2.7.1: Python Assignment 2A

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Chemical Structure Inputs for PUG-REST

Downloadable Files

Lecture02_structure_input.ipynb

lecture02_exb_compound1.sdf

lecture02_exb_compound2.sdf

lecture02_exb_compound3.sdf

lecture02_exb_compound4.sdf

lecture02_exb_compound5.sdf

Structure2D_CID_5288826.sdf

Download the ipynb file and run your Jupyter notebook.
- You can use the notebook you created in section 1.5 or the Jupyter hub at LibreText: https://jupyter.libretexts.org (see your instructor if you do not have access to the hub).
- This page is an html version of the above .ipynb file.
  - If you have questions on this assignment you should use this web page and the hypothes.is annotation to post a question (or comment) to the 2019OLCCStu class group. Contact your instructor for the link to join the discussion group.
The SDF files will be needed to complete the assignment

Objectives

Use SMILES and InChI strings to specify the input compound for a PUG-REST request.
Use a structure-data (SD) file to specify the input compound for a PUG-REST request.
Learn to submit a PUG-REST request using the HTTP-POST method.

You can use a chemical structure as an input for a PUG-REST request. PUG-REST accepts some popular chemical structure line notations such as SMILES and InChI strings. It is also possible to use an Structure-Data File (SDF) as a structure input.

To learn how to specify the structure input in a PUG-REST request, one needs to know that there are two methods by which data are transferred from clients (users) and servers (PubChem) through PUG-REST. Discussing what these methods are in detail is beyond the scope of this material, and it is enough to know three things:

When you make a PUG-REST request by typing the request URL in the address bar of your web browser (such as Google Chrome, MS Internet Explorer), the HTTP GET method is used
The HTTP GET method transfers information encoded in a single-line URL.
Some chemical structure inputs are not appropriate to encode in a single-line URL (because they may contain special characters not compatible with the URL syntax, span over multiple lines, or too long), and the HTTP POST needs to be used for such cases.

For more information on HTTP GET and POST, read the following documents.

HTTP request methods (https://www.w3schools.com/tags/ref_httpmethods.asp)
Get vs. POST (https://www.diffen.com/difference/GET-vs-POST-HTTP-Requests)

Here, import the Requests library, necessary to make web service requests to PubChem.

In [1]:

import requests

Using the HTTP GET method.

Structure encoded in the URL path.

In some cases, you can encode a chemical structure in the PUG-REST request URL path as in the following example.

In [2]:

prolog = 'https://pubchem.ncbi.nlm.nih.gov/rest/pug'

In [3]:

smiles1 = "CC(C)CC1=CC=C(C=C1)C(C)C(=O)O"
url = prolog + "/compound/smiles/" + smiles1 + "/cids/txt"
print(url)

https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/smiles/CC(C)CC1=CC=C(C=C1)C(C)C(=O)O/cids/txt

This request URL returns ibuprofen (CID 3672).

In [4]:

res = requests.get(url)
print(res.text)

Try to run the following

In [5]:

smiles2 = "CC1=C([C@@](SC1=O)(C)/C=C(\C)/C=C)O"

url = prolog + "/compound/smiles/" + smiles2 + "/cids/txt"
res = requests.get(url)
print(res.text)

Status: 400
Code: PUGREST.BadRequest
Message: Unable to standardize the given structure - perhaps some special characters need to be escaped or data packed in a MIME form?
Detail: error: 
Detail: status: 400
Detail: output: Caught ncbi::CException: Standardization failed
Detail: Output Log:
Detail: Record 1: Warning: Cactvs Ensemble cannot be created from input string
Detail: Record 1: Error: Unable to convert input into a compound object
Detail: 
Detail:

Note in the above example that the SMILES string contains special characters. In this case a forward slash ("/"), which is also used in the URL path. These special characters conflict with the PUG-REST request URL syntax, causing an error when used in the PUG-REST request URL.

Structure encoded as a URL argument

To circumvent the issue mentioned above, the SMILES string may be encoded as the URL argments (as an optional parameter followed by the "?" character).

In [6]:

url = prolog + "/compound/smiles/cids/txt?" + "smiles=" + smiles2
print(url)
res2 = requests.get(url)
print(res2.text)

https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/smiles/cids/txt?smiles=CC1=C([C@@](SC1=O)(C)/C=C(\C)/C=C)O
135403829

Structure passed in a dictionary

It is also possible to pass the structure query as a key-value pair in a dictionary.

Tutorial on Python Dictionaries

The following tutorial goes over python dictionaries: https://www.w3schools.com/python/python_dictionaries.asp

The following example does the same task as the previous example does.

In [7]:

url = prolog + "/compound/smiles/cids/txt"
struct = { 'smiles': smiles2 }
res3 = requests.get(url, params = struct)
print(res3.text)

135403829

The object returned from a web service request (res, res2, and res3 in our examples) contains information on the request URL through which the data have been retrieved. This information can be accessed using the ".url" attribute of the object, as shown in this example:

In [8]:

print(smiles2)    # the orginal smiles string unencoded
print(res2.url)   # from (request 2) structure encoded as a URL argument
print()
print(struct)     # to show the smiles string in the dictionary is unencoded for URL
print(res3.url)   # from (request 3) structure passed in a dictionary

CC1=C([C@@](SC1=O)(C)/C=C(\C)/C=C)O
https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/smiles/cids/txt?smiles=CC1=C(%5BC@@%5D(SC1=O)(C)/C=C(%5CC)/C=C)O

{'smiles': 'CC1=C([C@@](SC1=O)(C)/C=C(\\C)/C=C)O'}
https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/smiles/cids/txt?smiles=CC1%3DC%28%5BC%40%40%5D%28SC1%3DO%29%28C%29%2FC%3DC%28%5CC%29%2FC%3DC%29O

From these two URLs, we can see two important things:

When the structure is passed using a key-value pair in a dictionary (i.e., "res3"), the structure is automatically encoded as a URL argument (after the "?" mark).
When the structure is passed in a dictionary, the special characters in the SMILES string are converted according to the URL encoding rules: https://www.w3schools.com/tags/ref_urlencode.asp. [for example, the equal sign "=" changes into "%3D", and "(" into "%28", "/" into "%2F", etc]

It illustrates that the last two approaches using HTTP GET are essentially the same.

Exercise 1a Retrieve (in the CSV (comma-separated values) format) the Hydrogen bond donor and acceptor counts, TPSA, and XLogP of the chemical represented by the SMILES string: "C1=CC(=C(C=C1Cl)O)OC2=C(C=C(C=C2)Cl)Cl". When you construct a PUG-REST url for this request, encode the structure in the URL path.

In [9]:

# Write your code in this cell.

Exercise 1b Get the CID corresponding to the following InChI string, using the HTTP GET method. Pay attention to the case sensitivity of the URL parameter part after the "?" mark.

In [10]:

inchi = "InChI=1S/C17H14O4S/c1-22(19,20)14-9-7-12(8-10-14)15-11-21-17(18)16(15)13-5-3-2-4-6-13/h2-10H,11H2,1H3"

In [11]:

# Write your code in this cell

Using the HTTP POST method

Comparison of HTTP POST and GET

All the three examples above use the HTTP GET method, as implied in the use of "requests.get()". Alternatively, one can use the HTTP POST method. For example, the following example returns the identical result as the last two HTTP GET examples.

In [12]:

url = prolog + "/compound/smiles/cids/txt"
struct = { 'smiles': smiles2 }
res = requests.post(url, params = struct)   # the SMILES as a URL parameter
print(res.url)
print(res.text)

https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/smiles/cids/txt?smiles=CC1%3DC%28%5BC%40%40%5D%28SC1%3DO%29%28C%29%2FC%3DC%28%5CC%29%2FC%3DC%29O
135403829

In [13]:

url = prolog + "/compound/smiles/cids/txt"
struct = { 'smiles': smiles2 }
res = requests.post(url, data = struct)    # the SMILES as data
print(res.url)
print(res.text)

https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/smiles/cids/txt
135403829

Note that the first one passes the input SMILES string as a parameter, while the second one passes it as data. Because of this, the URL stored in the "res.url" variable in the second code does not contain structure informaion.

HTTP POST for multi-line structure input

The HTTP POST method should be used if the input molecular structure for PUG-REST request span over multiple lines (e.g., stored in a structure-data file (SDF) format). The SDF file contains structure information of a molecule in a multi-line format, along with other data.

In [14]:

mysdf = '''1983
  -OEChem-07241917072D

 20 20  0     0  0  0  0  0  0999 V2000
    2.8660   -2.5950    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5981    1.4050    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8660    1.4050    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8660    0.4050    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7320   -0.0950    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0000   -0.0950    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7320   -1.0950    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0000   -1.0950    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8660   -1.5950    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7320    1.9050    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7320    2.9050    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2690    0.2150    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4631    0.2150    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3291    1.7150    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2690   -1.4050    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4631   -1.4050    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3520    2.9050    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7320    3.5250    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1120    2.9050    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3291   -2.9050    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  9  1  0  0  0  0
  1 20  1  0  0  0  0
  2 10  2  0  0  0  0
  3  4  1  0  0  0  0
  3 10  1  0  0  0  0
  3 14  1  0  0  0  0
  4  5  2  0  0  0  0
  4  6  1  0  0  0  0
  5  7  1  0  0  0  0
  5 12  1  0  0  0  0
  6  8  2  0  0  0  0
  6 13  1  0  0  0  0
  7  9  2  0  0  0  0
  7 15  1  0  0  0  0
  8  9  1  0  0  0  0
  8 16  1  0  0  0  0
 10 11  1  0  0  0  0
 11 17  1  0  0  0  0
 11 18  1  0  0  0  0
 11 19  1  0  0  0  0
M  END
> <PUBCHEM_COMPOUND_CID>
1983

> <PUBCHEM_COMPOUND_CANONICALIZED>
1

> <PUBCHEM_CACTVS_COMPLEXITY>
139

> <PUBCHEM_CACTVS_HBOND_ACCEPTOR>
2

> <PUBCHEM_CACTVS_HBOND_DONOR>
2

> <PUBCHEM_CACTVS_ROTATABLE_BOND>
1
$$$$
'''

In this example, the triple quotes (''') are used to enclose a multi-line string. This multi-line sdf data is used as an input for a PUG-REST request through the HTTP POST.

In [19]:

url = prolog + "/compound/sdf/cids/txt"
mydata = { 'sdf': mysdf }
res = requests.post(url, data=mydata) # the multiline sdf as URL data
print(res.url)
print(res.text)

https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/sdf/cids/txt
1983

HTTP POST for SDF file input

One may want to use the structure stored in a file as the input for a PUG-REST request. The following code shows how to read an SDF file into a variable. This code cell assumes that the 'Structure2D_CID_5288826.sdf' file is in the current directory. The file can be downloaded from the Chapter 2 Assignments page.

In [20]:

with open('Structure2D_CID_5288826.sdf', 'r') as file:
    mysdf = file.read()
    
print(mysdf)

5288826
  -OEChem-08171913162D

 40 44  0     1  0  0  0  0  0999 V2000
    2.2314    0.0528    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0000   -2.4021    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0000    2.4021    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.1607   -0.9511    0.0000 N   0  0  3  0  0  0  0  0  0  0  0  0
    3.6897   -0.4755    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.5133   -0.9511    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.3370   -0.4755    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8660   -0.9511    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.2392    0.2219    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6897    0.4755    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3370    0.4755    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5918    0.2219    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5133    0.9511    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8660   -1.9022    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.5133   -1.9022    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8660    0.9511    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6897   -2.3777    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8418   -1.6832    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5133    1.9022    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8660    1.9022    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6897    2.3777    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0597   -1.6022    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6284   -1.2740    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0496   -1.1875    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3760    0.8266    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6795    0.4887    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9476    0.3679    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5490    1.0581    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1840    0.4057    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4989    0.8349    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8660   -2.5222    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0503   -2.2122    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6897   -2.9977    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3879   -2.1055    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.2641   -2.1371    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.2957   -1.2609    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0503    2.2122    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6897    2.9977    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0000   -3.0222    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0000    3.0222    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  8  1  0  0  0  0
  1 16  1  0  0  0  0
 14  2  1  6  0  0  0
  2 39  1  0  0  0  0
  3 20  1  0  0  0  0
  3 40  1  0  0  0  0
  4  7  1  0  0  0  0
  4 12  1  0  0  0  0
  4 18  1  0  0  0  0
  5  6  1  0  0  0  0
  5  8  1  0  0  0  0
  5  9  1  1  0  0  0
  5 10  1  0  0  0  0
  6  7  1  0  0  0  0
  6 15  1  0  0  0  0
  6 22  1  1  0  0  0
  7 11  1  0  0  0  0
  7 23  1  6  0  0  0
  8 14  1  0  0  0  0
  8 24  1  1  0  0  0
  9 12  1  0  0  0  0
  9 25  1  0  0  0  0
  9 26  1  0  0  0  0
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 10 16  1  0  0  0  0
 11 13  1  0  0  0  0
 11 27  1  0  0  0  0
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 12 29  1  0  0  0  0
 12 30  1  0  0  0  0
 13 19  1  0  0  0  0
 14 17  1  0  0  0  0
 14 31  1  0  0  0  0
 15 17  2  0  0  0  0
 15 32  1  0  0  0  0
 16 20  2  0  0  0  0
 17 33  1  0  0  0  0
 18 34  1  0  0  0  0
 18 35  1  0  0  0  0
 18 36  1  0  0  0  0
 19 21  2  0  0  0  0
 19 37  1  0  0  0  0
 20 21  1  0  0  0  0
 21 38  1  0  0  0  0
M  END
> <PUBCHEM_COMPOUND_CID>
5288826

> <PUBCHEM_COMPOUND_CANONICALIZED>
1

> <PUBCHEM_CACTVS_COMPLEXITY>
494

> <PUBCHEM_CACTVS_HBOND_ACCEPTOR>
4

> <PUBCHEM_CACTVS_HBOND_DONOR>
2

> <PUBCHEM_CACTVS_ROTATABLE_BOND>
0

> <PUBCHEM_CACTVS_SUBSKEYS>
AAADceB6MAAAAAAAAAAAAAAAAAAAASAAAAA8YIEAAAAWAEjBAAAAHgAACAAADzzhmAYyBoMABgCAAiBCAAACCAAgIAAIiAAOiIgNNiKGsRuGeCOkwBGLuAew8PcPoAABAAAYQADQAAaAADSAAAAAAAAAAA==

> <PUBCHEM_IUPAC_OPENEYE_NAME>
(4R,4aR,7S,7aR,12bS)-3-methyl-2,4,4a,7,7a,13-hexahydro-1H-4,12-methanobenzofuro[3,2-e]isoquinoline-7,9-diol

> <PUBCHEM_IUPAC_CAS_NAME>
(4R,4aR,7S,7aR,12bS)-3-methyl-2,4,4a,7,7a,13-hexahydro-1H-4,12-methanobenzofuro[3,2-e]isoquinoline-7,9-diol

> <PUBCHEM_IUPAC_NAME_MARKUP>
(4<I>R</I>,4<I>a</I><I>R</I>,7<I>S</I>,7<I>a</I><I>R</I>,12<I>b</I><I>S</I>)-3-methyl-2,4,4<I>a</I>,7,7<I>a</I>,13-hexahydro-1<I>H</I>-4,12-methanobenzofuro[3,2-e]isoquinoline-7,9-diol

> <PUBCHEM_IUPAC_NAME>
(4R,4aR,7S,7aR,12bS)-3-methyl-2,4,4a,7,7a,13-hexahydro-1H-4,12-methanobenzofuro[3,2-e]isoquinoline-7,9-diol

> <PUBCHEM_IUPAC_SYSTEMATIC_NAME>
(4R,4aR,7S,7aR,12bS)-3-methyl-2,4,4a,7,7a,13-hexahydro-1H-4,12-methanobenzofuro[3,2-e]isoquinoline-7,9-diol

> <PUBCHEM_IUPAC_TRADITIONAL_NAME>
(4R,4aR,7S,7aR,12bS)-3-methyl-2,4,4a,7,7a,13-hexahydro-1H-4,12-methanobenzofuro[3,2-e]isoquinoline-7,9-diol

> <PUBCHEM_IUPAC_INCHI>
InChI=1S/C17H19NO3/c1-18-7-6-17-10-3-5-13(20)16(17)21-15-12(19)4-2-9(14(15)17)8-11(10)18/h2-5,10-11,13,16,19-20H,6-8H2,1H3/t10-,11+,13-,16-,17-/m0/s1

> <PUBCHEM_IUPAC_INCHIKEY>
BQJCRHHNABKAKU-KBQPJGBKSA-N

> <PUBCHEM_XLOGP3>
0.8

> <PUBCHEM_EXACT_MASS>
285.136493

> <PUBCHEM_MOLECULAR_FORMULA>
C17H19NO3

> <PUBCHEM_MOLECULAR_WEIGHT>
285.34

> <PUBCHEM_OPENEYE_CAN_SMILES>
CN1CCC23C4C1CC5=C2C(=C(C=C5)O)OC3C(C=C4)O

> <PUBCHEM_OPENEYE_ISO_SMILES>
CN1CC[C@]23[C@@H]4[C@H]1CC5=C2C(=C(C=C5)O)O[C@H]3[C@H](C=C4)O

> <PUBCHEM_CACTVS_TPSA>
52.9

> <PUBCHEM_MONOISOTOPIC_WEIGHT>
285.136493

> <PUBCHEM_TOTAL_CHARGE>
0

> <PUBCHEM_HEAVY_ATOM_COUNT>
21

> <PUBCHEM_ATOM_DEF_STEREO_COUNT>
5

> <PUBCHEM_ATOM_UDEF_STEREO_COUNT>
0

> <PUBCHEM_BOND_DEF_STEREO_COUNT>
0

> <PUBCHEM_BOND_UDEF_STEREO_COUNT>
0

> <PUBCHEM_ISOTOPIC_ATOM_COUNT>
0

> <PUBCHEM_COMPONENT_COUNT>
1

> <PUBCHEM_CACTVS_TAUTO_COUNT>
-1

> <PUBCHEM_COORDINATE_TYPE>
1
5
255

> <PUBCHEM_BONDANNOTATIONS>
10  13  8
10  16  8
13  19  8
16  20  8
19  21  8
14  2  6
20  21  8
5  9  5
6  22  5
7  23  6
8  24  5

$$$$

Now the structure stored in the "mysdf" can be used in a PUG-REST request through HTTP-POST. For example, the code cell below shows how to retrieve various names (also called "synonyms") of the input structure.

In [17]:

url = prolog + "/compound/sdf/synonyms/txt"
mydata = { 'sdf': mysdf }
res = requests.post(url, data=mydata)
print(res.text)

morphine
Morphia
Morphinum
Morphium
Morphina
Morphin
(-)-Morphine
Duromorph
MS Contin
DepoDur
Meconium
Morphinism
Moscontin
Ospalivina
Morfina
l-Morphine
Dulcontin
Nepenthe
Roxanol
Kadian
57-27-2
MORPHINE SULFATE
Infumorph
Dreamer
Morpho
Avinza
Hocus
Unkie
Cube juice
Hard stuff
Oramorph SR
Statex SR
M-Eslon
Ms Emma
Morphin [German]
Morfina [Italian]
Duramorph
Morphina [Italian]
Morphine [BAN]
Astramorph PF
Duramorph PF
CCRIS 5762
Dolcontin
HSDB 2134
(5R,6S,9R,13S,14R)-4,5-Epoxy-N-methyl-7-morphinen-3,6-diol
UNII-76I7G6D29C
D-(-)-Morphine
CHEBI:17303
CHEMBL70
EINECS 200-320-2
4,5alpha-Epoxy-17-methyl-7-morphinen-3,6alpha-diol
7,8-Didehydro-4,5-epoxy-17-methyl-morphinan-3,6-diol
(7R,7AS,12BS)-3-METHYL-2,3,4,4A,7,7A-HEXAHYDRO-1H-4,12-METHANO[1]BENZOFURO[3,2-E]ISOQUINOLINE-7,9-DIOL
DEA No. 9300
Morphine Anhydrate
76I7G6D29C
(5alpha,6alpha)-17-methyl-7,8-didehydro-4,5-epoxymorphinan-3,6-diol
Morphine (BAN)
Morphine Forte
RMS
Morphine H.P
(5alpha,6alpha)-Didehydro-4,5-epoxy-17-methylmorphinan-3,6-diol
Morphinan-3,6-alpha-diol, 7,8-didehydro-4,5-alpha-epoxy-17-methyl-
Morphine Extra-Forte
Morphinan-3,6-diol, 7,8-didehydro-4,5-epoxy-17-methyl-, (5alpha,6alpha)-
9H-9,9c-Iminoethanophenanthro(4,5-bcd)furan-3,5-diol, 4a,5,7a,8-tetrahydro-12-methyl-
methyl[?]diol
Aguettant
Dinamorf
Sevredol
Dimorf
MOI
Epimorph
Morphitec
Oramorph
Rescudose
Statex Drops
OMS Concentrate
RMS Uniserts
Roxanol UD
(Morphine)
Substitol (TN)
Mscontin, Oramorph
(4R,4aR,7S,7aR,12bS)-3-methyl-2,4,4a,7,7a,13-hexahydro-1H-4,12-methanobenzofuro[3,2-e]isoquinoline-7,9-diol
(-)-(etorphine)
MSIR
Roxanol 100
(-)Morphine sulfate
Morfina Dosa (TN)
SDZ202-250
NSC11441
SDZ 202-250
MS/L
MS/S
Epitope ID:116646
Morphinan-3,6-diol, 7,8-didehydro-4,5-epoxy-17-methyl- (5alpha,6alpha)-
SCHEMBL2997
M.O.S
BIDD:GT0147
GTPL1627
DTXSID9023336
Morphine 0.1 mg/ml in Methanol
Morphine 1.0 mg/ml in Methanol
BQJCRHHNABKAKU-KBQPJGBKSA-N
ZINC3812983
BDBM50000092
AKOS015966554
DB00295
AN-23579
AN-23737
LS-91748
C01516
D08233
7,8-Didehydro-4,5-epoxy-17-methylmorphinan-3,6-diol
UNII-1M5VY6ITRT component BQJCRHHNABKAKU-KBQPJGBKSA-N
17-methyl-7,8-didehydro-4,5alpha-epoxymorphinan-3,6alpha-diol
7,8-Didehydro-4,5-epoxy-17-methylmorphinan-3,6-diol(morphine)
(5A,6A)-7,8-DIDEHYDRO-4,5-EPOXY-17-METHYLMORPHINIAN-3,6-DIOL
(5alpha,6alpha)-7,8-Didehydro-4,5-epoxy-17-methylmorphinan-3,6-diol
(5alpha,6beta)-17-methyl-7,8-didehydro-4,5-epoxymorphinan-3,6-diol
3-(4-Hydroxy-phenyl)-1-propyl-piperidine-3-carboxylic acid ethyl ester
6-tert-Butyl-3-methyl-1,2,3,4,5,6-hexahydro-2,6-methano-benzo[d]azocine
(-)(5.alpha.,6.alpha.)-7,8-Didehydro-4,5-epoxy-17-methylmorphinan-3,6-diol
Morphinan-3,6-diol, 7,8-didehydro-4,5-epoxy-17-methyl- (5..alpha.,6.alpha.)-
Morphine solution, 1.0 mg/mL in methanol, ampule of 1 mL, certified reference material
(1S,5R,13R,14S)-12-oxa-4-azapentacyclo[9.6.1.01,13.05,17.07,18]octadeca-7(18),8,10,15-tetraene-10,14-diol
(1S,5R,13R,14S,17R)-4-methyl-12-oxa-4-azapentacyclo[9.6.1.0;{1,13}.0;{5,17}.0;{7,18}]octadeca-7(18),8,10,15-tetraene-10,14-diol
(1S,5R,13R,14S,17R)-4-methyl-12-oxa-4-azapentacyclo[9.6.1.0^{1,13}.0^{5,17}.0^{7,18}]octadeca-7,9,11(18),15-tetraene-10,14-diol
(morphine) 4-methyl-(1S,5R,13R,14S,17R)-12-oxa-4-azapentacyclo[9.6.1.01,13.05,17.07,18]octadeca-7(18),8,10,15-tetraene-10,14-diol
2-{4-[2,4-diamino-6-pteridinylmethyl(methyl)amino]phenylcarboxamido}pentanedioic acid(morphine)
4-methyl-(1S,5R,13R,14S,17R)-12-oxa-4-azapentacyclo[9.6.1.01,13.05,17.07,18]octadeca-7(18),8,10,15-tetraene-10,14-diol
4-methyl-(1S,5R,13R,14S,17R)-12-oxa-4-azapentacyclo[9.6.1.01,13.05,17.07,18]octadeca-7(18),8,10,15-tetraene-10,14-diol ; HydroChloride
4-methyl-(1S,5R,13R,14S,17R)-12-oxa-4-azapentacyclo[9.6.1.01,13.05,17.07,18]octadeca-7(18),8,10,15-tetraene-10,14-diol ;sulphate salt(morphine)
4-methyl-(1S,5R,13R,14S,17R)-12-oxa-4-azapentacyclo[9.6.1.01,13.05,17.07,18]octadeca-7(18),8,10,15-tetraene-10,14-diol((Morphine))
4-methyl-(1S,5R,13R,14S,17R)-12-oxa-4-azapentacyclo[9.6.1.01,13.05,17.07,18]octadeca-7(18),8,10,15-tetraene-10,14-diol(morphine sulfate)
4-methyl-(1S,5R,13R,14S,17R)-12-oxa-4-azapentacyclo[9.6.1.01,13.05,17.07,18]octadeca-7(18),8,10,15-tetraene-10,14-diol(morphine)
4-methyl-(1S,5R,13R,14S,17R)-12-oxa-4-azapentacyclo[9.6.1.01,13.05,17.07,18]octadeca-7(18),8,10,15-tetraene-10,14-diol(Morphine)(HCl)
4-methyl-(1S,5R,13R,14S,17R)-12-oxa-4-azapentacyclo[9.6.1.01,13.05,17.07,18]octadeca-7(18),8,10,15-tetraene-10,14-diol,sulfate(Morphinesulfate)
4-methyl-(1S,5R,13R,14S,17R)-12-oxa-4-azapentacyclo[9.6.1.01,13.05,17.07,18]octadeca-7(18),8,10,15-tetraene-10,14-diolMorphine
4-methyl-12-oxa-4-azapentacyclo[9.6.1.01,13.05,17.07,18]octadeca-7(18),8,10,15-tetraene-10,14-diol
4-methyl-12-oxa-4-azapentacyclo[9.6.1.01,13.05,17.07,18]octadeca-7(18),8,10,15-tetraene-10,14-diol (morphine)
4-methyl-12-oxa-4-azapentacyclo[9.6.1.01,13.05,17.07,18]octadeca-7(18),8,10,15-tetraene-10,14-diol(Morphine)
6,11-Dimethyl-3-(3-methyl-but-2-enyl)-1,2,3,4,5,6-hexahydro-2,6-methano-benzo[d]azocin-8-ol(Morphine)
9H-9,9c-Iminoethanophenanthro(4,5-bcd)furan-3,5-diol, 4alpha,5,7alpha,8-tetrahydro-12-methyl-
MORPHINE, (5A,6A)-7,8-DIDEHYDRO-4,5-EPOXY-17-METHYLMORPHINIAN-3,6-DIOL, MORPHIUM, MORPHIA, DOLCONTIN, DUROMORPH, MORPHINA, NEPENTHE
Morphine;4-methyl-(1S,5R,13R,14S,17R)-12-oxa-4-azapentacyclo[9.6.1.01,13.05,17.07,18]octadeca-7(18),8,10,15-tetraene-10,14-diol

Exercise 2a Retrieve (in the CSV format) the XlogP, molecular weight, hydrogen bond donor count, hydrogen bond aceptor count, and TPSA of the compounds contained in the five sdf files below, which can be downloaded from the Chapter 2 Assignments page.

Use a for loop to retrieve the data for each compound.
Import the time package and add "time.sleep(0.2)" to sleep 0.2 seconds after retrieving the data for each compound.
Refer to the "lecture 1" notebook to see how to merge the multiple CSV outputs into a single CSV output.

In [18]:

files = ['lecture02_ex2b_compound1.sdf','lecture02_ex2b_compound2.sdf','lecture02_ex2b_compound3.sdf', \
         'lecture02_ex2b_compound4.sdf','lecture02_ex2b_compound5.sdf']

In [ ]:

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Tutorial on Python Dictionaries