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resi_atoms.py
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resi_atoms.py
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"""
Author: Eric J. Ma, Arian Jamasb
Purpose: This is a set of utility variables and functions that can be used
across the Graphein project.
These include various collections of standard & non-standard/modified amino acids and their names, identifiers and properties.
We also include mappings of covalent radii and bond lengths for the amino acids used in assembling atomic protein graphs.
"""
# Graphein
# Author: Eric J. Ma, Arian Jamasb <arian@jamasb.io>
# License: MIT
# Project Website: https://github.com/a-r-j/graphein
# Code Repository: https://github.com/a-r-j/graphein
from typing import Dict, List
import numpy as np
from sklearn.preprocessing import StandardScaler
BACKBONE_ATOMS: List[str] = ["N", "CA", "C", "O"]
"""Atoms present in Amino Acid Backbones."""
BASE_AMINO_ACIDS: List[str] = [
"A",
"C",
"D",
"E",
"F",
"G",
"H",
"I",
"K",
"L",
"M",
"N",
"P",
"Q",
"R",
"S",
"T",
"V",
"W",
"Y",
]
"""Vocabulary of 20 standard amino acids."""
STANDARD_AMINO_ACIDS: List[str] = [
"A",
"B",
"C",
"D",
"E",
"F",
"G",
"H",
"I",
"J",
"K",
"L",
"M",
"N",
"P",
"Q",
"R",
"S",
"T",
"V",
"W",
"X",
"Y",
"Z",
]
"""
Vocabulary of amino acids with one-letter codes. Includes `fuzzy` standard amino acids:
``"B"`` denotes ``"ASX"`` which corresponds to ``"ASP"`` (``"D"``) **or** ``"ASN"`` (``"N"``)
and ``"Z"`` denotes ``"GLX"`` which corresponds to ``"GLU"`` (``"E"``) **or** ``"GLN"`` (``"Q"``).
"""
NON_STANDARD_AMINO_ACIDS: List[str] = ["O", "U"]
"""Non-standard amino acids with one-letter codes."""
AMINO_ACIDS: List[str] = [
"A",
"B",
"C",
"D",
"E",
"F",
"G",
"H",
"I",
"J",
"K",
"L",
"M",
"N",
"O",
"P",
"Q",
"R",
"S",
"T",
"U",
"V",
"W",
"X",
"Y",
"Z",
]
"""Vocabulary of amino acids with one-letter codes. Includes `fuzzy` standard amino acids:
``"B"`` denotes ``"ASX"`` which corresponds to ``"ASP"`` (``"D"``) **or** ``"ASN"`` (``"N"``),
``"J"`` denotes ``"XLE"`` which corresponds to ``"LEU"`` (``"L"``) **or** ``"ILE"`` (``"I"``),
and ``"Z"`` denotes ``"GLX"`` which corresponds to``"GLU"`` (``"E"``) **or** ``"GLN"`` (``"Q"``).
``"X"`` denotes unknown (``"UNK"`` or sometimes ``"XAA"``).
"""
STANDARD_AMINO_ACID_MAPPING_TO_1_3: Dict[str, str] = {
"A": "ALA",
"C": "CYS",
"D": "ASP",
"E": "GLU",
"F": "PHE",
"G": "GLY",
"H": "HIS",
"I": "ILE",
"K": "LYS",
"L": "LEU",
"M": "MET",
"N": "ASN",
"O": "PYL",
"P": "PRO",
"Q": "GLN",
"R": "ARG",
"S": "SER",
"T": "THR",
"U": "SEC",
"V": "VAL",
"W": "TRP",
"Y": "TYR",
"X": "UNK",
}
NON_STANDARD_AMINO_ACID_MAPPING_3_TO_1: Dict[str, str] = {
"CGU": "E",
"HID": "H",
"HIE": "H",
"HIP": "H",
"PYL": "O",
"SEC": "U",
}
"""
Mapping of 3-letter non-standard amino acids codes to their one-letter form.
See: http://ligand-expo.rcsb.org/
"""
BOND_TYPES: List[str] = [
"hydrophobic",
"disulfide",
"hbond",
"ionic",
"aromatic",
"aromatic_sulphur",
"cation_pi",
"backbone",
"delaunay",
"vdw",
"salt_bridge",
"proximal",
"bb_carbonyl_carbonyl",
]
"""List of supported bond types."""
STANDARD_RESI_NAMES: List[str] = [
"ALA",
"ARG",
"ASN",
"ASP",
"ASX",
"CYS",
"GLN",
"GLU",
"GLX",
"GLY",
"HIS",
"ILE",
"LEU",
"LYS",
"MET",
"PHE",
"PRO",
"SER",
"THR",
"TRP",
"TYR",
"UNK",
"VAL",
]
"""
List of standard residue 3-letter names.
Includes ``"UNK"`` for unknown residues.
``"ASX"`` denotes ``"ASP"`` **or** ``"ASN"`` and ``"GLX"`` denotes ``"GLU"`` **or** ``"GLN"``.
"""
NON_STANDARD_RESI_NAMES: List[str] = [
"5HP",
"ABA",
"ACE",
"AIB",
"BMT",
"BOC",
"CBX",
"CEA",
"CGU",
"CME",
"CRO",
"CSD",
"CSO",
"CSS",
"CSW",
"CSX",
"CXM",
"DAL",
"DAR",
"DCY",
"DGL",
"DGN",
"DHI",
"DIL",
"DIV",
"DLE",
"DLY",
"DPN",
"DPR",
"DSG",
"DSN",
"DSP",
"DTH",
"DTR",
"DTY",
"DVA",
"FME",
"FOR",
"HID",
"HIE",
"HIP",
"HYP",
"IVA",
"KCX",
"LLP",
"MLE",
"MVA",
"NH2",
"NLE",
"OCS",
"ORN",
"PCA",
"PTR",
"PVL",
"PYL",
"SAR",
"SEC",
"SEP",
"STY",
"TPO",
"TPQ",
"TYS",
]
"""
List of non-standard residue 3-letter names.
Collected from: https://www.globalphasing.com/buster/manual/maketnt/manual/lib_val/library_validation.html
"""
RESI_NAMES: List[str] = [
"5HP",
"ABA",
"ACE",
"AIB",
"ALA",
"ARG",
"ASN",
"ASP",
"ASX",
"BMT",
"BOC",
"CBX",
"CEA",
"CGU",
"CME",
"CRO",
"CSD",
"CSO",
"CSS",
"CSW",
"CSX",
"CXM",
"CYS",
"DAL",
"DAR",
"DCY",
"DGL",
"DGN",
"DHI",
"DIL",
"DIV",
"DLE",
"DLY",
"DPN",
"DPR",
"DSG",
"DSN",
"DSP",
"DTH",
"DTR",
"DTY",
"DVA",
"FME",
"FOR",
"GLN",
"GLU",
"GLX",
"GLY",
"HID",
"HIE",
"HIP",
"HIS",
"HYP",
"ILE",
"IVA",
"KCX",
"LEU",
"LLP",
"LYS",
"MET",
"MLE",
"MVA",
"NH2",
"NLE",
"OCS",
"ORN",
"PCA",
"PHE",
"PRO",
"PTR",
"PVL",
"PYL",
"SAR",
"SEC",
"SEP",
"SER",
"STY",
"THR",
"TPO",
"TPQ",
"TRP",
"TYR",
"TYS",
"UNK",
"VAL",
]
"""
3-letter residue names for all amino acids.
Non-standard/modified amino acids are mapped to their parent amino acid.
Includes ``"UNK"`` to denote unknown residues.
"""
# https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound
RESI_THREE_TO_1: Dict[str, str] = {
"3HP": "X",
"4HP": "X",
"5HP": "Q",
"ABA": "A",
"ACE": "X",
"AIB": "A",
"ALA": "A",
"ARG": "R",
"ASN": "N",
"ASP": "D",
"ASX": "B",
"BMT": "T",
"BOC": "X",
"CBX": "X",
"CEA": "C",
"CGU": "E",
"CME": "C",
"CRO": "TYG",
"CSD": "C",
"CSO": "C",
"CSS": "C",
"CSW": "C",
"CSX": "C",
"CXM": "M",
"CYS": "C",
"DAL": "A",
"DAR": "R",
"DCY": "C",
"DGL": "E",
"DGN": "Q",
"DHI": "H",
"DIL": "I",
"DIV": "V",
"DLE": "L",
"DLY": "K",
"DPN": "F",
"DPR": "P",
"DSG": "N",
"DSN": "S",
"DSP": "D",
"DTH": "T",
"DTR": "W",
"DTY": "Y",
"DVA": "V",
"FME": "M",
"FOR": "X",
"GLN": "Q",
"GLU": "E",
"GLX": "Z",
"GLY": "G",
"HID": "H", # Different protonation states of HIS
"HIE": "H", # Different protonation states of HIS
"HIP": "H", # Different protonation states of HIS
"HIS": "H",
"HYP": "P",
"ILE": "I",
"IVA": "X",
"KCX": "K",
"LEU": "L",
"LLP": "K",
"LYS": "K",
"MET": "M",
"MLE": "L",
"MVA": "V",
"NH2": "X",
"NLE": "L",
"OCS": "C",
"ORN": "A",
"PCA": "Q",
"PHE": "F",
"PRO": "P",
"PTR": "Y",
"PVL": "X",
"PYL": "O",
"SAR": "G",
"SEC": "U",
"SEP": "S",
"SER": "S",
"STY": "Y",
"THR": "T",
"TPO": "T",
"TPQ": "Y",
"TRP": "W",
"TYR": "Y",
"TYS": "Y",
"UNK": "X",
"VAL": "V",
}
"""
Mapping of 3-letter residue names to 1-letter residue names.
Non-standard/modified amino acids are mapped to their parent amino acid.
Includes ``"UNK"`` to denote unknown residues.
"""
NON_STANDARD_RESIS_NAME: List[str] = [
"3-SULFINOALANINE",
"4-HYDROXYPROLINE",
"4-METHYL-4-[(E)-2-BUTENYL]-4,N-METHYL-THREONINE",
"5-HYDROXYPROLINE",
"ACETYL_GROUP",
"ALPHA-AMINOBUTYRIC_ACID",
"ALPHA-AMINOISOBUTYRIC_ACID",
"AMINO_GROUP",
"CARBOXY_GROUP",
"CYSTEINE-S-DIOXIDE",
"CYSTEINESULFONIC_ACID",
"D-ALANINE",
"D-ARGININE",
"D-ASPARAGINE",
"D-ASPARTATE",
"D-CYSTEINE",
"DECARBOXY(PARAHYDROXYBENZYLIDENE-IMIDAZOLIDINONE)THREONINE",
"D-GLUTAMATE",
"D-GLUTAMINE",
"D-HISTIDINE",
"D-ISOLEUCINE",
"D-ISOVALINE",
"D-LEUCINE",
"D-LYSINE",
"D-PHENYLALANINE",
"D-PROLINE",
"D-SERINE",
"D-THREONINE",
"D-TRYPTOPHANE",
"D-TYROSINE",
"D-VALINE",
"FORMYL_GROUP",
"GAMMA-CARBOXY-GLUTAMIC_ACID",
"ISOVALERIC_ACID",
"LYSINE_NZ-CARBOXYLIC_ACID",
"LYSINE-PYRIDOXAL-5'-PHOSPHATE",
"N-CARBOXYMETHIONINE",
"N-FORMYLMETHIONINE",
"N-METHYLLEUCINE",
"N-METHYLVALINE",
"NORLEUCINE",
"O-PHOSPHOTYROSINE",
"ORNITHINE",
"PHOSPHOSERINE",
"PHOSPHOTHREONINE",
"PYROGLUTAMIC_ACID",
"PYRUVOYL_GROUP",
"SARCOSINE",
"S-HYDROXY-CYSTEINE",
"S-HYDROXYCYSTEINE",
"S-MERCAPTOCYSTEINE",
"S-OXY_CYSTEINE",
"S,S-(2-HYDROXYETHYL)THIOCYSTEINE",
"SULFONATED_TYROSINE",
"TERT-BUTYLOXYCARBONYL_GROUP",
"TOPO-QUINONE",
"TYROSINE-O-SULPHONIC_ACID",
]
"""
Non-standard residue info taken from: https://www.globalphasing.com/buster/manual/maketnt/manual/lib_val/library_validation.html
``PYL`` (pyrolysine) and ``SEC`` are added
"""
NON_STANDARD_RESIS_PARENT: Dict[str, str] = {
"5HP": "GLU",
"ABA": "ALA",
"ACE": "-",
"AIB": "ALA",
"BMT": "THR",
"BOC": "-",
"CBX": "-",
"CEA": "CYS",
"CGU": "GLU",
"CME": "CYS",
"CRO": "CRO",
"CSD": "CYS",
"CSO": "CYS",
"CSS": "CYS",
"CSW": "CYS",
"CSX": "CYS",
"CXM": "MET",
"DAL": "ALA",
"DAR": "ARG",
"DCY": "CYS",
"DGL": "GLU",
"DGN": "GLN",
"DHI": "HIS",
"DIL": "ILE",
"DIV": "VAL",
"DLE": "LEU",
"DLY": "LYS",
"DPN": "PHE",
"DPR": "PRO",
"DSG": "ASN",
"DSN": "SER",
"DSP": "ASP",
"DTH": "THR",
"DTR": "DTR",
"DTY": "TYR",
"DVA": "VAL",
"FME": "MET",
"FOR": "-",
"HYP": "PRO",
"IVA": "-",
"KCX": "LYS",
"LLP": "LYS",
"MLE": "LEU",
"MVA": "VAL",
"NH2": "-",
"NLE": "LEU",
"OCS": "CYS",
"ORN": "ALA",
"PCA": "GLU",
"PTR": "TYR",
"PVL": "-",
"PYL": "LYS",
"SAR": "GLY",
"SEC": "CYS",
"SEP": "SER",
"STY": "TYR",
"TPO": "THR",
"TPQ": "PHE",
"TYS": "TYR",
}
"""
Mapping of 3-letter non-standard/modified residues to their 3-letter parent residue names.
"""
HYDROGEN_BOND_DONORS: Dict[str, Dict[str, int]] = {
"ARG": {"NE": 1, "NH1": 2, "NH2": 2},
"ASN": {"ND2": 2},
"GLN": {"NE2": 2},
"HIS": {"ND1": 2, "NE2": 2},
"LYS": {"NZ": 3},
"SER": {"OG": 1},
"THR": {"OG1": 1},
"TYR": {"OH": 1},
"TRP": {"NE1": 1},
}
"""
Number of hydrogen bonds that a donor atom can donate, if more than one.
9 amino acids (alanine, cysteine, glycine, isoleucine, leucine, methionine,
phenylalanine, proline, valine) have no hydrogen donor or acceptor atoms in
their side chains.
https://www.imgt.org/IMGTeducation/Aide-memoire/_UK/aminoacids/charge/
"""
HYDROGEN_BOND_ACCEPTORS: Dict[str, Dict[str, int]] = {
"ASN": {"OD1": 2},
"ASP": {"OD1": 2, "OD2": 2},
"GLN": {"OE1": 2},
"GLU": {"OE1": 2, "OE2": 2},
"HIS": {"ND1": 1, "NE2": 1},
"SER": {"OG": 2},
"THR": {"OG1": 2},
"TYR": {"OH": 1},
}
"""
Number of hydrogen bonds that an acceptor atom can accept, if more than one.
9 amino acids (alanine, cysteine, glycine, isoleucine, leucine, methionine,
phenylalanine, proline, valine) have no hydrogen donor or acceptor atoms in
their side chains.
https://www.imgt.org/IMGTeducation/Aide-memoire/_UK/aminoacids/charge/
"""
COFACTOR_NAMES: List[str] = [
"ADP",
"AMP",
"ATP",
"cAMP",
"COENZYME_A",
"FAD",
"FLAVIN_MONONUCLEOTIDE",
"NADP",
"NADPH",
]
"""
Names of cofactors commonly found in PDB structures.
See: http://ligand-expo.rcsb.org/ and https://www.globalphasing.com/buster/manual/maketnt/manual/lib_val/library_validation.html
"""
COFACTOR_CODES: List[str] = [
"ADP",
"AMP",
"ATP",
"CMP",
"COA",
"FAD",
"FMN",
"NAP",
"NDP",
]
"""
Three letter codes of cofactors commonly found in PDB structures.
See: http://ligand-expo.rcsb.org/ and https://www.globalphasing.com/buster/manual/maketnt/manual/lib_val/library_validation.html
"""
COFACTOR_CODE_NAME_MAPPING: Dict[str, str] = {
"ADP": "ADP",
"AMP": "AMP",
"ATP": "ATP",
"CMP": "cAMP",
"COA": "COENZYME_A",
"FAD": "FAD",
"FMN": "FLAVIN_MONONUCLEOTIDE",
"NAP": "NADP",
"NDP": "NADPH",
}
"""
Mapping between 3-letter PDB ligand codes and cofactor names.
See http://ligand-expo.rcsb.org/ and https://www.globalphasing.com/buster/manual/maketnt/manual/lib_val/library_validation.html
"""
CARBOHYDRATE_NAMES: List[str] = [
"D-GALACTOSE",
"D-GLUCOSE",
"D-MANNOSE",
"D-XYLOPYRANOSE",
"FUCOSE",
"N-ACETYL-D-GALACTOSAMINE",
"N-ACETYL-D-GLUCOSAMINE",
"O-SIALIC_ACID",
]
"""
Names of commonly found carbohydrates in protein structures.
See http://ligand-expo.rcsb.org/ and https://www.globalphasing.com/buster/manual/maketnt/manual/lib_val/library_validation.html
"""
CARBOHYDRATE_CODES: List[str] = [
"BGC",
"BMA",
"FUC",
"GAL",
"GLA",
"GLC",
"MAN",
"NAG",
"NGA",
"SIA",
"XYS",
]
"""
Three letter codes of commonly found carbohydrates in protein structures.
See http://ligand-expo.rcsb.org/ and https://www.globalphasing.com/buster/manual/maketnt/manual/lib_val/library_validation.html
"""
CARBOHYDRATE_CODE_NAME_MAPPING: Dict[str, str] = {
"BGC": "D-GLUCOSE",
"BMA": "D-MANNOSE",
"FUC": "FUCOSE",
"GAL": "D-GALACTOSE",
"GLA": "D-GALACTOSE",
"GLC": "D-GLUCOSE",
"MAN": "D-MANNOSE",
"NAG": "N-ACETYL-D-GLUCOSAMINE",
"NGA": "N-ACETYL-D-GALACTOSAMINE",
"SIA": "O-SIALIC_ACID",
"XYS": "D-XYLOPYRANOSE",
}
"""
Mapping of 3-letter PDB ligand accession codes for common carbohydrates to their full names.
See http://ligand-expo.rcsb.org/ and https://www.globalphasing.com/buster/manual/maketnt/manual/lib_val/library_validation.html
"""
HYDROPHOBIC_RESIS: List[str] = [
"ALA",
"ILE",
"LEU",
"MET",
"PHE",
"PRO",
"TRP",
"TYR",
"VAL",
]
"""List of residues that are considered to be hydrophobic."""
DISULFIDE_RESIS: List[str] = ["CYS"]
"""Residues capable of forming disulfide bonds."""
DISULFIDE_ATOMS: List[str] = ["SG"]
"""List of atoms capable of forming disulphide bonds."""
IONIC_RESIS: List[str] = ["ARG", "LYS", "HIS", "ASP", "GLU"]
"""Residues capable of forming ionic interactions."""
POS_AA: List[str] = ["HIS", "LYS", "ARG"]
"""Positively charged amino acids."""
NEG_AA: List[str] = ["GLU", "ASP"]
"""Negatively charged amino acids."""
AA_RING_ATOMS: Dict[str, List[str]] = {
# "HIS": ["CG", "CD", "CE", "ND", "NE"],
"HIS": ["CG", "CD", "CE", "ND", "NE", "CD2", "ND1", "CE1", "NE2"],
# "PHE": ["CG", "CD", "CE", "CZ"],
"PHE": ["CG", "CD", "CE", "CZ", "CD1", "CD2", "CE1", "CE2"],
# "TRP": ["CD", "CE", "CH", "CZ"],
"TRP": ["CD2", "CE2", "CE3", "CZ2", "CZ3", "CH2"],
# "TYR": ["CG", "CD", "CE", "CZ"],
"TYR": ["CG", "CD", "CE", "CZ", "CD1", "CD2", "CE1", "CE2"],
}
"""
Dictionary mapping amino acid 3-letter codes to lists of atoms that are part of rings.
"""
RING_NORMAL_ATOMS: Dict[str, List[str]] = {
"PHE": ["CG", "CE1", "CE2"],
"TRP": ["CD2", "CZ2", "CZ3"],
"TYR": ["CG", "CE1", "CE2"],
}
"""Dictionary of atoms used to compute ring normals for each residue."""
AROMATIC_RESIS: List[str] = ["PHE", "TRP", "HIS", "TYR"]
"""List of aromatic residues."""
CATION_PI_RESIS: List[str] = ["LYS", "ARG", "PHE", "TYR", "TRP"]
"""List of residues involved in cation-pi interactions."""
CATION_RESIS: List[str] = ["LYS", "ARG"]
"""List of cationic residues."""
PI_RESIS: List[str] = ["PHE", "TYR", "TRP"]
"""List of residues involved in pi interactions."""
SULPHUR_RESIS: List[str] = ["MET", "CYS"]
"""Residues containing sulphur atoms."""
SALT_BRIDGE_ANIONS: List[str] = ["ASP", "GLU"]
"""List of anionic residues that can form salt bridges."""
SALT_BRIDGE_CATIONS: List[str] = ["LYS", "ARG"]
"""List of cationic residues that can form salt bridges."""
SALT_BRIDGE_RESIDUES: List[str] = SALT_BRIDGE_ANIONS + SALT_BRIDGE_CATIONS
"""List of residues that can form salt bridges."""
SALT_BRIDGE_ATOMS: List[str] = ["OD1", "OD2", "OE1", "OE2", "NZ", "NH1", "NH2"]
"""List of atoms that can form salt bridges."""
VDW_RADII: Dict[str, float] = {
"H": 1.2, # 1.09
"C": 1.7,
"N": 1.55,
"O": 1.52,
"F": 1.47,
"P": 1.8,
"S": 1.8,
"Cl": 1.75,
"Cu": 1.4,
}
"""van der Waals radii of the most common atoms. Taken from:
> Bondi, A. (1964). "van der Waals Volumes and Radii".
> J. Phys. Chem. 68 (3): 441–451.
https://pubs.acs.org/doi/10.1021/j100785a001
"""
ISOELECTRIC_POINTS: Dict[str, float] = {
"ALA": 6.11,
"ARG": 10.76,
"ASN": 10.76,
"ASP": 2.98,
"ASX": 6.87, # the average of D and N
"CYS": 5.02,
"GLN": 5.65,
"GLU": 3.08,
"GLX": 4.35, # the average of E and Q
"GLY": 6.06,
"HIS": 7.64,
"ILE": 6.04,
"LEU": 6.04,
"LYS": 9.74,
"MET": 5.74,
"PHE": 5.91,
"PRO": 6.30,
"SER": 5.68,
"THR": 5.60,
"TRP": 5.88,
"TYR": 5.63,
"UNK": 7.00, # unknown so assign neutral
"VAL": 6.02,
}
"""
Dictionary of isoelectric points for standard amino acids. For ``"UNK"`` residues, neutral (pH 7.0) is assigned.
For ``"ASX"`` and ``"GLX"`` the average of their constituents (``"D"`` and ``"N"``, and ``"E"`` and ``"Q"``, respectively) is assigned.
"""
scaler = StandardScaler()
scaler.fit(np.array(list(ISOELECTRIC_POINTS.values())).reshape(-1, 1))
ISOELECTRIC_POINTS_STD = {
k: scaler.transform(np.array([v]).reshape(-1, 1))
for k, v in ISOELECTRIC_POINTS.items()
}
"""
Standardized (sklearn.StandardScaler) isoelectric points for standard amino acids.
See :const:`~graphein.protein.resi_atoms.ISOELECTRIC_POINTS` for details.
"""
MOLECULAR_WEIGHTS: Dict[str, float] = {
"ALA": 89.0935,
"ARG": 174.2017,
"ASN": 132.1184,
"ASP": 133.1032,
"ASX": 132.6108, # the average of D and N
"CYS": 121.1590,
"GLN": 146.1451,
"GLU": 147.1299,
"GLX": 146.6375, # the average of E and Q
"GLY": 75.0669,
"HIS": 155.1552,
"ILE": 131.1736,
"LEU": 131.1736,
"LYS": 146.1882,
"MET": 149.2124,
"PHE": 165.1900,
"PRO": 115.1310,
"SER": 105.0930,
"THR": 119.1197,
"TRP": 204.2262,
"TYR": 181.1894,
"UNK": 137.1484, # unknown, therefore assign average of knowns
"VAL": 117.1469,
}
"""Mapping of 3-letter amino acid names to molecular weights.
``UNK`` is used for unknown residues and takes the mean of known weights.
For ``"ASX"`` and ``"GLX"`` the average of their constituents (``"D"`` and ``"N"``, and ``"E"`` and ``"Q"``, respectively) is assigned.
"""
scaler.fit(np.array(list(MOLECULAR_WEIGHTS.values())).reshape(-1, 1))
MOLECULAR_WEIGHTS_STD = {
k: scaler.transform(np.array([v]).reshape(-1, 1))
for k, v in MOLECULAR_WEIGHTS.items()
}
"""
Standardized (sklearn.StandardScaler) molecular weights for standard amino acids.
See :const:`~graphein.protein.resi_atoms.MOLECULAR_WEIGHTS` for details.
"""
GRANTHAM_CHEMICAL_DISTANCE_MATRIX: Dict[str, float] = {
"AA": 0.0,
"AC": 0.112,
"AD": 0.819,
"AE": 0.827,
"AF": 0.54,
"AG": 0.208,
"AH": 0.696,
"AI": 0.407,
"AK": 0.891,
"AL": 0.406,
"AM": 0.379,
"AN": 0.318,
"AP": 0.191,
"AQ": 0.372,
"AR": 1.0,
"AS": 0.094,
"AT": 0.22,
"AV": 0.273,
"AW": 0.739,
"AY": 0.552,
"CA": 0.114,
"CC": 0.0,
"CD": 0.847,
"CE": 0.838,
"CF": 0.437,
"CG": 0.32,
"CH": 0.66,
"CI": 0.304,
"CK": 0.887,
"CL": 0.301,
"CM": 0.277,
"CN": 0.324,
"CP": 0.157,
"CQ": 0.341,
"CR": 1.0,
"CS": 0.176,
"CT": 0.233,
"CV": 0.167,
"CW": 0.639,
"CY": 0.457,
"DA": 0.729,
"DC": 0.742,
"DD": 0.0,
"DE": 0.124,
"DF": 0.924,
"DG": 0.697,
"DH": 0.435,
"DI": 0.847,
"DK": 0.249,
"DL": 0.841,
"DM": 0.819,
"DN": 0.56,
"DP": 0.657,
"DQ": 0.584,
"DR": 0.295,
"DS": 0.667,
"DT": 0.649,
"DV": 0.797,
"DW": 1.0,
"DY": 0.836,
"EA": 0.79,
"EC": 0.788,
"ED": 0.133,
"EE": 0.0,
"EF": 0.932,
"EG": 0.779,
"EH": 0.406,
"EI": 0.86,
"EK": 0.143,
"EL": 0.854,
"EM": 0.83,
"EN": 0.599,
"EP": 0.688,
"EQ": 0.598,
"ER": 0.234,
"ES": 0.726,