CCL: free software for calculation of TPSA or PSA for ligands databases

[Kyle Lutz <kyle.r.lutz!=!gmail.com>]

 Sent to CCL by: Kyle Lutz [kyle.r.lutz^gmail.com]
 Hi Andrew,
 You can do this quite easily using chemkit's (http://www.chemkit.org)
 python API as follows:
 --- tpsa-sort.py
 -----------------------------------------------------------------------
 import sys
 import chemkit
 # open and read file
 file = chemkit.MoleculeFile(sys.argv[1])
 file.read()
 # calculate tpsa values
 values = []
 for molecule in file.molecules():
  values.append((molecule.descriptor("tpsa"), molecule))
 # print sorted tpsa values and the names of the molecules
 for tpsa, molecule in sorted(values):
  print "%f, %s" % (tpsa, molecule.name())
 --- end tpsa-sort.py
 ------------------------------------------------------------------
 This can also be extended to sort by any of the other molecular
 descriptors that chemkit can calculate by changing the "tpsa" string
 to another descriptor name. See
 http://wiki.chemkit.org/Features#Molecular_Descriptors for a
 list of
 available descriptors.
 Cheers,
 Kyle
 On Mon, Apr 23, 2012 at 1:56 PM, Wolf Ihlenfeldt wdi .. xemistry.com
 <owner-chemistry#%#ccl.net> wrote:
 >
 > Sent to CCL by: Wolf Ihlenfeldt [wdi!A!xemistry.com]
 > Easily done with a tiny Cactvs script (www.xemistry.com/academic for
 > free academic downloads)
 >
 > ---snip--
 > set th [table create]
 > table addcol $th E_SMILES
 > table addcol $th E_TPSA
 > molfile hloop [lindex $argv 0] eh {
 >        table addens $th $eh
 > }
 > table sort $th {E_TPSA ascending}
 > table write $th tpsa.tsv
 > --snip--
 >
 > Run as 'csts -f script.tcl structurefile'.
 >
 > Of course the table output format, additional columns, etc. can be
 > further customized. The script automatically detects the input format,
 > so you can process SMILES, SDF, SLN, Mol2, or any other multi-record
 > format without change.
 >
 >
 >
 >
 >
 > On Mon, Apr 23, 2012 at 2:01 PM, Andrew Voronkov drugdesign++yandex.ru
 > <owner-chemistry-,-ccl.net> wrote:
 >>
 >> Sent to CCL by: Andrew Voronkov [drugdesign[-]yandex.ru]
 >> Dear CCL users, can anyone recommend free software for TPSA calculation
 where I can load database of ligands, for example several hundreds and ideally
 get the ranked according PSA. I am using now free Molinspiration server, but
 there is no file upload option, onl one by one option. Best regards, Andrew>
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 >
 >
 >
 > --
 > Wolf-D. Ihlenfeldt -  Xemistry GmbH - wdi-,-xemistry.com
 > Phone: +49 6174 201455 - Fax +49 6174 209665
 > ---
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 D. Ihlenfeldt
 > Address: Hainholzweg 11, D-61462 Königstein, Germany
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