"""Chemical Engineering Design Library (ChEDL). Utilities for process modeling.
Copyright (C) 2016, 2017, 2018, 2019, 2020 Caleb Bell
<Caleb.Andrew.Bell@gmail.com>
Copyright (C) 2020 Yoel Rene Cortes-Pena
<yoelcortes@gmail.com>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
This module contains a complete periodic table, routines for working with
chemical formulas, computing molecular weight, computing mass fractions and
atom fractions, and assorted other tasks.
For reporting bugs, adding feature requests, or submitting pull requests,
please use the `GitHub issue tracker <https://github.com/CalebBell/chemicals/>`_.
.. contents:: :local:
Periodic Table and Elements
---------------------------
.. autodata:: chemicals.elements.periodic_table
.. autoclass:: chemicals.elements.Element
.. autoclass:: chemicals.elements.PeriodicTable
Working with Formulas
---------------------
.. autofunction:: chemicals.elements.simple_formula_parser
.. autofunction:: chemicals.elements.nested_formula_parser
.. autofunction:: chemicals.elements.charge_from_formula
.. autofunction:: chemicals.elements.serialize_formula
.. autofunction:: chemicals.elements.atoms_to_Hill
Working with Parsed Formulas
----------------------------
.. autofunction:: chemicals.elements.molecular_weight
.. autofunction:: chemicals.elements.similarity_variable
.. autofunction:: chemicals.elements.index_hydrogen_deficiency
.. autofunction:: chemicals.elements.atom_fractions
.. autofunction:: chemicals.elements.mass_fractions
.. autofunction:: chemicals.elements.mixture_atomic_composition
.. autofunction:: chemicals.elements.mixture_atomic_composition_ordered
.. autofunction:: chemicals.elements.atom_matrix
"""
__all__ = ['PeriodicTable', 'molecular_weight', 'mass_fractions',
'atom_fractions','mixture_atomic_composition', 'atom_matrix',
'similarity_variable', 'atoms_to_Hill', 'index_hydrogen_deficiency',
'simple_formula_parser', 'nested_formula_parser', 'CAS_by_number',
'periods', 'groups', 'homonuclear_elements',
'blocks', 'homonuclear_elemental_gases', 'charge_from_formula',
'serialize_formula', 'mixture_atomic_composition_ordered',
'periodic_table']
import re
from chemicals.utils import mark_numba_incompatible
CAS_by_number_standard = ['1333-74-0', '7440-59-7', '7439-93-2', '7440-41-7', '7440-42-8', '7440-44-0', '7727-37-9', '7782-44-7', '7782-41-4', '7440-01-9', '7440-23-5', '7439-95-4', '7429-90-5', '7440-21-3', '7723-14-0', '7704-34-9', '7782-50-5', '7440-37-1', '7440-09-7', '7440-70-2', '7440-20-2', '7440-32-6', '7440-62-2', '7440-47-3', '7439-96-5', '7439-89-6', '7440-48-4', '7440-02-0', '7440-50-8', '7440-66-6', '7440-55-3', '7440-56-4', '7440-38-2', '7782-49-2', '7726-95-6', '7439-90-9', '7440-17-7', '7440-24-6', '7440-65-5', '7440-67-7', '7440-03-1', '7439-98-7', '7440-26-8', '7440-18-8', '7440-16-6', '7440-05-3', '7440-22-4', '7440-43-9', '7440-74-6', '7440-31-5', '7440-36-0', '13494-80-9', '7553-56-2', '7440-63-3', '7440-46-2', '7440-39-3', '7439-91-0', '7440-45-1', '7440-10-0', '7440-00-8', '7440-12-2', '7440-19-9', '7440-53-1', '7440-54-2', '7440-27-9', '7429-91-6', '7440-60-0', '7440-52-0', '7440-30-4', '7440-64-4', '7439-94-3', '7440-58-6', '7440-25-7', '7440-33-7', '7440-15-5', '7440-04-2', '7439-88-5', '7440-06-4', '7440-57-5', '7439-97-6', '7440-28-0', '7439-92-1', '7440-69-9', '7440-08-6', '7440-68-8', '10043-92-2', '7440-73-5', '7440-14-4', '7440-34-8', '7440-29-1', '7440-13-3', '7440-61-1', '7439-99-8', '7440-07-5', '7440-35-9', '7440-51-9', '7440-40-6', '7440-71-3', '7429-92-7', '7440-72-4', '7440-11-1', '10028-14-5', '22537-19-5', '53850-36-5', '53850-35-4', '54038-81-2', '54037-14-8', '54037-57-9', '54038-01-6', '54083-77-1', '54386-24-2', '54084-26-3', '54084-70-7', '54085-16-4', '54085-64-2', '54100-71-9', '54101-14-3', '54144-19-3']
"""Standard CAS numbers of the elements, indexed by atomic numbers off-by-one up to 118."""
CAS_by_number = list(CAS_by_number_standard)
"""CAS numbers of the monatomic elements, indexed by atomic numbers off-by-one up to 118."""
periods = [1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
"""Periods of the elements, indexed by atomic numbers off-by-one up to 118."""
groups = [1, 18, 1, 2, 13, 14, 15, 16, 17, 18, 1, 2, 13, 14, 15, 16, 17, 18, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 1, 2, None, None, None, None, None, None, None, None, None, None, None, None, None, None, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 1, 2, None, None, None, None, None, None, None, None, None, None, None, None, None, None, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18]
"""Groups of the elements, indexed by atomic numbers off-by-one up to 118.
Lanthanides and Actinides are set to None."""
s_block = [1, 2, 3, 4, 11, 12, 19, 20, 37, 38, 55, 56, 87, 88]
d_block = [21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 72, 73, 74, 75, 76, 77, 78, 79, 80, 104, 105, 106, 107, 108, 109, 110, 111, 112]
f_block = [57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103] # 57, 89 are sometimes placed in the d block
p_block = [5, 6, 7, 8, 9, 10, 13, 14, 15, 16, 17, 18, 31, 32, 33, 34, 35, 36, 49, 50, 51, 52, 53, 54, 81, 82, 83, 84, 85, 86, 113, 114, 115, 116, 117, 118]
blocks = {'s': s_block, 'd': d_block, 'f': f_block, 'p': p_block}
"""Blocks of the elements, stored in a dictionary with four keys and lists.
Indexed by atomic numbers off-by-one up to 118."""
InChI_keys = ['YZCKVEUIGOORGS-UHFFFAOYSA-N', 'SWQJXJOGLNCZEY-UHFFFAOYSA-N', 'WHXSMMKQMYFTQS-UHFFFAOYSA-N', 'ATBAMAFKBVZNFJ-UHFFFAOYSA-N', 'ZOXJGFHDIHLPTG-UHFFFAOYSA-N', 'OKTJSMMVPCPJKN-UHFFFAOYSA-N', 'QJGQUHMNIGDVPM-UHFFFAOYSA-N', 'QVGXLLKOCUKJST-UHFFFAOYSA-N', 'YCKRFDGAMUMZLT-UHFFFAOYSA-N', 'GKAOGPIIYCISHV-UHFFFAOYSA-N', 'KEAYESYHFKHZAL-UHFFFAOYSA-N', 'FYYHWMGAXLPEAU-UHFFFAOYSA-N', 'XAGFODPZIPBFFR-UHFFFAOYSA-N', 'XUIMIQQOPSSXEZ-UHFFFAOYSA-N', 'OAICVXFJPJFONN-UHFFFAOYSA-N', 'NINIDFKCEFEMDL-UHFFFAOYSA-N', 'ZAMOUSCENKQFHK-UHFFFAOYSA-N', 'XKRFYHLGVUSROY-UHFFFAOYSA-N', 'ZLMJMSJWJFRBEC-UHFFFAOYSA-N', 'OYPRJOBELJOOCE-UHFFFAOYSA-N', 'SIXSYDAISGFNSX-UHFFFAOYSA-N', 'RTAQQCXQSZGOHL-UHFFFAOYSA-N', 'LEONUFNNVUYDNQ-UHFFFAOYSA-N', 'VYZAMTAEIAYCRO-UHFFFAOYSA-N', 'PWHULOQIROXLJO-UHFFFAOYSA-N', 'XEEYBQQBJWHFJM-UHFFFAOYSA-N', 'GUTLYIVDDKVIGB-UHFFFAOYSA-N', 'PXHVJJICTQNCMI-UHFFFAOYSA-N', 'RYGMFSIKBFXOCR-UHFFFAOYSA-N', 'HCHKCACWOHOZIP-UHFFFAOYSA-N', 'GYHNNYVSQQEPJS-UHFFFAOYSA-N', 'GNPVGFCGXDBREM-UHFFFAOYSA-N', 'RQNWIZPPADIBDY-UHFFFAOYSA-N', 'BUGBHKTXTAQXES-UHFFFAOYSA-N', 'WKBOTKDWSSQWDR-UHFFFAOYSA-N', 'DNNSSWSSYDEUBZ-UHFFFAOYSA-N', 'IGLNJRXAVVLDKE-UHFFFAOYSA-N', 'CIOAGBVUUVVLOB-UHFFFAOYSA-N', 'VWQVUPCCIRVNHF-UHFFFAOYSA-N', 'QCWXUUIWCKQGHC-UHFFFAOYSA-N', 'GUCVJGMIXFAOAE-UHFFFAOYSA-N', 'ZOKXTWBITQBERF-UHFFFAOYSA-N', 'GKLVYJBZJHMRIY-UHFFFAOYSA-N', 'KJTLSVCANCCWHF-UHFFFAOYSA-N', 'MHOVAHRLVXNVSD-UHFFFAOYSA-N', 'KDLHZDBZIXYQEI-UHFFFAOYSA-N', 'BQCADISMDOOEFD-UHFFFAOYSA-N', 'BDOSMKKIYDKNTQ-UHFFFAOYSA-N', 'APFVFJFRJDLVQX-UHFFFAOYSA-N', 'ATJFFYVFTNAWJD-UHFFFAOYSA-N', 'WATWJIUSRGPENY-UHFFFAOYSA-N', 'PORWMNRCUJJQNO-UHFFFAOYSA-N', 'ZCYVEMRRCGMTRW-UHFFFAOYSA-N', 'FHNFHKCVQCLJFQ-UHFFFAOYSA-N', 'TVFDJXOCXUVLDH-UHFFFAOYSA-N', 'DSAJWYNOEDNPEQ-UHFFFAOYSA-N', 'FZLIPJUXYLNCLC-UHFFFAOYSA-N', 'GWXLDORMOJMVQZ-UHFFFAOYSA-N', 'PUDIUYLPXJFUGB-UHFFFAOYSA-N', 'QEFYFXOXNSNQGX-UHFFFAOYSA-N', 'VQMWBBYLQSCNPO-UHFFFAOYSA-N', 'KZUNJOHGWZRPMI-UHFFFAOYSA-N', 'OGPBJKLSAFTDLK-UHFFFAOYSA-N', 'UIWYJDYFSGRHKR-UHFFFAOYSA-N', 'GZCRRIHWUXGPOV-UHFFFAOYSA-N', 'KBQHZAAAGSGFKK-UHFFFAOYSA-N', 'KJZYNXUDTRRSPN-UHFFFAOYSA-N', 'UYAHIZSMUZPPFV-UHFFFAOYSA-N', 'FRNOGLGSGLTDKL-UHFFFAOYSA-N', 'NAWDYIZEMPQZHO-UHFFFAOYSA-N', 'OHSVLFRHMCKCQY-UHFFFAOYSA-N', 'VBJZVLUMGGDVMO-UHFFFAOYSA-N', 'GUVRBAGPIYLISA-UHFFFAOYSA-N', 'WFKWXMTUELFFGS-UHFFFAOYSA-N', 'WUAPFZMCVAUBPE-UHFFFAOYSA-N', 'SYQBFIAQOQZEGI-UHFFFAOYSA-N', 'GKOZUEZYRPOHIO-UHFFFAOYSA-N', 'BASFCYQUMIYNBI-UHFFFAOYSA-N', 'PCHJSUWPFVWCPO-UHFFFAOYSA-N', 'QSHDDOUJBYECFT-UHFFFAOYSA-N', 'BKVIYDNLLOSFOA-UHFFFAOYSA-N', 'WABPQHHGFIMREM-UHFFFAOYSA-N', 'JCXGWMGPZLAOME-UHFFFAOYSA-N', 'HZEBHPIOVYHPMT-UHFFFAOYSA-N', 'RYXHOMYVWAEKHL-UHFFFAOYSA-N', 'SYUHGPGVQRZVTB-UHFFFAOYSA-N', 'KLMCZVJOEAUDNE-UHFFFAOYSA-N', 'HCWPIIXVSYCSAN-UHFFFAOYSA-N', 'QQINRWTZWGJFDB-UHFFFAOYSA-N', 'ZSLUVFAKFWKJRC-UHFFFAOYSA-N', 'XLROVYAPLOFLNU-UHFFFAOYSA-N', 'JFALSRSLKYAFGM-UHFFFAOYSA-N', 'LFNLGNPSGWYGGD-UHFFFAOYSA-N', 'OYEHPCDNVJXUIW-UHFFFAOYSA-N', 'LXQXZNRPTYVCNG-UHFFFAOYSA-N', 'NIWWFAAXEMMFMS-UHFFFAOYSA-N', 'PWVKJRSRVJTHTR-UHFFFAOYSA-N', 'HGLDOAKPQXAFKI-UHFFFAOYSA-N', 'CKBRQZNRCSJHFT-UHFFFAOYSA-N', 'MIORUQGGZCBUGO-UHFFFAOYSA-N', 'MQVSLOYRCXQRPM-UHFFFAOYSA-N', 'ORQBXQOJMQIAOY-UHFFFAOYSA-N', 'CNQCVBJFEGMYDW-UHFFFAOYSA-N', 'YGPLJIIQQIDVFJ-UHFFFAOYSA-N', 'PUKKTGLVJQVIOF-UHFFFAOYSA-N', 'VAOUCABZIBBBJH-UHFFFAOYSA-N', 'INOXRQQPOOCQPH-UHFFFAOYSA-N', 'OBDWMWVOVYJOMI-UHFFFAOYSA-N', 'VAJSJTKWMRUWBF-UHFFFAOYSA-N', 'NCBMSFCPDGXTHD-UHFFFAOYSA-N', 'LJROPTGWFUZRDB-UHFFFAOYSA-N', 'NOTIIDSZELDPOP-UHFFFAOYSA-N', 'KUGNSLWRKGRKGS-UHFFFAOYSA-N', 'WIHJCBVMYKIGOT-UHFFFAOYSA-N', 'QDXZEHQJHSHEQF-UHFFFAOYSA-N', 'ONFASNXETZOODS-UHFFFAOYSA-N', 'INMSAURDCVBGHH-UHFFFAOYSA-N', 'GOANEQIZDYDFCO-UHFFFAOYSA-N']
# Big problem: Atoms like N2, O2 point to only the singlet
homonuclear_elements = [1, 7, 8, 9, 17, 35, 53] # includes Br2, I2
homonuclear_elements_set = frozenset(homonuclear_elements)
# homonuclear_elemental_gases = [periodic_table[i] for i in ['hydrogen', 'nitrogen', 'oxygen', 'fluorine', 'chlorine', 'bromine', 'iodine']]
homonuclear_elemental_gases = [1, 7, 8, 9, 17] # 35, 53
homonuclear_elemental_singlets_CASs = ["12385-13-6", "17778-88-0", "17778-80-2", "14762-94-8", "22537-15-1"]
homonuclear_elements_CASs = homonuclear_elemental_singlets_CASs + ['10097-32-2', '14362-44-8']
homonuclear_elements_CASs_set = frozenset(homonuclear_elements_CASs)
for i, CAS in zip(homonuclear_elements, homonuclear_elements_CASs):
CAS_by_number[i-1] = CAS
cids = [783, 23987, 3028194, 5460467, 5462311, 5462310, 222, 962, 14917, 23935, 5360545, 5462224, 5359268, 5461123, 24404, 402, 313, 23968, 5462222, 5460341, 23952, 23963, 23990, 23976, 23930, 23925, 104730, 935, 23978, 23994, 5360835, 6326954, 5359596, 6326970, 260, 5416, 5357696, 5359327, 23993, 23995, 23936, 23932, 23957, 23950, 23948, 23938, 23954, 23973, 5359967, 5352426, 5354495, 6327182, 24841, 23991, 5354618, 5355457, 23926, 23974, 23942, 23934, 23944, 23951, 23981, 23982, 23958, 23912, 23988, 23980, 23961, 23992, 23929, 23986, 23956, 23964, 23947, 23937, 23924, 23939, 23985, 23931, 5359464, 5352425, 5359367, 6328143, 5460479, 24857, 6328145, 6328144, 23965, 23960, 23945, 23989, 23933, 23940, 23966, 23979, 23971, 23997, 23913, 23998, 23943, 24822, 31192, 56951715, 56951718, 56951717, 56951713, 56951714, 56951716, None, None, None, None, None, None, None, None, None]
# https://periodictable.com/Properties/A/AllotropeNames.html
# Shows reference state https://janaf.nist.gov/tables/P-001.html
# https://janaf.nist.gov/tables/Br-038.html
# format: (name, count, phase, stp_ref, smiles, inchi, inchi_key, closest_CAS, unique_CAS_maybe_fake,)
allotropes = {}
allotropes['N'] = [
('dinitrogen', 2, 'g', True, 'N#N', 'N2/c1-2', 'IJGRMHOSHXDMSA-UHFFFAOYSA-N', '7727-37-9', '7727-37-9'),
('atomic nitrogen', 1, 'g', False, '[N]', 'N', 'QJGQUHMNIGDVPM-UHFFFAOYSA-N', '17778-88-0', '17778-88-0'),
('linear trinitrogen', 3, 'g', False, '[N-]=[N+]=[N]', '1S/N3/c1-3-2', 'QJGQUHMNIGDVPM-UHFFFAOYSA-N', '12596-60-0', '12596-60-0'),
('cyclic trinitrogen', 3, 'g', False, 'N1=N[N]1', '1S/N3/c1-2-3-1', 'RLXSTAGCZQYHDL-UHFFFAOYSA-N', '12596-60-0', '2099958000-00-0'),
]
allotropes['H'] = [
('dihydrogen', 2, 'g', True, '[HH]', 'H2/h1H', 'UFHFLCQGNIYNRP-UHFFFAOYSA-N', '1333-74-0', '1333-74-0'),
('atomic hydrogen', 1, 'g', False, '[H]', 'H', 'YZCKVEUIGOORGS-UHFFFAOYSA-N', '12385-13-6', '12385-13-6')
]
allotropes['F'] = [
('difluorine', 2, 'g', True, 'FF', 'F2/c1-2', 'PXGOKWXKJXAPGV-UHFFFAOYSA-N', '7782-41-4', '7782-41-4'),
('atomic fluorine', 1, 'g', False, '[F]', 'F', 'YCKRFDGAMUMZLT-UHFFFAOYSA-N', '14762-94-8', '14762-94-8')
]
allotropes['I'] = [
('diiodine', 2, 's', True, 'II', 'I2/c1-2', 'PNDPGZBMCMUPRI-UHFFFAOYSA-N', '7553-56-2', '7553-56-2'),
('atomic iodine', 1, 'g', False, '[I]', 'I', 'ZCYVEMRRCGMTRW-UHFFFAOYSA-N', '14362-44-8', '14362-44-8'),
]
allotropes['Br'] = [
('dibromine', 2, 'l', True, 'BrBr', '1S/Br2/c1-2', 'GDTBXPJZTBHREO-UHFFFAOYSA-N', '7726-95-6', '7726-95-6'),
('atomic bromine', 1, 'g', False, '[Br]', 'Br', 'WKBOTKDWSSQWDR-UHFFFAOYSA-N', '10097-32-2', '10097-32-2')
]
allotropes['Cl'] = [
('dichlorine', 2, 'g', True, 'ClCl', 'Cl2/c1-2', 'KZBUYRJDOAKODT-UHFFFAOYSA-N', '7782-50-5', '7782-50-5'),
('atomic chlorine', 1, 'g', False, '[Cl]', 'Cl', 'ZAMOUSCENKQFHK-UHFFFAOYSA-N', '22537-15-1', '22537-15-1')
]
allotropes['C'] = [
('diamond', 1, 's', False, 'C', 'CH4/h1H4', 'VNWKTOKETHGBQD-UHFFFAOYSA-N', '7782-40-3', '7782-40-3'),
('graphite', 1, 's', True, 'C', 'CH4/h1H4', 'VNWKTOKETHGBQD-UHFFFAOYSA-N', '7782-42-5', '7782-42-5'),
('atomic carbon', 1, 's', False, 'C', 'CH4/h1H4', 'VNWKTOKETHGBQD-UHFFFAOYSA-N', '7440-44-0', '7440-44-0'),# also carbon black
]
allotropes['Po'] = [
# assuming alpha is more stable
('alpha polonium', 1, 's', True, '[Po]', 'Po', 'HZEBHPIOVYHPMT-UHFFFAOYSA-N', '7440-08-6', '2099953000-00-0'),
('beta polonium', 1, 's', False, '[Po]', 'Po', 'HZEBHPIOVYHPMT-UHFFFAOYSA-N', '7440-08-6', '2099937000-00-0'),
]
allotropes['Sn'] = [
# unfortunately sources report the same CAS
('white tin', 1, 's', True, '[Sn]', 'Sn', 'ATJFFYVFTNAWJD-UHFFFAOYSA-N', '7440-31-5', '2099932000-00-0'),
('gray tin', 1, 's', False, '[Sn]', 'Sn', 'ATJFFYVFTNAWJD-UHFFFAOYSA-N', '7440-31-5', '2099916000-00-0'),
('gamma tin', 1, 's', False, '[Sn]', 'Sn', 'ATJFFYVFTNAWJD-UHFFFAOYSA-N', '7440-31-5', '2099911000-00-0'), # not common
('sigma tin', 1, 's', False, '[Sn]', 'Sn', 'ATJFFYVFTNAWJD-UHFFFAOYSA-N', '7440-31-5', '2099898000-00-0'), # not common
]
allotropes['Se'] = [
# most stable at STP, chiral hexagonal crystal lattice
('gray selenium', 1, 's', True, '[Se]', 'Se', 'BUGBHKTXTAQXES-UHFFFAOYSA-N', '7782-49-2', '7782-49-2'),
# monocrystaline puckered cyclooctaselenium (Se8) rings
('red gamma selenium', 8, 's', False, '[Se]1[Se][Se][Se][Se][Se][Se][Se]1', 'Se8/c1-2-4-6-8-7-5-3-1',
'JWMKWLJGSKAGLH-UHFFFAOYSA-N', '12597-33-0', '2099893000-00-0'),
# monocrystaline puckered cyclooctaselenium (Se8) rings
('red beta selenium', 8, 's', False, '[Se]1[Se][Se][Se][Se][Se][Se][Se]1', 'Se8/c1-2-4-6-8-7-5-3-1',
'JWMKWLJGSKAGLH-UHFFFAOYSA-N', '12597-33-0', '2099877000-00-0'),
('amorphous black selenium', 1, 's', False, '[Se]', 'Se', 'BUGBHKTXTAQXES-UHFFFAOYSA-N', '7782-49-2',
'2099872000-00-0'), # amorphous, up to 1000 atoms per ring
('amorphous red selenium', 1, 's', False, '[Se]', 'Se', 'BUGBHKTXTAQXES-UHFFFAOYSA-N', '7782-49-2',
'2099856000-00-0'), # amorphous
]
allotropes['As'] = [
('gray arsenic', 1, 's', True, '[As]', 'As', 'RQNWIZPPADIBDY-UHFFFAOYSA-N', '7440-38-2', '2099851000-00-0'), # most stable form
('yellow arsenic', 1, 's', False, '[As]', 'As', 'RQNWIZPPADIBDY-UHFFFAOYSA-N', '7440-38-2', '2099835000-00-0'),
('black arsenic', 1, 's', False, '[As]', 'As', 'RQNWIZPPADIBDY-UHFFFAOYSA-N', '7440-38-2', '2099830000-00-0'),
]
allotropes['P'] = [
# most stable form at room Body-centred cubic or Triclinic also heard yellow phosphorus; CAS is tetraphosphorus
('alpha white phosphorus', 4, 's', True, 'P12P3P1P23', 'P4/c1-2-3(1)4(1)2', 'OBSZRRSYVTXPNB-UHFFFAOYSA-N', '12185-10-3', '2099819000-00-0'),
# Triclinic also heard yellow phosphorus
('beta white phosphorus', 4, 's', False, 'P12P3P1P23', 'P4/c1-2-3(1)4(1)2', 'OBSZRRSYVTXPNB-UHFFFAOYSA-N', '12185-10-3', '2099814000-00-0'),
# CAS is phosphorus
('red phosphorus', 1, 's', False, '[P]', 'P', 'OAICVXFJPJFONN-UHFFFAOYSA-N', '7723-14-0', '2099796000-00-0'),
('violet phosphorus', 1, 's', False, '[P]', 'P', 'OAICVXFJPJFONN-UHFFFAOYSA-N', '7723-14-0', '2099791000-00-0'), # Monoclinic
('black phosphorus', 1, 's', False, '[P]', 'P', 'OAICVXFJPJFONN-UHFFFAOYSA-N', '7723-14-0', '2099775000-00-0'), # Orthorhombic
('diphosphorus', 2, 'g', False, 'P#P', '1S/P2/c1-2', 'FOBPTJZYDGNHLR-UHFFFAOYSA-N', '12185-09-0', '12185-09-0'), # gas
]
allotropes['Sb'] = [
('white antimony', 1, 's', True, '[Sb]', 'Sb', 'WATWJIUSRGPENY-UHFFFAOYSA-N', '7440-36-0', '2099770000-00-0'),# most stable form
('yellow antimony', 1, 's', False, '[Sb]', 'Sb', 'WATWJIUSRGPENY-UHFFFAOYSA-N', '7440-36-0', '2099759000-00-0'),# metastable
('black antimony', 1, 's', False, '[Sb]', 'Sb', 'WATWJIUSRGPENY-UHFFFAOYSA-N', '7440-36-0', '2099754000-00-0'),# metastable
('explosive antimony', 1, 's', False, '[Sb]', 'Sb', 'WATWJIUSRGPENY-UHFFFAOYSA-N', '7440-36-0', '2099738000-00-0'),# eep
]
allotropes['S'] = [
('atomic sulfur', 1, 's', False, '[S]', 'S', 'NINIDFKCEFEMDL-UHFFFAOYSA-N', '7704-34-9', '7704-34-9'),
# orthorhombic most common
('alpha S8 sulfur', 8, 's', True, 'S1SSSSSSS1', 'S8/c1-2-4-6-8-7-5-3-1', 'JLQNHALFVCURHW-UHFFFAOYSA-N', '10544-50-0', '2099733000-00-0'),
# orthorhombicform from alpha when raised to 95.3 °C
('beta S8 sulfur', 8, 's', False, 'S1SSSSSSS1', 'S8/c1-2-4-6-8-7-5-3-1', 'JLQNHALFVCURHW-UHFFFAOYSA-N', '10544-50-0', '2099717000-00-0'),
# orthorhombic nacreous sulfur or mother of pearl sulfur
('gamma S8 sulfur', 8, 's', False, 'S1SSSSSSS1', 'S8/c1-2-4-6-8-7-5-3-1', 'JLQNHALFVCURHW-UHFFFAOYSA-N', '10544-50-0', '2099712000-00-0'),
# most common component of sulfur vapour above 720 °C
('disulfur', 2, 'g', False, 'S=S', 'S2/c1-2', 'MAHNFPMIPQKPPI-UHFFFAOYSA-N', '23550-45-0', '23550-45-0'),
# vapor species 10% at 440 °C
('trisulfur', 3, 'g', False, 'S=S=S', 'S3/c1-3-2', 'NVSDADJBGGUCLP-UHFFFAOYSA-N', '12597-03-4', '12597-03-4'),
# gas only not characterized
('tetrasulfur', 4, 'g', False, 'S1SSS1', 'S4/c1-2-4-3-1', 'NWWQJUISNMIVLJ-UHFFFAOYSA-N', '19269-85-3', '19269-85-3'),
# gas only not characterized
('pentasulfur', 5, 'g', False, 'S1SSSS1', 'S5/c1-2-4-5-3-1', 'DEVHCWHUQVZNMT-UHFFFAOYSA-N', '12597-10-3', '12597-10-3'),
# solid ring form
('cyclo-S6', 6, 's', False, 'S1SSSSS1', 'S6/c1-2-4-6-5-3-1', 'FEXCMMPRRBSCRG-UHFFFAOYSA-N', '13798-23-7', '13798-23-7'),
# solid ring S7 forms
('alpha S7 sulfur', 7, 's', False, 'S1SSSSSS1', 'S7/c1-2-4-6-7-5-3-1', 'VVNDVBPCYWJYSK-UHFFFAOYSA-N', '21459-04-1', '2099699000-00-0'),
('beta S7 sulfur', 7, 's', False, 'S1SSSSSS1', 'S7/c1-2-4-6-7-5-3-1', 'VVNDVBPCYWJYSK-UHFFFAOYSA-N', '21459-04-1', '2099694000-00-0'),
('gamma S7 sulfur', 7, 's', False, 'S1SSSSSS1', 'S7/c1-2-4-6-7-5-3-1', 'VVNDVBPCYWJYSK-UHFFFAOYSA-N', '21459-04-1', '2099678000-00-0'),
('delta S7 sulfur', 7, 's', False, 'S1SSSSSS1', 'S7/c1-2-4-6-7-5-3-1', 'VVNDVBPCYWJYSK-UHFFFAOYSA-N', '21459-04-1', '2099673000-00-0'),
]
allotropes['O'] = [
('dioxygen', 2, 'g', True, 'O=O', 'O2/c1-2', 'MYMOFIZGZYHOMD-UHFFFAOYSA-N', '7782-44-7', '7782-44-7'),
('atomic oxygen', 1, 'g', False, '[O]', 'O', 'QVGXLLKOCUKJST-UHFFFAOYSA-N', '17778-80-2', '17778-80-2'),
('ozone', 3, 'g', False, '[O-][O+]=O', 'O3/c1-3-2', 'CBENFWSGALASAD-UHFFFAOYSA-N', '10028-15-6', '10028-15-6'),
# theorized wikipedia only and chemspider
('cyclic ozone', 3, 'g', False, 'o1oo1', '1S/O3/c1-2-3-1', 'XQOAKYYZMDCSIA-UHFFFAOYSA-N', '153851-84-4', '153851-84-4'),
('alpha oxygen', 2, 's', False, 'O=O', 'O2/c1-2', 'MYMOFIZGZYHOMD-UHFFFAOYSA-N', '7782-44-7', '2099550000-00-0'),
('beta oxygen', 2, 's', False, 'O=O', 'O2/c1-2', 'MYMOFIZGZYHOMD-UHFFFAOYSA-N', '7782-44-7', '2099539000-00-0'),
('gamma oxygen', 2, 's', False, 'O=O', 'O2/c1-2', 'MYMOFIZGZYHOMD-UHFFFAOYSA-N', '7782-44-7', '2099534000-00-0'),
('delta oxygen', 2, 's', False, 'O=O', 'O2/c1-2', 'MYMOFIZGZYHOMD-UHFFFAOYSA-N', '7782-44-7', '2099518000-00-0'), # orange high pressure
('epsilon oxygen', 2, 's', False, 'O=O', 'O2/c1-2', 'MYMOFIZGZYHOMD-UHFFFAOYSA-N', '7782-44-7', '2099513000-00-0'), # red high pressure
('zeta oxygen', 2, 's', False, 'O=O', 'O2/c1-2', 'MYMOFIZGZYHOMD-UHFFFAOYSA-N', '7782-44-7', '2099495000-00-0'), # metallic high pressure
# Don't have structures for these
# 'tetraoxygen': '852461-27-9', # cyclotetraoxygen D2d structure form
# 'Octaoxygen': '176740-46-8', # wikidata for CAS, also called ε-oxygen or red oxygen, 600 K & 16 GPa and higher
]
# https://janaf.nist.gov/tables/B-001.html
allotropes['B'] = [
('alpha rhombohedral boron', 1, 's', False, '[B]', 'B', 'ZOXJGFHDIHLPTG-UHFFFAOYSA-N', '7440-42-8', '2099657000-00-0'),
('beta rhombohedral boron', 1, 's', True, '[B]', 'B', 'ZOXJGFHDIHLPTG-UHFFFAOYSA-N', '7440-42-8', '2099652000-00-0'),# most stable
('beta tetragonal boron', 1, 's', False, '[B]', 'B', 'ZOXJGFHDIHLPTG-UHFFFAOYSA-N', '7440-42-8', '2099636000-00-0'),
('alpha tetragonal boron', 1, 's', False, '[B]', 'B', 'ZOXJGFHDIHLPTG-UHFFFAOYSA-N', '7440-42-8', '2099631000-00-0'),
('gamma orthorhombic boron', 1, 's', False, '[B]', 'B', 'ZOXJGFHDIHLPTG-UHFFFAOYSA-N', '7440-42-8', '2099615000-00-0'),
('powder boron', 1, 's', False, '[B]', 'B', 'ZOXJGFHDIHLPTG-UHFFFAOYSA-N', '7440-42-8', '2099610000-00-0'),
('glassy boron', 1, 's', False, '[B]', 'B', 'ZOXJGFHDIHLPTG-UHFFFAOYSA-N', '7440-42-8', '2099597000-00-0'),
# not sure actually exists but is in common chemistry
('diboron', 2, 's', False, 'B#B', 'B2/c1-2', 'ZOCHARZZJNPSEU-UHFFFAOYSA-N', '14452-61-0', '14452-61-0'),
]
allotropes['Zr'] = [
('alpha zirconium', 1, 's', False, '[Zr]', 'Zr', 'QCWXUUIWCKQGHC-UHFFFAOYSA-N', '7440-67-7', '2099592000-00-0'),
('beta zirconium', 1, 's', True, '[Zr]', 'Zr', 'QCWXUUIWCKQGHC-UHFFFAOYSA-N', '7440-67-7', '2099576000-00-0'),
]
allotropes['Ti'] = [
# format: (name, count, phase, stp_ref, smiles, inchi, inchi_key, closest_CAS, unique_CAS_maybe_fake,)
('alpha titanium', 1, 's', True, '[Ti]', 'Ti', 'RTAQQCXQSZGOHL-UHFFFAOYSA-N', '7440-67-7', '2099571000-00-0'),
('beta titanium', 1, 's', False, '[Ti]', 'Ti', 'RTAQQCXQSZGOHL-UHFFFAOYSA-N', '7440-67-7', '2099555000-00-0'),
]
solid_allotrope_map = {
'7440-32-6': {'T_transitions': [1166], 'CASs_transitions': ['2099571000-00-0', '2099555000-00-0'], 'all_CASs': ['2099555000-00-0', '2099571000-00-0']},
'7782-44-7': {'T_transitions': [23.876, 43.7964], 'H_transitions': [0.0, 742], #Freiman, Yu. A., and H. J. Jodl. “Solid Oxygen.” Physics Reports 401, no. 1 (November 1, 2004): 1–228. https://doi.org/10.1016/j.physrep.2004.06.002.
'CASs_transitions': ['2099550000-00-0', '2099539000-00-0', '2099534000-00-0'],
'all_CASs': ['2099550000-00-0', '2099539000-00-0', '2099534000-00-0']},
}
allotrope_CAS_to_name = {v[8]: v[0] for t in allotropes.values() for v in t}
# For each element that has allotropes, the allotrope which is used as a reference state at STP
allotropic_standard_states = {'H': 'dihydrogen',
'N': 'dinitrogen',
'O': 'dioxygen',
'F': 'difluorine',
'I': 'diiodine',
'Br': 'dibromine',
'Cl': 'dichlorine',
'C': 'graphite', # consistent with NBS/JANAF
'Po': 'alpha polonium',
'Sb': 'white antimony',
'Sn': 'white tin', # consistent with NBS/JANAF
'P': 'alpha white phosphorus', # consistent with NBS/JANAF
'S': 'alpha S8 sulfur', # JANAF consistent 298.15 K then switches to beta then gas
'Se': 'gray selenium',
'As': 'gray arsenic',
'B': 'beta rhombohedral boron',
'Ti': 'alpha titanium',
'Zr': 'beta zirconium',
}
"""
liquids = ['Hg', 'Br']
gases = ['He', 'Ne', 'Ar', 'Kr', 'Xe', 'Rn', 'F', 'Cl', 'H', 'O', 'N']
phases = ['s' for i in periodic_table]
for i, ele in enumerate(periodic_table):
if ele.symbol in liquids:
phases[i] = 'l'
elif ele.symbol in gases:
phases[i] = 'g'
"""
phases = ['g', 'g', 's', 's', 's', 's', 'g', 'g', 'g', 'g', 's', 's', 's', 's', 's', 's', 'g', 'g', 's', 's', 's', 's', 's', 's', 's', 's', 's', 's', 's', 's', 's', 's', 's', 's', 'l', 'g', 's', 's', 's', 's', 's', 's', 's', 's', 's', 's', 's', 's', 's', 's', 's', 's', 's', 'g', 's', 's', 's', 's', 's', 's', 's', 's', 's', 's', 's', 's', 's', 's', 's', 's', 's', 's', 's', 's', 's', 's', 's', 's', 's', 'l', 's', 's', 's', 's', 's', 'g', 's', 's', 's', 's', 's', 's', 's', 's', 's', 's', 's', 's', 's', 's', 's', 's', 's', 's', 's', 's', 's', 's', 's', 's', 's', 's', 's', 's', 's', 's', 's', 's']
"""# From CRC Table:
from chemicals.heat_capacity import CRC_standard_data
S0s = []
Hfs = []
other_values = {
'7440-31-5': (0, 51.18), # Tin (white) instead of gray from CODATA
'10097-32-2': (0, 152.2) # bromine as a liquid
}
for ele in periodic_table:
try:
CAS = ele.CAS_standard
if CAS == '7440-44-0': # carbon -> graphite (which is the standard state)
CAS = '7782-42-5'
S0c = CRC_standard_data.at[CAS, 'S0s']
S0l = CRC_standard_data.at[CAS, 'S0l']
S0g = CRC_standard_data.at[CAS, 'S0g']
Hfs = CRC_standard_data.at[CAS, 'Hfs']
Hfl = CRC_standard_data.at[CAS, 'Hfl']
Hfg = CRC_standard_data.at[CAS, 'Hfg']
if ele.phase == 's':
S0 = S0c
Hf = Hfs
elif ele.phase == 'l':
S0 = S0l
Hf = Hfl
elif ele.phase == 'g':
S0 = S0g
Hf = Hfg
if isnan(S0):
S0 = None
if isnan(Hf):
Hf = None
if CAS in other_values:
Hf, S0 = other_values[CAS]
S0s.append(S0)
Hfs.append(Hf)
except Exception as e:
S0s.append(None)
Hfs.append(None)
for Hf, ele in zip(Hfs, periodic_table):
if Hf != 0 and Hf is not None:
print(Hf, ele.name, ele.CAS)
"""
# Note that atoms like Br2, I2, O2, N2 have values of S for two atoms not one
S0s = [130.7, 126.2, 29.1, 9.5, 5.9, 5.7, 191.6, 205.2, 202.8, 146.3, 51.3, 32.7, 28.3, 18.8, 41.1, 32.1, 223.1, 154.8, 64.7, 41.6, 34.6, 30.7, 28.9, 23.8, 32.0, 27.3, 30.0, 29.9, 33.2, 41.6, 40.8, 31.1, 35.1, 42.4, 152.2, 164.1, 76.8, 55.0, 44.4, 39.0, 36.4, 28.7, None, 28.5, 31.5, 37.6, 42.6, 51.8, 57.8, 51.18, 45.7, 49.7, 116.1, 169.7, 85.2, 62.5, 56.9, 72.0, 73.2, 71.5, None, 69.6, 77.8, 68.1, 73.2, 75.6, 75.3, 73.2, 74.0, 59.9, 51.0, 43.6, 41.5, 32.6, 36.9, 32.6, 35.5, 41.6, 47.4, 75.9, 64.2, 64.8, 56.7, None, None, 176.2, 95.4, 71.0, 56.5, 51.8, 51.9, 50.2, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None]
Hfs = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, None, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None]
[docs]class PeriodicTable:
"""Periodic Table object for use in dealing with elements.
As there is only one periodic table of elements, this is automatically
initialized into the object `periodic_table`; there is no need to
construct a new instance of this class.
Parameters
----------
elements : list[Element]
List of Element objects, [-]
Notes
-----
Can be checked to sese if an element in in this, can be iterated over,
and as a current length of 118 elements.
See Also
--------
periodic_table
Element
References
----------
.. [1] N M O'Boyle, M Banck, C A James, C Morley, T Vandermeersch, and
G R Hutchison. "Open Babel: An open chemical toolbox." J. Cheminf.
(2011), 3, 33. DOI:10.1186/1758-2946-3-33
"""
__slots__ = ('_number_to_elements', '_symbol_to_elements',
'_name_to_elements', '_CAS_to_elements', '_indexes')
def __init__(self, elements):
#: Dictionary lookup of number(int) -> Element;
#: also has number(str) -> Element for convenience.
self._number_to_elements = number_to_elements = {}
#: Dictionary lookup of symbol(str) -> Element.
self._symbol_to_elements = symbol_to_elements = {}
#: Dictionary lookup of name(str) -> Element;
#: also has name(str.lower()) -> Element for convenience.
self._name_to_elements = name_to_elements = {}
#: Dictionary lookup of CAS(str) -> Element.
self._CAS_to_elements = CAS_to_elements = {}
for ele in elements:
number_to_elements[ele.number] = ele
number_to_elements[str(ele.number)] = ele
symbol_to_elements[ele.symbol] = ele
name_to_elements[ele.name] = ele
name_to_elements[ele.name.lower()] = ele
CAS_to_elements[ele.CAS] = ele
self._indexes = (symbol_to_elements, number_to_elements,
name_to_elements, CAS_to_elements)
def __contains__(self, key):
return any(key in i for i in self._indexes)
def __len__(self):
return 118
def __iter__(self):
return iter([self._number_to_elements[i] for i in range(1,119)])
def __getitem__(self, key):
for i in self._indexes:
if key in i: return i[key]
raise KeyError("'%s' is not in the periodic table" %(key))
def __getattr__(self, key):
for i in self._indexes:
if key in i: return i[key]
raise AttributeError("'%s' is not in the periodic table" %(key))
[docs]class Element:
"""Class for storing data on chemical elements. Supports most common
properties. If a property is not available, it is set to None.
The elements are created automatically and should be accessed via the
`periodic_table` interface.
Attributes
----------
number : int
Atomic number, [-]
name : str
name, [-]
symbol : str
Elemental symbol, [-]
MW : float
Molecular weight, [g/mol]
CAS : str
CAS number, [-]
period : str
Period in the periodic table, [-]
group : str
Group in the periodic table, [-]
block : str
Block in the periodic table, [-]
AReneg : float
Allred and Rochow electronegativity, [-]
rcov : float
Covalent radius, [Angstrom]
rvdw : float
Van der Waals radius, [Angstrom]
maxbonds : float
Maximum valence of a bond with this element, [-]
elneg : float
Pauling electronegativity, [-]
ionization : float
Ionization potential, [eV]
elaffinity : float
Electron affinity, [eV]
protons : int
Number of protons, [-]
electrons : int
Number of electrons of the element in the ground state, [-]
InChI : str
Standard InChI string of the element, [-]
InChI_key : str
25-character hash of the compound's InChI, [-]
smiles : str
Standard smiles string of the element, [-]
PubChem : int
PubChem Compound identifier (CID) of the chemical, [-]
phase : str
Standard state at 1 atm and 298.15 K, [-]
Hf : float
Enthalpy of formation of the element in its standard state (0 by
definition), [J/mol]
S0 : float
Standard absolute entropy of the element in its standard state (1 bar,
298.15 K), [J/mol/K]
"""
__slots__ = ['number', 'symbol', 'name', 'CAS', 'MW', 'AReneg', 'rcov',
'rvdw', 'maxbonds', 'elneg', 'ionization', 'elaffinity',
'period', 'group',
'InChI_key', 'PubChem', 'phase', 'Hf', 'S0']
def __repr__(self):
return "<Element %s (%s), number %d, MW=%s>" %(self.name, self.symbol, self.number, self.MW)
def __init__(self, number, symbol, name, MW, CAS, AReneg, rcov, rvdw,
maxbonds, elneg, ionization, elaffinity, period, group,
PubChem, phase, Hf, S0, InChI_key=None):
self.number = number
self.symbol = symbol
self.name = name
self.MW = MW
self.CAS = CAS
self.period = period
self.group = group
self.AReneg = AReneg
self.rcov = rcov
self.rvdw = rvdw
self.maxbonds = maxbonds
self.elneg = elneg
self.ionization = ionization
self.elaffinity = elaffinity
self.InChI_key = InChI_key
self.PubChem = PubChem
self.phase = phase
self.S0 = S0
self.Hf = Hf
@property
def CAS_standard(self):
r'''CAS number of the compound of the element used as a standard state
; i.e. the typically diatomic molecules hydrogen, nitrogen, oxygen,
fluorine, and chlorine, have different CAS numbers for the monoatomic
form and the diatomic form. This method returns the conventionally used
CAS number.
'''
return CAS_by_number_standard[self.number-1]
@property
def formula_standard(self):
r'''The formula of the element in its standard state. For homonuclear elements `2` is added to the formula.'''
if self.number in homonuclear_elements_set:
return self.symbol + '2'
return self.symbol
@property
def MW_standard(self):
r'''The molecular weight of the element in its standard state. For homonuclear elements the MW is doubled.'''
if self.number in homonuclear_elements_set:
return self.MW*2.0
return self.MW
@property
def protons(self):
r'''The number of protons of the element.'''
return self.number
@property
def electrons(self):
r'''The number of electrons of the element.'''
return self.number
@property
def neutrons(self):
r'''The number of neutrons of the element.'''
return int(round(self.MW - self.number, 0))
@property
def smiles(self):
r'''The SMILES identification string of the element.'''
return f'[{self.symbol}]'
@property
def InChI(self):
r'''The InChI identifier of the element. One of 's', 'd', 'f', or 'p'.'''
return self.symbol # 'InChI=1S/' +
@property
def block(self):
r'''Which block of the periodic table the element is in.'''
for k, v in blocks.items():
if self.number in v:
return k
# New file format; same data, coverted to Python lists for convenience with a few regular expressions
# https://github.com/openbabel/openbabel/blob/master/src/elementtable.h
openbabel_element_data = [
[ 1, "H", 2.20, 0.31, 0.31, 1.10, 1, 1.00794, 2.20, 13.5984, 0.75420375, 0.75, 0.75, 0.75, "Hydrogen"],
[ 2, "He", 0.00, 0.28, 0.28, 1.40, 0, 4.002602, 0.00, 24.5874, 0, 0.85, 1.00, 1.00, "Helium"],
[ 3, "Li", 0.97, 1.28, 1.28, 1.81, 1, 6.941, 0.98, 5.3917, 0.618049, 0.80, 0.50, 1.00, "Lithium"],
[ 4, "Be", 1.47, 0.96, 0.96, 1.53, 2, 9.012182, 1.57, 9.3227, 0, 0.76, 1.00, 0.00, "Beryllium"],
[ 5, "B", 2.01, 0.84, 0.84, 1.92, 4, 10.811, 2.04, 8.298, 0.279723, 1.00, 0.71, 0.71, "Boron"],
[ 6, "C", 2.50, 0.76, 0.76, 1.70, 4, 12.0107, 2.55, 11.2603, 1.262118, 0.40, 0.40, 0.40, "Carbon"],
[ 7, "N", 3.07, 0.71, 0.71, 1.55, 4, 14.0067, 3.04, 14.5341, -0.07, 0.05, 0.05, 1.00, "Nitrogen"],
[ 8, "O", 3.50, 0.66, 0.66, 1.52, 2, 15.9994, 3.44, 13.6181, 1.461112, 1.00, 0.05, 0.05, "Oxygen"],
[ 9, "F", 4.10, 0.57, 0.57, 1.47, 1, 18.9984032, 3.98, 17.4228, 3.4011887, 0.50, 0.70, 1.00, "Fluorine"],
[ 10, "Ne", 0.00, 0.58, 0.58, 1.54, 0, 20.1797, 0.00, 21.5645, 0, 0.70, 0.89, 0.96, "Neon"],
[ 11, "Na", 1.01, 1.66, 1.66, 2.27, 1, 22.98977, 0.93, 5.1391, 0.547926, 0.67, 0.36, 0.95, "Sodium"],
[ 12, "Mg", 1.23, 1.41, 1.41, 1.73, 2, 24.3050, 1.31, 7.6462, 0, 0.54, 1.00, 0.00, "Magnesium"],
[ 13, "Al", 1.47, 1.21, 1.21, 1.84, 6, 26.981538, 1.61, 5.9858, 0.43283, 0.75, 0.65, 0.65, "Aluminium"],
[ 14, "Si", 1.74, 1.11, 1.11, 2.10, 6, 28.0855, 1.90, 8.1517, 1.389521, 0.50, 0.60, 0.60, "Silicon"],
[ 15, "P", 2.06, 1.07, 1.07, 1.80, 6, 30.973761, 2.19, 10.4867, 0.7465, 1.00, 0.50, 0.00, "Phosphorus"],
[ 16, "S", 2.44, 1.05, 1.05, 1.80, 6, 32.065, 2.58, 10.36, 2.0771029, 0.70, 0.70, 0.00, "Sulfur"],
[ 17, "Cl", 2.83, 1.02, 1.02, 1.75, 1, 35.453, 3.16, 12.9676, 3.612724, 0.12, 0.94, 0.12, "Chlorine"],
[ 18, "Ar", 0.00, 1.06, 1.06, 1.88, 0, 39.948, 0.00, 15.7596, 0, 0.50, 0.82, 0.89, "Argon"],
[ 19, "K", 0.91, 2.03, 2.03, 2.75, 1, 39.0983, 0.82, 4.3407, 0.501459, 0.56, 0.25, 0.83, "Potassium"],
[ 20, "Ca", 1.04, 1.76, 1.76, 2.31, 2, 40.078, 1.00, 6.1132, 0.02455, 0.24, 1.00, 0.00, "Calcium"],
[ 21, "Sc", 1.20, 1.70, 1.70, 2.30, 6, 44.95591, 1.36, 6.5615, 0.188, 0.90, 0.90, 0.90, "Scandium"],
[ 22, "Ti", 1.32, 1.60, 1.60, 2.15, 6, 47.867, 1.54, 6.8281, 0.084, 0.75, 0.76, 0.78, "Titanium"],
[ 23, "V", 1.45, 1.53, 1.53, 2.05, 6, 50.9415, 1.63, 6.7462, 0.525, 0.65, 0.65, 0.67, "Vanadium"],
[ 24, "Cr", 1.56, 1.39, 1.39, 2.05, 6, 51.9961, 1.66, 6.7665, 0.67584, 0.54, 0.60, 0.78, "Chromium"],
[ 25, "Mn", 1.60, 1.39, 1.39, 2.05, 8, 54.938049, 1.55, 7.434, 0, 0.61, 0.48, 0.78, "Manganese"],
[ 26, "Fe", 1.64, 1.32, 1.32, 2.05, 6, 55.845, 1.83, 7.9024, 0.151, 0.88, 0.40, 0.20, "Iron"],
[ 27, "Co", 1.70, 1.26, 1.26, 2.00, 6, 58.9332, 1.88, 7.881, 0.6633, 0.94, 0.56, 0.63, "Cobalt"],
[ 28, "Ni", 1.75, 1.24, 1.24, 2.00, 6, 58.6934, 1.91, 7.6398, 1.15716, 0.31, 0.82, 0.31, "Nickel"],
[ 29, "Cu", 1.75, 1.32, 1.32, 2.00, 6, 63.546, 1.90, 7.7264, 1.23578, 0.78, 0.50, 0.20, "Copper"],
[ 30, "Zn", 1.66, 1.22, 1.22, 2.10, 6, 65.38, 1.65, 9.3942, 0, 0.49, 0.50, 0.69, "Zinc"],
[ 31, "Ga", 1.82, 1.22, 1.22, 1.87, 3, 69.723, 1.81, 5.9993, 0.41, 0.76, 0.56, 0.56, "Gallium"],
[ 32, "Ge", 2.02, 1.20, 1.20, 2.11, 4, 72.64, 2.01, 7.8994, 1.232712, 0.40, 0.56, 0.56, "Germanium"],
[ 33, "As", 2.20, 1.19, 1.19, 1.85, 3, 74.92160, 2.18, 9.7886, 0.814, 0.74, 0.50, 0.89, "Arsenic"],
[ 34, "Se", 2.48, 1.20, 1.20, 1.90, 2, 78.96, 2.55, 9.7524, 2.02067, 1.00, 0.63, 0.00, "Selenium"],
[ 35, "Br", 2.74, 1.20, 1.20, 1.83, 1, 79.904, 2.96, 11.8138, 3.363588, 0.65, 0.16, 0.16, "Bromine"],
[ 36, "Kr", 0.00, 1.16, 1.16, 2.02, 0, 83.798, 3.00, 13.9996, 0, 0.36, 0.72, 0.82, "Krypton"],
[ 37, "Rb", 0.89, 2.20, 2.20, 3.03, 1, 85.4678, 0.82, 4.1771, 0.485916, 0.44, 0.18, 0.69, "Rubidium"],
[ 38, "Sr", 0.99, 1.95, 1.95, 2.49, 2, 87.62, 0.95, 5.6949, 0.05206, 0.00, 1.00, 0.00, "Strontium"],
[ 39, "Y", 1.11, 1.90, 1.90, 2.40, 6, 88.90585, 1.22, 6.2173, 0.307, 0.58, 1.00, 1.00, "Yttrium"],
[ 40, "Zr", 1.22, 1.75, 1.75, 2.30, 6, 91.224, 1.33, 6.6339, 0.426, 0.58, 0.88, 0.88, "Zirconium"],
[ 41, "Nb", 1.23, 1.64, 1.64, 2.15, 6, 92.90638, 1.60, 6.7589, 0.893, 0.45, 0.76, 0.79, "Niobium"],
[ 42, "Mo", 1.30, 1.54, 1.54, 2.10, 6, 95.96, 2.16, 7.0924, 0.7472, 0.33, 0.71, 0.71, "Molybdenum"],
[ 43, "Tc", 1.36, 1.47, 1.47, 2.05, 6, 98, 1.90, 7.28, 0.55, 0.23, 0.62, 0.62, "Technetium"],
[ 44, "Ru", 1.42, 1.46, 1.46, 2.05, 6, 101.07, 2.20, 7.3605, 1.04638, 0.14, 0.56, 0.56, "Ruthenium"],
[ 45, "Rh", 1.45, 1.42, 1.42, 2.00, 6, 102.90550, 2.28, 7.4589, 1.14289, 0.04, 0.49, 0.55, "Rhodium"],
[ 46, "Pd", 1.35, 1.39, 1.39, 2.05, 6, 106.42, 2.20, 8.3369, 0.56214, 0.00, 0.41, 0.52, "Palladium"],
[ 47, "Ag", 1.42, 1.45, 1.45, 2.10, 6, 107.8682, 1.93, 7.5762, 1.30447, 0.88, 0.88, 1.00, "Silver"],
[ 48, "Cd", 1.46, 1.44, 1.44, 2.20, 6, 112.411, 1.69, 8.9938, 0, 1.00, 0.85, 0.56, "Cadmium"],
[ 49, "In", 1.49, 1.42, 1.42, 2.20, 3, 114.818, 1.78, 5.7864, 0.404, 0.65, 0.46, 0.45, "Indium"],
[ 50, "Sn", 1.72, 1.39, 1.39, 1.93, 4, 118.701, 1.96, 7.3439, 1.112066, 0.40, 0.50, 0.50, "Tin"],
[ 51, "Sb", 1.82, 1.39, 1.39, 2.17, 3, 121.760, 2.05, 8.6084, 1.047401, 0.62, 0.39, 0.71, "Antimony"],
[ 52, "Te", 2.01, 1.38, 1.38, 2.06, 2, 127.60, 2.10, 9.0096, 1.970875, 0.83, 0.48, 0.00, "Tellurium"],
[ 53, "I", 2.21, 1.39, 1.39, 1.98, 1, 126.90447, 2.66, 10.4513, 3.059038, 0.58, 0.00, 0.58, "Iodine"],
[ 54, "Xe", 0.00, 1.40, 1.40, 2.16, 0, 131.293, 2.60, 12.1298, 0, 0.26, 0.62, 0.69, "Xenon"],
[ 55, "Cs", 0.86, 2.44, 2.44, 3.43, 1, 132.90545, 0.79, 3.8939, 0.471626, 0.34, 0.09, 0.56, "Caesium"],
[ 56, "Ba", 0.97, 2.15, 2.15, 2.68, 2, 137.327, 0.89, 5.2117, 0.14462, 0.00, 0.79, 0.00, "Barium"],
[ 57, "La", 1.08, 2.07, 2.07, 2.50, 12, 138.9055, 1.10, 5.5769, 0.47, 0.44, 0.83, 1.00, "Lanthanum"],
[ 58, "Ce", 0.00, 2.04, 2.04, 2.48, 6, 140.116, 1.12, 5.5387, 0.5, 1.00, 1.00, 0.78, "Cerium"],
[ 59, "Pr", 0.00, 2.03, 2.03, 2.47, 6, 140.90765, 1.13, 5.473, 0.5, 0.85, 1.00, 0.78, "Praseodymium"],
[ 60, "Nd", 0.00, 2.01, 2.01, 2.45, 6, 144.24, 1.14, 5.525, 0.5, 0.78, 1.00, 0.78, "Neodymium"],
[ 61, "Pm", 0.00, 1.99, 1.99, 2.43, 6, 145, 0.00, 5.582, 0.5, 0.64, 1.00, 0.78, "Promethium"],
[ 62, "Sm", 0.00, 1.98, 1.98, 2.42, 6, 150.36, 1.17, 5.6437, 0.5, 0.56, 1.00, 0.78, "Samarium"],
[ 63, "Eu", 0.00, 1.98, 1.98, 2.40, 6, 151.964, 0.00, 5.6704, 0.5, 0.38, 1.00, 0.78, "Europium"],
[ 64, "Gd", 0.00, 1.96, 1.96, 2.38, 6, 157.25, 1.20, 6.1498, 0.5, 0.27, 1.00, 0.78, "Gadolinium"],
[ 65, "Tb", 0.00, 1.94, 1.94, 2.37, 6, 158.92534, 0.00, 5.8638, 0.5, 0.19, 1.00, 0.78, "Terbium"],
[ 66, "Dy", 0.00, 1.92, 1.92, 2.35, 6, 162.500, 1.22, 5.9389, 0.5, 0.12, 1.00, 0.78, "Dysprosium"],
[ 67, "Ho", 0.00, 1.92, 1.92, 2.33, 6, 164.93032, 1.23, 6.0215, 0.5, 0.00, 1.00, 0.61, "Holmium"],
[ 68, "Er", 0.00, 1.89, 1.89, 2.32, 6, 167.259, 1.24, 6.1077, 0.5, 0.00, 0.90, 0.46, "Erbium"],
[ 69, "Tm", 0.00, 1.90, 1.90, 2.30, 6, 168.93421, 1.25, 6.1843, 0.5, 0.00, 0.83, 0.32, "Thulium"],
[ 70, "Yb", 0.00, 1.87, 1.87, 2.28, 6, 173.054, 0.00, 6.2542, 0.5, 0.00, 0.75, 0.22, "Ytterbium"],
[ 71, "Lu", 0.00, 1.87, 1.87, 2.27, 6, 174.9668, 1.27, 5.4259, 0.5, 0.00, 0.67, 0.14, "Lutetium"],
[ 72, "Hf", 1.23, 1.75, 1.75, 2.25, 6, 178.49, 1.30, 6.8251, 0, 0.30, 0.76, 1.00, "Hafnium"],
[ 73, "Ta", 1.33, 1.70, 1.70, 2.20, 6, 180.9479, 1.50, 7.5496, 0.322, 0.30, 0.65, 1.00, "Tantalum"],
[ 74, "W", 1.40, 1.62, 1.62, 2.10, 6, 183.84, 2.36, 7.864, 0.815, 0.13, 0.58, 0.84, "Tungsten"],
[ 75, "Re", 1.46, 1.51, 1.51, 2.05, 6, 186.207, 1.90, 7.8335, 0.15, 0.15, 0.49, 0.67, "Rhenium"],
[ 76, "Os", 1.52, 1.44, 1.44, 2.00, 6, 190.23, 2.20, 8.4382, 1.0778, 0.15, 0.40, 0.59, "Osmium"],
[ 77, "Ir", 1.55, 1.41, 1.41, 2.00, 6, 192.217, 2.20, 8.967, 1.56436, 0.09, 0.33, 0.53, "Iridium"],
[ 78, "Pt", 1.44, 1.36, 1.36, 2.05, 6, 195.078, 2.28, 8.9588, 2.1251, 0.90, 0.85, 0.68, "Platinum"],
[ 79, "Au", 1.42, 1.36, 1.36, 2.10, 6, 196.96655, 2.54, 9.2255, 2.30861, 0.80, 0.82, 0.12, "Gold"],
[ 80, "Hg", 1.44, 1.32, 1.32, 2.05, 6, 200.59, 2.00, 10.4375, 0, 0.71, 0.71, 0.76, "Mercury"],
[ 81, "Tl", 1.44, 1.45, 1.45, 1.96, 3, 204.3833, 1.62, 6.1082, 0.377, 0.65, 0.33, 0.30, "Thallium"],
[ 82, "Pb", 1.55, 1.46, 1.46, 2.02, 4, 207.2, 2.33, 7.4167, 0.364, 0.34, 0.35, 0.38, "Lead"],
[ 83, "Bi", 1.67, 1.48, 1.48, 2.07, 3, 208.98040, 2.02, 7.2855, 0.942363, 0.62, 0.31, 0.71, "Bismuth"],
[ 84, "Po", 1.76, 1.40, 1.40, 1.97, 2, 209, 2.00, 8.414, 1.9, 0.67, 0.36, 0.00, "Polonium"],
[ 85, "At", 1.90, 1.50, 1.50, 2.02, 1, 210, 2.20, 0, 2.8, 0.46, 0.31, 0.27, "Astatine"],
[ 86, "Rn", 0.00, 1.50, 1.50, 2.20, 0, 222, 0.00, 10.7485, 0, 0.26, 0.51, 0.59, "Radon"],
[ 87, "Fr", 0.00, 2.60, 2.60, 3.48, 1, 223, 0.70, 4.0727, 0, 0.26, 0.00, 0.40, "Francium"],
[ 88, "Ra", 0.00, 2.21, 2.21, 2.83, 2, 226, 0.90, 5.2784, 0, 0.00, 0.49, 0.00, "Radium"],
[ 89, "Ac", 0.00, 2.15, 2.15, 2.00, 6, 227, 1.10, 5.17, 0, 0.44, 0.67, 0.98, "Actinium"],
[ 90, "Th", 0.00, 2.06, 2.06, 2.40, 6, 232.0381, 1.30, 6.3067, 0, 0.00, 0.73, 1.00, "Thorium"],
[ 91, "Pa", 0.00, 2.00, 2.00, 2.00, 6, 231.03588, 1.50, 5.89, 0, 0.00, 0.63, 1.00, "Protactinium"],
[ 92, "U", 0.00, 1.96, 1.96, 2.30, 6, 238.02891, 1.38, 6.1941, 0, 0.00, 0.56, 1.00, "Uranium"],
[ 93, "Np", 0.00, 1.90, 1.90, 2.00, 6, 237.05, 1.36, 6.2657, 0, 0.00, 0.50, 1.00, "Neptunium"],
[ 94, "Pu", 0.00, 1.87, 1.87, 2.00, 6, 244.06, 1.28, 6.026, 0, 0.00, 0.42, 1.00, "Plutonium"],
[ 95, "Am", 0.00, 1.80, 1.80, 2.00, 6, 243.06, 1.30, 5.9738, 0, 0.33, 0.36, 0.95, "Americium"],
[ 96, "Cm", 0.00, 1.69, 1.69, 2.00, 6, 247.07, 1.30, 5.9914, 0, 0.47, 0.36, 0.89, "Curium"],
[ 97, "Bk", 0.00, 1.60, 1.60, 2.00, 6, 247.07, 1.30, 6.1979, 0, 0.54, 0.31, 0.89, "Berkelium"],
[ 98, "Cf", 0.00, 1.60, 1.60, 2.00, 6, 251.08, 1.30, 6.2817, 0, 0.63, 0.21, 0.83, "Californium"],
[ 99, "Es", 0.00, 1.60, 1.60, 2.00, 6, 252.08, 1.30, 6.42, 0, 0.70, 0.12, 0.83, "Einsteinium"],
[100, "Fm", 0.00, 1.60, 1.60, 2.00, 6, 257.10, 1.30, 6.5, 0, 0.70, 0.12, 0.73, "Fermium"],
[101, "Md", 0.00, 1.60, 1.60, 2.00, 6, 258.10, 1.30, 6.58, 0, 0.70, 0.05, 0.65, "Mendelevium"],
[102, "No", 0.00, 1.60, 1.60, 2.00, 6, 259.10, 1.30, 6.65, 0, 0.74, 0.05, 0.53, "Nobelium"],
[103, "Lr", 0.00, 1.60, 1.60, 2.00, 6, 262.11, 0.00, 4.9, 0, 0.78, 0.00, 0.40, "Lawrencium"],
[104, "Rf", 0.00, 1.60, 1.60, 2.00, 6, 265.12, 0.00, 6, 0, 0.80, 0.00, 0.35, "Rutherfordium"],
[105, "Db", 0.00, 1.60, 1.60, 2.00, 6, 268.13, 0.00, 0, 0, 0.82, 0.00, 0.31, "Dubnium"],
[106, "Sg", 0.00, 1.60, 1.60, 2.00, 6, 271.13, 0.00, 0, 0, 0.85, 0.00, 0.27, "Seaborgium"],
[107, "Bh", 0.00, 1.60, 1.60, 2.00, 6, 270, 0.00, 0, 0, 0.88, 0.00, 0.22, "Bohrium"],
[108, "Hs", 0.00, 1.60, 1.60, 2.00, 6, 277.15, 0.00, 0, 0, 0.90, 0.00, 0.18, "Hassium"],
[109, "Mt", 0.00, 1.60, 1.60, 2.00, 6, 276.15, 0.00, 0, 0, 0.92, 0.00, 0.15, "Meitnerium"],
[110, "Ds", 0.00, 1.60, 1.60, 2.00, 6, 281.16, 0.00, 0, 0, 0.93, 0.00, 0.14, "Darmstadtium"],
[111, "Rg", 0.00, 1.60, 1.60, 2.00, 6, 280.16, 0.00, 0, 0, 0.94, 0.00, 0.13, "Roentgenium"],
[112, "Cn", 0.00, 1.60, 1.60, 2.00, 6, 285.17, 0.00, 0, 0, 0.95, 0.00, 0.12, "Copernicium"],
[113, "Nh", 0.00, 1.60, 1.60, 2.00, 6, 284.18, 0.00, 0, 0, 0.96, 0.00, 0.11, "Nihonium"],
[114, "Fl", 0.00, 1.60, 1.60, 2.00, 6, 289.19, 0.00, 0, 0, 0.97, 0.00, 0.10, "Flerovium"],
[115, "Mc", 0.00, 1.60, 1.60, 2.00, 6, 288.19, 0.00, 0, 0, 0.98, 0.00, 0.09, "Moscovium"],
[116, "Lv", 0.00, 1.60, 1.60, 2.00, 6, 293, 0.00, 0, 0, 0.99, 0.00, 0.08, "Livermorium"],
[117, "Ts", 0.00, 1.60, 1.60, 2.00, 6, 294, 0.00, 0, 0, 0.99, 0.00, 0.07, "Tennessine"],
[118, "Og", 0.00, 1.60, 1.60, 2.00, 6, 294, 0.00, 0, 0, 0.99, 0.00, 0.06, "Oganesson"],
]
element_list = []
"""Load the data from OpenBabel, and store it as both a
list of elements first, and then as an instance of Periodic Table."""
for values in openbabel_element_data:
number, symbol, AReneg, rcov, _, rvdw, maxbonds, MW, elneg, ionization, elaffinity, _, _, _, name = values
AReneg = None if AReneg == 0 else AReneg
rcov = None if rcov == 1.6 else rcov # in Angstrom
rvdw = None if rvdw == 2.0 else rvdw # in Angstrom
maxbonds = None if maxbonds == 6.0 else int(maxbonds)
elneg = None if elneg == 0.0 else elneg
ionization = None if ionization == 0.0 else ionization # in eV
elaffinity = None if elaffinity == 0.0 else elaffinity # in eV
index = number-1
period = periods[index]
group = groups[index]
InChI_key = InChI_keys[index]
cid = cids[index]
phase = phases[index]
Hf = Hfs[index]
S0 = S0s[index]
CAS = CAS_by_number[index]
ele = Element(number, symbol, name, MW, CAS, AReneg, rcov, rvdw,
maxbonds, elneg, ionization, elaffinity, period, group,
cid, phase, Hf, S0, InChI_key)
element_list.append(ele)
periodic_table = PeriodicTable(element_list)
"""Single instance of the PeriodicTable class. Use this, not the PeriodicTable
class directly.
A brief overview of using the periodic table and its elements:
>>> periodic_table.Na
<Element Sodium (Na), number 11, MW=22.98977>
>>> periodic_table.U.MW
238.02891
>>> periodic_table['Th'].CAS
'7440-29-1'
>>> periodic_table.lead.protons
82
>>> periodic_table['7440-57-5'].symbol
'Au'
>>> len(periodic_table)
118
>>> 'gold' in periodic_table
True
>>> periodic_table.He.protons, periodic_table.He.neutrons, periodic_table.He.electrons # Standard number of protons, neutrons, electrons
(2, 2, 2)
>>> periodic_table.He.phase # Phase of the element in the standard state
'g'
>>> periodic_table.He.Hf # Heat of formation in standard state in J/mol - by definition 0
0.0
>>> periodic_table.He.S0 # Absolute entropy (J/(mol*K) in standard state - non-zero)
126.2
>>> periodic_table.Kr.block, periodic_table.Kr.period, periodic_table.Kr.group
('p', 4, 18)
>>> periodic_table.Rn.InChI
'Rn'
>>> periodic_table.Rn.smiles
'[Rn]'
>>> periodic_table.Pu.number
94
>>> periodic_table.Pu.PubChem
23940
>>> periodic_table.Bi.InChI_key
'JCXGWMGPZLAOME-UHFFFAOYSA-N'
"""
del openbabel_element_data
[docs]@mark_numba_incompatible
def molecular_weight(atoms):
r'''Calculates molecular weight of a molecule given a dictionary of its
atoms and their counts, in the format {symbol: count}.
.. math::
MW = \sum_i n_i MW_i
Parameters
----------
atoms : dict
Dictionary of counts of individual atoms, indexed by symbol with
proper capitalization, [-]
Returns
-------
MW : float
Calculated molecular weight [g/mol]
Notes
-----
Elemental data is from rdkit, with CAS numbers added. An exception is
raised if an incorrect element symbol is given. Elements up to 118 are
supported, as are deutreium and tritium.
Examples
--------
>>> molecular_weight({'H': 12, 'C': 20, 'O': 5}) # DNA
332.30628
References
----------
.. [1] RDKit: Open-source cheminformatics; http://www.rdkit.org
'''
MW = 0
for i in atoms:
if i in periodic_table:
MW += periodic_table[i].MW*atoms[i]
elif i == 'D':
# Hardcoded MW until an actual isotope db is created
MW += 2.014102*atoms[i]
elif i == 'T':
# Hardcoded MW until an actual isotope db is created
MW += 3.0160492*atoms[i]
else:
raise ValueError('Molecule includes unknown atoms')
return MW
[docs]@mark_numba_incompatible
def mass_fractions(atoms, MW=None):
r'''Calculates the mass fractions of each element in a compound,
given a dictionary of its atoms and their counts, in the format
{symbol: count}.
.. math::
w_i = \frac{n_i MW_i}{\sum_i n_i MW_i}
Parameters
----------
atoms : dict
Dictionary of counts of individual atoms, indexed by symbol with
proper capitalization, [-]
MW : float, optional
Molecular weight, [g/mol]
Returns
-------
mfracs : dict
Dictionary of mass fractions of individual atoms, indexed by symbol
with proper capitalization, [-]
Notes
-----
Molecular weight is optional, but speeds up the calculation slightly. It
is calculated using the function `molecular_weight` if not specified.
Elemental data is from rdkit, with CAS numbers added. An exception is
raised if an incorrect element symbol is given. Elements up to 118 are
supported.
Examples
--------
>>> mass_fractions({'H': 12, 'C': 20, 'O': 5})
{'H': 0.03639798802478244, 'C': 0.7228692758981262, 'O': 0.24073273607709128}
References
----------
.. [1] RDKit: Open-source cheminformatics; http://www.rdkit.org
'''
if not MW:
MW = molecular_weight(atoms)
mfracs = {}
for i in atoms:
if i in periodic_table:
mfracs[i] = periodic_table[i].MW*atoms[i]/MW
else:
raise ValueError('Molecule includes unknown atoms')
return mfracs
[docs]@mark_numba_incompatible
def atom_fractions(atoms):
r'''Calculates the atomic fractions of each element in a compound,
given a dictionary of its atoms and their counts, in the format
{symbol: count}.
.. math::
a_i = \frac{n_i}{\sum_i n_i}
Parameters
----------
atoms : dict
dictionary of counts of individual atoms, indexed by symbol with
proper capitalization, [-]
Returns
-------
afracs : dict
dictionary of atomic fractions of individual atoms, indexed by symbol
with proper capitalization, [-]
Notes
-----
No actual data on the elements is used, so incorrect or custom compounds
would not raise an error.
Examples
--------
>>> atom_fractions({'H': 12, 'C': 20, 'O': 5})
{'H': 0.32432432432432434, 'C': 0.5405405405405406, 'O': 0.13513513513513514}
References
----------
.. [1] RDKit: Open-source cheminformatics; http://www.rdkit.org
'''
count = sum(atoms.values())
afracs = {}
for i in atoms:
afracs[i] = atoms[i]/count
return afracs
[docs]@mark_numba_incompatible
def mixture_atomic_composition(atomss, zs):
r'''Simple function to calculate the atomic average composition of a
mixture, using the mole fractions of each species and their own atomic
compositions.
Parameters
----------
atomss : list[dict[(str, int)]]
List of dictionaries of atomic compositions, [-]
zs : list[float]
Mole fractions of each component, [-]
Returns
-------
atoms : dict[(str, int)]
Atomic composition
Notes
-----
Examples
--------
>>> mixture_atomic_composition([{'O': 2}, {'N': 1, 'O': 2}, {'C': 1, 'H': 4}], [0.95, 0.025, .025])
{'O': 1.95, 'N': 0.025, 'C': 0.025, 'H': 0.1}
'''
ans = {}
for atoms, zs_i in zip(atomss, zs):
for key, val in atoms.items():
if key in ans:
ans[key] += val*zs_i
else:
ans[key] = val*zs_i
return ans
[docs]@mark_numba_incompatible
def mixture_atomic_composition_ordered(atomss, zs):
r'''Simple function to calculate the atomic average composition of a
mixture, using the mole fractions of each species and their own atomic
compositions. Returns the result as a sorted list with atomic numbers from
low to high.
Parameters
----------
atomss : list[dict[(str, int)]]
List of dictionaries of atomic compositions, [-]
zs : list[float]
Mole fractions of each component; this can also be a molar flow rate
and then the `abundances` will be flows, [-]
Returns
-------
abundances : list[float]
Number of atoms of each element per mole of the feed, [-]
atom_keys : list[str]
Atomic elements, sorted from lowest atomic number to highest
Notes
-----
Useful to ensure a matrix order is consistent in multiple steps.
Examples
--------
>>> mixture_atomic_composition_ordered([{'O': 2}, {'N': 1, 'O': 2}, {'C': 1, 'H': 4}], [0.95, 0.025, .025])
([0.1, 0.025, 0.025, 1.95], ['H', 'C', 'N', 'O'])
'''
ans = mixture_atomic_composition(atomss, zs)
nums = []
eles = []
for k, n in sorted(ans.items(), key=lambda x: periodic_table[x[0]].number):
nums.append(n)
eles.append(k)
return nums, eles
[docs]@mark_numba_incompatible
def atom_matrix(atomss, atom_IDs=None):
r'''Simple function to create a matrix of elements in each compound, where
each row has the same elements.
Parameters
----------
atomss : list[dict[(str, int)]]
List of dictionaries of atomic compositions, [-]
atom_IDs : list[str], optional
Optionally, a subset (or simply ordered differently) of elements to
consider, [-]
Returns
-------
matrix : list[list[float]]
The number of each element in each compound as a matrix, indexed as
[compound][element], [-]
Notes
-----
Examples
--------
>>> atom_matrix([{'C': 1, 'H': 4}, {'C': 2, 'H': 6}, {'N': 2}, {'O': 2}, {'H': 2, 'O': 1}, {'C': 1, 'O': 2}])
[[4, 1, 0.0, 0.0], [6, 2, 0.0, 0.0], [0.0, 0.0, 2, 0.0], [0.0, 0.0, 0.0, 2], [2, 0.0, 0.0, 1], [0.0, 1, 0.0, 2]]
'''
if atom_IDs is None:
ans = set()
for atoms in atomss:
for i in atoms.keys():
ans.add(i)
atom_IDs = sorted(list(ans), key=lambda x: periodic_table[x].number)
atom_idx = {k: i for i, k in enumerate(atom_IDs)}
n_atoms = len(atom_IDs)
element_matrix = []
for atoms in atomss:
l = [0.0]*n_atoms
for k, v in atoms.items():
try:
l[atom_idx[k]] = v
except KeyError:
pass
element_matrix.append(l)
return element_matrix
[docs]@mark_numba_incompatible
def similarity_variable(atoms, MW=None):
r'''Calculates the similarity variable of an compound, as defined in [1]_.
Currently only applied for certain heat capacity estimation routines.
.. math::
\alpha = \frac{N}{MW} = \frac{\sum_i n_i}{\sum_i n_i MW_i}
Parameters
----------
atoms : dict
dictionary of counts of individual atoms, indexed by symbol with
proper capitalization, [-]
MW : float, optional
Molecular weight, [g/mol]
Returns
-------
similarity_variable : float
Similarity variable as defined in [1]_, [mol/g]
Notes
-----
Molecular weight is optional, but speeds up the calculation slightly. It
is calculated using the function `molecular_weight` if not specified.
Examples
--------
>>> similarity_variable({'H': 32, 'C': 15})
0.2212654140784498
References
----------
.. [1] Laštovka, Václav, Nasser Sallamie, and John M. Shaw. "A Similarity
Variable for Estimating the Heat Capacity of Solid Organic Compounds:
Part I. Fundamentals." Fluid Phase Equilibria 268, no. 1-2
(June 25, 2008): 51-60. doi:10.1016/j.fluid.2008.03.019.
'''
if not MW:
MW = molecular_weight(atoms)
return sum(atoms.values())/MW
[docs]@mark_numba_incompatible
def atoms_to_Hill(atoms):
r'''Determine the Hill formula of a compound, given a dictionary of its
atoms and their counts, in the format {symbol: count}.
Parameters
----------
atoms : dict
dictionary of counts of individual atoms, indexed by symbol with
proper capitalization, [-]
Returns
-------
Hill_formula : str
Hill formula, [-]
Notes
-----
The Hill system is as follows:
If the chemical has 'C' in it, this is listed first, and then if it has
'H' in it as well as 'C', then that goes next. All elements are sorted
alphabetically afterwards, including 'H' if 'C' is not present.
All elements are followed by their count, unless it is 1.
Examples
--------
>>> atoms_to_Hill({'H': 5, 'C': 2, 'Br': 1})
'C2H5Br'
References
----------
.. [1] Hill, Edwin A."“ON A SYSTEM OF INDEXING CHEMICAL LITERATURE;
ADOPTED BY THE CLASSIFICATION DIVISION OF THE U. S. PATENT OFFICE.1."
Journal of the American Chemical Society 22, no. 8 (August 1, 1900):
478-94. doi:10.1021/ja02046a005.
'''
def str_ele_count(ele):
if atoms[ele] == 1:
count = ''
else:
count = str(atoms[ele])
return count
atoms = atoms.copy()
s = ''
if 'C' in atoms.keys():
s += 'C' + str_ele_count('C')
del atoms['C']
if 'H' in atoms.keys():
s += 'H' + str_ele_count('H')
del atoms['H']
for ele in sorted(atoms.keys()):
s += ele + str_ele_count(ele)
else:
for ele in sorted(atoms.keys()):
s += ele + str_ele_count(ele)
return s
_simple_formula_parser_re_str = r'([A-Z][a-z]{0,2})([\d\.\d]+)?'
_simple_formula_parser_re = None # Delay creation to simple_formula_parser to speedup start
# Delay creation to simple_formula_parser to speedup start
formula_token_matcher_rational_re_str = r'[A-Z][a-z]?|(?:\d*[.])?\d+|\d+|[()]'
bracketed_charge_re_str = r'\([+-]?\d+\)$|\(\d+[+-]?\)$|\([+-]+\)$'
formula_token_matcher_rational = bracketed_charge_re = None
letter_set = set('abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ')
subscripts = '₀₁₂₃₄₅₆₇₈₉'
numbers = '0123456789'
# translate_subscripts = str.maketrans(subscripts, numbers)# missing in micropython
translate_subscripts = {8320: 48, 8321: 49, 8322: 50, 8323: 51, 8324: 52, 8325: 53, 8326: 54, 8327: 55, 8328: 56, 8329: 57}
allowable_atoms_index_hydrogen_deficiency = frozenset(['C', 'O', 'H', 'N', 'F', 'Cl', 'Br', 'I', 'At'])
[docs]@mark_numba_incompatible
def index_hydrogen_deficiency(atoms):
r'''Calculate the index of hydrogen deficiency of a compound, given a
dictionary of its atoms and their counts, in the format {symbol: count}.
Parameters
----------
atoms : dict
dictionary of counts of individual atoms, indexed by symbol with
proper capitalization, [-]
Returns
-------
HDI : float
Hydrogen deficiency index, [-]
Notes
-----
The calculation is according to:
.. math::
\text{IDH} = 0.5\left(2C + 2 + N - H -X + 0O \right)
where `X` is the number of halogen atoms. The number of oxygen atoms does
not impact this calculation.
Examples
--------
Agelastatin A:
>>> index_hydrogen_deficiency({'C': 12, 'H': 13, 'Br': 1, 'N': 4, 'O': 3})
8.0
References
----------
.. [1] Brown, William H., and Thomas Poon. Introduction to Organic
Chemistry. 4th edition. Hoboken, NJ: Wiley, 2010.
'''
if not set(atoms.keys()).issubset(allowable_atoms_index_hydrogen_deficiency):
raise ValueError("Atoms contain unsupported element; supported elements are 'C', 'O', 'H', 'N', 'F', 'Cl', 'Br', 'I', 'At'.")
# https://www.chem.ucalgary.ca/courses/350/Carey5th/Ch13/ch13-ihd.html
halogens = ('F', 'Cl', 'Br', 'I', 'At')
halogen_count = 0
for atom in halogens:
halogen_count += atoms.get(atom, 0)
# Oxygen is OK also, does not alter the calculation
IDH = 0.5*(2*atoms.get('C', 0) + 2 - atoms.get('H', 0) - halogen_count + atoms.get('N', 0))
return IDH