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root/owl/trunk/proteinstructure/Pdb.java

#	Line 1 | Line 1
1		package proteinstructure;
2
3	+	import java.io.BufferedReader;
4	+	import java.io.File;
5		import java.io.FileOutputStream;
6	+	import java.io.FileReader;
7		import java.io.PrintStream;
8	+	import java.io.FileNotFoundException;
9		import java.io.IOException;
10		import java.util.HashMap;
11		import java.util.TreeMap;
12		import java.util.ArrayList;
13		import java.util.Collections;
14	+	import java.util.regex.Matcher;
15	+	import java.util.regex.Pattern;
16
17		public class Pdb {
18
#	Line 34 | Line 40
40		read_pdb_data_from_pdbase(db);
41		}
42
43	<	public Pdb (String pdbfile) {
44	<	//TODO implement read_pdb_data_from_file
45	<	//read_pdb_data_from_file(pdbfile);
43	>	public Pdb (String pdbfile) throws FileNotFoundException, IOException {
44	>	this.accode="";
45	>	read_pdb_data_from_file(pdbfile);
46		}
47
48		public void read_pdb_data_from_pdbase(String db) throws PdbaseInconsistencyError, PdbaseAcCodeNotFoundError{
#	Line 73 | Line 79
79		}
80		}
81
82	+	public void read_pdb_data_from_file(String pdbfile) throws FileNotFoundException, IOException{
83	+	resser_atom2atomserial = new HashMap<String,Integer>();
84	+	resser2restype = new HashMap<Integer,String>();
85	+	atomser2coord = new HashMap<Integer,Double[]>();
86	+	atomser2resser = new HashMap<Integer,Integer>();
87	+
88	+	BufferedReader fpdb = new BufferedReader(new FileReader(new File(pdbfile)));
89	+	String line;
90	+	while ((line = fpdb.readLine() ) != null ) {
91	+	Pattern p = Pattern.compile("^ATOM");
92	+	Matcher m = p.matcher(line);
93	+	if (m.find()){
94	+	Pattern pl = Pattern.compile(".{6}(.....).{2}(...).{1}(...).{2}(.{4}).{4}(.{8})(.{8})(.{8})",Pattern.CASE_INSENSITIVE);
95	+	Matcher ml = pl.matcher(line);
96	+	if (ml.find()) {
97	+	int atomserial=Integer.parseInt(ml.group(1).trim());
98	+	String atom = ml.group(2).trim();
99	+	String res_type = ml.group(3).trim();
100	+	int res_serial = Integer.parseInt(ml.group(4).trim());
101	+	double x = Double.parseDouble(ml.group(5).trim());
102	+	double y = Double.parseDouble(ml.group(6).trim());
103	+	double z = Double.parseDouble(ml.group(7).trim());
104	+	Double[] coords = {x, y, z};
105	+	ArrayList<String> aalist=AA.aas();
106	+	if (aalist.contains(res_type)) {
107	+	atomser2coord.put(atomserial, coords);
108	+	atomser2resser.put(atomserial, res_serial);
109	+	resser2restype.put(res_serial, res_type);
110	+	ArrayList<String> atomlist = aas2atoms.get(res_type);
111	+	if (atomlist.contains(atom)){
112	+	resser_atom2atomserial.put(res_serial+"_"+atom, atomserial);
113	+	}
114	+	}
115	+	}
116	+	}
117	+	}
118	+	fpdb.close();
119	+	// now we read the sequence from the resser2restype HashMap
120	+	// NOTE: we must make sure elsewhere that there are no unobserved residues, we can't check that here!
121	+	ArrayList<Integer> ressers = new ArrayList<Integer>();
122	+	for (int resser:resser2restype.keySet()) {
123	+	ressers.add(resser);
124	+	}
125	+	Collections.sort(ressers);
126	+	sequence="";
127	+	for (int resser:ressers){
128	+	String oneletter = AA.threeletter2oneletter(resser2restype.get(resser));
129	+	sequence += oneletter;
130	+	}
131	+	// finally we set accode and chaincode to unknown
132	+	//TODO: we should parse accode and chaincode from appropriate fields in pdb file,
133	+	// problem: in case of a non-original pdb file there won't be accession code
134	+	accode="?";
135	+	chaincode="?";
136	+	}
137	+
138		public void dump2pdbfile(String outfile) throws IOException {
139		String chainstr=chain;
140		if (chain.equals("NULL")){
#	Line 87 | Line 149
149		String res_type = resser2restype.get(res_serial);
150		Double[] coords = atomser2coord.get(atomserial);
151		Object[] fields = {atomserial, atom, res_type, chainstr, res_serial, coords[0], coords[1], coords[2]};
152	<	Out.printf("ATOM  %5d  %3s %3s %1s%4d    %8.3f%8.3f%8.3f",fields);
152	>	Out.printf("ATOM  %5d  %3s %3s %1s%4d    %8.3f%8.3f%8.3f\n",fields);
153		}
154		Out.println("END");
155		Out.close();

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