'Syntax Error: invalid syntax' for no apparent reason

You're missing a close paren in this line:

fi2=0.460*scipy.sqrt(1-(Tr-0.566)**2/(0.434**2)+0.494

There are three ( and only two ).

For problems where it seems to be an error on a line you think is correct, you can often remove/comment the line where the error appears to be and, if the error moves to the next line, there are two possibilities:

• Either both lines have a problem (and the second may have been hidden by the first); or
• The previous line has a problem which is being carried forward.

The most likely case is the second option (even more so if you remove another line and it moves again).

For example, the following Python program twisty_passages.py:

xyzzy = (1 +
plugh = 7

generates the error:

  File "twisty_passages.py", line 2
    plugh = 7
          ^
SyntaxError: invalid syntax

despite the problem clearly being on line 1.

---

In your particular case, that second case is the zctual problem. The parentheses in the line before your error line are unmatched, as per the following annotated snippet:

# open parentheses: 1  2             3
#                   v  v             v
fi2=0.460*scipy.sqrt(1-(Tr-0.566)**2/(0.434**2)+0.494
#                               ^             ^
# close parentheses:            1             2

Depending on what you're trying to achieve, the solution may be as simple as just adding another closing parenthesis at the end, to close off the sqrt function.

I can't say for certain since I don't recognise the expression off the top of my head. Hardly surprising if (assuming PSAT is the enzyme, and the use of the typeMolecule identifier) it's to do with molecular biology - I seem to recall failing Biology consistently in my youth :-)

If you are running the program with python, try running it with python3.