- added documentation to methods

- added chemimg method
- added cas validation with check digit verification
- added inchikey validation
- improved query to check for '*' and added exact option
- improved key2cas to get casrn of smallest molecule (assuming other hits are polymers)

Author: stuchalk

comchem/__init__.py

@@ -1,4 +1,7 @@
 import json
+import re
+import cairosvg
+import os
 from bs4 import BeautifulSoup
 from urllib.request import urlopen
 
@@ -7,13 +10,19 @@
           'properties', 'synonyms', 'replaceRns', 'hasMolefile']
 
 
-# get data from a page
 def detail(casrn, field="all"):
-    """ access the common chemistry detail api """
+    """
+    Access the Common Chemistry detail API at
+    https://commonchemistry.cas.org/api/detail?cas_rn=<casrn>
+    :param casrn: CAS Registry Number
+    :param field: field to return or all fields (default)
+    :return mixed
+    """
+    if not _validcas(casrn):
+        return ''  # false
     url = ccpath + 'detail?cas_rn=' + casrn
     respnse = urlopen(url)
     jsn = json.loads(respnse.read())
-
     if field == "all":
         return jsn
     elif field in fields:
@@ -25,23 +34,125 @@ def detail(casrn, field="all"):
         else:
             return jsn[field]
     else:
-        return "Field not available..."
+        return ''  # false
 
 
-# run a search
-def query(term):
-    url = ccpath + 'search?q=' + term
+def query(term='', exact=False):
+    """
+    Search the CommonChemistry database API at
+    https://commonchemistry.cas.org/api/search?q=<term>
+    :param term: string to be searched
+    :param exact: boolean to indicate an exact match
+    :return: string
+    """
+    url = ''
+    if exact is False:
+        url = ccpath + 'search?q=' + term + '*'
+    elif term[-1:] == '*' or exact is True:
+        url = ccpath + 'search?q=' + term
     respnse = urlopen(url)
     jsn = json.loads(respnse.read())
-    out = []
-    for hit in jsn['results']:
-        textname = BeautifulSoup(hit["name"], "lxml").text
-        out.append({"textname": textname, "htmlname": hit["name"].lower(), "rn": hit["rn"]})
+    out = []  # false
+    if jsn['results']:
+        for hit in jsn['results']:
+            textname = BeautifulSoup(hit["name"], "lxml").text
+            out.append({"textname": textname, "htmlname": hit["name"].lower(), "rn": hit["rn"]})
     return out
 
 
-# search for a compound using an InChIKey
 def key2cas(key):
-    """ search the api for an InChKey"""
-    hits = query('InChIKey=' + key)
-    return hits[0]['rn']  # only returns the casne of the first hit
+    """
+    Find the CAS Registry Number of a chemical substance using an IUPAC InChIKey
+    :param key - a valid InChIKey
+    """
+    if _validkey(key):
+        hits = query('InChIKey=' + key, True)
+        if hits:
+            if len(hits) == 1:
+                return hits[0]['rn']
+            else:
+                # check hits for smallest molar mass compound, i.e., not polymer
+                minmm = 100000
+                minrn = ''
+                for i, hit in enumerate(hits):
+                    mm = detail(hit['rn'], 'molecularMass')
+                    if mm != '':
+                        if float(mm) < minmm:
+                            minmm = float(mm)
+                            minrn = hit['rn']
+                return minrn
+        else:
+            return ''
+    else:
+        return ''
+
+
+def _validkey(key):
+    """
+    Validate and IUPAC InChIKey
+    :param key: a string to be validated as an IUPAC InChIKey
+    :return: bool
+    """
+    test = re.search(r'^[A-Z]{14}-[A-Z]{8}[SN][A]-[A-Z]$', key)
+    if test is None:
+        return False
+    return True
+
+
+def _validcas(cas):
+    """
+    Validate a CAS Registry Number
+    See: https://en.wikipedia.org/wiki/CAS_Registry_Number#Format
+    :param cas: a string to be validated as a CAS Registry Number
+    :return: bool
+    """
+    test = re.search(r'^\d{2,8}-\d{2}-\d$', cas)
+    # if format of string does not match then it's not CAS RN
+    if test is None:
+        return False
+    # verify check digit
+    reverse = cas[::-1]  # reverse the CAS Registry Number (needed for checksum math and split out checksum)
+    digits = reverse.replace('-', '')  # remove the dashes
+    nochk = digits[1:]  # all but first digit
+    chksum = int(digits[:1])  # first digit
+    total = 0
+    for i, digit in enumerate(nochk):
+        total += (i + 1) * int(digit)  # index of chars starts at 0
+    newsum = total % 10
+    if newsum == chksum:
+        return True
+    else:
+        return False
+
+
+def chemimg(chemid='', imgtype='svg'):
+    """
+    Get an image for a compound from either a CAS Registry Number, InChIKey, SMILES, or name
+    :param chemid: the CAS Registry Number, InChIKey, SMILES, or name
+    :param imgtype: the type of image file to produce - svg, png, or ps
+    :return:
+    """
+    # check identifier for type so checking can be done
+    if chemid == '':
+        return False
+    if _validkey(chemid):
+        casrn = key2cas(chemid)
+    elif not _validcas(chemid):
+        casrn = query(chemid, True)
+    else:
+        casrn = chemid
+    if not casrn:
+        return casrn
+    # get svg data and save
+    svg = detail(casrn, "image")
+    f = open(casrn + ".svg", "w")
+    f.write(svg)
+    f.close()
+    if imgtype == 'png':
+        cairosvg.svg2png(url=casrn + ".svg", write_to=casrn + ".png")
+    elif imgtype == 'ps':
+        cairosvg.svg2ps(url=casrn + ".svg", write_to=casrn + ".ps")
+    if imgtype == 'png' or imgtype == 'ps':
+        if os.path.exists(casrn + ".svg"):
+            os.remove(casrn + ".svg")
+    return True

example.py

@@ -1,10 +1,12 @@
 from comchem import *
 
-name = detail("9003-07-0", "properties")
-print(name)
+# name = detail("9003-07-0", "properties")
+# print(name)
+#
+# find = query("trifluoro*")
+# print(find)
 
-find = query("trifluoro*")
-print(find)
+# find = key2cas('UHOVQNZJYSORNB-UHFFFAOYSA-N')
+# print(find)
 
-find = key2cas('UHOVQNZJYSORNB-UHFFFAOYSA-N')
-print(find)
+chemimg("71-43-2", 'png')

pyproject.toml

@@ -19,6 +19,7 @@ packages = [
 [tool.poetry.dependencies]
 python = "^3.7"
 bs4 = "0.0.1"
+cairosvg = "^2.5.2"
 
 [tool.poetry.dev-dependencies]
 pytest = "^5.2"