Programming Forums > Script Programming > Python

arranta · May 29th, 2006, 11:53 AM

I'm girl and I'm not into computers and programming. I'm studying chemistry and I have a course of programming in python. I don't know much about it but this is the last thing I need to pass to get my M.Sc. in chemistry.

I need to write a simple (I guess) programm and send it to my teacher until midnight tommorow. Please help me!

This is my taski:

Quote:

Write a program which reads a file and prints atoms' coordinates. Thease coordinates are in the line beginning with "Standard orientation:". Be careful. This line occures few times in the input file so you need to use the last one.

(Toggle Plain Text)

                         Standard orientation:                         

 ---------------------------------------------------------------------

 Center     Atomic     Atomic              Coordinates (Angstroms)

 Number     Number      Type              X           Y           Z

 ---------------------------------------------------------------------

    1          8             0        1.134793   -0.271635   -0.000036

    2          6             0        0.144813    0.402688    0.000046

    3          8             0       -1.115077   -0.083365   -0.000108

    4          1             0        0.115449    1.476364    0.000260

    5          1             0       -1.142054   -1.052488    0.000615

 ---------------------------------------------------------------------

A name of the file should be an argument used in shell and should print results in four columns - atomic number, x coordinate, y coordinate, z coordinate).

A file to use in this program you can find here:
http://ar.ch.pwr.wroc.pl/file.php/4/...domowe/opt.log

PLEASE HELP!

PS Sorry for my english. I'm from Eastern Europe.

Arevos · May 29th, 2006, 12:04 PM

Quote:

Originally Posted by arranta

I need to write a simple (I guess) programm and send it to my teacher until midnight tommorow. Please help me!

What have you created so far?

I can't think of much advice I can give without completing the task for you. You should probably use the re.split command to turn a single line of numerical data into a list of numbers. You should also read each line in the file into a list for easy processing.

Apart from this, it's difficult to give any advice without seeing the program you have constructed, or explaining what part of the assignment you are having problems with.

arranta · May 29th, 2006, 12:36 PM

I'm doing exactly the same thing. I'm converting data into list of lines. It's very hard for me. I'm reading the manuals and trying to create somethin but it is a pain in the a..

thanx

Arevos · May 29th, 2006, 12:52 PM

So... what have you written so far?

uman · May 29th, 2006, 1:04 PM

Sorry, I can't help, as I don't know Python, but I just want to say that your English is almost perfect. The only thing is that we would say "by midnight tommorow" rather than "until midnight tomorrow".

arranta · May 29th, 2006, 1:08 PM

I realize that it could be total crap but...

(Toggle Plain Text)

file=open('opt.log')
   list=file.readlines()
   list.reverse()
   A=list.index (Standard orientation:)
   list_new=[['A'+5],['A'+9]]

Arevos · May 29th, 2006, 3:42 PM

That's a good start. The first problem you have in your code is that list.index will only find exact matches. This is a problem because there appears to be a lot of whitespace in the file.

Instead, you probably want a command which says, "Find me the first line that has the 'Standard orientation' text in it". List comprehensions come in useful here: you can filter a list based on certain criteria.

(Toggle Plain Text)

stdori_list = [line for line in list if "Standard orientation:" in line]

And you can use standard indices to get the first value:

(Toggle Plain Text)

a = [line for line in list if "Standard orientation:" in line][0]

However, this isn't much good, as it returns the line itself, rather than the index. The enumerate function was introduced in Python 2.4, which hopefully you'll have. This function adds in the index to any for loop or list comprehension. For instance:

(Toggle Plain Text)

>>> for index, letter in enumerate(["a", "b", "c"]):
...    print index, letter
...    
0 a
1 b
2 c

Using this, you can get the index thus:

(Toggle Plain Text)

a = [i for i, x in enumerate(list) if "Standard orientation:" in x][0]

From here, you'll need to find the lines that contain numerical data. I'll leave that as an exercise for the reader.

Once you have the lines, there is a simple way to extract the data, using the re.split function. Again, I won't go into much detail, but you can split up a line based on a regular expression.

Regular expressions are a kind of universal sub-language for text searching and manipulation. It contains several special symbols. The two which you need are \s, which means "any whitespace", and +, which means "one or more of the previous character. Thus, the regular expression "\s+" means "one or more whitespace".

Using this in the split command, getting information from a line can be as easy as:

(Toggle Plain Text)

center, number, type, x, y, z = re.split("\s+", line.strip())

(The .strip() method removes trailing and preceeding whitespace)

arranta · May 29th, 2006, 4:36 PM

Thank you very much. I'll check it out in a moment. There is one concern I've got. What is enumerate function and how to check out if I have it?

Sorry for super-noobie-like questions but as I said. I'm dealing more with chemicals rather than computers

Dietrich · May 29th, 2006, 4:46 PM

I can't get a hold of your data file, but you got that part figured out anyway. So here is my wooden nickle's worth:

(Toggle Plain Text)

# let's assume that opt.log looks like str1

str1 = """\
                        Standard orientation:

 ---------------------------------------------------------------------

 Center     Atomic     Atomic              Coordinates (Angstroms)

 Number     Number      Type              X           Y           Z

 ---------------------------------------------------------------------

    1          8             0        1.134793   -0.271635   -0.000036

    2          6             0        0.144813    0.402688    0.000046

    3          8             0       -1.115077   -0.083365   -0.000108

    4          1             0        0.115449    1.476364    0.000260

    5          1             0       -1.142054   -1.052488    0.000615

 ---------------------------------------------------------------------
"""

list1 = str1.split("\n")
numeric_list = []
for line in list1:
    # strip leading whitspace
    line = line.lstrip()
    # find all the lines that start with a number
    # and extract all the numbers, no spaces
    if len(line) > 0 and line[0].isdigit():
        numeric_list.append(line.split(None))

print "%14s %14s % 14s %14s" % ("atomic number", "x coordinate", "y coordinate", "z coordinate")
for line in numeric_list:
    print "%14s %14s % 14s %14s" % (line[1], line[3], line[4], line[5])

"""
 atomic number   x coordinate   y coordinate   z coordinate
             8       1.134793      -0.271635      -0.000036
             6       0.144813       0.402688       0.000046
             8      -1.115077      -0.083365      -0.000108
             1       0.115449       1.476364       0.000260
             1      -1.142054      -1.052488       0.000615
"""

If you want to see what's going on, then insert some interim print statements like print list1, or print line, or print numeric_list. I think its easy to understand this way.

Pizentios · May 29th, 2006, 5:09 PM

Quote:

Originally Posted by arranta

Thank you very much. I'll check it out in a moment. There is one concern I've got. What is enumerate function and how to check out if I have it?

Sorry for super-noobie-like questions but as I said. I'm dealing more with chemicals rather than computers

Don't say sorry for asking questions! That's what this forum is for. Now, had you asked us to code it for you, it might have been a different story. Our users have no problem answering newbie questions as long as the user has shown some effort on their part (like you have).

Keep asking questions, it's the only real way to learn :-)

May 29th, 2006, 1:04 PM	#5
uman Expert Programmer Join Date: Dec 2004 Posts: 794 Rep Power: 4	Sorry, I can't help, as I don't know Python, but I just want to say that your English is almost perfect. The only thing is that we would say "by midnight tommorow" rather than "until midnight tomorrow". __________________ Few people deserve to be compared to (Rush) Limbaugh, most of them were convicted at the Nuremburg trials. --WilliamSChips on Slashdot

May 29th, 2006, 1:08 PM	#6
arranta Newbie Join Date: May 2006 Posts: 5 Rep Power: 0	I realize that it could be total crap but... (Toggle Plain Text) file=open('opt.log') list=file.readlines() list.reverse() A=list.index (Standard orientation:) list_new=[['A'+5],['A'+9]] file=open('opt.log') list=file.readlines() list.reverse() A=list.index (Standard orientation:) list_new=[['A'+5],['A'+9]]

May 29th, 2006, 3:42 PM	#7
Arevos Programming Guru Join Date: Aug 2005 Location: England Posts: 1,499 Rep Power: 5	That's a good start. The first problem you have in your code is that list.index will only find exact matches. This is a problem because there appears to be a lot of whitespace in the file. Instead, you probably want a command which says, "Find me the first line that has the 'Standard orientation' text in it". List comprehensions come in useful here: you can filter a list based on certain criteria. (Toggle Plain Text) stdori_list = [line for line in list if "Standard orientation:" in line] stdori_list = [line for line in list if "Standard orientation:" in line] And you can use standard indices to get the first value: (Toggle Plain Text) a = [line for line in list if "Standard orientation:" in line][0] a = [line for line in list if "Standard orientation:" in line][0] However, this isn't much good, as it returns the line itself, rather than the index. The enumerate function was introduced in Python 2.4, which hopefully you'll have. This function adds in the index to any for loop or list comprehension. For instance: (Toggle Plain Text) >>> for index, letter in enumerate(["a", "b", "c"]): ... print index, letter ... 0 a 1 b 2 c >>> for index, letter in enumerate(["a", "b", "c"]): ... print index, letter ... 0 a 1 b 2 c Using this, you can get the index thus: (Toggle Plain Text) a = [i for i, x in enumerate(list) if "Standard orientation:" in x][0] a = [i for i, x in enumerate(list) if "Standard orientation:" in x][0] From here, you'll need to find the lines that contain numerical data. I'll leave that as an exercise for the reader. Once you have the lines, there is a simple way to extract the data, using the re.split function. Again, I won't go into much detail, but you can split up a line based on a regular expression. Regular expressions are a kind of universal sub-language for text searching and manipulation. It contains several special symbols. The two which you need are \s, which means "any whitespace", and +, which means "one or more of the previous character. Thus, the regular expression "\s+" means "one or more whitespace". Using this in the split command, getting information from a line can be as easy as: (Toggle Plain Text) center, number, type, x, y, z = re.split("\s+", line.strip()) center, number, type, x, y, z = re.split("\s+", line.strip()) (The .strip() method removes trailing and preceeding whitespace)

May 29th, 2006, 4:46 PM	#9
Dietrich Professional Programmer Join Date: Feb 2005 Posts: 434 Rep Power: 4	I can't get a hold of your data file, but you got that part figured out anyway. So here is my wooden nickle's worth: (Toggle Plain Text) # let's assume that opt.log looks like str1 str1 = """\ Standard orientation: --------------------------------------------------------------------- Center Atomic Atomic Coordinates (Angstroms) Number Number Type X Y Z --------------------------------------------------------------------- 1 8 0 1.134793 -0.271635 -0.000036 2 6 0 0.144813 0.402688 0.000046 3 8 0 -1.115077 -0.083365 -0.000108 4 1 0 0.115449 1.476364 0.000260 5 1 0 -1.142054 -1.052488 0.000615 --------------------------------------------------------------------- """ list1 = str1.split("\n") numeric_list = [] for line in list1: # strip leading whitspace line = line.lstrip() # find all the lines that start with a number # and extract all the numbers, no spaces if len(line) > 0 and line[0].isdigit(): numeric_list.append(line.split(None)) print "%14s %14s % 14s %14s" % ("atomic number", "x coordinate", "y coordinate", "z coordinate") for line in numeric_list: print "%14s %14s % 14s %14s" % (line[1], line[3], line[4], line[5]) """ atomic number x coordinate y coordinate z coordinate 8 1.134793 -0.271635 -0.000036 6 0.144813 0.402688 0.000046 8 -1.115077 -0.083365 -0.000108 1 0.115449 1.476364 0.000260 1 -1.142054 -1.052488 0.000615 """ # let's assume that opt.log looks like str1 str1 = """\ Standard orientation: --------------------------------------------------------------------- Center Atomic Atomic Coordinates (Angstroms) Number Number Type X Y Z --------------------------------------------------------------------- 1 8 0 1.134793 -0.271635 -0.000036 2 6 0 0.144813 0.402688 0.000046 3 8 0 -1.115077 -0.083365 -0.000108 4 1 0 0.115449 1.476364 0.000260 5 1 0 -1.142054 -1.052488 0.000615 --------------------------------------------------------------------- """ list1 = str1.split("\n") numeric_list = [] for line in list1: # strip leading whitspace line = line.lstrip() # find all the lines that start with a number # and extract all the numbers, no spaces if len(line) > 0 and line[0].isdigit(): numeric_list.append(line.split(None)) print "%14s %14s % 14s %14s" % ("atomic number", "x coordinate", "y coordinate", "z coordinate") for line in numeric_list: print "%14s %14s % 14s %14s" % (line[1], line[3], line[4], line[5]) """ atomic number x coordinate y coordinate z coordinate 8 1.134793 -0.271635 -0.000036 6 0.144813 0.402688 0.000046 8 -1.115077 -0.083365 -0.000108 1 0.115449 1.476364 0.000260 1 -1.142054 -1.052488 0.000615 """ If you want to see what's going on, then insert some interim print statements like print list1, or print line, or print numeric_list. I think its easy to understand this way. __________________ I looked it up on the Intergnats!

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May 29th, 2006, 12:36 PM	#3
arranta Newbie Join Date: May 2006 Posts: 5 Rep Power: 0	I'm doing exactly the same thing. I'm converting data into list of lines. It's very hard for me. I'm reading the manuals and trying to create somethin but it is a pain in the a.. thanx

May 29th, 2006, 12:52 PM	#4
Arevos Programming Guru Join Date: Aug 2005 Location: England Posts: 1,499 Rep Power: 5	So... what have you written so far?

May 29th, 2006, 4:36 PM	#8
arranta Newbie Join Date: May 2006 Posts: 5 Rep Power: 0	Thank you very much. I'll check it out in a moment. There is one concern I've got. What is enumerate function and how to check out if I have it? Sorry for super-noobie-like questions but as I said. I'm dealing more with chemicals rather than computers

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Programming Forums > Script Programming > Python

Please help me graduate!