trunk/proteinstructure/AA.java

package proteinstructure;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.sql.Statement;
import java.util.HashMap;
import java.util.ArrayList;
import tools.MySQLConnection;

public class AA {
        
        public final static String MYSQLSERVER="white";
        public final static String MYSQLUSER=getUserName();
        public final static String MYSQLPWD="nieve";
        public final static String DB = "aa_info";

        //public static final ArrayList<String> AAS = aas();
        //public static final HashMap<String,String> THREELETTER2ONELETTER = threeletter2oneletter();

        /** get user name from operating system (for use as database username) */
        private static String getUserName() {
                String user = null;
                user = System.getProperty("user.name");
                if(user == null) {
                        System.err.println("Could not get user name from operating system. Exiting");
                        System.exit(1);
                }
                return user;
        }
        
        public static HashMap<String,String> getThreeletter2oneletter() {
                HashMap<String,String> three2oneletter = new HashMap<String,String>();
                three2oneletter.put("CYS", "C");
                three2oneletter.put("ASP", "D");
                three2oneletter.put("SER", "S");
                three2oneletter.put("GLN", "Q");
                three2oneletter.put("LYS", "K");
                three2oneletter.put("ILE", "I");
                three2oneletter.put("PRO", "P");
                three2oneletter.put("THR", "T");
                three2oneletter.put("PHE", "F");
                three2oneletter.put("ALA", "A");
                three2oneletter.put("GLY", "G");
                three2oneletter.put("HIS", "H");
                three2oneletter.put("GLU", "E");
                three2oneletter.put("LEU", "L");
                three2oneletter.put("ARG", "R");
                three2oneletter.put("TRP", "W");
                three2oneletter.put("VAL", "V");
                three2oneletter.put("ASN", "N");
                three2oneletter.put("TYR", "Y") ;
                three2oneletter.put("MET", "M");
                return three2oneletter;
        }
        
        public static String threeletter2oneletter(String three) {
                HashMap<String,String> three2oneletter = getThreeletter2oneletter();
                return three2oneletter.get(three);
        }
        
        public static HashMap<String,String> getOneletter2Threeletter(){
                HashMap<String,String> one2threeletter = new HashMap<String,String>();
                one2threeletter.put("C", "CYS");
                one2threeletter.put("D", "ASP");
                one2threeletter.put("S", "SER");
                one2threeletter.put("Q", "GLN");
                one2threeletter.put("K", "LYS");
                one2threeletter.put("I", "ILE");
                one2threeletter.put("P", "PRO");
                one2threeletter.put("T", "THR");
                one2threeletter.put("F", "PHE");
                one2threeletter.put("A", "ALA");
                one2threeletter.put("G", "GLY");
                one2threeletter.put("H", "HIS");
                one2threeletter.put("E", "GLU");
                one2threeletter.put("L", "LEU");
                one2threeletter.put("R", "ARG");
                one2threeletter.put("W", "TRP");
                one2threeletter.put("V", "VAL");
                one2threeletter.put("N", "ASN");
                one2threeletter.put("Y", "TYR");
                one2threeletter.put("M", "MET");
                return one2threeletter;
        }
        
        public static String oneletter2threeletter(String one) {
                HashMap<String,String> one2threeletter = getOneletter2Threeletter();
                return one2threeletter.get(one);
        }
        
        public static ArrayList<String> aas() {
                HashMap<String,String> three2oneletter = getThreeletter2oneletter();
                ArrayList<String> aas = new ArrayList<String>();
                for (String aa:three2oneletter.keySet()) {
                        aas.add(aa);
                }
                return aas;
        }
        
        public static HashMap<String,ArrayList<String>> getaas2atoms() {
                HashMap<String,ArrayList<String>> aas2atoms = new HashMap<String,ArrayList<String>>();
                MySQLConnection conn = new MySQLConnection(MYSQLSERVER,MYSQLUSER,MYSQLPWD,DB);
                String sql="SELECT code_3_letter, group_concat(chem_atom_name) FROM atom_names GROUP BY code_3_letter ORDER BY code_3_letter";
                try {
                        Statement stmt = conn.createStatement();
                        ResultSet rsst = stmt.executeQuery(sql);
                        while (rsst.next()) {
                                String res_type=rsst.getString(1);
                                String atomsStr = rsst.getString(2);
                                String[] atoms = atomsStr.split(",");
                                ArrayList<String> atomsAL = new ArrayList<String>();
                                for (String atom:atoms){
                                        if (! atom.equals("OXT")){
                                                atomsAL.add(atom);
                                        }
                                }
                                aas2atoms.put(res_type, atomsAL);       
                        } 
                        rsst.close();
                        stmt.close();
                } catch (SQLException e) {
                        e.printStackTrace();
                }
                conn.close();
                return aas2atoms;
                
        }
        
        public static HashMap<String,String[]> ct2atoms(String ct) {
                ArrayList<String> aas = aas();
                HashMap<String,String[]> ct2atoms = new HashMap<String,String[]>();
                if (ct.equals("Ca")){
                        String[] atoms = {"CA"};
                        for (String aa:aas) {
                                ct2atoms.put(aa, atoms);
                        }
                } 
                else if (ct.equals("Cb")){
                        String[] atoms = {"CB"};
                        for (String aa:aas) {
                                ct2atoms.put(aa, atoms);
                        }
                        atoms = new String[1];
                        atoms[0]="CA";
                        ct2atoms.put("GLY", atoms);
                }
                else if (ct.equals("C")){
                        String[] atoms = {"C"};
                        for (String aa:aas) {                           
                                ct2atoms.put(aa, atoms);
                        }                       
                }
                else if (ct.equals("Cg")){
                        String[] atoms = {"SG"};
                        ct2atoms.put("CYS", atoms);
                        atoms = new String[1];
                        atoms[0]= "CG";
                        ct2atoms.put("ASP", atoms);
                        atoms = new String[1];
                        atoms[0]="OG";
                        ct2atoms.put("SER", atoms);
                        atoms = new String[1];
                        atoms[0]="CG";
                        ct2atoms.put("GLN", atoms);
                        atoms = new String[1];
                        atoms[0]="CD";
                        ct2atoms.put("LYS", atoms);
                        atoms = new String[1];
                        atoms[0]="CG1";
                        ct2atoms.put("ILE", atoms);
                        atoms = new String[1];
                        atoms[0]="CG";
                        ct2atoms.put("PRO", atoms);
                        atoms = new String[1];
                        atoms[0]="OG1";
                        ct2atoms.put("THR", atoms);
                        atoms = new String[1];
                        atoms[0]="CG";
                        ct2atoms.put("PHE", atoms);
                        ct2atoms.put("ALA", new String[0]);
                        ct2atoms.put("GLY", new String[0]);
                        atoms = new String[1];
                        atoms[0]="CG";
                        ct2atoms.put("HIS", atoms);
                        atoms = new String[1];
                        atoms[0]="CG";
                        ct2atoms.put("GLU", atoms);
                        atoms = new String[1];
                        atoms[0]="CG";
                        ct2atoms.put("LEU", atoms);
                        atoms = new String[1];
                        atoms[0]="NE";
                        ct2atoms.put("ARG", atoms);
                        atoms = new String[1];
                        atoms[0]="CD2";
                        ct2atoms.put("TRP", atoms);
                        atoms = new String[1];
                        atoms[0]="CG1";
                        ct2atoms.put("VAL", atoms);
                        atoms = new String[1];
                        atoms[0]="CG";
                        ct2atoms.put("ASN", atoms);
                        atoms = new String[1];
                        atoms[0]="CG";
                        ct2atoms.put("TYR", atoms);
                        atoms = new String[1];
                        atoms[0]="CG";
                        ct2atoms.put("MET", atoms);                     
                }
                else if (ct.equals("BB")){
                        String[] atoms = {"CA", "N", "C", "O"};
                        for (String aa:aas) {
                                ct2atoms.put(aa, atoms);
                        }
                }
                else if (ct.equals("SC")){
                        HashMap<String,ArrayList<String>> aas2atoms = getaas2atoms();                   
                        for (String aa:aas) {
                                ArrayList<String> SCatoms =aas2atoms.get(aa);
                                SCatoms.remove("CA");
                                SCatoms.remove("N");
                                SCatoms.remove("C");
                                SCatoms.remove("O");
                                String[] SCatomsar= new String[SCatoms.size()];
                                SCatomsar=SCatoms.toArray(SCatomsar);
                                ct2atoms.put(aa, SCatomsar);
                        }
                }
                else if (ct.equals("ALL")){
                        HashMap<String,ArrayList<String>> aas2atoms = getaas2atoms();
                        for (String aa:aas) {
                                ArrayList<String> ALLatoms = aas2atoms.get(aa);
                                String[] ALLatomsar= new String[ALLatoms.size()];
                                ALLatomsar=ALLatoms.toArray(ALLatomsar);                                
                                ct2atoms.put(aa,ALLatomsar);
                        }
                }               
                return ct2atoms;
        }
}
Revision:	135
Committed:	Mon May 14 09:49:04 2007 UTC (17 years, 4 months ago) by duarte
File size:	7097 byte(s)
Log Message:	NEW FUNCTIONALITY: reading of graph from db is fully implemented for all cases New chain member variable in the Info classes, read in get_asym_id (Pdbase) and in get_chain_id (Msdsd) Reading chain also in Pdb in read_pdb_data_from_file Not reading chain anymore in read_atomData of PdbaseInfo Added oneletter2threeletter and getoneletter2threeletter to AA class Changes in Graph: - added db static vars and getUserName method - new member variables graphid and sm_id - new method read_graph_from_db to read contacts, nodes (and sequence from nodes) from db - new method getgraphid New Exception class GraphIdNotFoundError
Line	User	Rev	File contents
1	duarte	123	package proteinstructure;
2			import java.sql.ResultSet;
3			import java.sql.SQLException;
4			import java.sql.Statement;
5			import java.util.HashMap;
6			import java.util.ArrayList;
7			import tools.MySQLConnection;
8
9			public class AA {
10
11			public final static String MYSQLSERVER="white";
12	duarte	126	public final static String MYSQLUSER=getUserName();
13	duarte	123	public final static String MYSQLPWD="nieve";
14			public final static String DB = "aa_info";
15
16			//public static final ArrayList<String> AAS = aas();
17			//public static final HashMap<String,String> THREELETTER2ONELETTER = threeletter2oneletter();
18	duarte	126
19			/** get user name from operating system (for use as database username) */
20			private static String getUserName() {
21			String user = null;
22			user = System.getProperty("user.name");
23			if(user == null) {
24			System.err.println("Could not get user name from operating system. Exiting");
25			System.exit(1);
26			}
27			return user;
28			}
29	duarte	123
30			public static HashMap<String,String> getThreeletter2oneletter() {
31			HashMap<String,String> three2oneletter = new HashMap<String,String>();
32			three2oneletter.put("CYS", "C");
33			three2oneletter.put("ASP", "D");
34			three2oneletter.put("SER", "S");
35			three2oneletter.put("GLN", "Q");
36			three2oneletter.put("LYS", "K");
37			three2oneletter.put("ILE", "I");
38			three2oneletter.put("PRO", "P");
39			three2oneletter.put("THR", "T");
40			three2oneletter.put("PHE", "F");
41			three2oneletter.put("ALA", "A");
42			three2oneletter.put("GLY", "G");
43			three2oneletter.put("HIS", "H");
44			three2oneletter.put("GLU", "E");
45			three2oneletter.put("LEU", "L");
46			three2oneletter.put("ARG", "R");
47			three2oneletter.put("TRP", "W");
48			three2oneletter.put("VAL", "V");
49			three2oneletter.put("ASN", "N");
50			three2oneletter.put("TYR", "Y") ;
51			three2oneletter.put("MET", "M");
52			return three2oneletter;
53			}
54
55			public static String threeletter2oneletter(String three) {
56			HashMap<String,String> three2oneletter = getThreeletter2oneletter();
57			return three2oneletter.get(three);
58			}
59
60	duarte	135	public static HashMap<String,String> getOneletter2Threeletter(){
61			HashMap<String,String> one2threeletter = new HashMap<String,String>();
62			one2threeletter.put("C", "CYS");
63			one2threeletter.put("D", "ASP");
64			one2threeletter.put("S", "SER");
65			one2threeletter.put("Q", "GLN");
66			one2threeletter.put("K", "LYS");
67			one2threeletter.put("I", "ILE");
68			one2threeletter.put("P", "PRO");
69			one2threeletter.put("T", "THR");
70			one2threeletter.put("F", "PHE");
71			one2threeletter.put("A", "ALA");
72			one2threeletter.put("G", "GLY");
73			one2threeletter.put("H", "HIS");
74			one2threeletter.put("E", "GLU");
75			one2threeletter.put("L", "LEU");
76			one2threeletter.put("R", "ARG");
77			one2threeletter.put("W", "TRP");
78			one2threeletter.put("V", "VAL");
79			one2threeletter.put("N", "ASN");
80			one2threeletter.put("Y", "TYR");
81			one2threeletter.put("M", "MET");
82			return one2threeletter;
83			}
84
85			public static String oneletter2threeletter(String one) {
86			HashMap<String,String> one2threeletter = getOneletter2Threeletter();
87			return one2threeletter.get(one);
88			}
89
90	duarte	123	public static ArrayList<String> aas() {
91			HashMap<String,String> three2oneletter = getThreeletter2oneletter();
92			ArrayList<String> aas = new ArrayList<String>();
93			for (String aa:three2oneletter.keySet()) {
94			aas.add(aa);
95			}
96			return aas;
97			}
98
99			public static HashMap<String,ArrayList<String>> getaas2atoms() {
100			HashMap<String,ArrayList<String>> aas2atoms = new HashMap<String,ArrayList<String>>();
101			MySQLConnection conn = new MySQLConnection(MYSQLSERVER,MYSQLUSER,MYSQLPWD,DB);
102			String sql="SELECT code_3_letter, group_concat(chem_atom_name) FROM atom_names GROUP BY code_3_letter ORDER BY code_3_letter";
103			try {
104			Statement stmt = conn.createStatement();
105			ResultSet rsst = stmt.executeQuery(sql);
106			while (rsst.next()) {
107			String res_type=rsst.getString(1);
108			String atomsStr = rsst.getString(2);
109			String[] atoms = atomsStr.split(",");
110			ArrayList<String> atomsAL = new ArrayList<String>();
111			for (String atom:atoms){
112			if (! atom.equals("OXT")){
113			atomsAL.add(atom);
114			}
115			}
116			aas2atoms.put(res_type, atomsAL);
117			}
118			rsst.close();
119			stmt.close();
120			} catch (SQLException e) {
121			e.printStackTrace();
122			}
123			conn.close();
124			return aas2atoms;
125
126			}
127
128			public static HashMap<String,String[]> ct2atoms(String ct) {
129			ArrayList<String> aas = aas();
130			HashMap<String,String[]> ct2atoms = new HashMap<String,String[]>();
131			if (ct.equals("Ca")){
132			String[] atoms = {"CA"};
133			for (String aa:aas) {
134			ct2atoms.put(aa, atoms);
135			}
136			}
137			else if (ct.equals("Cb")){
138			String[] atoms = {"CB"};
139			for (String aa:aas) {
140			ct2atoms.put(aa, atoms);
141			}
142			atoms = new String[1];
143			atoms[0]="CA";
144			ct2atoms.put("GLY", atoms);
145			}
146			else if (ct.equals("C")){
147			String[] atoms = {"C"};
148			for (String aa:aas) {
149			ct2atoms.put(aa, atoms);
150			}
151			}
152			else if (ct.equals("Cg")){
153			String[] atoms = {"SG"};
154			ct2atoms.put("CYS", atoms);
155			atoms = new String[1];
156			atoms[0]= "CG";
157			ct2atoms.put("ASP", atoms);
158			atoms = new String[1];
159			atoms[0]="OG";
160			ct2atoms.put("SER", atoms);
161			atoms = new String[1];
162			atoms[0]="CG";
163			ct2atoms.put("GLN", atoms);
164			atoms = new String[1];
165			atoms[0]="CD";
166			ct2atoms.put("LYS", atoms);
167			atoms = new String[1];
168			atoms[0]="CG1";
169			ct2atoms.put("ILE", atoms);
170			atoms = new String[1];
171			atoms[0]="CG";
172			ct2atoms.put("PRO", atoms);
173			atoms = new String[1];
174			atoms[0]="OG1";
175			ct2atoms.put("THR", atoms);
176			atoms = new String[1];
177			atoms[0]="CG";
178			ct2atoms.put("PHE", atoms);
179			ct2atoms.put("ALA", new String[0]);
180			ct2atoms.put("GLY", new String[0]);
181			atoms = new String[1];
182			atoms[0]="CG";
183			ct2atoms.put("HIS", atoms);
184			atoms = new String[1];
185			atoms[0]="CG";
186			ct2atoms.put("GLU", atoms);
187			atoms = new String[1];
188			atoms[0]="CG";
189			ct2atoms.put("LEU", atoms);
190			atoms = new String[1];
191			atoms[0]="NE";
192			ct2atoms.put("ARG", atoms);
193			atoms = new String[1];
194			atoms[0]="CD2";
195			ct2atoms.put("TRP", atoms);
196			atoms = new String[1];
197			atoms[0]="CG1";
198			ct2atoms.put("VAL", atoms);
199			atoms = new String[1];
200			atoms[0]="CG";
201			ct2atoms.put("ASN", atoms);
202			atoms = new String[1];
203			atoms[0]="CG";
204			ct2atoms.put("TYR", atoms);
205			atoms = new String[1];
206			atoms[0]="CG";
207			ct2atoms.put("MET", atoms);
208			}
209			else if (ct.equals("BB")){
210			String[] atoms = {"CA", "N", "C", "O"};
211			for (String aa:aas) {
212			ct2atoms.put(aa, atoms);
213			}
214			}
215			else if (ct.equals("SC")){
216			HashMap<String,ArrayList<String>> aas2atoms = getaas2atoms();
217			for (String aa:aas) {
218			ArrayList<String> SCatoms =aas2atoms.get(aa);
219			SCatoms.remove("CA");
220			SCatoms.remove("N");
221			SCatoms.remove("C");
222			SCatoms.remove("O");
223			String[] SCatomsar= new String[SCatoms.size()];
224			SCatomsar=SCatoms.toArray(SCatomsar);
225			ct2atoms.put(aa, SCatomsar);
226			}
227			}
228			else if (ct.equals("ALL")){
229			HashMap<String,ArrayList<String>> aas2atoms = getaas2atoms();
230			for (String aa:aas) {
231			ArrayList<String> ALLatoms = aas2atoms.get(aa);
232			String[] ALLatomsar= new String[ALLatoms.size()];
233			ALLatomsar=ALLatoms.toArray(ALLatomsar);
234			ct2atoms.put(aa,ALLatomsar);
235			}
236			}
237			return ct2atoms;
238			}
239			}