diff --git a/datasources/goldbook_api.html b/datasources/goldbook_api.html index 773ef006..3840990f 100644 --- a/datasources/goldbook_api.html +++ b/datasources/goldbook_api.html @@ -574,7 +574,7 @@

Step 5: Use the term code to retrieve its definition
-
{'term': {'id': '01093', 'doi': '10.1351/goldbook.C01093', 'code': 'C01093', 'status': 'current', 'longtitle': 'IUPAC Gold Book - cis-trans isomers', 'title': '<i>cis</i>-<i>trans</i> isomers', 'termversion': '2.3.3', 'lastupdated': '2014-02-24', 'definitions': [{'id': '1', 'text': 'Stereoisomeric olefins or cycloalkanes (or hetero-analogues) which differ in the positions of atoms (or groups) relative to a reference plane: in the cis-isomer the atoms are on the same side, in the trans-isomer they are on opposite sides. [image: molecular structures showing cis/trans isomerism]', 'chemicals': [{'type': 'chemimage', 'title': 'molecular structures showing cis/trans isomerism', 'file': 'https://goldbook.iupac.org/img/inline/C01093.png'}], 'links': [{'title': 'Stereoisomeric', 'type': 'internal', 'url': 'https://goldbook.iupac.org/terms/view/S05983'}, {'title': 'olefins', 'type': 'goldify', 'url': 'https://goldbook.iupac.org/terms/view/O04281'}, {'title': 'cycloalkanes', 'type': 'goldify', 'url': 'https://goldbook.iupac.org/terms/view/C01497'}, {'title': 'isomer', 'type': 'goldify', 'url': 'https://goldbook.iupac.org/terms/view/I03289'}, {'title': 'trans', 'type': 'goldify', 'url': 'https://goldbook.iupac.org/terms/view/C01092'}], 'sources': ["PAC, 1996, 68, 2193. 'Basic terminology of stereochemistry (IUPAC Recommendations 1996)' on page 2204 (https://doi.org/10.1351/pac199668122193)"]}], 'referencedin': [{'title': 'Wikipedia - Cis-trans izomerie (cs)', 'url': 'https://cs.wikipedia.org/wiki/Cis-trans_izomerie'}, {'title': 'Wikipedia - Cis-trans izoméria (sk)', 'url': 'https://sk.wikipedia.org/wiki/Cis-trans_izoméria'}, {'title': 'Wikipedia - Cis–trans isomerism (en)', 'url': 'https://en.wikipedia.org/wiki/Cis–trans_isomerism'}, {'title': 'Wikipedia - Isomeria (it)', 'url': 'https://it.wikipedia.org/wiki/Isomeria'}, {'title': 'Wikipedia - Isomeria cis-trans (it)', 'url': 'https://it.wikipedia.org/wiki/Isomeria_cis-trans'}, {'title': 'Wikipedia - Isomeria geométrica (pt)', 'url': 'https://pt.wikipedia.org/wiki/Isomeria_geométrica'}, {'title': 'Wikipedia - Isomería cis-trans (es)', 'url': 'https://es.wikipedia.org/wiki/Isomería_cis-trans'}, {'title': 'Wikipedia - Talk:Isomer (en)', 'url': 'https://en.wikipedia.org/wiki/Talk:Isomer'}, {'title': 'Wikipedia - Talk:Stereoisomerism (en)', 'url': 'https://en.wikipedia.org/wiki/Talk:Stereoisomerism'}, {'title': 'Wikipedia - Цис-транс изомеризъм (bg)', 'url': 'https://bg.wikipedia.org/wiki/Цис-транс_изомеризъм'}, {'title': 'Wikipedia - Цис–транс ізомерія (uk)', 'url': 'https://uk.wikipedia.org/wiki/Цис–транс_ізомерія'}, {'title': 'Wikipedia - ایزومری سیس–ترانس (fa)', 'url': 'https://fa.wikipedia.org/wiki/ایزومری_سیس–ترانس'}, {'title': 'Wikipedia - 顺反异构 (zh)', 'url': 'https://zh.wikipedia.org/wiki/顺反异构'}], 'links': {'html': 'https://goldbook.iupac.org/terms/view/C01093/html', 'json': 'https://goldbook.iupac.org/terms/view/C01093/json', 'xml': 'https://goldbook.iupac.org/terms/view/C01093/xml', 'plain': 'https://goldbook.iupac.org/terms/view/C01093/plain', 'pdf': 'https://goldbook.iupac.org/terms/view/C01093/pdf'}, 'citation': "Citation: '<i>cis</i>-<i>trans</i> isomers' in IUPAC Compendium of Chemical Terminology, 3rd ed. International Union of Pure and Applied Chemistry; 2006. Online version 3.0.1, 2019. 10.1351/goldbook.C01093", 'license': 'The IUPAC Gold Book is licensed under Creative Commons Attribution-ShareAlike CC BY-SA 4.0 International (https://creativecommons.org/licenses/by-sa/4.0/) for individual terms.', 'collection': 'If you are interested in licensing the Gold Book for commercial use, please contact the IUPAC Executive Director at executivedirector@iupac.org .', 'disclaimer': 'The International Union of Pure and Applied Chemistry (IUPAC) is continuously reviewing and, where needed, updating terms in the Compendium of Chemical Terminology (the IUPAC Gold Book). Users of these terms are encouraged to include the version of a term with its use and to check regularly for updates to term definitions that you are using.', 'accessed': '2024-01-18T16:40:42+00:00'}}
+
{'term': {'id': '01093', 'doi': '10.1351/goldbook.C01093', 'code': 'C01093', 'status': 'current', 'longtitle': 'IUPAC Gold Book - cis-trans isomers', 'title': '<i>cis</i>-<i>trans</i> isomers', 'termversion': '2.3.3', 'lastupdated': '2014-02-24', 'definitions': [{'id': '1', 'text': 'Stereoisomeric olefins or cycloalkanes (or hetero-analogues) which differ in the positions of atoms (or groups) relative to a reference plane: in the cis-isomer the atoms are on the same side, in the trans-isomer they are on opposite sides. [image: molecular structures showing cis/trans isomerism]', 'chemicals': [{'type': 'chemimage', 'title': 'molecular structures showing cis/trans isomerism', 'file': 'https://goldbook.iupac.org/img/inline/C01093.png'}], 'links': [{'title': 'Stereoisomeric', 'type': 'internal', 'url': 'https://goldbook.iupac.org/terms/view/S05983'}, {'title': 'olefins', 'type': 'goldify', 'url': 'https://goldbook.iupac.org/terms/view/O04281'}, {'title': 'cycloalkanes', 'type': 'goldify', 'url': 'https://goldbook.iupac.org/terms/view/C01497'}, {'title': 'isomer', 'type': 'goldify', 'url': 'https://goldbook.iupac.org/terms/view/I03289'}, {'title': 'trans', 'type': 'goldify', 'url': 'https://goldbook.iupac.org/terms/view/C01092'}], 'sources': ["PAC, 1996, 68, 2193. 'Basic terminology of stereochemistry (IUPAC Recommendations 1996)' on page 2204 (https://doi.org/10.1351/pac199668122193)"]}], 'referencedin': [{'title': 'Wikipedia - Cis-trans izomerie (cs)', 'url': 'https://cs.wikipedia.org/wiki/Cis-trans_izomerie'}, {'title': 'Wikipedia - Cis-trans izoméria (sk)', 'url': 'https://sk.wikipedia.org/wiki/Cis-trans_izoméria'}, {'title': 'Wikipedia - Cis–trans isomerism (en)', 'url': 'https://en.wikipedia.org/wiki/Cis–trans_isomerism'}, {'title': 'Wikipedia - Isomeria (it)', 'url': 'https://it.wikipedia.org/wiki/Isomeria'}, {'title': 'Wikipedia - Isomeria cis-trans (it)', 'url': 'https://it.wikipedia.org/wiki/Isomeria_cis-trans'}, {'title': 'Wikipedia - Isomeria geométrica (pt)', 'url': 'https://pt.wikipedia.org/wiki/Isomeria_geométrica'}, {'title': 'Wikipedia - Isomería cis-trans (es)', 'url': 'https://es.wikipedia.org/wiki/Isomería_cis-trans'}, {'title': 'Wikipedia - Talk:Isomer (en)', 'url': 'https://en.wikipedia.org/wiki/Talk:Isomer'}, {'title': 'Wikipedia - Talk:Stereoisomerism (en)', 'url': 'https://en.wikipedia.org/wiki/Talk:Stereoisomerism'}, {'title': 'Wikipedia - Цис-транс изомеризъм (bg)', 'url': 'https://bg.wikipedia.org/wiki/Цис-транс_изомеризъм'}, {'title': 'Wikipedia - Цис–транс ізомерія (uk)', 'url': 'https://uk.wikipedia.org/wiki/Цис–транс_ізомерія'}, {'title': 'Wikipedia - ایزومری سیس–ترانس (fa)', 'url': 'https://fa.wikipedia.org/wiki/ایزومری_سیس–ترانس'}, {'title': 'Wikipedia - 顺反异构 (zh)', 'url': 'https://zh.wikipedia.org/wiki/顺反异构'}], 'links': {'html': 'https://goldbook.iupac.org/terms/view/C01093/html', 'json': 'https://goldbook.iupac.org/terms/view/C01093/json', 'xml': 'https://goldbook.iupac.org/terms/view/C01093/xml', 'plain': 'https://goldbook.iupac.org/terms/view/C01093/plain', 'pdf': 'https://goldbook.iupac.org/terms/view/C01093/pdf'}, 'citation': "Citation: '<i>cis</i>-<i>trans</i> isomers' in IUPAC Compendium of Chemical Terminology, 3rd ed. International Union of Pure and Applied Chemistry; 2006. Online version 3.0.1, 2019. 10.1351/goldbook.C01093", 'license': 'The IUPAC Gold Book is licensed under Creative Commons Attribution-ShareAlike CC BY-SA 4.0 International (https://creativecommons.org/licenses/by-sa/4.0/) for individual terms.', 'collection': 'If you are interested in licensing the Gold Book for commercial use, please contact the IUPAC Executive Director at executivedirector@iupac.org .', 'disclaimer': 'The International Union of Pure and Applied Chemistry (IUPAC) is continuously reviewing and, where needed, updating terms in the Compendium of Chemical Terminology (the IUPAC Gold Book). Users of these terms are encouraged to include the version of a term with its use and to check regularly for updates to term definitions that you are using.', 'accessed': '2024-01-22T13:45:48+00:00'}}
 
diff --git a/datasources/pubchem_pugrest1.html b/datasources/pubchem_pugrest1.html index 14773efa..6aff5f16 100644 --- a/datasources/pubchem_pugrest1.html +++ b/datasources/pubchem_pugrest1.html @@ -523,9 +523,7 @@

2. Construct a PUG-REST API and retrieve data
REQEST URL: https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/2244/property/MolecularFormula/txt
-
-
-
OUTPUT    : C9H8O4
+OUTPUT    : C9H8O4
 

@@ -586,19 +584,15 @@

3. Getting Computed Molecular Properties
MolecularWeight  : 180.16
+HBondDonorCount  : 1
 
-
HBondDonorCount  : 1
-HBondAcceptorCoun: 4
-
-
-
HeavyAtomCount   : 13
+
HBondAcceptorCoun: 4
+HeavyAtomCount   : 13
 
XLogP            : 1.200
-
-
-
TPSA             : 63.6
+TPSA             : 63.6
 
diff --git a/datasources/pubchem_pugrest2.html b/datasources/pubchem_pugrest2.html index a5055209..de99a1b2 100644 --- a/datasources/pubchem_pugrest2.html +++ b/datasources/pubchem_pugrest2.html @@ -492,11 +492,13 @@

1. Accessing PubChem data using a chemical name
CID             : 2244
-MolecularFormula: C9H8O4
 
-
-
PSEUDOEPHEDRINE HYDROCHLORIDE
+PSEUDOEPHEDRINE HYDROCHLORIDE
 Pseudoephedrine Hcl
 345-78-8
 Rhinalair
@@ -812,11 +812,10 @@ 

2. Getting chemical names for a given chemical structure
Aleve PM
+
#-- CID 77098502
+Aleve PM
 Naproxen sodium/DPH combination
 Diphenhydramine HCl / naproxen sodium
 BAY98-7111
diff --git a/datasources/pubchem_pugrest3.html b/datasources/pubchem_pugrest3.html
index 77f06ca6..213cacc4 100644
--- a/datasources/pubchem_pugrest3.html
+++ b/datasources/pubchem_pugrest3.html
@@ -702,8 +702,8 @@ 

3. Performing 2-D and 3-D similarity search -
25
-['155903259', '167331698', '166157194', '163362001', '162396459', '169240696', '168301133', '168290284', '167094316', '167094315', '167065082', '164701818', '164701813', '164701812', '164701760', '164701758', '164040179', '163362031', '163362005', '163361849', '169240702', '163341926', '163285815', '166642632', '168476190']
+
8
+['Status:', '504', 'Code:', 'PUGREST.Timeout', 'Message:', 'Request', 'timed', 'out']
 
@@ -777,7 +777,135 @@

5. Performing substructure/superstructure search -
40602
+
---------------------------------------------------------------------------
+KeyboardInterrupt                         Traceback (most recent call last)
+Cell In[15], line 2
+      1 smiles = "C2CN=C(C1=C(C=CC=C1)N2)C3=CC=CC=C3"
+----> 2 cids = requests.post("https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/fastsubstructure/smiles/cids/txt", data={'smiles':smiles}).text.strip().split()
+      3 print(len(cids))
+
+File /opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/requests/api.py:115, in post(url, data, json, **kwargs)
+    103 def post(url, data=None, json=None, **kwargs):
+    104     r"""Sends a POST request.
+    105 
+    106     :param url: URL for the new :class:`Request` object.
+   (...)
+    112     :rtype: requests.Response
+    113     """
+--> 115     return request("post", url, data=data, json=json, **kwargs)
+
+File /opt/hostedtoolcache/Python/3.11.7/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/3.11.7/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/3.11.7/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/3.11.7/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/3.11.7/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/3.11.7/x64/lib/python3.11/site-packages/urllib3/connectionpool.py:467, in HTTPConnectionPool._make_request(self, conn, method, url, body, headers, retries, timeout, chunked, response_conn, preload_content, decode_content, enforce_content_length)
+    464 try:
+    465     # Trigger any extra validation we need to do.
+    466     try:
+--> 467         self._validate_conn(conn)
+    468     except (SocketTimeout, BaseSSLError) as e:
+    469         self._raise_timeout(err=e, url=url, timeout_value=conn.timeout)
+
+File /opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/urllib3/connectionpool.py:1096, in HTTPSConnectionPool._validate_conn(self, conn)
+   1094 # Force connect early to allow us to validate the connection.
+   1095 if conn.is_closed:
+-> 1096     conn.connect()
+   1098 if not conn.is_verified:
+   1099     warnings.warn(
+   1100         (
+   1101             f"Unverified HTTPS request is being made to host '{conn.host}'. "
+   (...)
+   1106         InsecureRequestWarning,
+   1107     )
+
+File /opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/urllib3/connection.py:611, in HTTPSConnection.connect(self)
+    609 def connect(self) -> None:
+    610     sock: socket.socket | ssl.SSLSocket
+--> 611     self.sock = sock = self._new_conn()
+    612     server_hostname: str = self.host
+    613     tls_in_tls = False
+
+File /opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/urllib3/connection.py:203, in HTTPConnection._new_conn(self)
+    198 """Establish a socket connection and set nodelay settings on it.
+    199 
+    200 :return: New socket connection.
+    201 """
+    202 try:
+--> 203     sock = connection.create_connection(
+    204         (self._dns_host, self.port),
+    205         self.timeout,
+    206         source_address=self.source_address,
+    207         socket_options=self.socket_options,
+    208     )
+    209 except socket.gaierror as e:
+    210     raise NameResolutionError(self.host, self, e) from e
+
+File /opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/urllib3/util/connection.py:73, in create_connection(address, timeout, source_address, socket_options)
+     71 if source_address:
+     72     sock.bind(source_address)
+---> 73 sock.connect(sa)
+     74 # Break explicitly a reference cycle
+     75 err = None
+
+KeyboardInterrupt: 
 
@@ -791,7 +919,7 @@

5. Performing substructure/superstructure search -
6817
+
6746
 
@@ -808,7 +936,7 @@

7. Molecular Formula search - @@ -860,7 +988,7 @@

7. Molecular Formula search -

diff --git a/manipulations/computing_inchis.html b/manipulations/computing_inchis.html index bfacc5e1..7f2c2dc3 100644 --- a/manipulations/computing_inchis.html +++ b/manipulations/computing_inchis.html @@ -526,7 +526,7 @@

1.2 Create a Molecular Object from SMILES -
<rdkit.Chem.rdchem.Mol object at 0x7fd7affd0c10>
+
<rdkit.Chem.rdchem.Mol object at 0x7fbb92fc4c10>
 
@@ -607,7 +607,7 @@

1.4 Calculate InChIs for a List of Molecules -
[<rdkit.Chem.rdchem.Mol object at 0x7fd7affd1070>, <rdkit.Chem.rdchem.Mol object at 0x7fd7affd10e0>, <rdkit.Chem.rdchem.Mol object at 0x7fd7affd15b0>, <rdkit.Chem.rdchem.Mol object at 0x7fd7affd1620>, <rdkit.Chem.rdchem.Mol object at 0x7fd7affd1690>, <rdkit.Chem.rdchem.Mol object at 0x7fd7affd1700>]
+
[<rdkit.Chem.rdchem.Mol object at 0x7fbb92fc4eb0>, <rdkit.Chem.rdchem.Mol object at 0x7fbb92fc50e0>, <rdkit.Chem.rdchem.Mol object at 0x7fbb92fc55b0>, <rdkit.Chem.rdchem.Mol object at 0x7fbb92fc5620>, <rdkit.Chem.rdchem.Mol object at 0x7fbb92fc5690>, <rdkit.Chem.rdchem.Mol object at 0x7fbb92fc5700>]
 
@@ -766,7 +766,7 @@

2.4 Calculate InChIs for a List of Molecules -
[<openbabel.pybel.Molecule object at 0x7fd7aeffc710>, <openbabel.pybel.Molecule object at 0x7fd7aeffc910>, <openbabel.pybel.Molecule object at 0x7fd7ae764550>, <openbabel.pybel.Molecule object at 0x7fd7ae765dd0>, <openbabel.pybel.Molecule object at 0x7fd7ae766ed0>, <openbabel.pybel.Molecule object at 0x7fd7ae766e90>]
+
[<openbabel.pybel.Molecule object at 0x7fbb9135cf10>, <openbabel.pybel.Molecule object at 0x7fbb9135e990>, <openbabel.pybel.Molecule object at 0x7fbb9135eb10>, <openbabel.pybel.Molecule object at 0x7fbb9135e810>, <openbabel.pybel.Molecule object at 0x7fbb9135e590>, <openbabel.pybel.Molecule object at 0x7fbb9135e450>]
 
diff --git a/manipulations/dataset_search.html b/manipulations/dataset_search.html index 8dbcac09..6691553b 100644 --- a/manipulations/dataset_search.html +++ b/manipulations/dataset_search.html @@ -1015,7 +1015,7 @@

2.1 - Authentication to the FAIRSharing API -
{'success': True, 'jwt': 'eyJhbGciOiJIUzI1NiJ9.eyJqdGkiOiI0YjVkNzQyMi1hOTg3LTRlZWYtYjQyYi1hN2U3Yjc2MTM0ZTEiLCJzdWIiOiI4NTA5Iiwic2NwIjoidXNlciIsImF1ZCI6bnVsbCwiaWF0IjoxNzA1NTk2MDk5LCJleHAiOjE3MDU2ODI0OTl9.6yAMqLN95YnwleUIUq_xUDg2yMYximXN_k-c-ABN4v4', 'username': 'ChemCookbook', 'id': 8509, 'role': 'user', 'profile_type': 'none', 'watched_records': [], 'is_curator': False, 'is_super_curator': False, 'third_party': False, 'expiry': 1705682499, 'message': 'Authentication successful'}
+
{'success': True, 'jwt': 'eyJhbGciOiJIUzI1NiJ9.eyJqdGkiOiI0YjVkNzQyMi1hOTg3LTRlZWYtYjQyYi1hN2U3Yjc2MTM0ZTEiLCJzdWIiOiI4NTA5Iiwic2NwIjoidXNlciIsImF1ZCI6bnVsbCwiaWF0IjoxNzA1OTMxMzI3LCJleHAiOjE3MDYwMTc3Mjd9.HxBqNA_9ssKQlNOvPptCKsacRaXIVh0r8uwDoGTMzCs', 'username': 'ChemCookbook', 'id': 8509, 'role': 'user', 'profile_type': 'none', 'watched_records': [], 'is_curator': False, 'is_super_curator': False, 'third_party': False, 'expiry': 1706017727, 'message': 'Authentication successful'}
 
@@ -1187,22 +1187,22 @@

2.3 - Output the data in a presentable format