PFMBench/src/data/constants/geometry.py

# Copyright Generate Biomedicines, Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#      http://www.apache.org/licenses/LICENSE-2.0
#
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# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

"""Dictionary containing ideal internal coordinates and chi angle assignments
 for building amino acid 3D coordinates"""
from typing import Dict

"""
+--------------+--------+----------------------------------------------------------+
| 氨基酸       | 单字母 | 原子名列表                                                |
+--------------+--------+----------------------------------------------------------+
| 甘氨酸 (Gly) | 'G'    | 'N',  'CA', 'C',  'O'                                     |
| 丙氨酸 (Ala) | 'A'    | 'N',  'CA', 'C',  'O',  'CB'                               |
| 缬氨酸 (Val) | 'V'    | 'N',  'CA', 'C',  'O',  'CB',  'CG1', 'CG2'                |
| 亮氨酸 (Leu) | 'L'    | 'N',  'CA', 'C',  'O',  'CB',  'CG',  'CD1', 'CD2'         |
| 异亮氨酸 (Ile)| 'I'   | 'N',  'CA', 'C',  'O',  'CB',  'CG1', 'CG2', 'CD1'         |
| 丝氨酸 (Ser) | 'S'    | 'N',  'CA', 'C',  'O',  'CB',  'OG'                        |
| 苏氨酸 (Thr) | 'T'    | 'N',  'CA', 'C',  'O',  'CB',  'OG1', 'CG2'                |
| 半胱氨酸 (Cys)| 'C'   | 'N',  'CA', 'C',  'O',  'CB',  'SG'                        |
| 甲硫氨酸 (Met)| 'M'   | 'N',  'CA', 'C',  'O',  'CB',  'CG',  'SD',  'CE'          |
| 脯氨酸 (Pro) | 'P'    | 'N',  'CA', 'C',  'O',  'CB',  'CG',  'CD'                 |
| 苯丙氨酸 (Phe)| 'F'   | 'N',  'CA', 'C',  'O',  'CB',  'CG',  'CD1', 'CD2', 'CE1', |
|              |        | 'CE2', 'CZ'                                                |
| 酪氨酸 (Tyr) | 'Y'    | 'N',  'CA', 'C',  'O',  'CB',  'CG',  'CD1', 'CD2', 'CE1', |
|              |        | 'CE2', 'CZ',  'OH'                                         |
| 色氨酸 (Trp) | 'W'    | 'N',  'CA', 'C',  'O',  'CB',  'CG',  'CD1', 'CD2', 'NE1', |
|              |        | 'CE2','CE3', 'CZ2','CZ3', 'CH2'                            |
| 天冬氨酸 (Asp)| 'D'   | 'N',  'CA', 'C',  'O',  'CB',  'CG',  'OD1', 'OD2'          |
| 谷氨酸 (Glu) | 'E'    | 'N',  'CA', 'C',  'O',  'CB',  'CG',  'CD',  'OE1', 'OE2'   |
| 天冬酰胺 (Asn)| 'N'   | 'N',  'CA', 'C',  'O',  'CB',  'CG',  'OD1', 'ND2'          |
| 谷酰胺 (Gln) | 'Q'    | 'N',  'CA', 'C',  'O',  'CB',  'CG',  'CD',  'OE1', 'NE2'   |
| 赖氨酸 (Lys) | 'K'    | 'N',  'CA', 'C',  'O',  'CB',  'CG',  'CD',  'CE',  'NZ'    |
| 精氨酸 (Arg) | 'R'    | 'N',  'CA', 'C',  'O',  'CB',  'CG',  'CD',  'NE',  'CZ',   |
|              |        | 'NH1','NH2'                                                |
| 组氨酸 (His) | 'H'    | 'N',  'CA', 'C',  'O',  'CB',  'CG',  'ND1', 'CD2', 'CE1', |
|              |        | 'NE2'                                                      |
+--------------+--------+----------------------------------------------------------+
"""




AA_GEOMETRY: Dict[str, dict] = {
    "ALA": {
        "atoms": ["CB"],
        "chi_indices": [],
        "parents": [["N", "C", "CA"]],
        "types": {"C": "C", "CA": "CT1", "CB": "CT3", "N": "NH1", "O": "O"},
        "z-angles": [111.09],
        "z-dihedrals": [123.23],
        "z-lengths": [1.55],
    },
    "ARG": {
        "atoms": ["CB", "CG", "CD", "NE", "CZ", "NH1", "NH2"],
        "chi_indices": [1, 2, 3, 4],
        "parents": [
            ["N", "C", "CA"],
            ["N", "CA", "CB"],
            ["CA", "CB", "CG"],
            ["CB", "CG", "CD"],
            ["CG", "CD", "NE"],
            ["CD", "NE", "CZ"],
            ["NH1", "NE", "CZ"],
        ],
        "types": {
            "C": "C",
            "CA": "CT1",
            "CB": "CT2",
            "CD": "CT2",
            "CG": "CT2",
            "CZ": "C",
            "N": "NH1",
            "NE": "NC2",
            "NH1": "NC2",
            "NH2": "NC2",
            "O": "O",
        },
        "z-angles": [112.26, 115.95, 114.01, 107.09, 123.05, 118.06, 122.14],
        "z-dihedrals": [123.64, 180.0, 180.0, 180.0, 180.0, 180.0, 178.64],
        "z-lengths": [1.56, 1.55, 1.54, 1.5, 1.34, 1.33, 1.33],
    },
    "ASN": {
        "atoms": ["CB", "CG", "OD1", "ND2"],
        "chi_indices": [1, 2],
        "parents": [
            ["N", "C", "CA"],
            ["N", "CA", "CB"],
            ["CA", "CB", "CG"],
            ["OD1", "CB", "CG"],
        ],
        "types": {
            "C": "C",
            "CA": "CT1",
            "CB": "CT2",
            "CG": "CC",
            "N": "NH1",
            "ND2": "NH2",
            "O": "O",
            "OD1": "O",
        },
        "z-angles": [113.04, 114.3, 122.56, 116.15],
        "z-dihedrals": [121.18, 180.0, 180.0, -179.19],
        "z-lengths": [1.56, 1.53, 1.23, 1.35],
    },
    "ASP": {
        "atoms": ["CB", "CG", "OD1", "OD2"],
        "chi_indices": [1, 2],
        "parents": [
            ["N", "C", "CA"],
            ["N", "CA", "CB"],
            ["CA", "CB", "CG"],
            ["OD1", "CB", "CG"],
        ],
        "types": {
            "C": "C",
            "CA": "CT1",
            "CB": "CT2A",
            "CG": "CC",
            "N": "NH1",
            "O": "O",
            "OD1": "OC",
            "OD2": "OC",
        },
        "z-angles": [114.1, 112.6, 117.99, 117.7],
        "z-dihedrals": [122.33, 180.0, 180.0, -170.23],
        "z-lengths": [1.56, 1.52, 1.26, 1.25],
    },
    "CYS": {
        "atoms": ["CB", "SG"],
        "chi_indices": [1],
        "parents": [["N", "C", "CA"], ["N", "CA", "CB"]],
        "types": {"C": "C", "CA": "CT1", "CB": "CT2", "N": "NH1", "O": "O", "SG": "S"},
        "z-angles": [111.98, 113.87],
        "z-dihedrals": [121.79, 180.0],
        "z-lengths": [1.56, 1.84],
    },
    "GLN": {
        "atoms": ["CB", "CG", "CD", "OE1", "NE2"],
        "chi_indices": [1, 2, 3],
        "parents": [
            ["N", "C", "CA"],
            ["N", "CA", "CB"],
            ["CA", "CB", "CG"],
            ["CB", "CG", "CD"],
            ["OE1", "CG", "CD"],
        ],
        "types": {
            "C": "C",
            "CA": "CT1",
            "CB": "CT2",
            "CD": "CC",
            "CG": "CT2",
            "N": "NH1",
            "NE2": "NH2",
            "O": "O",
            "OE1": "O",
        },
        "z-angles": [111.68, 115.52, 112.5, 121.52, 116.84],
        "z-dihedrals": [121.91, 180.0, 180.0, 180.0, 179.57],
        "z-lengths": [1.55, 1.55, 1.53, 1.23, 1.35],
    },
    "GLU": {
        "atoms": ["CB", "CG", "CD", "OE1", "OE2"],
        "chi_indices": [1, 2, 3],
        "parents": [
            ["N", "C", "CA"],
            ["N", "CA", "CB"],
            ["CA", "CB", "CG"],
            ["CB", "CG", "CD"],
            ["OE1", "CG", "CD"],
        ],
        "types": {
            "C": "C",
            "CA": "CT1",
            "CB": "CT2A",
            "CD": "CC",
            "CG": "CT2",
            "N": "NH1",
            "O": "O",
            "OE1": "OC",
            "OE2": "OC",
        },
        "z-angles": [111.71, 115.69, 115.73, 114.99, 120.08],
        "z-dihedrals": [121.9, 180.0, 180.0, 180.0, -179.1],
        "z-lengths": [1.55, 1.56, 1.53, 1.26, 1.25],
    },
    "GLY": {
        "atoms": [],
        "chi_indices": [],
        "parents": [],
        "types": {"C": "C", "CA": "CT2", "N": "NH1", "O": "O"},
        "z-angles": [],
        "z-dihedrals": [],
        "z-lengths": [],
    },
    "HIS": {
        "atoms": ["CB", "CG", "ND1", "CD2", "CE1", "NE2"],
        "chi_indices": [1, 2],
        "parents": [
            ["N", "C", "CA"],
            ["N", "CA", "CB"],
            ["CA", "CB", "CG"],
            ["ND1", "CB", "CG"],
            ["CB", "CG", "ND1"],
            ["CB", "CG", "CD2"],
        ],
        "types": {
            "C": "C",
            "CA": "CT1",
            "CB": "CT2",
            "CD2": "CPH1",
            "CE1": "CPH2",
            "CG": "CPH1",
            "N": "NH1",
            "ND1": "NR1",
            "NE2": "NR2",
            "O": "O",
        },
        "z-angles": [109.99, 114.05, 124.1, 129.6, 107.03, 110.03],
        "z-dihedrals": [122.46, 180.0, 90.0, -171.29, -173.21, 171.99],
        "z-lengths": [1.55, 1.5, 1.38, 1.36, 1.35, 1.38],
    },
    "HSD": {
        "atoms": ["CB", "CG", "ND1", "CD2", "CE1", "NE2"],
        "chi_indices": [1, 2],
        "parents": [
            ["N", "C", "CA"],
            ["N", "CA", "CB"],
            ["CA", "CB", "CG"],
            ["ND1", "CB", "CG"],
            ["CB", "CG", "ND1"],
            ["CB", "CG", "CD2"],
        ],
        "types": {
            "C": "C",
            "CA": "CT1",
            "CB": "CT2",
            "CD2": "CPH1",
            "CE1": "CPH2",
            "CG": "CPH1",
            "N": "NH1",
            "ND1": "NR1",
            "NE2": "NR2",
            "O": "O",
        },
        "z-angles": [109.99, 114.05, 124.1, 129.6, 107.03, 110.03],
        "z-dihedrals": [122.46, 180.0, 90.0, -171.29, -173.21, 171.99],
        "z-lengths": [1.55, 1.5, 1.38, 1.36, 1.35, 1.38],
    },
    "HSE": {
        "atoms": ["CB", "CG", "ND1", "CD2", "CE1", "NE2"],
        "chi_indices": [],
        "parents": [
            ["N", "C", "CA"],
            ["N", "CA", "CB"],
            ["CA", "CB", "CG"],
            ["ND1", "CB", "CG"],
            ["CB", "CG", "ND1"],
            ["CB", "CG", "CD2"],
        ],
        "types": {
            "C": "C",
            "CA": "CT1",
            "CB": "CT2",
            "CD2": "CPH1",
            "CE1": "CPH2",
            "CG": "CPH1",
            "N": "NH1",
            "ND1": "NR2",
            "NE2": "NR1",
            "O": "O",
        },
        "z-angles": [111.67, 116.94, 120.17, 129.71, 105.2, 105.8],
        "z-dihedrals": [123.52, 180.0, 90.0, -178.26, -179.2, 178.66],
        "z-lengths": [1.56, 1.51, 1.39, 1.36, 1.32, 1.38],
    },
    "HSP": {
        "atoms": ["CB", "CG", "ND1", "CD2", "CE1", "NE2"],
        "chi_indices": [],
        "parents": [
            ["N", "C", "CA"],
            ["N", "CA", "CB"],
            ["CA", "CB", "CG"],
            ["ND1", "CB", "CG"],
            ["CB", "CG", "ND1"],
            ["CB", "CG", "CD2"],
        ],
        "types": {
            "C": "C",
            "CA": "CT1",
            "CB": "CT2A",
            "CD2": "CPH1",
            "CE1": "CPH2",
            "CG": "CPH1",
            "N": "NH1",
            "ND1": "NR3",
            "NE2": "NR3",
            "O": "O",
        },
        "z-angles": [109.38, 114.18, 122.94, 128.93, 108.9, 106.93],
        "z-dihedrals": [125.13, 180.0, 90.0, -165.26, -167.62, 167.13],
        "z-lengths": [1.55, 1.52, 1.37, 1.35, 1.33, 1.37],
    },
    "ILE": {
        "atoms": ["CB", "CG1", "CG2", "CD1"],
        "chi_indices": [1, 3],
        "parents": [
            ["N", "C", "CA"],
            ["N", "CA", "CB"],
            ["CG1", "CA", "CB"],
            ["CA", "CB", "CG1"],
        ],
        "types": {
            "C": "C",
            "CA": "CT1",
            "CB": "CT1",
            "CD": "CT3",
            "CG1": "CT2",
            "CG2": "CT3",
            "N": "NH1",
            "O": "O",
        },
        "z-angles": [112.93, 113.63, 113.93, 114.09],
        "z-dihedrals": [124.22, 180.0, -130.04, 180.0],
        "z-lengths": [1.57, 1.55, 1.55, 1.54],
    },
    "LEU": {
        "atoms": ["CB", "CG", "CD1", "CD2"],
        "chi_indices": [1, 2],
        "parents": [
            ["N", "C", "CA"],
            ["N", "CA", "CB"],
            ["CA", "CB", "CG"],
            ["CD1", "CB", "CG"],
        ],
        "types": {
            "C": "C",
            "CA": "CT1",
            "CB": "CT2",
            "CD1": "CT3",
            "CD2": "CT3",
            "CG": "CT1",
            "N": "NH1",
            "O": "O",
        },
        "z-angles": [112.12, 117.46, 110.48, 112.57],
        "z-dihedrals": [121.52, 180.0, 180.0, 120.0],
        "z-lengths": [1.55, 1.55, 1.54, 1.54],
    },
    "LYS": {
        "atoms": ["CB", "CG", "CD", "CE", "NZ"],
        "chi_indices": [1, 2, 3, 4],
        "parents": [
            ["N", "C", "CA"],
            ["N", "CA", "CB"],
            ["CA", "CB", "CG"],
            ["CB", "CG", "CD"],
            ["CG", "CD", "CE"],
        ],
        "types": {
            "C": "C",
            "CA": "CT1",
            "CB": "CT2",
            "CD": "CT2",
            "CE": "CT2",
            "CG": "CT2",
            "N": "NH1",
            "NZ": "NH3",
            "O": "O",
        },
        "z-angles": [111.36, 115.76, 113.28, 112.33, 110.46],
        "z-dihedrals": [122.23, 180.0, 180.0, 180.0, 180.0],
        "z-lengths": [1.56, 1.54, 1.54, 1.53, 1.46],
    },
    "MET": {
        "atoms": ["CB", "CG", "SD", "CE"],
        "chi_indices": [1, 2, 3],
        "parents": [
            ["N", "C", "CA"],
            ["N", "CA", "CB"],
            ["CA", "CB", "CG"],
            ["CB", "CG", "SD"],
        ],
        "types": {
            "C": "C",
            "CA": "CT1",
            "CB": "CT2",
            "CE": "CT3",
            "CG": "CT2",
            "N": "NH1",
            "O": "O",
            "SD": "S",
        },
        "z-angles": [111.88, 115.92, 110.28, 98.94],
        "z-dihedrals": [121.62, 180.0, 180.0, 180.0],
        "z-lengths": [1.55, 1.55, 1.82, 1.82],
    },
    "PHE": {
        "atoms": ["CB", "CG", "CD1", "CD2", "CE1", "CE2", "CZ"],
        "chi_indices": [1, 2],
        "parents": [
            ["N", "C", "CA"],
            ["N", "CA", "CB"],
            ["CA", "CB", "CG"],
            ["CD1", "CB", "CG"],
            ["CB", "CG", "CD1"],
            ["CB", "CG", "CD2"],
            ["CG", "CD1", "CE1"],
        ],
        "types": {
            "C": "C",
            "CA": "CT1",
            "CB": "CT2",
            "CD1": "CA",
            "CD2": "CA",
            "CE1": "CA",
            "CE2": "CA",
            "CG": "CA",
            "CZ": "CA",
            "N": "NH1",
            "O": "O",
        },
        "z-angles": [112.45, 112.76, 120.32, 120.76, 120.63, 120.62, 119.93],
        "z-dihedrals": [122.49, 180.0, 90.0, -177.96, -177.37, 177.2, -0.12],
        "z-lengths": [1.56, 1.51, 1.41, 1.41, 1.4, 1.4, 1.4],
    },
    "PRO": {
        "atoms": ["CB", "CG", "CD"],
        "chi_indices": [1, 2],
        "parents": [["N", "C", "CA"], ["N", "CA", "CB"], ["CA", "CB", "CG"]],
        "types": {
            "C": "C",
            "CA": "CP1",
            "CB": "CP2",
            "CD": "CP3",
            "CG": "CP2",
            "N": "N",
            "O": "O",
        },
        "z-angles": [111.74, 104.39, 103.21],
        "z-dihedrals": [113.74, 31.61, -34.59],
        "z-lengths": [1.54, 1.53, 1.53],
    },
    "SER": {
        "atoms": ["CB", "OG"],
        "chi_indices": [1],
        "parents": [["N", "C", "CA"], ["N", "CA", "CB"]],
        "types": {
            "C": "C",
            "CA": "CT1",
            "CB": "CT2",
            "N": "NH1",
            "O": "O",
            "OG": "OH1",
        },
        "z-angles": [111.4, 112.45],
        "z-dihedrals": [124.75, 180.0],
        "z-lengths": [1.56, 1.43],
    },
    "THR": {
        "atoms": ["CB", "OG1", "CG2"],
        "chi_indices": [1],
        "parents": [["N", "C", "CA"], ["N", "CA", "CB"], ["OG1", "CA", "CB"]],
        "types": {
            "C": "C",
            "CA": "CT1",
            "CB": "CT1",
            "CG2": "CT3",
            "N": "NH1",
            "O": "O",
            "OG1": "OH1",
        },
        "z-angles": [112.74, 112.16, 115.91],
        "z-dihedrals": [126.46, 180.0, -124.13],
        "z-lengths": [1.57, 1.43, 1.53],
    },
    "TRP": {
        "atoms": ["CB", "CG", "CD2", "CD1", "CE2", "NE1", "CE3", "CZ3", "CH2", "CZ2"],
        "chi_indices": [1, 2],
        "parents": [
            ["N", "C", "CA"],
            ["N", "CA", "CB"],
            ["CA", "CB", "CG"],
            ["CD2", "CB", "CG"],
            ["CD1", "CG", "CD2"],
            ["CG", "CD2", "CE2"],
            ["CE2", "CG", "CD2"],
            ["CE2", "CD2", "CE3"],
            ["CD2", "CE3", "CZ3"],
            ["CE3", "CZ3", "CH2"],
        ],
        "types": {
            "C": "C",
            "CA": "CT1",
            "CB": "CT2",
            "CD1": "CA",
            "CD2": "CPT",
            "CE2": "CPT",
            "CE3": "CAI",
            "CG": "CY",
            "CH2": "CA",
            "CZ2": "CAI",
            "CZ3": "CA",
            "N": "NH1",
            "NE1": "NY",
            "O": "O",
        },
        "z-angles": [
            111.23,
            115.14,
            123.95,
            129.18,
            106.65,
            107.87,
            132.54,
            118.16,
            120.97,
            120.87,
        ],
        "z-dihedrals": [
            122.68,
            180.0,
            90.0,
            -172.81,
            -0.08,
            0.14,
            179.21,
            -0.2,
            0.1,
            0.01,
        ],
        "z-lengths": [1.56, 1.52, 1.44, 1.37, 1.41, 1.37, 1.4, 1.4, 1.4, 1.4],
    },
    "TYR": {
        "atoms": ["CB", "CG", "CD1", "CD2", "CE1", "CE2", "CZ", "OH"],
        "chi_indices": [1, 2],
        "parents": [
            ["N", "C", "CA"],
            ["N", "CA", "CB"],
            ["CA", "CB", "CG"],
            ["CD1", "CB", "CG"],
            ["CB", "CG", "CD1"],
            ["CB", "CG", "CD2"],
            ["CG", "CD1", "CE1"],
            ["CE1", "CE2", "CZ"],
        ],
        "types": {
            "C": "C",
            "CA": "CT1",
            "CB": "CT2",
            "CD1": "CA",
            "CD2": "CA",
            "CE1": "CA",
            "CE2": "CA",
            "CG": "CA",
            "CZ": "CA",
            "N": "NH1",
            "O": "O",
            "OH": "OH1",
        },
        "z-angles": [112.34, 112.94, 120.49, 120.46, 120.4, 120.56, 120.09, 120.25],
        "z-dihedrals": [122.27, 180.0, 90.0, -176.46, -175.49, 175.32, -0.19, -178.98],
        "z-lengths": [1.56, 1.51, 1.41, 1.41, 1.4, 1.4, 1.4, 1.41],
    },
    "VAL": {
        "atoms": ["CB", "CG1", "CG2"],
        "chi_indices": [1],
        "parents": [["N", "C", "CA"], ["N", "CA", "CB"], ["CG1", "CA", "CB"]],
        "types": {
            "C": "C",
            "CA": "CT1",
            "CB": "CT1",
            "CG1": "CT3",
            "CG2": "CT3",
            "N": "NH1",
            "O": "O",
        },
        "z-angles": [111.23, 113.97, 112.17],
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