🌐 Mailman 3 September 2019 - Tutor - python.org

Scripting Calligra sheets with Python
by Jim Byrnes Jan. 31, 2022

Jan. 31, 2022

I am trying to script Calligra Sheets (formerly KSpread) with python. I have gotten some of the included example scripts to run so I know python scripting is running. I found the following snippet on their website: import KSpread sheet = KSpread.view().sheet() # swap text of B5 and C6 t1 = sheet.text("B5") t2 = sheet.text(6,3) sheet.setText("B5", t2) sheet.setText(6, 3, t1) # swap value of D7 and E8 v1 = sheet.value("D7") v2 = sheet.value(8,5) sheet.setValue("D7", v2) sheet.setValue(8, 5, v1) Error: 'str' object has no attribute 'text' File "file:///usr/share/kde4/apps/sheets/scripts/extensions/myswap.py", line 4, in <module> This error message appeared in a dialog box. I've taught myself some Python but I don't understand what is happening here. Shouldn't t1 be a sheet object? What would cause it to be a str instead? Thanks, Jim

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Pointers Towards Appropriate Python Methods
by Stephen P. Molnar Oct. 8, 2019

Oct. 8, 2019

First, let me state that this is not a homework problem. I happen to be a retired Research Chemist whose rathre meager programming skills are in FORTRAN. I have managed to write, and with help from the list debug, a very short Python script to extract a column of data from an ASCII file: #!/usr/bin/env python3 # -*- coding: utf-8 -*- """ Created on Tue Sep 24 07:51:11 2019 """ import numpy as np fileName = [] name = input("Enter Molecule ID: ") name_in = name+'_apo-1acl.RMSD' data = np.genfromtxt(name_in, usecols=(3), dtype=None, skip_header=8, skip_footer=1, encoding=None) I have uploaded the script and an example of the input file to my Dropbox account in order to avoid scrambling of the file format. https://www.dropbox.com/sh/xwsv17vkh48tsaa/AAAfIe0miWrrk49hqZCkxe-aa?dl=0 My problem is that I have a large number of data files that I wish to process for input to several other different Python scripts that I use as part of my Computational Chemistry research program. I've also uploaded a bash script that illustrates what I want to do in Python. At this point what I would like are pointers towards python method for processing a large number of data files. I'm not asking anyone to write the coed for me. Thanks in advance. -- Stephen P. Molnar, Ph.D. www.molecular-modeling.net 614.312.7528 (c) Skype: smolnar1

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NumPy Generates ValueError: Some errors were detected ! Line #9 (got 42 columns instead of 1)
by Stephen P. Molnar Oct. 1, 2019

Oct. 1, 2019

0 I am writing code to combine text files and I have encountered an error that I am having trouble solving. Google is no help. The code is: |#!/usr/bin/env python3# -*- coding: utf-8 -*-""" Created on Thu Sep 26 09:51:55 2019 @author: comp """importnumpy asnp NAME =input("Enter Molecule ID: ")NAME_IN =NAME+'_apo-1acl.RMSD'DATA =[]DATA =np.genfromtxt(NAME_IN,skip_header=8,dtype=None)| The text file is: |RMSD TABLE __________ _____________________________________________________________________ ||||||Rank|Sub-|Run|Binding|Cluster|Reference|Grep|Rank||Energy|RMSD |RMSD |Pattern_____|______|______|___________|_________|_________________|___________ 118-7.230.0093.07RANKING 129-6.791.3992.64RANKING 2116-7.180.0093.19RANKING 312-6.930.0093.38RANKING 3217-6.840.2393.45RANKING 4115-6.550.0091.83RANKING 427-6.340.3391.77RANKING 515-6.410.0093.05RANKING 613-6.360.0092.84RANKING 6210-6.280.4792.92RANKING 636-6.270.4392.82RANKING 6418-6.250.3292.88RANKING 6513-6.240.9692.75RANKING 661-6.240.8792.60RANKING 6714-6.210.5192.90RANKING 6811-6.140.9892.78RANKING 6920-6.110.7192.67RANKING 61019-6.011.3693.00RANKING 7112-6.300.0093.28RANKING 814-5.850.0092.97RANKING _______________________________________________________________________| and the error is: |runfile('/home/comp/Apps/Models/1-PhosphorusLigands/CombinedLigands/MOL/Docking/Results/RMSDTable/CombineRMSDFiles.py') Enter Molecule ID: 13-7 13-7_apo-1acl.RMSD Traceback (most recent call last): File "/home/comp/Apps/Models/1-PhosphorusLigands/CombinedLigands/MOL/Docking/Results/RMSDTable/CombineRMSDFiles.py", line 15, in <module> DATA = np.genfromtxt(NAME_IN, dtype=None, skip_header=8) File "/home/comp/Apps/Miniconda3/lib/python3.7/site-packages/numpy/lib/npyio.py", line 2075, in genfromtxt raise ValueError(errmsg) ValueError: Some errors were detected ! Line #29 (got 1 columns instead of 7)| At this point, I'm not even sure how to ask the question. Thanks in advance. -- Stephen P. Molnar, Ph.D. Life is a fuzzy set http://www.Molecular-Modeling.net Multivariate and stochastic 614.312.7528 (c) Skype: smolnar1

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Python Calculator Help needed ASAP!!
by Raj Patel Oct. 1, 2019

Oct. 1, 2019

Hi so Im a university student new to python, and I’ve been given a mini assignment to create a calculate on python, on of the function it must have is that once the user has already calculated something and wants to recalculate something with that result the second time the input calls the result becomes one of the two nums Ex. Choose an operator: + Enter the first number: 56 Enter the second number: 8 Result: 64 Choose an operator:+ Enter the first number: (since I’d be leaving this blank the result from the last equation would become the number here) Enter the second number: 10 Result: 74

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Type error when doing Pygame
by Cravan Sept. 28, 2019

Sept. 28, 2019

Hi guys, Recently tried doing a pygame project (which is still half-finished). However I received a TypeError code that 5 positional arguments have been inserted when I have only inserted four in my function. Have no idea why its not working. Here’s my code: ``` import pygame import random import math import os import time import sys from os import path from newsettings import * from spritesdata import * class Game: def __init__(self): pygame.init() self.clock = pygame.time.Clock() self.screen = pygame.display.set_mode((WIDTH, HEIGHT)) pygame.display.set_caption(TITLE) self.time = pygame.time.get_ticks() pygame.key.set_repeat(500, 100) self.all_sprites = pygame.sprite.Group() self.console = Console(self, 0) self.player = Player(self, 390, 595) self.work = Work(self, 450, 250) self.food_station = Food_Station(self, 750, 200) self.food = Food(self, 0, 10) self.education = Education(self, 300, 10) self.school = School(self, 100, 200) self.family = Family(self, 600, 10) self.money = Money(self, 850, 15) self.food_bar = 100 def run(self): self.playing = True while self.playing: self.dt = self.clock.tick(FPS) / 1000 self.hunger() self.events() self.update() self.draw() def hunger(self): HUNGEREVENT = pygame.USEREVENT + 1 pygame.time.set_timer(HUNGEREVENT, 10000) def food_food(self, x, y, cool): if cool < 0: cool = 0 BAR_LENGTH = 100 BAR_HEIGHT = 10 fill = (cool / 100) * BAR_LENGTH outline_rect = pygame.Rect(x, y, BAR_LENGTH, BAR_HEIGHT) fill_rect = pygame.Rect(x, y, fill, BAR_HEIGHT) pygame.draw.rect(self, GREEN, fill_rect) pygame.draw.rect(self, WHITE, outline_rect, 2) def quit(self): pygame.quit() sys.exit() def update(self): self.all_sprites.update() def draw(self): self.screen.fill(BGCOLOR) self.all_sprites.draw(self.screen) font = pygame.font.SysFont('Arial', 15, True, False) self.food_food(screen, 5, 5, self.food_bar) text = font.render("Number of days:" , True, BLACK) screen.blit(text, [0, 110]) font = pygame.font.SysFont('Arial', 30, True, False) text = font.render("=" , True, BLACK) screen.blit(text, [120, 40]) font = pygame.font.SysFont('Arial', 30, True, False) text = font.render("=" , True, BLACK) screen.blit(text, [400, 40]) font = pygame.font.SysFont('Arial', 30, True, False) text = font.render("=" , True, BLACK) screen.blit(text, [700, 40]) font = pygame.font.SysFont('Arial', 30, True, False) text = font.render("=" , True, BLACK) screen.blit(text, [950, 40]) self.all_sprites.update() pygame.display.flip() def events(self): # catch all events here HUNGEREVENT = pygame.USEREVENT + 1 pygame.time.set_timer(HUNGEREVENT, 10000) if pygame.event.get(HUNGEREVENT): self.food_bar = self.food_bar - 10 for event in pygame.event.get(): if event.type == pygame.QUIT: self.quit() if event.key == pygame.K_ESCAPE: self.quit() def end_screen(self): screen.fill(BLUE) font = pygame.font.SysFont('Arial', 30, True, False) text = font.render("Life Simulator V2" , True, WHITE) screen.blit(text, [400, 100]) font = pygame.font.SysFont('Arial', 30, True, False) text = font.render("Controls: F for food, E for education, W for work", True, WHITE) screen.blit(text, [175, 250]) font = pygame.font.SysFont('Arial', 30, True, False) text = font.render("Hard mode: h Easy mode: e Normal mode: m", True, WHITE) screen.blit(text, [175, 400]) font = pygame.font.SysFont('Arial', 30, True, False) text = font.render("Start by pressing a key corresponding to that mode", True, WHITE) screen.blit(text, [150, 600]) pygame.display.flip() waiting = True while waiting: pygame.init() clock = pygame.time.Clock() clock.tick(60) for event in pygame.event.get(): if event.type == pygame.QUIT: sys.exit() if event.type == pygame.KEYDOWN: if event.key == pygame.K_h: waiting = False initial_money = 50 self.food_bar = 100 if event.key == pygame.K_m: waiting = False initial_money = 100 self.food_bar = 100 if event.key == pygame.K_e: waiting = False initial_money = 200 self.food_bar = 100 g = Game() g.end_screen() g.run() ``` And here’s the Error I’m receiving: ################################ Traceback (most recent call last): File "final_project.py", line 135, in <module> g.run() File "final_project.py", line 37, in run self.draw() File "final_project.py", line 65, in draw self.food_food(screen, 5, 5, self.food_bar) TypeError: food_food() takes 4 positional arguments but 5 were given Any help is appreciated. Thanks in advance! Cravan

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Re: [Tutor] NumPy Generates ValueError: Some errors were detected ! Line #9 (got 42 columns instead of 1)
by David Sept. 27, 2019

Sept. 27, 2019

On Sat, 28 Sep 2019 at 03:49, Stephen P. Molnar <s.molnar(a)sbcglobal.net> wrote: > On 09/27/2019 09:55 AM, Stephen P. Molnar wrote: > > On 09/27/2019 09:28 AM, Mats Wichmann wrote: > >> On 9/27/19 5:47 AM, Stephen P. Molnar wrote: > >>> I am writing code to combine text files and I have encountered an > >>> error that I am having trouble solving. Google is no help. > >>> > >>> The code is: > >>> > >>> |#!/usr/bin/env python3# -*- coding: utf-8 -*-""" Created on Thu Sep > >>> 26 09:51:55 2019 @author: comp """importnumpy asnp NAME > >>> =input("Enter Molecule ID: ")NAME_IN =NAME+'_apo-1acl.RMSD'DATA > >>> =[]DATA =np.genfromtxt(NAME_IN,skip_header=8,dtype=None)| > >>> > >>> The text file is: > >>> > >>> |RMSD TABLE __________ > >>> _____________________________________________________________________ ||||||Rank|Sub-|Run|Binding|Cluster|Reference|Grep|Rank||Energy|RMSD > >>> |RMSD > >>> |Pattern_____|______|______|___________|_________|_________________|___________ > >>> 118-7.230.0093.07RANKING 129-6.791.3992.64RANKING > >>> 2116-7.180.0093.19RANKING 312-6.930.0093.38RANKING > >>> 3217-6.840.2393.45RANKING 4115-6.550.0091.83RANKING > >>> 427-6.340.3391.77RANKING 515-6.410.0093.05RANKING > >>> 613-6.360.0092.84RANKING 6210-6.280.4792.92RANKING > >>> 636-6.270.4392.82RANKING 6418-6.250.3292.88RANKING > >>> 6513-6.240.9692.75RANKING 661-6.240.8792.60RANKING > >>> 6714-6.210.5192.90RANKING 6811-6.140.9892.78RANKING > >>> 6920-6.110.7192.67RANKING 61019-6.011.3693.00RANKING > >>> 7112-6.300.0093.28RANKING 814-5.850.0092.97RANKING > >>> _______________________________________________________________________| > >>> > >>> and the error is: > >>> > >>> |runfile('/home/comp/Apps/Models/1-PhosphorusLigands/CombinedLigands/MOL/Docking/Results/RMSDTable/CombineRMSDFiles.py') > >>> Enter Molecule ID: 13-7 13-7_apo-1acl.RMSD Traceback (most recent > >>> call last): File > >>> "/home/comp/Apps/Models/1-PhosphorusLigands/CombinedLigands/MOL/Docking/Results/RMSDTable/CombineRMSDFiles.py", > >>> line 15, in <module> DATA = np.genfromtxt(NAME_IN, dtype=None, > >>> skip_header=8) File > >>> "/home/comp/Apps/Miniconda3/lib/python3.7/site-packages/numpy/lib/npyio.py", > >>> line 2075, in genfromtxt raise ValueError(errmsg) ValueError: Some > >>> errors were detected ! Line #29 (got 1 columns instead of 7)| > >>> > >>> At this point, I'm not even sure how to ask the question. > >>> > >> > >> your posting has come across mangled, seemingly spaces have been > >> stripped. But trying to disentangle it: > >> > >> "...pyio.py", line 2075, in genfromtxt > >> raise ValueError(errmsg) > >> ValueError: Some errors were detected ! Line #29 (got 1 columns > >> instead of 7)| > >> > >> and in your data you have lines which are clearly not seven columns. > >> You've done skip_header=8 and it doesn't look here that's eight lines > >> in the data pasted, but maybe that's due to whatever happened to the > >> pasted data between the source and the email. It looks at the very > >> least like you should use a skip_footer keyword as well since you > >> show a footer line. Beyond that it's really hard to tell as the data > >> portion of the table looks like it has no separators... > >> _______________________________________________ > >> Tutor maillist - Tutor(a)python.org > >> To unsubscribe or change subscription options: > >> https://mail.python.org/mailman/listinfo/tutor > > > > Sorry about the mangled files. > > > > > > I put both the python script and the data file in my Dropbox account. > > Here are the URL's: > > > > https://www.dropbox.com/s/aattr8qnjwd8b8e/13-7a_apo-1acl.RMSD?dl=0 > > https://www.dropbox.com/s/aattr8qnjwd8b8e/13-7a_apo-1acl.RMSD?dl=0 > > > Oh, dear. Just noticed my mistake. > > Here are the correct URL's: > > Data\ File: > https://www.dropbox.com/s/aattr8qnjwd8b8e/13-7a_apo-1acl.RMSD?dl=0 > Python Script: > https://www.dropbox.com/s/ni3pk0342q7o0qz/CombineRMSDFiles.py?dl=0 I get the feeling that you don't put much effort into asking questions on the mailing lists that I see you on. Here you have: 1) somehow posted your question to Python Tutor <tutor(a)python.org>, but posted your followup message to <debian-user(a)lists.debian.net> 2) somehow ignored the error message from python: ValueError: Some errors were detected ! Line #29 (got 1 columns instead of 7)| 3) somehow ignored the advice you were given on Python Tutor: > >> It looks at the very > >> least like you should use a skip_footer keyword as well since you > >> show a footer line I checked your dropbox data file at your corrected URL. Line 29 is a sequence of 71 underscore characters. Like Mats Wichmann replied, I think that would explain the error message "got 1 columns instead of 7", although I haven't bothered to test it.

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Pandas Problem?
by Stephen P. Molnar Sept. 24, 2019

Sept. 24, 2019

I am using the Spyder3 IDE with Python 3.7.3 and have encountered, what to me at least, is a rather strange problem. The code, at this point is: #!/usr/bin/env python3 # -*- coding: utf-8 -*- """ Created on Sat Apr 8 15:17:07 2017 @author: comp """ #import numpy as np #import matplotlib.pyplot as plt import pandas as pd name = input("Enter Molecule ID: ") print(name) ligand_file = name+'_apo-1acl.RMSD' print('Ligand file = ',ligand_file) data = pd.read_table('ligand_file',skiprows = 7) print(data) The input file, in this example, 17-3_apo-1acl.RMSD is: RMSD TABLE __________ _____________________________________________________________________ | | | | | | Rank | Sub- | Run | Binding | Cluster | Reference | Grep | Rank | | Energy | RMSD | RMSD | Pattern _____|______|______|___________|_________|_________________|___________ 1 1 8 -7.23 0.00 93.07 RANKING 1 2 9 -6.79 1.39 92.64 RANKING 2 1 16 -7.18 0.00 93.19 RANKING 3 1 2 -6.93 0.00 93.38 RANKING 3 2 17 -6.84 0.23 93.45 RANKING 4 1 15 -6.55 0.00 91.83 RANKING 4 2 7 -6.34 0.33 91.77 RANKING 5 1 5 -6.41 0.00 93.05 RANKING 6 1 3 -6.36 0.00 92.84 RANKING 6 2 10 -6.28 0.47 92.92 RANKING 6 3 6 -6.27 0.43 92.82 RANKING 6 4 18 -6.25 0.32 92.88 RANKING 6 5 13 -6.24 0.96 92.75 RANKING 6 6 1 -6.24 0.87 92.60 RANKING 6 7 14 -6.21 0.51 92.90 RANKING 6 8 11 -6.14 0.98 92.78 RANKING 6 9 20 -6.11 0.71 92.67 RANKING 6 10 19 -6.01 1.36 93.00 RANKING 7 1 12 -6.30 0.00 93.28 RANKING 8 1 4 -5.85 0.00 92.97 RANKING _______________________________________________________________________ The output at this point is: Enter Molecule ID: 17-3 17-3 Ligand file = 17-3_apo-1acl.RMSD Traceback (most recent call last): File "<ipython-input-3-48de0a8fd907>", line 1, in <module> runfile('/home/comp/Apps/Models/1-PhosphorusLigands/CombinedLigands/MOL/Docking/Results/RMSDTable/RMSDTable_3.py.', wdir='/home/comp/Apps/Models/1-PhosphorusLigands/CombinedLigands/MOL/Docking/Results/RMSDTable') File "/usr/local/lib/python3.7/dist-packages/spyder_kernels/customize/spydercustomize.py", line 827, in runfile execfile(filename, namespace) File "/usr/local/lib/python3.7/dist-packages/spyder_kernels/customize/spydercustomize.py", line 110, in execfile exec(compile(f.read(), filename, 'exec'), namespace) File "/home/comp/Apps/Models/1-PhosphorusLigands/CombinedLigands/MOL/Docking/Results/RMSDTable/RMSDTable_3.py.", line 23, in <module> data = pd.read_table('ligand_file',skiprows = 7) File "/usr/local/lib/python3.7/dist-packages/pandas/io/parsers.py", line 685, in parser_f return _read(filepath_or_buffer, kwds) File "/usr/local/lib/python3.7/dist-packages/pandas/io/parsers.py", line 457, in _read parser = TextFileReader(fp_or_buf, **kwds) File "/usr/local/lib/python3.7/dist-packages/pandas/io/parsers.py", line 895, in __init__ self._make_engine(self.engine) File "/usr/local/lib/python3.7/dist-packages/pandas/io/parsers.py", line 1135, in _make_engine self._engine = CParserWrapper(self.f, **self.options) File "/usr/local/lib/python3.7/dist-packages/pandas/io/parsers.py", line 1917, in __init__ self._reader = parsers.TextReader(src, **kwds) File "pandas/_libs/parsers.pyx", line 382, in pandas._libs.parsers.TextReader.__cinit__ File "pandas/_libs/parsers.pyx", line 689, in pandas._libs.parsers.TextReader._setup_parser_source FileNotFoundError: [Errno 2] File b'ligand_file' does not exist: b'ligand_file' However, if I change the data = line to: data = pd.read_table('13-7_apo-1acl.RMSD',skiprows = 7) The output is: runfile('/home/comp/Apps/Models/1-PhosphorusLigands/CombinedLigands/MOL/Docking/Results/RMSDTable/RMSDTable_3.py.', wdir='/home/comp/Apps/Models/1-PhosphorusLigands/CombinedLigands/MOL/Docking/Results/RMSDTable') Enter Molecule ID: 13-7 13-7 Ligand file = 13-7_apo-1acl.RMSD _____|______|______|___________|_________|_________________|___________ 0 1 1 8 -7.23 0.00 9... 1 1 2 9 -6.79 1.39 9... 2 2 1 16 -7.18 0.00 9... 3 3 1 2 -6.93 0.00 9... 4 3 2 17 -6.84 0.23 9... 5 4 1 15 -6.55 0.00 9... 6 4 2 7 -6.34 0.33 9... 7 5 1 5 -6.41 0.00 9... 8 6 1 3 -6.36 0.00 9... 9 6 2 10 -6.28 0.47 9... 10 6 3 6 -6.27 0.43 9... 11 6 4 18 -6.25 0.32 9... 12 6 5 13 -6.24 0.96 9... 13 6 6 1 -6.24 0.87 9... 14 6 7 14 -6.21 0.51 9... 15 6 8 11 -6.14 0.98 9... 16 6 9 20 -6.11 0.71 9... 17 6 10 19 -6.01 1.36 9... 18 7 1 12 -6.30 0.00 9... 19 8 1 4 -5.85 0.00 9... 20 ______________________________________________... I have used the ligand_file = line in other Python script that has worked without any errors. Google has not been a solution in his case. Pointers towards wolutions to this problem will be much appreciated. Thanks in advance. -- Stephen P. Molnar, Ph.D. Life is a fuzzy set http://www.Molecular-Modeling.net Multivariate and stochastic 614.312.7528 (c) Skype: smolnar1

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Python3 : Yes --- Python2 : No ?
by Hendrickx Marcel Sept. 22, 2019

Sept. 22, 2019

Link with the info => https://www.python.org/doc/sunset-python-2/ News for me... Greetings.

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Most efficient way to replace ", " with "." in a array and/or dataframe
by Markos Sept. 22, 2019

Sept. 22, 2019

Hi, I have a table.csv file with the following structure: , Polyarene conc ,, mg L-1 ,,,,,,, Spectrum, Py, Ace, Anth, 1, "0,456", "0,120", "0,168" 2, "0,456", "0,040", "0,280" 3, "0,152", "0,200", "0,280" I open as dataframe with the command: data = pd.read_csv ('table.csv', sep = ',', skiprows = 1) and the variable "data" has the structure: Spectrum, Py, Ace, Anth, 0 1 0,456 0,120 0,168 1 2 0,456 0,040 0,280 2 3 0,152 0,200 0,280 I copy the numeric fields to an array with the command: data_array = data.values [:, 1:] And the data_array variable gets the fields in string format: [['0,456' '0,120' '0,168'] ['0,456' '0,040' '0,280'] ['0,152' '0,200' '0,280']] The only way I found to change comma "," to dot "." was using the method replace(): for i, line in enumerate (data_array): data_array [i] = ([float (element.replace (',', '.')) for element in data_array [i]]) But I'm wondering if there is another, more "efficient" way to make this change without having to "iterate" all elements of the array with a loop "for". Also I'm also wondering if there would be any benefit of making this modification in dataframe before extracting the numeric fields to the array. Please, any comments or tip? Thanks you, Markos

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How to get all methods of "object"?
by boB Stepp Sept. 22, 2019

Sept. 22, 2019

Python 3.7.4 I tried to do this with: >>> for attribute in dir(object): print(attribute) __class__ __delattr__ __dir__ __doc__ __eq__ __format__ __ge__ __getattribute__ __gt__ __hash__ __init__ __init_subclass__ __le__ __lt__ __ne__ __new__ __reduce__ __reduce_ex__ __repr__ __setattr__ __sizeof__ __str__ __subclasshook__ But I know at least one that is not listed: __dict__ And I would not be surprised if there are others. Basically, I am wondering what are *all* the things inherited from "object" when one creates one's own class? I am currently trying to find such a list in the Python 3 docs, but so far I have been unsuccessful. -- boB

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