Detect and report SMILES and SDF parsing errors

Parse the strings "Q" and "C1C1" as if they were SMILES and store any error or warning messages to a file. These should not be accepted as valid SMILES strings.

There needs to be a similar test for SD files.

Hmm, even better would be to parse a SMILES file and SD file containing errors, to see if the respective readers can skip the errors.

The idea here is that an application (including a web app) may want to report that an input structure was incorrect, and give some information about what was wrong.

OpenBabel/Rubabel

require 'rubabel'
File.open("log.txt", 'w') do |out|
     %w(Q C1C).each do |smile|
          Rubabel[smile] rescue out.puts "bad smiles #{smile}"
     end
end

Cactvs/Tcl

set fh [open log.txt w]
foreach smiles [list "Q" "C1C"] {
   if {[catch {ens create $smiles} msg]} {
      puts $fh $msg
   }
}
close $fh

The message is "Error: ens create failed: Failed to decode structure data specification"

For file input, you can do something like

while 1 {
  if {[catch {molfile read $fh} eh]} {
     if {[molfile get $fh eof]} {
        break
     } else {
        puts $eh
        continue
     }
  }
}

All I/O modules in the toolkit have the capability to re-sync the file (trivial for SMILES, not so simple for SDF). In the read loop, this happens automatically.