compute the number of hbonds in pdb

[wpena1]

loada pdb file and computes number of hydrogen bonds

[github-actions]

2021.03.5
2021.03.5
2021.03.5
2021.03.5
2021.03.5
1.9.6
1.9.6
1.9.6
No protein molecules found
1.9.6
1.9.6
1.9.6
No protein molecules found
2021.03.5
2021.03.5
2021.03.5
2021.03.5
2021.03.5
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
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
hbonds	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	Fail	Fail	Fail	Fail	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
pair_wise	Fail	Fail	Fail	Fail	Fail
pi	Fail	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	Pass
rmse-ch	Pass	Pass	Pass	Pass	Pass
rmse	Pass	Pass	Pass	Pass	Pass
rog	Fail	Fail	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

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

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 1

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

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'

hbonds

Exception on response 0

invalid syntax (<string>, line 20)

Exception on response 1

invalid syntax (<string>, line 20)

Exception on response 2

invalid syntax (<string>, line 20)

Exception on response 3

name 'angle_' is not defined

Exception on response 4

module 'mdtraj' has no attribute 'baker_hub'

hydrophobic_res

Exception on response 0

invalid syntax (<string>, line 23)

integral

Exception on response 4

invalid syntax (<string>, line 21)

trap

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

expected an indented block (<string>, line 25)

Exception on response 4

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

matrix_factorial

Exception on response 0

only integer scalar arrays can be converted to a scalar index

Exception on response 4

only integer scalar arrays can be converted to a scalar index

pair_wise

Exception on response 0

invalid syntax (<string>, line 23)

Exception on response 1

invalid syntax (<string>, line 23)

Exception on response 2

invalid syntax (<string>, line 22)

Exception on response 3

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

Exception on response 4

invalid syntax (<string>, line 23)

pi

Exception on response 0

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

unexpected EOF while parsing (<string>, line 17)

random_walk

Exception on response 1

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

Exception on response 2

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

Exception on response 3

invalid syntax (<string>, line 20)

Exception on response 4

invalid syntax (<string>, line 20)

remove-water-ch

Exception on response 0

'Trajectory' object has no attribute 'restrict_'

Exception on response 1

'Trajectory' object has no attribute 'rest'

Exception on response 2

'NoneType' object has no attribute 'n_atoms'

Exception on response 3

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

Exception on response 4

invalid syntax (<string>, line 20)

remove-water

Exception on response 1

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

Exception on response 2

name 'tra' is not defined

Exception on response 3

'NoneType' object has no attribute 'n_atoms'

rmse-ch

rmse

rog

Exception on response 0

name 'radius' is not defined

Exception on response 1

name 'radius' 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_of_' is not defined

select_frames

sequence

smoke