Generating chemical properties

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Calculating chemical properties with OrChem

OrChem can calculate chemical properties by invoking the CDK. Functions to do this are located in OrChem's PL/SQL package 'orchem_calculate', they take in molecule data and an input type (either 'SMILES' or 'MOL'). There's also an option to have hydrogens added to the molecular input before calculating the property. Examples below. 
> desc orchem_calculate

    FUNCTION CHARGE RETURNS NUMBER
     Argument Name                  Type                    In/Out Default?
     ------------------------------ ----------------------- ------ --------
     MOLECULE                       CLOB                    IN
     INPUT_TYPE                     VARCHAR2                IN

    FUNCTION FORMULA RETURNS VARCHAR2
     Argument Name                  Type                    In/Out Default?
     ------------------------------ ----------------------- ------ --------
     MOLECULE                       CLOB                    IN
     INPUT_TYPE                     VARCHAR2                IN
     ADD_HYDROGENS                  VARCHAR2                IN

    FUNCTION MASS RETURNS NUMBER
     Argument Name                  Type                    In/Out Default?
     ------------------------------ ----------------------- ------ --------
     MOLECULE                       CLOB                    IN
     INPUT_TYPE                     VARCHAR2                IN
     ADD_HYDROGENS                  VARCHAR2                IN

orchem_calculate.formula

Generates the chemical formula for a SMILES or Molfile, with or without hydrogens added.
Examples: 
		    

> select orchem_calculate.formula('O5CCN(CC=3C=1C=CC=CC=1C(=C2C=CC=CC2=3)CN4CCOCC4)CC5','SMILES','Y') as F from dual;

  F
  -----------------------------------------------------------------------------------------------------------------------------------
  C24H28N2O2
  
 
> select orchem_calculate.formula('O5CCN(CC=3C=1C=CC=CC=1C(=C2C=CC=CC2=3)CN4CCOCC4)CC5','SMILES','N') as F from dual;

  F
  -----------------------------------------------------------------------------------------------------------------------------------
  C24N2O2

orchem_calculate.mass

Generates the mass for a SMILES or Molfile, with or without hydrogens added.
Examples: 
		    
> select orchem_calculate.formula('C','SMILES','Y') F, orchem_calculate.mass('C','SMILES','Y') M from dual;

  F                             M
  -------------------- ----------
  CH4                  16.0424989
  
> select orchem_calculate.formula('C','SMILES','N') F, orchem_calculate.mass('C','SMILES','N') M from dual;
  
  F                             M
  -------------------- ----------
  C                    12.0107359

orchem_calculate.charge

Generates the charge for a SMILES or Molfile.
Examples: 
		    
> select orchem_calculate.charge('[O-]C([N+])C([N+])C','SMILES')  C from dual;

         C
----------
         1


> select id, orchem_calculate.charge(molfile,'MOL') as chrg 
  from orchem_compound_sample 
  where   orchem_calculate.charge(molfile,'MOL') != 0;

        ID       CHRG
---------- ----------
      1051          2
      1052          2
      1053          2
      1055          2
      1056          2
      1057         -1
      ........




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