-
Notifications
You must be signed in to change notification settings - Fork 79
/
parsing.py
708 lines (589 loc) · 20 KB
/
parsing.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
# -*- coding: utf-8 -*-
""" Functions for chemical formulae and reactions """
from collections import defaultdict
import re
from .pyutil import memoize
from .periodic import symbols
parsing_library = "pyparsing" # info used for selective testing.
def get_parsing_context():
"""returns the default dictionary for parsing strings in chempy"""
import chempy
from chempy.kinetics import rates
from chempy.units import default_units, default_constants, to_unitless
globals_ = dict(to_unitless=to_unitless, chempy=chempy)
def _update(mod, keys=None):
if keys is None:
keys = dir(mod)
globals_.update({k: getattr(mod, k) for k in keys if not k.startswith("_")})
try:
import numpy
except ImportError:
def _numpy_not_installed_raise(*args, **kwargs):
raise ImportError("numpy not installed, no such method")
class numpy:
array = staticmethod(_numpy_not_installed_raise)
log = staticmethod(_numpy_not_installed_raise)
exp = staticmethod(_numpy_not_installed_raise)
_update(numpy, keys="array log exp".split()) # could of course add more
_update(rates)
_update(chempy)
for df in [default_units, default_constants]:
if df is not None:
globals_.update(df.as_dict())
return globals_
@memoize()
def _get_formula_parser():
"""Create a forward pyparsing parser for chemical formulae
BNF for simple chemical formula (no nesting)
integer :: '0'..'9'+
element :: 'A'..'Z' 'a'..'z'*
term :: element [integer]
formula :: term+
BNF for nested chemical formula
integer :: '0'..'9'+
element :: 'A'..'Z' 'a'..'z'*
term :: (element | '(' formula ')') [integer]
formula :: term+
Notes
-----
The code in this function is from an answer on StackOverflow:
http://stackoverflow.com/a/18555142/790973
written by:
Paul McGuire, http://stackoverflow.com/users/165216/paul-mcguire
in answer to the question formulated by:
Thales MG, http://stackoverflow.com/users/2708711/thales-mg
the code is licensed under 'CC-WIKI'.
(see: http://blog.stackoverflow.com/2009/06/attribution-required/)
Documentation for the desired product. Original documentation
above.
Create a chemical formula parser.
Parse a chemical formula, including elements, nested ions,
complexes, charges (ions), hydrates, and state symbols.
BNF for nested chemical formula with complexes
count :: ( '1'..'9'? | '1'..'9'' '0'..'9'+ )
element :: 'A'..'Z' 'a'..'z'*
charge :: ( '-' | '+' ) ( '1'..'9'? | '1'..'9'' '0'..'9'+ )
prime :: ( "*" | "'" )*
term :: (element
| '(' formula ')'
| '{' formula '}'
| '[' formula ']' ) count prime charge?
formula :: term+
hydrate :: ( '..' | '\u00B7' ) count? formula
state :: '(' ( 's' | 'l' | 'g' | 'aq' | 'cr' ) ')'
compound :: count formula hydrate? state?
Parse a chemical formula, including elements, non-integer
subscripts, nested ions, complexes, charges (ions), hydrates, and
state symbols.
BNF for nested chemical formula with complexes
count :: ( '1'..'9'? | '1'..'9'' '0'..'9'+ | '0'..'9'+ '.' '0'..'9'+ )
element :: 'A'..'Z' 'a'..'z'*
charge :: ( '-' | '+' ) ( '1'..'9'? | '1'..'9'' '0'..'9'+ )
prime :: ( "*" | "'" )*
term :: (element
| '(' formula ')'
| '{' formula '}'
| '[' formula ']' ) count prime charge?
formula :: term+
hydrate :: ( '..' | '\u00B7' ) count? formula
state :: '(' ( 's' | 'l' | 'g' | 'aq' | 'cr' ) ')'
compound :: count formula hydrate? state?
"""
_p = __import__(parsing_library)
Forward, Group, OneOrMore = _p.Forward, _p.Group, _p.OneOrMore
Optional, ParseResults, Regex = _p.Optional, _p.ParseResults, _p.Regex
Suppress = _p.Suppress
# Define and suppress the grouping symbols.
LCB = Suppress(Regex(r"\{"))
RCB = Suppress(Regex(r"\}"))
LSB = Suppress(Regex(r"\["))
RSB = Suppress(Regex(r"\]"))
LP = Suppress(Regex(r"\("))
RP = Suppress(Regex(r"\)"))
# Define and suppress the caged symbol.
caged = Suppress(Regex(r"\@"))
# Primes/stars for marking special species in reactions.
primes = Suppress(Regex(r"[*']+"))
# Parse counts (subscripts and coefficients).
count = Regex(r"(\d+\.\d+|\d*)")
count.setParseAction(lambda t: 1 if t[0] == "" else float(t[0]))
# Parse states.
state = Suppress(Regex(r"\((s|l|g|aq|cr)\)"))
# Elements, 1-118, official symbols.
element = Regex(
r"A[cglmrstu]"
"|B[aehikr]?"
"|C[adeflmnorsu]?"
"|D[bsy]"
"|E[rsu]"
"|F[elmr]?"
"|G[ade]"
"|H[efgos]?"
"|I[nr]?"
"|Kr?"
"|L[airuv]"
"|M[cdgnot]"
"|N[abdehiop]?"
"|O[gs]?"
"|P[abdmortu]?"
"|R[abefghnu]"
"|S[bcegimnr]?"
"|T[abcehilms]"
"|U"
"|V"
"|W"
"|Xe"
"|Yb?"
"|Z[nr]"
).setResultsName("element", listAllMatches=True)
# forward declare 'formula' so it can be used in definition of 'term'
formula = Forward()
term = Group(
(
element
| Group(LP + formula + RP)("subgroup")
| Group(LSB + formula + RSB)("subgroup")
| Group(LCB + formula + RCB)("subgroup")
| Group(caged + formula)("subgroup")
)
+ Optional(count, default=1)("mult")
+ Optional(state)("state")
+ Optional(primes)("primes")
)
# add parse actions for parse-time processing
# parse action to multiply out subgroups
def multiplyContents(tokens):
t = tokens[0]
# if these tokens contain a subgroup, then use multiplier to
# extend counts of all elements in the subgroup
if t.subgroup:
mult = t.mult
for term in t.subgroup:
term[1] *= mult
return t.subgroup
term.setParseAction(multiplyContents)
# add parse action to sum up multiple references to the same element
def sumByElement(tokens):
elementsList = [t[0] for t in tokens]
# construct set to see if there are duplicates
duplicates = len(elementsList) > len(set(elementsList))
# if there are duplicate element names, sum up by element and
# return a new nested ParseResults
if duplicates:
ctr = defaultdict(int)
for t in tokens:
ctr[t[0]] += t[1]
return ParseResults([ParseResults([k, v]) for k, v in ctr.items()])
# define contents of a formula as one or more terms
formula << OneOrMore(term)
formula.setParseAction(sumByElement)
return formula
def _get_charge(chgstr):
if chgstr == "+":
return 1
elif chgstr == "-":
return -1
for token, anti, sign in zip("+-", "-+", (1, -1)):
if token in chgstr:
if anti in chgstr:
raise ValueError("Invalid charge description (+ & - present)")
before, after = chgstr.split(token)
if len(before) > 0 and len(after) > 0:
raise ValueError("Values both before and after charge token")
if len(after) > 0:
return sign * int(1 if after == "" else after)
raise ValueError("Invalid charge description (+ or - missing)")
def _formula_to_parts(formula, prefixes, suffixes):
# Drop prefixes and suffixes.
drop_pref, drop_suff = [], []
for ign in prefixes:
if formula.startswith(ign):
drop_pref.append(ign)
formula = formula[len(ign) :]
for ign in suffixes:
if formula.endswith(ign):
drop_suff.append(ign)
formula = formula[: -len(ign)]
# Extract charge.
if "/" in formula:
raise ValueError(
"Slashes ('/') in charge strings are deprecated."
" Use `Fe+3` instead of `Fe/3+`."
)
else:
for token in "+-":
if token in formula:
if formula.count(token) > 1:
raise ValueError("Multiple tokens: %s" % token)
parts = formula.split(token)
parts[1] = token + parts[1]
break
else:
parts = [formula, None]
return parts + [tuple(drop_pref), tuple(drop_suff[::-1])]
def _parse_stoich(stoich):
# Special case: the electron is not an element.
if stoich == "e":
return {}
comp = {}
for k, n in _get_formula_parser().parseString(stoich, parseAll=True):
# Only use rational subscripts if necessary as
# ``sympy.linsolve()`` does not like non-integers when
# balancing reactions.
if n == int(n):
comp[symbols.index(k) + 1] = int(n)
else:
comp[symbols.index(k) + 1] = n
return comp
_greek_letters = (
"alpha",
"beta",
"gamma",
"delta",
"epsilon",
"zeta",
"eta",
"theta",
"iota",
"kappa",
"lambda",
"mu",
"nu",
"xi",
"omicron",
"pi",
"rho",
"sigma",
"tau",
"upsilon",
"phi",
"chi",
"psi",
"omega",
)
_greek_u = "αβγδεζηθικλμνξοπρστυφχψω"
_latex_mapping = {k + "-": "\\" + k + "-" for k in _greek_letters}
_latex_mapping["epsilon-"] = "\\varepsilon-"
_latex_mapping["omicron-"] = "o-"
_latex_mapping["."] = "^\\bullet "
_latex_infix_mapping = {"..": "\\cdot "}
_unicode_mapping = {k + "-": v + "-" for k, v in zip(_greek_letters, _greek_u)}
_unicode_mapping["."] = "⋅"
_unicode_infix_mapping = {"..": "\u00b7"} # 0x00b7: '·'
_html_mapping = {k + "-": "&" + k + ";-" for k in _greek_letters}
_html_mapping["."] = "⋅"
# _html_infix_mapping = _html_mapping
_html_infix_mapping = {"..": "⋅"}
def _get_leading_integer(s):
m = re.findall(r"^\d+", s)
if len(m) == 0:
m = 1
elif len(m) == 1:
s = s[len(m[0]) :]
m = int(m[0])
else:
raise ValueError("Failed to parse: %s" % s)
return m, s
def formula_to_composition(
formula, prefixes=None, suffixes=("(s)", "(l)", "(g)", "(aq)")
):
"""Parse composition of formula representing a chemical formula
Composition is represented as a dict mapping int -> int (atomic
number -> multiplicity). "Atomic number" 0 represents net charge.
Parameters
----------
formula: str
Chemical formula, e.g. 'H2O', 'Fe+3', 'Cl-'
prefixes: iterable strings
Prefixes to ignore, e.g. ('.', 'alpha-')
suffixes: tuple of strings
Suffixes to ignore, e.g. ('(g)', '(s)')
Examples
--------
>>> formula_to_composition('NH4+') == {0: 1, 1: 4, 7: 1}
True
>>> formula_to_composition('.NHO-(aq)') == {0: -1, 1: 1, 7: 1, 8: 1}
True
>>> formula_to_composition('Na2CO3..7H2O') == {11: 2, 6: 1, 8: 10, 1: 14}
True
>>> formula_to_composition('UO2.3') == {92: 1, 8: 2.3}
True
"""
if prefixes is None:
prefixes = _latex_mapping.keys()
stoich_tok, chg_tok = _formula_to_parts(formula, prefixes, suffixes)[:2]
tot_comp = {}
if '\u00b7' in stoich_tok:
parts = stoich_tok.split('\u00b7')
else:
parts = stoich_tok.split("..")
for idx, stoich in enumerate(parts):
if idx == 0:
m = 1
else:
m, stoich = _get_leading_integer(stoich)
comp = _parse_stoich(stoich)
for k, v in comp.items():
if k not in tot_comp:
tot_comp[k] = m * v
else:
tot_comp[k] += m * v
if chg_tok is not None:
tot_comp[0] = _get_charge(chg_tok)
return tot_comp
def _subs(string, patterns):
for patt, repl in patterns.items():
string = string.replace(patt, repl)
return string
def _parse_multiplicity(strings, substance_keys=None):
"""
Examples
--------
>>> _parse_multiplicity(['2 H2O2', 'O2']) == {'H2O2': 2, 'O2': 1}
True
>>> _parse_multiplicity(['2 * H2O2', 'O2']) == {'H2O2': 2, 'O2': 1}
True
>>> _parse_multiplicity(['']) == {}
True
>>> _parse_multiplicity(['H2O', 'H2O']) == {'H2O': 2}
True
"""
result = {}
for items in [re.split(" \\* | ", s) for s in strings]:
items = [x for x in items if x != ""]
if len(items) == 0:
continue
elif len(items) == 1:
if items[0] not in result:
result[items[0]] = 0
result[items[0]] += 1
elif len(items) == 2:
if items[1] not in result:
result[items[1]] = 0
result[items[1]] += (
float(items[0]) if "." in items[0] or "e" in items[0] else int(items[0])
)
else:
raise ValueError("To many parts in substring")
if substance_keys is not None:
for k in result:
if k not in substance_keys:
raise ValueError("Unknown substance_key: %s" % k)
return result
def to_reaction(line, substance_keys, token, Cls, globals_=None, **kwargs):
"""Parses a string into a Reaction object and substances
Reac1 + 2 Reac2 + (2 Reac1) -> Prod1 + Prod2; 10**3.7; ref='doi:12/ab'
Reac1 = Prod1; 2.1;
Parameters
----------
line: str
string representation to be parsed
substance_keys: iterable of strings
Allowed names, e.g. ('H2O', 'H+', 'OH-')
token : str
delimiter token between reactant and product side
Cls : class
e.g. subclass of Reaction
globals_: dict (optional)
Globals passed on to :func:`eval`, when ``None``:
`chempy.units.default_units` is used with 'chempy'
and 'default_units' extra entries.
Notes
-----
This function calls :func:`eval`, hence there are severe security concerns
with running this on untrusted data.
"""
if globals_ is None:
globals_ = get_parsing_context()
parts = line.rstrip("\n").split(";")
stoich = parts[0].strip()
if len(parts) > 2:
kwargs.update(eval("dict(" + ";".join(parts[2:]) + "\n)", globals_ or {}))
if len(parts) > 1:
param = parts[1].strip()
else:
param = kwargs.pop("param", "None")
if isinstance(param, str):
if param.startswith("'") and param.endswith("'") and "'" not in param[1:-1]:
from ..kinetics.rates import MassAction
from ._expr import Symbol
param = MassAction(Symbol(unique_keys=(param[1:-1],)))
else:
param = None if globals_ is False else eval(param, globals_)
if token not in stoich:
raise ValueError("Missing token: %s" % token)
reac_prod = [[y.strip() for y in x.split(" + ")] for x in stoich.split(token)]
act, inact = [], []
for elements in reac_prod:
act.append(
_parse_multiplicity(
[x for x in elements if not x.startswith("(")], substance_keys
)
)
inact.append(
_parse_multiplicity(
[x[1:-1] for x in elements if x.startswith("(") and x.endswith(")")],
substance_keys,
)
)
# stoich coeff -> dict
return Cls(
act[0], act[1], param, inact_reac=inact[0], inact_prod=inact[1], **kwargs
)
def _formula_to_format(
sub,
sup,
formula,
prefixes=None,
infixes=None,
suffixes=("(s)", "(l)", "(g)", "(aq)"),
):
parts = _formula_to_parts(formula, prefixes.keys(), suffixes)
if '\u00b7' in parts[0]:
stoichs = parts[0].split('\u00b7')
else:
stoichs = parts[0].split("..")
string = ""
for idx, stoich in enumerate(stoichs):
if idx == 0:
m = 1
else:
m, stoich = _get_leading_integer(stoich)
string += _subs("..", infixes)
if m != 1:
string += str(m)
string += re.sub(r"([0-9]+\.[0-9]+|[0-9]+)", lambda m: sub(m.group(1)), stoich)
if parts[1] is not None:
chg = _get_charge(parts[1])
if chg < 0:
token = "-" if chg == -1 else "%d-" % -chg
if chg > 0:
token = "+" if chg == 1 else "%d+" % chg
string += sup(token)
if len(parts) > 4:
raise ValueError("Incorrect formula")
pre_str = "".join(map(lambda x: _subs(x, prefixes), parts[2]))
return pre_str + string + "".join(parts[3])
def formula_to_latex(formula, prefixes=None, infixes=None, **kwargs):
r"""Convert formula string to latex representation
Parameters
----------
formula: str
Chemical formula, e.g. 'H2O', 'Fe+3', 'Cl-'
prefixes: dict
Prefix transformations, default: greek letters and .
infixes: dict
Infix transformations, default: .
suffixes: iterable of str
What suffixes not to interpret, default: (s), (l), (g), (aq)
Examples
--------
>>> formula_to_latex('NH4+')
'NH_{4}^{+}'
>>> formula_to_latex('Fe(CN)6+2')
'Fe(CN)_{6}^{2+}'
>>> formula_to_latex('Fe(CN)6+2(aq)')
'Fe(CN)_{6}^{2+}(aq)'
>>> formula_to_latex('.NHO-(aq)')
'^\\bullet NHO^{-}(aq)'
>>> formula_to_latex('alpha-FeOOH(s)')
'\\alpha-FeOOH(s)'
"""
if prefixes is None:
prefixes = _latex_mapping
if infixes is None:
infixes = _latex_infix_mapping
return _formula_to_format(
lambda x: "_{%s}" % x,
lambda x: "^{%s}" % x,
# formula,
re.sub(r"([{}])", r"\\\1", formula) if re.search(r"[{}]", formula) else formula,
prefixes,
infixes,
**kwargs
)
_unicode_sub = {
".": ".",
}
for k, v in enumerate("₀₁₂₃₄₅₆₇₈₉."):
_unicode_sub[str(k)] = v
_unicode_sup = {
"+": "⁺",
"-": "⁻",
}
for k, v in enumerate("⁰¹²³⁴⁵⁶⁷⁸⁹"):
_unicode_sup[str(k)] = v
def formula_to_unicode(formula, prefixes=None, infixes=None, **kwargs):
"""Convert formula string to unicode string representation
Parameters
----------
formula : str
Chemical formula, e.g. 'H2O', 'Fe+3', 'Cl-'
prefixes : dict
Prefix transofmrations, default: greek letters and .
infixes : dict
Infix transofmrations, default: .
suffixes : tuple of strings
Suffixes to keep, e.g. ('(g)', '(s)')
Examples
--------
>>> formula_to_unicode('NH4+') == u'NH₄⁺'
True
>>> formula_to_unicode('Fe(CN)6+2') == u'Fe(CN)₆²⁺'
True
>>> formula_to_unicode('Fe(CN)6+2(aq)') == u'Fe(CN)₆²⁺(aq)'
True
>>> formula_to_unicode('.NHO-(aq)') == u'⋅NHO⁻(aq)'
True
>>> formula_to_unicode('alpha-FeOOH(s)') == u'α-FeOOH(s)'
True
"""
if prefixes is None:
prefixes = _unicode_mapping
if infixes is None:
infixes = _unicode_infix_mapping
return _formula_to_format(
lambda x: "".join(_unicode_sub[str(_)] for _ in x),
lambda x: "".join(_unicode_sup[str(_)] for _ in x),
formula,
prefixes,
infixes,
**kwargs
)
def formula_to_html(formula, prefixes=None, infixes=None, **kwargs):
"""Convert formula string to html string representation
Parameters
----------
formula : str
Chemical formula, e.g. 'H2O', 'Fe+3', 'Cl-'
prefixes : dict
Prefix transformations, default: greek letters and .
infixes : dict
Infix transformations, default: .
suffixes : tuple of strings
Suffixes to keep, e.g. ('(g)', '(s)')
Examples
--------
>>> formula_to_html('NH4+')
'NH<sub>4</sub><sup>+</sup>'
>>> formula_to_html('Fe(CN)6+2')
'Fe(CN)<sub>6</sub><sup>2+</sup>'
>>> formula_to_html('Fe(CN)6+2(aq)')
'Fe(CN)<sub>6</sub><sup>2+</sup>(aq)'
>>> formula_to_html('.NHO-(aq)')
'⋅NHO<sup>-</sup>(aq)'
>>> formula_to_html('alpha-FeOOH(s)')
'α-FeOOH(s)'
"""
if prefixes is None:
prefixes = _html_mapping
if infixes is None:
infixes = _html_infix_mapping
return _formula_to_format(
lambda x: "<sub>%s</sub>" % x,
lambda x: "<sup>%s</sup>" % x,
formula,
prefixes,
infixes,
**kwargs
)