rigid_group_atom_positions ========================== 各个氨基酸中原子相对于8个刚体变换群(rigid_group)的位置。 8种group为 - 0 - backbone-group 氨基酸 :math:`N-C\alpha-C-C\beta` 原子之间的扭转角 `backbone` 对应主链刚体变换群，CA为坐标原点，C在x轴正向，N在X-Y平面。 - 1 - pre-omega-group 氨基酸 :math:`N_i-C\alpha_i-N_{i-1}-C\alpha_{i-1}` 原子之间的扭转角 `pre-omega` 对应刚体变换群。 - 2 - phi-group 氨基酸 :math:`C_i-C\alpha_i-N_i-C_{i+1}` 原子之间的扭转角 `phi` 对应刚体变换群。 - 3 - psi-group 氨基酸 :math:`N_{i-1}-C_i-C\alpha_i-N_i` 原子之间的扭转角 `psi` 对应刚体变换群。 - 4 - chi1-group - 5 - chi2-group - 6 - chi3-group - 7 - chi4-group chi1,2,3,4-group 在 `chi_angle_atoms` 相应氨基酸的相应扭转角中，扭转角由四个原子[A,B,C,D]的坐标确定，中间两个原子B,C为旋转轴，在x轴上；第3个原子C为坐标原点，原子B在x负半轴；第1个原子A在xy平面，从而确定该坐标下第4个原子坐标。 pre-omega-group到backbone-group的坐标系相同，坐标变换为恒等变换。 phi-group到backbone-group，psi-group到backbone-group，chi1-group到backbone-group，chi2-group到chi1-group，chi3-group到chi2-group，chi4-group到chi3-group的坐标变换矩阵需要通过_make_rigid_transformation_4x4函数计算得到。 +------------+------+-------+---------------------------+ | amino acid | Atom | group | positions | +============+======+=======+===========================+ || || N || 0 || (-0.525, 1.363, 0.0) | || || CA || 0 || (0.0, 0.0, 0.0) | || ALA || C || 0 || (1.526, -0.0, -0.0) | || || CB || 0 || (-0.529, -0.774, -1.205) | || || O || 3 || (0.627, 1.062, 0.0) | +------------+------+-------+---------------------------+ || || N || 0 || (-0.524, 1.363, 0.0) | || || CA || 0 || (0.0, 0.0, 0.0) | || || C || 0 || (1.525, -0.0, -0.0) | || || CB || 0 || (-0.524, -0.778, -1.209) | || || O || 3 || (0.627, 1.062, 0.0) | || || CG || 4 || (0.616, 1.39, -0.0) | || ARG || CD || 5 || (0.564, 1.414, 0.0) | || || NE || 6 || (0.539, 1.357, -0.0) | || || NH1 || 7 || (0.206, 2.301, 0.0) | || || NH2 || 7 || (2.078, 0.978, -0.0) | || || CZ || 7 || (0.758, 1.093, -0.0) | +------------+------+-------+---------------------------+ || || N || 0 || (-0.536, 1.357, 0.0) | || || CA || 0 || (0.0, 0.0, 0.0) | || || C || 0 || (1.526, -0.0, -0.0) | || || CB || 0 || (-0.531, -0.787, -1.2) | || || O || 3 || (0.625, 1.062, 0.0) | || ASN || CG || 4 || (0.584, 1.399, 0.0) | || || ND2 || 5 || (0.593, -1.188, 0.001) | || || OD1 || 5 || (0.633, 1.059, 0.0) | +------------+------+-------+---------------------------+ || || N || 0 || (-0.525, 1.362, -0.0) | || || CA || 0 || (0.0, 0.0, 0.0) | || || C || 0 || (1.527, 0.0, -0.0) | || || CB || 0 || (-0.526, -0.778, -1.208) | || ASP || O || 3 || (0.626, 1.062, -0.0) | || || CG || 4 || (0.593, 1.398, -0.0) | || || OD1 || 5 || (0.61, 1.091, 0.0) | || || OD2 || 5 || (0.592, -1.101, -0.003) | +------------+------+-------+---------------------------+ || || N || 0 || (-0.525, 1.362, -0.0) | || || CA || 0 || (0.0, 0.0, 0.0) | || CYS || C || 0 || (1.524, 0.0, -0.0) | || || CB || 0 || (-0.519, -0.773, -1.212) | || || O || 3 || (0.625, 1.062, -0.0) | || || SG || 4 || (0.728, 1.653, 0.0) | +------------+------+-------+---------------------------+ || || N || 0 || (-0.525, 1.362, -0.0) | || || CA || 0 || (0.0, 0.0, 0.0) | || || C || 0 || (1.524, 0.0, -0.0) | || || CB || 0 || (-0.519, -0.773, -1.212) | || GLN || O || 3 || (0.625, 1.062, -0.0) | || || CG || 4 || (0.584, 1.399, 0.0) | || || CD || 5 || (0.587, 1.399, -0.000) | || || NE2 || 6 || (0.593, -1.189, -0.001) | || || OE1 || 6 || (0.634, 1.060, 0.000) | +------------+------+-------+---------------------------+ || || N || 0 || (-0.528, 1.361, 0.000) | || || CA || 0 || (0.0, 0.0, 0.0) | || || C || 0 || (1.526, -0.000, -0.000) | || || CB || 0 || (-0.526, -0.781, -1.207) | || GLU || O || 3 || (0.626, 1.062, 0.000) | || || CG || 4 || (0.615, 1.392, 0.000) | || || CD || 5 || (0.589, -1.104, -0.001) | || || OE1 || 6 || (0.607, 1.095, -0.000) | || || OE2 || 6 || (0.589, -1.104, -0.001) | +------------+------+-------+---------------------------+ || || N || 0 || (-0.528, 1.361, 0.000) | || || CA || 0 || (0.0, 0.0, 0.0) | || GLY || C || 0 || (1.526, -0.000, -0.000) | || || O || 3 || (0.626, 1.062, 0.000) | +------------+------+-------+---------------------------+ || || N || 0 || (-0.527, 1.361, 0.000) | || || CA || 0 || (0.0, 0.0, 0.0) | || || C || 0 || (1.526, -0.000, -0.000) | || || CB || 0 || (-0.526, -0.781, -1.207) | || HIS || O || 3 || (0.626, 1.062, 0.000) | || || CG || 4 || (0.615, 1.392, 0.000) | || || CD2 || 5 || (0.607, 1.095, -0.000) | || || ND1 || 6 || (0.589, -1.104, -0.001) | || || CE1 || 5 || (2.030, 0.851, 0.002) | || || NE2 || 5 || (2.145, -0.466, 0.004) | +------------+------+-------+---------------------------+ || || N || 0 || (-0.493, 1.373, -0.000) | || || CA || 0 || (0.0, 0.0, 0.0) | || || C || 0 || (1.526, -0.000, -0.000) | || || CB || 0 || (-0.536, -0.793, -1.213) | || ILE || O || 3 || (0.627, 1.062, -0.000) | || || CG1 || 4 || (0.534, 1.437, -0.000) | || || CG2 || 3 || (0.540, -0.785, -1.199) | || || CD1 || 5 || (0.619, 1.391, 0.000) | +------------+------+-------+---------------------------+ || || N || 0 || (-0.520, 1.363, 0.000) | || || CA || 0 || (0.0, 0.0, 0.0) | || || C || 0 || (1.525, -0.000, -0.000) | || || CB || 0 || (-0.522, -0.773, -1.214) | || LEU || O || 3 || (0.625, 1.063, -0.000) | || || CG || 4 || (0.678, 1.371, 0.000) | || || CD1 || 5 || (0.530, 1.430, -0.000) | || || CD2 || 5 || (0.535, -0.774, 1.200) | +------------+------+-------+---------------------------+ || || N || 0 || (-0.526, 1.362, -0.000) | || || CA || 0 || (0.0, 0.0, 0.0) | || || C || 0 || (1.526, 0.000, 0.000) | || || CB || 0 || (-0.524, -0.778, -1.208) | || LYS || O || 3 || (0.626, 1.062, -0.000) | || || CG || 4 || (0.619, 1.390, 0.000) | || || CD || 5 || (0.559, 1.417, 0.000) | || || CE || 6 || (0.560, 1.416, 0.000) | || || NZ || 7 || (0.554, 1.387, 0.000) | +------------+------+-------+---------------------------+ || || N || 0 || (-0.521, 1.364, -0.000) | || || CA || 0 || (0.0, 0.0, 0.0) | || || C || 0 || (1.525, 0.000, 0.000) | || || CB || 0 || (-0.523, -0.776, -1.210) | || MET || O || 3 || (0.625, 1.062, -0.000) | || || CG || 4 || (0.613, 1.391, -0.000) | || || SD || 5 || (0.703, 1.695, 0.000) | || || CE || 6 || (0.320, 1.786, -0.000) | +------------+------+-------+---------------------------+ || || N || 0 || (-0.518, 1.363, 0.000) | || || CA || 0 || (0.0, 0.0, 0.0) | || || C || 0 || (1.524, 0.000, -0.000) | || || CB || 0 || (-0.525, -0.776, -1.212) | || PHE || O || 3 || (0.626, 1.062, -0.000) | || || CG || 4 || (0.607, 1.377, 0.000) | || || CD1 || 5 || (0.709, 1.195, -0.000) | || || CD2 || 5 || (0.706, -1.196, 0.000) | || || CE1 || 5 || (2.102, 1.198, -0.000) | || || CE2 || 5 || (2.098, -1.201, -0.000) | || || CZ || 5 || (2.794, -0.003, -0.001) | +------------+------+-------+---------------------------+ || || N || 0 || (-0.566, 1.351, -0.000) | || || CA || 0 || (0.0, 0.0, 0.0) | || || C || 0 || (1.527, -0.000, 0.000) | || PRO || CB || 0 || (-0.546, -0.611, -1.293) | || || O || 3 || (0.621, 1.066, 0.000) | || || CG || 4 || (0.382, 1.445, 0.0) | || || CD || 5 || (0.477, 1.424, 0.0) | +------------+------+-------+---------------------------+ || || N || 0 || (-0.529, 1.360, -0.000) | || || CA || 0 || (0.0, 0.0, 0.0) | || || C || 0 || (1.525, -0.000, -0.000) | || SER || CB || 0 || (-0.518, -0.777, -1.211) | || || O || 3 || (0.626, 1.062, -0.000) | || || CG || 4 || (0.503, 1.325, 0.000) | +------------+------+-------+---------------------------+ || || N || 0 || (-0.517, 1.364, 0.000) | || || CA || 0 || (0.0, 0.0, 0.0) | || || C || 0 || (1.526, 0.000, -0.000) | || THR || CB || 0 || (-0.516, -0.793, -1.215) | || || O || 3 || (0.626, 1.062, 0.000) | || || CG2 || 4 || (0.550, -0.718, -1.228) | || || OG1 || 4 || (0.472, 1.353, 0.000) | +------------+------+-------+---------------------------+ || || N || 0 || (-0.521, 1.363, 0.000) | || || CA || 0 || (0.0, 0.0, 0.0) | || || C || 0 || (1.525, -0.000, 0.000) | || || CB || 0 || (-0.523, -0.776, -1.212) | || || O || 3 || (0.627, 1.062, 0.000) | || || CG || 4 || (0.609, 1.370, -0.000) | || TRP || CD1 || 5 || (0.824, 1.091, 0.000) | || || CD2 || 5 || (0.854, -1.148, -0.005) | || || CE2 || 5 || (2.186, -0.678, -0.007) | || || CE3 || 5 || (0.622, -2.530, -0.007) | || || NE1 || 5 || (2.140, 0.690, -0.004) | || || CH2 || 5 || (3.028, -2.890, -0.013) | || || CZ2 || 5 || (3.283, -1.543, -0.011) | || || CZ3 || 5 || (1.715, -3.389, -0.011) | +------------+------+-------+---------------------------+ || || N || 0 || (-0.522, 1.362, 0.000) | || || CA || 0 || (0.0, 0.0, 0.0) | || || C || 0 || (1.524, -0.000, -0.000) | || || CB || 0 || (-0.522, -0.776, -1.213) | || || O || 3 || (0.627, 1.062, -0.000) | || || CG || 4 || (0.607, 1.382, -0.000) | || TYR || CD1 || 5 || (0.716, 1.195, -0.000) | || || CD2 || 5 || (0.713, -1.194, -0.001) | || || CE1 || 5 || (2.107, 1.200, -0.002) | || || CE2 || 5 || (2.104, -1.201, -0.003) | || || OH || 5 || (4.168, -0.002, -0.005) | || || CZ || 5 || (2.791, -0.001, -0.003) | +------------+------+-------+---------------------------+ || || N || 0 || (-0.494, 1.373, -0.000) | || || CA || 0 || (0.000, 0.000, 0.000) | || || C || 0 || (1.527, -0.000, -0.000) | || VAL || CB || 3 || (-0.533, -0.795, -1.213) | || || O || 4 || (0.627, 1.062, -0.000) | || || CG1 || 5 || (0.540, 1.429, -0.000) | || || CG2 || 5 || (0.533, -0.776, 1.203) | +------------+------+-------+---------------------------+