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="";
        public String accode="";
    // given "external" pdb chain code, i.e. the classic pdb code ("NULL" if it is blank in original pdb file)  
        String chaincode="";
        int model=DEFAULT_MODEL;
        String db;
        
    // Our internal chain identifier (taken from dbs or pdb):
    // - in reading from pdbase or from msdsd it will be set to the internal chain id (asym_id field for pdbase, pchain_id for msdsd)
    // - in reading from pdb file it gets set to whatever parsed from the pdb file
        public 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);
        }

        //TODO implement read of pdb file given 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();
                chain = mypdbaseinfo.chain;
                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);
                        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);
                                }
                        }
                }
        }
        
        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();
                chain = mymsdsdinfo.chain;
                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()){
                                //                                 serial    atom   res_type chain res_ser     x     y     z
                                Pattern pl = Pattern.compile(".{6}(.....).{2}(...).{1}(...).{1}(.)(.{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();
                                        chain = ml.group(4).trim();
                                        int res_serial = Integer.parseInt(ml.group(5).trim());
                                        double x = Double.parseDouble(ml.group(6).trim());
                                        double y = Double.parseDouble(ml.group(7).trim());
                                        double z = Double.parseDouble(ml.group(8).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="Unknown";
                chaincode="Unknown";
        }

        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 chain identifier) 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:	140
Committed:	Mon May 14 15:34:21 2007 UTC (17 years, 5 months ago) by stehr
File size:	13465 byte(s)
Log Message:	Made Pdb.acccode public
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	stehr	140	public String accode="";
26	duarte	135	// given "external" pdb chain code, i.e. the classic pdb code ("NULL" if it is blank in original pdb file)
27	duarte	123	String chaincode="";
28	duarte	133	int model=DEFAULT_MODEL;
29	duarte	123	String db;
30	duarte	135
31			// Our internal chain identifier (taken from dbs or pdb):
32			// - in reading from pdbase or from msdsd it will be set to the internal chain id (asym_id field for pdbase, pchain_id for msdsd)
33			// - in reading from pdb file it gets set to whatever parsed from the pdb file
34	stehr	137	public String chain;
35	duarte	123
36	duarte	133	public static int DEFAULT_MODEL=1;
37
38	duarte	130	public Pdb (String accode, String chaincode) throws PdbaseInconsistencyError, PdbaseAcCodeNotFoundError, MsdsdAcCodeNotFoundError, MsdsdInconsistentResidueNumbersError {
39	duarte	133	this(accode,chaincode,DEFAULT_MODEL,PdbaseInfo.pdbaseDB);
40	duarte	123	}
41	duarte	133
42			public Pdb (String accode, String chaincode, int model_serial) throws PdbaseInconsistencyError, PdbaseAcCodeNotFoundError, MsdsdAcCodeNotFoundError, MsdsdInconsistentResidueNumbersError {
43			this(accode,chaincode,model_serial,PdbaseInfo.pdbaseDB);
44			}
45
46	duarte	130	public Pdb (String accode, String chaincode, String db) throws PdbaseInconsistencyError, PdbaseAcCodeNotFoundError, MsdsdAcCodeNotFoundError, MsdsdInconsistentResidueNumbersError {
47	duarte	133	this(accode,chaincode,DEFAULT_MODEL,db);
48			}
49
50			public Pdb (String accode, String chaincode, int model_serial, String db) throws PdbaseInconsistencyError, PdbaseAcCodeNotFoundError, MsdsdAcCodeNotFoundError, MsdsdInconsistentResidueNumbersError {
51	duarte	123	this.accode=accode;
52			this.chaincode=chaincode;
53	duarte	133	this.model=model_serial;
54	duarte	123	this.db=db;
55	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
56			this.chain=chaincode;
57			if (db.contains("msdsd")){
58			read_pdb_data_from_msdsd(db);
59			} else if (db.contains("pdbase")){
60			read_pdb_data_from_pdbase(db);
61			}
62	duarte	123	}
63
64	duarte	127	public Pdb (String pdbfile) throws FileNotFoundException, IOException {
65	duarte	133	this(pdbfile,DEFAULT_MODEL);
66			}
67
68	duarte	139	//TODO implement read of pdb file given model
69	duarte	133	public Pdb (String pdbfile, int model_serial) throws FileNotFoundException, IOException {
70	duarte	127	this.accode="";
71	duarte	133	this.model=model_serial;
72	duarte	127	read_pdb_data_from_file(pdbfile);
73	duarte	123	}
74	duarte	133
75	duarte	124	public void read_pdb_data_from_pdbase(String db) throws PdbaseInconsistencyError, PdbaseAcCodeNotFoundError{
76	duarte	123	resser_atom2atomserial = new HashMap<String,Integer>();
77			resser2restype = new HashMap<Integer,String>();
78			atomser2coord = new HashMap<Integer,Double[]>();
79			atomser2resser = new HashMap<Integer,Integer>();
80
81	duarte	133	PdbaseInfo mypdbaseinfo = new PdbaseInfo(accode,chaincode,model,db);
82	duarte	123	ArrayList<ArrayList> resultset = mypdbaseinfo.read_atomData();
83	duarte	135	chain = mypdbaseinfo.chain;
84	duarte	123	sequence = mypdbaseinfo.read_seq();
85			mypdbaseinfo.close();
86
87			for (ArrayList result:resultset){
88			int atomserial = (Integer) result.get(0);
89			String atom = (String) result.get(1);
90			String res_type = (String) result.get(2);
91	duarte	135	int res_serial = (Integer) result.get(3);
92			double x = (Double) result.get(4);
93			double y = (Double) result.get(5);
94			double z = (Double) result.get(6);
95	duarte	123	Double[] coords = {x, y, z};
96			ArrayList<String> aalist=AA.aas();
97			if (aalist.contains(res_type)) {
98			atomser2coord.put(atomserial, coords);
99			atomser2resser.put(atomserial, res_serial);
100			resser2restype.put(res_serial, res_type);
101			ArrayList<String> atomlist = aas2atoms.get(res_type);
102			if (atomlist.contains(atom)){
103			resser_atom2atomserial.put(res_serial+"_"+atom, atomserial);
104			}
105			}
106			}
107			}
108
109	duarte	130	public void read_pdb_data_from_msdsd(String db) throws MsdsdAcCodeNotFoundError, MsdsdInconsistentResidueNumbersError {
110			resser_atom2atomserial = new HashMap<String,Integer>();
111			resser2restype = new HashMap<Integer,String>();
112			atomser2coord = new HashMap<Integer,Double[]>();
113			atomser2resser = new HashMap<Integer,Integer>();
114
115	duarte	133	MsdsdInfo mymsdsdinfo = new MsdsdInfo(accode,chaincode,model,db);
116	duarte	130	ArrayList<ArrayList> resultset = mymsdsdinfo.read_atomData();
117			sequence = mymsdsdinfo.read_seq();
118	duarte	138	chain = mymsdsdinfo.chain;
119	duarte	130	mymsdsdinfo.close();
120
121			for (ArrayList result:resultset){
122			int atomserial = (Integer) result.get(0);
123			String atom = (String) result.get(1);
124			String res_type = (String) result.get(2);
125			int res_serial = (Integer) result.get(3);
126			double x = (Double) result.get(4);
127			double y = (Double) result.get(5);
128			double z = (Double) result.get(6);
129			Double[] coords = {x, y, z};
130			ArrayList<String> aalist=AA.aas();
131			if (aalist.contains(res_type)) {
132			atomser2coord.put(atomserial, coords);
133			atomser2resser.put(atomserial, res_serial);
134			resser2restype.put(res_serial, res_type);
135			ArrayList<String> atomlist = aas2atoms.get(res_type);
136			if (atomlist.contains(atom)){
137			resser_atom2atomserial.put(res_serial+"_"+atom, atomserial);
138			}
139			}
140			}
141			}
142
143	duarte	133	/**
144			* To read the pdb data (atom coordinates, residue serials, atom serials) from file
145			* NOTE: for now they must be single model, single chain files!! Nothing else implemented!
146			* @param pdbfile
147			* @throws FileNotFoundException
148			* @throws IOException
149			*/
150	duarte	127	public void read_pdb_data_from_file(String pdbfile) throws FileNotFoundException, IOException{
151			resser_atom2atomserial = new HashMap<String,Integer>();
152			resser2restype = new HashMap<Integer,String>();
153			atomser2coord = new HashMap<Integer,Double[]>();
154			atomser2resser = new HashMap<Integer,Integer>();
155
156			BufferedReader fpdb = new BufferedReader(new FileReader(new File(pdbfile)));
157			String line;
158			while ((line = fpdb.readLine() ) != null ) {
159			Pattern p = Pattern.compile("^ATOM");
160			Matcher m = p.matcher(line);
161			if (m.find()){
162	duarte	135	// serial atom res_type chain res_ser x y z
163			Pattern pl = Pattern.compile(".{6}(.....).{2}(...).{1}(...).{1}(.)(.{4}).{4}(.{8})(.{8})(.{8})",Pattern.CASE_INSENSITIVE);
164	duarte	127	Matcher ml = pl.matcher(line);
165			if (ml.find()) {
166			int atomserial=Integer.parseInt(ml.group(1).trim());
167			String atom = ml.group(2).trim();
168			String res_type = ml.group(3).trim();
169	duarte	135	chain = ml.group(4).trim();
170			int res_serial = Integer.parseInt(ml.group(5).trim());
171			double x = Double.parseDouble(ml.group(6).trim());
172			double y = Double.parseDouble(ml.group(7).trim());
173			double z = Double.parseDouble(ml.group(8).trim());
174	duarte	127	Double[] coords = {x, y, z};
175			ArrayList<String> aalist=AA.aas();
176			if (aalist.contains(res_type)) {
177			atomser2coord.put(atomserial, coords);
178			atomser2resser.put(atomserial, res_serial);
179			resser2restype.put(res_serial, res_type);
180			ArrayList<String> atomlist = aas2atoms.get(res_type);
181			if (atomlist.contains(atom)){
182			resser_atom2atomserial.put(res_serial+"_"+atom, atomserial);
183			}
184			}
185			}
186			}
187			}
188			fpdb.close();
189			// now we read the sequence from the resser2restype HashMap
190			// NOTE: we must make sure elsewhere that there are no unobserved residues, we can't check that here!
191			ArrayList<Integer> ressers = new ArrayList<Integer>();
192			for (int resser:resser2restype.keySet()) {
193			ressers.add(resser);
194			}
195			Collections.sort(ressers);
196			sequence="";
197			for (int resser:ressers){
198			String oneletter = AA.threeletter2oneletter(resser2restype.get(resser));
199			sequence += oneletter;
200			}
201			// finally we set accode and chaincode to unknown
202			//TODO: we should parse accode and chaincode from appropriate fields in pdb file,
203			// problem: in case of a non-original pdb file there won't be accession code
204	duarte	139	accode="Unknown";
205			chaincode="Unknown";
206	duarte	127	}
207
208	duarte	123	public void dump2pdbfile(String outfile) throws IOException {
209			String chainstr=chain;
210			if (chain.equals("NULL")){
211			chainstr="A";
212			}
213	duarte	130	TreeMap<Integer,Object[]> lines = new TreeMap<Integer,Object[]>();
214	duarte	123	PrintStream Out = new PrintStream(new FileOutputStream(outfile));
215			Out.println("HEADER Dumped from "+db+". pdb accession code="+accode+", pdb chain code="+chaincode);
216			for (String resser_atom:resser_atom2atomserial.keySet()){
217			int atomserial = resser_atom2atomserial.get(resser_atom);
218			int res_serial = Integer.parseInt(resser_atom.split("_")[0]);
219			String atom = resser_atom.split("_")[1];
220			String res_type = resser2restype.get(res_serial);
221			Double[] coords = atomser2coord.get(atomserial);
222			Object[] fields = {atomserial, atom, res_type, chainstr, res_serial, coords[0], coords[1], coords[2]};
223	duarte	130	lines.put(atomserial, fields);
224	duarte	123	}
225	duarte	130	for (int atomserial:lines.keySet()){
226			Out.printf("ATOM %5d %3s %3s %1s%4d %8.3f%8.3f%8.3f\n",lines.get(atomserial));
227			}
228	duarte	123	Out.println("END");
229			Out.close();
230			}
231
232			public void dumpseq(String seqfile) throws IOException {
233			PrintStream Out = new PrintStream(new FileOutputStream(seqfile));
234			Out.println(">"+accode+"_"+chaincode);
235			Out.println(sequence);
236			Out.close();
237			}
238
239			public int get_length(){
240			return resser2restype.size();
241			}
242
243			public HashMap<Integer,Double[]> get_coords_for_ct(String ct) {
244			HashMap<Integer,Double[]> coords = new HashMap<Integer,Double[]>();
245			HashMap<String,String[]> restype2atoms = AA.ct2atoms(ct);
246			for (int resser:resser2restype.keySet()){
247			String[] atoms = restype2atoms.get(resser2restype.get(resser));
248			for (String atom:atoms){
249			if (resser_atom2atomserial.containsKey(resser+"_"+atom)){
250			int atomser = resser_atom2atomserial.get(resser+"_"+atom);
251			Double[] coord = atomser2coord.get(atomser);
252			coords.put(atomser, coord);
253			}
254			else if (atom.equals("O") && resser_atom2atomserial.containsKey(resser+"_"+"OXT")){
255			int atomser = resser_atom2atomserial.get(resser+"_"+"OXT");
256			Double[] coord = atomser2coord.get(atomser);
257			coords.put(atomser, coord);
258			}
259			else {
260			System.err.println("Couldn't find "+atom+" atom for resser="+resser+". Continuing without that atom for this resser.");
261			}
262			}
263			}
264			return coords;
265			}
266
267			public TreeMap<Contact, Double> calculate_dist_matrix(String ct){
268			TreeMap<Contact,Double> dist_matrix = new TreeMap<Contact,Double>();
269			if (!ct.contains("/")){
270			HashMap<Integer,Double[]> coords = get_coords_for_ct(ct);
271			for (int i_atomser:coords.keySet()){
272			for (int j_atomser:coords.keySet()){
273			if (j_atomser>i_atomser) {
274			Contact pair = new Contact(i_atomser,j_atomser);
275			dist_matrix.put(pair, distance(coords.get(i_atomser),coords.get(j_atomser)));
276			}
277			}
278			}
279			} else {
280			String i_ct = ct.split("/")[0];
281			String j_ct = ct.split("/")[1];
282			HashMap<Integer,Double[]> i_coords = get_coords_for_ct(i_ct);
283			HashMap<Integer,Double[]> j_coords = get_coords_for_ct(j_ct);
284			for (int i_atomser:i_coords.keySet()){
285			for (int j_atomser:j_coords.keySet()){
286			if (j_atomser!=i_atomser){
287			Contact pair = new Contact(i_atomser,j_atomser);
288			dist_matrix.put(pair, distance(i_coords.get(i_atomser),j_coords.get(j_atomser)));
289			}
290			}
291			}
292			}
293			return dist_matrix;
294			}
295
296	duarte	129	/**
297			* Get the contacts for given contact type and cutoff for this Pdb object.
298			* Returns a Graph object with the contacts
299			* The graph is always directional, i.e. in crossed cases xx/yy: i corresponds to xx and j to yy
300			* ct here can be single contact type (e.g. Ca, BB) or crossed (e.g. BB/SC or Ca/Cb)
301			* @param ct
302			* @param cutoff
303			* @return
304			*/
305	duarte	123	public Graph get_graph(String ct, double cutoff){
306			TreeMap<Contact,Double> dist_matrix = calculate_dist_matrix(ct);
307			ArrayList<Contact> contacts = new ArrayList<Contact>();
308	duarte	129	// we loop here over all indices of dist_matrix,
309			// we took care already that in symmetric cases (i.e. single contact type, not crossed) we have only one side of the matrix and
310			// in asymmetrical cases (i.e. crossed cases) we have both sides of the matrix
311	duarte	123	for (Contact pair:dist_matrix.keySet()){
312			int i_atomser=pair.i;
313			int j_atomser=pair.j;
314			if (dist_matrix.get(pair)<=cutoff){
315			int i_resser = atomser2resser.get(i_atomser);
316			int j_resser = atomser2resser.get(j_atomser);
317			Contact resser_pair = new Contact(i_resser,j_resser);
318	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
319	duarte	123	if (i_resser!=j_resser && (! contacts.contains(resser_pair))){
320			contacts.add(resser_pair);
321			}
322			}
323			}
324			Collections.sort(contacts);
325	duarte	129	TreeMap<Integer,String> nodes = new TreeMap<Integer,String>();
326			for (int resser:resser2restype.keySet()){
327			nodes.put(resser,resser2restype.get(resser));
328			}
329	duarte	135	// NOTE: we pass to the graph object the chain (internal chain identifier) not the pdb chain code!
330	duarte	129	Graph graph = new Graph (contacts,nodes,sequence,cutoff,ct,accode,chain);
331	duarte	123	return graph;
332			}
333
334			public Double distance(Double[] coords1, Double[] coords2){
335			return Math.sqrt(Math.pow((coords1[0]-coords2[0]),2)+Math.pow((coords1[1]-coords2[1]),2)+Math.pow((coords1[2]-coords2[2]),2));
336			}
337			}