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Discretize a continuous space #84

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1.9.6
No protein molecules found in file: data/hydrophobic_res/e22g.pdb
1.9.6
There is only one chain in the pdb file
1.9.6
1.9.6
No protein molecules found
2.0.0
1.9.6
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1.9.6
1.9.6

Test Report

Global Parameters

  • Engine = openai
  • n = 5

Results

Test Run 0 Run 1 Run 2 Run 3 Run 4
cubes Pass Pass Fail Fail Pass
derivative1d-ch Fail Fail Fail Fail Pass
derivative_2deg Fail Pass Fail Fail Fail
dipole Fail Fail Fail Fail Fail
discretize Fail Fail Fail Fail Fail
hydrophobic_res Fail Fail Fail Fail Fail
integral Fail Fail Fail Fail Fail
trap Pass Fail Pass Pass Pass
invert_matrix Fail Fail Fail Pass Pass
mape Pass Fail Fail Fail Fail
mapping_operator Fail Fail Fail Fail Fail
matrix_factorial Fail Fail Fail Fail Fail
pair_wise Fail Fail Fail Fail Fail
pi Pass Fail Fail Fail Fail
random_walk Fail Fail Fail Fail Fail
remove-water-ch Fail Fail Fail Fail Fail
remove-water Fail Fail Fail Fail Fail
rmse-ch Pass Pass Pass Pass Pass
rmse Pass Pass Pass Pass Pass
rog Pass Fail Fail Fail Fail
select_frames Fail Pass Pass Pass Pass
sequence Fail Pass Pass Pass Pass
smoke Pass Pass Pass Pass Pass

Test Details

cubes
derivative1d-ch
derivative_2deg
dipole

Exception on response 1

non-broadcastable output operand with shape (3,1) doesn't match the broadcast shape (3,3)

Exception on response 2

unsupported operand type(s) for -: 'float' and 'NoneType'

Exception on response 3

unsupported operand type(s) for -: 'float' and 'NoneType'

Exception on response 4

unsupported operand type(s) for -: 'float' and 'NoneType'
discretize

Exception on response 0

list indices must be integers or slices, not tuple

Exception on response 1

list indices must be integers or slices, not tuple

Exception on response 2

list indices must be integers or slices, not tuple

Exception on response 3

list indices must be integers or slices, not tuple

Exception on response 4

list indices must be integers or slices, not float
hydrophobic_res

Exception on response 3

invalid syntax (<string>, line 23)
integral
trap

Exception on response 1

invalid syntax (<string>, line 19)
invert_matrix

Exception on response 1

invalid syntax (<string>, line 23)
mape
mapping_operator

Exception on response 0

invalid syntax (<string>, line 19)

Exception on response 1

invalid syntax (<string>, line 20)

Exception on response 2

invalid syntax (<string>, line 19)

Exception on response 3

[Errno 2] No such file or directory: 'water.gro'

Exception on response 4

invalid syntax (<string>, line 19)
matrix_factorial

Exception on response 0

only integer scalar arrays can be converted to a scalar index

Exception on response 1

The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()

Exception on response 4

EOF while scanning triple-quoted string literal (<string>, line 31)
pair_wise

Exception on response 0

unsupported operand type(s) for /: 'NoneType' and 'int'

Exception on response 1

invalid syntax (<string>, line 23)

Exception on response 2

unsupported operand type(s) for /: 'NoneType' and 'int'

Exception on response 3

name 'alpha_carbon_coord' is not defined

Exception on response 4

invalid syntax (<string>, line 23)
pi

Exception on response 1

unsupported operand type(s) for -: 'NoneType' and 'float'

Exception on response 2

unsupported operand type(s) for -: 'NoneType' and 'float'

Exception on response 3

unsupported operand type(s) for -: 'NoneType' and 'float'

Exception on response 4

unsupported operand type(s) for -: 'NoneType' and 'float'
random_walk

Exception on response 0

unsupported operand type(s) for *: 'NoneType' and 'NoneType'

Exception on response 1

expected an indented block (<string>, line 22)

Exception on response 2

unsupported operand type(s) for *: 'NoneType' and 'NoneType'

Exception on response 3

invalid syntax (<string>, line 21)
remove-water-ch

Exception on response 0

'NoneType' object has no attribute 'n_atoms'

Exception on response 1

'NoneType' object has no attribute 'n_atoms'

Exception on response 2

'NoneType' object has no attribute 'n_atoms'

Exception on response 3

'NoneType' object has no attribute 'n_atoms'

Exception on response 4

'Trajectory' object has no attribute 'rest'
remove-water

Exception on response 0

invalid syntax (<string>, line 20)

Exception on response 1

'NoneType' object has no attribute 'n_atoms'

Exception on response 2

'NoneType' object has no attribute 'n_atoms'

Exception on response 3

'NoneType' object has no attribute 'n_atoms'

Exception on response 4

invalid syntax (<string>, line 18)
rmse-ch
rmse
rog

Exception on response 1

name 'radius_of_gy' is not defined

Exception on response 2

name 'radius' is not defined

Exception on response 3

name 'radius' is not defined

Exception on response 4

name 'radius' is not defined
select_frames

Exception on response 0

invalid syntax (<string>, line 20)
sequence
smoke

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1.9.6
No protein molecules found
1.9.6
1.9.6
No protein molecules found
[[1. 1. 1. 1. 1. 1. 1. 1. 1. 1.]
[1. 1. 1. 1. 1. 1. 1. 1. 1. 1.]
[1. 1. 1. 1. 1. 1. 1. 1. 1. 1.]
[1. 1. 1. 1. 1. 1. 1. 1. 1. 1.]
[1. 1. 1. 1. 1. 1. 1. 1. 1. 1.]]
1.9.6
1.9.6
1.9.6
1.9.6
1.9.6
1.9.6
1.9.6
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1.9.6
1.9.6
1.9.6
1.9.6
1.9.6
1.9.6
1.9.6
1.9.6
1.9.6
1.9.6
1.9.6
1.9.6
1.9.6

Test Report

Global Parameters

  • Engine = openai
  • n = 5

Results

Test Run 0 Run 1 Run 2 Run 3 Run 4
cubes Pass Pass Pass Pass Pass
derivative1d-ch Fail Fail Fail Fail Fail
derivative_2deg Fail Fail Fail Fail Fail
dipole Fail Fail Fail Fail Fail
discretize Fail Fail Fail Fail Fail
hydrophobic_res Fail Fail Fail Fail Fail
integral Fail Fail Fail Fail Fail
trap Pass Pass Pass Pass Pass
invert_matrix Pass Fail Fail Fail Fail
mape Fail Fail Pass Fail Fail
mapping_operator Fail Fail Fail Fail Fail
matrix_factorial Fail Fail Fail Fail Fail
pair_wise Fail Fail Fail Fail Fail
pi Pass Fail Pass Pass Pass
random_walk Fail Fail Pass Fail Fail
remove-water-ch Fail Fail Fail Fail Fail
remove-water Fail Fail Fail Fail Pass
rmse-ch Pass Pass Pass Pass Pass
rmse Pass Pass Pass Pass Pass
rog Fail Fail Fail Pass Pass
select_frames Pass Pass Pass Pass Pass
sequence Fail Fail Fail Pass Pass
smoke Pass Pass Pass Pass Pass

Test Details

cubes
derivative1d-ch

Exception on response 3

invalid syntax (<string>, line 21)
derivative_2deg
dipole

Exception on response 0

unsupported operand type(s) for -: 'float' and 'NoneType'

Exception on response 1

unsupported operand type(s) for -: 'float' and 'NoneType'

Exception on response 2

unsupported operand type(s) for -: 'float' and 'NoneType'

Exception on response 3

unsupported operand type(s) for -: 'float' and 'NoneType'

Exception on response 4

unsupported operand type(s) for -: 'float' and 'NoneType'
discretize

Exception on response 0

invalid syntax (<string>, line 18)

Exception on response 1

can't multiply sequence by non-int of type 'float'

Exception on response 2

unsupported operand type(s) for /: 'float' and 'list'

Exception on response 3

unsupported operand type(s) for /: 'float' and 'list'

Exception on response 4

invalid syntax (<string>, line 18)
hydrophobic_res

Exception on response 1

invalid syntax (<string>, line 23)

Exception on response 4

invalid syntax (<string>, line 23)
integral
trap
invert_matrix
mape
mapping_operator

Exception on response 0

expected an indented block (<string>, line 19)

Exception on response 1

expected an indented block (<string>, line 21)

Exception on response 2

expected an indented block (<string>, line 20)

Exception on response 3

invalid syntax (<string>, line 19)

Exception on response 4

invalid syntax (<string>, line 18)
matrix_factorial

Exception on response 4

EOF while scanning triple-quoted string literal (<string>, line 31)
pair_wise

Exception on response 0

name 'n' is not defined

Exception on response 1

unsupported operand type(s) for /: 'NoneType' and 'int'

Exception on response 2

name 'itertools' is not defined

Exception on response 3

invalid syntax (<string>, line 22)

Exception on response 4

unsupported operand type(s) for /: 'NoneType' and 'int'
pi

Exception on response 1

unsupported operand type(s) for -: 'NoneType' and 'float'
random_walk

Exception on response 0

unsupported operand type(s) for /: 'float' and 'module'

Exception on response 1

expected an indented block (<string>, line 22)

Exception on response 3

unsupported operand type(s) for *: 'NoneType' and 'NoneType'

Exception on response 4

invalid syntax (<string>, line 21)
remove-water-ch

Exception on response 0

'NoneType' object has no attribute 'n_atoms'

Exception on response 1

'Trajectory' object has no attribute 'atom'

Exception on response 2

'Trajectory' object has no attribute 'rest'

Exception on response 3

EOL while scanning string literal (<string>, line 17)

Exception on response 4

'NoneType' object has no attribute 'n_atoms'
remove-water

Exception on response 0

invalid syntax (<string>, line 20)

Exception on response 1

name 'tra' is not defined

Exception on response 2

'NoneType' object has no attribute 'n_atoms'

Exception on response 3

EOL while scanning string literal (<string>, line 17)
rmse-ch
rmse
rog

Exception on response 0

name 'radius' is not defined

Exception on response 1

name 'radius' is not defined
select_frames
sequence
smoke

@whitead whitead requested a review from ziyueyang37 September 21, 2021 02:40
ziyueyang37
ziyueyang37 reviewed Sep 21, 2021
View reviewed changes
data/discretize/discretize.py
import numpy as np

def discretize(location, grid):
return tuple(int(np.digitize(l, g)) for l, g in zip(location, grid))
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  1. Is the grid necessarily to be int? If not, the test is not exhausted. Otherwise should modify the description to specify the grid is int.
  2. Take a look at this https://numpy.org/doc/stable/reference/generated/numpy.digitize.html. Maybe should specify right argument. Consider the edge case that the location falls exactly on grid point, and the grid array is increasing/decreasing.

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