Revision 02c131e7-26c3-4710-a331-2a9de4bc8c37 - Code Golf Stack Exchange

#Python (<strike>312</strike> 309 chars)

 import re
 a,d,o,e=[],{},"",len(i)-1
 for b in i:a.append(dict(re.findall(r"([A-Z][a-z]*)(\d*)",b)))
 a=[{b:int(c[b])if c[b]else 1for b in c}for c in a]
 for b in a:
 for c in b:d[c]=d[c]+b[c]if c in d else b[c]
 if"H"not in b:d["-"]=0
 d["H"]-=2*e
 d["O"]-=e
 for b in d:o+=b+(str(d[b])if d[b]-1else"")if d[b]else""
The input for this piece of code is the array of strings `i`, and the output is `o`. Here is an example of the code with input, output, and comments added in:

 import re
 i=["HgHO4","C6H12O6"] #input, as an array of strings
 a,d,o,e=[],{},"",len(i)-1 #vars b and c are used for iterating, and are not defined here
 for b in i:a.append(dict(re.findall(r"([A-Z][a-z]*)(\d*)",b))) #convert each molecule from string to a dictionary and store into a
 a=[{b:int(c[b])if c[b]else 1for b in c}for c in a] #convert all "subscripts" in a to ints, making empty strings into 1s
 for b in a:
 for c in b:d[c]=d[c]+b[c]if c in d else b[c] #add key/value pairs of array of dictionaries a to dictionary d
 if"H"not in b:d["-"]=0 #check that all molecules have at least one H(ydrogen)
 d["H"]-=2*e #remove H(ydrogen)
 d["O"]-=e #remove O(xygen)
 for b in d:o+=b+(str(d[b])if d[b]-1else"")if d[b]else"" #convert dictionary d into output string o
 print(o) #print output