How to use STDIN in between a URL?

[piscean]

Hello Monks!

I am using PUBCHEM's PUG REST service to download properties of a specific chemical compound. I want to give STDIN input of the chemical compound in the form of a SMILES string (it's a format to represent a chemical compound, like a molecular formula). The PUG REST URL format looks like this:

http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/smiles/CCC/property/MolecularFormula,MolecularWeight,TPSA/CSV/

http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/smiles/<smiles string>/property/<properties of interest>/<output file format>/

Now, how do I STDIN my smiles string in the above format of URL? I've tried some little tricks like this:

 
#!/usr/bin/perl
use LWP::Simple;
my $smiles = <STDIN>;
my $url = 'http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/smiles/';
+  
my $finalurl = get "$url$smiles/property/MolecularFormula,MolecularWei
+ght,TPSA/CSV/";
print $finalurl;

and warning was: Use of uninitialized value $finalurl in print at test_lwp.pl line 12. Thanks in advance :)

[ikegami]

You didn't remove the line terminator.

chomp($smiles);

You should at least have printed "$url$smiles/property/MolecularFormula,MolecularWeight,TPSA/CSV/" when trying to find the problem. And it would have found it.

[piscean]

Oops! Thanks @ikegami :)

[InfiniteSilence]

chomp is your friend.

  DB<1> p $smiles
CCC

  DB<2> chomp $smiles

  DB<3> p $smiles
CCC
  DB<4> n
main::(monks1083655.pl:8):    my $finalurl = get "$url$smiles/property
+/MolecularFormula,MolecularWeight,TPSA/CSV/";
  DB<4> n
main::(monks1083655.pl:9):    print $finalurl;
  DB<4> p $finalurl
"CID","MolecularFormula","MolecularWeight","TPSA"
6334,"C3H8",44.095620,0.0

  DB<5> q

[piscean]

Thanks, my friend :)