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,Integer> pdbresser2resser; // only used when reading from database
        HashMap<Integer,String> resser2pdbresser; // only used when reading from database
        
        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);
                }
                // we initialise resser2pdbresser from the pdbresser2resser HashMap
                resser2pdbresser = new HashMap<Integer, String>();
                for (String pdbresser:pdbresser2resser.keySet()){
                        resser2pdbresser.put(pdbresser2resser.get(pdbresser), pdbresser);
                }
        }
        
        /**
         * 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();
                pdbresser2resser = mypdbaseinfo.get_ressers_mapping();
                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;
                pdbresser2resser = mymsdsdinfo.get_ressers_mapping();
                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
         */
        @SuppressWarnings("unchecked")
        public Graph get_graph(String ct, double cutoff){
                TreeMap<Contact,Double> dist_matrix = calculate_dist_matrix(ct);
                ContactList contacts = new ContactList();
        // 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));
        }
        
        public int get_resser_from_pdbresser (String pdbresser){
                return pdbresser2resser.get(pdbresser);
        }
        
        public String get_pdbresser_from_resser (int resser){
                return resser2pdbresser.get(resser);
        }

}
Revision:	190
Committed:	Tue Jun 12 13:38:46 2007 UTC (17 years, 3 months ago) by duarte
File size:	17584 byte(s)
Log Message:	NEW FEATURE: mapping of pdb residue serials and internal serials in the Pdb object
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	duarte	153	public final static int DEFAULT_MODEL=1;
20
21	duarte	123	HashMap<String,Integer> resser_atom2atomserial;
22			HashMap<Integer,String> resser2restype;
23			HashMap<Integer,Double[]> atomser2coord;
24			HashMap<Integer,Integer> atomser2resser;
25	duarte	190	HashMap<String,Integer> pdbresser2resser; // only used when reading from database
26			HashMap<Integer,String> resser2pdbresser; // only used when reading from database
27
28	duarte	123	HashMap<String,ArrayList<String>> aas2atoms = AA.getaas2atoms();
29	duarte	145	public String sequence="";
30	stehr	140	public String accode="";
31	duarte	135	// given "external" pdb chain code, i.e. the classic pdb code ("NULL" if it is blank in original pdb file)
32	duarte	145	public String chaincode="";
33			public int model=DEFAULT_MODEL;
34	duarte	123	String db;
35	duarte	135
36			// Our internal chain identifier (taken from dbs or pdb):
37			// - 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)
38	duarte	153	// - in reading from pdb file it gets set to whatever parsed from the pdb file (i.e. can be also ' ')
39	stehr	137	public String chain;
40	duarte	123
41	duarte	153	/**
42			* Constructs Pdb object given accession code and pdb chain code. Model will be DEFAULT_MODEL
43			* Takes data from default pdbase-like database: PdbaseInfo.pdbaseDB
44			* @param accode
45			* @param chaincode
46			* @throws PdbaseInconsistencyError
47			* @throws PdbaseAcCodeNotFoundError
48			* @throws MsdsdAcCodeNotFoundError
49			* @throws MsdsdInconsistentResidueNumbersError
50			*/
51	duarte	130	public Pdb (String accode, String chaincode) throws PdbaseInconsistencyError, PdbaseAcCodeNotFoundError, MsdsdAcCodeNotFoundError, MsdsdInconsistentResidueNumbersError {
52	duarte	133	this(accode,chaincode,DEFAULT_MODEL,PdbaseInfo.pdbaseDB);
53	duarte	123	}
54	duarte	133
55	duarte	153	/**
56			* Constructs Pdb object given accession code, pdb chain code and a model serial
57			* Takes data from default pdbase-like database: PdbaseInfo.pdbaseDB
58			* @param accode
59			* @param chaincode
60			* @param model_serial
61			* @throws PdbaseInconsistencyError
62			* @throws PdbaseAcCodeNotFoundError
63			* @throws MsdsdAcCodeNotFoundError
64			* @throws MsdsdInconsistentResidueNumbersError
65			*/
66	duarte	133	public Pdb (String accode, String chaincode, int model_serial) throws PdbaseInconsistencyError, PdbaseAcCodeNotFoundError, MsdsdAcCodeNotFoundError, MsdsdInconsistentResidueNumbersError {
67			this(accode,chaincode,model_serial,PdbaseInfo.pdbaseDB);
68			}
69	duarte	153
70			/**
71			* Constructs Pdb object given accession code, pdb chain code and a source db for the data. Model will be DEFAULT_MODEL
72			* The db can be pdbase-like or msdsd-like
73			* @param accode
74			* @param chaincode
75			* @param db
76			* @throws PdbaseInconsistencyError
77			* @throws PdbaseAcCodeNotFoundError
78			* @throws MsdsdAcCodeNotFoundError
79			* @throws MsdsdInconsistentResidueNumbersError
80			*/
81	duarte	130	public Pdb (String accode, String chaincode, String db) throws PdbaseInconsistencyError, PdbaseAcCodeNotFoundError, MsdsdAcCodeNotFoundError, MsdsdInconsistentResidueNumbersError {
82	duarte	133	this(accode,chaincode,DEFAULT_MODEL,db);
83			}
84
85	duarte	153	/**
86			* Constructs Pdb object given accession code, pdb chain code, model serial and a source db for the data.
87			* The db can be pdbase-like or msdsd-like
88			* @param accode
89			* @param chaincode
90			* @param model_serial
91			* @param db
92			* @throws PdbaseInconsistencyError
93			* @throws PdbaseAcCodeNotFoundError
94			* @throws MsdsdAcCodeNotFoundError
95			* @throws MsdsdInconsistentResidueNumbersError
96			*/
97	duarte	133	public Pdb (String accode, String chaincode, int model_serial, String db) throws PdbaseInconsistencyError, PdbaseAcCodeNotFoundError, MsdsdAcCodeNotFoundError, MsdsdInconsistentResidueNumbersError {
98	duarte	123	this.accode=accode;
99			this.chaincode=chaincode;
100	duarte	133	this.model=model_serial;
101	duarte	123	this.db=db;
102	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
103			this.chain=chaincode;
104			if (db.contains("msdsd")){
105			read_pdb_data_from_msdsd(db);
106			} else if (db.contains("pdbase")){
107			read_pdb_data_from_pdbase(db);
108			}
109	duarte	190	// we initialise resser2pdbresser from the pdbresser2resser HashMap
110			resser2pdbresser = new HashMap<Integer, String>();
111			for (String pdbresser:pdbresser2resser.keySet()){
112			resser2pdbresser.put(pdbresser2resser.get(pdbresser), pdbresser);
113			}
114	duarte	123	}
115
116	duarte	153	/**
117			* Constructs Pdb object reading from pdb file given pdb chain code. Model will be DEFAULT_MODEL
118			* @param pdbfile
119			* @param chaincode
120			* @param dummy dummy parameter to distinguish the method from other with the same signature
121			* TODO dummy parameter is a dirty hack, must solve it in other way: subclassing
122			* @throws FileNotFoundException
123			* @throws IOException
124			*/
125			public Pdb (String pdbfile, String chaincode, boolean dummy) throws FileNotFoundException, IOException {
126			this(pdbfile,chaincode,DEFAULT_MODEL,dummy);
127	duarte	133	}
128	duarte	153
129			/**
130			* Constructs Pdb object reading from pdb file given pdb chain code and model serial
131			* @param pdbfile
132			* @param chaincode
133			* @param model_serial
134			* @param dummy dummy parameter to distinguish the method from other with the same signature
135			* TODO dummy parameter is a dirty hack, must solve it in other way: subclassing
136			* @throws FileNotFoundException
137			* @throws IOException
138			*/
139			public Pdb (String pdbfile, String chaincode, int model_serial, boolean dummy) throws FileNotFoundException, IOException {
140	duarte	133	this.model=model_serial;
141	duarte	153	this.chaincode=chaincode;
142	duarte	127	read_pdb_data_from_file(pdbfile);
143	duarte	123	}
144	duarte	133
145	duarte	124	public void read_pdb_data_from_pdbase(String db) throws PdbaseInconsistencyError, PdbaseAcCodeNotFoundError{
146	duarte	123	resser_atom2atomserial = new HashMap<String,Integer>();
147			resser2restype = new HashMap<Integer,String>();
148			atomser2coord = new HashMap<Integer,Double[]>();
149			atomser2resser = new HashMap<Integer,Integer>();
150
151	duarte	133	PdbaseInfo mypdbaseinfo = new PdbaseInfo(accode,chaincode,model,db);
152	duarte	123	ArrayList<ArrayList> resultset = mypdbaseinfo.read_atomData();
153	duarte	135	chain = mypdbaseinfo.chain;
154	duarte	123	sequence = mypdbaseinfo.read_seq();
155	duarte	190	pdbresser2resser = mypdbaseinfo.get_ressers_mapping();
156	duarte	123	mypdbaseinfo.close();
157
158			for (ArrayList result:resultset){
159			int atomserial = (Integer) result.get(0);
160			String atom = (String) result.get(1);
161			String res_type = (String) result.get(2);
162	duarte	135	int res_serial = (Integer) result.get(3);
163			double x = (Double) result.get(4);
164			double y = (Double) result.get(5);
165			double z = (Double) result.get(6);
166	duarte	123	Double[] coords = {x, y, z};
167			ArrayList<String> aalist=AA.aas();
168			if (aalist.contains(res_type)) {
169			atomser2coord.put(atomserial, coords);
170			atomser2resser.put(atomserial, res_serial);
171			resser2restype.put(res_serial, res_type);
172			ArrayList<String> atomlist = aas2atoms.get(res_type);
173			if (atomlist.contains(atom)){
174			resser_atom2atomserial.put(res_serial+"_"+atom, atomserial);
175			}
176			}
177			}
178			}
179
180	duarte	130	public void read_pdb_data_from_msdsd(String db) throws MsdsdAcCodeNotFoundError, MsdsdInconsistentResidueNumbersError {
181			resser_atom2atomserial = new HashMap<String,Integer>();
182			resser2restype = new HashMap<Integer,String>();
183			atomser2coord = new HashMap<Integer,Double[]>();
184			atomser2resser = new HashMap<Integer,Integer>();
185
186	duarte	133	MsdsdInfo mymsdsdinfo = new MsdsdInfo(accode,chaincode,model,db);
187	duarte	130	ArrayList<ArrayList> resultset = mymsdsdinfo.read_atomData();
188			sequence = mymsdsdinfo.read_seq();
189	duarte	138	chain = mymsdsdinfo.chain;
190	duarte	190	pdbresser2resser = mymsdsdinfo.get_ressers_mapping();
191	duarte	130	mymsdsdinfo.close();
192
193			for (ArrayList result:resultset){
194			int atomserial = (Integer) result.get(0);
195			String atom = (String) result.get(1);
196			String res_type = (String) result.get(2);
197			int res_serial = (Integer) result.get(3);
198			double x = (Double) result.get(4);
199			double y = (Double) result.get(5);
200			double z = (Double) result.get(6);
201			Double[] coords = {x, y, z};
202			ArrayList<String> aalist=AA.aas();
203			if (aalist.contains(res_type)) {
204			atomser2coord.put(atomserial, coords);
205			atomser2resser.put(atomserial, res_serial);
206			resser2restype.put(res_serial, res_type);
207			ArrayList<String> atomlist = aas2atoms.get(res_type);
208			if (atomlist.contains(atom)){
209			resser_atom2atomserial.put(res_serial+"_"+atom, atomserial);
210			}
211			}
212			}
213			}
214
215	duarte	133	/**
216			* To read the pdb data (atom coordinates, residue serials, atom serials) from file
217	duarte	153	* chain gets set to internal identifier: if input chain code NULL then chain will be ' '
218			* accode gets set to the one parsed in HEADER or to 'Unknown' if not found
219			* sequence gets set to the sequence read from ATOM lines (i.e. observed resdiues only)
220	duarte	133	* @param pdbfile
221			* @throws FileNotFoundException
222			* @throws IOException
223			*/
224	duarte	127	public void read_pdb_data_from_file(String pdbfile) throws FileNotFoundException, IOException{
225			resser_atom2atomserial = new HashMap<String,Integer>();
226			resser2restype = new HashMap<Integer,String>();
227			atomser2coord = new HashMap<Integer,Double[]>();
228			atomser2resser = new HashMap<Integer,Integer>();
229	duarte	153	boolean empty = true; // controls whether we don't find any atom line for given chaincode and model
230	duarte	154	// we set chain to chaincode except for case NULL where we use " " (NULL is a blank chain code in pdb files)
231			chain=chaincode;
232			if (chaincode.equals("NULL")) chain=" ";
233	duarte	153	int thismodel=DEFAULT_MODEL; // we initialise to DEFAULT_MODEL, in case file doesn't have MODEL lines
234	duarte	127	BufferedReader fpdb = new BufferedReader(new FileReader(new File(pdbfile)));
235			String line;
236			while ((line = fpdb.readLine() ) != null ) {
237	duarte	153	Pattern p = Pattern.compile("^HEADER");
238	duarte	127	Matcher m = p.matcher(line);
239			if (m.find()){
240	duarte	153	Pattern ph = Pattern.compile("^HEADER.{56}(\\d\\w{3})");
241			Matcher mh = ph.matcher(line);
242			if (mh.find()) {
243			accode=mh.group(1).toLowerCase();
244			} else {
245			accode="Unknown";
246			}
247			}
248			p = Pattern.compile("^MODEL\\s+(\\d+)");
249			m = p.matcher(line);
250			if (m.find()){
251			thismodel=Integer.parseInt(m.group(1));
252			}
253			if (thismodel!=model) continue; // we skip reading of atom lines if we are not in the desired model
254			p = Pattern.compile("^ATOM");
255			m = p.matcher(line);
256			if (m.find()){
257	duarte	154	// serial atom res_type chain res_ser x y z
258			Pattern pl = Pattern.compile(".{6}(.....).{2}(...).{1}(...).{1}"+chain+"(.{4}).{4}(.{8})(.{8})(.{8})",Pattern.CASE_INSENSITIVE);
259	duarte	127	Matcher ml = pl.matcher(line);
260			if (ml.find()) {
261	duarte	153	empty=false;
262	duarte	127	int atomserial=Integer.parseInt(ml.group(1).trim());
263			String atom = ml.group(2).trim();
264			String res_type = ml.group(3).trim();
265	duarte	154	int res_serial = Integer.parseInt(ml.group(4).trim());
266			double x = Double.parseDouble(ml.group(5).trim());
267			double y = Double.parseDouble(ml.group(6).trim());
268			double z = Double.parseDouble(ml.group(7).trim());
269	duarte	127	Double[] coords = {x, y, z};
270			ArrayList<String> aalist=AA.aas();
271			if (aalist.contains(res_type)) {
272			atomser2coord.put(atomserial, coords);
273			atomser2resser.put(atomserial, res_serial);
274			resser2restype.put(res_serial, res_type);
275			ArrayList<String> atomlist = aas2atoms.get(res_type);
276			if (atomlist.contains(atom)){
277			resser_atom2atomserial.put(res_serial+"_"+atom, atomserial);
278			}
279	duarte	153	}
280			}
281	duarte	127	}
282			}
283			fpdb.close();
284	duarte	153	if (empty) System.err.println("Couldn't find any atom line for given chaincode: "+chaincode+", model: "+model);
285	duarte	127	// now we read the sequence from the resser2restype HashMap
286			// NOTE: we must make sure elsewhere that there are no unobserved residues, we can't check that here!
287			ArrayList<Integer> ressers = new ArrayList<Integer>();
288			for (int resser:resser2restype.keySet()) {
289			ressers.add(resser);
290			}
291			Collections.sort(ressers);
292			sequence="";
293			for (int resser:ressers){
294			String oneletter = AA.threeletter2oneletter(resser2restype.get(resser));
295			sequence += oneletter;
296			}
297			}
298
299	duarte	153	/**
300			* Dumps coordinate data into a file in pdb format (ATOM lines only)
301			* The chain dumped is the value of the chain field, i.e. our internal chain identifier for Pdb objects
302			* @param outfile
303			* @throws IOException
304			*/
305	duarte	123	public void dump2pdbfile(String outfile) throws IOException {
306	duarte	130	TreeMap<Integer,Object[]> lines = new TreeMap<Integer,Object[]>();
307	duarte	123	PrintStream Out = new PrintStream(new FileOutputStream(outfile));
308	duarte	153	Out.println("HEADER Dumped from "+db+". pdb accession code="+accode+", chain='"+chain+"'");
309	duarte	123	for (String resser_atom:resser_atom2atomserial.keySet()){
310			int atomserial = resser_atom2atomserial.get(resser_atom);
311			int res_serial = Integer.parseInt(resser_atom.split("_")[0]);
312			String atom = resser_atom.split("_")[1];
313			String res_type = resser2restype.get(res_serial);
314			Double[] coords = atomser2coord.get(atomserial);
315	duarte	153	Object[] fields = {atomserial, atom, res_type, chain, res_serial, coords[0], coords[1], coords[2]};
316	duarte	130	lines.put(atomserial, fields);
317	duarte	123	}
318	duarte	130	for (int atomserial:lines.keySet()){
319			Out.printf("ATOM %5d %3s %3s %1s%4d %8.3f%8.3f%8.3f\n",lines.get(atomserial));
320			}
321	duarte	123	Out.println("END");
322			Out.close();
323			}
324
325			public void dumpseq(String seqfile) throws IOException {
326			PrintStream Out = new PrintStream(new FileOutputStream(seqfile));
327			Out.println(">"+accode+"_"+chaincode);
328			Out.println(sequence);
329			Out.close();
330			}
331
332			public int get_length(){
333			return resser2restype.size();
334			}
335
336			public HashMap<Integer,Double[]> get_coords_for_ct(String ct) {
337			HashMap<Integer,Double[]> coords = new HashMap<Integer,Double[]>();
338			HashMap<String,String[]> restype2atoms = AA.ct2atoms(ct);
339			for (int resser:resser2restype.keySet()){
340			String[] atoms = restype2atoms.get(resser2restype.get(resser));
341			for (String atom:atoms){
342			if (resser_atom2atomserial.containsKey(resser+"_"+atom)){
343			int atomser = resser_atom2atomserial.get(resser+"_"+atom);
344			Double[] coord = atomser2coord.get(atomser);
345			coords.put(atomser, coord);
346			}
347			else if (atom.equals("O") && resser_atom2atomserial.containsKey(resser+"_"+"OXT")){
348			int atomser = resser_atom2atomserial.get(resser+"_"+"OXT");
349			Double[] coord = atomser2coord.get(atomser);
350			coords.put(atomser, coord);
351			}
352			else {
353			System.err.println("Couldn't find "+atom+" atom for resser="+resser+". Continuing without that atom for this resser.");
354			}
355			}
356			}
357			return coords;
358			}
359
360			public TreeMap<Contact, Double> calculate_dist_matrix(String ct){
361			TreeMap<Contact,Double> dist_matrix = new TreeMap<Contact,Double>();
362			if (!ct.contains("/")){
363			HashMap<Integer,Double[]> coords = get_coords_for_ct(ct);
364			for (int i_atomser:coords.keySet()){
365			for (int j_atomser:coords.keySet()){
366			if (j_atomser>i_atomser) {
367			Contact pair = new Contact(i_atomser,j_atomser);
368			dist_matrix.put(pair, distance(coords.get(i_atomser),coords.get(j_atomser)));
369			}
370			}
371			}
372			} else {
373			String i_ct = ct.split("/")[0];
374			String j_ct = ct.split("/")[1];
375			HashMap<Integer,Double[]> i_coords = get_coords_for_ct(i_ct);
376			HashMap<Integer,Double[]> j_coords = get_coords_for_ct(j_ct);
377			for (int i_atomser:i_coords.keySet()){
378			for (int j_atomser:j_coords.keySet()){
379			if (j_atomser!=i_atomser){
380			Contact pair = new Contact(i_atomser,j_atomser);
381			dist_matrix.put(pair, distance(i_coords.get(i_atomser),j_coords.get(j_atomser)));
382			}
383			}
384			}
385			}
386			return dist_matrix;
387			}
388
389	duarte	129	/**
390			* Get the contacts for given contact type and cutoff for this Pdb object.
391			* Returns a Graph object with the contacts
392			* The graph is always directional, i.e. in crossed cases xx/yy: i corresponds to xx and j to yy
393			* ct here can be single contact type (e.g. Ca, BB) or crossed (e.g. BB/SC or Ca/Cb)
394			* @param ct
395			* @param cutoff
396			* @return
397			*/
398	duarte	190	@SuppressWarnings("unchecked")
399	duarte	123	public Graph get_graph(String ct, double cutoff){
400			TreeMap<Contact,Double> dist_matrix = calculate_dist_matrix(ct);
401	duarte	175	ContactList contacts = new ContactList();
402	duarte	129	// we loop here over all indices of dist_matrix,
403			// we took care already that in symmetric cases (i.e. single contact type, not crossed) we have only one side of the matrix and
404			// in asymmetrical cases (i.e. crossed cases) we have both sides of the matrix
405	duarte	123	for (Contact pair:dist_matrix.keySet()){
406			int i_atomser=pair.i;
407			int j_atomser=pair.j;
408			if (dist_matrix.get(pair)<=cutoff){
409			int i_resser = atomser2resser.get(i_atomser);
410			int j_resser = atomser2resser.get(j_atomser);
411			Contact resser_pair = new Contact(i_resser,j_resser);
412	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
413	duarte	123	if (i_resser!=j_resser && (! contacts.contains(resser_pair))){
414			contacts.add(resser_pair);
415			}
416			}
417			}
418			Collections.sort(contacts);
419	duarte	129	TreeMap<Integer,String> nodes = new TreeMap<Integer,String>();
420			for (int resser:resser2restype.keySet()){
421			nodes.put(resser,resser2restype.get(resser));
422			}
423	duarte	156	Graph graph = new Graph (contacts,nodes,sequence,cutoff,ct,accode,chain,chaincode);
424	duarte	123	return graph;
425			}
426
427			public Double distance(Double[] coords1, Double[] coords2){
428			return Math.sqrt(Math.pow((coords1[0]-coords2[0]),2)+Math.pow((coords1[1]-coords2[1]),2)+Math.pow((coords1[2]-coords2[2]),2));
429			}
430	duarte	190
431			public int get_resser_from_pdbresser (String pdbresser){
432			return pdbresser2resser.get(pdbresser);
433			}
434
435			public String get_pdbresser_from_resser (int resser){
436			return resser2pdbresser.get(resser);
437			}
438
439	duarte	123	}