### Install Mordred via Pip

Source: https://github.com/mordred-descriptor/mordred/blob/develop/README.rst

Shows how to install Mordred using pip, with an option to include extra dependencies.

```console
$ pip install 'mordred[full]'
```

```console
# or
$ pip install mordred
```

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

### Run Mordred Tests

Source: https://github.com/mordred-descriptor/mordred/blob/develop/README.rst

Command to execute the built-in tests for the Mordred installation.

```console
$ python -m mordred.tests
```

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

### Install Mordred via Conda

Source: https://github.com/mordred-descriptor/mordred/blob/develop/README.rst

Provides the command to install the Mordred library using Conda, including necessary channels for dependencies like RDKit.

```console
$ conda install -c rdkit -c mordred-descriptor mordred
```

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

### Electronegativity Data for Period 6 (Part 1)

Source: https://github.com/mordred-descriptor/mordred/blob/develop/mordred/data/allred_rocow_electron_negativity.txt

This snippet contains electronegativity values for elements in Period 6, from Cesium to Barium, and the start of the Lanthanoid series. The data is presented as a list of values, with '-' indicating missing entries.

```text
0.86 #  55 Cs
0.97 #  56 Ba

# Lanthanoid
1.08 #  57 La
-    #  58 Ce
-    #  59 Pr
-    #  60 Nd
-    #  61 Pm
-    #  62 Sm
-    #  63 Eu
-    #  64 Gd
-    #  65 Tb
-    #  66 Dy
-    #  67 Ho
-    #  68 Er
-    #  69 Tm
-    #  70 Yb
-    #  71 Lu
```

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

### Display Mordred Help Information

Source: https://github.com/mordred-descriptor/mordred/blob/develop/README.rst

Shows the help message for the Mordred command-line interface, detailing all available options and arguments.

```console
$ python -m mordred --help
```

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

### Mordred Descriptor Calculation

Source: https://github.com/mordred-descriptor/mordred/blob/develop/README.rst

Demonstrates how to initialize the Mordred Calculator with all descriptors, calculate descriptors for a single molecule using SMILES, and calculate descriptors for multiple molecules, including outputting to a pandas DataFrame.

```python
from rdkit import Chem
from mordred import Calculator, descriptors

# create descriptor calculator with all descriptors
calc = Calculator(descriptors, ignore_3D=True)

print(len(calc.descriptors))

# calculate single molecule
mol = Chem.MolFromSmiles('c1ccccc1')
print(calc(mol)[:3])

# calculate multiple molecule
mols = [Chem.MolFromSmiles(smi) for smi in ['c1ccccc1Cl', 'c1ccccc1O', 'c1ccccc1N']]

# as pandas
df = calc.pandas(mols)
print(df['SLogP'])
```

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

### Sphinx Extensions for Documentation

Source: https://github.com/mordred-descriptor/mordred/blob/develop/extra/requirements/requirements-pip.txt

This section details Sphinx extensions used for generating project documentation. These tools enhance the documentation process, particularly for projects with bibliographies and specific themes.

```text
sphinx-rtd-theme
sphinxcontrib-bibtex
```

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

### Descriptor Retrieval Functions

Source: https://github.com/mordred-descriptor/mordred/blob/develop/docs/mordred.rst

Documentation for functions used to retrieve descriptors within the mordred package.

```APIDOC
get_descriptors_in_module(module)
    - Retrieves all descriptor classes available in a given module.
    - Parameters:
        - module: The module object to inspect.
    - Returns: A list of descriptor classes.

get_descriptors_from_module(module)
    - Retrieves all descriptor instances from a given module.
    - Parameters:
        - module: The module object to inspect.
    - Returns: A list of descriptor instances.
```

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

### Flake8 Plugins for Code Quality

Source: https://github.com/mordred-descriptor/mordred/blob/develop/extra/requirements/requirements-pip.txt

This section lists various flake8 plugins used to enforce coding standards, improve readability, and catch common errors. These plugins help maintain a consistent and high-quality codebase.

```text
flake8-quotes
flake8-print
flake8-black
flake8-comprehensions
flake8-docstrings
flake8-sorted-keys
flake8-regex
flake8-string-format
```

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

### Calculate Multiple Specific Descriptors (ABCIndex and AcidBase)

Source: https://github.com/mordred-descriptor/mordred/blob/develop/README.rst

Calculates both ABCIndex and AcidBase descriptors for molecules in a SMILES file and outputs the results.

```console
$ python -m mordred example.smi -d ABCIndex -d AcidBase
```

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

### Process Multiple Input Files

Source: https://github.com/mordred-descriptor/mordred/blob/develop/README.rst

Calculates specified descriptors (ABCIndex in this case) for molecules from multiple input SMILES files.

```console
$ python -m mordred example.smi example2.smi -d ABCIndex
```

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

### mordred.Calculator Class

Source: https://github.com/mordred-descriptor/mordred/blob/develop/docs/mordred.rst

Documentation for the Calculator class in the mordred package. This class is likely responsible for performing descriptor calculations.

```APIDOC
mordred.Calculator
    :members:
    - Handles the calculation of molecular descriptors.
    - Likely manages a collection of descriptors and applies them to molecules.
```

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

### Calculate Number of Descriptors

Source: https://github.com/mordred-descriptor/mordred/blob/develop/README.rst

Demonstrates how to calculate the total number of 2D and 3D descriptors available in the Mordred library. It initializes a Calculator with specified descriptor sets and counts the available descriptors.

```python
from mordred import Calculator, descriptors
n_all = len(Calculator(descriptors, ignore_3D=False).descriptors)
n_2D = len(Calculator(descriptors, ignore_3D=True).descriptors)
print("2D:    {:5}\\n3D:    {:5}\\n------------\\ntotal: {:5}".format(n_2D, n_all - n_2D, n_all))
```

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

### mordred.Descriptor Class

Source: https://github.com/mordred-descriptor/mordred/blob/develop/docs/mordred.rst

Documentation for the Descriptor class in the mordred package. This class is likely the base class for all descriptor implementations.

```APIDOC
mordred.Descriptor
    :members:
    - Base class for all molecular descriptors in mordred.
    - Likely defines the interface for calculating descriptors.
```

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

### Calculate Descriptors and Save to CSV with Progress

Source: https://github.com/mordred-descriptor/mordred/blob/develop/README.rst

Calculates molecular descriptors and saves them to a CSV file, displaying a progress bar during the process.

```console
$ python -m mordred example.smi -o example.csv
```

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

### Element Data from Handbook of Chemistry and Physics

Source: https://github.com/mordred-descriptor/mordred/blob/develop/mordred/data/ionization_potential.txt

This snippet represents data extracted from the Handbook of Chemistry and Physics, listing atomic numbers and associated numerical values for chemical elements. The data is presented in a simple, human-readable format.

```python
# Project: /mordred-descriptor/mordred

# Handbook of Chemistry and Physics, 94th Edition, 2013-2014, pg10-197

# 1
13.598443  #   1 H
24.587387  #   2 He

# 2
 5.391719  #   3 Li
9.32270   #   4 Be
8.29802   #   5 B
11.26030   #   6 C
14.5341    #   7 N
13.61805   #   8 O
17.4228    #   9 F
21.56454   #  10 Ne

# 3
 5.139076  #  11 Na
7.646235  #  12 Mg
5.985768  #  13 Al
8.15168   #  14 Si
10.48669   #  15 P
10.36001   #  16 S
12.96763   #  17 Cl
15.759610  #  18 Ar

# 4
 4.3406633 #  19 K
6.11316   #  20 Ca
6.56149   #  21 Sc
6.82812   #  22 Ti
6.74619   #  23 V
6.76651   #  24 Cr
7.43402   #  25 Mn
7.9024    #  26 Fe
7.88101   #  27 Co
7.6398    #  28 Ni
7.72638   #  29 Cu
9.394199  #  30 Zn
5.999301  #  31 Ga
7.89943   #  32 Ge
9.7886    #  33 As
9.75239   #  34 Se
11.8138    #  35 Br
13.99961   #  36 Kr

# 5
 4.177128  #  37 Rb
5.69485   #  38 Sr
6.2173    #  39 Y
6.63390   #  40 Zr
6.75885   #  41 Nb
7.09243   #  42 Mo
7.28      #  43 Tc
7.36050   #  44 Ru
7.45890   #  45 Rh
8.3369    #  46 Pd
7.57623   #  47 Ag
8.99382   #  48 Cd
5.78636   #  49 In
7.34392   #  50 Sn
8.60839   #  51 Sb
9.0096    #  52 Te
10.45126   #  53 I
12.12984   #  54 Xe

# 6
 3.893905  #  55 Cs
5.211664  #  56 Ba

# Lanthanoid
5.5769    #  57 La
5.5387    #  58 Ce
5.473     #  59 Pr
5.5250    #  60 Nd
5.582     #  61 Pm
5.6437    #  62 Sm
5.67038   #  63 Eu
6.14980   #  64 Gd
5.8638    #  65 Tb
5.9389    #  66 Dy
6.0215    #  67 Ho
6.1077    #  68 Er
6.18431   #  69 Tm
6.25416   #  70 Yb
5.42586   #  71 Lu

# 6 cont.
6.82507   #  72 Hf
7.54957   #  73 Ta
7.86403   #  74 W
7.83352   #  75 Re
8.43823   #  76 Os
8.96702   #  77 Ir
8.9588    #  78 Pt
9.22553   #  79 Au
10.4375    #  80 Hg
6.108194  #  81 Tl
7.41663   #  82 Pb
7.2855    #  83 Bi
8.414     #  84 Po
-          #  85 At
10.7485    #  86 Rn

# 7
 4.072741  #  87 Fr
5.278423  #  88 Ra

# Actinoid
5.17      #  89 Ac
6.3067    #  90 Th
5.89      #  91 Pa
6.1941    #  92 U
6.2657    #  93 Np
6.0260    #  94 Pu
5.9738    #  95 Am
5.9914    #  96 Cm
6.1979    #  97 Bk
6.2817    #  98 Cf
6.42      #  99 Es
6.50      # 100 Fm
6.58      # 101 Md
6.65      # 102 No
4.9       # 103 Lr

# 7 cont.
6.0       # 104 Rf

```

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

### mordred.descriptors Module Documentation

Source: https://github.com/mordred-descriptor/mordred/blob/develop/docs/subpackages/mordred.descriptors.rst

This section details the members, undocumented members, and inheritance of the mordred.descriptors module. It is generated using Sphinx's automodule directive.

```python
.. automodule:: mordred.descriptors
    :members:
    :undoc-members:
    :show-inheritance:
```

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

### Electronegativity Data for Period 6 (Part 2)

Source: https://github.com/mordred-descriptor/mordred/blob/develop/mordred/data/allred_rocow_electron_negativity.txt

This snippet contains electronegativity values for the continuation of Period 6 elements, from Hafnium to Astatine. The data is presented as a list of values, with '-' indicating missing entries.

```text
# 6 cont.
1.23 #  72 Hf
1.33 #  73 Ta
1.40 #  74 W
1.46 #  75 Re
1.52 #  76 Os
1.55 #  77 Ir
1.44 #  78 Pt
1.42 #  79 Au
1.44 #  80 Hg
1.44 #  81 Tl
1.55 #  82 Pb
1.67 #  83 Bi
1.76 #  84 Po
1.90 #  85 At
```

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

### Calculate All Descriptors from SMILES

Source: https://github.com/mordred-descriptor/mordred/blob/develop/README.rst

Calculates all available molecular descriptors for molecules listed in a SMILES file and outputs the results in CSV format.

```console
$ python -m mordred example.smi
```

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

### Mordred Descriptor Data Sections

Source: https://github.com/mordred-descriptor/mordred/blob/develop/mordred/data/mc_gowan_volume.txt

This snippet displays the categorized data from the Mordred descriptor project. Each section contains numerical values and corresponding element identifiers.

```plaintext
# 1
 8.71 #   1 H
 6.75 #   2 He

# 2
22.23 #   3 Li
20.27 #   4 Be
18.31 #   5 B
16.35 #   6 C
14.39 #   7 N
12.43 #   8 O
10.47 #   9 F
 8.51 #  10 Ne

# 3
32.71 #  11 Na
30.75 #  12 Mg
28.79 #  13 Al
26.83 #  14 Si
24.87 #  15 P
22.91 #  16 S
20.95 #  17 Cl
18.99 #  18 Ar

# 4
51.89 #  19 K
50.28 #  20 Ca
48.68 #  21 Sc
47.07 #  22 Ti
45.47 #  23 V
43.86 #  24 Cr
42.26 #  25 Mn
40.65 #  26 Fe
39.05 #  27 Co
37.44 #  28 Ni
35.84 #  29 Cu
34.23 #  30 Zn
32.63 #  31 Ga
31.02 #  32 Ge
29.42 #  33 As
27.81 #  34 Se
26.21 #  35 Br
24.60 #  36 Kr

# 5
60.22 #  37 Rb
58.61 #  38 Sr
57.01 #  39 Y
55.40 #  40 Zr
53.80 #  41 Nb
52.19 #  42 Mo
50.59 #  43 Tc
48.98 #  44 Ru
47.38 #  45 Rh
45.77 #  46 Pd
44.17 #  47 Ag
42.56 #  48 Cd
40.96 #  49 In
39.35 #  50 Sn
37.75 #  51 Sb
36.14 #  52 Te
34.54 #  53 I
32.93 #  54 Xe

# 6
77.25 #  55 Cs
76.00 #  56 Ba

# Lanthanoid
74.75 #  57 La
73.49 #  58 Ce
72.24 #  59 Pr
70.99 #  60 Nd
69.74 #  61 Pm
68.49 #  62 Sm
67.23 #  63 Eu
65.98 #  64 Gd
64.73 #  65 Tb
63.48 #  66 Dy
62.23 #  67 Ho
60.97 #  68 Er
59.72 #  69 Tm
58.47 #  70 Yb
57.22 #  71 Lu

# 6 cont.
55.97 #  72 Hf
54.71 #  73 Ta
53.46 #  74 W
52.21 #  75 Re
50.96 #  76 Os
49.71 #  77 Ir
48.45 #  78 Pt
47.20 #  79 Au
45.95 #  80 Hg
44.70 #  81 Tl
43.45 #  82 Pb
42.19 #  83 Bi
40.94 #  84 Po
39.69 #  85 At
38.44 #  86 Rn

# 7
75.59 #  87 Fr
74.34 #  88 Ra

# Actinoid
73.09 #  89 Ac
71.83 #  90 Th
70.58 #  91 Pa
69.33 #  92 U
68.08 #  93 Np
66.83 #  94 Pu
65.57 #  95 Am
64.32 #  96 Cm
63.07 #  97 Bk
61.82 #  98 Cf
60.57 #  99 Es
59.31 # 100 Fm
58.06 # 101 Md
56.81 # 102 No
55.56 # 103 Lr
```

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

### Electronegativity Values by Atomic Number

Source: https://github.com/mordred-descriptor/mordred/blob/develop/mordred/data/sanderson_electron_negativity.txt

This snippet lists electronegativity values for elements, indexed by their atomic number. It includes data for periods 1 through 6, with some elements marked as '-' indicating missing or not applicable values. The data is sourced from scientific publications and web resources.

```data
# Project: /mordred-descriptor/mordred
# Content:
# # Sanderson, RT. Electronegativity and Bond Energy.  J. Am. Chem. Soc. 1983, 105: 2259-2261.
# # Remaining values come from http://www.talete.mi.it/help/dragon_help/weighting_schemes.htm

# 1
2.592 #   1 H
-     #   2 He

# 2
0.670 #   3 Li
1.810 #   4 Be
2.275 #   5 B
2.746 #   6 C
3.194 #   7 N
3.654 #   8 O
4.000 #   9 F
4.5   #  10 Ne

# 3
0.560 #  11 Na
1.318 #  12 Mg
1.714 #  13 Al
2.138 #  14 Si
2.515 #  15 P
2.957 #  16 S
3.475 #  17 Cl
3.31  #  18 Ar

# 4
0.445 #  19 K
0.946 #  20 Ca
1.02  #  21 Sc
1.09  #  22 Ti
1.39  #  23 V
1.66  #  24 Cr
2.2   #  25 Mn
2.2   #  26 Fe
2.56  #  27 Co
1.94  #  28 Ni
2.033 #  29 Cu
2.223 #  30 Zn
2.419 #  31 Ga
2.618 #  32 Ge
2.816 #  33 As
3.014 #  34 Se
3.219 #  35 Br
2.91  #  36 Kr

# 5
0.312 #  37 Rb
0.721 #  38 Sr
0.65  #  39 Y
0.9   #  40 Zr
1.42  #  41 Nb
1.15  #  42 Mo
-     #  43 Tc
-     #  44 Ru
-     #  45 Rh
-     #  46 Pd
1.826 #  47 Ag
1.978 #  48 Cd
2.138 #  49 In
2.298 #  50 Sn
2.458 #  51 Sb
2.618 #  52 Te
2.778 #  53 I
2.34  #  54 Xe

# 6
0.220 #  55 Cs
0.651 #  56 Ba

# Lanthanoid
-     #  57 La
-     #  58 Ce
-     #  59 Pr
-     #  60 Nd
-     #  61 Pm
-     #  62 Sm
-     #  63 Eu
-     #  64 Gd
-     #  65 Tb
-     #  66 Dy
-     #  67 Ho
-     #  68 Er
-     #  69 Tm
-     #  70 Yb
-     #  71 Lu

# 6 cont.
-     #  72 Hf
-     #  73 Ta
0.98  #  74 W
-     #  75 Re
-     #  76 Os
-     #  77 Ir
-     #  78 Pt
-     #  79 Au
2.195 #  80 Hg
2.246 #  81 Tl
2.291 #  82 Pb
2.342 #  83 Bi

```

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

### Stream Read for Low Memory Usage

Source: https://github.com/mordred-descriptor/mordred/blob/develop/README.rst

Calculates descriptors by streaming input molecules, which is suitable for large files with limited memory. It also saves the output to a CSV file.

```console
$ python -m mordred example.smi -s -o example.csv
```

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

### mordred.error Module Documentation

Source: https://github.com/mordred-descriptor/mordred/blob/develop/docs/subpackages/mordred.error.rst

This section details the mordred.error module, which contains custom exception classes used within the mordred library. It lists all members, including undocumented ones, and shows inheritance relationships.

```APIDOC
.. automodule:: mordred.error
    :members:
    :undoc-members:
    :show-inheritance:
```

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

### mordred.Result Class

Source: https://github.com/mordred-descriptor/mordred/blob/develop/docs/mordred.rst

Documentation for the Result class in the mordred package. This class likely holds the results of descriptor calculations.

```APIDOC
mordred.Result
    :members:
    - Represents the result of a descriptor calculation.
    - Likely contains methods and attributes for accessing calculated descriptor values.
```

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

### Calculate Specific Descriptors (ABCIndex)

Source: https://github.com/mordred-descriptor/mordred/blob/develop/README.rst

Calculates only the ABCIndex descriptor for molecules in a SMILES file and outputs the results.

```console
$ python -m mordred example.smi -d ABCIndex
```