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import insilico.core.descriptor.Descriptor;
import insilico.core.descriptor.DescriptorBlock;
import insilico.core.descriptor.blocks.AtomCenteredFragments;
import insilico.core.descriptor.blocks.Constitutional;
import insilico.core.descriptor.blocks.FunctionalGroups;
import insilico.core.descriptor.blocks.logp.MLogP;
import insilico.core.exception.DescriptorNotFoundException;
import insilico.core.molecule.InsilicoMolecule;
import insilico.core.molecule.conversion.file.MoleculeFileSmiles;
import java.util.ArrayList;
/**
* Descriptors needed by Nestle' models, based on VEGA core descriptor with
* some modification in order to be compliant with older Dragon descriptors
* used in their original model.
*
* @author Alberto Manganaro (a.manganaro@kode-solutions.net)
* modified by helma@in-silico.ch
*/
public class LoaelMazzatorta {
public LoaelMazzatorta() {
}
/**
* Main method to calculate the descriptors, from a given input file
* containing just the SMILES of the molecules. The results are written
* in a tab-separated text file.
*
* @param InputFile full path+filename of the input file (with the SMILES
* to be processed)
* @param OutFile full path+filename of the file to be written with the
* calculated descriptors
*/
public void Calculate(String InputFile) {
ArrayList<InsilicoMolecule> mols;
MoleculeFileSmiles sfile = new MoleculeFileSmiles();
try {
sfile.OpenFile(InputFile);
mols = sfile.ReadAll();
} catch (Throwable ex) {
System.out.println("Unable to read and import molecules - " + ex.getMessage());
return;
}
// build descriptors blocks
AtomCenteredFragments b_acf = new AtomCenteredFragments();
Constitutional b_const = new Constitutional();
FunctionalGroups b_func = new FunctionalGroups();
MLogP b_mlogp = new MLogP();
// run calculation
int idx = 0;
int dNum = 0;
int nErr = 0;
for (InsilicoMolecule m : mols) {
idx++;
// check mol
if (!m.IsValid()) {
nErr++;
System.out.println("INVALID MOLECULE\t" + idx);
continue;
}
// calculate
b_mlogp.Calculate(m);
b_const.Calculate(m);
b_func.Calculate(m);
b_acf.Calculate(m);
CustomDescriptors otherDesc = new CustomDescriptors(m);
double MLogP;
try {
MLogP = b_mlogp.GetByName("MLogP").getValue();
MLogP = MLogP + otherDesc.N_MlogP_Correction * (-3.684);
} catch (DescriptorNotFoundException ex) {
MLogP = -999;
}
double MLogP_square = -999;
if (MLogP != -999)
MLogP_square = Math.pow(MLogP,2);
double log10_loael = 1.80710
+ 0.05150*otherDesc.RBN
- 0.16676*getDescriptor(b_const, "nN")
- 0.91947*otherDesc.nHM
- 0.11135*getDescriptor(b_const, "nX")
- 0.09491*getDescriptor(b_func, "nCt")
+ 0.68498*getDescriptor(b_func, "nArCOOH")
+ 0.46493*getDescriptor(b_func, "nOHp")
- 0.13636*getDescriptor(b_func, "nArOR")
- 0.32953*getDescriptor(b_func, "nRSR")
- 1.78510*getDescriptor(b_func, "nSO")
- 0.50694*getDescriptor(b_func, "nCXr=")
+ 0.52406*getDescriptor(b_func, "nCconjX")
- 0.02561*getDescriptor(b_acf, "H-052")
- 0.16168*getDescriptor(b_acf, "H-054")
+ 0.17824*getDescriptor(b_acf, "O-058")
- 0.26345*getDescriptor(b_acf, "S-107")
- 1.36840*getDescriptor(b_acf, "P-117")
+ 0.13760*otherDesc.Hy
+ 0.07871*MLogP
- 0.02219*MLogP_square;
System.out.println(log10_loael);
}
}
private double getDescriptor(DescriptorBlock block, String name) {
double res;
try {
res = Double.parseDouble(block.GetByName(name).getFormattedValue());
} catch (DescriptorNotFoundException e) {
return -999;
}
return res;
}
/**
* @param args the command line arguments
*/
public static void main(String[] args) {
LoaelMazzatorta loael = new LoaelMazzatorta();
loael.Calculate(args[0]);
}
}
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