diff --git a/pyaptamer/pseaac/_props.py b/pyaptamer/pseaac/_props.py index a05c4b90..e8d4f2e6 100644 --- a/pyaptamer/pseaac/_props.py +++ b/pyaptamer/pseaac/_props.py @@ -608,473 +608,6 @@ def aa_props(prop_indices=None, type="numpy", normalize=True): ] ).T # shape (20, 21) - if normalize: - props = np.array( - [ - [ - 0.636, - 0.298, - -0.924, - -0.759, - 1.221, - 0.493, - -0.41, - 1.416, - -1.539, - 1.088, - 0.657, - -0.8, - 0.123, - -0.872, - -2.596, - -0.185, - -0.051, - 1.108, - 0.831, - 0.267, - ], - [ - -0.152, - -0.418, - 1.713, - 1.713, - -1.218, - 0.115, - -0.152, - -0.845, - 1.713, - -0.845, - -0.578, - 0.221, - 0.115, - 0.221, - 1.713, - 0.274, - -0.099, - -0.685, - -1.697, - -1.111, - ], - [ - -1.592, - -0.53, - -0.131, - 0.334, - 0.931, - -2.057, - 0.632, - -0.198, - 0.334, - -0.198, - 0.4, - -0.164, - -0.696, - 0.3, - 1.263, - -1.061, - -0.596, - -0.662, - 2.226, - 1.462, - ], - [ - 0.329, - 1.417, - -0.487, - 1.417, - -1.303, - 0.057, - -0.215, - 1.036, - 1.689, - -0.922, - -0.65, - 0.166, - -0.704, - 0.166, - 1.689, - 0.22, - -0.16, - -0.759, - -1.792, - -1.194, - ], - [ - 1.755, - 0.429, - -1.365, - 0.195, - -0.585, - 1.365, - -1.287, - 0.039, - 0.819, - 1.287, - -1.521, - -0.039, - -0.429, - -0.507, - -0.351, - 1.131, - 0.507, - 0.897, - -1.755, - -0.585, - ], - [ - -0.659, - -1.007, - 0.593, - -1.633, - 0.697, - -0.416, - -0.277, - 1.671, - -0.798, - 0.836, - 0.176, - -1.32, - -1.355, - -0.068, - -0.52, - -0.277, - 0.628, - 2.297, - 0.628, - 0.802, - ], - [ - 0.735, - -0.968, - 1.372, - -1.341, - 1.108, - -0.023, - -0.704, - 1.273, - -0.166, - 1.141, - 0.955, - -0.924, - -0.77, - -1.429, - -1.924, - -0.276, - 0.021, - 1.196, - 0.746, - -0.023, - ], - [ - 0.219, - 1.552, - -0.811, - 0.69, - -1.427, - 0.575, - -0.314, - -1.42, - 1.335, - -1.554, - -1.281, - 1.087, - 1.08, - 0.662, - 0.212, - 0.697, - 0.686, - -1.247, - 0.117, - -0.857, - ], - [ - 0.56, - 1.13, - -1.484, - 2.509, - -0.975, - 0.933, - -0.696, - -0.722, - 1.645, - -0.181, - -0.991, - 0.158, - -0.067, - 0.076, - 0.592, - 0.13, - 0.114, - -0.453, - -1.411, - -0.867, - ], - [ - -0.479, - -0.663, - 0.09, - -0.654, - 1.271, - -1.153, - -0.479, - 1.516, - 0.195, - 0.658, - 0.221, - -1.161, - 1.183, - -1.24, - -0.496, - -1.179, - -1.179, - 0.396, - 2.058, - 1.096, - ], - [ - 0.253, - -0.338, - -0.836, - -0.061, - -0.836, - 0.548, - -0.522, - -0.541, - 0.548, - -0.947, - -0.928, - 0.345, - 3.703, - -0.227, - 0.031, - 0.474, - 0.696, - -0.725, - -0.614, - -0.024, - ], - [ - -0.223, - 1.256, - -0.163, - -0.042, - -0.797, - 1.588, - -0.254, - -1.008, - -0.495, - -1.189, - -1.219, - 1.98, - 2.04, - -0.133, - 0.048, - 0.743, - 0.169, - -1.159, - -0.948, - -0.193, - ], - [ - -0.277, - -1.356, - 0.311, - -1.037, - 0.532, - -1.037, - -0.253, - 1.905, - -0.816, - 0.655, - 0.385, - -1.062, - -1.552, - -0.203, - -0.253, - -0.522, - 0.213, - 1.905, - 1.243, - 1.219, - ], - [ - -0.187, - -0.393, - 0.397, - -2.352, - 1.221, - -0.393, - -0.496, - 1.805, - -0.703, - 0.843, - 0.947, - -1.012, - -0.909, - 0.569, - -1.184, - -0.84, - 0.74, - 1.359, - 0.397, - 0.191, - ], - [ - -0.402, - -1.503, - 0.469, - -1.119, - 0.443, - -1.273, - 0.161, - 1.237, - -0.812, - 0.52, - 0.085, - -1.119, - -1.631, - 0.315, - -0.095, - -0.479, - 0.622, - 1.211, - 1.775, - 1.595, - ], - [ - -0.078, - -0.667, - -2.081, - -0.562, - -0.401, - -0.097, - 0.907, - -0.066, - 2.24, - -0.091, - -0.24, - -0.444, - 0.108, - -0.295, - 2.872, - -0.277, - -0.289, - -0.103, - -0.147, - -0.289, - ], - [ - 1.728, - -0.604, - -0.7, - -1.671, - -1.152, - 1.25, - -0.292, - -0.273, - -0.47, - -0.273, - -0.082, - 0.008, - 2.445, - -0.534, - 1.371, - 0.333, - -0.097, - 0.097, - 0.218, - -1.302, - ], - [ - -0.025, - -1.322, - -1.322, - -1.249, - 1.601, - -0.81, - -0.335, - 1.291, - -1.194, - 1.382, - 0.852, - -0.847, - 0.871, - -0.189, - -0.993, - -0.573, - -0.098, - 0.779, - 1.273, - 0.907, - ], - [ - 0.549, - -1.863, - 0.137, - 0.173, - -2.131, - 0.111, - 0.152, - 0.131, - 0.853, - 0.147, - -0.946, - 1.167, - 0.229, - 1.059, - 2.172, - 0.147, - 0.126, - 0.085, - -1.116, - -1.183, - ], - [ - -0.099, - 1.717, - -0.227, - -0.277, - 2.339, - -0.385, - 0.009, - -0.223, - -0.857, - -0.231, - 0.82, - -1.081, - -0.289, - -0.976, - -1.996, - -0.358, - -0.281, - -0.18, - 1.431, - 1.145, - ], - [ - -0.2, - 1.276, - -0.28, - -0.348, - 2.725, - -0.052, - 0.578, - -0.28, - -0.602, - -0.28, - 0.538, - -0.576, - -0.254, - -0.482, - -1.126, - -0.71, - -0.495, - -0.254, - 2.215, - -1.394, - ], - ] - ).T # shape (20, 21) if prop_indices is not None: props = props[:, prop_indices] @@ -1082,9 +615,12 @@ def aa_props(prop_indices=None, type="numpy", normalize=True): else: selected_names = prop_names + if normalize: + props = (props - props.mean(axis=0)) / props.std(axis=0) + if type == "pandas": return pd.DataFrame(props, index=aa_order, columns=selected_names) elif type == "numpy": return props else: - raise ValueError("type must be 'numpy' or 'pandas'") + raise ValueError("type must be 'numpy' or 'pandas'") \ No newline at end of file