(self):
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"""Fix elements that should accumulate/increment values."""
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either = [list(child.children) for child in transform(self).children]
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for case in either:
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for e in [child for child in case if case.count(child) > 1]:
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if isinstance(
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e,
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Argument) or isinstance(
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e,
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Option) and e.argcount:
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if e.value is None:
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e.value = []
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elif not isinstance(e.value, list):
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e.value = e.value.split()
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if isinstance(
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e,
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Command) or isinstance(
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e,
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Option) and e.argcount == 0:
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e.value = 0
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return self
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def transform(pattern):
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"""Expand pattern into an (almost) equivalent one, but with single Either.
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Example: ((-a | -b) (-c | -d)) => (-a -c | -a -d | -b -c | -b -d)
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Quirks: [-a] => (-a), (-a...) => (-a -a)
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"""
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result = []
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groups = [[pattern]]
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while groups:
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children = groups.pop(0)
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parents = [Required, Optional, OptionsShortcut, Either, OneOrMore]
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if any(t in map(type, children) for t in parents):
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child = [c for c in children if type(c) in parents][0]
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children.remove(child)
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if isinstance(child, Either):
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for c in child.children:
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groups.append([c] + children)
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elif isinstance(child, OneOrMore):
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groups.append(child.children * 2 + children)
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else:
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groups.append(child.children + children)
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else:
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result.append(children)
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return Either(*[Required(*e) for e in result])
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class LeafPattern(Pattern):
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"""Leaf/terminal node of a pattern tree."""
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def __init__(self, name, value=None):
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self.name, self.value = name, value
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def __repr__(self):
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return '%s(%r, %r)' % (self.__class__.__name__, self.name, self.value)
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def flat(self, *types):
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return [self] if not types or type(self) in types else []
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def match(self, left, collected=None):
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collected = [] if collected is None else collected
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pos, match = self.single_match(left)
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if match is None:
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return False, left, collected
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left_ = left[:pos] + left[pos + 1:]
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same_name = [a for a in collected if a.name == self.name]
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if type(self.value) in (int, list):
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if isinstance(self.value, int):
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increment = 1
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else:
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increment = ([match.value] if isinstance(match.value, str)
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else match.value)
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if not same_name:
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match.value = increment
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return True, left_, collected + [match]
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same_name[0].value += increment
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return True, left_, collected
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return True, left_, collected + [match]
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class BranchPattern(Pattern):
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"""Branch/inner node of a pattern tree."""
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def __init__(self, *children):
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self.children = list(children)
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def __repr__(self):
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return '%s(%s)' % (self.__class__.__name__,
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', '.join(repr(a) for a in self.children))
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def flat(self, *types):
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if type(self) in types:
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return [self]
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return sum([child.flat(*types) for child in self.children], [])
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class Argument(LeafPattern):
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def single_match(self, left):
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for n, pattern in enumerate(left):
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if isinstance(pattern, Argument):
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return n, Argument(self.name, pattern.value)
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return None, None
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@classmethod
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def parse(class_, source):
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name = re.findall('(<\S*?>)', source)[0]
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value = re.findall('\[default: (.*)\]', source, flags=re.I)
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return class_(name, value[0] if value else None)
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class Command(Argument):
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def __init__(self, name, value=False):
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self.name, self.value = name, value
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def single_match(self, left):
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for n, pattern in enumerate(left):
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if isinstance(pattern, Argument):
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if pattern.value == self.name:
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return n, Command(self.name, True)
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else:
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break
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return None, None
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class Option(LeafPattern):
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def __init__(self, short=None, long=None, argcount=0, value=False):
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assert argcount in (0, 1)
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self.short, self.long, self.argcount = short, long, argcount
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self.value = None if value is False and argcount else value
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@classmethod
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def parse(class_, option_description):
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short, long, argcount, value = None, None, 0, False
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options, _, description = option_description.strip().partition(' ')
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options = options.replace(',', ' ').replace('=', ' ')
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for s in options.split():
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if s.startswith('--'):
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long = s
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elif s.startswith('-'):
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short = s
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else:
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argcount = 1
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if argcount:
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matched = re.findall('\[default: (.*)\]', description, flags=re.I)
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value = matched[0] if matched else None
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return class_(short, long, argcount, value)
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def single_match(self, left):
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for n, pattern in enumerate(left):
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if self.name == pattern.name:
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return n, pattern
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return None, None
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@property
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def name(self):
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return self.long or self.short
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def __repr__(self):
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return 'Option(%r, %r, %r, %r)' % (self.short, self.long,
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self.argcount, self.value)
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class Required(BranchPattern):
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def match(self, left, collected=None):
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collected = [] if collected is None else collected
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l = left
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c = collected
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for pattern in self.children:
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matched, l, c = pattern.match(l, c)
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if not matched:
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return False, left, collected
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return True, l, c
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class Optional(BranchPattern):
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def match(self, left, collected=None):
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collected = [] if collected is None else collected
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for pattern in self.children:
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m, left, collected = pattern.match(left, collected)
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return True, left, collected
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class OptionsShortcut(Optional):
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"""Marker/placeholder for [options] shortcut."""
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class OneOrMore(BranchPattern):
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def match(self, left, collected=None):
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assert len(self.children) == 1
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collected = [] if collected is None else collected
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l = left
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c = collected
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l_ = None
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matched = True
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times = 0
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while matched:
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# could it be that something didn't match but changed l or c?
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matched, l, c = self.children[0].match(l, c)
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times += 1 if matched else 0
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if l_ == l:
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break
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l_ = l
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if times >= 1:
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return True, l, c
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return False, left, collected
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class Either(BranchPattern):
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def match(self, left, collected=None):
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collected = [] if collected is None else collected
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outcomes = []
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for pattern in self.children:
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matched, _, _ = outcome = pattern.match(left, collected)
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if matched:
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outcomes.append(outcome)
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if outcomes:
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return min(outcomes, key=lambda outcome: len(outcome[1]))
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return False, left, collected
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class Tokens(list):
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def __init__(self, source, error=DocoptExit):
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self += source.split() if hasattr(source, 'split') else source
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self.error = error
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@staticmethod
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def from_pattern(source):
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source = re.sub(r'([\[\]\(\)\|]|\.\.\.)', r' \1 ', source)
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source = [s for s in re.split('\s+|(\S*<.*?>)', source) if s]
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return Tokens(source, error=DocoptLanguageError)
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def move(self):
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return self.pop(0) if len(self) else None
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def current(self):
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return self[0] if len(self) else None
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def parse_long(tokens, options):
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"""long ::= '--' chars [ ( ' ' | '=' ) chars ] ;"""
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long, eq, value = tokens.move().partition('=')
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assert long.startswith('--')
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value = None if eq == value == '' else value
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similar = [o for o in options if o.long == long]
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if tokens.error is DocoptExit and similar == []: # if no exact match
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similar = [o for o in options if o.long and o.long.startswith(long)]
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if len(similar) > 1: # might be simply specified ambiguously 2+ times?
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raise tokens.error('%s is not a unique prefix: %s?' %
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(long, ', '.join(o.long for o in similar)))
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elif len(similar) < 1:
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argcount = 1 if eq == '=' else 0
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o = Option(None, long, argcount)
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options.append(o)
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if tokens.error is DocoptExit:
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o = Option(None, long, argcount, value if argcount else True)
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else:
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o = Option(similar[0].short, similar[0].long,
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similar[0].argcount, similar[0].value)
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if o.argcount == 0:
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if value is not None:
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raise tokens.error('%s must not have an argument' % o.long)
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else:
|
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if value is None:
|
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if tokens.current() in [None, '--']:
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raise tokens.error('%s requires argument' % o.long)
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value = tokens.move()
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if tokens.error is DocoptExit:
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o.value = value if value is not None else True
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return [o]
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def parse_shorts(tokens, options):
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"""shorts ::= '-' ( chars )* [ [ ' ' ] chars ] ;"""
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token = tokens.move()
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assert token.startswith('-') and not token.startswith('--')
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left = token.lstrip('-')
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parsed = []
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while left != '':
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short, left = '-' + left[0], left[1:]
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similar = [o for o in options if o.short == short]
|
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if len(similar) > 1:
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raise tokens.error('%s is specified ambiguously %d times' %
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(short, len(similar)))
|
||||
elif len(similar) < 1:
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o = Option(short, None, 0)
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options.append(o)
|
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if tokens.error is DocoptExit:
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o = Option(short, None, 0, True)
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else: # why copying is necessary here?
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o = Option(short, similar[0].long,
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similar[0].argcount, similar[0].value)
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value = None
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if o.argcount != 0:
|
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if left == '':
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if tokens.current() in [None, '--']:
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raise tokens.error('%s requires argument' % short)
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value = tokens.move()
|
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else:
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value = left
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left = ''
|
||||
if tokens.error is DocoptExit:
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o.value = value if value is not None else True
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parsed.append(o)
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return parsed
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|
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|
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def parse_pattern(source, options):
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tokens = Tokens.from_pattern(source)
|
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result = parse_expr(tokens, options)
|
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if tokens.current() is not None:
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raise tokens.error('unexpected ending: %r' % ' '.join(tokens))
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return Required(*result)
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|
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|
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def parse_expr(tokens, options):
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"""expr ::= seq ( '|' seq )* ;"""
|
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seq = parse_seq(tokens, options)
|
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if tokens.current() != '|':
|
||||
return seq
|
||||
result = [Required(*seq)] if len(seq) > 1 else seq
|
||||
while tokens.current() == '|':
|
||||
tokens.move()
|
||||
seq = parse_seq(tokens, options)
|
||||
result += [Required(*seq)] if len(seq) > 1 else seq
|
||||
return [Either(*result)] if len(result) > 1 else result
|
||||
|
||||
|
||||
def parse_seq(tokens, options):
|
||||
"""seq ::= ( atom [ '...' ] )* ;"""
|
||||
result = []
|
||||
while tokens.current() not in [None, ']', ')', '|']:
|
||||
atom = parse_atom(tokens, options)
|
||||
if tokens.current() == '...':
|
||||
atom = [OneOrMore(*atom)]
|
||||
tokens.move()
|
||||
result += atom
|
||||
return result
|
||||
|
||||
|
||||
def parse_atom(tokens, options):
|
||||
"""atom ::= '(' expr ')' | '[' expr ']' | 'options'
|
||||
| long | shorts | argument | command ;
|
||||
"""
|
||||
token = tokens.current()
|
||||
result = []
|
||||
if token in '([':
|
||||
tokens.move()
|
||||
matching, pattern = {'(': [')', Required], '[': [']', Optional]}[token]
|
||||
result = pattern(*parse_expr(tokens, options))
|
||||
if tokens.move() != matching:
|
||||
raise tokens.error("unmatched '%s'" % token)
|
||||
return [result]
|
||||
elif token == 'options':
|
||||
tokens.move()
|
||||
return [OptionsShortcut()]
|
||||
elif token.startswith('--') and token != '--':
|
||||
return parse_long(tokens, options)
|
||||
elif token.startswith('-') and token not in ('-', '--'):
|
||||
return parse_shorts(tokens, options)
|
||||
elif token.startswith('<') and token.endswith('>') or token.isupper():
|
||||
return [Argument(tokens.move())]
|
||||
else:
|
||||
return [Command(tokens.move())]
|
||||
|
||||
|
||||
def parse_argv(tokens, options, options_first=False):
|
||||
"""Parse command-line argument vector.
|
||||
|
||||
If options_first:
|
||||
argv ::= [ long | shorts ]* [ argument ]* [ '--' [ argument ]* ] ;
|
||||
else:
|
||||
argv ::= [ long | shorts | argument ]* [ '--' [ argument ]* ] ;
|
||||
|
||||
"""
|
||||
parsed = []
|
||||
while tokens.current() is not None:
|
||||
if tokens.current() == '--':
|
||||
return parsed + [Argument(None, v) for v in tokens]
|
||||
elif tokens.current().startswith('--'):
|
||||
parsed += parse_long(tokens, options)
|
||||
elif tokens.current().startswith('-') and tokens.current() != '-':
|
||||
parsed += parse_shorts(tokens, options)
|
||||
elif options_first:
|
||||
return parsed + [Argument(None, v) for v in tokens]
|
||||
else:
|
||||
parsed.append(Argument(None, tokens.move()))
|
||||
return parsed
|
||||
|
||||
|
||||
def parse_defaults(doc):
|
||||
defaults = []
|
||||
for s in parse_section('options:', doc):
|
||||
# FIXME corner case "bla: options: --foo"
|
||||
_, _, s = s.partition(':') # get rid of "options:"
|
||||
split = re.split('\n[ \t]*(-\S+?)', '\n' + s)[1:]
|
||||
split = [s1 + s2 for s1, s2 in zip(split[::2], split[1::2])]
|
||||
options = [Option.parse(s) for s in split if s.startswith('-')]
|
||||
defaults += options
|
||||
return defaults
|
||||
|
||||
|
||||
def parse_section(name, source):
|
||||
pattern = re.compile('^([^\n]*' + name + '[^\n]*\n?(?:[ \t].*?(?:\n|$))*)',
|
||||
re.IGNORECASE | re.MULTILINE)
|
||||
return [s.strip() for s in pattern.findall(source)]
|
||||
|
||||
|
||||
def formal_usage(section):
|
||||
_, _, section = section.partition(':') # drop "usage:"
|
||||
pu = section.split()
|
||||
return '( ' + ' '.join(') | (' if s == pu[0] else s for s in pu[1:]) + ' )'
|
||||
|
||||
|
||||
def extras(help, version, options, doc):
|
||||
if help and any((o.name in ('-h', '--help')) and o.value for o in options):
|
||||
print(doc.strip("\n"))
|
||||
sys.exit()
|
||||
if version and any(o.name == '--version' and o.value for o in options):
|
||||
print(version)
|
||||
sys.exit()
|
||||
|
||||
|
||||
class Dict(dict):
|
||||
|
||||
def __repr__(self):
|
||||
return '{%s}' % ',\n '.join('%r: %r' % i for i in sorted(self.items()))
|
||||
|
||||
|
||||
def docopt(doc, argv=None, help=True, version=None, options_first=False):
|
||||
"""Parse `argv` based on command-line interface described in `doc`.
|
||||
|
||||
`docopt` creates your command-line interface based on its
|
||||
description that you pass as `doc`. Such description can contain
|
||||
--options, <positional-argument>, commands, which could be
|
||||
[optional], (required), (mutually | exclusive) or repeated...
|
||||
|
||||
Parameters
|
||||
----------
|
||||
doc : str
|
||||
Description of your command-line interface.
|
||||
argv : list of str, optional
|
||||
Argument vector to be parsed. sys.argv[1:] is used if not
|
||||
provided.
|
||||
help : bool (default: True)
|
||||
Set to False to disable automatic help on -h or --help
|
||||
options.
|
||||
version : any object
|
||||
If passed, the object will be printed if --version is in
|
||||
`argv`.
|
||||
options_first : bool (default: False)
|
||||
Set to True to require options precede positional arguments,
|
||||
i.e. to forbid options and positional arguments intermix.
|
||||
|
||||
Returns
|
||||
-------
|
||||
args : dict
|
||||
A dictionary, where keys are names of command-line elements
|
||||
such as e.g. "--verbose" and "<path>", and values are the
|
||||
parsed values of those elements.
|
||||
|
||||
Example
|
||||
-------
|
||||
>>> from docopt import docopt
|
||||
>>> doc = '''
|
||||
... Usage:
|
||||
... my_program tcp <host> <port> [--timeout=<seconds>]
|
||||
... my_program serial <port> [--baud=<n>] [--timeout=<seconds>]
|
||||
... my_program (-h | --help | --version)
|
||||
...
|
||||
... Options:
|
||||
... -h, --help Show this screen and exit.
|
||||
... --baud=<n> Baudrate [default: 9600]
|
||||
... '''
|
||||
>>> argv = ['tcp', '127.0.0.1', '80', '--timeout', '30']
|
||||
>>> docopt(doc, argv)
|
||||
{'--baud': '9600',
|
||||
'--help': False,
|
||||
'--timeout': '30',
|
||||
'--version': False,
|
||||
'<host>': '127.0.0.1',
|
||||
'<port>': '80',
|
||||
'serial': False,
|
||||
'tcp': True}
|
||||
|
||||
See also
|
||||
--------
|
||||
* For video introduction see http://docopt.org
|
||||
* Full documentation is available in README.rst as well as online
|
||||
at https://github.com/docopt/docopt#readme
|
||||
|
||||
"""
|
||||
argv = sys.argv[1:] if argv is None else argv
|
||||
|
||||
usage_sections = parse_section('usage:', doc)
|
||||
if len(usage_sections) == 0:
|
||||
raise DocoptLanguageError('"usage:" (case-insensitive) not found.')
|
||||
if len(usage_sections) > 1:
|
||||
raise DocoptLanguageError('More than one "usage:" (case-insensitive).')
|
||||
DocoptExit.usage = usage_sections[0]
|
||||
|
||||
options = parse_defaults(doc)
|
||||
pattern = parse_pattern(formal_usage(DocoptExit.usage), options)
|
||||
# [default] syntax for argument is disabled
|
||||
# for a in pattern.flat(Argument):
|
||||
# same_name = [d for d in arguments if d.name == a.name]
|
||||
# if same_name:
|
||||
# a.value = same_name[0].value
|
||||
argv = parse_argv(Tokens(argv), list(options), options_first)
|
||||
pattern_options = set(pattern.flat(Option))
|
||||
for options_shortcut in pattern.flat(OptionsShortcut):
|
||||
doc_options = parse_defaults(doc)
|
||||
options_shortcut.children = list(set(doc_options) - pattern_options)
|
||||
# if any_options:
|
||||
# options_shortcut.children += [Option(o.short, o.long, o.argcount)
|
||||
# for o in argv if type(o) is Option]
|
||||
extras(help, version, argv, doc)
|
||||
matched, left, collected = pattern.fix().match(argv)
|
||||
if matched and left == []: # better error message if left?
|
||||
return Dict((a.name, a.value) for a in (pattern.flat() + collected))
|
||||
raise DocoptExit()
|
||||
|
|
@ -1,118 +0,0 @@
|
|||
1 - H - Hydrogen
|
||||
2 - He - Helium
|
||||
3 - Li - Lithium
|
||||
4 - Be - Beryllium
|
||||
5 - B - Boron
|
||||
6 - C - Carbon
|
||||
7 - N - Nitrogen
|
||||
8 - O - Oxygen
|
||||
9 - F - Fluorine
|
||||
10 - Ne - Neon
|
||||
11 - Na - Sodium
|
||||
12 - Mg - Magnesium
|
||||
13 - Al - Aluminum
|
||||
14 - Si - Silicon
|
||||
15 - P - Phosphorus
|
||||
16 - S - Sulfur
|
||||
17 - Cl - Chlorine
|
||||
18 - Ar - Argon
|
||||
19 - K - Potassium
|
||||
20 - Ca - Calcium
|
||||
21 - Sc - Scandium
|
||||
22 - Ti - Titanium
|
||||
23 - V - Vanadium
|
||||
24 - Cr - Chromium
|
||||
25 - Mn - Manganese
|
||||
26 - Fe - Iron
|
||||
27 - Co - Cobalt
|
||||
28 - Ni - Nickel
|
||||
29 - Cu - Copper
|
||||
30 - Zn - Zinc
|
||||
31 - Ga - Gallium
|
||||
32 - Ge - Germanium
|
||||
33 - As - Arsenic
|
||||
34 - Se - Selenium
|
||||
35 - Br - Bromine
|
||||
36 - Kr - Krypton
|
||||
37 - Rb - Rubidium
|
||||
38 - Sr - Strontium
|
||||
39 - Y - Yttrium
|
||||
40 - Zr - Zirconium
|
||||
41 - Nb - Niobium
|
||||
42 - Mo - Molybdenum
|
||||
43 - Tc - Technetium
|
||||
44 - Ru - Ruthenium
|
||||
45 - Rh - Rhodium
|
||||
46 - Pd - Palladium
|
||||
47 - Ag - Silver
|
||||
48 - Cd - Cadmium
|
||||
49 - In - Indium
|
||||
50 - Sn - Tin
|
||||
51 - Sb - Antimony
|
||||
52 - Te - Tellurium
|
||||
53 - I - Iodine
|
||||
54 - Xe - Xenon
|
||||
55 - Cs - Cesium
|
||||
56 - Ba - Barium
|
||||
57 - La - Lanthanum
|
||||
58 - Ce - Cerium
|
||||
59 - Pr - Praseodymium
|
||||
60 - Nd - Neodymium
|
||||
61 - Pm - Promethium
|
||||
62 - Sm - Samarium
|
||||
63 - Eu - Europium
|
||||
64 - Gd - Gadolinium
|
||||
65 - Tb - Terbium
|
||||
66 - Dy - Dysprosium
|
||||
67 - Ho - Holmium
|
||||
68 - Er - Erbium
|
||||
69 - Tm - Thulium
|
||||
70 - Yb - Ytterbium
|
||||
71 - Lu - Lutetium
|
||||
72 - Hf - Hafnium
|
||||
73 - Ta - Tantalum
|
||||
74 - W - Tungsten
|
||||
75 - Re - Rhenium
|
||||
76 - Os - Osmium
|
||||
77 - Ir - Iridium
|
||||
78 - Pt - Platinum
|
||||
79 - Au - Gold
|
||||
80 - Hg - Mercury
|
||||
81 - Tl - Thallium
|
||||
82 - Pb - Lead
|
||||
83 - Bi - Bismuth
|
||||
84 - Po - Polonium
|
||||
85 - At - Astatine
|
||||
86 - Rn - Radon
|
||||
87 - Fr - Francium
|
||||
88 - Ra - Radium
|
||||
89 - Ac - Actinium
|
||||
90 - Th - Thorium
|
||||
91 - Pa - Protactinium
|
||||
92 - U - Uranium
|
||||
93 - Np - Neptunium
|
||||
94 - Pu - Plutonium
|
||||
95 - Am - Americium
|
||||
96 - Cm - Curium
|
||||
97 - Bk - Berkelium
|
||||
98 - Cf - Californium
|
||||
99 - Es - Einsteinium
|
||||
100 - Fm - Fermium
|
||||
101 - Md - Mendelevium
|
||||
102 - No - Nobelium
|
||||
103 - Lr - Lawrencium
|
||||
104 - Rf - Rutherfordium
|
||||
105 - Db - Dubnium
|
||||
106 - Sg - Seaborgium
|
||||
107 - Bh - Bohrium
|
||||
108 - Hs - Hassium
|
||||
109 - Mt - Meitnerium
|
||||
110 - Ds - Darmstadtium
|
||||
111 - Rg - Roentgenium
|
||||
112 - Cn - Copernicium
|
||||
113 - Uut - Ununtrium
|
||||
114 - Fl - Flerovium
|
||||
115 - Uup - Ununpentium
|
||||
116 - Lv - Livermorium
|
||||
117 - Uus - Ununseptium
|
||||
118 - Uuo - Ununoctium
|
||||
326
src/parser.py
326
src/parser.py
|
|
@ -1,326 +0,0 @@
|
|||
import sys
|
||||
import os
|
||||
import re
|
||||
|
||||
|
||||
def get_dict_ele():
|
||||
"""Return dict[atom]=[abreviation]"""
|
||||
elt_path = os.path.dirname(sys.argv[0]) + "/src/elts_abrev.dat"
|
||||
|
||||
with open(elt_path, "r") as f:
|
||||
data = f.readlines()
|
||||
|
||||
dict_ele = dict()
|
||||
for i in data:
|
||||
l = i.split("-")
|
||||
dict_ele[l[1].strip().lower()] = l[2].strip().lower()
|
||||
|
||||
return dict_ele
|
||||
|
||||
|
||||
# ______
|
||||
# | ___ \
|
||||
# | |_/ /_ _ _ __ ___ ___ _ __
|
||||
# | __/ _` | '__/ __|/ _ \ '__|
|
||||
# | | | (_| | | \__ \ __/ |
|
||||
# \_| \__,_|_| |___/\___|_|
|
||||
#
|
||||
|
||||
# __
|
||||
# /__ _. ._ _ _ _ _ _
|
||||
# \_| (_| | | | (/_ _> _> |_| _>
|
||||
#
|
||||
def parse_basis_data_gamess_us(data, name, des, elts, debug=False):
|
||||
"""Parse the basis data raw html of gamess-us to get a nice tuple
|
||||
Return [name, description, [[ele, data_ele],...]]"""
|
||||
basis_data = []
|
||||
|
||||
b = data.find("$DATA")
|
||||
e = data.find("$END")
|
||||
if (b == -1 or data.find("$DATA$END") != -1):
|
||||
if debug:
|
||||
print data
|
||||
raise Exception("WARNING not DATA")
|
||||
else:
|
||||
dict_replace = {"PHOSPHOROUS": "PHOSPHORUS",
|
||||
"D+": "E+",
|
||||
"D-": "E-"}
|
||||
|
||||
for k, v in dict_replace.iteritems():
|
||||
data = data.replace(k, v)
|
||||
|
||||
data = data[b + 5:e - 1].split('\n\n')
|
||||
|
||||
dict_ele = get_dict_ele()
|
||||
|
||||
for (elt, data_elt) in zip(elts, data):
|
||||
|
||||
elt_long_th = dict_ele[elt.lower()]
|
||||
elt_long_exp = data_elt.split()[0].lower()
|
||||
|
||||
if "$" in data_elt:
|
||||
if debug:
|
||||
print "Eror",
|
||||
raise Exception("WARNING bad split")
|
||||
|
||||
if elt_long_th == elt_long_exp:
|
||||
basis_data.append([elt, data_elt.strip()])
|
||||
else:
|
||||
if debug:
|
||||
print "th", elt_long_th
|
||||
print "exp", elt_long_exp
|
||||
print "abv", elt
|
||||
raise Exception("WARNING not a good ELEMENT")
|
||||
|
||||
return [name, des, basis_data]
|
||||
|
||||
|
||||
symmetry_regex = re.compile(ur'^(\w)\s+\d+\b')
|
||||
|
||||
|
||||
def l_symmetry_gamess_us(atom_basis):
|
||||
"""
|
||||
Return the begin and the end of all the type of orbital
|
||||
input: atom_basis = [name, S 1, 12 0.12 12212, ...]
|
||||
output: [ [type, begin, end], ...]
|
||||
"""
|
||||
# Example
|
||||
# [[u'S', 1, 5], [u'L', 5, 9], [u'L', 9, 12], [u'D', 16, 18]]"
|
||||
|
||||
l = []
|
||||
for i, line in enumerate(atom_basis):
|
||||
m = re.search(symmetry_regex, line)
|
||||
if m:
|
||||
# Cause of L !
|
||||
read_symmetry = m.group(1)
|
||||
|
||||
# L is real L or special SP
|
||||
# Just check the number of exponant
|
||||
if read_symmetry == "L" and len(atom_basis[i + 1].split()) == 4:
|
||||
real_symmetry = "SP"
|
||||
else:
|
||||
real_symmetry = read_symmetry
|
||||
|
||||
l.append([real_symmetry, i])
|
||||
try:
|
||||
l[-2].append(i)
|
||||
except IndexError:
|
||||
pass
|
||||
|
||||
l[-1].append(i + 1)
|
||||
return l
|
||||
|
||||
|
||||
def handle_l_gamess_us(l_atom_basis):
|
||||
"""
|
||||
Read l_atom_basis and change the SP in L and P
|
||||
"""
|
||||
|
||||
l_data = []
|
||||
for atom_basis in l_atom_basis:
|
||||
|
||||
# Split the data in line
|
||||
l_line_raw = atom_basis.split("\n")
|
||||
l_line = [l_line_raw[0]]
|
||||
# l_line_raw[0] containt the name of the Atom
|
||||
|
||||
for symmetry, begin, end in l_symmetry_gamess_us(l_line_raw):
|
||||
|
||||
if symmetry == "SP":
|
||||
|
||||
body_s = []
|
||||
body_p = []
|
||||
|
||||
for i_l in l_line_raw[begin + 1:end]:
|
||||
|
||||
# one L => S & P
|
||||
a = i_l.split()
|
||||
|
||||
common = "{:>3}".format(a[0])
|
||||
common += "{:>15.7f}".format(float(a[1]))
|
||||
|
||||
tail_s = common + "{:>23.7f}".format(float(a[2]))
|
||||
body_s.append(tail_s)
|
||||
|
||||
tail_p = common + "{:>23.7f}".format(float(a[3]))
|
||||
body_p.append(tail_p)
|
||||
|
||||
l_line += [l_line_raw[begin].replace("L", "S")]
|
||||
l_line += body_s
|
||||
|
||||
l_line += [l_line_raw[begin].replace("L", "P")]
|
||||
l_line += body_p
|
||||
else:
|
||||
l_line += l_line_raw[begin:end]
|
||||
|
||||
l_data.append("\n".join(l_line))
|
||||
|
||||
return l_data
|
||||
|
||||
|
||||
# __ _
|
||||
# /__ _. _ _ o _. ._ (_| |_|_
|
||||
# \_| (_| |_| _> _> | (_| | | | |
|
||||
#
|
||||
def parse_basis_data_gaussian94(data, name, description, elements, debug=True):
|
||||
"""Parse the Gaussian94 basis data raw html to get a nice tuple.
|
||||
|
||||
The data-pairs item is actually expected to be a 2 item list:
|
||||
[symbol, data]
|
||||
|
||||
e.g. ["Ca", "#BASIS SET..."]
|
||||
|
||||
N.B.: Currently ignores ECP data!
|
||||
|
||||
@param data: raw HTML from BSE
|
||||
@type data : unicode
|
||||
@param name: basis set name
|
||||
@type name : str
|
||||
@param des: basis set description
|
||||
@type des : str
|
||||
@param elements: element symbols e.g. ['H', 'C', 'N', 'O', 'Cl']
|
||||
@type elements : list
|
||||
@return: (name, description, data-pairs)
|
||||
@rtype : tuple
|
||||
"""
|
||||
|
||||
d = []
|
||||
|
||||
# Each basis set block starts and ends with ****. Find the region
|
||||
# containing all the basis blocks using the first and last ****.
|
||||
mark = "****"
|
||||
begin = data.find(mark)
|
||||
end = data.rfind(mark)
|
||||
|
||||
if begin == -1 or end == -1:
|
||||
if debug:
|
||||
print(data)
|
||||
str_ = " No basis set data found while attempting to process {0} ({1})"
|
||||
raise ValueError(str_.format(name, description))
|
||||
|
||||
trimmed = data[begin + len(mark): end - len(mark)].strip()
|
||||
chunks = []
|
||||
lines = []
|
||||
|
||||
# group lines of data delimited by mark into per-element chunks
|
||||
for line in trimmed.split("\n"):
|
||||
if line.startswith(mark):
|
||||
if lines:
|
||||
chunks.append(lines)
|
||||
lines = [line]
|
||||
else:
|
||||
lines.append(line)
|
||||
|
||||
# handle trailing chunk that is not followed by another basis set block
|
||||
# also remove the marker lines from the chunk itself
|
||||
if lines and (not chunks or lines != chunks[-1]):
|
||||
chunks.append(lines)
|
||||
|
||||
# join lines back into solid text blocks
|
||||
chunks = ["\n".join([L for L in c if mark not in L]) for c in chunks]
|
||||
|
||||
# check each block for element and assign symbols to final pairs
|
||||
pairs = []
|
||||
unused_elements = set([e.upper() for e in elements])
|
||||
for chunk in chunks:
|
||||
# get first 3 chars of first line in block
|
||||
symbol = chunk.split("\n")[0][:3].strip()
|
||||
try:
|
||||
unused_elements.remove(symbol.upper())
|
||||
except KeyError:
|
||||
if debug:
|
||||
msg = "Warning: already processed {0}\n".format(symbol)
|
||||
sys.stderr.write(msg)
|
||||
pairs.append([symbol, chunk])
|
||||
|
||||
if unused_elements:
|
||||
msg = "Warning: elements {0} left over for {1}".format(
|
||||
list(unused_elements),
|
||||
name)
|
||||
print(msg)
|
||||
|
||||
return [name, description, pairs]
|
||||
|
||||
|
||||
# ______ _ _ _ _
|
||||
# | ___| | | | (_) | |
|
||||
# | |_ _ __ ___ _ __ ___ __ _| |_ __| |_ ___| |_
|
||||
# | _| '__/ _ \| '_ ` _ \ / _` | __| / _` | |/ __| __|
|
||||
# | | | | | (_) | | | | | | (_| | |_ | (_| | | (__| |_
|
||||
# \_| |_| \___/|_| |_| |_|\__,_|\__| \__,_|_|\___|\__|
|
||||
#
|
||||
|
||||
format_dict = {"Gaussian94": parse_basis_data_gaussian94,
|
||||
"GAMESS-US": parse_basis_data_gamess_us,
|
||||
"GAMESS-UK": None,
|
||||
"Turbomole": None,
|
||||
"TX93": None,
|
||||
"Molpro": None,
|
||||
"MolproInt": None,
|
||||
"Hondo": None,
|
||||
"SuperMolecule": None,
|
||||
"Molcas": None,
|
||||
"HyperChem": None,
|
||||
"Dalton": None,
|
||||
"deMon-KS": None,
|
||||
"deMon2k": None,
|
||||
"AcesII": None}
|
||||
|
||||
# _____ _ _ _ _
|
||||
# / ___| | | | (_) | |
|
||||
# \ `--. _ _ _ __ ___ _ __ ___ ___| |_ _ __ _ _ __| |_ ___| |_
|
||||
# `--. \ | | | '_ ` _ \| '_ ` _ \ / _ \ __| '__| | | | / _` | |/ __| __|
|
||||
# /\__/ / |_| | | | | | | | | | | | __/ |_| | | |_| | | (_| | | (__| |_
|
||||
# \____/ \__, |_| |_| |_|_| |_| |_|\___|\__|_| \__, | \__,_|_|\___|\__|
|
||||
# __/ | __/ |
|
||||
# |___/ |___/
|
||||
|
||||
"""
|
||||
Return the begin and the end of all the type of orbital
|
||||
input: atom_basis = [name, S 1, 12 0.12 12212, ...]
|
||||
output: [ [type, begin, end], ...]
|
||||
"""
|
||||
|
||||
symmetry_dict = {"GAMESS-US": l_symmetry_gamess_us}
|
||||
|
||||
|
||||
def get_symmetry_function(format):
|
||||
"""
|
||||
Return the begin and the end of all the type of orbital
|
||||
input: atom_basis = [name, S 1, 12 0.12 12212, ...]
|
||||
output: [ [type, begin, end], ...]
|
||||
"""
|
||||
try:
|
||||
f = symmetry_dict[format]
|
||||
except KeyError:
|
||||
print >> sys.stderr, "You need to add a function in symmetry_dict"
|
||||
print >> sys.stderr, "for your format ({0})".format(format)
|
||||
sys.exit(1)
|
||||
return f
|
||||
|
||||
# _ _ _ _ _ _ _ _ _ ______ _ _
|
||||
# | | | | | | | ( | ) | ( | ) | _ (_) | |
|
||||
# | |_| | __ _ _ __ __| | | ___ V V| | V V | | | |_ ___| |_
|
||||
# | _ |/ _` | '_ \ / _` | |/ _ \ | | | | | | |/ __| __|
|
||||
# | | | | (_| | | | | (_| | | __/ | |____ | |/ /| | (__| |_
|
||||
# \_| |_/\__,_|_| |_|\__,_|_|\___| \_____/ |___/ |_|\___|\__|
|
||||
|
||||
"""
|
||||
Tranforme SP special function (create using get_symmetry_function) into S and P
|
||||
"""
|
||||
|
||||
handle_l_dict = {"GAMESS-US": handle_l_gamess_us}
|
||||
|
||||
|
||||
def get_handle_l_function(format):
|
||||
"""
|
||||
Tranforme SP special function (create using get_symmetry_function)
|
||||
into S and P
|
||||
"""
|
||||
try:
|
||||
f = handle_l_dict[format]
|
||||
except KeyError:
|
||||
print >> sys.stderr, "You need to add a function in handle_l_dict"
|
||||
print >> sys.stderr, "for your format ({0})".format(format)
|
||||
sys.exit(1)
|
||||
return f
|
||||
|
|
@ -0,0 +1,109 @@
|
|||
import sys
|
||||
import os
|
||||
import re
|
||||
|
||||
|
||||
def get_dict_ele():
|
||||
"""Return dict[atom]=[abreviation]"""
|
||||
elt_path = os.path.dirname(sys.argv[0]) + "/src/misc/elts_abrev.dat"
|
||||
|
||||
with open(elt_path, "r") as f:
|
||||
data = f.readlines()
|
||||
|
||||
dict_ele = dict()
|
||||
for i in data:
|
||||
l = i.split("-")
|
||||
dict_ele[l[1].strip().lower()] = l[2].strip().lower()
|
||||
|
||||
return dict_ele
|
||||
|
||||
# ______ _ _ _ _
|
||||
# | ___| | | | (_) | |
|
||||
# | |_ _ __ ___ _ __ ___ __ _| |_ __| |_ ___| |_
|
||||
# | _| '__/ _ \| '_ ` _ \ / _` | __| / _` | |/ __| __|
|
||||
# | | | | | (_) | | | | | | (_| | |_ | (_| | | (__| |_
|
||||
# \_| |_| \___/|_| |_| |_|\__,_|\__| \__,_|_|\___|\__|
|
||||
#
|
||||
from src.parser.gamess_us import parse_basis_data_gamess_us
|
||||
from src.parser.gaussian94 import parse_basis_data_gaussian94
|
||||
from src.parser.nwchem import parse_basis_data_nwchem
|
||||
|
||||
|
||||
format_dict = {"Gaussian94": parse_basis_data_gaussian94,
|
||||
"GAMESS-US": parse_basis_data_gamess_us,
|
||||
"GAMESS-UK": None,
|
||||
"Turbomole": None,
|
||||
"TX93": None,
|
||||
"Molpro": None,
|
||||
"MolproInt": None,
|
||||
"Hondo": None,
|
||||
"SuperMolecule": None,
|
||||
"Molcas": None,
|
||||
"HyperChem": None,
|
||||
"Dalton": None,
|
||||
"deMon-KS": None,
|
||||
"deMon2k": None,
|
||||
"AcesII": None,
|
||||
"NWChem": parse_basis_data_nwchem}
|
||||
|
||||
# _____ _ _ _ _
|
||||
# / ___| | | | (_) | |
|
||||
# \ `--. _ _ _ __ ___ _ __ ___ ___| |_ _ __ _ _ __| |_ ___| |_
|
||||
# `--. \ | | | '_ ` _ \| '_ ` _ \ / _ \ __| '__| | | | / _` | |/ __| __|
|
||||
# /\__/ / |_| | | | | | | | | | | | __/ |_| | | |_| | | (_| | | (__| |_
|
||||
# \____/ \__, |_| |_| |_|_| |_| |_|\___|\__|_| \__, | \__,_|_|\___|\__|
|
||||
# __/ | __/ |
|
||||
# |___/ |___/
|
||||
|
||||
"""
|
||||
Return the begin and the end of all the type of orbital
|
||||
input: atom_basis = [name, S 1, 12 0.12 12212, ...]
|
||||
output: [ [type, begin, end], ...]
|
||||
"""
|
||||
|
||||
from src.parser.gamess_us import l_symmetry_gamess_us
|
||||
|
||||
symmetry_dict = {"GAMESS-US": l_symmetry_gamess_us}
|
||||
|
||||
|
||||
def get_symmetry_function(format):
|
||||
"""
|
||||
Return the begin and the end of all the type of orbital
|
||||
input: atom_basis = [name, S 1, 12 0.12 12212, ...]
|
||||
output: [ [type, begin, end], ...]
|
||||
"""
|
||||
try:
|
||||
f = symmetry_dict[format]
|
||||
except KeyError:
|
||||
print >> sys.stderr, "You need to add a function in symmetry_dict"
|
||||
print >> sys.stderr, "for your format ({0})".format(format)
|
||||
sys.exit(1)
|
||||
return f
|
||||
|
||||
# _ _ _ _ _ _ _ _ _ ______ _ _
|
||||
# | | | | | | | ( | ) | ( | ) | _ (_) | |
|
||||
# | |_| | __ _ _ __ __| | | ___ V V| | V V | | | |_ ___| |_
|
||||
# | _ |/ _` | '_ \ / _` | |/ _ \ | | | | | | |/ __| __|
|
||||
# | | | | (_| | | | | (_| | | __/ | |____ | |/ /| | (__| |_
|
||||
# \_| |_/\__,_|_| |_|\__,_|_|\___| \_____/ |___/ |_|\___|\__|
|
||||
|
||||
"""
|
||||
Tranforme SP special function (create using get_symmetry_function) into S and P
|
||||
"""
|
||||
from src.parser.gamess_us import handle_l_gamess_us
|
||||
|
||||
handle_l_dict = {"GAMESS-US": handle_l_gamess_us}
|
||||
|
||||
|
||||
def get_handle_l_function(format):
|
||||
"""
|
||||
Tranforme SP special function (create using get_symmetry_function)
|
||||
into S and P
|
||||
"""
|
||||
try:
|
||||
f = handle_l_dict[format]
|
||||
except KeyError:
|
||||
print >> sys.stderr, "You need to add a function in handle_l_dict"
|
||||
print >> sys.stderr, "for your format ({0})".format(format)
|
||||
sys.exit(1)
|
||||
return f
|
||||
Loading…
Reference in New Issue