User 677b9c22ff
12-09-2007 04:15:16
Hi,
I have the following component SMARTS and I use MolImporter and force
SMARTS detection with setquerymode(true)
| Code: |
Molecule myQuery = null;
MolImporter mi = createMolImporter(queryfilename );
// needed for SMARTS
mi.setQueryMode(true);
while ((mi.read()) != null) {
//needed for SMARTS
mi.setQueryMode(true);
myQuery = mi.read();
}
|
However either the import crashes or the SMARTS are detected as CXSMILES:
The SMARTS are:
[#7]
[#7].[#7]
[#7].[#7].[#7]
N
N.N
N.N.N
output:
cxsmiles chemaxon.formats.MolImporter@1ef9157
cxsmiles chemaxon.formats.MolImporter@1ef9157
cxsmiles chemaxon.formats.MolImporter@1ef9157
cxsmiles chemaxon.formats.MolImporter@1ef9157
If I start with other SMARTS:
[!#1!#6][!#1!#6]
*
[#6]~*
[#6]~[#6]
[#7]
[#7].[#7]
[#7].[#7].[#7]
N
N.N
N.N.N
output:
cxsmarts chemaxon.formats.MolImporter@17431b9
cxsmarts chemaxon.formats.MolImporter@17431b9
cxsmarts chemaxon.formats.MolImporter@17431b9
cxsmarts chemaxon.formats.MolImporter@17431b9
cxsmarts chemaxon.formats.MolImporter@17431b9
cxsmarts chemaxon.formats.MolImporter@17431b9
In either way I never can fully read all the SMARTS, probably due to conversion errors. I can read them into Instant-JChem. So is there
a better way to force SMARTS detection within the API?
Thank you
Tobias
ChemAxon 7c2d26e5cf
12-09-2007 07:52:01
Define the input format to MolImporter to prefer this in MolImporter by format recognition. You can assign import options to the input file name (in '{' and '}' brackets). See the API:
MolImporter(String)
| Code: |
| MolImporter importer = new MolImporter(filename+"{smarts}"); |
To check the format of imported molecule, you can use the Molecule.getInputFormat() method.
User 677b9c22ff
12-09-2007 18:48:32
Hi Tamas,
thanks, unfortunately this does not resolve the problematic component SMARTS issue.
bad-smarts3.smi
| Code: |
[!#1!#6][!#1!#6]
*
[#6]~*
[#6]~[#6]
[#7]
[#7].[#7]
[#7].[#7].[#7]
N
N.N
N.N.N |
JAVA example code
| Code: |
package examples;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.IOException;
import chemaxon.formats.MolFormatException;
import chemaxon.formats.MolImporter;
import chemaxon.marvin.plugin.PluginException;
import chemaxon.struc.Molecule;
public class SMARTSproblem {
/** Defines a MolImporter object to the structure file. */
private static MolImporter createMolImporter(String filename,String format) throws IOException{
MolImporter mi = null;
try {
File f = new File(filename);
// FileInputStream fis = new FileInputStream(f);
mi = new MolImporter(f + format);
// following "get" code has no function?
System.out.println("LineCount: "+mi.getLineCount());
System.out.println("NumRecords: "+mi.estimateNumRecords());
System.out.println("RecordCount: "+mi.getRecordCount());
System.out.println("RecordCountMax: "+mi.getRecordCountMax());
} catch (FileNotFoundException ex) {
System.err.println(filename + ": not found");
System.exit(1);
} catch (MolFormatException ex) {
System.err.println(filename + ": " + ex.getMessage());
System.exit(1);
} catch (Exception ex) {
System.err.println("Error: " + filename
+ " is not a structure file.");
System.exit(1);
}
return mi;
}
public static void main(String[] args) throws PluginException , MolFormatException, IOException {
String queryfilename = "Z:bad-smarts3.smi";
try {
MolImporter mi = createMolImporter(queryfilename, "{smarts}" );
Molecule myQuery = null;
int i = 0;
while ((mi.read()) != null) {
i++;
//*** This does not work for certain SMARTS
mi.setQueryMode(true);
String myformat = mi.getFormat();
String out = mi.toString();
System.out.print (myformat+" "+out+" ");
myQuery = mi.read();
System.out.println(myQuery.getInputFormat());
}
mi.close();
System.out.println("Input contained 10 SMARTS - imported: "+i);
} catch (IOException ioe) {
ioe.printStackTrace();
}
}
}
|
Output:
| Code: |
LineCount: 0
NumRecords: -1
RecordCount: 0
RecordCountMax: 0
smarts chemaxon.formats.MolImporter@9173ef smarts
smarts chemaxon.formats.MolImporter@9173ef smarts
smarts chemaxon.formats.MolImporter@9173ef smarts
smarts chemaxon.formats.MolImporter@9173ef smarts
smarts chemaxon.formats.MolImporter@9173ef smarts
Input contained 10 SMARTS - imported: 5
|
Still it reads only 5 SMARTS instead of all 10.
Tobias
ChemAxon 25dcd765a3
14-09-2007 13:10:03
Hi!
You read every second molecule only:
| Code: |
while ((mi.read()) != null) {
i++;
//*** This does not work for certain SMARTS
mi.setQueryMode(true);
String myformat = mi.getFormat();
String out = mi.toString();
System.out.print (myformat+" "+out+" ");
myQuery = mi.read();
System.out.println(myQuery.getInputFormat());
}
|
mi.read() returns a molecule or null
in your code you store every even molecule in "myQuery = mi.read();".
The odd ones are not used in the while cycle condition.
So the correct code is the following:
| Code: |
while ((myQuery=mi.read()) != null) {
i++;
//*** This does not work for certain SMARTS
mi.setQueryMode(true);
String myformat = mi.getFormat();
String out = mi.toString();
System.out.print (myformat+" "+out+" ");
System.out.println(myQuery.getInputFormat());
}
|
Andras
User 677b9c22ff
14-09-2007 18:44:26
Hi Andras and Tamas,
thank you for the solution.
Running it with MolImporter mi = createMolImporter(queryfilename, "{
smiles}" );
| Code: |
LineCount: 0
NumRecords: -1
RecordCount: 0
RecordCountMax: 0
smiles chemaxon.formats.MolImporter@9173ef smarts [!#1!#6][!#1!#6]
smiles chemaxon.formats.MolImporter@9173ef smiles *
smiles chemaxon.formats.MolImporter@9173ef smarts [#6]~*
smiles chemaxon.formats.MolImporter@9173ef smarts [#6]~[#6]
smiles chemaxon.formats.MolImporter@9173ef smarts [#7]
smiles chemaxon.formats.MolImporter@9173ef smarts [#7].[#7]
smiles chemaxon.formats.MolImporter@9173ef smarts [#7].[#7].[#7]
smiles chemaxon.formats.MolImporter@9173ef smiles N
smiles chemaxon.formats.MolImporter@9173ef smiles N.N
smiles chemaxon.formats.MolImporter@9173ef smiles N.N.N
Input contained 10 SMARTS - imported: 10 |
Running it with MolImporter mi = createMolImporter(queryfilename, "{smarts}" ); does it correctly.
| Code: |
LineCount: 0
NumRecords: -1
RecordCount: 0
RecordCountMax: 0
smarts chemaxon.formats.MolImporter@9173ef smarts
smarts chemaxon.formats.MolImporter@9173ef smarts
smarts chemaxon.formats.MolImporter@9173ef smarts
smarts chemaxon.formats.MolImporter@9173ef smarts
smarts chemaxon.formats.MolImporter@9173ef smarts
smarts chemaxon.formats.MolImporter@9173ef smarts
smarts chemaxon.formats.MolImporter@9173ef smarts
smarts chemaxon.formats.MolImporter@9173ef smarts
smarts chemaxon.formats.MolImporter@9173ef smarts
smarts chemaxon.formats.MolImporter@9173ef smarts
Input contained 10 SMARTS - imported: 10 |
Code:
| Code: |
package examples;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.IOException;
import chemaxon.formats.MolFormatException;
import chemaxon.formats.MolImporter;
import chemaxon.marvin.plugin.PluginException;
import chemaxon.struc.Molecule;
public class SMARTSimporter {
/** Defines a MolImporter object to the structure file. */
private static MolImporter createMolImporter(String filename,String format) throws IOException{
MolImporter mi = null;
try {
File f = new File(filename);
// FileInputStream fis = new FileInputStream(f);
mi = new MolImporter(f + format);
// following "get" code has no function?
System.out.println("LineCount: "+mi.getLineCount());
System.out.println("NumRecords: "+mi.estimateNumRecords());
System.out.println("RecordCount: "+mi.getRecordCount());
System.out.println("RecordCountMax: "+mi.getRecordCountMax());
} catch (FileNotFoundException ex) {
System.err.println(filename + ": not found");
System.exit(1);
} catch (MolFormatException ex) {
System.err.println(filename + ": " + ex.getMessage());
System.exit(1);
} catch (Exception ex) {
System.err.println("Error: " + filename
+ " is not a structure file.");
System.exit(1);
}
return mi;
}
public static void main(String[] args) throws PluginException , MolFormatException, IOException {
String queryfilename = "Z:bad-smarts3.smi";
try {
MolImporter mi = createMolImporter(queryfilename, "{smarts}" );
Molecule myQuery = null;
int i = 0;
while ((myQuery = mi.read()) != null) {
i++;
String myformat = mi.getFormat();
String out = mi.toString();
System.out.print (myformat+" "+out+" ");
//myQuery mi.read();
System.out.println(myQuery.getInputFormat());
}
mi.close();
System.out.println("Input contained 10 SMARTS - imported: "+i);
} catch (IOException ioe) {
ioe.printStackTrace();
}
}
}
|
Tobias