While reproducing virtual_screening_pipeline, I faced with this error:
# compute descriptors as an array
whales_template, lab = do_whales.whales_from_mol(template)
# convert the arrays into a pandas dataframe
df_whales_template = pd.DataFrame(whales_template.reshape(-1, len(whales_template)),index=['template'],columns=lab)
df_whales_template
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
Input In [26], in <cell line: 2>()
1 # compute descriptors as an array
----> 2 whales_template, lab = do_whales.whales_from_mol(template)
3 # convert the arrays into a pandas dataframe
4 df_whales_template = pd.DataFrame(whales_template.reshape(-1, len(whales_template)),index=['template'],columns=lab)
File ~/Documents/scaffold_hopping_whales/code/do_whales.py:40, in whales_from_mol(mol, charge_threshold, do_charge, property_name)
37 coords, w, err = mol_properties.get_coordinates_and_prop(mol, property_name, do_charge)
38 if err == 0: # no errors in charge
39 # does descriptors
---> 40 x, lab = do_lcd(coords, w, charge_threshold)
41 else:
42 x = np.full((33,), -999.0)
File ~/Documents/scaffold_hopping_whales/code/do_whales.py:87, in do_lcd(coords, w, thr)
84 # applies sign
85 res = apply_sign(w, res, thr)
---> 87 x_all, lab_all = extract_lcm(res) # MDs and labels
89 return x_all, lab_all
File ~/Documents/scaffold_hopping_whales/code/do_whales.py:132, in extract_lcm(data, start, end, step, lab_string)
130 # Calculates percentiles according to the specified settings
131 perc = range(start, end + 1, step)
--> 132 x = np.percentile(data, list(perc), axis=0)
133 x = np.concatenate((x[:, 0], x[:, 1], x[:, 2]), axis=0) # Flattens preserving the ordering
135 # rounds the descriptors to the third decimal place
File <__array_function__ internals>:180, in percentile(*args, **kwargs)
File ~/opt/anaconda3/envs/td_test/lib/python3.8/site-packages/numpy/lib/function_base.py:4166, in percentile(a, q, axis, out, overwrite_input, method, keepdims, interpolation)
4164 if not _quantile_is_valid(q):
4165 raise ValueError("Percentiles must be in the range [0, 100]")
-> 4166 return _quantile_unchecked(
4167 a, q, axis, out, overwrite_input, method, keepdims)
File ~/opt/anaconda3/envs/td_test/lib/python3.8/site-packages/numpy/lib/function_base.py:4424, in _quantile_unchecked(a, q, axis, out, overwrite_input, method, keepdims)
4416 def _quantile_unchecked(a,
4417 q,
4418 axis=None,
(...)
4421 method="linear",
4422 keepdims=False):
4423 """Assumes that q is in [0, 1], and is an ndarray"""
-> 4424 r, k = _ureduce(a,
4425 func=_quantile_ureduce_func,
4426 q=q,
4427 axis=axis,
4428 out=out,
4429 overwrite_input=overwrite_input,
4430 method=method)
4431 if keepdims:
4432 return r.reshape(q.shape + k)
File ~/opt/anaconda3/envs/td_test/lib/python3.8/site-packages/numpy/lib/function_base.py:3725, in _ureduce(a, func, **kwargs)
3722 else:
3723 keepdim = (1,) * a.ndim
-> 3725 r = func(a, **kwargs)
3726 return r, keepdim
File ~/opt/anaconda3/envs/td_test/lib/python3.8/site-packages/numpy/lib/function_base.py:4593, in _quantile_ureduce_func(a, q, axis, out, overwrite_input, method)
4591 else:
4592 arr = a.copy()
-> 4593 result = _quantile(arr,
4594 quantiles=q,
4595 axis=axis,
4596 method=method,
4597 out=out)
4598 return result
File ~/opt/anaconda3/envs/td_test/lib/python3.8/site-packages/numpy/lib/function_base.py:4710, in _quantile(arr, quantiles, axis, method, out)
4708 result_shape = virtual_indexes.shape + (1,) * (arr.ndim - 1)
4709 gamma = gamma.reshape(result_shape)
-> 4710 result = _lerp(previous,
4711 next,
4712 gamma,
4713 out=out)
4714 if np.any(slices_having_nans):
4715 if result.ndim == 0 and out is None:
4716 # can't write to a scalar
File ~/opt/anaconda3/envs/td_test/lib/python3.8/site-packages/numpy/lib/function_base.py:4529, in _lerp(a, b, t, out)
4527 diff_b_a = subtract(b, a)
4528 # asanyarray is a stop-gap until gh-13105
-> 4529 lerp_interpolation = asanyarray(add(a, diff_b_a * t, out=out))
4530 subtract(b, diff_b_a * (1 - t), out=lerp_interpolation, where=t >= 0.5)
4531 if lerp_interpolation.ndim == 0 and out is None:
File ~/opt/anaconda3/envs/td_test/lib/python3.8/site-packages/numpy/matrixlib/defmatrix.py:218, in matrix.__mul__(self, other)
215 def __mul__(self, other):
216 if isinstance(other, (N.ndarray, list, tuple)) :
217 # This promotes 1-D vectors to row vectors
--> 218 return N.dot(self, asmatrix(other))
219 if isscalar(other) or not hasattr(other, '__rmul__') :
220 return N.dot(self, other)
File <__array_function__ internals>:180, in dot(*args, **kwargs)
ValueError: shapes (11,3) and (11,1) not aligned: 3 (dim 1) != 11 (dim 0)
I made no changes in code and tried a couple of different molecules but this error didn't disappear.
While reproducing virtual_screening_pipeline, I faced with this error:
I made no changes in code and tried a couple of different molecules but this error didn't disappear.