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 {
        
        public final static int DEFAULT_MODEL=1;
        
        HashMap<String,Integer> resser_atom2atomserial;
        HashMap<Integer,String> resser2restype;
        HashMap<Integer,Double[]> atomser2coord;
        HashMap<Integer,Integer> atomser2resser;
        HashMap<String,ArrayList<String>> aas2atoms = AA.getaas2atoms();
        public 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)  
        public String chaincode="";
        public 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 (i.e. can be also ' ')
        public String chain;
        
        /**
         * Constructs Pdb object given accession code and pdb chain code. Model will be DEFAULT_MODEL
         * Takes data from default pdbase-like database: PdbaseInfo.pdbaseDB
         * @param accode
         * @param chaincode
         * @throws PdbaseInconsistencyError
         * @throws PdbaseAcCodeNotFoundError
         * @throws MsdsdAcCodeNotFoundError
         * @throws MsdsdInconsistentResidueNumbersError
         */
        public Pdb (String accode, String chaincode) throws PdbaseInconsistencyError, PdbaseAcCodeNotFoundError, MsdsdAcCodeNotFoundError, MsdsdInconsistentResidueNumbersError {
                this(accode,chaincode,DEFAULT_MODEL,PdbaseInfo.pdbaseDB);               
        }

        /**
         * Constructs Pdb object given accession code, pdb chain code and a model serial
         * Takes data from default pdbase-like database: PdbaseInfo.pdbaseDB
         * @param accode
         * @param chaincode
         * @param model_serial
         * @throws PdbaseInconsistencyError
         * @throws PdbaseAcCodeNotFoundError
         * @throws MsdsdAcCodeNotFoundError
         * @throws MsdsdInconsistentResidueNumbersError
         */
        public Pdb (String accode, String chaincode, int model_serial) throws PdbaseInconsistencyError, PdbaseAcCodeNotFoundError, MsdsdAcCodeNotFoundError, MsdsdInconsistentResidueNumbersError {
                this(accode,chaincode,model_serial,PdbaseInfo.pdbaseDB);                
        }
        
        /**
         * Constructs Pdb object given accession code, pdb chain code and a source db for the data. Model will be DEFAULT_MODEL
         * The db can be pdbase-like or msdsd-like
         * @param accode
         * @param chaincode
         * @param db
         * @throws PdbaseInconsistencyError
         * @throws PdbaseAcCodeNotFoundError
         * @throws MsdsdAcCodeNotFoundError
         * @throws MsdsdInconsistentResidueNumbersError
         */
        public Pdb (String accode, String chaincode, String db) throws PdbaseInconsistencyError, PdbaseAcCodeNotFoundError, MsdsdAcCodeNotFoundError, MsdsdInconsistentResidueNumbersError {
                this(accode,chaincode,DEFAULT_MODEL,db);                
        }

        /**
         * Constructs Pdb object given accession code, pdb chain code, model serial and a source db for the data.
         * The db can be pdbase-like or msdsd-like 
         * @param accode
         * @param chaincode
         * @param model_serial
         * @param db
         * @throws PdbaseInconsistencyError
         * @throws PdbaseAcCodeNotFoundError
         * @throws MsdsdAcCodeNotFoundError
         * @throws MsdsdInconsistentResidueNumbersError
         */
        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);
                }
        }
        
        /**
         * Constructs Pdb object reading from pdb file given pdb chain code. Model will be DEFAULT_MODEL
         * @param pdbfile
         * @param chaincode
         * @param dummy dummy parameter to distinguish the method from other with the same signature
         * TODO dummy parameter is a dirty hack, must solve it in other way: subclassing
         * @throws FileNotFoundException
         * @throws IOException
         */
        public Pdb (String pdbfile, String chaincode, boolean dummy) throws FileNotFoundException, IOException {
                this(pdbfile,chaincode,DEFAULT_MODEL,dummy);
        }
        
        /**
         * Constructs Pdb object reading from pdb file given pdb chain code and model serial
         * @param pdbfile
         * @param chaincode
         * @param model_serial
         * @param dummy dummy parameter to distinguish the method from other with the same signature
         * TODO dummy parameter is a dirty hack, must solve it in other way: subclassing
         * @throws FileNotFoundException
         * @throws IOException
         */
        public Pdb (String pdbfile, String chaincode, int model_serial, boolean dummy) throws FileNotFoundException, IOException {
                this.model=model_serial;
                this.chaincode=chaincode;
                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
         * chain gets set to internal identifier: if input chain code NULL then chain will be ' '
         * accode gets set to the one parsed in HEADER or to 'Unknown' if not found
         * sequence gets set to the sequence read from ATOM lines (i.e. observed resdiues only)
         * @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>();
                boolean empty = true; // controls whether we don't find any atom line for given chaincode and model
                // we set chain to chaincode except for case NULL where we use " " (NULL is a blank chain code in pdb files)
                chain=chaincode;
                if (chaincode.equals("NULL")) chain=" ";
                int thismodel=DEFAULT_MODEL; // we initialise to DEFAULT_MODEL, in case file doesn't have MODEL lines 
                BufferedReader fpdb = new BufferedReader(new FileReader(new File(pdbfile)));
                String line;
                while ((line = fpdb.readLine() ) != null ) {
                        Pattern p = Pattern.compile("^HEADER");
                        Matcher m = p.matcher(line);
                        if (m.find()){
                                Pattern ph = Pattern.compile("^HEADER.{56}(\\d\\w{3})");
                                Matcher mh = ph.matcher(line);
                                if (mh.find()) {
                                        accode=mh.group(1).toLowerCase();
                                } else {
                                        accode="Unknown";
                                }
                        }
                        p = Pattern.compile("^MODEL\\s+(\\d+)");
                        m = p.matcher(line);
                        if (m.find()){
                                thismodel=Integer.parseInt(m.group(1));
                        }
                        if (thismodel!=model) continue; // we skip reading of atom lines if we are not in the desired model
                        p = Pattern.compile("^ATOM");
                        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}"+chain+"(.{4}).{4}(.{8})(.{8})(.{8})",Pattern.CASE_INSENSITIVE);
                                Matcher ml = pl.matcher(line);
                                if (ml.find()) {
                                        empty=false;
                                        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();
                if (empty) System.err.println("Couldn't find any atom line for given chaincode: "+chaincode+", model: "+model);
                // 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;
                }
        }

        /**
         * Dumps coordinate data into a file in pdb format (ATOM lines only)
         * The chain dumped is the value of the chain field, i.e. our internal chain identifier for Pdb objects
         * @param outfile
         * @throws IOException
         */
        public void dump2pdbfile(String outfile) throws IOException {
                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+", chain='"+chain+"'");
                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, chain, 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));
                }
                Graph graph = new Graph (contacts,nodes,sequence,cutoff,ct,accode,chain,chaincode);
                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:	159
Committed:	Thu May 24 09:37:25 2007 UTC (17 years, 5 months ago) by duarte
File size:	16832 byte(s)
Log Message:	Moved ContactMap and EdgeState out of this repository. Extra functionality of ContactMap now in Graph: - new member variables fullLength, obsLength, numContacts. New method getIntMatrix - removed getCM method
Line	File contents
1	package proteinstructure;
2
3	import java.io.BufferedReader;
4	import java.io.File;
5	import java.io.FileOutputStream;
6	import java.io.FileReader;
7	import java.io.PrintStream;
8	import java.io.FileNotFoundException;
9	import java.io.IOException;
10	import java.util.HashMap;
11	import java.util.TreeMap;
12	import java.util.ArrayList;
13	import java.util.Collections;
14	import java.util.regex.Matcher;
15	import java.util.regex.Pattern;
16
17	public class Pdb {
18
19	public final static int DEFAULT_MODEL=1;
20
21	HashMap<String,Integer> resser_atom2atomserial;
22	HashMap<Integer,String> resser2restype;
23	HashMap<Integer,Double[]> atomser2coord;
24	HashMap<Integer,Integer> atomser2resser;
25	HashMap<String,ArrayList<String>> aas2atoms = AA.getaas2atoms();
26	public String sequence="";
27	public String accode="";
28	// given "external" pdb chain code, i.e. the classic pdb code ("NULL" if it is blank in original pdb file)
29	public String chaincode="";
30	public int model=DEFAULT_MODEL;
31	String db;
32
33	// Our internal chain identifier (taken from dbs or pdb):
34	// - 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)
35	// - in reading from pdb file it gets set to whatever parsed from the pdb file (i.e. can be also ' ')
36	public String chain;
37
38	/**
39	* Constructs Pdb object given accession code and pdb chain code. Model will be DEFAULT_MODEL
40	* Takes data from default pdbase-like database: PdbaseInfo.pdbaseDB
41	* @param accode
42	* @param chaincode
43	* @throws PdbaseInconsistencyError
44	* @throws PdbaseAcCodeNotFoundError
45	* @throws MsdsdAcCodeNotFoundError
46	* @throws MsdsdInconsistentResidueNumbersError
47	*/
48	public Pdb (String accode, String chaincode) throws PdbaseInconsistencyError, PdbaseAcCodeNotFoundError, MsdsdAcCodeNotFoundError, MsdsdInconsistentResidueNumbersError {
49	this(accode,chaincode,DEFAULT_MODEL,PdbaseInfo.pdbaseDB);
50	}
51
52	/**
53	* Constructs Pdb object given accession code, pdb chain code and a model serial
54	* Takes data from default pdbase-like database: PdbaseInfo.pdbaseDB
55	* @param accode
56	* @param chaincode
57	* @param model_serial
58	* @throws PdbaseInconsistencyError
59	* @throws PdbaseAcCodeNotFoundError
60	* @throws MsdsdAcCodeNotFoundError
61	* @throws MsdsdInconsistentResidueNumbersError
62	*/
63	public Pdb (String accode, String chaincode, int model_serial) throws PdbaseInconsistencyError, PdbaseAcCodeNotFoundError, MsdsdAcCodeNotFoundError, MsdsdInconsistentResidueNumbersError {
64	this(accode,chaincode,model_serial,PdbaseInfo.pdbaseDB);
65	}
66
67	/**
68	* Constructs Pdb object given accession code, pdb chain code and a source db for the data. Model will be DEFAULT_MODEL
69	* The db can be pdbase-like or msdsd-like
70	* @param accode
71	* @param chaincode
72	* @param db
73	* @throws PdbaseInconsistencyError
74	* @throws PdbaseAcCodeNotFoundError
75	* @throws MsdsdAcCodeNotFoundError
76	* @throws MsdsdInconsistentResidueNumbersError
77	*/
78	public Pdb (String accode, String chaincode, String db) throws PdbaseInconsistencyError, PdbaseAcCodeNotFoundError, MsdsdAcCodeNotFoundError, MsdsdInconsistentResidueNumbersError {
79	this(accode,chaincode,DEFAULT_MODEL,db);
80	}
81
82	/**
83	* Constructs Pdb object given accession code, pdb chain code, model serial and a source db for the data.
84	* The db can be pdbase-like or msdsd-like
85	* @param accode
86	* @param chaincode
87	* @param model_serial
88	* @param db
89	* @throws PdbaseInconsistencyError
90	* @throws PdbaseAcCodeNotFoundError
91	* @throws MsdsdAcCodeNotFoundError
92	* @throws MsdsdInconsistentResidueNumbersError
93	*/
94	public Pdb (String accode, String chaincode, int model_serial, String db) throws PdbaseInconsistencyError, PdbaseAcCodeNotFoundError, MsdsdAcCodeNotFoundError, MsdsdInconsistentResidueNumbersError {
95	this.accode=accode;
96	this.chaincode=chaincode;
97	this.model=model_serial;
98	this.db=db;
99	// 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
100	this.chain=chaincode;
101	if (db.contains("msdsd")){
102	read_pdb_data_from_msdsd(db);
103	} else if (db.contains("pdbase")){
104	read_pdb_data_from_pdbase(db);
105	}
106	}
107
108	/**
109	* Constructs Pdb object reading from pdb file given pdb chain code. Model will be DEFAULT_MODEL
110	* @param pdbfile
111	* @param chaincode
112	* @param dummy dummy parameter to distinguish the method from other with the same signature
113	* TODO dummy parameter is a dirty hack, must solve it in other way: subclassing
114	* @throws FileNotFoundException
115	* @throws IOException
116	*/
117	public Pdb (String pdbfile, String chaincode, boolean dummy) throws FileNotFoundException, IOException {
118	this(pdbfile,chaincode,DEFAULT_MODEL,dummy);
119	}
120
121	/**
122	* Constructs Pdb object reading from pdb file given pdb chain code and model serial
123	* @param pdbfile
124	* @param chaincode
125	* @param model_serial
126	* @param dummy dummy parameter to distinguish the method from other with the same signature
127	* TODO dummy parameter is a dirty hack, must solve it in other way: subclassing
128	* @throws FileNotFoundException
129	* @throws IOException
130	*/
131	public Pdb (String pdbfile, String chaincode, int model_serial, boolean dummy) throws FileNotFoundException, IOException {
132	this.model=model_serial;
133	this.chaincode=chaincode;
134	read_pdb_data_from_file(pdbfile);
135	}
136
137	public void read_pdb_data_from_pdbase(String db) throws PdbaseInconsistencyError, PdbaseAcCodeNotFoundError{
138	resser_atom2atomserial = new HashMap<String,Integer>();
139	resser2restype = new HashMap<Integer,String>();
140	atomser2coord = new HashMap<Integer,Double[]>();
141	atomser2resser = new HashMap<Integer,Integer>();
142
143	PdbaseInfo mypdbaseinfo = new PdbaseInfo(accode,chaincode,model,db);
144	ArrayList<ArrayList> resultset = mypdbaseinfo.read_atomData();
145	chain = mypdbaseinfo.chain;
146	sequence = mypdbaseinfo.read_seq();
147	mypdbaseinfo.close();
148
149	for (ArrayList result:resultset){
150	int atomserial = (Integer) result.get(0);
151	String atom = (String) result.get(1);
152	String res_type = (String) result.get(2);
153	int res_serial = (Integer) result.get(3);
154	double x = (Double) result.get(4);
155	double y = (Double) result.get(5);
156	double z = (Double) result.get(6);
157	Double[] coords = {x, y, z};
158	ArrayList<String> aalist=AA.aas();
159	if (aalist.contains(res_type)) {
160	atomser2coord.put(atomserial, coords);
161	atomser2resser.put(atomserial, res_serial);
162	resser2restype.put(res_serial, res_type);
163	ArrayList<String> atomlist = aas2atoms.get(res_type);
164	if (atomlist.contains(atom)){
165	resser_atom2atomserial.put(res_serial+"_"+atom, atomserial);
166	}
167	}
168	}
169	}
170
171	public void read_pdb_data_from_msdsd(String db) throws MsdsdAcCodeNotFoundError, MsdsdInconsistentResidueNumbersError {
172	resser_atom2atomserial = new HashMap<String,Integer>();
173	resser2restype = new HashMap<Integer,String>();
174	atomser2coord = new HashMap<Integer,Double[]>();
175	atomser2resser = new HashMap<Integer,Integer>();
176
177	MsdsdInfo mymsdsdinfo = new MsdsdInfo(accode,chaincode,model,db);
178	ArrayList<ArrayList> resultset = mymsdsdinfo.read_atomData();
179	sequence = mymsdsdinfo.read_seq();
180	chain = mymsdsdinfo.chain;
181	mymsdsdinfo.close();
182
183	for (ArrayList result:resultset){
184	int atomserial = (Integer) result.get(0);
185	String atom = (String) result.get(1);
186	String res_type = (String) result.get(2);
187	int res_serial = (Integer) result.get(3);
188	double x = (Double) result.get(4);
189	double y = (Double) result.get(5);
190	double z = (Double) result.get(6);
191	Double[] coords = {x, y, z};
192	ArrayList<String> aalist=AA.aas();
193	if (aalist.contains(res_type)) {
194	atomser2coord.put(atomserial, coords);
195	atomser2resser.put(atomserial, res_serial);
196	resser2restype.put(res_serial, res_type);
197	ArrayList<String> atomlist = aas2atoms.get(res_type);
198	if (atomlist.contains(atom)){
199	resser_atom2atomserial.put(res_serial+"_"+atom, atomserial);
200	}
201	}
202	}
203	}
204
205	/**
206	* To read the pdb data (atom coordinates, residue serials, atom serials) from file
207	* chain gets set to internal identifier: if input chain code NULL then chain will be ' '
208	* accode gets set to the one parsed in HEADER or to 'Unknown' if not found
209	* sequence gets set to the sequence read from ATOM lines (i.e. observed resdiues only)
210	* @param pdbfile
211	* @throws FileNotFoundException
212	* @throws IOException
213	*/
214	public void read_pdb_data_from_file(String pdbfile) throws FileNotFoundException, IOException{
215	resser_atom2atomserial = new HashMap<String,Integer>();
216	resser2restype = new HashMap<Integer,String>();
217	atomser2coord = new HashMap<Integer,Double[]>();
218	atomser2resser = new HashMap<Integer,Integer>();
219	boolean empty = true; // controls whether we don't find any atom line for given chaincode and model
220	// we set chain to chaincode except for case NULL where we use " " (NULL is a blank chain code in pdb files)
221	chain=chaincode;
222	if (chaincode.equals("NULL")) chain=" ";
223	int thismodel=DEFAULT_MODEL; // we initialise to DEFAULT_MODEL, in case file doesn't have MODEL lines
224	BufferedReader fpdb = new BufferedReader(new FileReader(new File(pdbfile)));
225	String line;
226	while ((line = fpdb.readLine() ) != null ) {
227	Pattern p = Pattern.compile("^HEADER");
228	Matcher m = p.matcher(line);
229	if (m.find()){
230	Pattern ph = Pattern.compile("^HEADER.{56}(\\d\\w{3})");
231	Matcher mh = ph.matcher(line);
232	if (mh.find()) {
233	accode=mh.group(1).toLowerCase();
234	} else {
235	accode="Unknown";
236	}
237	}
238	p = Pattern.compile("^MODEL\\s+(\\d+)");
239	m = p.matcher(line);
240	if (m.find()){
241	thismodel=Integer.parseInt(m.group(1));
242	}
243	if (thismodel!=model) continue; // we skip reading of atom lines if we are not in the desired model
244	p = Pattern.compile("^ATOM");
245	m = p.matcher(line);
246	if (m.find()){
247	// serial atom res_type chain res_ser x y z
248	Pattern pl = Pattern.compile(".{6}(.....).{2}(...).{1}(...).{1}"+chain+"(.{4}).{4}(.{8})(.{8})(.{8})",Pattern.CASE_INSENSITIVE);
249	Matcher ml = pl.matcher(line);
250	if (ml.find()) {
251	empty=false;
252	int atomserial=Integer.parseInt(ml.group(1).trim());
253	String atom = ml.group(2).trim();
254	String res_type = ml.group(3).trim();
255	int res_serial = Integer.parseInt(ml.group(4).trim());
256	double x = Double.parseDouble(ml.group(5).trim());
257	double y = Double.parseDouble(ml.group(6).trim());
258	double z = Double.parseDouble(ml.group(7).trim());
259	Double[] coords = {x, y, z};
260	ArrayList<String> aalist=AA.aas();
261	if (aalist.contains(res_type)) {
262	atomser2coord.put(atomserial, coords);
263	atomser2resser.put(atomserial, res_serial);
264	resser2restype.put(res_serial, res_type);
265	ArrayList<String> atomlist = aas2atoms.get(res_type);
266	if (atomlist.contains(atom)){
267	resser_atom2atomserial.put(res_serial+"_"+atom, atomserial);
268	}
269	}
270	}
271	}
272	}
273	fpdb.close();
274	if (empty) System.err.println("Couldn't find any atom line for given chaincode: "+chaincode+", model: "+model);
275	// now we read the sequence from the resser2restype HashMap
276	// NOTE: we must make sure elsewhere that there are no unobserved residues, we can't check that here!
277	ArrayList<Integer> ressers = new ArrayList<Integer>();
278	for (int resser:resser2restype.keySet()) {
279	ressers.add(resser);
280	}
281	Collections.sort(ressers);
282	sequence="";
283	for (int resser:ressers){
284	String oneletter = AA.threeletter2oneletter(resser2restype.get(resser));
285	sequence += oneletter;
286	}
287	}
288
289	/**
290	* Dumps coordinate data into a file in pdb format (ATOM lines only)
291	* The chain dumped is the value of the chain field, i.e. our internal chain identifier for Pdb objects
292	* @param outfile
293	* @throws IOException
294	*/
295	public void dump2pdbfile(String outfile) throws IOException {
296	TreeMap<Integer,Object[]> lines = new TreeMap<Integer,Object[]>();
297	PrintStream Out = new PrintStream(new FileOutputStream(outfile));
298	Out.println("HEADER Dumped from "+db+". pdb accession code="+accode+", chain='"+chain+"'");
299	for (String resser_atom:resser_atom2atomserial.keySet()){
300	int atomserial = resser_atom2atomserial.get(resser_atom);
301	int res_serial = Integer.parseInt(resser_atom.split("_")[0]);
302	String atom = resser_atom.split("_")[1];
303	String res_type = resser2restype.get(res_serial);
304	Double[] coords = atomser2coord.get(atomserial);
305	Object[] fields = {atomserial, atom, res_type, chain, res_serial, coords[0], coords[1], coords[2]};
306	lines.put(atomserial, fields);
307	}
308	for (int atomserial:lines.keySet()){
309	Out.printf("ATOM %5d %3s %3s %1s%4d %8.3f%8.3f%8.3f\n",lines.get(atomserial));
310	}
311	Out.println("END");
312	Out.close();
313	}
314
315	public void dumpseq(String seqfile) throws IOException {
316	PrintStream Out = new PrintStream(new FileOutputStream(seqfile));
317	Out.println(">"+accode+"_"+chaincode);
318	Out.println(sequence);
319	Out.close();
320	}
321
322	public int get_length(){
323	return resser2restype.size();
324	}
325
326	public HashMap<Integer,Double[]> get_coords_for_ct(String ct) {
327	HashMap<Integer,Double[]> coords = new HashMap<Integer,Double[]>();
328	HashMap<String,String[]> restype2atoms = AA.ct2atoms(ct);
329	for (int resser:resser2restype.keySet()){
330	String[] atoms = restype2atoms.get(resser2restype.get(resser));
331	for (String atom:atoms){
332	if (resser_atom2atomserial.containsKey(resser+"_"+atom)){
333	int atomser = resser_atom2atomserial.get(resser+"_"+atom);
334	Double[] coord = atomser2coord.get(atomser);
335	coords.put(atomser, coord);
336	}
337	else if (atom.equals("O") && resser_atom2atomserial.containsKey(resser+"_"+"OXT")){
338	int atomser = resser_atom2atomserial.get(resser+"_"+"OXT");
339	Double[] coord = atomser2coord.get(atomser);
340	coords.put(atomser, coord);
341	}
342	else {
343	System.err.println("Couldn't find "+atom+" atom for resser="+resser+". Continuing without that atom for this resser.");
344	}
345	}
346	}
347	return coords;
348	}
349
350	public TreeMap<Contact, Double> calculate_dist_matrix(String ct){
351	TreeMap<Contact,Double> dist_matrix = new TreeMap<Contact,Double>();
352	if (!ct.contains("/")){
353	HashMap<Integer,Double[]> coords = get_coords_for_ct(ct);
354	for (int i_atomser:coords.keySet()){
355	for (int j_atomser:coords.keySet()){
356	if (j_atomser>i_atomser) {
357	Contact pair = new Contact(i_atomser,j_atomser);
358	dist_matrix.put(pair, distance(coords.get(i_atomser),coords.get(j_atomser)));
359	}
360	}
361	}
362	} else {
363	String i_ct = ct.split("/")[0];
364	String j_ct = ct.split("/")[1];
365	HashMap<Integer,Double[]> i_coords = get_coords_for_ct(i_ct);
366	HashMap<Integer,Double[]> j_coords = get_coords_for_ct(j_ct);
367	for (int i_atomser:i_coords.keySet()){
368	for (int j_atomser:j_coords.keySet()){
369	if (j_atomser!=i_atomser){
370	Contact pair = new Contact(i_atomser,j_atomser);
371	dist_matrix.put(pair, distance(i_coords.get(i_atomser),j_coords.get(j_atomser)));
372	}
373	}
374	}
375	}
376	return dist_matrix;
377	}
378
379	/**
380	* Get the contacts for given contact type and cutoff for this Pdb object.
381	* Returns a Graph object with the contacts
382	* The graph is always directional, i.e. in crossed cases xx/yy: i corresponds to xx and j to yy
383	* ct here can be single contact type (e.g. Ca, BB) or crossed (e.g. BB/SC or Ca/Cb)
384	* @param ct
385	* @param cutoff
386	* @return
387	*/
388	public Graph get_graph(String ct, double cutoff){
389	TreeMap<Contact,Double> dist_matrix = calculate_dist_matrix(ct);
390	ArrayList<Contact> contacts = new ArrayList<Contact>();
391	// we loop here over all indices of dist_matrix,
392	// we took care already that in symmetric cases (i.e. single contact type, not crossed) we have only one side of the matrix and
393	// in asymmetrical cases (i.e. crossed cases) we have both sides of the matrix
394	for (Contact pair:dist_matrix.keySet()){
395	int i_atomser=pair.i;
396	int j_atomser=pair.j;
397	if (dist_matrix.get(pair)<=cutoff){
398	int i_resser = atomser2resser.get(i_atomser);
399	int j_resser = atomser2resser.get(j_atomser);
400	Contact resser_pair = new Contact(i_resser,j_resser);
401	// 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
402	if (i_resser!=j_resser && (! contacts.contains(resser_pair))){
403	contacts.add(resser_pair);
404	}
405	}
406	}
407	Collections.sort(contacts);
408	TreeMap<Integer,String> nodes = new TreeMap<Integer,String>();
409	for (int resser:resser2restype.keySet()){
410	nodes.put(resser,resser2restype.get(resser));
411	}
412	Graph graph = new Graph (contacts,nodes,sequence,cutoff,ct,accode,chain,chaincode);
413	return graph;
414	}
415
416	public Double distance(Double[] coords1, Double[] coords2){
417	return Math.sqrt(Math.pow((coords1[0]-coords2[0]),2)+Math.pow((coords1[1]-coords2[1]),2)+Math.pow((coords1[2]-coords2[2]),2));
418	}
419	}