trunk/tools/Msdsd2Pdb.java

package tools;

import java.io.*;

/**
 * Package:             tools
 * Class:               PyMol
 * Author:              Ioannis Filippis, filippis@molgen.mpg.de
 * Date:                21/03/2006
 *
 * Msdsd2Pdb's static export2File method creates a pdb file by exporting the atom
 * lines directly from the msdsd. This is needed for the visualization of the
 * biological units since pdb files contain the ASUs. Moreover, contact graphs
 * are defined using msdsd-custom fields (like chain code and residue serial)
 * and mapping to pdb fields would be necessary for the graph visualisation 
 * if the original pdb files were preferred.
 * 
 * Notes:
 * - Hetatoms are excluded (pdb_group = "A") and in case of multiple locations of
 *       amino acids, only the default location is considered (alt_code = "A") 
 *       (VendruscoloM_00_PSFG.pdf currently found in LitNet/incomingPDF/LAST_ROUND/)
 * - The filename is either accessionCode_assemblyId_modelId.pdb (biological unit)
 *   or accessionCode.pdb (asu)
 * - There is also the oportunity to send the atom lines directly to PyMol and 
 *       loading the structure without intermediate files. Look at PyMol class and
 *   sendAtomLines method.
 * 
 * Changelog:
 * 21/03/06 first created by IF
 */

public class Msdsd2Pdb {
        
    /**
     * exports to file the atom lines of a model (modelId) of a biological unit (assemblyId) 
     * of a protein (accessionCode) directly from msdsd. The filename is returned.
     * 
     * Notes:
     * - Hetatoms are excluded (pdb_group = "A") and in case of multiple locations of
     *   amino acids, only the default location is considered (alt_code = "A") 
     *   (VendruscoloM_00_PSFG.pdf currently found in LitNet/incomingPDF/LAST_ROUND/)
     * - The filename is accessionCode_assemblyId_modelId.pdb (biological unit).
     * - The chain_pdb_code is used in the chainID field in the atom line, while the chain_code is used 
     *   the segID field (due to its length). Therefore, "segi" and not "chain" must be used in pymol
     *   selections.
     * - There are two versions of export2File. One that takes the atomic coordinates from the 
     *   partial atom_data tables (needs the table number e.g. 1 for atom_data_1, but is faster), 
     *   while the other uses the merged table (really slow - should be avoided)
     */ 
        public static String export2File(String accessionCode, int assemblyId, int modelId, String pdbDir) {

                String pdbFileName = accessionCode+"_"+assemblyId+"_"+modelId+".pdb";
                String query = "SELECT CONCAT("+
                    "RPAD(\"ATOM\", 6, \" \"), "+
                    "LPAD(serial, 5, \" \"), "+
                    "\" \", "+
                    "LPAD(chem_atom_name, 4, \" \"), "+
                    "IF(alt_code IS NULL, \" \", alt_code), "+
                    "code_3_letter, "+
                    "\" \", "+
                    "IF(chain_pdb_code IS NULL, \" \", chain_pdb_code), "+
                    "LPAD(residue_serial, 4, \" \"), "+
                    "IF(residue_pdb_insert_code IS NULL, \" \", residue_pdb_insert_code), "+
                    "REPEAT(\" \", 3), "+
                    "LPAD(x, 8, \" \"), "+
                    "LPAD(y, 8, \" \"), "+
                    "LPAD(z, 8, \" \"), "+
                    "LPAD(occupancy, 6, \" \"), "+
                    "REPEAT(\" \", 6), "+
                    "REPEAT(\" \", 6), "+
                    "RPAD(chain_code, 4, \" \") "+
                    ") AS atom_lines FROM msdsd.atom_data WHERE "+
                    "(assembly_id = "+assemblyId+") AND "+
                    "(model_id = "+modelId+") AND "+
                    "((alt_code = \"A\") OR (alt_code IS NULL)) AND "+
                    "(pdb_group = \"A\") "+
                    "ORDER BY chain_code, residue_serial, serial;";
                
                gen(pdbDir+"/"+pdbFileName, query);
        
                return pdbFileName;

    }

    /**
     * exports to file the atom lines of a model (modelId) of a biological unit (assemblyId) 
     * of a protein (accessionCode) directly from msdsd. The filename is returned.
     * 
     * Notes:
     * - Hetatoms are excluded (pdb_group = "A") and in case of multiple locations of
     *   amino acids, only the default location is considered (alt_code = "A") 
     *   (VendruscoloM_00_PSFG.pdf currently found in LitNet/incomingPDF/LAST_ROUND/)
     * - The filename is accessionCode_assemblyId_modelId.pdb (biological unit).
     * - The chain_pdb_code is used in the chainID field in the atom line, while the chain_code is used 
     *   the segID field (due to its length). Therefore, "segi" and not "chain" must be used in pymol
     *   selections.
     * - There are two versions of export2File. One that takes the atomic coordinates from the 
     *   partial atom_data tables (needs the table number e.g. 1 for atom_data_1, but is faster), 
     *   while the other uses the merged table (really slow - should be avoided)
     */         
    public static String export2File(String accessionCode, int assemblyId, int modelId, int atomDataTblNum, String pdbDir) {

                String pdbFileName = accessionCode+"_"+assemblyId+"_"+modelId+".pdb";
                String query = "SELECT CONCAT("+
                    "RPAD(\"ATOM\", 6, \" \"), "+
                    "LPAD(serial, 5, \" \"), "+
                    "\" \", "+
                    "LPAD(chem_atom_name, 4, \" \"), "+
                    "IF(alt_code IS NULL, \" \", alt_code), "+
                    "code_3_letter, "+
                    "\" \", "+
                    "IF(chain_pdb_code IS NULL, \" \", chain_pdb_code), "+
                    "LPAD(residue_serial, 4, \" \"), "+
                    "IF(residue_pdb_insert_code IS NULL, \" \", residue_pdb_insert_code), "+
                    "REPEAT(\" \", 3), "+
                    "LPAD(x, 8, \" \"), "+
                    "LPAD(y, 8, \" \"), "+
                    "LPAD(z, 8, \" \"), "+
                    "LPAD(occupancy, 6, \" \"), "+
                    "REPEAT(\" \", 6), "+
                    "REPEAT(\" \", 6), "+
                    "RPAD(chain_code, 4, \" \") "+
                    ") AS atom_lines FROM msdsd.atom_data_"+atomDataTblNum+" WHERE "+
                    "(assembly_id = "+assemblyId+") AND "+
                    "(model_id = "+modelId+") AND "+
                    "((alt_code = \"A\") OR (alt_code IS NULL)) AND "+
                    "(pdb_group = \"A\") "+
                    "ORDER BY chain_code, residue_serial, serial;";
                
                gen(pdbDir+"/"+pdbFileName, query);

                return pdbFileName;

    }
    
    /**
     * exports to file the atom lines of the assymetric unit of a protein (accessionCode) 
     * directly from msdsd. The filename is returned.
     * 
     * Notes:
     * - Hetatoms are excluded (pdb_group = "A") and in case of multiple locations of
     *   amino acids, only the default location is considered (alt_code = "A") 
     *   (VendruscoloM_00_PSFG.pdf currently found in LitNet/incomingPDF/LAST_ROUND/)
     * - The filename is accessionCode.pdb (asu).
     * - The chain_pdb_code is used in the chainID field in the atom line, while the chain_code is used 
     *   the segID field (due to its length). Therefore, "segi" and not "chain" must be used in pymol
     *   selections.
     * - There are two versions of export2File. One that takes the atomic coordinates from the 
     *   partial atom_data tables (needs the table number e.g. 1 for atom_data_1, but is faster), 
     *   while the other uses the merged table (really slow - should be avoided)
     */ 
        public static String export2File(String accessionCode, String pdbDir) {

                String pdbFileName = accessionCode+".pdb";
                String query = "SELECT CONCAT("+
                    "RPAD(\"ATOM\", 6, \" \"), "+
                    "LPAD(serial, 5, \" \"), "+
                    "\" \", "+
                    "LPAD(chem_atom_name, 4, \" \"), "+
                    "IF(alt_code IS NULL, \" \", alt_code), "+
                    "code_3_letter, "+
                    "\" \", "+
                    "IF(chain_pdb_code IS NULL, \" \", chain_pdb_code), "+
                    "LPAD(residue_serial, 4, \" \"), "+
                    "IF(residue_pdb_insert_code IS NULL, \" \", residue_pdb_insert_code), "+
                    "REPEAT(\" \", 3), "+
                    "LPAD(x, 8, \" \"), "+
                    "LPAD(y, 8, \" \"), "+
                    "LPAD(z, 8, \" \"), "+
                    "LPAD(occupancy, 6, \" \"), "+
                    "REPEAT(\" \", 6), "+
                    "REPEAT(\" \", 6), "+
                    "RPAD(chain_code, 4, \" \") "+
                    ") AS atom_lines FROM msdsd.atom_data WHERE "+
                    "(accession_code = \""+accessionCode+"\") AND "+
                    "(non_assembly_valid = \"Y\") AND "+
                    "((alt_code = \"A\") OR (alt_code IS NULL)) AND "+
                    "(pdb_group = \"A\") "+
                    "ORDER BY chain_code, residue_serial, serial;";
                
                gen(pdbDir+"/"+pdbFileName, query);
        
                return pdbFileName;

    }

    /**
     * exports to file the atom lines of the assymetric unit of a protein (accessionCode) 
     * directly from msdsd. The filename is returned.
     * 
     * Notes:
     * - Hetatoms are excluded (pdb_group = "A") and in case of multiple locations of
     *   amino acids, only the default location is considered (alt_code = "A") 
     *   (VendruscoloM_00_PSFG.pdf currently found in LitNet/incomingPDF/LAST_ROUND/)
     * - The filename is accessionCode.pdb (asu).
     * - The chain_pdb_code is used in the chainID field in the atom line, while the chain_code is used 
     *   the segID field (due to its length). Therefore, "segi" and not "chain" must be used in pymol
     *   selections.
     * - There are two versions of export2File. One that takes the atomic coordinates from the 
     *   partial atom_data tables (needs the table number e.g. 1 for atom_data_1, but is faster), 
     *   while the other uses the merged table (really slow - should be avoided)
     */ 
        public static String export2File(String accessionCode, int atomDataTblNum, String pdbDir) {

                String pdbFileName = accessionCode+".pdb";
                String query = "SELECT CONCAT("+
                    "RPAD(\"ATOM\", 6, \" \"), "+
                    "LPAD(serial, 5, \" \"), "+
                    "\" \", "+
                    "LPAD(chem_atom_name, 4, \" \"), "+
                    "IF(alt_code IS NULL, \" \", alt_code), "+
                    "code_3_letter, "+
                    "\" \", "+
                    "IF(chain_pdb_code IS NULL, \" \", chain_pdb_code), "+
                    "LPAD(residue_serial, 4, \" \"), "+
                    "IF(residue_pdb_insert_code IS NULL, \" \", residue_pdb_insert_code), "+
                    "REPEAT(\" \", 3), "+
                    "LPAD(x, 8, \" \"), "+
                    "LPAD(y, 8, \" \"), "+
                    "LPAD(z, 8, \" \"), "+
                    "LPAD(occupancy, 6, \" \"), "+
                    "REPEAT(\" \", 6), "+
                    "REPEAT(\" \", 6), "+
                    "RPAD(chain_code, 4, \" \") "+
                    ") AS atom_lines FROM msdsd.atom_data_"+atomDataTblNum+" WHERE "+
                    "(accession_code = \""+accessionCode+"\") AND "+
                    "(non_assembly_valid = \"Y\") AND "+
                    "((alt_code = \"A\") OR (alt_code IS NULL)) AND "+
                    "(pdb_group = \"A\") "+
                    "ORDER BY chain_code, residue_serial, serial;";
                
                gen(pdbDir+"/"+pdbFileName, query);
        
                return pdbFileName;

    }

        /**
     * creates a temporary sql script called export.sql with the necessary sql query to dump the atom lines,
     * executes the script redirecting the output to a file and deletes the sql script
     */         
    private static void gen(String pdbFileName, String query) {
        
        try {

                    File sqlScript = new File("export.sql");
                    PrintWriter scriptOut = new PrintWriter(new FileWriter(sqlScript));
                    scriptOut.println(query);
                    if (scriptOut != null) { scriptOut.close(); }
                    
                    System.out.println(SystemCmd.exec(new String[] {"/bin/sh", "-c", "my_lila < export.sql > "+pdbFileName}));
        
                    sqlScript.delete();

                } catch (Exception e) { 
                        System.out.println(e); 
                }
                
        }

} // end of class Msdsd2Pdb
Revision:	40
Committed:	Tue Mar 21 18:21:00 2006 UTC (18 years, 6 months ago) by filippis
File size:	10883 byte(s)
Log Message:	Adding Msdsd2Pdb and PyMol classes
Line	File contents
1	package tools;
2
3	import java.io.*;
4
5	/**
6	* Package: tools
7	* Class: PyMol
8	* Author: Ioannis Filippis, filippis@molgen.mpg.de
9	* Date: 21/03/2006
10	*
11	* Msdsd2Pdb's static export2File method creates a pdb file by exporting the atom
12	* lines directly from the msdsd. This is needed for the visualization of the
13	* biological units since pdb files contain the ASUs. Moreover, contact graphs
14	* are defined using msdsd-custom fields (like chain code and residue serial)
15	* and mapping to pdb fields would be necessary for the graph visualisation
16	* if the original pdb files were preferred.
17	*
18	* Notes:
19	* - Hetatoms are excluded (pdb_group = "A") and in case of multiple locations of
20	* amino acids, only the default location is considered (alt_code = "A")
21	* (VendruscoloM_00_PSFG.pdf currently found in LitNet/incomingPDF/LAST_ROUND/)
22	* - The filename is either accessionCode_assemblyId_modelId.pdb (biological unit)
23	* or accessionCode.pdb (asu)
24	* - There is also the oportunity to send the atom lines directly to PyMol and
25	* loading the structure without intermediate files. Look at PyMol class and
26	* sendAtomLines method.
27	*
28	* Changelog:
29	* 21/03/06 first created by IF
30	*/
31
32	public class Msdsd2Pdb {
33
34	/**
35	* exports to file the atom lines of a model (modelId) of a biological unit (assemblyId)
36	* of a protein (accessionCode) directly from msdsd. The filename is returned.
37	*
38	* Notes:
39	* - Hetatoms are excluded (pdb_group = "A") and in case of multiple locations of
40	* amino acids, only the default location is considered (alt_code = "A")
41	* (VendruscoloM_00_PSFG.pdf currently found in LitNet/incomingPDF/LAST_ROUND/)
42	* - The filename is accessionCode_assemblyId_modelId.pdb (biological unit).
43	* - The chain_pdb_code is used in the chainID field in the atom line, while the chain_code is used
44	* the segID field (due to its length). Therefore, "segi" and not "chain" must be used in pymol
45	* selections.
46	* - There are two versions of export2File. One that takes the atomic coordinates from the
47	* partial atom_data tables (needs the table number e.g. 1 for atom_data_1, but is faster),
48	* while the other uses the merged table (really slow - should be avoided)
49	*/
50	public static String export2File(String accessionCode, int assemblyId, int modelId, String pdbDir) {
51
52	String pdbFileName = accessionCode+"_"+assemblyId+"_"+modelId+".pdb";
53	String query = "SELECT CONCAT("+
54	"RPAD(\"ATOM\", 6, \" \"), "+
55	"LPAD(serial, 5, \" \"), "+
56	"\" \", "+
57	"LPAD(chem_atom_name, 4, \" \"), "+
58	"IF(alt_code IS NULL, \" \", alt_code), "+
59	"code_3_letter, "+
60	"\" \", "+
61	"IF(chain_pdb_code IS NULL, \" \", chain_pdb_code), "+
62	"LPAD(residue_serial, 4, \" \"), "+
63	"IF(residue_pdb_insert_code IS NULL, \" \", residue_pdb_insert_code), "+
64	"REPEAT(\" \", 3), "+
65	"LPAD(x, 8, \" \"), "+
66	"LPAD(y, 8, \" \"), "+
67	"LPAD(z, 8, \" \"), "+
68	"LPAD(occupancy, 6, \" \"), "+
69	"REPEAT(\" \", 6), "+
70	"REPEAT(\" \", 6), "+
71	"RPAD(chain_code, 4, \" \") "+
72	") AS atom_lines FROM msdsd.atom_data WHERE "+
73	"(assembly_id = "+assemblyId+") AND "+
74	"(model_id = "+modelId+") AND "+
75	"((alt_code = \"A\") OR (alt_code IS NULL)) AND "+
76	"(pdb_group = \"A\") "+
77	"ORDER BY chain_code, residue_serial, serial;";
78
79	gen(pdbDir+"/"+pdbFileName, query);
80
81	return pdbFileName;
82
83	}
84
85	/**
86	* exports to file the atom lines of a model (modelId) of a biological unit (assemblyId)
87	* of a protein (accessionCode) directly from msdsd. The filename is returned.
88	*
89	* Notes:
90	* - Hetatoms are excluded (pdb_group = "A") and in case of multiple locations of
91	* amino acids, only the default location is considered (alt_code = "A")
92	* (VendruscoloM_00_PSFG.pdf currently found in LitNet/incomingPDF/LAST_ROUND/)
93	* - The filename is accessionCode_assemblyId_modelId.pdb (biological unit).
94	* - The chain_pdb_code is used in the chainID field in the atom line, while the chain_code is used
95	* the segID field (due to its length). Therefore, "segi" and not "chain" must be used in pymol
96	* selections.
97	* - There are two versions of export2File. One that takes the atomic coordinates from the
98	* partial atom_data tables (needs the table number e.g. 1 for atom_data_1, but is faster),
99	* while the other uses the merged table (really slow - should be avoided)
100	*/
101	public static String export2File(String accessionCode, int assemblyId, int modelId, int atomDataTblNum, String pdbDir) {
102
103	String pdbFileName = accessionCode+"_"+assemblyId+"_"+modelId+".pdb";
104	String query = "SELECT CONCAT("+
105	"RPAD(\"ATOM\", 6, \" \"), "+
106	"LPAD(serial, 5, \" \"), "+
107	"\" \", "+
108	"LPAD(chem_atom_name, 4, \" \"), "+
109	"IF(alt_code IS NULL, \" \", alt_code), "+
110	"code_3_letter, "+
111	"\" \", "+
112	"IF(chain_pdb_code IS NULL, \" \", chain_pdb_code), "+
113	"LPAD(residue_serial, 4, \" \"), "+
114	"IF(residue_pdb_insert_code IS NULL, \" \", residue_pdb_insert_code), "+
115	"REPEAT(\" \", 3), "+
116	"LPAD(x, 8, \" \"), "+
117	"LPAD(y, 8, \" \"), "+
118	"LPAD(z, 8, \" \"), "+
119	"LPAD(occupancy, 6, \" \"), "+
120	"REPEAT(\" \", 6), "+
121	"REPEAT(\" \", 6), "+
122	"RPAD(chain_code, 4, \" \") "+
123	") AS atom_lines FROM msdsd.atom_data_"+atomDataTblNum+" WHERE "+
124	"(assembly_id = "+assemblyId+") AND "+
125	"(model_id = "+modelId+") AND "+
126	"((alt_code = \"A\") OR (alt_code IS NULL)) AND "+
127	"(pdb_group = \"A\") "+
128	"ORDER BY chain_code, residue_serial, serial;";
129
130	gen(pdbDir+"/"+pdbFileName, query);
131
132	return pdbFileName;
133
134	}
135
136	/**
137	* exports to file the atom lines of the assymetric unit of a protein (accessionCode)
138	* directly from msdsd. The filename is returned.
139	*
140	* Notes:
141	* - Hetatoms are excluded (pdb_group = "A") and in case of multiple locations of
142	* amino acids, only the default location is considered (alt_code = "A")
143	* (VendruscoloM_00_PSFG.pdf currently found in LitNet/incomingPDF/LAST_ROUND/)
144	* - The filename is accessionCode.pdb (asu).
145	* - The chain_pdb_code is used in the chainID field in the atom line, while the chain_code is used
146	* the segID field (due to its length). Therefore, "segi" and not "chain" must be used in pymol
147	* selections.
148	* - There are two versions of export2File. One that takes the atomic coordinates from the
149	* partial atom_data tables (needs the table number e.g. 1 for atom_data_1, but is faster),
150	* while the other uses the merged table (really slow - should be avoided)
151	*/
152	public static String export2File(String accessionCode, String pdbDir) {
153
154	String pdbFileName = accessionCode+".pdb";
155	String query = "SELECT CONCAT("+
156	"RPAD(\"ATOM\", 6, \" \"), "+
157	"LPAD(serial, 5, \" \"), "+
158	"\" \", "+
159	"LPAD(chem_atom_name, 4, \" \"), "+
160	"IF(alt_code IS NULL, \" \", alt_code), "+
161	"code_3_letter, "+
162	"\" \", "+
163	"IF(chain_pdb_code IS NULL, \" \", chain_pdb_code), "+
164	"LPAD(residue_serial, 4, \" \"), "+
165	"IF(residue_pdb_insert_code IS NULL, \" \", residue_pdb_insert_code), "+
166	"REPEAT(\" \", 3), "+
167	"LPAD(x, 8, \" \"), "+
168	"LPAD(y, 8, \" \"), "+
169	"LPAD(z, 8, \" \"), "+
170	"LPAD(occupancy, 6, \" \"), "+
171	"REPEAT(\" \", 6), "+
172	"REPEAT(\" \", 6), "+
173	"RPAD(chain_code, 4, \" \") "+
174	") AS atom_lines FROM msdsd.atom_data WHERE "+
175	"(accession_code = \""+accessionCode+"\") AND "+
176	"(non_assembly_valid = \"Y\") AND "+
177	"((alt_code = \"A\") OR (alt_code IS NULL)) AND "+
178	"(pdb_group = \"A\") "+
179	"ORDER BY chain_code, residue_serial, serial;";
180
181	gen(pdbDir+"/"+pdbFileName, query);
182
183	return pdbFileName;
184
185	}
186
187	/**
188	* exports to file the atom lines of the assymetric unit of a protein (accessionCode)
189	* directly from msdsd. The filename is returned.
190	*
191	* Notes:
192	* - Hetatoms are excluded (pdb_group = "A") and in case of multiple locations of
193	* amino acids, only the default location is considered (alt_code = "A")
194	* (VendruscoloM_00_PSFG.pdf currently found in LitNet/incomingPDF/LAST_ROUND/)
195	* - The filename is accessionCode.pdb (asu).
196	* - The chain_pdb_code is used in the chainID field in the atom line, while the chain_code is used
197	* the segID field (due to its length). Therefore, "segi" and not "chain" must be used in pymol
198	* selections.
199	* - There are two versions of export2File. One that takes the atomic coordinates from the
200	* partial atom_data tables (needs the table number e.g. 1 for atom_data_1, but is faster),
201	* while the other uses the merged table (really slow - should be avoided)
202	*/
203	public static String export2File(String accessionCode, int atomDataTblNum, String pdbDir) {
204
205	String pdbFileName = accessionCode+".pdb";
206	String query = "SELECT CONCAT("+
207	"RPAD(\"ATOM\", 6, \" \"), "+
208	"LPAD(serial, 5, \" \"), "+
209	"\" \", "+
210	"LPAD(chem_atom_name, 4, \" \"), "+
211	"IF(alt_code IS NULL, \" \", alt_code), "+
212	"code_3_letter, "+
213	"\" \", "+
214	"IF(chain_pdb_code IS NULL, \" \", chain_pdb_code), "+
215	"LPAD(residue_serial, 4, \" \"), "+
216	"IF(residue_pdb_insert_code IS NULL, \" \", residue_pdb_insert_code), "+
217	"REPEAT(\" \", 3), "+
218	"LPAD(x, 8, \" \"), "+
219	"LPAD(y, 8, \" \"), "+
220	"LPAD(z, 8, \" \"), "+
221	"LPAD(occupancy, 6, \" \"), "+
222	"REPEAT(\" \", 6), "+
223	"REPEAT(\" \", 6), "+
224	"RPAD(chain_code, 4, \" \") "+
225	") AS atom_lines FROM msdsd.atom_data_"+atomDataTblNum+" WHERE "+
226	"(accession_code = \""+accessionCode+"\") AND "+
227	"(non_assembly_valid = \"Y\") AND "+
228	"((alt_code = \"A\") OR (alt_code IS NULL)) AND "+
229	"(pdb_group = \"A\") "+
230	"ORDER BY chain_code, residue_serial, serial;";
231
232	gen(pdbDir+"/"+pdbFileName, query);
233
234	return pdbFileName;
235
236	}
237
238	/**
239	* creates a temporary sql script called export.sql with the necessary sql query to dump the atom lines,
240	* executes the script redirecting the output to a file and deletes the sql script
241	*/
242	private static void gen(String pdbFileName, String query) {
243
244	try {
245
246	File sqlScript = new File("export.sql");
247	PrintWriter scriptOut = new PrintWriter(new FileWriter(sqlScript));
248	scriptOut.println(query);
249	if (scriptOut != null) { scriptOut.close(); }
250
251	System.out.println(SystemCmd.exec(new String[] {"/bin/sh", "-c", "my_lila < export.sql > "+pdbFileName}));
252
253	sqlScript.delete();
254
255	} catch (Exception e) {
256	System.out.println(e);
257	}
258
259	}
260
261	} // end of class Msdsd2Pdb