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Suggest alternative for find number of columns; Other typos and lintings #54

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Suggestion alternative for find numbers of columns; Other typos and l…
khoivan88 Mar 16, 2020
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Revert back to original document
khoivan88 Mar 26, 2020
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Merge branch 'gh-pages' into patch-4
khoivan88 Mar 26, 2020
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65 changes: 38 additions & 27 deletions _episodes/04-tabular_data.md
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Original file line number Diff line number Diff line change
Expand Up @@ -253,6 +253,13 @@ In our example, the "end" value needs to be the number of columns of data.
>> ~~~
>> {: .language-python}
>>
>> Alternatively:
>> ~~~
>> num_rows, num_columns = data.shape # data.shape returns (10000, 5) which is the numbers of rows and columns, respectively
>> print(num_columns)
>> ~~~
>> {: .language-python}
>>
>> ~~~
>> 5
>> ~~~
Expand All @@ -262,10 +269,10 @@ In our example, the "end" value needs to be the number of columns of data.

Now that we know the number of columns, we can use the `range()` function to set up our `for` loop.
```
for i in range(1,num_columns):
column = data[:,i]
for i in range(1, num_columns):
column = data[:, i]
avg_col = numpy.mean(column)
print(F'{headers[i]} : {avg_col}')
print(f'{headers[i]} : {avg_col}')
```
{: .language-python}
```
Expand Down Expand Up @@ -308,17 +315,17 @@ TYR6_ASP : 10.9934435
>>
>> file_location = os.path.join('data', 'water.xyz')
>> xyz_file = numpy.genfromtxt(fname=file_location, skip_header=2, dtype='unicode')
>> symbols = xyz_file[:,0]
>> coordinates = (xyz_file[:,1:])
>> symbols = xyz_file[:, 0]
>> coordinates = xyz_file[:, 1:]
>> coordinates = coordinates.astype(numpy.float)
>> num_atoms = len(symbols)
>> for num1 in range(0,num_atoms):
>> for num2 in range(0,num_atoms):
>> for num1 in range(0, num_atoms):
>> for num2 in range(0, num_atoms):
>> x_distance = coordinates[num1,0] - coordinates[num2,0]
>> y_distance = coordinates[num1,1] - coordinates[num2,1]
>> z_distance = coordinates[num1,2] - coordinates[num2,2]
>> bond_length_12 = numpy.sqrt(x_distance**2+y_distance**2+z_distance**2)
>> print(F'{symbols[num1]} to {symbols[num2]} : {bond_length_12:.3f}')
>> bond_length_12 = numpy.sqrt(x_distance ** 2 + y_distance ** 2 + z_distance ** 2)
>> print(f'{symbols[num1]} to {symbols[num2]} : {bond_length_12:.3f}') # print result to screen
>>
>> ~~~
>> {: .language-python}
Expand All @@ -327,9 +334,11 @@ TYR6_ASP : 10.9934435
>> ~~~
>> import numpy
>> import os
>>
>> file_location = os.path.join('data', 'water.xyz')
>> xyzfile = open(file_location,"r")
>> data=xyzfile.readlines()
>> data = xyzfile.readlines()
>> xyzfile.close()
>> num_atoms = int(data[0])
>> data = data[2:]
>>
Expand All @@ -343,15 +352,15 @@ TYR6_ASP : 10.9934435
>> x, y, z = atom_data[1], atom_data[2], atom_data[3]
>> coordinates.append([float(x), float(y), float(z)])
>>
>> for num1 in range(0,num_atoms):
>> for num2 in range(0,num_atoms):
>> for num1 in range(0, num_atoms):
>> for num2 in range(0, num_atoms):
>> atom1 = coordinates[num1]
>> atom2 = coordinates[num2]
>> x_distance = atom1[0] - atom2[0]
>> y_distance = atom1[1] - atom2[1]
>> z_distance = atom1[2] - atom2[2]
>> bond_length_12 = numpy.sqrt(x_distance**2+y_distance**2+z_distance**2)
>> print(F'{symbols[num1]} to {symbols[num2]} : {bond_length_12:.3f}')
>> bond_length_12 = numpy.sqrt(x_distance ** 2 + y_distance ** 2 + z_distance ** 2)
>> print(f'{symbols[num1]} to {symbols[num2]} : {bond_length_12:.3f}')
>> ~~~
>> {: .language-python}
> {: .solution}
Expand All @@ -360,7 +369,7 @@ TYR6_ASP : 10.9934435

> ## Variable Names
>
> In our solution above, we called our bond length variable `bond_length_AB`. We could have called this variable anything we wanted. Consider the following two potential variable names for bond length - `BL_AB` and `bond_length_AB`. Which is more clear to you? While you might know what `BL` means, and it is possible for others to figure it out through context, it's easier on others if you give your variables clear names.
> In our solution above, we called our bond length variable `bond_length_12`. We could have called this variable anything we wanted. Consider the following two potential variable names for bond length - `BL_12` and `bond_length_12`. Which is more clear to you? While you might know what `BL` means, and it is possible for others to figure it out through context, it's easier on others if you give your variables clear names.
{: .callout}

> ## Project Extension 1
Expand All @@ -372,7 +381,7 @@ TYR6_ASP : 10.9934435
>> Add an `if` statement before your print statement.
>> ~~~
>> if bond_length_12 > 0 and bond_length_12 <= 1.5:
>> print(F'{symbols[num1]} to {symbols[num2]} : {bond_length_12:.3f}')
>> print(f'{symbols[num1]} to {symbols[num2]} : {bond_length_12:.3f}')
>> ~~~
>> {: .language-python}
>>
Expand All @@ -399,19 +408,19 @@ TYR6_ASP : 10.9934435
>>
>> file_location = os.path.join('data', 'water.xyz')
>> xyz_file = numpy.genfromtxt(fname=file_location, skip_header=2, dtype='unicode')
>> symbols = xyz_file[:,0]
>> coordinates = (xyz_file[:,1:])
>> symbols = xyz_file[:, 0]
>> coordinates = xyz_file[:, 1:]
>> coordinates = coordinates.astype(numpy.float)
>> num_atoms = len(symbols)
>> for num1 in range(0,num_atoms):
>> for num2 in range(0,num_atoms):
>> if num1<num2:
>> x_distance = coordinates[num1,0] - coordinates[num2,0]
>> y_distance = coordinates[num1,1] - coordinates[num2,1]
>> z_distance = coordinates[num1,2] - coordinates[num2,2]
>> bond_length_12 = numpy.sqrt(x_distance**2+y_distance**2+z_distance**2)
>> for num1 in range(0, num_atoms):
>> for num2 in range(0, num_atoms):
>> if num1 < num2:
>> x_distance = coordinates[num1, 0] - coordinates[num2, 0]
>> y_distance = coordinates[num1, 1] - coordinates[num2, 1]
>> z_distance = coordinates[num1, 2] - coordinates[num2, 2]
>> bond_length_12 = numpy.sqrt(x_distance ** 2 + y_distance ** 2 + z_distance ** 2)
>> if bond_length_12 > 0 and bond_length_12 <= 1.5:
>> print(F'{symbols[num1]} to {symbols[num2]} : {bond_length_12:.3f}')
>> print(f'{symbols[num1]} to {symbols[num2]} : {bond_length_12:.3f}')
>> ~~~
>> {: .language-python}
>>
Expand All @@ -437,10 +446,12 @@ TYR6_ASP : 10.9934435
>>
>> Then inside your loop change your `print` statement to a `BLfile.write()` statement.
>> ~~~
>> BLfile.write(F'{symbols[num1]} to {symbols[num2]} : {bond_length_12:.3f}')
>> BLfile.write(f'{symbols[num1]} to {symbols[num2]} : {bond_length_12:.3f}\n')
>> ~~~
>> {: .language-python}
>>
>> Note: `write()` does not add a new line at the end of each line so `\n` is required!
>>
>> Don't forget to close the file at the end of your code.
>> ~~~
>> BLfile.close() #Close the file so it will write
Expand Down