pychnosz 1.1.1__cp310-cp310-win_amd64.whl

pychnosz/data/extdata/src/README.txt

@@ -0,0 +1,5 @@
+[20220322]
+
+H2O92D.f.orig is a source file taken from the SUPCRT92 package without
+modification (timestamp: Nov 15, 1991). It is provided here to enable diffs
+between it and the H2O92D.f that has been modified for use in CHNOSZ.

pychnosz/data/extdata/taxonomy/names.dmp

@@ -0,0 +1,215 @@
+1	|	all	|		|	synonym	|
+1	|	root	|		|	scientific name	|
+2	|	Bacteria	|	Bacteria <prokaryote>	|	scientific name	|
+2	|	Monera	|	Monera <Bacteria>	|	in-part	|
+2	|	Procaryotae	|	Procaryotae <Bacteria>	|	in-part	|
+2	|	Prokaryota	|	Prokaryota <Bacteria>	|	in-part	|
+2	|	Prokaryotae	|	Prokaryotae <Bacteria>	|	in-part	|
+2	|	bacteria	|	bacteria <blast2>	|	blast name	|
+2	|	eubacteria	|		|	genbank common name	|
+2	|	not Bacteria Haeckel 1894	|		|	synonym	|
+2	|	prokaryotes	|	prokaryotes <Bacteria>	|	in-part	|
+543	|	Enterobacteraceae	|		|	synonym	|
+543	|	Enterobacteraceae (ex Lapage 1979) Lapage 1982, fam. nov., nom. rev.	|		|	synonym	|
+543	|	Enterobacteriaceae	|		|	scientific name	|
+543	|	Enterobacteriaceae (ex Rahn 1937) Ewing et al. 1980, fam. nov., nom. rev.	|		|	synonym	|
+543	|	Enterobacteriaceae Rahn 1937	|		|	synonym	|
+543	|	gamma-3 proteobacteria	|	gamma-3 proteobacteria <#1>	|	in-part	|
+561	|	Escherchia	|		|	misspelling	|
+561	|	Escherichia	|		|	scientific name	|
+561	|	Escherichia Castellani and Chalmers 1919	|		|	authority	|
+562	|	"Bacillus coli" Migula 1895	|		|	synonym	|
+562	|	"Bacterium coli commune" Escherich 1885	|		|	synonym	|
+562	|	"Bacterium coli" (Migula 1895) Lehmann and Neumann 1896	|		|	synonym	|
+562	|	Bacillus coli	|		|	synonym	|
+562	|	Bacterium coli	|		|	synonym	|
+562	|	Bacterium coli commune	|		|	synonym	|
+562	|	Enterococcus coli	|		|	synonym	|
+562	|	Escherchia coli	|		|	misspelling	|
+562	|	Escherichia coli	|		|	scientific name	|
+562	|	Escherichia coli (Migula 1895) Castellani and Chalmers 1919	|		|	synonym	|
+562	|	Escherichia coli retron Ec107	|		|	includes	|
+562	|	Escherichia coli retron Ec67	|		|	includes	|
+562	|	Escherichia coli retron Ec79	|		|	includes	|
+562	|	Escherichia coli retron Ec86	|		|	includes	|
+562	|	Eschericia coli	|		|	misspelling	|
+562	|	bacterium 10a	|		|	includes	|
+562	|	bacterium E3	|		|	synonym	|
+1224	|	Proteobacteria	|		|	scientific name	|
+1224	|	Proteobacteria (as class) Stackebrandt et al. 1988	|		|	synonym	|
+1224	|	Proteobacteria Garrity et al. 2005	|		|	synonym	|
+1224	|	not Proteobacteria Cavalier-Smith 2002	|		|	synonym	|
+1224	|	proteobacteria	|	proteobacteria<blast1224>	|	blast name	|
+1224	|	purple bacteria	|		|	common name	|
+1224	|	purple bacteria and relatives	|		|	common name	|
+1224	|	purple non-sulfur bacteria	|		|	common name	|
+1224	|	purple photosynthetic bacteria	|		|	common name	|
+1224	|	purple photosynthetic bacteria and relatives	|		|	common name	|
+1236	|	Gammaproteobacteria	|		|	scientific name	|
+1236	|	Gammaproteobacteria Garrity et al. 2005	|		|	synonym	|
+1236	|	Proteobacteria gamma subdivision	|		|	synonym	|
+1236	|	Purple bacteria, gamma subdivision	|		|	synonym	|
+1236	|	g-proteobacteria	|	gamma proteos<blast1236>	|	blast name	|
+1236	|	gamma proteobacteria	|		|	synonym	|
+1236	|	gamma subdivision	|		|	synonym	|
+1236	|	gamma subgroup	|		|	synonym	|
+2157	|	"Archaea" Woese et al. 1990	|		|	authority	|
+2157	|	"Archaebacteria" (sic) Woese and Fox 1977	|		|	authority	|
+2157	|	Archaea	|		|	scientific name	|
+2157	|	Archaebacteria	|		|	synonym	|
+2157	|	Mendosicutes	|		|	synonym	|
+2157	|	Metabacteria	|		|	synonym	|
+2157	|	Monera	|	Monera <Archaea>	|	in-part	|
+2157	|	Procaryotae	|	Procaryotae <Archaea>	|	in-part	|
+2157	|	Prokaryota	|	Prokaryota <Archaea>	|	in-part	|
+2157	|	Prokaryotae	|	Prokaryotae <Archaea>	|	in-part	|
+2157	|	archaea	|	Archaea<blast2157>	|	blast name	|
+2157	|	prokaryotes	|	prokaryotes <Archaea>	|	in-part	|
+2182	|	Methanococcales	|		|	scientific name	|
+2182	|	Methanococcales Balch and Wolfe 1981	|		|	authority	|
+2190	|	Methanocaldococcus jannaschii	|		|	scientific name	|
+2190	|	Methanocaldococcus jannaschii (Jones et al. 1984) Whitman 2002	|		|	authority	|
+2190	|	Methanococcus jannaschii	|		|	synonym	|
+2190	|	Methanococcus jannaschii Jones et al. 1984	|		|	authority	|
+2258	|	Thermococcales	|		|	scientific name	|
+2258	|	Thermococcales Zillig et al. 1988	|		|	authority	|
+2259	|	Thermococcaceae	|		|	scientific name	|
+2259	|	Thermococcaceae Zillig et al. 1988	|		|	authority	|
+2260	|	Pyrococcus	|		|	scientific name	|
+2260	|	Pyrococcus Fiala and Stetter 1986	|		|	authority	|
+2261	|	Pyrococcus furiosus	|		|	scientific name	|
+2261	|	Pyrococcus furiosus Fiala and Stetter 1986	|		|	authority	|
+2759	|	Eucarya	|		|	synonym	|
+2759	|	Eucaryotae	|		|	synonym	|
+2759	|	Eukarya	|		|	synonym	|
+2759	|	Eukaryota	|		|	scientific name	|
+2759	|	Eukaryotae	|		|	synonym	|
+2759	|	eucaryotes	|		|	genbank common name	|
+2759	|	eukaryotes	|		|	common name	|
+2759	|	eukaryotes	|	eukaryotes<blast2759>	|	blast name	|
+4751	|	Fungi	|		|	scientific name	|
+4751	|	fungi	|	fungi<blast4751>	|	blast name	|
+4751	|	fungi	|	fungi<preferred>	|	genbank common name	|
+4890	|	Ascomycota	|		|	scientific name	|
+4890	|	ascomycetes	|		|	genbank common name	|
+4890	|	ascomycetes	|	ascomycetes<blast4890>	|	blast name	|
+4890	|	sac fungi	|		|	common name	|
+4891	|	Hemiascomycetes	|		|	synonym	|
+4891	|	Saccharomycetes	|		|	scientific name	|
+4892	|	Endomycetales	|		|	synonym	|
+4892	|	Saccharomycetales	|		|	scientific name	|
+4892	|	budding yeasts	|		|	genbank common name	|
+4893	|	Eremotheciaceae	|		|	includes	|
+4893	|	Saccharomycetaceae	|		|	scientific name	|
+4930	|	Pachytichospora	|		|	synonym	|
+4930	|	Saccharomyces	|		|	scientific name	|
+4932	|	Candida robusta	|		|	anamorph	|
+4932	|	Saccaromyces cerevisiae	|		|	misspelling	|
+4932	|	Saccharomyces capensis	|		|	synonym	|
+4932	|	Saccharomyces cerevisiae	|		|	scientific name	|
+4932	|	Saccharomyces italicus	|		|	synonym	|
+4932	|	Saccharomyces oviformis	|		|	synonym	|
+4932	|	Saccharomyces uvarum var. melibiosus	|		|	synonym	|
+4932	|	Saccharomyes cerevisiae	|		|	misspelling	|
+4932	|	Sccharomyces cerevisiae	|		|	misspelling	|
+4932	|	baker's yeast	|		|	genbank common name	|
+4932	|	brewer's yeast	|		|	common name	|
+4932	|	lager beer yeast	|		|	common name	|
+4932	|	yeast	|		|	common name	|
+6072	|	Eumetazoa	|		|	scientific name	|
+7711	|	Chordata	|		|	scientific name	|
+7711	|	chordates	|		|	genbank common name	|
+7711	|	chordates	|	chordates<blast7711>	|	blast name	|
+7742	|	Vertebrata	|		|	scientific name	|
+7742	|	vertebrates	|		|	genbank common name	|
+7742	|	vertebrates	|	vertebrates<blast7742>	|	blast name	|
+7776	|	Gnathostomata	|	Gnathostomata <vertebrate>	|	scientific name	|
+7776	|	jawed vertebrates	|		|	genbank common name	|
+8287	|	Sarcopterygii	|		|	scientific name	|
+9347	|	Eutheria	|		|	scientific name	|
+9347	|	Placentalia	|		|	synonym	|
+9347	|	eutherian mammals	|		|	common name	|
+9347	|	placental mammals	|		|	common name	|
+9347	|	placentals	|		|	genbank common name	|
+9347	|	placentals	|	placentals <blast9347>	|	blast name	|
+9443	|	Primata	|		|	synonym	|
+9443	|	Primates	|		|	scientific name	|
+9443	|	primate	|		|	equivalent name	|
+9443	|	primates	|	primates <blast9443>	|	blast name	|
+9526	|	Catarrhini	|		|	scientific name	|
+9604	|	Hominidae	|		|	scientific name	|
+9604	|	Pongidae	|		|	synonym	|
+9604	|	great apes	|		|	common name	|
+9605	|	Homo	|		|	scientific name	|
+9606	|	Homo sapiens	|		|	scientific name	|
+9606	|	human	|		|	genbank common name	|
+9606	|	man	|		|	common name	|
+28890	|	"Euryarchaeota" Woese et al. 1990	|		|	authority	|
+28890	|	Euryarchaeota	|		|	scientific name	|
+28890	|	Euryarchaeota Garrity and Holt 2002	|		|	authority	|
+28890	|	euryarchaeotes	|	euryarchaeotes<blast28890>	|	blast name	|
+28890	|	not Euryarchaeota Cavalier-Smith 2002	|		|	synonym	|
+32523	|	Tetrapoda	|		|	scientific name	|
+32523	|	tetrapods	|		|	genbank common name	|
+32524	|	Amniota	|		|	scientific name	|
+32524	|	amniotes	|		|	genbank common name	|
+32525	|	Theria	|		|	scientific name	|
+33154	|	Fungi/Metazoa group	|		|	scientific name	|
+33154	|	Opisthokonta	|		|	synonym	|
+33154	|	opisthokonts	|		|	synonym	|
+33208	|	Animalia	|		|	synonym	|
+33208	|	Metazoa	|		|	scientific name	|
+33208	|	animals	|		|	blast name	|
+33208	|	metazoans	|		|	genbank common name	|
+33208	|	multicellular animals	|		|	common name	|
+33213	|	Bilateria	|		|	scientific name	|
+33316	|	Coelomata	|		|	scientific name	|
+33511	|	Deuterostomia	|		|	scientific name	|
+40674	|	Mammalia	|		|	scientific name	|
+40674	|	mammals	|		|	genbank common name	|
+40674	|	mammals	|	mammals<blast40674>	|	blast name	|
+83333	|	Escherichia coli K-12	|		|	scientific name	|
+83333	|	Escherichia coli K12	|		|	equivalent name	|
+89593	|	Craniata	|	Craniata <chordata>	|	scientific name	|
+91347	|	'Enterobacteriales'	|		|	synonym	|
+91347	|	Enterobacteriaceae and related endosymbionts	|		|	synonym	|
+91347	|	Enterobacteriaceae group	|		|	synonym	|
+91347	|	Enterobacteriales	|		|	scientific name	|
+91347	|	enterobacteria	|	enterobacteria<blast91347>	|	blast name	|
+91347	|	gamma-3 proteobacteria	|	gamma-3 proteobacteria <#5>	|	in-part	|
+117570	|	Teleostomi	|		|	scientific name	|
+117571	|	Euteleostomi	|		|	scientific name	|
+117571	|	bony vertebrates	|		|	genbank common name	|
+131567	|	biota	|		|	synonym	|
+131567	|	cellular organisms	|		|	scientific name	|
+147537	|	Saccharomycotina	|		|	scientific name	|
+183939	|	Methanococci	|		|	scientific name	|
+183939	|	Methanococci Boone 2002	|		|	authority	|
+183939	|	Methanothermea	|		|	synonym	|
+183939	|	Methanothermea Cavalier-Smith 2002	|		|	authority	|
+183968	|	Protoarchaea	|		|	synonym	|
+183968	|	Protoarchaea Cavalier-Smith 2002	|		|	authority	|
+183968	|	Thermococci	|		|	scientific name	|
+183968	|	Thermococci Zillig and Reysenbach 2002	|		|	authority	|
+186497	|	Pyrococcus furiosus DSM 3638	|		|	scientific name	|
+186497	|	Pyrococcus furiosus DSM3638	|		|	misspelling	|
+186497	|	Pyrococcus furiosus str. DSM 3638	|		|	equivalent name	|
+186497	|	Pyrococcus furiosus strain DSM 3638	|		|	equivalent name	|
+196117	|	Methanocaldococcaceae	|		|	scientific name	|
+196117	|	Methanocaldococcaceae Whitman et al. 2002	|		|	authority	|
+196118	|	Methanocaldococcus	|		|	scientific name	|
+196118	|	Methanocaldococcus Whitman 2002	|		|	authority	|
+207598	|	Homininae	|		|	scientific name	|
+207598	|	Homo/Pan/Gorilla group	|		|	synonym	|
+243232	|	Methanocaldococcus jannaschii DSM 2661	|		|	scientific name	|
+243232	|	Methanocaldococcus jannaschii str. DSM 2661	|		|	equivalent name	|
+243232	|	Methanococcus jannaschii DSM 2661	|		|	synonym	|
+314146	|	Euarchontoglires	|		|	scientific name	|
+314293	|	Anthropoidea	|		|	synonym	|
+314293	|	Simiiformes	|		|	scientific name	|
+314295	|	Hominoidea	|		|	scientific name	|
+314295	|	ape	|	ape <Hominoidea>	|	common name	|
+314295	|	apes	|		|	common name	|
+376913	|	Haplorrhini	|		|	scientific name	|
+451864	|	Dikarya	|		|	scientific name	|
+716545	|	Saccharomyceta	|		|	scientific name	|

pychnosz/data/extdata/taxonomy/nodes.dmp

@@ -0,0 +1,63 @@
+1	|	1	|	no rank	|		|	8	|	0	|	1	|	0	|	0	|	0	|	0	|	0	|		|
+2	|	131567	|	superkingdom	|		|	0	|	0	|	11	|	0	|	0	|	0	|	0	|	0	|		|
+543	|	91347	|	family	|		|	0	|	1	|	11	|	1	|	0	|	1	|	0	|	0	|		|
+561	|	543	|	genus	|		|	0	|	1	|	11	|	1	|	0	|	1	|	0	|	0	|		|
+562	|	561	|	species	|	EC	|	0	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
+1224	|	2	|	phylum	|		|	0	|	1	|	11	|	1	|	0	|	1	|	0	|	0	|		|
+1236	|	1224	|	class	|		|	0	|	1	|	11	|	1	|	0	|	1	|	0	|	0	|		|
+2157	|	131567	|	superkingdom	|		|	0	|	0	|	11	|	0	|	0	|	0	|	0	|	0	|		|
+2182	|	183939	|	order	|		|	0	|	1	|	11	|	1	|	0	|	1	|	0	|	0	|		|
+2190	|	196118	|	species	|	MJ	|	0	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
+2258	|	183968	|	order	|		|	0	|	1	|	11	|	1	|	0	|	1	|	0	|	0	|		|
+2259	|	2258	|	family	|		|	0	|	1	|	11	|	1	|	0	|	1	|	0	|	0	|		|
+2260	|	2259	|	genus	|		|	0	|	1	|	11	|	1	|	0	|	1	|	0	|	0	|		|
+2261	|	2260	|	species	|	PF	|	0	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
+2759	|	131567	|	superkingdom	|		|	1	|	0	|	1	|	0	|	1	|	0	|	0	|	0	|		|
+4751	|	33154	|	kingdom	|		|	4	|	0	|	1	|	1	|	4	|	0	|	0	|	0	|		|
+4890	|	451864	|	phylum	|		|	4	|	1	|	1	|	1	|	4	|	1	|	0	|	0	|		|
+4891	|	147537	|	class	|		|	4	|	0	|	1	|	1	|	3	|	0	|	0	|	0	|		|
+4892	|	4891	|	order	|		|	4	|	1	|	1	|	1	|	3	|	1	|	0	|	0	|		|
+4893	|	4892	|	family	|		|	4	|	1	|	1	|	1	|	3	|	1	|	0	|	0	|		|
+4930	|	4893	|	genus	|		|	4	|	1	|	1	|	1	|	3	|	1	|	0	|	0	|		|
+4932	|	4930	|	species	|	SC	|	4	|	1	|	1	|	1	|	3	|	1	|	1	|	0	|		|
+6072	|	33208	|	no rank	|		|	1	|	1	|	1	|	1	|	5	|	0	|	1	|	0	|		|
+7711	|	33511	|	phylum	|		|	1	|	1	|	1	|	1	|	5	|	1	|	0	|	0	|		|
+7742	|	89593	|	no rank	|		|	10	|	0	|	1	|	1	|	2	|	1	|	0	|	0	|		|
+7776	|	7742	|	superclass	|		|	10	|	1	|	1	|	1	|	2	|	1	|	1	|	0	|		|
+8287	|	117571	|	no rank	|		|	10	|	1	|	1	|	1	|	2	|	1	|	1	|	0	|		|
+9347	|	32525	|	no rank	|		|	2	|	1	|	1	|	1	|	2	|	1	|	0	|	0	|		|
+9443	|	314146	|	order	|		|	5	|	0	|	1	|	1	|	2	|	1	|	0	|	0	|		|
+9526	|	314293	|	parvorder	|		|	5	|	1	|	1	|	1	|	2	|	1	|	0	|	0	|		|
+9604	|	314295	|	family	|		|	5	|	1	|	1	|	1	|	2	|	1	|	0	|	0	|		|
+9605	|	207598	|	genus	|		|	5	|	1	|	1	|	1	|	2	|	1	|	0	|	0	|		|
+9606	|	9605	|	species	|	HS	|	5	|	1	|	1	|	1	|	2	|	1	|	1	|	0	|		|
+28890	|	2157	|	phylum	|		|	0	|	1	|	11	|	1	|	0	|	1	|	0	|	0	|		|
+32523	|	8287	|	no rank	|		|	10	|	1	|	1	|	1	|	2	|	1	|	1	|	0	|		|
+32524	|	32523	|	no rank	|		|	10	|	1	|	1	|	1	|	2	|	1	|	1	|	0	|		|
+32525	|	40674	|	no rank	|		|	2	|	1	|	1	|	1	|	2	|	1	|	1	|	0	|		|
+33154	|	2759	|	no rank	|		|	4	|	0	|	1	|	1	|	1	|	1	|	1	|	0	|		|
+33208	|	33154	|	kingdom	|		|	1	|	0	|	1	|	1	|	1	|	1	|	0	|	0	|		|
+33213	|	6072	|	no rank	|		|	1	|	1	|	1	|	1	|	5	|	1	|	1	|	0	|		|
+33316	|	33213	|	no rank	|		|	1	|	1	|	1	|	1	|	5	|	1	|	1	|	0	|		|
+33511	|	33316	|	no rank	|		|	1	|	1	|	1	|	1	|	5	|	1	|	1	|	0	|		|
+40674	|	32524	|	class	|		|	2	|	0	|	1	|	1	|	2	|	1	|	0	|	0	|		|
+83333	|	562	|	no rank	|		|	0	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
+89593	|	7711	|	subphylum	|		|	10	|	0	|	1	|	1	|	2	|	0	|	0	|	0	|		|
+91347	|	1236	|	order	|		|	0	|	1	|	11	|	1	|	0	|	1	|	0	|	0	|		|
+117570	|	7776	|	no rank	|		|	10	|	1	|	1	|	1	|	2	|	1	|	1	|	0	|		|
+117571	|	117570	|	no rank	|		|	10	|	1	|	1	|	1	|	2	|	1	|	0	|	0	|		|
+131567	|	1	|	no rank	|		|	8	|	1	|	1	|	1	|	0	|	1	|	1	|	0	|		|
+147537	|	716545	|	subphylum	|		|	4	|	1	|	1	|	1	|	4	|	1	|	0	|	0	|		|
+183939	|	28890	|	class	|		|	0	|	1	|	11	|	1	|	0	|	1	|	0	|	0	|		|
+183968	|	28890	|	class	|		|	0	|	1	|	11	|	1	|	0	|	1	|	0	|	0	|		|
+186497	|	2261	|	no rank	|		|	0	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
+196117	|	2182	|	family	|		|	0	|	1	|	11	|	1	|	0	|	1	|	0	|	0	|		|
+196118	|	196117	|	genus	|		|	0	|	1	|	11	|	1	|	0	|	1	|	0	|	0	|		|
+207598	|	9604	|	subfamily	|		|	5	|	1	|	1	|	1	|	2	|	1	|	1	|	0	|		|
+243232	|	2190	|	no rank	|		|	0	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
+314146	|	9347	|	superorder	|		|	2	|	1	|	1	|	1	|	2	|	1	|	0	|	0	|		|
+314293	|	376913	|	infraorder	|		|	5	|	1	|	1	|	1	|	2	|	1	|	1	|	0	|		|
+314295	|	9526	|	superfamily	|		|	5	|	1	|	1	|	1	|	2	|	1	|	1	|	0	|		|
+376913	|	9443	|	suborder	|		|	5	|	1	|	1	|	1	|	2	|	1	|	0	|	0	|		|
+451864	|	4751	|	subkingdom	|		|	4	|	1	|	1	|	1	|	4	|	1	|	0	|	0	|		|
+716545	|	4890	|	no rank	|		|	4	|	1	|	1	|	1	|	4	|	1	|	0	|	0	|		|

pychnosz/data/extdata/thermo/Bdot_acirc.csv

@@ -0,0 +1,60 @@
+species,acirc
+Rb+,2.5
+Cs+,2.5
+NH4+,2.5
+Tl+,2.5
+Ag+,2.5
+K+,3
+Cl-,3
+Br-,3
+I-,3
+NO3-,3
+OH-,3.5
+F-,3.5
+HS-,3.5
+BrO3-,3.5
+IO3-,3.5
+MnO4-,3.5
+Na+,4
+HCO3-,4
+H2PO4-,4
+HSO3-,4
+Hg2+2,4
+SO4-2,4
+SeO4-2,4
+CrO4-2,4
+HPO4-2,4
+PO4-3,4
+Pb+2,4.5
+CO3-2,4.5
+SO3-2,4.5
+MoO4-2,4.5
+Sr+2,5
+Ba+2,5
+Ra+2,5
+Cd+2,5
+Hg+2,5
+S-2,5
+WO4-2,5
+Li+,6
+Ca+2,6
+Cu+2,6
+Zn+2,6
+Sn+2,6
+Mn+2,6
+Fe+2,6
+Ni+2,6
+Co+2,6
+Mg+2,8
+Be+2,8
+H+,9
+Al+3,9
+Cr+3,9
+La+3,9
+Ce+3,9
+Y+3,9
+Eu+3,9
+Th+4,11
+Zr+4,11
+Ce+4,11
+Sn+4,11

pychnosz/data/extdata/thermo/buffer.csv

@@ -0,0 +1,40 @@
+name,species,state,logact
+AC,"acetic acid",aq,-3
+FORM,"formic acid",aq,-3
+AL,alanine,aq,-3
+GLN,glutamine,aq,-3
+UREA,urea,aq,-3
+ATP,H4ATP,aq,-3
+GSH,glutathione,aq,-3
+LYS,lysine,aq,-3
+RIBOSE,ribose,aq,-3
+GLUCOSE,glucose,aq,-3
+CYSTINE,cystine,aq,-3
+ETHANOL,ethanol,aq,-3
+MAMINE,methanamine,aq,-3
+HM,hematite,cr,0
+HM,magnetite,cr,0
+FeFeO,iron,cr,0
+FeFeO,FeO,cr,0
+CO2-AC,CO2,aq,-3
+CO2-AC,"acetic acid",aq,-3
+C2H4-AC,C2H4,aq,-3
+C2H4-AC,"acetic acid",aq,-3
+CH4-AC,CH4,aq,-3
+CH4-AC,"acetic acid",aq,-10
+ET-H,C2H4,aq,-3
+ET-H,C2H6,aq,-15
+cysteine-cystine,cysteine,aq,-3
+cysteine-cystine,cystine,aq,-3
+GSH-GSSG,GSH,aq,-3
+GSH-GSSG,GSSG,aq,-9
+NADred-NADox,HNAD(red)-,aq,-3
+NADred-NADox,NAD(ox)-,aq,-3
+QFM,quartz,cr,0
+QFM,fayalite,cr,0
+QFM,magnetite,cr,0
+PPM,pyrite,cr,0
+PPM,pyrrhotite,cr,0
+PPM,magnetite,cr,0
+water,water,liq,0
+quartz,quartz,cr,0

pychnosz/data/extdata/thermo/element.csv

@@ -0,0 +1,135 @@
+element,state,source,mass,s,n
+Z,aq,CWM89,0,-15.6166347992352,1
+O,gas,CWM89,15.9994,49.0325047801147,2
+H,gas,CWM89,1.00794,31.2332695984704,2
+He,gas,CWM89,4.0026,30.1512906309751,1
+Ne,gas,CWM89,20.179,34.9732313575526,1
+Ar,gas,CWM89,39.948,37.0090822179732,1
+Kr,gas,CWM89,83.8,39.2172562141491,1
+Xe,gas,CWM89,131.29,40.5556883365201,1
+F,gas,CWM89,18.9984,48.4682122370937,2
+Cl,gas,CWM89,35.453,53.317638623327,2
+Br,liq,CWM89,79.904,36.3790631,2
+I,cr,CWM89,126.9045,27.7581261950287,2
+S,cr,CWM89,32.06,7.66108986615679,1
+N,gas,CWM89,14.0067,45.7956500956023,2
+P,cr,CWM89,30.97376,9.82074569789675,1
+C,cr,CWM89,12.011,1.37189292543021,1
+Si,cr,CWM89,28.0855,4.49569789674952,1
+Ge,cr,CWM89,72.59,7.43068833652008,1
+Sn,cr,CWM89,118.69,12.2323135755258,1
+Pb,cr,CWM89,207.2,15.4875717017208,1
+B,cr,CWM89,10.81,1.41013384321224,1
+Al,cr,CWM89,26.98154,6.76386233269599,1
+Zn,cr,CWM89,65.38,9.94980879541109,1
+Cd,cr,CWM89,112.41,12.3804971319312,1
+Hg,liq,CWM89,200.59,18.1405353728489,1
+Cu,cr,CWM89,63.546,7.92304015296367,1
+Ag,cr,CWM89,107.8682,10.1696940726577,1
+Ti,cr,CWM89,47.88,7.34225621414914,1
+U,cr,CWM89,238.0289,11.9980879541109,1
+Th,cr,CWM89,232.0381,12.3804971319312,1
+Be,cr,CWM89,9.01218,2.27055449330784,1
+Mg,cr,CWM89,24.305,7.80831739961759,1
+Ca,cr,CWM89,40.08,9.94024856596558,1
+Li,cr,CWM89,6.941,6.95984703632887,1
+Na,cr,CWM89,22.98977,12.2609942638623,1
+K,cr,CWM89,39.0983,15.4588910133843,1
+Rb,cr,CWM89,85.4678,18.3508604206501,1
+Cs,cr,CWM89,132.9054,20.3704588910134,1
+O,gas,WEP+82,15.9994,49.0291586998088,2
+H,gas,WEP+82,1.008,31.2342256214149,2
+He,gas,WEP+82,4.0026,30.1505736137667,1
+Ne,gas,WEP+82,20.183,34.9732313575526,1
+Ar,gas,WEP+82,39.948,37.0083652007648,1
+Kr,gas,WEP+82,83.8,39.2165391969407,1
+Xe,gas,WEP+82,131.3,40.5552103250478,1
+Rn,gas,WEP+82,222,42.1152007648184,1
+F,gas,WEP+82,18.9984,48.4655831739962,2
+Cl,gas,WEP+82,35.453,53.3140535372849,2
+Br,liq,WEP+82,79.909,36.3840822179732,2
+I,cr,WEP+82,126.9044,27.756931166348,2
+At,cr,WEP+82,210,NA,2
+S,cr,WEP+82,32.064,7.60038240917782,1
+Se,cr,WEP+82,78.96,10.1438814531549,1
+Te,cr,WEP+82,127.6,11.8809751434034,1
+Po,cr,WEP+82,210,NA,1
+N,cr,WEP+82,14.0067,45.7958891013384,2
+P,cr,WEP+82,30.9738,9.82074569789675,1
+As,cr,WEP+82,74.9216,8.38910133843212,1
+Sb,cr,WEP+82,121.75,10.92017208413,1
+Bi,cr,WEP+82,208.98,13.5611854684512,1
+C,cr,WEP+82,12.0112,1.37189292543021,1
+Si,cr,WEP+82,28.086,4.50047801147227,1
+Ge,cr,WEP+82,72.59,7.43068833652008,1
+Sn,cr,WEP+82,118.69,12.3207456978967,1
+Pb,cr,WEP+82,207.19,15.4899617590822,1
+B,cr,WEP+82,10.811,1.40057361376673,1
+Al,cr,WEP+82,26.9815,6.77103250478011,1
+Ga,cr,WEP+82,69.72,9.77055449330784,1
+In,cr,WEP+82,114.82,13.8193116634799,1
+Tl,cr,WEP+82,204.37,15.3393881453155,1
+Zn,cr,WEP+82,65.37,9.94980879541109,1
+Cd,cr,WEP+82,112.4,12.3709369024857,1
+Hg,liq,WEP+82,200.59,18.1692160611855,1
+Cu,cr,WEP+82,63.54,7.92304015296367,1
+Ag,cr,WEP+82,107.87,10.1696940726577,1
+Au,cr,WEP+82,196.967,11.3288718929254,1
+Ni,cr,WEP+82,58.71,7.13910133843212,1
+Co,cr,WEP+82,58.9332,7.17973231357553,1
+Fe,cr,WEP+82,55.847,6.52007648183556,1
+Pd,cr,WEP+82,106.4,8.97944550669216,1
+Rh,cr,WEP+82,102.905,7.5310707456979,1
+Ru,cr,WEP+82,101.07,6.81883365200765,1
+Pt,cr,WEP+82,195.09,9.94980879541109,1
+Ir,cr,WEP+82,192.2,8.47992351816444,1
+Os,cr,WEP+82,190.2,7.79158699808795,1
+Mn,cr,WEP+82,54.938,7.65057361376673,1
+Tc,cr,WEP+82,98.906,NA,1
+Re,cr,WEP+82,186.2,8.80975143403442,1
+Cr,cr,WEP+82,51.996,5.68116634799235,1
+Mo,cr,WEP+82,95.94,6.84990439770554,1
+W,cr,WEP+82,183.85,7.80114722753346,1
+V,cr,WEP+82,50.942,6.90965583173996,1
+Nb,cr,WEP+82,92.906,8.69980879541109,1
+Ta,cr,WEP+82,180.948,9.92112810707457,1
+Ti,cr,WEP+82,47.9,7.32074569789675,1
+Zr,cr,WEP+82,91.22,9.31883365200765,1
+Hf,cr,WEP+82,178.49,10.4110898661568,1
+Sc,cr,WEP+82,44.956,8.27915869980879,1
+Y,cr,WEP+82,88.905,10.6190248565966,1
+Lu,cr,WEP+82,174.97,12.1797323135755,1
+Yb,cr,WEP+82,173.04,14.3092734225621,1
+Tm,cr,WEP+82,168.934,17.6888145315488,1
+Er,cr,WEP+82,167.26,17.4904397705545,1
+Ho,cr,WEP+82,164.93,17.9971319311663,1
+Dy,cr,WEP+82,162.5,17.8704588910134,1
+Tb,cr,WEP+82,158.924,17.5,1
+Gd,cr,WEP+82,157.25,16.269120458891,1
+Eu,cr,WEP+82,151.96,18.5898661567878,1
+Sm,cr,WEP+82,150.35,16.6300191204589,1
+Pm,cr,WEP+82,146.915,NA,1
+Nd,cr,WEP+82,144.24,17.0889101338432,1
+Pr,cr,WEP+82,140.907,17.4952198852772,1
+Ce,cr,WEP+82,140.12,17.208413001912,1
+La,cr,WEP+82,138.91,13.5994263862333,1
+U,cr,WEP+82,238.029,12.0004780114723,1
+Pa,cr,WEP+82,231.0359,12.4043977055449,1
+Th,cr,WEP+82,232.0381,12.7605162523901,1
+Ac,cr,WEP+82,227.028,13.5038240917782,1
+Be,cr,WEP+82,9.0122,2.27055449330784,1
+Mg,cr,WEP+82,24.312,7.81070745697897,1
+Ca,cr,WEP+82,40.08,9.89961759082218,1
+Sr,cr,WEP+82,87.62,12.5,1
+Ba,cr,WEP+82,137.34,15.0095602294455,1
+Ra,cr,WEP+82,226.025,16.9694072657744,1
+Li,cr,WEP+82,6.941,6.95984703632887,1
+Na,cr,WEP+82,22.9898,12.2394837476099,1
+K,cr,WEP+82,39.102,15.3393881453155,1
+Rb,cr,WEP+82,85.4678,18.3508604206501,1
+Cs,cr,WEP+82,132.9054,20.3704588910134,1
+Fr,cr,WEP+82,223,22.8011472275335,1
+Pu,cr,THBC14,NA,13.01625,1
+Am,cr,THBC14,NA,13.24092,1
+Np,cr,THBC14,NA,12.06023,1
+Cm,cr,THBC14,NA,16.92161,1

pychnosz/data/extdata/thermo/groups.csv

@@ -0,0 +1,6 @@
+"","[Ala]","[Cys]","[Asp]","[Glu]","[Phe]","[Gly]","[His]","[Ile]","[Lys]","[Leu]","[Met]","[Asn]","[Pro]","[Gln]","[Arg]","[Ser]","[Thr]","[Val]","[Trp]","[Tyr]","[AABB]","[UPBB]"
+"C",1,1,2,3,7,0,4,4,4,4,3,2,3,3,4,1,2,3,9,7,2,2
+"H",3,3,3,5,7,1,5,9,10,9,7,4,5,6,10,3,5,7,8,7,4,2
+"N",0,0,0,0,0,0,2,0,1,0,0,1,0,1,3,0,0,0,1,0,1,1
+"O",0,0,2,2,0,0,0,0,0,0,0,1,0,1,0,1,1,0,0,1,2,1
+"S",0,1,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0

pychnosz/data/extdata/thermo/opt.csv

@@ -0,0 +1,2 @@
+E.units,T.units,P.units,state,water,G.tol,Cp.tol,V.tol,varP,IAPWS.sat,paramin,ideal.H,ideal.e,nonideal,Setchenow,Berman,maxcores,ionize.aa
+J,C,bar,aq,SUPCRT92,100,1,1,FALSE,liquid,1000,TRUE,TRUE,Bdot,bgamma0,NA,2,TRUE