trunk/proteinstructure/Pdb.java

package proteinstructure;

import java.io.BufferedReader;
import java.io.File;
import java.io.FileOutputStream;
import java.io.FileReader;
import java.io.PrintStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.HashMap;
import java.util.TreeMap;
import java.util.ArrayList;
import java.util.Collections;
import java.util.regex.Matcher;
import java.util.regex.Pattern;

public class Pdb {
        
        HashMap<String,Integer> resser_atom2atomserial;
        HashMap<Integer,String> resser2restype;
        HashMap<Integer,Double[]> atomser2coord;
        HashMap<Integer,Integer> atomser2resser;
        HashMap<String,ArrayList<String>> aas2atoms = AA.getaas2atoms();
        String sequence="";
        String accode="";
        String chaincode="";
        String db;
        String chain;
        
        public Pdb (String accode, String chaincode) throws PdbaseInconsistencyError, PdbaseAcCodeNotFoundError {
                this(accode,chaincode,PdbaseInfo.pdbaseDB);
                
        }
        
        public Pdb (String accode, String chaincode, String db) throws PdbaseInconsistencyError, PdbaseAcCodeNotFoundError {
                this.accode=accode;
                this.chaincode=chaincode;
                this.db=db;
                this.chain=chaincode; // we initialise it to chaincode, in read_pdb_data_from_pdbase gets reset to the right internal chain id
                read_pdb_data_from_pdbase(db);
        }
        
        public Pdb (String pdbfile) throws FileNotFoundException, IOException {
                this.accode="";
                read_pdb_data_from_file(pdbfile);
        }
        
        public void read_pdb_data_from_pdbase(String db) throws PdbaseInconsistencyError, PdbaseAcCodeNotFoundError{
                resser_atom2atomserial = new HashMap<String,Integer>();
                resser2restype = new HashMap<Integer,String>();
                atomser2coord = new HashMap<Integer,Double[]>();
                atomser2resser = new HashMap<Integer,Integer>();

                PdbaseInfo mypdbaseinfo = new PdbaseInfo(accode,chaincode,db);
                ArrayList<ArrayList> resultset = mypdbaseinfo.read_atomData();
                sequence = mypdbaseinfo.read_seq();
                mypdbaseinfo.close();
                
                for (ArrayList result:resultset){
                        int atomserial = (Integer) result.get(0);
                        String atom = (String) result.get(1);
                        String res_type = (String) result.get(2);
                        chain=(String) result.get(3);
                        int res_serial = (Integer) result.get(4);
                        double x = (Double) result.get(5);
                        double y = (Double) result.get(6);
                        double z = (Double) result.get(7);
                        Double[] coords = {x, y, z};
                        ArrayList<String> aalist=AA.aas();
                        if (aalist.contains(res_type)) {
                                atomser2coord.put(atomserial, coords);
                                atomser2resser.put(atomserial, res_serial);
                                resser2restype.put(res_serial, res_type);
                                ArrayList<String> atomlist = aas2atoms.get(res_type);
                                if (atomlist.contains(atom)){
                                        resser_atom2atomserial.put(res_serial+"_"+atom, atomserial);
                                }
                        }
                }
        }
        
        public void read_pdb_data_from_file(String pdbfile) throws FileNotFoundException, IOException{
                resser_atom2atomserial = new HashMap<String,Integer>();
                resser2restype = new HashMap<Integer,String>();
                atomser2coord = new HashMap<Integer,Double[]>();
                atomser2resser = new HashMap<Integer,Integer>();

                BufferedReader fpdb = new BufferedReader(new FileReader(new File(pdbfile)));
                String line;
                while ((line = fpdb.readLine() ) != null ) {
                        Pattern p = Pattern.compile("^ATOM");
                        Matcher m = p.matcher(line);
                        if (m.find()){
                                Pattern pl = Pattern.compile(".{6}(.....).{2}(...).{1}(...).{2}(.{4}).{4}(.{8})(.{8})(.{8})",Pattern.CASE_INSENSITIVE);
                                Matcher ml = pl.matcher(line);
                                if (ml.find()) {
                                        int atomserial=Integer.parseInt(ml.group(1).trim());
                                        String atom = ml.group(2).trim();
                                        String res_type = ml.group(3).trim();
                                        int res_serial = Integer.parseInt(ml.group(4).trim());
                                        double x = Double.parseDouble(ml.group(5).trim());
                                        double y = Double.parseDouble(ml.group(6).trim());
                                        double z = Double.parseDouble(ml.group(7).trim());
                                        Double[] coords = {x, y, z};
                                        ArrayList<String> aalist=AA.aas();
                                        if (aalist.contains(res_type)) {
                                                atomser2coord.put(atomserial, coords);
                                                atomser2resser.put(atomserial, res_serial);
                                                resser2restype.put(res_serial, res_type);
                                                ArrayList<String> atomlist = aas2atoms.get(res_type);
                                                if (atomlist.contains(atom)){
                                                        resser_atom2atomserial.put(res_serial+"_"+atom, atomserial);
                                                }
                                        }
                                }                               
                        }
                }
                fpdb.close();
                // now we read the sequence from the resser2restype HashMap
                // NOTE: we must make sure elsewhere that there are no unobserved residues, we can't check that here!
                ArrayList<Integer> ressers = new ArrayList<Integer>();
                for (int resser:resser2restype.keySet()) {
                        ressers.add(resser);
                }
                Collections.sort(ressers);
                sequence="";
                for (int resser:ressers){
                        String oneletter = AA.threeletter2oneletter(resser2restype.get(resser));
                        sequence += oneletter;
                }
        // finally we set accode and chaincode to unknown 
        //TODO: we should parse accode and chaincode from appropriate fields in pdb file, 
                // problem: in case of a non-original pdb file there won't be accession code            
                accode="?";
                chaincode="?";
        }

        public void dump2pdbfile(String outfile) throws IOException {
                String chainstr=chain;
                if (chain.equals("NULL")){
                        chainstr="A";
                }
                PrintStream Out = new PrintStream(new FileOutputStream(outfile));
                Out.println("HEADER  Dumped from "+db+". pdb accession code="+accode+", pdb chain code="+chaincode);
                for (String resser_atom:resser_atom2atomserial.keySet()){
                        int atomserial = resser_atom2atomserial.get(resser_atom);
                        int res_serial = Integer.parseInt(resser_atom.split("_")[0]);
                        String atom = resser_atom.split("_")[1];
                        String res_type = resser2restype.get(res_serial);
                        Double[] coords = atomser2coord.get(atomserial);
                        Object[] fields = {atomserial, atom, res_type, chainstr, res_serial, coords[0], coords[1], coords[2]};
                        Out.printf("ATOM  %5d  %3s %3s %1s%4d    %8.3f%8.3f%8.3f\n",fields);
                }
                Out.println("END");
                Out.close();
        }
        
        public void dumpseq(String seqfile) throws IOException {
                PrintStream Out = new PrintStream(new FileOutputStream(seqfile));
                Out.println(">"+accode+"_"+chaincode);
                Out.println(sequence);
                Out.close();
        }
        
        public int get_length(){
                return resser2restype.size();
        }
        
        public HashMap<Integer,Double[]> get_coords_for_ct(String ct) {
                HashMap<Integer,Double[]> coords = new HashMap<Integer,Double[]>(); 
                HashMap<String,String[]> restype2atoms = AA.ct2atoms(ct);
                for (int resser:resser2restype.keySet()){
                        String[] atoms = restype2atoms.get(resser2restype.get(resser));
                        for (String atom:atoms){
                                if (resser_atom2atomserial.containsKey(resser+"_"+atom)){
                                        int atomser = resser_atom2atomserial.get(resser+"_"+atom);
                                        Double[] coord = atomser2coord.get(atomser);
                                        coords.put(atomser, coord);
                                }
                                else if (atom.equals("O") && resser_atom2atomserial.containsKey(resser+"_"+"OXT")){
                                        int atomser = resser_atom2atomserial.get(resser+"_"+"OXT");
                                        Double[] coord = atomser2coord.get(atomser);
                                        coords.put(atomser, coord);
                                }
                                else {
                                        System.err.println("Couldn't find "+atom+" atom for resser="+resser+". Continuing without that atom for this resser.");
                                }
                        }
                }
                return coords;
        }
        
        public TreeMap<Contact, Double> calculate_dist_matrix(String ct){
                TreeMap<Contact,Double> dist_matrix = new TreeMap<Contact,Double>();
                if (!ct.contains("/")){
                        HashMap<Integer,Double[]> coords = get_coords_for_ct(ct);
                        for (int i_atomser:coords.keySet()){
                                for (int j_atomser:coords.keySet()){
                                        if (j_atomser>i_atomser) {
                                                Contact pair = new Contact(i_atomser,j_atomser);
                                                dist_matrix.put(pair, distance(coords.get(i_atomser),coords.get(j_atomser)));
                                        }
                                }
                        }
                } else {
                        String i_ct = ct.split("/")[0];
                        String j_ct = ct.split("/")[1];
                        HashMap<Integer,Double[]> i_coords = get_coords_for_ct(i_ct);
                        HashMap<Integer,Double[]> j_coords = get_coords_for_ct(j_ct);
                        for (int i_atomser:i_coords.keySet()){
                                for (int j_atomser:j_coords.keySet()){
                                        if (j_atomser!=i_atomser){
                                                Contact pair = new Contact(i_atomser,j_atomser);
                                                dist_matrix.put(pair, distance(i_coords.get(i_atomser),j_coords.get(j_atomser)));
                                        }
                                }
                        }
                }
                return dist_matrix;
        }
        
        /**
         * Get the contacts for given contact type and cutoff for this Pdb object.
         * Returns a Graph object with the contacts
         * The graph is always directional, i.e. in crossed cases xx/yy: i corresponds to xx and j to yy
         * ct here can be single contact type (e.g. Ca, BB) or crossed (e.g. BB/SC or Ca/Cb)
         * @param ct
         * @param cutoff
         * @return
         */
        public Graph get_graph(String ct, double cutoff){
                TreeMap<Contact,Double> dist_matrix = calculate_dist_matrix(ct);
                ArrayList<Contact> contacts = new ArrayList<Contact>();
        // we loop here over all indices of dist_matrix, 
        // we took care already that in symmetric cases (i.e. single contact type, not crossed) we have only one side of the matrix and 
        // in asymmetrical cases (i.e. crossed cases) we have both sides of the matrix
                for (Contact pair:dist_matrix.keySet()){
                        int i_atomser=pair.i;
                        int j_atomser=pair.j;
                        if (dist_matrix.get(pair)<=cutoff){
                                int i_resser = atomser2resser.get(i_atomser);
                                int j_resser = atomser2resser.get(j_atomser);
                                Contact resser_pair = new Contact(i_resser,j_resser);
                // for multi-atom models (BB, SC, ALL or BB/SC) we need to make sure that we don't have contacts from residue to itself or that we don't have duplicates                                
                                if (i_resser!=j_resser && (! contacts.contains(resser_pair))){
                                        contacts.add(resser_pair);
                                }
                        }
                }
                Collections.sort(contacts);
                TreeMap<Integer,String> nodes = new TreeMap<Integer,String>();
                for (int resser:resser2restype.keySet()){
                        nodes.put(resser,resser2restype.get(resser));
                }
        // NOTE: we pass to the graph object the chain (internal pdbase id) not the pdb chain code!
                Graph graph = new Graph (contacts,nodes,sequence,cutoff,ct,accode,chain);
                return graph;
        }
        
        public Double distance(Double[] coords1, Double[] coords2){
                return Math.sqrt(Math.pow((coords1[0]-coords2[0]),2)+Math.pow((coords1[1]-coords2[1]),2)+Math.pow((coords1[2]-coords2[2]),2));
        }
}
Revision:	129
Committed:	Thu May 10 13:12:32 2007 UTC (17 years, 4 months ago) by duarte
File size:	10095 byte(s)
Log Message:	NEW FUNCTIONALITY: can retrieve now a ContactMap object from a Graph object New method getCM in Graph. New member variables: sequence, accode, chain, nodes, directed Passing more data from Pdb to Graph in get_graph New constructor in ContactMap
Line	User	Rev	File contents
1	duarte	123	package proteinstructure;
2
3	duarte	127	import java.io.BufferedReader;
4			import java.io.File;
5	duarte	123	import java.io.FileOutputStream;
6	duarte	127	import java.io.FileReader;
7	duarte	123	import java.io.PrintStream;
8	duarte	127	import java.io.FileNotFoundException;
9	duarte	123	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	duarte	127	import java.util.regex.Matcher;
15			import java.util.regex.Pattern;
16	duarte	123
17			public class Pdb {
18
19			HashMap<String,Integer> resser_atom2atomserial;
20			HashMap<Integer,String> resser2restype;
21			HashMap<Integer,Double[]> atomser2coord;
22			HashMap<Integer,Integer> atomser2resser;
23			HashMap<String,ArrayList<String>> aas2atoms = AA.getaas2atoms();
24			String sequence="";
25			String accode="";
26			String chaincode="";
27			String db;
28			String chain;
29
30	duarte	124	public Pdb (String accode, String chaincode) throws PdbaseInconsistencyError, PdbaseAcCodeNotFoundError {
31	duarte	123	this(accode,chaincode,PdbaseInfo.pdbaseDB);
32
33			}
34
35	duarte	124	public Pdb (String accode, String chaincode, String db) throws PdbaseInconsistencyError, PdbaseAcCodeNotFoundError {
36	duarte	123	this.accode=accode;
37			this.chaincode=chaincode;
38			this.db=db;
39			this.chain=chaincode; // we initialise it to chaincode, in read_pdb_data_from_pdbase gets reset to the right internal chain id
40			read_pdb_data_from_pdbase(db);
41			}
42
43	duarte	127	public Pdb (String pdbfile) throws FileNotFoundException, IOException {
44			this.accode="";
45			read_pdb_data_from_file(pdbfile);
46	duarte	123	}
47
48	duarte	124	public void read_pdb_data_from_pdbase(String db) throws PdbaseInconsistencyError, PdbaseAcCodeNotFoundError{
49	duarte	123	resser_atom2atomserial = new HashMap<String,Integer>();
50			resser2restype = new HashMap<Integer,String>();
51			atomser2coord = new HashMap<Integer,Double[]>();
52			atomser2resser = new HashMap<Integer,Integer>();
53
54			PdbaseInfo mypdbaseinfo = new PdbaseInfo(accode,chaincode,db);
55			ArrayList<ArrayList> resultset = mypdbaseinfo.read_atomData();
56			sequence = mypdbaseinfo.read_seq();
57			mypdbaseinfo.close();
58
59			for (ArrayList result:resultset){
60			int atomserial = (Integer) result.get(0);
61			String atom = (String) result.get(1);
62			String res_type = (String) result.get(2);
63			chain=(String) result.get(3);
64			int res_serial = (Integer) result.get(4);
65			double x = (Double) result.get(5);
66			double y = (Double) result.get(6);
67			double z = (Double) result.get(7);
68			Double[] coords = {x, y, z};
69			ArrayList<String> aalist=AA.aas();
70			if (aalist.contains(res_type)) {
71			atomser2coord.put(atomserial, coords);
72			atomser2resser.put(atomserial, res_serial);
73			resser2restype.put(res_serial, res_type);
74			ArrayList<String> atomlist = aas2atoms.get(res_type);
75			if (atomlist.contains(atom)){
76			resser_atom2atomserial.put(res_serial+"_"+atom, atomserial);
77			}
78			}
79			}
80			}
81
82	duarte	127	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	duarte	123	public void dump2pdbfile(String outfile) throws IOException {
139			String chainstr=chain;
140			if (chain.equals("NULL")){
141			chainstr="A";
142			}
143			PrintStream Out = new PrintStream(new FileOutputStream(outfile));
144			Out.println("HEADER Dumped from "+db+". pdb accession code="+accode+", pdb chain code="+chaincode);
145			for (String resser_atom:resser_atom2atomserial.keySet()){
146			int atomserial = resser_atom2atomserial.get(resser_atom);
147			int res_serial = Integer.parseInt(resser_atom.split("_")[0]);
148			String atom = resser_atom.split("_")[1];
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	duarte	127	Out.printf("ATOM %5d %3s %3s %1s%4d %8.3f%8.3f%8.3f\n",fields);
153	duarte	123	}
154			Out.println("END");
155			Out.close();
156			}
157
158			public void dumpseq(String seqfile) throws IOException {
159			PrintStream Out = new PrintStream(new FileOutputStream(seqfile));
160			Out.println(">"+accode+"_"+chaincode);
161			Out.println(sequence);
162			Out.close();
163			}
164
165			public int get_length(){
166			return resser2restype.size();
167			}
168
169			public HashMap<Integer,Double[]> get_coords_for_ct(String ct) {
170			HashMap<Integer,Double[]> coords = new HashMap<Integer,Double[]>();
171			HashMap<String,String[]> restype2atoms = AA.ct2atoms(ct);
172			for (int resser:resser2restype.keySet()){
173			String[] atoms = restype2atoms.get(resser2restype.get(resser));
174			for (String atom:atoms){
175			if (resser_atom2atomserial.containsKey(resser+"_"+atom)){
176			int atomser = resser_atom2atomserial.get(resser+"_"+atom);
177			Double[] coord = atomser2coord.get(atomser);
178			coords.put(atomser, coord);
179			}
180			else if (atom.equals("O") && resser_atom2atomserial.containsKey(resser+"_"+"OXT")){
181			int atomser = resser_atom2atomserial.get(resser+"_"+"OXT");
182			Double[] coord = atomser2coord.get(atomser);
183			coords.put(atomser, coord);
184			}
185			else {
186			System.err.println("Couldn't find "+atom+" atom for resser="+resser+". Continuing without that atom for this resser.");
187			}
188			}
189			}
190			return coords;
191			}
192
193			public TreeMap<Contact, Double> calculate_dist_matrix(String ct){
194			TreeMap<Contact,Double> dist_matrix = new TreeMap<Contact,Double>();
195			if (!ct.contains("/")){
196			HashMap<Integer,Double[]> coords = get_coords_for_ct(ct);
197			for (int i_atomser:coords.keySet()){
198			for (int j_atomser:coords.keySet()){
199			if (j_atomser>i_atomser) {
200			Contact pair = new Contact(i_atomser,j_atomser);
201			dist_matrix.put(pair, distance(coords.get(i_atomser),coords.get(j_atomser)));
202			}
203			}
204			}
205			} else {
206			String i_ct = ct.split("/")[0];
207			String j_ct = ct.split("/")[1];
208			HashMap<Integer,Double[]> i_coords = get_coords_for_ct(i_ct);
209			HashMap<Integer,Double[]> j_coords = get_coords_for_ct(j_ct);
210			for (int i_atomser:i_coords.keySet()){
211			for (int j_atomser:j_coords.keySet()){
212			if (j_atomser!=i_atomser){
213			Contact pair = new Contact(i_atomser,j_atomser);
214			dist_matrix.put(pair, distance(i_coords.get(i_atomser),j_coords.get(j_atomser)));
215			}
216			}
217			}
218			}
219			return dist_matrix;
220			}
221
222	duarte	129	/**
223			* Get the contacts for given contact type and cutoff for this Pdb object.
224			* Returns a Graph object with the contacts
225			* The graph is always directional, i.e. in crossed cases xx/yy: i corresponds to xx and j to yy
226			* ct here can be single contact type (e.g. Ca, BB) or crossed (e.g. BB/SC or Ca/Cb)
227			* @param ct
228			* @param cutoff
229			* @return
230			*/
231	duarte	123	public Graph get_graph(String ct, double cutoff){
232			TreeMap<Contact,Double> dist_matrix = calculate_dist_matrix(ct);
233			ArrayList<Contact> contacts = new ArrayList<Contact>();
234	duarte	129	// we loop here over all indices of dist_matrix,
235			// we took care already that in symmetric cases (i.e. single contact type, not crossed) we have only one side of the matrix and
236			// in asymmetrical cases (i.e. crossed cases) we have both sides of the matrix
237	duarte	123	for (Contact pair:dist_matrix.keySet()){
238			int i_atomser=pair.i;
239			int j_atomser=pair.j;
240			if (dist_matrix.get(pair)<=cutoff){
241			int i_resser = atomser2resser.get(i_atomser);
242			int j_resser = atomser2resser.get(j_atomser);
243			Contact resser_pair = new Contact(i_resser,j_resser);
244	duarte	129	// for multi-atom models (BB, SC, ALL or BB/SC) we need to make sure that we don't have contacts from residue to itself or that we don't have duplicates
245	duarte	123	if (i_resser!=j_resser && (! contacts.contains(resser_pair))){
246			contacts.add(resser_pair);
247			}
248			}
249			}
250			Collections.sort(contacts);
251	duarte	129	TreeMap<Integer,String> nodes = new TreeMap<Integer,String>();
252			for (int resser:resser2restype.keySet()){
253			nodes.put(resser,resser2restype.get(resser));
254			}
255			// NOTE: we pass to the graph object the chain (internal pdbase id) not the pdb chain code!
256			Graph graph = new Graph (contacts,nodes,sequence,cutoff,ct,accode,chain);
257	duarte	123	return graph;
258			}
259
260			public Double distance(Double[] coords1, Double[] coords2){
261			return Math.sqrt(Math.pow((coords1[0]-coords2[0]),2)+Math.pow((coords1[1]-coords2[1]),2)+Math.pow((coords1[2]-coords2[2]),2));
262			}
263			}