Error in running script, plot is not defined?

[HenryPD96]

I have been trying to run the test.py script to see if it works and I keep getting 'NameError: plot is not defined'?

Can you help me on this please?

I have attached a screenshot of my terminal window and the script which I used.

Many Thanks,

Henry

`#! /usr/bin/python

Boilerplate

import sys
sys.path.insert(1,"C:\Users\Henry\rxnlvl") #

Plot

p = plot([25.0,10.0],vbuf=10.0,hbuf=5.0,bgcolour=None, qualified='sortof')

p + level(energy( 00, 'kjmol'), 1, '1', 0x0)
p + level(energy( -85.5, 'kjmol'), 2, 'EC1', 0x0)
p + level(energy( 244, 'kjmol'), 3, 'TS1a', 0xFF4444)
p + level(energy( 51, 'kjmol'), 3, 'TS1b', 0x0)
p + level(energy( -102, 'kjmol'), 4, 'DC1', 0x0)
p + level(energy( -82, 'kjmol'), 5, '2', 0x0)
p + level(energy( -111, 'kjmol'), 6, 'EC2', 0x0)
p + level(energy( -83, 'kjmol'), 7, 'TS2b', 0x0)
p + level(energy( 18, 'kjmol'), 7, 'TS2a', 0x44FF44)
p + level(energy( -103, 'kjmol'), 8, 'DC2', 0x0)
p + level(energy( 85, 'kjmol'), 9, '3', 0x0)
p + level(energy( 185, 'kjmol'), 10, '4', 0x0)
p + level(energy( 25, 'kjmol'), 11, '5', 0x0)

p + edge( '1', 'EC1', 0x0, 0.4, 'normal')
p + edge( 'EC1', 'TS1a', 0x0, 0.2, 'normal')
p + edge( 'EC1', 'TS1b', 0x0, 0.4, 'normal')
p + edge( 'TS1a', 'DC1', 0x0, 0.2, 'normal')
p + edge( 'TS1b', 'DC1', 0x0, 0.4, 'normal')
p + edge( 'DC1', '2', 0x0, 0.4, 'normal')
p + edge( '2', 'EC2', 0x0, 0.4, 'normal')
p + edge( 'EC2', 'TS2b', 0x0, 0.4, 'normal')
p + edge( 'EC2', 'TS2a', 0x0, 0.2, 'normal')
p + edge( 'TS2a', 'DC2', 0x0, 0.2, 'normal')
p + edge( 'TS2b', 'DC2', 0x0, 0.4, 'normal')
p + edge( 'DC2', '3', 0x0, 0.4, 'normal')
p + edge( '3', '4', 0x0, 0.4, 'normal')
p + edge( '4', '5', 0x0, 0.4, 'normal')

p + baseline(energy( 0.0, 'kjmol'),colour=0x0,mode='dashed',opacity=0.1)

p.write()

[esguerra]

Hi,
It might be a python3 problem. Which python version are you using?

Try running the test with:

python2.7 test.py

[HenryPD96]

Hi, I am using python 2.7 but I do not understand how to use python as I am a beginner. How do I edit the code? I don’t know what the file has to include? Can you advise me on how to run the program, please? Thank you, Henry

…

On Tuesday, January 2, 2018, Mauricio Esguerra ***@***.***> wrote: Hi, It might be a python3 problem. Which python version are you using. Try running the test with: python2.7 test.py — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#2 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AhaTwuRCBeLzsrEMs_dF2XUfk7PKv5jrks5tGkSHgaJpZM4RQpkP> .

[ericchansen]

You can see from your error message that plot isn't defined. You have to import it (from here). For the test script to work as the author intended, you have to edit line 5, which could be one reason (out of many) that it's not working.

You'll probably need some degree of Python knowledge to get this package to do what you'd like it to do. Here's a pretty well written introduction to how import works in Python. I'd start there.

[HenryPD96]

That's great thank you very much, I'll try this. What does the import * on line 6 mean? Do I have to change the * to something else?

I'll have a read of that introduction, if you could advise me further I'd appreciate it very much.

[HenryPD96]

I have done as suggested but now cannot find the outputted file. Here is the code:

`#! /usr/bin/python
import matplotlib.pyplot as plt

Boilerplate

import sys
sys.path.insert(1,"/Users/henry/Desktop/rxnlvl-master/rxnlvl")
from rxnlvl import *

Plot

p = plot([25.0,10.0],vbuf=10.0,hbuf=5.0,bgcolour=None, qualified='sortof')

p + level(energy( 00, 'kjmol'), 1, '1', 0x0)
p + level(energy( -85.5, 'kjmol'), 2, 'EC1', 0x0)
p + level(energy( 244, 'kjmol'), 3, 'TS1a', 0xFF4444)
p + level(energy( 51, 'kjmol'), 3, 'TS1b', 0x0)
p + level(energy( -102, 'kjmol'), 4, 'DC1', 0x0)
p + level(energy( -82, 'kjmol'), 5, '2', 0x0)
p + level(energy( -111, 'kjmol'), 6, 'EC2', 0x0)
p + level(energy( -83, 'kjmol'), 7, 'TS2b', 0x0)
p + level(energy( 18, 'kjmol'), 7, 'TS2a', 0x44FF44)
p + level(energy( -103, 'kjmol'), 8, 'DC2', 0x0)
p + level(energy( 85, 'kjmol'), 9, '3', 0x0)
p + level(energy( 185, 'kjmol'), 10, '4', 0x0)
p + level(energy( 25, 'kjmol'), 11, '5', 0x0)

p + edge( '1', 'EC1', 0x0, 0.4, 'normal')
p + edge( 'EC1', 'TS1a', 0x0, 0.2, 'normal')
p + edge( 'EC1', 'TS1b', 0x0, 0.4, 'normal')
p + edge( 'TS1a', 'DC1', 0x0, 0.2, 'normal')
p + edge( 'TS1b', 'DC1', 0x0, 0.4, 'normal')
p + edge( 'DC1', '2', 0x0, 0.4, 'normal')
p + edge( '2', 'EC2', 0x0, 0.4, 'normal')
p + edge( 'EC2', 'TS2b', 0x0, 0.4, 'normal')
p + edge( 'EC2', 'TS2a', 0x0, 0.2, 'normal')
p + edge( 'TS2a', 'DC2', 0x0, 0.2, 'normal')
p + edge( 'TS2b', 'DC2', 0x0, 0.4, 'normal')
p + edge( 'DC2', '3', 0x0, 0.4, 'normal')
p + edge( '3', '4', 0x0, 0.4, 'normal')
p + edge( '4', '5', 0x0, 0.4, 'normal')

p + baseline(energy( 0.0, 'kjmol'),colour=0x0,mode='dashed',opacity=0.1)

p.write()`

The output from this code is attached - what have I done wrong?

Please help!

Henry
Terminal Saved Output.pdf

[esguerra]

Hi,

That is the expected result.
The format is svg.
If you change the extension of the produced file to svg, you should be able to see it.

[esguerra]

Try this:

python2.7 test.py > energyplot.svg

Then you should be able to see the svg file.

[esguerra]

https://en.wikipedia.org/wiki/Scalable_Vector_Graphics

[ericchansen]

It looks like the write function in the plot class is trying to piece together the contents of an SVG file inside the svgstring variable. It writes svgstring to standard output, which you could redirect to a file. Perhaps try something like python test.py > outputfile.svg. Most operating systems and browsers can display SVG files.