CAS Common Chemistry API#
About this interactive 
recipe
Author: Vincent Scalfani
Reviewer: Stuart Chalk
Topics: How to interact with the CAS Common Chemistry API using Python.
Attribution: Adapted from the MIT licensed University of Alabama Scholarly API Cookbook Use of the CAS Common Chemistry API requires registration: https://www.cas.org/services/commonchemistry-api. Example data shown is credited to CAS Common Chemistry, which is licensed under the CC BY-NC 4.0 license.
Format: Interactive Jupyter Notebook (Python)
Scenarios: You are search for identifiers and general property of common chemical substances.
Skills: You should be familiar with
Learning outcomes: After completing this example you should understand:
What kind of data is available through the CAS Common Chemistry API
How to interact with the CAS Common Chemistry API using Python
Citation: ‘CAS Common Chemistry API’, Vincent Scalfani, The IUPAC FAIR Chemistry Cookbook, Contributed: 2024-02-14 https://w3id.org/ifcc/IFCC011.
Reuse: This notebook is made available under a CC-BY-4.0 license.
1. Common Chemistry Record Detail Retrieval#
Information about substances in CAS Common Chemistry can be retrieved using the /detail API and a CAS RN identifier:
Import libraries#
import requests
from pprint import pprint
Setup API parameters#
detail_base_url = "https://commonchemistry.cas.org/api/detail?"
casrn1 = "10094-36-7" # ethyl cyclohexanepropionate
Request data from CAS Common Chemistry Detail API#
casrn1_data = requests.get(detail_base_url + "cas_rn=" + casrn1).json()
pprint(casrn1_data)
{'canonicalSmile': 'O=C(OCC)CCC1CCCCC1',
'experimentalProperties': [{'name': 'Boiling Point',
'property': '105-113 °C @ Press: 17 Torr',
'sourceNumber': 1}],
'hasMolfile': True,
'image': '<svg width="215" viewBox="0 0 215 101" style="fill-opacity:1; '
'color-rendering:auto; color-interpolation:auto; '
'text-rendering:auto; stroke:black; stroke-linecap:square; '
'stroke-miterlimit:10; shape-rendering:auto; stroke-opacity:1; '
'fill:black; stroke-dasharray:none; font-weight:normal; '
"stroke-width:1; font-family:'Open Sans'; font-style:normal; "
'stroke-linejoin:miter; font-size:12; stroke-dashoffset:0; '
'image-rendering:auto;" height="101" class="cas-substance-image" '
'xmlns:xlink="http://www.w3.org/1999/xlink" '
'xmlns="http://www.w3.org/2000/svg"><svg '
'class="cas-substance-single-component"><rect y="0" x="0" '
'width="215" stroke="none" ry="7" rx="7" height="101" fill="white" '
'class="cas-substance-group"/><svg y="0" x="0" width="215" '
'viewBox="0 0 215 101" style="fill:black;" height="101" '
'class="cas-substance-single-component-image"><svg><g><g '
'transform="translate(107,49)" '
'style="text-rendering:geometricPrecision; '
'color-rendering:optimizeQuality; color-interpolation:linearRGB; '
'stroke-linecap:butt; image-rendering:optimizeQuality;"><line y2="0" '
'y1="15" x2="0" x1="-25.98" style="fill:none;"/><line y2="0" y1="15" '
'x2="-51.963" x1="-25.98" style="fill:none;"/><line y2="15" y1="0" '
'x2="25.98" x1="0" style="fill:none;"/><line y2="3.1886" y1="15" '
'x2="46.4398" x1="25.98" style="fill:none;"/><line y2="38.5234" '
'y1="13.9896" x2="24.23" x1="24.23" style="fill:none;"/><line '
'y2="38.5234" y1="13.9897" x2="27.73" x1="27.73" '
'style="fill:none;"/><line y2="15" y1="3.1786" x2="77.943" '
'x1="57.4684" style="fill:none;"/><line y2="0" y1="15" x2="103.923" '
'x1="77.943" style="fill:none;"/><line y2="15" y1="0" x2="-77.943" '
'x1="-51.963" style="fill:none;"/><line y2="-30" y1="0" x2="-51.963" '
'x1="-51.963" style="fill:none;"/><line y2="0" y1="15" x2="-103.923" '
'x1="-77.943" style="fill:none;"/><line y2="-45" y1="-30" '
'x2="-77.943" x1="-51.963" style="fill:none;"/><line y2="-30" y1="0" '
'x2="-103.923" x1="-103.923" style="fill:none;"/><line y2="-30" '
'y1="-45" x2="-103.923" x1="-77.943" style="fill:none;"/><path '
'style="fill:none; stroke-miterlimit:5;" d="M-25.547 14.75 L-25.98 '
'15 L-26.413 14.75"/><path style="fill:none; stroke-miterlimit:5;" '
'd="M-0.433 0.25 L0 0 L0.433 0.25"/><path style="fill:none; '
'stroke-miterlimit:5;" d="M25.547 14.75 L25.98 15 L26.413 '
'14.75"/></g><g transform="translate(107,49)" '
'style="stroke-linecap:butt; fill:rgb(230,0,0); '
'text-rendering:geometricPrecision; color-rendering:optimizeQuality; '
"image-rendering:optimizeQuality; font-family:'Open Sans'; "
'stroke:rgb(230,0,0); color-interpolation:linearRGB; '
'stroke-miterlimit:5;"><path style="stroke:none;" d="M55.9005 '
'-0.0703 Q55.9005 1.9922 54.8614 3.1719 Q53.8224 4.3516 51.9786 '
'4.3516 Q50.088 4.3516 49.0568 3.1875 Q48.0255 2.0234 48.0255 '
'-0.0859 Q48.0255 -2.1797 49.0568 -3.3281 Q50.088 -4.4766 51.9786 '
'-4.4766 Q53.838 -4.4766 54.8693 -3.3047 Q55.9005 -2.1328 55.9005 '
'-0.0703 ZM49.0724 -0.0703 Q49.0724 1.6641 49.8146 2.5703 Q50.5568 '
'3.4766 51.9786 3.4766 Q53.4005 3.4766 54.1271 2.5781 Q54.8536 '
'1.6797 54.8536 -0.0703 Q54.8536 -1.8047 54.1271 -2.6953 Q53.4005 '
'-3.5859 51.9786 -3.5859 Q50.5568 -3.5859 49.8146 -2.6875 Q49.0724 '
'-1.7891 49.0724 -0.0703 Z"/><path style="stroke:none;" d="M29.9175 '
'44.9297 Q29.9175 46.9922 28.8784 48.1719 Q27.8394 49.3516 25.9956 '
'49.3516 Q24.105 49.3516 23.0737 48.1875 Q22.0425 47.0234 22.0425 '
'44.9141 Q22.0425 42.8203 23.0737 41.6719 Q24.105 40.5234 25.9956 '
'40.5234 Q27.855 40.5234 28.8862 41.6953 Q29.9175 42.8672 29.9175 '
'44.9297 ZM23.0894 44.9297 Q23.0894 46.6641 23.8316 47.5703 Q24.5737 '
'48.4766 25.9956 48.4766 Q27.4175 48.4766 28.1441 47.5781 Q28.8706 '
'46.6797 28.8706 44.9297 Q28.8706 43.1953 28.1441 42.3047 Q27.4175 '
'41.4141 25.9956 41.4141 Q24.5737 41.4141 23.8316 42.3125 Q23.0894 '
'43.2109 23.0894 44.9297 Z"/><path style="fill:none; stroke:black;" '
'd="M77.51 14.75 L77.943 15 L78.376 14.75"/><path style="fill:none; '
'stroke:black;" d="M-77.51 14.75 L-77.943 15 L-78.376 14.75"/><path '
'style="fill:none; stroke:black;" d="M-51.963 -29.5 L-51.963 -30 '
'L-52.396 -30.25"/><path style="fill:none; stroke:black;" '
'd="M-103.49 0.25 L-103.923 0 L-103.923 -0.5"/><path '
'style="fill:none; stroke:black;" d="M-77.51 -44.75 L-77.943 -45 '
'L-78.376 -44.75"/><path style="fill:none; stroke:black;" '
'd="M-103.923 -29.5 L-103.923 -30 L-103.49 '
'-30.25"/></g></g></svg></svg></svg></svg>',
'inchi': 'InChI=1S/C11H20O2/c1-2-13-11(12)9-8-10-6-4-3-5-7-10/h10H,2-9H2,1H3',
'inchiKey': 'InChIKey=NRVPMFHPHGBQLP-UHFFFAOYSA-N',
'molecularFormula': 'C<sub>11</sub>H<sub>20</sub>O<sub>2</sub>',
'molecularMass': '184.28',
'name': 'Ethyl cyclohexanepropionate',
'propertyCitations': [{'docUri': 'document/pt/document/22252593',
'source': 'De Benneville, Peter L.; Journal of the '
'American Chemical Society, (1940), 62, '
'283-7, CAplus',
'sourceNumber': 1}],
'replacedRns': [],
'rn': '10094-36-7',
'smile': 'C(CC(OCC)=O)C1CCCCC1',
'synonyms': ['Cyclohexanepropanoic acid, ethyl ester',
'Cyclohexanepropionic acid, ethyl ester',
'Ethyl cyclohexanepropionate',
'Ethyl cyclohexylpropanoate',
'Ethyl 3-cyclohexylpropionate',
'Ethyl 3-cyclohexylpropanoate',
'3-Cyclohexylpropionic acid ethyl ester',
'NSC 71463',
'Ethyl 3-cyclohexanepropionate'],
'uri': 'substance/pt/10094367'}
Display the Molecule Drawing#
# get svg image text
svg_string1 = casrn1_data["image"]
# display the molecule
from IPython.display import SVG
SVG(svg_string1)
Select some specific data#
# Get Experimental Properties
casrn1_data["experimentalProperties"][0]
{'name': 'Boiling Point',
'property': '105-113 °C @ Press: 17 Torr',
'sourceNumber': 1}
# Get Boiling Point property
casrn1_data["experimentalProperties"][0]["property"]
'105-113 °C @ Press: 17 Torr'
# Get InChIKey
casrn1_data["inchiKey"]
'InChIKey=NRVPMFHPHGBQLP-UHFFFAOYSA-N'
# Get Canonical SMILES
casrn1_data["canonicalSmile"]
'O=C(OCC)CCC1CCCCC1'
2. Common Chemistry API record detail retrieval in a loop#
Import libraries#
import requests
from pprint import pprint
from time import sleep
Setup API parameters#
detail_base_url = "https://commonchemistry.cas.org/api/detail?"
casrn_list = ["10094-36-7", "10031-92-2", "10199-61-8", "10036-21-2", "1019020-13-3"]
Request data for each CAS RN and save to a list#
casrn_data = []
for casrn in casrn_list:
casrn_data.append(requests.get(detail_base_url + "cas_rn=" + casrn).json())
sleep(1) # add a delay between API calls
casrn_data[0:2] # view first 2
[{'uri': 'substance/pt/10094367',
'rn': '10094-36-7',
'name': 'Ethyl cyclohexanepropionate',
'image': '<svg width="215" viewBox="0 0 215 101" style="fill-opacity:1; color-rendering:auto; color-interpolation:auto; text-rendering:auto; stroke:black; stroke-linecap:square; stroke-miterlimit:10; shape-rendering:auto; stroke-opacity:1; fill:black; stroke-dasharray:none; font-weight:normal; stroke-width:1; font-family:\'Open Sans\'; font-style:normal; stroke-linejoin:miter; font-size:12; stroke-dashoffset:0; image-rendering:auto;" height="101" class="cas-substance-image" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns="http://www.w3.org/2000/svg"><svg class="cas-substance-single-component"><rect y="0" x="0" width="215" stroke="none" ry="7" rx="7" height="101" fill="white" class="cas-substance-group"/><svg y="0" x="0" width="215" viewBox="0 0 215 101" style="fill:black;" height="101" class="cas-substance-single-component-image"><svg><g><g transform="translate(107,49)" style="text-rendering:geometricPrecision; color-rendering:optimizeQuality; color-interpolation:linearRGB; stroke-linecap:butt; image-rendering:optimizeQuality;"><line y2="0" y1="15" x2="0" x1="-25.98" style="fill:none;"/><line y2="0" y1="15" x2="-51.963" x1="-25.98" style="fill:none;"/><line y2="15" y1="0" x2="25.98" x1="0" style="fill:none;"/><line y2="3.1886" y1="15" x2="46.4398" x1="25.98" style="fill:none;"/><line y2="38.5234" y1="13.9896" x2="24.23" x1="24.23" style="fill:none;"/><line y2="38.5234" y1="13.9897" x2="27.73" x1="27.73" style="fill:none;"/><line y2="15" y1="3.1786" x2="77.943" x1="57.4684" style="fill:none;"/><line y2="0" y1="15" x2="103.923" x1="77.943" style="fill:none;"/><line y2="15" y1="0" x2="-77.943" x1="-51.963" style="fill:none;"/><line y2="-30" y1="0" x2="-51.963" x1="-51.963" style="fill:none;"/><line y2="0" y1="15" x2="-103.923" x1="-77.943" style="fill:none;"/><line y2="-45" y1="-30" x2="-77.943" x1="-51.963" style="fill:none;"/><line y2="-30" y1="0" x2="-103.923" x1="-103.923" style="fill:none;"/><line y2="-30" y1="-45" x2="-103.923" x1="-77.943" style="fill:none;"/><path style="fill:none; stroke-miterlimit:5;" d="M-25.547 14.75 L-25.98 15 L-26.413 14.75"/><path style="fill:none; stroke-miterlimit:5;" d="M-0.433 0.25 L0 0 L0.433 0.25"/><path style="fill:none; stroke-miterlimit:5;" d="M25.547 14.75 L25.98 15 L26.413 14.75"/></g><g transform="translate(107,49)" style="stroke-linecap:butt; fill:rgb(230,0,0); text-rendering:geometricPrecision; color-rendering:optimizeQuality; image-rendering:optimizeQuality; font-family:\'Open Sans\'; stroke:rgb(230,0,0); color-interpolation:linearRGB; stroke-miterlimit:5;"><path style="stroke:none;" d="M55.9005 -0.0703 Q55.9005 1.9922 54.8614 3.1719 Q53.8224 4.3516 51.9786 4.3516 Q50.088 4.3516 49.0568 3.1875 Q48.0255 2.0234 48.0255 -0.0859 Q48.0255 -2.1797 49.0568 -3.3281 Q50.088 -4.4766 51.9786 -4.4766 Q53.838 -4.4766 54.8693 -3.3047 Q55.9005 -2.1328 55.9005 -0.0703 ZM49.0724 -0.0703 Q49.0724 1.6641 49.8146 2.5703 Q50.5568 3.4766 51.9786 3.4766 Q53.4005 3.4766 54.1271 2.5781 Q54.8536 1.6797 54.8536 -0.0703 Q54.8536 -1.8047 54.1271 -2.6953 Q53.4005 -3.5859 51.9786 -3.5859 Q50.5568 -3.5859 49.8146 -2.6875 Q49.0724 -1.7891 49.0724 -0.0703 Z"/><path style="stroke:none;" d="M29.9175 44.9297 Q29.9175 46.9922 28.8784 48.1719 Q27.8394 49.3516 25.9956 49.3516 Q24.105 49.3516 23.0737 48.1875 Q22.0425 47.0234 22.0425 44.9141 Q22.0425 42.8203 23.0737 41.6719 Q24.105 40.5234 25.9956 40.5234 Q27.855 40.5234 28.8862 41.6953 Q29.9175 42.8672 29.9175 44.9297 ZM23.0894 44.9297 Q23.0894 46.6641 23.8316 47.5703 Q24.5737 48.4766 25.9956 48.4766 Q27.4175 48.4766 28.1441 47.5781 Q28.8706 46.6797 28.8706 44.9297 Q28.8706 43.1953 28.1441 42.3047 Q27.4175 41.4141 25.9956 41.4141 Q24.5737 41.4141 23.8316 42.3125 Q23.0894 43.2109 23.0894 44.9297 Z"/><path style="fill:none; stroke:black;" d="M77.51 14.75 L77.943 15 L78.376 14.75"/><path style="fill:none; stroke:black;" d="M-77.51 14.75 L-77.943 15 L-78.376 14.75"/><path style="fill:none; stroke:black;" d="M-51.963 -29.5 L-51.963 -30 L-52.396 -30.25"/><path style="fill:none; stroke:black;" d="M-103.49 0.25 L-103.923 0 L-103.923 -0.5"/><path style="fill:none; stroke:black;" d="M-77.51 -44.75 L-77.943 -45 L-78.376 -44.75"/><path style="fill:none; stroke:black;" d="M-103.923 -29.5 L-103.923 -30 L-103.49 -30.25"/></g></g></svg></svg></svg></svg>',
'inchi': 'InChI=1S/C11H20O2/c1-2-13-11(12)9-8-10-6-4-3-5-7-10/h10H,2-9H2,1H3',
'inchiKey': 'InChIKey=NRVPMFHPHGBQLP-UHFFFAOYSA-N',
'smile': 'C(CC(OCC)=O)C1CCCCC1',
'canonicalSmile': 'O=C(OCC)CCC1CCCCC1',
'molecularFormula': 'C<sub>11</sub>H<sub>20</sub>O<sub>2</sub>',
'molecularMass': '184.28',
'experimentalProperties': [{'name': 'Boiling Point',
'property': '105-113 °C @ Press: 17 Torr',
'sourceNumber': 1}],
'propertyCitations': [{'docUri': 'document/pt/document/22252593',
'sourceNumber': 1,
'source': 'De Benneville, Peter L.; Journal of the American Chemical Society, (1940), 62, 283-7, CAplus'}],
'synonyms': ['Cyclohexanepropanoic acid, ethyl ester',
'Cyclohexanepropionic acid, ethyl ester',
'Ethyl cyclohexanepropionate',
'Ethyl cyclohexylpropanoate',
'Ethyl 3-cyclohexylpropionate',
'Ethyl 3-cyclohexylpropanoate',
'3-Cyclohexylpropionic acid ethyl ester',
'NSC 71463',
'Ethyl 3-cyclohexanepropionate'],
'replacedRns': [],
'hasMolfile': True},
{'uri': 'substance/pt/10031922',
'rn': '10031-92-2',
'name': 'Ethyl 2-nonynoate',
'image': '<svg width="292" viewBox="0 0 292 86" style="fill-opacity:1; color-rendering:auto; color-interpolation:auto; text-rendering:auto; stroke:black; stroke-linecap:square; stroke-miterlimit:10; shape-rendering:auto; stroke-opacity:1; fill:black; stroke-dasharray:none; font-weight:normal; stroke-width:1; font-family:\'Open Sans\'; font-style:normal; stroke-linejoin:miter; font-size:12; stroke-dashoffset:0; image-rendering:auto;" height="86" class="cas-substance-image" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns="http://www.w3.org/2000/svg"><svg class="cas-substance-single-component"><rect y="0" x="0" width="292" stroke="none" ry="7" rx="7" height="86" fill="white" class="cas-substance-group"/><svg y="0" x="0" width="292" viewBox="0 0 292 86" style="fill:black;" height="86" class="cas-substance-single-component-image"><svg><g><g transform="translate(146,41)" style="text-rendering:geometricPrecision; color-rendering:optimizeQuality; color-interpolation:linearRGB; stroke-linecap:butt; image-rendering:optimizeQuality;"><line y2="-7.5" y1="7.5" x2="-38.97" x1="-64.953" style="fill:none;"/><line y2="-4.3214" y1="7.5" x2="-85.4276" x1="-64.953" style="fill:none;"/><line y2="31.0234" y1="6.4896" x2="-66.703" x1="-66.703" style="fill:none;"/><line y2="31.0234" y1="6.4897" x2="-63.203" x1="-63.203" style="fill:none;"/><line y2="-22.5" y1="-7.5" x2="-12.99" x1="-38.97" style="fill:none;"/><line y2="-25.5311" y1="-10.5311" x2="-14.74" x1="-40.72" style="fill:none;"/><line y2="-19.4689" y1="-4.4689" x2="-11.24" x1="-37.22" style="fill:none;"/><line y2="7.5" y1="-4.3112" x2="-116.913" x1="-96.456" style="fill:none;"/><line y2="-37.5" y1="-22.5" x2="12.99" x1="-12.99" style="fill:none;"/><line y2="-7.5" y1="7.5" x2="-142.893" x1="-116.913" style="fill:none;"/><line y2="-22.5" y1="-37.5" x2="38.97" x1="12.99" style="fill:none;"/><line y2="-37.5" y1="-22.5" x2="64.953" x1="38.97" style="fill:none;"/><line y2="-22.5" y1="-37.5" x2="90.933" x1="64.953" style="fill:none;"/><line y2="-37.5" y1="-22.5" x2="116.913" x1="90.933" style="fill:none;"/><line y2="-22.5" y1="-37.5" x2="142.893" x1="116.913" style="fill:none;"/><path style="fill:none; stroke-miterlimit:5;" d="M-64.52 7.25 L-64.953 7.5 L-65.386 7.25"/><path style="fill:none; stroke-miterlimit:5;" d="M-39.403 -7.25 L-38.97 -7.5 L-38.537 -7.75"/></g><g transform="translate(146,41)" style="stroke-linecap:butt; fill:rgb(230,0,0); text-rendering:geometricPrecision; color-rendering:optimizeQuality; image-rendering:optimizeQuality; font-family:\'Open Sans\'; stroke:rgb(230,0,0); color-interpolation:linearRGB; stroke-miterlimit:5;"><path style="stroke:none;" d="M-86.9955 -7.5703 Q-86.9955 -5.5078 -88.0346 -4.3281 Q-89.0736 -3.1484 -90.9174 -3.1484 Q-92.808 -3.1484 -93.8392 -4.3125 Q-94.8705 -5.4766 -94.8705 -7.5859 Q-94.8705 -9.6797 -93.8392 -10.8281 Q-92.808 -11.9766 -90.9174 -11.9766 Q-89.058 -11.9766 -88.0267 -10.8047 Q-86.9955 -9.6328 -86.9955 -7.5703 ZM-93.8236 -7.5703 Q-93.8236 -5.8359 -93.0814 -4.9297 Q-92.3392 -4.0234 -90.9174 -4.0234 Q-89.4955 -4.0234 -88.7689 -4.9219 Q-88.0424 -5.8203 -88.0424 -7.5703 Q-88.0424 -9.3047 -88.7689 -10.1953 Q-89.4955 -11.0859 -90.9174 -11.0859 Q-92.3392 -11.0859 -93.0814 -10.1875 Q-93.8236 -9.2891 -93.8236 -7.5703 Z"/><path style="stroke:none;" d="M-61.0155 37.4297 Q-61.0155 39.4922 -62.0546 40.6719 Q-63.0936 41.8516 -64.9374 41.8516 Q-66.828 41.8516 -67.8593 40.6875 Q-68.8905 39.5234 -68.8905 37.4141 Q-68.8905 35.3203 -67.8593 34.1719 Q-66.828 33.0234 -64.9374 33.0234 Q-63.078 33.0234 -62.0468 34.1953 Q-61.0155 35.3672 -61.0155 37.4297 ZM-67.8436 37.4297 Q-67.8436 39.1641 -67.1014 40.0703 Q-66.3593 40.9766 -64.9374 40.9766 Q-63.5155 40.9766 -62.7889 40.0781 Q-62.0624 39.1797 -62.0624 37.4297 Q-62.0624 35.6953 -62.7889 34.8047 Q-63.5155 33.9141 -64.9374 33.9141 Q-66.3593 33.9141 -67.1014 34.8125 Q-67.8436 35.7109 -67.8436 37.4297 Z"/><path style="fill:none; stroke:black;" d="M-116.48 7.25 L-116.913 7.5 L-117.346 7.25"/><path style="fill:none; stroke:black;" d="M12.557 -37.25 L12.99 -37.5 L13.423 -37.25"/><path style="fill:none; stroke:black;" d="M38.537 -22.75 L38.97 -22.5 L39.403 -22.75"/><path style="fill:none; stroke:black;" d="M64.52 -37.25 L64.953 -37.5 L65.386 -37.25"/><path style="fill:none; stroke:black;" d="M90.5 -22.75 L90.933 -22.5 L91.366 -22.75"/><path style="fill:none; stroke:black;" d="M116.48 -37.25 L116.913 -37.5 L117.346 -37.25"/></g></g></svg></svg></svg></svg>',
'inchi': 'InChI=1S/C11H18O2/c1-3-5-6-7-8-9-10-11(12)13-4-2/h3-8H2,1-2H3',
'inchiKey': 'InChIKey=BFZNMUGAZYAMTG-UHFFFAOYSA-N',
'smile': 'C(C#CCCCCCC)(OCC)=O',
'canonicalSmile': 'O=C(C#CCCCCCC)OCC',
'molecularFormula': 'C<sub>11</sub>H<sub>18</sub>O<sub>2</sub>',
'molecularMass': '182.26',
'experimentalProperties': [],
'propertyCitations': [],
'synonyms': ['2-Nonynoic acid, ethyl ester',
'Ethyl 2-nonynoate',
'NSC 190985'],
'replacedRns': [],
'hasMolfile': True}]
Display Molecule Drawings#
from IPython.display import SVG
# get svg image text
svg_strings = []
for svg_idx in range(len(casrn_data)):
svg_strings.append(casrn_data[svg_idx]["image"])
# display the molecules
for svg_string in svg_strings:
display(SVG(svg_string))
Select some specific data#
# Get canonical SMILES
cansmiles = []
for cansmi in range(len(casrn_data)):
cansmiles.append(casrn_data[cansmi]["canonicalSmile"])
print(cansmiles)
['O=C(OCC)CCC1CCCCC1', 'O=C(C#CCCCCCC)OCC', 'O=C(OCC)CN1N=CC=C1', 'O=C(OCC)C1=CC=CC(=C1)CCC(=O)OCC', 'N=C(OCC)C1=CCCCC1']
# Get synonyms
synonyms_list = []
for syn in range(len(casrn_data)):
synonyms_list.append(casrn_data[syn]["synonyms"])
pprint(synonyms_list)
[['Cyclohexanepropanoic acid, ethyl ester',
'Cyclohexanepropionic acid, ethyl ester',
'Ethyl cyclohexanepropionate',
'Ethyl cyclohexylpropanoate',
'Ethyl 3-cyclohexylpropionate',
'Ethyl 3-cyclohexylpropanoate',
'3-Cyclohexylpropionic acid ethyl ester',
'NSC 71463',
'Ethyl 3-cyclohexanepropionate'],
['2-Nonynoic acid, ethyl ester', 'Ethyl 2-nonynoate', 'NSC 190985'],
['1<em>H</em>-Pyrazole-1-acetic acid, ethyl ester',
'Pyrazole-1-acetic acid, ethyl ester',
'Ethyl 1<em>H</em>-pyrazole-1-acetate',
'Ethyl 1-pyrazoleacetate',
'Ethyl 2-(1<em>H</em>-pyrazol-1-yl)acetate'],
['Benzenepropanoic acid, 3-(ethoxycarbonyl)-, ethyl ester',
'Hydrocinnamic acid, <em>m</em>-carboxy-, diethyl ester',
'Ethyl 3-(ethoxycarbonyl)benzenepropanoate'],
['1-Cyclohexene-1-carboximidic acid, ethyl ester',
'Ethyl 1-cyclohexene-1-carboximidate']]
# Transform synonym "list of lists" to a flat list
synonyms_flat = []
for sublist in synonyms_list:
for synonym in sublist:
synonyms_flat.append(synonym)
pprint(synonyms_flat)
['Cyclohexanepropanoic acid, ethyl ester',
'Cyclohexanepropionic acid, ethyl ester',
'Ethyl cyclohexanepropionate',
'Ethyl cyclohexylpropanoate',
'Ethyl 3-cyclohexylpropionate',
'Ethyl 3-cyclohexylpropanoate',
'3-Cyclohexylpropionic acid ethyl ester',
'NSC 71463',
'Ethyl 3-cyclohexanepropionate',
'2-Nonynoic acid, ethyl ester',
'Ethyl 2-nonynoate',
'NSC 190985',
'1<em>H</em>-Pyrazole-1-acetic acid, ethyl ester',
'Pyrazole-1-acetic acid, ethyl ester',
'Ethyl 1<em>H</em>-pyrazole-1-acetate',
'Ethyl 1-pyrazoleacetate',
'Ethyl 2-(1<em>H</em>-pyrazol-1-yl)acetate',
'Benzenepropanoic acid, 3-(ethoxycarbonyl)-, ethyl ester',
'Hydrocinnamic acid, <em>m</em>-carboxy-, diethyl ester',
'Ethyl 3-(ethoxycarbonyl)benzenepropanoate',
'1-Cyclohexene-1-carboximidic acid, ethyl ester',
'Ethyl 1-cyclohexene-1-carboximidate']
3. Common Chemistry Search#
In addition to the /detail API, the CAS Common Chemistry API has a /search method that allows searching by CAS RN, SMILES, InChI/InChIKey, and name.
Import libraries#
import requests
from pprint import pprint
from time import sleep
Setup API Parameters#
search_base_url = "https://commonchemistry.cas.org/api/search?q="
Request data from CAS Common Chemistry Search API#
# keyword search query
quinine_search_data = requests.get(search_base_url + "quinine").json()
pprint(quinine_search_data)
{'count': 1,
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'name': 'Quinine',
'rn': '130-95-0'}]}
Note that with the CAS Common Chemistry Search API, only the image data, name, and CAS RN is returned. In order to retrieve the full record, we can combine our search with the related detail API:
# search query
quinine_search_data = requests.get(search_base_url + "quinine").json()
# extract our CAS RN
quinine_rn = quinine_search_data["results"][0]["rn"]
print(quinine_rn)
130-95-0
# get detailed record for quinine
detail_base_url = "https://commonchemistry.cas.org/api/detail?"
quinine_detail_data = requests.get(detail_base_url + "cas_rn=" + quinine_rn).json()
pprint(quinine_detail_data)
{'canonicalSmile': 'OC(C=1C=CN=C2C=CC(OC)=CC21)C3N4CCC(C3)C(C=C)C4',
'experimentalProperties': [{'name': 'Melting Point',
'property': '177 °C (decomp)',
'sourceNumber': 1}],
'hasMolfile': True,
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'inchi': 'InChI=1S/C20H24N2O2/c1-3-13-12-22-9-7-14(13)10-19(22)20(23)16-6-8-21-18-5-4-15(24-2)11-17(16)18/h3-6,8,11,13-14,19-20,23H,1,7,9-10,12H2,2H3/t13-,14-,19-,20+/m0/s1',
'inchiKey': 'InChIKey=LOUPRKONTZGTKE-WZBLMQSHSA-N',
'molecularFormula': 'C<sub>20</sub>H<sub>24</sub>N<sub>2</sub>O<sub>2</sub>',
'molecularMass': '324.42',
'name': 'Quinine',
'propertyCitations': [{'docUri': '',
'source': 'Drugs - Synonyms and Properties data were '
'obtained from Ashgate Publishing Co. (US)',
'sourceNumber': 1}],
'replacedRns': ['6912-57-8',
'12239-42-8',
'21480-31-9',
'55980-20-6',
'72646-90-3',
'95650-40-1',
'128544-03-6',
'767303-40-2',
'840482-04-4',
'857212-53-4',
'864908-93-0',
'875538-34-4',
'888714-03-2',
'890027-24-4',
'894767-09-0',
'898813-59-7',
'898814-28-3',
'899813-83-3',
'900786-66-5',
'900789-95-9',
'906550-97-8',
'909263-47-4',
'909767-48-2',
'909882-78-6',
'910878-25-0',
'910880-97-6',
'911445-75-5',
'918778-04-8',
'1071756-51-8',
'1267651-57-9',
'1628705-47-4',
'2244812-93-7',
'2244812-97-1',
'2409557-51-1',
'2566761-34-8',
'2929261-86-7',
'3032276-91-5'],
'rn': '130-95-0',
'smile': '[C@@H](O)(C=1C2=C(C=CC(OC)=C2)N=CC1)[C@]3([N@@]4C[C@H](C=C)[C@](C3)(CC4)[H])[H]',
'synonyms': ['Cinchonan-9-ol, 6′-methoxy-, (8α,9<em>R</em>)-',
'Quinine',
'(8α,9<em>R</em>)-6′-Methoxycinchonan-9-ol',
'6′-Methoxycinchonidine',
'(-)-Quinine',
'(8<em>S</em>,9<em>R</em>)-Quinine',
'(<em>R</em>)-(-)-Quinine',
'NSC 192949',
'WR297608',
'Qualaquin',
'Mosgard',
'Quinlup',
'Quine 9',
'Cinkona',
'Quinex',
'Quinlex',
'Rezquin',
'QSM',
'SW 85833',
'(<em>R</em>)-(6-Methoxy-4-quinolyl)[(2<em>S</em>)-5-vinylquinuclidin-2-yl]methanol',
'MeSH ID: D011803'],
'uri': 'substance/pt/130950'}
Handle multiple results#
# setup search query parameters
search_base_url = "https://commonchemistry.cas.org/api/search?q="
# SMILES for butadiene
smi_bd = "C=CC=C"
# Request data from CAS Common Chemistry Search API
smi_search_data = requests.get(search_base_url + smi_bd).json()
# get results count
print(smi_search_data["count"])
7
# extract out CAS RNs
smi_casrn_list = []
for casrn_idx in range(len(smi_search_data["results"])):
smi_casrn_list.append(smi_search_data["results"][casrn_idx]["rn"])
print(smi_casrn_list)
['106-99-0', '16422-75-6', '26952-74-9', '29406-96-0', '29989-19-3', '31567-90-5', '9003-17-2']
# now use the detail API to retrieve the full records
detail_base_url = "https://commonchemistry.cas.org/api/detail?"
smi_detail_data = []
for casrn in smi_casrn_list:
smi_detail_data.append(requests.get(detail_base_url + "cas_rn=" + casrn).json())
sleep(1) # add a delay between API calls
# Get some specific data such as name from the detail records
names = []
for name_idx in range(len(smi_detail_data)):
names.append(smi_detail_data[name_idx]["name"])
print(names)
['1,3-Butadiene', 'Butadiene trimer', 'Butadiene dimer', '1,3-Butadiene, homopolymer, isotactic', '1,3-Butadiene-<em>1</em>,<em>1</em>,<em>2</em>,<em>3</em>,<em>4</em>,<em>4</em>-<em>d</em><sub>6</sub>, homopolymer', 'Syndiotactic polybutadiene', 'Polybutadiene']
Handle multiple page results#
The CAS Common Chemistry API returns 50 results per page, and only the first page is returned by default. If the search returns more than 50 results, the offset option can be added to page through and obtain all results:
# setup search query parameters
search_base_url = "https://commonchemistry.cas.org/api/search?q="
n = "selen*"
# get results count for CAS Common Chemistry Search
num_Results = requests.get(search_base_url + n).json()["count"]
print(num_Results)
194
# Request data and save to a list in a loop for each page
n_search_data = []
for page_idx in range(int(num_Results/50 +1)): # creates [0,1,2,3] for 4 pages
page_data = requests.get(search_base_url + n + "&offset=" + str(page_idx*50)).json()
sleep(1)
n_search_data.append(page_data)
# length of search data includes a top level list for each query
len(n_search_data)
4
# lists within lists contain the results
for idx in range(len(n_search_data)):
print(len(n_search_data[idx]["results"]))
50
50
50
44
# We can index and extract out the first casrn like this
pprint(n_search_data[0]["results"][0]["rn"])
'10025-68-0'
# extract out all CAS RNs from the list of lists
n_casrn_list = []
for n_idx in range(len(n_search_data)): # top level list
for casrn_idx in range(len(n_search_data[n_idx]["results"])): # lists within top level
n_casrn_list.append(n_search_data[n_idx]["results"][casrn_idx]["rn"])
len(n_casrn_list)
194
# show first 10
pprint(n_casrn_list[0:10])
['10025-68-0',
'10026-03-6',
'10026-23-0',
'10101-96-9',
'10102-18-8',
'10102-23-5',
'10112-94-4',
'10161-84-9',
'10214-40-1',
'10236-58-5']
# now we can loop through each casrn and use the detail API to obtain the entire record
# this will query CAS Common Chem 192 times and take ~ 5 min.
detail_base_url = "https://commonchemistry.cas.org/api/detail?"
n_detail_data = []
for casrn in n_casrn_list:
n_detail_data.append(requests.get(detail_base_url + "cas_rn=" + casrn).json())
sleep(1) # !! add a delay between API calls
---------------------------------------------------------------------------
KeyboardInterrupt Traceback (most recent call last)
Cell In[37], line 6
4 n_detail_data = []
5 for casrn in n_casrn_list:
----> 6 n_detail_data.append(requests.get(detail_base_url + "cas_rn=" + casrn).json())
7 sleep(1) # !! add a delay between API calls
File /opt/hostedtoolcache/Python/3.11.10/x64/lib/python3.11/site-packages/requests/api.py:73, in get(url, params, **kwargs)
62 def get(url, params=None, **kwargs):
63 r"""Sends a GET request.
64
65 :param url: URL for the new :class:`Request` object.
(...)
70 :rtype: requests.Response
71 """
---> 73 return request("get", url, params=params, **kwargs)
File /opt/hostedtoolcache/Python/3.11.10/x64/lib/python3.11/site-packages/requests/api.py:59, in request(method, url, **kwargs)
55 # By using the 'with' statement we are sure the session is closed, thus we
56 # avoid leaving sockets open which can trigger a ResourceWarning in some
57 # cases, and look like a memory leak in others.
58 with sessions.Session() as session:
---> 59 return session.request(method=method, url=url, **kwargs)
File /opt/hostedtoolcache/Python/3.11.10/x64/lib/python3.11/site-packages/requests/sessions.py:589, in Session.request(self, method, url, params, data, headers, cookies, files, auth, timeout, allow_redirects, proxies, hooks, stream, verify, cert, json)
584 send_kwargs = {
585 "timeout": timeout,
586 "allow_redirects": allow_redirects,
587 }
588 send_kwargs.update(settings)
--> 589 resp = self.send(prep, **send_kwargs)
591 return resp
File /opt/hostedtoolcache/Python/3.11.10/x64/lib/python3.11/site-packages/requests/sessions.py:703, in Session.send(self, request, **kwargs)
700 start = preferred_clock()
702 # Send the request
--> 703 r = adapter.send(request, **kwargs)
705 # Total elapsed time of the request (approximately)
706 elapsed = preferred_clock() - start
File /opt/hostedtoolcache/Python/3.11.10/x64/lib/python3.11/site-packages/requests/adapters.py:486, in HTTPAdapter.send(self, request, stream, timeout, verify, cert, proxies)
483 timeout = TimeoutSauce(connect=timeout, read=timeout)
485 try:
--> 486 resp = conn.urlopen(
487 method=request.method,
488 url=url,
489 body=request.body,
490 headers=request.headers,
491 redirect=False,
492 assert_same_host=False,
493 preload_content=False,
494 decode_content=False,
495 retries=self.max_retries,
496 timeout=timeout,
497 chunked=chunked,
498 )
500 except (ProtocolError, OSError) as err:
501 raise ConnectionError(err, request=request)
File /opt/hostedtoolcache/Python/3.11.10/x64/lib/python3.11/site-packages/urllib3/connectionpool.py:790, in HTTPConnectionPool.urlopen(self, method, url, body, headers, retries, redirect, assert_same_host, timeout, pool_timeout, release_conn, chunked, body_pos, preload_content, decode_content, **response_kw)
787 response_conn = conn if not release_conn else None
789 # Make the request on the HTTPConnection object
--> 790 response = self._make_request(
791 conn,
792 method,
793 url,
794 timeout=timeout_obj,
795 body=body,
796 headers=headers,
797 chunked=chunked,
798 retries=retries,
799 response_conn=response_conn,
800 preload_content=preload_content,
801 decode_content=decode_content,
802 **response_kw,
803 )
805 # Everything went great!
806 clean_exit = True
File /opt/hostedtoolcache/Python/3.11.10/x64/lib/python3.11/site-packages/urllib3/connectionpool.py:536, in HTTPConnectionPool._make_request(self, conn, method, url, body, headers, retries, timeout, chunked, response_conn, preload_content, decode_content, enforce_content_length)
534 # Receive the response from the server
535 try:
--> 536 response = conn.getresponse()
537 except (BaseSSLError, OSError) as e:
538 self._raise_timeout(err=e, url=url, timeout_value=read_timeout)
File /opt/hostedtoolcache/Python/3.11.10/x64/lib/python3.11/site-packages/urllib3/connection.py:461, in HTTPConnection.getresponse(self)
458 from .response import HTTPResponse
460 # Get the response from http.client.HTTPConnection
--> 461 httplib_response = super().getresponse()
463 try:
464 assert_header_parsing(httplib_response.msg)
File /opt/hostedtoolcache/Python/3.11.10/x64/lib/python3.11/http/client.py:1395, in HTTPConnection.getresponse(self)
1393 try:
1394 try:
-> 1395 response.begin()
1396 except ConnectionError:
1397 self.close()
File /opt/hostedtoolcache/Python/3.11.10/x64/lib/python3.11/http/client.py:325, in HTTPResponse.begin(self)
323 # read until we get a non-100 response
324 while True:
--> 325 version, status, reason = self._read_status()
326 if status != CONTINUE:
327 break
File /opt/hostedtoolcache/Python/3.11.10/x64/lib/python3.11/http/client.py:286, in HTTPResponse._read_status(self)
285 def _read_status(self):
--> 286 line = str(self.fp.readline(_MAXLINE + 1), "iso-8859-1")
287 if len(line) > _MAXLINE:
288 raise LineTooLong("status line")
File /opt/hostedtoolcache/Python/3.11.10/x64/lib/python3.11/socket.py:718, in SocketIO.readinto(self, b)
716 while True:
717 try:
--> 718 return self._sock.recv_into(b)
719 except timeout:
720 self._timeout_occurred = True
File /opt/hostedtoolcache/Python/3.11.10/x64/lib/python3.11/ssl.py:1314, in SSLSocket.recv_into(self, buffer, nbytes, flags)
1310 if flags != 0:
1311 raise ValueError(
1312 "non-zero flags not allowed in calls to recv_into() on %s" %
1313 self.__class__)
-> 1314 return self.read(nbytes, buffer)
1315 else:
1316 return super().recv_into(buffer, nbytes, flags)
File /opt/hostedtoolcache/Python/3.11.10/x64/lib/python3.11/ssl.py:1166, in SSLSocket.read(self, len, buffer)
1164 try:
1165 if buffer is not None:
-> 1166 return self._sslobj.read(len, buffer)
1167 else:
1168 return self._sslobj.read(len)
KeyboardInterrupt:
# Extract out some data such as molecularMass
mms = []
for mm_idx in range(len(n_detail_data)):
mms.append(n_detail_data[mm_idx]["molecularMass"])
len(mms)
192
# view first 20
# note that several do not have molecularMass values and have an empty string in the record
print(mms[0:20])
['228.83', '220.77', '', '', '', '', '', '300.24', '', '168.05', '', '', '', '', '', '241.11', '', '368.25', '265.00', '']
# finally, we can quickly create a simple visualization from the
# extracted molecularMass values (from the selen* search)
# remove empty strings
mms_values = list(filter(None, mms))
# convert to floats
mms_values_float = []
for mms_value in mms_values:
mms_values_float.append(float(mms_value))
# import numpy and matplotlib
import matplotlib.pyplot as plt
# plot data
plt.figure(figsize=(10,7))
plt.hist(mms_values_float, histtype='bar',bins = 20, facecolor="blue", alpha=0.5)
plt.title("Histogram of available molecularMass values for selen* search")
plt.xlabel("molecularMass")
plt.ylabel("Count")
plt.show()
