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="";
        int model=DEFAULT_MODEL;
        String db;
        String chain;
        
        public static int DEFAULT_MODEL=1;
        
        public Pdb (String accode, String chaincode) throws PdbaseInconsistencyError, PdbaseAcCodeNotFoundError, MsdsdAcCodeNotFoundError, MsdsdInconsistentResidueNumbersError {
                this(accode,chaincode,DEFAULT_MODEL,PdbaseInfo.pdbaseDB);               
        }

        public Pdb (String accode, String chaincode, int model_serial) throws PdbaseInconsistencyError, PdbaseAcCodeNotFoundError, MsdsdAcCodeNotFoundError, MsdsdInconsistentResidueNumbersError {
                this(accode,chaincode,model_serial,PdbaseInfo.pdbaseDB);                
        }

        public Pdb (String accode, String chaincode, String db) throws PdbaseInconsistencyError, PdbaseAcCodeNotFoundError, MsdsdAcCodeNotFoundError, MsdsdInconsistentResidueNumbersError {
                this(accode,chaincode,DEFAULT_MODEL,db);                
        }

        public Pdb (String accode, String chaincode, int model_serial, String db) throws PdbaseInconsistencyError, PdbaseAcCodeNotFoundError, MsdsdAcCodeNotFoundError, MsdsdInconsistentResidueNumbersError {
                this.accode=accode;
                this.chaincode=chaincode;
                this.model=model_serial;
                this.db=db;
                // we initialise it to chaincode, in read_pdb_data_from_pdbase gets reset to the right internal chain id. If reading msdsd it stays as chaincode
                this.chain=chaincode; 
                if (db.contains("msdsd")){
                        read_pdb_data_from_msdsd(db);
                } else if (db.contains("pdbase")){
                        read_pdb_data_from_pdbase(db);
                }
        }
        
        public Pdb (String pdbfile) throws FileNotFoundException, IOException {
                this(pdbfile,DEFAULT_MODEL);
        }

        public Pdb (String pdbfile, int model_serial) throws FileNotFoundException, IOException {
                this.accode="";
                this.model=model_serial;
                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,model,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_msdsd(String db) throws MsdsdAcCodeNotFoundError, MsdsdInconsistentResidueNumbersError {
                resser_atom2atomserial = new HashMap<String,Integer>();
                resser2restype = new HashMap<Integer,String>();
                atomser2coord = new HashMap<Integer,Double[]>();
                atomser2resser = new HashMap<Integer,Integer>();
                
                MsdsdInfo mymsdsdinfo = new MsdsdInfo(accode,chaincode,model,db);
                ArrayList<ArrayList> resultset = mymsdsdinfo.read_atomData();
                sequence = mymsdsdinfo.read_seq();
                mymsdsdinfo.close();

                for (ArrayList result:resultset){
                        int atomserial = (Integer) result.get(0);
                        String atom = (String) result.get(1);
                        String res_type = (String) result.get(2);
                        int res_serial = (Integer) result.get(3);
                        double x = (Double) result.get(4);
                        double y = (Double) result.get(5);
                        double z = (Double) result.get(6);
                        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);
                                }
                        }
                }
        }
        
        /**
         * To read the pdb data (atom coordinates, residue serials, atom serials) from file
         * NOTE: for now they must be single model, single chain files!! Nothing else implemented!
         * @param pdbfile
         * @throws FileNotFoundException
         * @throws IOException
         */
        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";
                }
                TreeMap<Integer,Object[]> lines = new TreeMap<Integer,Object[]>();
                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]};
                        lines.put(atomserial, fields);
                }
                for (int atomserial:lines.keySet()){
                        Out.printf("ATOM  %5d  %3s %3s %1s%4d    %8.3f%8.3f%8.3f\n",lines.get(atomserial));
                }
                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:	133
Committed:	Fri May 11 09:37:38 2007 UTC (17 years, 4 months ago) by duarte
File size:	12833 byte(s)
Log Message:	New functionality: now can create a Pdb object passing a model serial for NMR structures. Not implemented when reading from pdb files!
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	duarte	133	int model=DEFAULT_MODEL;
28	duarte	123	String db;
29			String chain;
30
31	duarte	133	public static int DEFAULT_MODEL=1;
32
33	duarte	130	public Pdb (String accode, String chaincode) throws PdbaseInconsistencyError, PdbaseAcCodeNotFoundError, MsdsdAcCodeNotFoundError, MsdsdInconsistentResidueNumbersError {
34	duarte	133	this(accode,chaincode,DEFAULT_MODEL,PdbaseInfo.pdbaseDB);
35	duarte	123	}
36	duarte	133
37			public Pdb (String accode, String chaincode, int model_serial) throws PdbaseInconsistencyError, PdbaseAcCodeNotFoundError, MsdsdAcCodeNotFoundError, MsdsdInconsistentResidueNumbersError {
38			this(accode,chaincode,model_serial,PdbaseInfo.pdbaseDB);
39			}
40
41	duarte	130	public Pdb (String accode, String chaincode, String db) throws PdbaseInconsistencyError, PdbaseAcCodeNotFoundError, MsdsdAcCodeNotFoundError, MsdsdInconsistentResidueNumbersError {
42	duarte	133	this(accode,chaincode,DEFAULT_MODEL,db);
43			}
44
45			public Pdb (String accode, String chaincode, int model_serial, String db) throws PdbaseInconsistencyError, PdbaseAcCodeNotFoundError, MsdsdAcCodeNotFoundError, MsdsdInconsistentResidueNumbersError {
46	duarte	123	this.accode=accode;
47			this.chaincode=chaincode;
48	duarte	133	this.model=model_serial;
49	duarte	123	this.db=db;
50	duarte	130	// we initialise it to chaincode, in read_pdb_data_from_pdbase gets reset to the right internal chain id. If reading msdsd it stays as chaincode
51			this.chain=chaincode;
52			if (db.contains("msdsd")){
53			read_pdb_data_from_msdsd(db);
54			} else if (db.contains("pdbase")){
55			read_pdb_data_from_pdbase(db);
56			}
57	duarte	123	}
58
59	duarte	127	public Pdb (String pdbfile) throws FileNotFoundException, IOException {
60	duarte	133	this(pdbfile,DEFAULT_MODEL);
61			}
62
63			public Pdb (String pdbfile, int model_serial) throws FileNotFoundException, IOException {
64	duarte	127	this.accode="";
65	duarte	133	this.model=model_serial;
66	duarte	127	read_pdb_data_from_file(pdbfile);
67	duarte	123	}
68	duarte	133
69	duarte	124	public void read_pdb_data_from_pdbase(String db) throws PdbaseInconsistencyError, PdbaseAcCodeNotFoundError{
70	duarte	123	resser_atom2atomserial = new HashMap<String,Integer>();
71			resser2restype = new HashMap<Integer,String>();
72			atomser2coord = new HashMap<Integer,Double[]>();
73			atomser2resser = new HashMap<Integer,Integer>();
74
75	duarte	133	PdbaseInfo mypdbaseinfo = new PdbaseInfo(accode,chaincode,model,db);
76	duarte	123	ArrayList<ArrayList> resultset = mypdbaseinfo.read_atomData();
77			sequence = mypdbaseinfo.read_seq();
78			mypdbaseinfo.close();
79
80			for (ArrayList result:resultset){
81			int atomserial = (Integer) result.get(0);
82			String atom = (String) result.get(1);
83			String res_type = (String) result.get(2);
84			chain=(String) result.get(3);
85			int res_serial = (Integer) result.get(4);
86			double x = (Double) result.get(5);
87			double y = (Double) result.get(6);
88			double z = (Double) result.get(7);
89			Double[] coords = {x, y, z};
90			ArrayList<String> aalist=AA.aas();
91			if (aalist.contains(res_type)) {
92			atomser2coord.put(atomserial, coords);
93			atomser2resser.put(atomserial, res_serial);
94			resser2restype.put(res_serial, res_type);
95			ArrayList<String> atomlist = aas2atoms.get(res_type);
96			if (atomlist.contains(atom)){
97			resser_atom2atomserial.put(res_serial+"_"+atom, atomserial);
98			}
99			}
100			}
101			}
102
103	duarte	130	public void read_pdb_data_from_msdsd(String db) throws MsdsdAcCodeNotFoundError, MsdsdInconsistentResidueNumbersError {
104			resser_atom2atomserial = new HashMap<String,Integer>();
105			resser2restype = new HashMap<Integer,String>();
106			atomser2coord = new HashMap<Integer,Double[]>();
107			atomser2resser = new HashMap<Integer,Integer>();
108
109	duarte	133	MsdsdInfo mymsdsdinfo = new MsdsdInfo(accode,chaincode,model,db);
110	duarte	130	ArrayList<ArrayList> resultset = mymsdsdinfo.read_atomData();
111			sequence = mymsdsdinfo.read_seq();
112			mymsdsdinfo.close();
113
114			for (ArrayList result:resultset){
115			int atomserial = (Integer) result.get(0);
116			String atom = (String) result.get(1);
117			String res_type = (String) result.get(2);
118			int res_serial = (Integer) result.get(3);
119			double x = (Double) result.get(4);
120			double y = (Double) result.get(5);
121			double z = (Double) result.get(6);
122			Double[] coords = {x, y, z};
123			ArrayList<String> aalist=AA.aas();
124			if (aalist.contains(res_type)) {
125			atomser2coord.put(atomserial, coords);
126			atomser2resser.put(atomserial, res_serial);
127			resser2restype.put(res_serial, res_type);
128			ArrayList<String> atomlist = aas2atoms.get(res_type);
129			if (atomlist.contains(atom)){
130			resser_atom2atomserial.put(res_serial+"_"+atom, atomserial);
131			}
132			}
133			}
134			}
135
136	duarte	133	/**
137			* To read the pdb data (atom coordinates, residue serials, atom serials) from file
138			* NOTE: for now they must be single model, single chain files!! Nothing else implemented!
139			* @param pdbfile
140			* @throws FileNotFoundException
141			* @throws IOException
142			*/
143	duarte	127	public void read_pdb_data_from_file(String pdbfile) throws FileNotFoundException, IOException{
144			resser_atom2atomserial = new HashMap<String,Integer>();
145			resser2restype = new HashMap<Integer,String>();
146			atomser2coord = new HashMap<Integer,Double[]>();
147			atomser2resser = new HashMap<Integer,Integer>();
148
149			BufferedReader fpdb = new BufferedReader(new FileReader(new File(pdbfile)));
150			String line;
151			while ((line = fpdb.readLine() ) != null ) {
152			Pattern p = Pattern.compile("^ATOM");
153			Matcher m = p.matcher(line);
154			if (m.find()){
155			Pattern pl = Pattern.compile(".{6}(.....).{2}(...).{1}(...).{2}(.{4}).{4}(.{8})(.{8})(.{8})",Pattern.CASE_INSENSITIVE);
156			Matcher ml = pl.matcher(line);
157			if (ml.find()) {
158			int atomserial=Integer.parseInt(ml.group(1).trim());
159			String atom = ml.group(2).trim();
160			String res_type = ml.group(3).trim();
161			int res_serial = Integer.parseInt(ml.group(4).trim());
162			double x = Double.parseDouble(ml.group(5).trim());
163			double y = Double.parseDouble(ml.group(6).trim());
164			double z = Double.parseDouble(ml.group(7).trim());
165			Double[] coords = {x, y, z};
166			ArrayList<String> aalist=AA.aas();
167			if (aalist.contains(res_type)) {
168			atomser2coord.put(atomserial, coords);
169			atomser2resser.put(atomserial, res_serial);
170			resser2restype.put(res_serial, res_type);
171			ArrayList<String> atomlist = aas2atoms.get(res_type);
172			if (atomlist.contains(atom)){
173			resser_atom2atomserial.put(res_serial+"_"+atom, atomserial);
174			}
175			}
176			}
177			}
178			}
179			fpdb.close();
180			// now we read the sequence from the resser2restype HashMap
181			// NOTE: we must make sure elsewhere that there are no unobserved residues, we can't check that here!
182			ArrayList<Integer> ressers = new ArrayList<Integer>();
183			for (int resser:resser2restype.keySet()) {
184			ressers.add(resser);
185			}
186			Collections.sort(ressers);
187			sequence="";
188			for (int resser:ressers){
189			String oneletter = AA.threeletter2oneletter(resser2restype.get(resser));
190			sequence += oneletter;
191			}
192			// finally we set accode and chaincode to unknown
193			//TODO: we should parse accode and chaincode from appropriate fields in pdb file,
194			// problem: in case of a non-original pdb file there won't be accession code
195			accode="?";
196			chaincode="?";
197			}
198
199	duarte	123	public void dump2pdbfile(String outfile) throws IOException {
200			String chainstr=chain;
201			if (chain.equals("NULL")){
202			chainstr="A";
203			}
204	duarte	130	TreeMap<Integer,Object[]> lines = new TreeMap<Integer,Object[]>();
205	duarte	123	PrintStream Out = new PrintStream(new FileOutputStream(outfile));
206			Out.println("HEADER Dumped from "+db+". pdb accession code="+accode+", pdb chain code="+chaincode);
207			for (String resser_atom:resser_atom2atomserial.keySet()){
208			int atomserial = resser_atom2atomserial.get(resser_atom);
209			int res_serial = Integer.parseInt(resser_atom.split("_")[0]);
210			String atom = resser_atom.split("_")[1];
211			String res_type = resser2restype.get(res_serial);
212			Double[] coords = atomser2coord.get(atomserial);
213			Object[] fields = {atomserial, atom, res_type, chainstr, res_serial, coords[0], coords[1], coords[2]};
214	duarte	130	lines.put(atomserial, fields);
215	duarte	123	}
216	duarte	130	for (int atomserial:lines.keySet()){
217			Out.printf("ATOM %5d %3s %3s %1s%4d %8.3f%8.3f%8.3f\n",lines.get(atomserial));
218			}
219	duarte	123	Out.println("END");
220			Out.close();
221			}
222
223			public void dumpseq(String seqfile) throws IOException {
224			PrintStream Out = new PrintStream(new FileOutputStream(seqfile));
225			Out.println(">"+accode+"_"+chaincode);
226			Out.println(sequence);
227			Out.close();
228			}
229
230			public int get_length(){
231			return resser2restype.size();
232			}
233
234			public HashMap<Integer,Double[]> get_coords_for_ct(String ct) {
235			HashMap<Integer,Double[]> coords = new HashMap<Integer,Double[]>();
236			HashMap<String,String[]> restype2atoms = AA.ct2atoms(ct);
237			for (int resser:resser2restype.keySet()){
238			String[] atoms = restype2atoms.get(resser2restype.get(resser));
239			for (String atom:atoms){
240			if (resser_atom2atomserial.containsKey(resser+"_"+atom)){
241			int atomser = resser_atom2atomserial.get(resser+"_"+atom);
242			Double[] coord = atomser2coord.get(atomser);
243			coords.put(atomser, coord);
244			}
245			else if (atom.equals("O") && resser_atom2atomserial.containsKey(resser+"_"+"OXT")){
246			int atomser = resser_atom2atomserial.get(resser+"_"+"OXT");
247			Double[] coord = atomser2coord.get(atomser);
248			coords.put(atomser, coord);
249			}
250			else {
251			System.err.println("Couldn't find "+atom+" atom for resser="+resser+". Continuing without that atom for this resser.");
252			}
253			}
254			}
255			return coords;
256			}
257
258			public TreeMap<Contact, Double> calculate_dist_matrix(String ct){
259			TreeMap<Contact,Double> dist_matrix = new TreeMap<Contact,Double>();
260			if (!ct.contains("/")){
261			HashMap<Integer,Double[]> coords = get_coords_for_ct(ct);
262			for (int i_atomser:coords.keySet()){
263			for (int j_atomser:coords.keySet()){
264			if (j_atomser>i_atomser) {
265			Contact pair = new Contact(i_atomser,j_atomser);
266			dist_matrix.put(pair, distance(coords.get(i_atomser),coords.get(j_atomser)));
267			}
268			}
269			}
270			} else {
271			String i_ct = ct.split("/")[0];
272			String j_ct = ct.split("/")[1];
273			HashMap<Integer,Double[]> i_coords = get_coords_for_ct(i_ct);
274			HashMap<Integer,Double[]> j_coords = get_coords_for_ct(j_ct);
275			for (int i_atomser:i_coords.keySet()){
276			for (int j_atomser:j_coords.keySet()){
277			if (j_atomser!=i_atomser){
278			Contact pair = new Contact(i_atomser,j_atomser);
279			dist_matrix.put(pair, distance(i_coords.get(i_atomser),j_coords.get(j_atomser)));
280			}
281			}
282			}
283			}
284			return dist_matrix;
285			}
286
287	duarte	129	/**
288			* Get the contacts for given contact type and cutoff for this Pdb object.
289			* Returns a Graph object with the contacts
290			* The graph is always directional, i.e. in crossed cases xx/yy: i corresponds to xx and j to yy
291			* ct here can be single contact type (e.g. Ca, BB) or crossed (e.g. BB/SC or Ca/Cb)
292			* @param ct
293			* @param cutoff
294			* @return
295			*/
296	duarte	123	public Graph get_graph(String ct, double cutoff){
297			TreeMap<Contact,Double> dist_matrix = calculate_dist_matrix(ct);
298			ArrayList<Contact> contacts = new ArrayList<Contact>();
299	duarte	129	// we loop here over all indices of dist_matrix,
300			// we took care already that in symmetric cases (i.e. single contact type, not crossed) we have only one side of the matrix and
301			// in asymmetrical cases (i.e. crossed cases) we have both sides of the matrix
302	duarte	123	for (Contact pair:dist_matrix.keySet()){
303			int i_atomser=pair.i;
304			int j_atomser=pair.j;
305			if (dist_matrix.get(pair)<=cutoff){
306			int i_resser = atomser2resser.get(i_atomser);
307			int j_resser = atomser2resser.get(j_atomser);
308			Contact resser_pair = new Contact(i_resser,j_resser);
309	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
310	duarte	123	if (i_resser!=j_resser && (! contacts.contains(resser_pair))){
311			contacts.add(resser_pair);
312			}
313			}
314			}
315			Collections.sort(contacts);
316	duarte	129	TreeMap<Integer,String> nodes = new TreeMap<Integer,String>();
317			for (int resser:resser2restype.keySet()){
318			nodes.put(resser,resser2restype.get(resser));
319			}
320			// NOTE: we pass to the graph object the chain (internal pdbase id) not the pdb chain code!
321			Graph graph = new Graph (contacts,nodes,sequence,cutoff,ct,accode,chain);
322	duarte	123	return graph;
323			}
324
325			public Double distance(Double[] coords1, Double[] coords2){
326			return Math.sqrt(Math.pow((coords1[0]-coords2[0]),2)+Math.pow((coords1[1]-coords2[1]),2)+Math.pow((coords1[2]-coords2[2]),2));
327			}
328			}