aldepyde 0.0.0a1__py3-none-any.whl → 0.0.0a32__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
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- aldepyde/Parsers/_mmcif_parser.py +0 -0
- aldepyde/Parsers/_pdb_parser.py +0 -0
- aldepyde/__init__.py +50 -0
- aldepyde/_config.py +113 -0
- aldepyde/biomolecule/Residue.py +9 -0
- aldepyde/biomolecule/_Atom.py +95 -0
- aldepyde/biomolecule/_AtomFactory.py +71 -0
- aldepyde/biomolecule/__init__.py +15 -0
- aldepyde/biomolecule/_amino_acid.py +6 -0
- aldepyde/biomolecule/_dna.py +6 -0
- aldepyde/biomolecule/_pdb.py +455 -0
- aldepyde/biomolecule/_rna.py +6 -0
- aldepyde/biomolecule/utils.py +60 -0
- aldepyde/cache/__init__.py +2 -0
- aldepyde/cache/_cache.py +257 -0
- aldepyde/cache/cachemanager.py +212 -0
- aldepyde/cache/downloader.py +13 -0
- aldepyde/cache/utils.py +32 -0
- aldepyde/configurable.py +7 -0
- aldepyde/data/RemoteFileHandler.py +32 -0
- aldepyde/data/__init__.py +1 -0
- aldepyde/data.py +148 -0
- aldepyde/databases/PDB.py +0 -0
- aldepyde/databases/RemoteFileHandler.py +43 -0
- aldepyde/databases/UniRef.py +75 -0
- aldepyde/databases/__init__.py +0 -0
- aldepyde/databases/_database.py +38 -0
- aldepyde/env.py +43 -0
- aldepyde/fetcher/__init__.py +0 -0
- aldepyde/fetcher/test.py +2 -0
- aldepyde/json/CHG.json +25 -0
- aldepyde/json/Swiss_Prot.json +25 -0
- aldepyde/json/chemistry.json +4622 -0
- aldepyde/rand/RandomProtein.py +402 -0
- aldepyde/rand/__init__.py +3 -0
- aldepyde/stats/ProteinStats.py +89 -0
- aldepyde/stats/__init__.py +0 -0
- aldepyde/utils.py +275 -0
- {aldepyde-0.0.0a1.dist-info → aldepyde-0.0.0a32.dist-info}/METADATA +4 -3
- aldepyde-0.0.0a32.dist-info/RECORD +43 -0
- {aldepyde-0.0.0a1.dist-info → aldepyde-0.0.0a32.dist-info}/WHEEL +1 -1
- aldepyde-0.0.0a32.dist-info/top_level.txt +1 -0
- aldepyde-0.0.0a1.dist-info/RECORD +0 -5
- aldepyde-0.0.0a1.dist-info/top_level.txt +0 -1
- {aldepyde-0.0.0a1.dist-info → aldepyde-0.0.0a32.dist-info/licenses}/LICENSE +0 -0
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"map": {
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"amino_acid": {
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"arginine": "arginine",
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"arg": "arginine",
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"r": "arginine",
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"histidine": "histidine",
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"his": "histidine",
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"h": "histidine",
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"lysine": "lysine",
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"lys": "lysine",
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"k": "lysine",
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"aspartic acid": "aspartate",
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"aspartate": "aspartate",
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"asp": "aspartate",
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"d": "aspartate",
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"glutamic acid": "glutamate",
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"glutamate": "glutamate",
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"glu": "glutamate",
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"e": "glutamate",
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"serine": "serine",
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"ser": "serine",
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"s": "serine",
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"threonine": "threonine",
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"thr": "threonine",
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"t": "threonine",
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"asparagine": "asparagine",
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"asn": "asparagine",
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"n": "asparagine",
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"glutamine": "glutamine",
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"gln": "glutamine",
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"q": "glutamine",
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"cysteine": "cysteine",
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"cys": "cysteine",
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"c": "cysteine",
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"glycine": "glycine",
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"gly": "glycine",
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"g": "glycine",
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"proline": "proline",
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"pro": "proline",
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"p": "proline",
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"alanine": "alanine",
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"ala": "alanine",
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"a": "alanine",
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"valine": "valine",
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"val": "valine",
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"v": "valine",
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"isoleucine": "isoleucine",
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"ile": "isoleucine",
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"i": "isoleucine",
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"leucine": "leucine",
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"leu": "leucine",
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"l": "leucine",
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"methionine": "methionine",
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"met": "methionine",
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"m": "methionine",
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"phenylalanine": "phenylalanine",
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"phe": "phenylalanine",
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"f": "phenylalanine",
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"tyrosine": "tyrosine",
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"tyr": "tyrosine",
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"y": "tyrosine",
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"tryptophan": "tryptophan",
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"trp": "tryptophan",
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"w": "tryptophan"
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"dna": {
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"adenine": "adenine",
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"da": "adenine",
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"a": "adenine",
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"cytosine": "cytosine",
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"dc": "cytosine",
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"c": "cytosine",
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"guanine": "guanine",
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"dg": "guanine",
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"g": "guanine",
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"thymine": "thymine",
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"dt": "thymine",
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"t": "thymine",
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"uracil": "uracil",
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"du": "uracil",
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"u": "uracil",
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"dr": [
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"adenine",
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"guanine"
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"r": [
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"adenine",
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"dy": [
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"cytosine",
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"y": [
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"ds": [
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"s": [
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"dw": [
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"w": [
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"dm": [
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"m": [
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"db": [
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"b": [
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"dd": [
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"d": [
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"dh": [
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"h": [
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"dv": [
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"v": [
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"dn": [
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"n": [
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"-": [],
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".": []
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},
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"rna": {
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"adenine": "adenine",
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"a": "adenine",
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"cytosine": "cytosine",
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"c": "cytosine",
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"guanine": "guanine",
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"g": "guanine",
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"thymine": "thymine",
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"t": "thymine",
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"uracil": "uracil",
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"u": "uracil",
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"r": [
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"y": [
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"s": [
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"w": [
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"m": [
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"b": [
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"d": [
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"v": [
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"n": [
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"element": {
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"hydrogen": "hydrogen",
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"h": "hydrogen",
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"helium": "helium",
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"he": "helium",
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"lithium": "lithium",
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"li": "lithium",
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"beryllium": "beryllium",
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"be": "beryllium",
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"boron": "boron",
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"b": "boron",
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"carbon": "carbon",
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"c": "carbon",
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"nitrogen": "nitrogen",
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"n": "nitrogen",
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"oxygen": "oxygen",
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"o": "oxygen",
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"fluorine": "fluorine",
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"f": "fluorine",
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"neon": "neon",
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"ne": "neon",
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"sodium": "sodium",
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"na": "sodium",
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"magnesium": "magnesium",
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"mg": "magnesium",
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"aluminum": "aluminum",
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"al": "aluminum",
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"silicon": "silicon",
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"si": "silicon",
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"phosphorus": "phosphorus",
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"p": "phosphorus",
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"sulfur": "sulfur",
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"s": "sulfur",
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"chlorine": "chlorine",
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"cl": "chlorine",
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"argon": "argon",
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"ar": "argon",
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"potassium": "potassium",
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"k": "potassium",
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"calcium": "calcium",
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"ca": "calcium",
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"scandium": "scandium",
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"sc": "scandium",
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"titanium": "titanium",
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"ti": "titanium",
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"vanadium": "vanadium",
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"v": "vanadium",
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"chromium": "chromium",
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"cr": "chromium",
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"manganese": "manganese",
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"mn": "manganese",
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"iron": "iron",
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"fe": "iron",
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"cobalt": "cobalt",
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"co": "cobalt",
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"nickel": "nickel",
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"ni": "nickel",
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"copper": "copper",
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"cu": "copper",
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"zinc": "zinc",
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"zn": "zinc",
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"gallium": "gallium",
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"ga": "gallium",
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"germanium": "germanium",
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"ge": "germanium",
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315
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+
"arsenic": "arsenic",
|
|
316
|
+
"as": "arsenic",
|
|
317
|
+
"selenium": "selenium",
|
|
318
|
+
"se": "selenium",
|
|
319
|
+
"bromine": "bromine",
|
|
320
|
+
"br": "bromine",
|
|
321
|
+
"krypton": "krypton",
|
|
322
|
+
"kr": "krypton",
|
|
323
|
+
"rubidium": "rubidium",
|
|
324
|
+
"rb": "rubidium",
|
|
325
|
+
"strontium": "strontium",
|
|
326
|
+
"sr": "strontium",
|
|
327
|
+
"yttrium": "yttrium",
|
|
328
|
+
"y": "yttrium",
|
|
329
|
+
"zirconium": "zirconium",
|
|
330
|
+
"zr": "zirconium",
|
|
331
|
+
"niobium": "niobium",
|
|
332
|
+
"nb": "niobium",
|
|
333
|
+
"molybdenum": "molybdenum",
|
|
334
|
+
"mo": "molybdenum",
|
|
335
|
+
"technetium": "technetium",
|
|
336
|
+
"tc": "technetium",
|
|
337
|
+
"ruthenium": "ruthenium",
|
|
338
|
+
"ru": "ruthenium",
|
|
339
|
+
"rhodium": "rhodium",
|
|
340
|
+
"rh": "rhodium",
|
|
341
|
+
"palladium": "palladium",
|
|
342
|
+
"pd": "palladium",
|
|
343
|
+
"silver": "silver",
|
|
344
|
+
"ag": "silver",
|
|
345
|
+
"cadmium": "cadmium",
|
|
346
|
+
"cd": "cadmium",
|
|
347
|
+
"indium": "indium",
|
|
348
|
+
"in": "indium",
|
|
349
|
+
"tin": "tin",
|
|
350
|
+
"sn": "tin",
|
|
351
|
+
"antimony": "antimony",
|
|
352
|
+
"sb": "antimony",
|
|
353
|
+
"tellurium": "tellurium",
|
|
354
|
+
"te": "tellurium",
|
|
355
|
+
"iodine": "iodine",
|
|
356
|
+
"i": "iodine",
|
|
357
|
+
"xenon": "xenon",
|
|
358
|
+
"xe": "xenon",
|
|
359
|
+
"cesium": "cesium",
|
|
360
|
+
"caesium": "caesium",
|
|
361
|
+
"cs": "caesium",
|
|
362
|
+
"barium": "barium",
|
|
363
|
+
"ba": "barium",
|
|
364
|
+
"lanthanum": "lanthanum",
|
|
365
|
+
"la": "lanthanum",
|
|
366
|
+
"cerium": "cerium",
|
|
367
|
+
"ce": "cerium",
|
|
368
|
+
"praseodymium": "praseodymium",
|
|
369
|
+
"pr": "praseodymium",
|
|
370
|
+
"neodymium": "neodymium",
|
|
371
|
+
"nd": "neodymium",
|
|
372
|
+
"promethium": "promethium",
|
|
373
|
+
"pm": "promethium",
|
|
374
|
+
"samarium": "samarium",
|
|
375
|
+
"sm": "samarium",
|
|
376
|
+
"europium": "europium",
|
|
377
|
+
"eu": "europium",
|
|
378
|
+
"gadolinium": "gadolinium",
|
|
379
|
+
"gd": "gadolinium",
|
|
380
|
+
"terbium": "terbium",
|
|
381
|
+
"tb": "terbium",
|
|
382
|
+
"dysprosium": "dysprosium",
|
|
383
|
+
"dy": "dysprosium",
|
|
384
|
+
"holmium": "holmium",
|
|
385
|
+
"ho": "holmium",
|
|
386
|
+
"erbium": "erbium",
|
|
387
|
+
"er": "erbium",
|
|
388
|
+
"thulium": "thulium",
|
|
389
|
+
"tm": "thulium",
|
|
390
|
+
"ytterbium": "ytterbium",
|
|
391
|
+
"yb": "ytterbium",
|
|
392
|
+
"lutetium": "lutetium",
|
|
393
|
+
"lu": "lutetium",
|
|
394
|
+
"hafnium": "hafnium",
|
|
395
|
+
"hf": "hafnium",
|
|
396
|
+
"tantalum": "tantalum",
|
|
397
|
+
"ta": "tantalum",
|
|
398
|
+
"tungsten": "tungsten",
|
|
399
|
+
"w": "tungsten",
|
|
400
|
+
"rhenium": "rhenium",
|
|
401
|
+
"re": "rhenium",
|
|
402
|
+
"osmium": "osmium",
|
|
403
|
+
"os": "osmium",
|
|
404
|
+
"iridium": "iridium",
|
|
405
|
+
"ir": "iridium",
|
|
406
|
+
"platinum": "platinum",
|
|
407
|
+
"pt": "platinum",
|
|
408
|
+
"gold": "gold",
|
|
409
|
+
"au": "gold",
|
|
410
|
+
"mercury": "mercury",
|
|
411
|
+
"hg": "mercury",
|
|
412
|
+
"thallium": "thallium",
|
|
413
|
+
"tl": "thallium",
|
|
414
|
+
"lead": "lead",
|
|
415
|
+
"pb": "lead",
|
|
416
|
+
"bismuth": "bismuth",
|
|
417
|
+
"bi": "bismuth",
|
|
418
|
+
"polonium": "polonium",
|
|
419
|
+
"po": "polonium",
|
|
420
|
+
"astatine": "astatine",
|
|
421
|
+
"at": "astatine",
|
|
422
|
+
"radon": "radon",
|
|
423
|
+
"rn": "radon",
|
|
424
|
+
"francium": "francium",
|
|
425
|
+
"fr": "francium",
|
|
426
|
+
"radium": "radium",
|
|
427
|
+
"ra": "radium",
|
|
428
|
+
"actinium": "actinium",
|
|
429
|
+
"ac": "actinium",
|
|
430
|
+
"thorium": "thorium",
|
|
431
|
+
"th": "thorium",
|
|
432
|
+
"protactinium": "protactinium",
|
|
433
|
+
"pa": "protactinium",
|
|
434
|
+
"uranium": "uranium",
|
|
435
|
+
"u": "uranium",
|
|
436
|
+
"neptunium": "neptunium",
|
|
437
|
+
"np": "neptunium",
|
|
438
|
+
"plutonium": "plutonium",
|
|
439
|
+
"pu": "plutonium",
|
|
440
|
+
"americium": "americium",
|
|
441
|
+
"am": "americium",
|
|
442
|
+
"curium": "curium",
|
|
443
|
+
"cm": "curium",
|
|
444
|
+
"berkelium": "berkelium",
|
|
445
|
+
"bk": "berkelium",
|
|
446
|
+
"californium": "californium",
|
|
447
|
+
"cf": "californium",
|
|
448
|
+
"einsteinium": "einsteinium",
|
|
449
|
+
"es": "einsteinium",
|
|
450
|
+
"fermium": "fermium",
|
|
451
|
+
"fm": "fermium",
|
|
452
|
+
"mendelevium": "mendelevium",
|
|
453
|
+
"md": "mendelevium",
|
|
454
|
+
"nobelium": "nobelium",
|
|
455
|
+
"no": "nobelium",
|
|
456
|
+
"lawrencium": "lawrencium",
|
|
457
|
+
"lr": "lawrencium",
|
|
458
|
+
"rutherfordium": "rutherfordium",
|
|
459
|
+
"rf": "rutherfordium",
|
|
460
|
+
"dubnium": "dubnium",
|
|
461
|
+
"db": "dubnium",
|
|
462
|
+
"seaborgium": "seaborgium",
|
|
463
|
+
"sg": "seaborgium",
|
|
464
|
+
"bohrium": "bohrium",
|
|
465
|
+
"bh": "bohrium",
|
|
466
|
+
"hassium": "hassium",
|
|
467
|
+
"hs": "hassium",
|
|
468
|
+
"meitnerium": "meitnerium",
|
|
469
|
+
"mt": "meitnerium",
|
|
470
|
+
"darmstadtium": "darmstadtium",
|
|
471
|
+
"ds": "darmstadtium",
|
|
472
|
+
"roentgenium": "roentgenium",
|
|
473
|
+
"rg": "roentgenium",
|
|
474
|
+
"copernicium": "copernicium",
|
|
475
|
+
"cn": "copernicium",
|
|
476
|
+
"nihonium": "nihonium",
|
|
477
|
+
"nh": "nihonium",
|
|
478
|
+
"flerovium": "flerovium",
|
|
479
|
+
"fl": "flerovium",
|
|
480
|
+
"moscovium": "moscovium",
|
|
481
|
+
"mc": "moscovium",
|
|
482
|
+
"livermorium": "livermorium",
|
|
483
|
+
"lv": "livermorium",
|
|
484
|
+
"tennessine": "tennessine",
|
|
485
|
+
"ts": "tennessine",
|
|
486
|
+
"oganesson": "oganesson",
|
|
487
|
+
"og": "oganesson"
|
|
488
|
+
}
|
|
489
|
+
},
|
|
490
|
+
"amino_acid": {
|
|
491
|
+
"arginine": {
|
|
492
|
+
"1code": "r",
|
|
493
|
+
"3code": "arg",
|
|
494
|
+
"charge": "+",
|
|
495
|
+
"polarity": "polar",
|
|
496
|
+
"codons": [
|
|
497
|
+
"cgu",
|
|
498
|
+
"cgc",
|
|
499
|
+
"cga",
|
|
500
|
+
"cgg",
|
|
501
|
+
"aga",
|
|
502
|
+
"agg"
|
|
503
|
+
],
|
|
504
|
+
"centroid": [
|
|
505
|
+
"cg",
|
|
506
|
+
"cd",
|
|
507
|
+
"ne",
|
|
508
|
+
"cz",
|
|
509
|
+
"nh1",
|
|
510
|
+
"nh2"
|
|
511
|
+
],
|
|
512
|
+
"asa": {
|
|
513
|
+
"gly-x-gly asa w": 249.26,
|
|
514
|
+
"gly-x-gly asa sc": 190.24,
|
|
515
|
+
"ala-x-ala asa w": 235.45,
|
|
516
|
+
"ala-x-ala asa sc": 190.04
|
|
517
|
+
},
|
|
518
|
+
"std-alpha-prop": 0.88,
|
|
519
|
+
"formula": "c6h14n4o2"
|
|
520
|
+
},
|
|
521
|
+
"histidine": {
|
|
522
|
+
"1code": "h",
|
|
523
|
+
"3code": "his",
|
|
524
|
+
"charge": "+",
|
|
525
|
+
"polarity": "polar",
|
|
526
|
+
"codons": [
|
|
527
|
+
"cau",
|
|
528
|
+
"cac"
|
|
529
|
+
],
|
|
530
|
+
"centroid": [
|
|
531
|
+
"cg",
|
|
532
|
+
"nd1",
|
|
533
|
+
"cd2",
|
|
534
|
+
"ce1",
|
|
535
|
+
"ne2"
|
|
536
|
+
],
|
|
537
|
+
"asa": {
|
|
538
|
+
"gly-x-gly asa w": 198.51,
|
|
539
|
+
"gly-x-gly asa sc": 141.27,
|
|
540
|
+
"ala-x-ala asa w": 184.79,
|
|
541
|
+
"ala-x-ala asa sc": 141.17
|
|
542
|
+
},
|
|
543
|
+
"std-alpha-prop": 2.55,
|
|
544
|
+
"formula": "c6h9n3o2"
|
|
545
|
+
},
|
|
546
|
+
"lysine": {
|
|
547
|
+
"1code": "k",
|
|
548
|
+
"3code": "lys",
|
|
549
|
+
"charge": "+",
|
|
550
|
+
"polarity": "polar",
|
|
551
|
+
"codons": [
|
|
552
|
+
"aaa",
|
|
553
|
+
"aag"
|
|
554
|
+
],
|
|
555
|
+
"centroid": [
|
|
556
|
+
"cg",
|
|
557
|
+
"cd",
|
|
558
|
+
"ce",
|
|
559
|
+
"nz"
|
|
560
|
+
],
|
|
561
|
+
"asa": {
|
|
562
|
+
"gly-x-gly asa w": 207.49,
|
|
563
|
+
"gly-x-gly asa sc": 147.99,
|
|
564
|
+
"ala-x-ala asa w": 193.73,
|
|
565
|
+
"ala-x-ala asa sc": 147.83
|
|
566
|
+
},
|
|
567
|
+
"std-alpha-prop": 1.09,
|
|
568
|
+
"formula": "c6h14n2o2"
|
|
569
|
+
},
|
|
570
|
+
"aspartate": {
|
|
571
|
+
"1code": "d",
|
|
572
|
+
"3code": "asp",
|
|
573
|
+
"charge": "-",
|
|
574
|
+
"polarity": "polar",
|
|
575
|
+
"codons": [
|
|
576
|
+
"gau",
|
|
577
|
+
"gac"
|
|
578
|
+
],
|
|
579
|
+
"centroid": [
|
|
580
|
+
"cg",
|
|
581
|
+
"od1",
|
|
582
|
+
"od2"
|
|
583
|
+
],
|
|
584
|
+
"asa": {
|
|
585
|
+
"gly-x-gly asa w": 155.37,
|
|
586
|
+
"gly-x-gly asa sc": 97.8,
|
|
587
|
+
"ala-x-ala asa w": 141.61,
|
|
588
|
+
"ala-x-ala asa sc": 97.66
|
|
589
|
+
},
|
|
590
|
+
"std-alpha-prop": 2.89,
|
|
591
|
+
"formula": "c4h7no4"
|
|
592
|
+
},
|
|
593
|
+
"glutamate": {
|
|
594
|
+
"1code": "e",
|
|
595
|
+
"3code": "glu",
|
|
596
|
+
"charge": "-",
|
|
597
|
+
"polarity": "polar",
|
|
598
|
+
"codons": [
|
|
599
|
+
"gaa",
|
|
600
|
+
"gag"
|
|
601
|
+
],
|
|
602
|
+
"centroid": [
|
|
603
|
+
"cg",
|
|
604
|
+
"cd",
|
|
605
|
+
"oe1",
|
|
606
|
+
"oe2"
|
|
607
|
+
],
|
|
608
|
+
"asa": {
|
|
609
|
+
"gly-x-gly asa w": 187.16,
|
|
610
|
+
"gly-x-gly asa sc": 132.53,
|
|
611
|
+
"ala-x-ala asa w": 173.46,
|
|
612
|
+
"ala-x-ala asa sc": 132.42
|
|
613
|
+
},
|
|
614
|
+
"std-alpha-prop": 1.67,
|
|
615
|
+
"formula": "c5h9no4"
|
|
616
|
+
},
|
|
617
|
+
"serine": {
|
|
618
|
+
"1code": "s",
|
|
619
|
+
"3code": "ser",
|
|
620
|
+
"charge": "none",
|
|
621
|
+
"polarity": "polar",
|
|
622
|
+
"codons": [
|
|
623
|
+
"ucu",
|
|
624
|
+
"ucc",
|
|
625
|
+
"uca",
|
|
626
|
+
"ucg",
|
|
627
|
+
"agu",
|
|
628
|
+
"agc"
|
|
629
|
+
],
|
|
630
|
+
"centroid": [
|
|
631
|
+
"og"
|
|
632
|
+
],
|
|
633
|
+
"asa": {
|
|
634
|
+
"gly-x-gly asa w": 125.68,
|
|
635
|
+
"gly-x-gly asa sc": 69.08,
|
|
636
|
+
"ala-x-ala asa w": 111.97,
|
|
637
|
+
"ala-x-ala asa sc": 68.97
|
|
638
|
+
},
|
|
639
|
+
"std-alpha-prop": 2.09,
|
|
640
|
+
"formula": "c3h7no3"
|
|
641
|
+
},
|
|
642
|
+
"threonine": {
|
|
643
|
+
"1code": "t",
|
|
644
|
+
"3code": "thr",
|
|
645
|
+
"charge": "none",
|
|
646
|
+
"polarity": "polar",
|
|
647
|
+
"codons": [
|
|
648
|
+
"acu",
|
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1713
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1719
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1720
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1722
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1723
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1726
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1727
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1728
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1730
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1731
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1734
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1735
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|
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1741
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1742
|
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1743
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1744
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1745
|
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1746
|
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1747
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1748
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1749
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1750
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1751
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1752
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1753
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1754
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1755
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1756
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1757
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1758
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1759
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1760
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1761
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1762
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1763
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1764
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1765
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1766
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1767
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1768
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1770
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1771
|
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1772
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},
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1773
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1774
|
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1775
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1776
|
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1777
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1778
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1779
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1780
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1781
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1782
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|
1783
|
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},
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1784
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|
|
1785
|
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1786
|
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|
|
1787
|
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|
1788
|
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|
1789
|
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},
|
|
1790
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1791
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1792
|
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1793
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|
1794
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}
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|
1795
|
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},
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|
1796
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|
1797
|
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},
|
|
1798
|
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|
|
1799
|
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|
|
1800
|
+
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|
|
1801
|
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1802
|
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1803
|
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1804
|
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|
|
1805
|
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|
|
1806
|
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},
|
|
1807
|
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"ground configuration": "[ar]3d2 4s2",
|
|
1808
|
+
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|
|
1809
|
+
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|
|
1810
|
+
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|
|
1811
|
+
"crystal": 140
|
|
1812
|
+
},
|
|
1813
|
+
"stable": {
|
|
1814
|
+
"46": {
|
|
1815
|
+
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|
|
1816
|
+
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|
|
1817
|
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},
|
|
1818
|
+
"47": {
|
|
1819
|
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|
|
1820
|
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|
|
1821
|
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},
|
|
1822
|
+
"48": {
|
|
1823
|
+
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|
|
1824
|
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|
|
1825
|
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},
|
|
1826
|
+
"49": {
|
|
1827
|
+
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|
|
1828
|
+
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|
|
1829
|
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},
|
|
1830
|
+
"50": {
|
|
1831
|
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|
|
1832
|
+
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|
|
1833
|
+
}
|
|
1834
|
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},
|
|
1835
|
+
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|
|
1836
|
+
},
|
|
1837
|
+
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|
|
1838
|
+
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|
|
1839
|
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|
|
1840
|
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|
|
1841
|
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|
|
1842
|
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|
|
1843
|
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|
|
1844
|
+
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|
|
1845
|
+
},
|
|
1846
|
+
"ground configuration": "[ar]3d3 4s2",
|
|
1847
|
+
"radius": {
|
|
1848
|
+
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|
|
1849
|
+
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|
|
1850
|
+
"crystal": 135
|
|
1851
|
+
},
|
|
1852
|
+
"stable": {
|
|
1853
|
+
"50": {
|
|
1854
|
+
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|
|
1855
|
+
"abundance": 0.0025
|
|
1856
|
+
},
|
|
1857
|
+
"51": {
|
|
1858
|
+
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|
|
1859
|
+
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|
|
1860
|
+
}
|
|
1861
|
+
},
|
|
1862
|
+
"molar mass": 50.94147
|
|
1863
|
+
},
|
|
1864
|
+
"chromium": {
|
|
1865
|
+
"symbol": "cr",
|
|
1866
|
+
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|
|
1867
|
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|
|
1868
|
+
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|
|
1869
|
+
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|
|
1870
|
+
"thermochemical": 2.12,
|
|
1871
|
+
"allen": 1.65
|
|
1872
|
+
},
|
|
1873
|
+
"ground configuration": "[ar]3d5 4s",
|
|
1874
|
+
"radius": {
|
|
1875
|
+
"van der waals": null,
|
|
1876
|
+
"calculated": 166,
|
|
1877
|
+
"crystal": 140
|
|
1878
|
+
},
|
|
1879
|
+
"stable": {
|
|
1880
|
+
"50": {
|
|
1881
|
+
"mass": 49.9460495,
|
|
1882
|
+
"abundance": 0.04345
|
|
1883
|
+
},
|
|
1884
|
+
"52": {
|
|
1885
|
+
"mass": 51.9405115,
|
|
1886
|
+
"abundance": 0.83789
|
|
1887
|
+
},
|
|
1888
|
+
"53": {
|
|
1889
|
+
"mass": 52.9406534,
|
|
1890
|
+
"abundance": 0.09501
|
|
1891
|
+
},
|
|
1892
|
+
"54": {
|
|
1893
|
+
"mass": 53.9388846,
|
|
1894
|
+
"abundance": 0.02365
|
|
1895
|
+
}
|
|
1896
|
+
},
|
|
1897
|
+
"molar mass": 51.99614
|
|
1898
|
+
},
|
|
1899
|
+
"manganese": {
|
|
1900
|
+
"symbol": "mn",
|
|
1901
|
+
"number": 25,
|
|
1902
|
+
"ionization energy": 7.434038,
|
|
1903
|
+
"electronegativity": {
|
|
1904
|
+
"pauling": 1.55,
|
|
1905
|
+
"thermochemical": 2.2,
|
|
1906
|
+
"allen": 1.75
|
|
1907
|
+
},
|
|
1908
|
+
"ground configuration": "[ar]3d5 4s2",
|
|
1909
|
+
"radius": {
|
|
1910
|
+
"van der waals": null,
|
|
1911
|
+
"calculated": 161,
|
|
1912
|
+
"crystal": 140
|
|
1913
|
+
},
|
|
1914
|
+
"stable": {
|
|
1915
|
+
"55": {
|
|
1916
|
+
"mass": 54.9380493,
|
|
1917
|
+
"abundance": 1.0
|
|
1918
|
+
}
|
|
1919
|
+
},
|
|
1920
|
+
"molar mass": 54.93805
|
|
1921
|
+
},
|
|
1922
|
+
"iron": {
|
|
1923
|
+
"symbol": "fe",
|
|
1924
|
+
"number": 26,
|
|
1925
|
+
"ionization energy": 7.9024681,
|
|
1926
|
+
"electronegativity": {
|
|
1927
|
+
"pauling": 1.83,
|
|
1928
|
+
"thermochemical": 2.32,
|
|
1929
|
+
"allen": 1.8
|
|
1930
|
+
},
|
|
1931
|
+
"ground configuration": "[ar]3d6 4s2",
|
|
1932
|
+
"radius": {
|
|
1933
|
+
"van der waals": null,
|
|
1934
|
+
"calculated": 156,
|
|
1935
|
+
"crystal": 140
|
|
1936
|
+
},
|
|
1937
|
+
"stable": {
|
|
1938
|
+
"54": {
|
|
1939
|
+
"mass": 53.9396147,
|
|
1940
|
+
"abundance": 0.05845
|
|
1941
|
+
},
|
|
1942
|
+
"56": {
|
|
1943
|
+
"mass": 55.9349418,
|
|
1944
|
+
"abundance": 0.91754
|
|
1945
|
+
},
|
|
1946
|
+
"57": {
|
|
1947
|
+
"mass": 56.9353983,
|
|
1948
|
+
"abundance": 0.02119
|
|
1949
|
+
},
|
|
1950
|
+
"58": {
|
|
1951
|
+
"mass": 57.9332801,
|
|
1952
|
+
"abundance": 0.00282
|
|
1953
|
+
}
|
|
1954
|
+
},
|
|
1955
|
+
"molar mass": 55.84515
|
|
1956
|
+
},
|
|
1957
|
+
"cobalt": {
|
|
1958
|
+
"symbol": "co",
|
|
1959
|
+
"number": 27,
|
|
1960
|
+
"ionization energy": 7.88101,
|
|
1961
|
+
"electronegativity": {
|
|
1962
|
+
"pauling": 1.88,
|
|
1963
|
+
"thermochemical": 2.34,
|
|
1964
|
+
"allen": 1.84
|
|
1965
|
+
},
|
|
1966
|
+
"ground configuration": "[ar]3d7 4s2",
|
|
1967
|
+
"radius": {
|
|
1968
|
+
"van der waals": null,
|
|
1969
|
+
"calculated": 152,
|
|
1970
|
+
"crystal": 135
|
|
1971
|
+
},
|
|
1972
|
+
"stable": {
|
|
1973
|
+
"59": {
|
|
1974
|
+
"mass": 58.9331999,
|
|
1975
|
+
"abundance": 1.0
|
|
1976
|
+
}
|
|
1977
|
+
},
|
|
1978
|
+
"molar mass": 58.9332
|
|
1979
|
+
},
|
|
1980
|
+
"nickel": {
|
|
1981
|
+
"symbol": "ni",
|
|
1982
|
+
"number": 28,
|
|
1983
|
+
"ionization energy": 7.639878,
|
|
1984
|
+
"electronegativity": {
|
|
1985
|
+
"pauling": 1.91,
|
|
1986
|
+
"thermochemical": 2.32,
|
|
1987
|
+
"allen": 1.88
|
|
1988
|
+
},
|
|
1989
|
+
"ground configuration": "[ar]3d8 4s2",
|
|
1990
|
+
"radius": {
|
|
1991
|
+
"van der waals": null,
|
|
1992
|
+
"calculated": 149,
|
|
1993
|
+
"crystal": 135
|
|
1994
|
+
},
|
|
1995
|
+
"stable": {
|
|
1996
|
+
"58": {
|
|
1997
|
+
"mass": 57.9353477,
|
|
1998
|
+
"abundance": 0.680769
|
|
1999
|
+
},
|
|
2000
|
+
"60": {
|
|
2001
|
+
"mass": 59.9307903,
|
|
2002
|
+
"abundance": 0.262231
|
|
2003
|
+
},
|
|
2004
|
+
"61": {
|
|
2005
|
+
"mass": 60.9310601,
|
|
2006
|
+
"abundance": 0.011399
|
|
2007
|
+
},
|
|
2008
|
+
"62": {
|
|
2009
|
+
"mass": 61.9283484,
|
|
2010
|
+
"abundance": 0.036345
|
|
2011
|
+
},
|
|
2012
|
+
"64": {
|
|
2013
|
+
"mass": 63.9279692,
|
|
2014
|
+
"abundance": 0.009256
|
|
2015
|
+
}
|
|
2016
|
+
},
|
|
2017
|
+
"molar mass": 58.69336
|
|
2018
|
+
},
|
|
2019
|
+
"copper": {
|
|
2020
|
+
"symbol": "cu",
|
|
2021
|
+
"number": 29,
|
|
2022
|
+
"ionization energy": 7.72638,
|
|
2023
|
+
"electronegativity": {
|
|
2024
|
+
"pauling": 1.9,
|
|
2025
|
+
"thermochemical": 2.86,
|
|
2026
|
+
"allen": 1.85
|
|
2027
|
+
},
|
|
2028
|
+
"ground configuration": "[ar]3d10 4s",
|
|
2029
|
+
"radius": {
|
|
2030
|
+
"van der waals": null,
|
|
2031
|
+
"calculated": 145,
|
|
2032
|
+
"crystal": 135
|
|
2033
|
+
},
|
|
2034
|
+
"stable": {
|
|
2035
|
+
"63": {
|
|
2036
|
+
"mass": 62.9296007,
|
|
2037
|
+
"abundance": 0.6915
|
|
2038
|
+
},
|
|
2039
|
+
"65": {
|
|
2040
|
+
"mass": 64.9277938,
|
|
2041
|
+
"abundance": 0.3085
|
|
2042
|
+
}
|
|
2043
|
+
},
|
|
2044
|
+
"molar mass": 63.54604
|
|
2045
|
+
},
|
|
2046
|
+
"zinc": {
|
|
2047
|
+
"symbol": "zn",
|
|
2048
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"molar mass": 0
|
|
4463
|
+
},
|
|
4464
|
+
"copernicium": {
|
|
4465
|
+
"symbol": "cn",
|
|
4466
|
+
"number": 112,
|
|
4467
|
+
"ionization energy": null,
|
|
4468
|
+
"electronegativity": {
|
|
4469
|
+
"pauling": null,
|
|
4470
|
+
"thermochemical": 3.03,
|
|
4471
|
+
"allen": null
|
|
4472
|
+
},
|
|
4473
|
+
"ground configuration": null,
|
|
4474
|
+
"radius": {
|
|
4475
|
+
"van der waals": null,
|
|
4476
|
+
"calculated": null,
|
|
4477
|
+
"crystal": null
|
|
4478
|
+
},
|
|
4479
|
+
"stable": {},
|
|
4480
|
+
"molar mass": 0
|
|
4481
|
+
},
|
|
4482
|
+
"nihonium": {
|
|
4483
|
+
"symbol": "nh",
|
|
4484
|
+
"number": 113,
|
|
4485
|
+
"ionization energy": null,
|
|
4486
|
+
"electronegativity": {
|
|
4487
|
+
"pauling": null,
|
|
4488
|
+
"thermochemical": 2.49,
|
|
4489
|
+
"allen": null
|
|
4490
|
+
},
|
|
4491
|
+
"ground configuration": null,
|
|
4492
|
+
"radius": {
|
|
4493
|
+
"van der waals": null,
|
|
4494
|
+
"calculated": null,
|
|
4495
|
+
"crystal": null
|
|
4496
|
+
},
|
|
4497
|
+
"stable": {},
|
|
4498
|
+
"molar mass": 0
|
|
4499
|
+
},
|
|
4500
|
+
"flerovium": {
|
|
4501
|
+
"symbol": "fl",
|
|
4502
|
+
"number": 114,
|
|
4503
|
+
"ionization energy": null,
|
|
4504
|
+
"electronegativity": {
|
|
4505
|
+
"pauling": null,
|
|
4506
|
+
"thermochemical": 2.57,
|
|
4507
|
+
"allen": null
|
|
4508
|
+
},
|
|
4509
|
+
"ground configuration": null,
|
|
4510
|
+
"radius": {
|
|
4511
|
+
"van der waals": null,
|
|
4512
|
+
"calculated": null,
|
|
4513
|
+
"crystal": null
|
|
4514
|
+
},
|
|
4515
|
+
"stable": {},
|
|
4516
|
+
"molar mass": 0
|
|
4517
|
+
},
|
|
4518
|
+
"moscovium": {
|
|
4519
|
+
"symbol": "mc",
|
|
4520
|
+
"number": 115,
|
|
4521
|
+
"ionization energy": null,
|
|
4522
|
+
"electronegativity": {
|
|
4523
|
+
"pauling": null,
|
|
4524
|
+
"thermochemical": 2.21,
|
|
4525
|
+
"allen": null
|
|
4526
|
+
},
|
|
4527
|
+
"ground configuration": null,
|
|
4528
|
+
"radius": {
|
|
4529
|
+
"van der waals": null,
|
|
4530
|
+
"calculated": null,
|
|
4531
|
+
"crystal": null
|
|
4532
|
+
},
|
|
4533
|
+
"stable": {},
|
|
4534
|
+
"molar mass": 0
|
|
4535
|
+
},
|
|
4536
|
+
"livermorium": {
|
|
4537
|
+
"symbol": "lv",
|
|
4538
|
+
"number": 116,
|
|
4539
|
+
"ionization energy": null,
|
|
4540
|
+
"electronegativity": {
|
|
4541
|
+
"pauling": null,
|
|
4542
|
+
"thermochemical": 2.42,
|
|
4543
|
+
"allen": null
|
|
4544
|
+
},
|
|
4545
|
+
"ground configuration": null,
|
|
4546
|
+
"radius": {
|
|
4547
|
+
"van der waals": null,
|
|
4548
|
+
"calculated": null,
|
|
4549
|
+
"crystal": null
|
|
4550
|
+
},
|
|
4551
|
+
"stable": {},
|
|
4552
|
+
"molar mass": 0
|
|
4553
|
+
},
|
|
4554
|
+
"tennessine": {
|
|
4555
|
+
"symbol": "ts",
|
|
4556
|
+
"number": 117,
|
|
4557
|
+
"ionization energy": null,
|
|
4558
|
+
"electronegativity": {
|
|
4559
|
+
"pauling": null,
|
|
4560
|
+
"thermochemical": 2.61,
|
|
4561
|
+
"allen": null
|
|
4562
|
+
},
|
|
4563
|
+
"ground configuration": null,
|
|
4564
|
+
"radius": {
|
|
4565
|
+
"van der waals": null,
|
|
4566
|
+
"calculated": null,
|
|
4567
|
+
"crystal": null
|
|
4568
|
+
},
|
|
4569
|
+
"stable": {},
|
|
4570
|
+
"molar mass": 0
|
|
4571
|
+
},
|
|
4572
|
+
"oganesson": {
|
|
4573
|
+
"symbol": "og",
|
|
4574
|
+
"number": 118,
|
|
4575
|
+
"ionization energy": null,
|
|
4576
|
+
"electronegativity": {
|
|
4577
|
+
"pauling": null,
|
|
4578
|
+
"thermochemical": 2.59,
|
|
4579
|
+
"allen": null
|
|
4580
|
+
},
|
|
4581
|
+
"ground configuration": null,
|
|
4582
|
+
"radius": {
|
|
4583
|
+
"van der waals": null,
|
|
4584
|
+
"calculated": null,
|
|
4585
|
+
"crystal": null
|
|
4586
|
+
},
|
|
4587
|
+
"stable": {},
|
|
4588
|
+
"molar mass": 0
|
|
4589
|
+
}
|
|
4590
|
+
},
|
|
4591
|
+
"Sources": {
|
|
4592
|
+
"Atom Molar Masses": "STANDARD ATOMIC WEIGHTS, ciaaw 2020. Available online at www.ciaaw.org/atomic-masses.htm",
|
|
4593
|
+
"Isotopic Abundances": "CIAAW. Isotopic compositions of the elements 2019. Available online at www.ciaaw.org.",
|
|
4594
|
+
"Model Peptide SASAs or ASAs": "Uttamkumar Samanta, Ranjit P. Bahadur, Pinak Chakrabarti, Quantifying the accessible surface area of protein residues in their local environment, Protein Engineering, Design and Selection, Volume 15, Issue 8, August 2002, Pages 659-667, https://doi.org/10.1093/protein/15.8.659",
|
|
4595
|
+
"Atom Ionization Energies and Atom Ground State": "Kramida, A., Ralchenko, Yu., Reader, J., and NIST ASD Team (2021). NIST Atomic Spectra Database (ver. 5.9), [Online]. Available: https://physics.nist.gov/asd [2022, June 28]. National Institute of Standards and Technology, Gaithersburg, MD. DOI: https://doi.org/10.18434/T4W30F",
|
|
4596
|
+
"Pauling Electronegativity": "A.L. Allred, Electronegativity values from thermochemical data, Journal of Inorganic and Nuclear Chemistry, Volume 17, Issues 3-4, 1961, Pages 215-221, ISSN 0022-1902, https://doi.org/10.1016/0022-1902(61)80142-5. (https://www.sciencedirect.com/science/article/pii/0022190261801425)",
|
|
4597
|
+
"Thermochemical Electronegativity": "Tantardini, C., Oganov, A.R. Thermochemical electronegativities of the elements. Nat Commun 12, 2087 (2021). https://doi.org/10.1038/s41467-021-22429-0",
|
|
4598
|
+
"Allen Electronegativity (alkali metals, non-metals)": "Electronegativity is the average one-electron energy of the valence-shell electrons in ground-state free atoms, Leland C. Allen, Journal of the American Chemical Society 1989 111 (25), 9003-9014, DOI: 10.1021/ja00207a003",
|
|
4599
|
+
"Allen Electronegativity (metals)": "Configuration Energies of the d-Block Elements, Joseph B. Mann, Terry L. Meek, Eugene T. Knight, Joseph F. Capitani, and Leland C. Allen, Journal of the American Chemical Society 2000 122 (21), 5132-5137, DOI: 10.1021/ja9928677",
|
|
4600
|
+
"Van der Waals Radius": "Consistent van der Waals Radii for the Whole Main Group, Manjeera Mantina, Adam C. Chamberlin, Rosendo Valero, Christopher J. Cramer, and Donald G. Truhlar, The Journal of Physical Chemistry A 2009 113 (19), 5806-5812, DOI: 10.1021/jp8111556",
|
|
4601
|
+
"Calculated Radius": "Clementi, E., et al. Atomic Screening Constants from SCF Functions. II. Atoms with 37 to 86 Electrons. The Journal of Chemical Physics, vol. 47, no. 4, 10 Apr. 1967, pp. 1300-1307., https://doi.org/10.1063/1.1712084.",
|
|
4602
|
+
"Crystal Radius": "Slater, J. C. Atomic Radii in Crystals. The Journal of Chemical Physics, vol. 41, no. 10, 20 July 1964, pp. 3199-3204., https://doi.org/10.1063/1.1725697. "
|
|
4603
|
+
},
|
|
4604
|
+
"Special Thanks and Acknowledgment": [
|
|
4605
|
+
"This could not have been put together without the following individuals, 200ish man hours of manual data input, several hundred dollars of pizza, and collective rage against PDFs that don't support highlighting text. Thank you all for being the best <3",
|
|
4606
|
+
"Bechthold, H. C.",
|
|
4607
|
+
"Farwell, Taylor Cameron",
|
|
4608
|
+
"Holliday, Noah",
|
|
4609
|
+
"Howald, Curtis M.",
|
|
4610
|
+
"Jenkins, Chloe E.",
|
|
4611
|
+
"Loosli, Sarah",
|
|
4612
|
+
"Rivers, Ava D.",
|
|
4613
|
+
"Smith, Savannah R.",
|
|
4614
|
+
"Draney, Joshua",
|
|
4615
|
+
"Dunn, Kemery",
|
|
4616
|
+
"Dunn, Emma",
|
|
4617
|
+
"Mikami, Kyler M.",
|
|
4618
|
+
"Giraldez Chavez, Jose Humberto",
|
|
4619
|
+
"Hammarstrom, McKay",
|
|
4620
|
+
"Hine, Kutter R."
|
|
4621
|
+
]
|
|
4622
|
+
}
|