NameError: name 'atom2mass' is not defined

[MarcIsak]

Hi,

I am using Python 3.6.15 in Ubuntu 20.04 (Running inside a Docker container). The packages that I use are listed in the attached text file
packages_python.txt

I want to generate evidence/msms/peptide files from a Prosit spectral library that I have. However, when I run the following command:

python3.6 postprocess/main.py prosit postprocess/parameters.json

I get the error NameError: name 'atom2mass' is not defined. The full error log:

Using TensorFlow backend.
/usr/local/lib/python3.6/dist-packages/tensorflow/python/framework/dtypes.py:517: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_qint8 = np.dtype([("qint8", np.int8, 1)])
/usr/local/lib/python3.6/dist-packages/tensorflow/python/framework/dtypes.py:518: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_quint8 = np.dtype([("quint8", np.uint8, 1)])
/usr/local/lib/python3.6/dist-packages/tensorflow/python/framework/dtypes.py:519: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_qint16 = np.dtype([("qint16", np.int16, 1)])
/usr/local/lib/python3.6/dist-packages/tensorflow/python/framework/dtypes.py:520: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_quint16 = np.dtype([("quint16", np.uint16, 1)])
/usr/local/lib/python3.6/dist-packages/tensorflow/python/framework/dtypes.py:521: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_qint32 = np.dtype([("qint32", np.int32, 1)])
/usr/local/lib/python3.6/dist-packages/tensorflow/python/framework/dtypes.py:526: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
np_resource = np.dtype([("resource", np.ubyte, 1)])
Traceback (most recent call last):
File "postprocess/main.py", line 175, in
class Spectrum:
File "postprocess/main.py", line 219, in Spectrum
for aa, formula in aa2formula.items()}
File "postprocess/main.py", line 219, in
for aa, formula in aa2formula.items()}
File "postprocess/main.py", line 218, in
aa2mass = {aa: (sum([atom2mass[atom] * cnt for atom, cnt in formula.items()]) - 2 * atom2mass['H'] - atom2mass['O'])
NameError: name 'atom2mass' is not defined

Any idea what could be wrong here?

Best,

Marc

[AnStaes]

Hi,
I have the same problem. Any solution for this?

Thank you!
An

[temaia]

We ended up solving the error by adding a pre-calculated aa2mass object to the script and commenting out the original list comprehension line used to calculate aa2mass.