Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

monte carlo sampling #93

Open
wants to merge 2 commits into
base: main
Choose a base branch
from
Open

monte carlo sampling #93

wants to merge 2 commits into from

Conversation

SasmalSubarna
Copy link
Collaborator

No description provided.

@github-actions
Copy link

1.9.6
No protein molecules found in data/hydrophobic_res/e22g.pdb
1.9.6
No protein molecules found
1.9.6
1.9.6
1.0
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
1.9.6
[0.94689588]
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 Fail Fail Pass Pass
derivative1d-ch Fail Fail Fail Fail Fail
derivative_2deg Fail Fail Fail Fail Fail
dipole Fail Fail Fail Fail Fail
hydrophobic_res Fail Fail Fail Fail Fail
integral Fail Fail Pass Fail Fail
trap Pass Pass Pass Pass Pass
invert_matrix Pass Fail Fail Pass Fail
mape Fail Pass Pass Pass Fail
mapping_operator Fail Fail Fail Fail Fail
matrix_factorial Fail Fail Fail Fail Fail
monte_carlo Fail Fail Fail Fail Fail
pair_wise Fail Fail Fail Fail Fail
pi Pass Pass Fail Fail Fail
random_walk Pass Fail Fail Fail Fail
remove-water-ch Fail Fail Fail Fail Fail
remove-water Pass Fail Fail Fail Fail
rmse-ch Pass Pass Pass Pass Pass
rmse Pass Pass Pass Pass Pass
rog Fail Fail Fail Pass Fail
select_frames Pass Pass Pass Pass Pass
sequence Pass Pass Pass Pass Fail
smoke Pass Pass Pass Pass Pass

Test Details

cubes
derivative1d-ch
derivative_2deg
dipole

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'
hydrophobic_res

Exception on response 1

invalid syntax (<string>, line 22)

Exception on response 3

'Topology' object has no attribute 'resid'
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 20)

Exception on response 2

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

Exception on response 3

invalid syntax (<string>, line 22)

Exception on response 4

invalid syntax (<string>, line 19)
matrix_factorial

Exception on response 2

only integer scalar arrays can be converted to a scalar index

Exception on response 3

invalid syntax (<string>, line 19)

Exception on response 4

only integer scalar arrays can be converted to a scalar index
monte_carlo

Exception on response 0

invalid syntax (<string>, line 11)

Exception on response 1

invalid syntax (<string>, line 11)

Exception on response 2

invalid syntax (<string>, line 11)

Exception on response 3

invalid syntax (<string>, line 11)

Exception on response 4

invalid syntax (<string>, line 11)
pair_wise

Exception on response 0

module 'mdtraj' has no attribute 'compute'

Exception on response 1

invalid syntax (<string>, line 22)

Exception on response 2

invalid syntax (<string>, line 24)

Exception on response 3

name 'pair' is not defined

Exception on response 4

invalid syntax (<string>, line 24)
pi

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 1

invalid syntax (<string>, line 20)

Exception on response 3

invalid syntax (<string>, line 22)

Exception on response 4

unsupported operand type(s) for *: 'NoneType' and 'NoneType'
remove-water-ch

Exception on response 0

'NoneType' object has no attribute 'n_atoms'

Exception on response 1

invalid syntax (<string>, line 18)

Exception on response 2

'Topology' object has no attribute 'to_pdb'

Exception on response 3

'Trajectory' object has no attribute 'restrict_'

Exception on response 4

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

Exception on response 1

'NoneType' object has no attribute 'n_atoms'

Exception on response 2

EOL while scanning string literal (<string>, line 19)

Exception on response 3

'NoneType' object has no attribute 'n_atoms'

Exception on response 4

invalid syntax (<string>, line 19)
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 4

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

@github-actions
Copy link

2021.03.5
2021.03.5
2021.03.5
2021.03.5
1.9.6
1.9.6
No protein molecules found
1.9.6
1.9.6
There is only one chain in the pdb file
2021.03.5
2021.03.5
2021.03.5
2021.03.5
2021.03.5
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
Removing solvent
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
lipinski_rule_of_five Fail Fail Fail Fail Fail
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
hydrophobic_res Fail Fail Fail Fail Fail
integral Fail Fail Fail Fail Fail
trap Pass Pass Pass Fail Pass
invert_matrix Pass Fail Pass Pass Fail
iupac2smiles Fail Fail Fail Fail Fail
mape Fail Fail Fail Fail Fail
mapping_operator Fail Fail Fail Fail Fail
matrix_factorial Fail Fail Fail Fail Fail
monte_carlo Fail Fail Fail Fail Fail
pair_wise Fail Fail Fail Fail Fail
pi Pass Pass Fail Pass Pass
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 Pass Fail Fail Fail
select_frames Pass Pass Pass Pass Pass
sequence Pass Pass Pass Pass Pass
smoke Pass Pass Pass Pass Pass

Test Details

lipinski_rule_of_five

Exception on response 0

module 'rdkit.Chem' has no attribute 'rdMolDescriptors'

Exception on response 1

module 'rdkit.Chem' has no attribute 'rdMolDescriptors'

Exception on response 2

module 'rdkit.Chem' has no attribute 'rdMolDescriptors'

Exception on response 3

invalid syntax (<string>, line 26)

Exception on response 4

module 'rdkit.Chem' has no attribute 'rdMolDescriptors'
cubes
derivative1d-ch
derivative_2deg
dipole

Exception on response 0

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'
hydrophobic_res

Exception on response 0

invalid syntax (<string>, line 20)
integral
trap

Exception on response 3

invalid syntax (<string>, line 19)
invert_matrix
iupac2smiles

Exception on response 0

Python argument types in
   rdkit.Chem.rdmolfiles.MolToSmiles(NoneType)
did not match C++ signature:
   MolToSmiles(RDKit::ROMol mol, bool isomericSmiles=True, bool kekuleSmiles=False, int rootedAtAtom=-1, bool canonical=True, bool allBondsExplicit=False, bool allHsExplicit=False, bool doRandom=False)

Exception on response 1

Python argument types in
   rdkit.Chem.rdmolfiles.MolToSmiles(NoneType)
did not match C++ signature:
   MolToSmiles(RDKit::ROMol mol, bool isomericSmiles=True, bool kekuleSmiles=False, int rootedAtAtom=-1, bool canonical=True, bool allBondsExplicit=False, bool allHsExplicit=False, bool doRandom=False)

Exception on response 2

Python argument types in
   rdkit.Chem.rdmolfiles.MolToSmiles(NoneType)
did not match C++ signature:
   MolToSmiles(RDKit::ROMol mol, bool isomericSmiles=True, bool kekuleSmiles=False, int rootedAtAtom=-1, bool canonical=True, bool allBondsExplicit=False, bool allHsExplicit=False, bool doRandom=False)

Exception on response 3

Python argument types in
   rdkit.Chem.rdmolfiles.MolToSmiles(NoneType)
did not match C++ signature:
   MolToSmiles(RDKit::ROMol mol, bool isomericSmiles=True, bool kekuleSmiles=False, int rootedAtAtom=-1, bool canonical=True, bool allBondsExplicit=False, bool allHsExplicit=False, bool doRandom=False)

Exception on response 4

Python argument types in
   rdkit.Chem.rdmolfiles.MolToSmiles(NoneType)
did not match C++ signature:
   MolToSmiles(RDKit::ROMol mol, bool isomericSmiles=True, bool kekuleSmiles=False, int rootedAtAtom=-1, bool canonical=True, bool allBondsExplicit=False, bool allHsExplicit=False, bool doRandom=False)
mape
mapping_operator

Exception on response 0

invalid syntax (<string>, line 19)

Exception on response 1

invalid syntax (<string>, line 19)

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 19)
matrix_factorial

Exception on response 3

expected an indented block (<string>, line 23)
monte_carlo

Exception on response 0

invalid syntax (<string>, line 11)

Exception on response 1

invalid syntax (<string>, line 11)

Exception on response 2

invalid syntax (<string>, line 11)

Exception on response 3

invalid syntax (<string>, line 11)

Exception on response 4

invalid syntax (<string>, line 11)
pair_wise

Exception on response 0

invalid syntax (<string>, line 23)

Exception on response 1

name 'alpha_carbon_coordinates' is not defined

Exception on response 2

name 'pair' is not defined

Exception on response 3

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

Exception on response 4

invalid syntax (<string>, line 22)
pi

Exception on response 2

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

invalid syntax (<string>, line 21)

Exception on response 2

invalid syntax (<string>, line 19)

Exception on response 3

invalid syntax (<string>, line 21)

Exception on response 4

expected an indented block (<string>, line 22)
remove-water-ch

Exception on response 0

'NoneType' object has no attribute 'n_atoms'

Exception on response 1

'Trajectory' object has no attribute 'restrict_'

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

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

Exception on response 0

name 'tra' is not defined

Exception on response 1

invalid syntax (<string>, line 18)

Exception on response 2

'NoneType' object has no attribute 'n_atoms'

Exception on response 3

name 'tra' is not defined

Exception on response 4

'NoneType' object has no attribute 'n_atoms'
rmse-ch
rmse
rog

Exception on response 2

name 'radius' is not defined

Exception on response 3

name 'radius_of_' is not defined
select_frames
sequence
smoke

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers
No reviews
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
1 participant
@SasmalSubarna