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));
                }
        // 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:	154
Committed:	Fri May 18 09:32:28 2007 UTC (17 years, 9 months ago) by duarte
File size:	16929 byte(s)
Log Message:	Recoded chain reading in read_pdb_data_from_file to make it clearer, no change in functionality
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			HashMap<String,ArrayList<String>> aas2atoms = AA.getaas2atoms();
26	duarte	145	public String sequence="";
27	stehr	140	public String accode="";
28	duarte	135	// given "external" pdb chain code, i.e. the classic pdb code ("NULL" if it is blank in original pdb file)
29	duarte	145	public String chaincode="";
30			public int model=DEFAULT_MODEL;
31	duarte	123	String db;
32	duarte	135
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	duarte	153	// - in reading from pdb file it gets set to whatever parsed from the pdb file (i.e. can be also ' ')
36	stehr	137	public String chain;
37	duarte	123
38	duarte	153	/**
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	duarte	130	public Pdb (String accode, String chaincode) throws PdbaseInconsistencyError, PdbaseAcCodeNotFoundError, MsdsdAcCodeNotFoundError, MsdsdInconsistentResidueNumbersError {
49	duarte	133	this(accode,chaincode,DEFAULT_MODEL,PdbaseInfo.pdbaseDB);
50	duarte	123	}
51	duarte	133
52	duarte	153	/**
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	duarte	133	public Pdb (String accode, String chaincode, int model_serial) throws PdbaseInconsistencyError, PdbaseAcCodeNotFoundError, MsdsdAcCodeNotFoundError, MsdsdInconsistentResidueNumbersError {
64			this(accode,chaincode,model_serial,PdbaseInfo.pdbaseDB);
65			}
66	duarte	153
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	duarte	130	public Pdb (String accode, String chaincode, String db) throws PdbaseInconsistencyError, PdbaseAcCodeNotFoundError, MsdsdAcCodeNotFoundError, MsdsdInconsistentResidueNumbersError {
79	duarte	133	this(accode,chaincode,DEFAULT_MODEL,db);
80			}
81
82	duarte	153	/**
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	duarte	133	public Pdb (String accode, String chaincode, int model_serial, String db) throws PdbaseInconsistencyError, PdbaseAcCodeNotFoundError, MsdsdAcCodeNotFoundError, MsdsdInconsistentResidueNumbersError {
95	duarte	123	this.accode=accode;
96			this.chaincode=chaincode;
97	duarte	133	this.model=model_serial;
98	duarte	123	this.db=db;
99	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
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	duarte	123	}
107
108	duarte	153	/**
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	duarte	133	}
120	duarte	153
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	duarte	133	this.model=model_serial;
133	duarte	153	this.chaincode=chaincode;
134	duarte	127	read_pdb_data_from_file(pdbfile);
135	duarte	123	}
136	duarte	133
137	duarte	124	public void read_pdb_data_from_pdbase(String db) throws PdbaseInconsistencyError, PdbaseAcCodeNotFoundError{
138	duarte	123	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	duarte	133	PdbaseInfo mypdbaseinfo = new PdbaseInfo(accode,chaincode,model,db);
144	duarte	123	ArrayList<ArrayList> resultset = mypdbaseinfo.read_atomData();
145	duarte	135	chain = mypdbaseinfo.chain;
146	duarte	123	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	duarte	135	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	duarte	123	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	duarte	130	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	duarte	133	MsdsdInfo mymsdsdinfo = new MsdsdInfo(accode,chaincode,model,db);
178	duarte	130	ArrayList<ArrayList> resultset = mymsdsdinfo.read_atomData();
179			sequence = mymsdsdinfo.read_seq();
180	duarte	138	chain = mymsdsdinfo.chain;
181	duarte	130	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	duarte	133	/**
206			* To read the pdb data (atom coordinates, residue serials, atom serials) from file
207	duarte	153	* 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	duarte	133	* @param pdbfile
211			* @throws FileNotFoundException
212			* @throws IOException
213			*/
214	duarte	127	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	duarte	153	boolean empty = true; // controls whether we don't find any atom line for given chaincode and model
220	duarte	154	// 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	duarte	153	int thismodel=DEFAULT_MODEL; // we initialise to DEFAULT_MODEL, in case file doesn't have MODEL lines
224	duarte	127	BufferedReader fpdb = new BufferedReader(new FileReader(new File(pdbfile)));
225			String line;
226			while ((line = fpdb.readLine() ) != null ) {
227	duarte	153	Pattern p = Pattern.compile("^HEADER");
228	duarte	127	Matcher m = p.matcher(line);
229			if (m.find()){
230	duarte	153	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	duarte	154	// 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	duarte	127	Matcher ml = pl.matcher(line);
250			if (ml.find()) {
251	duarte	153	empty=false;
252	duarte	127	int atomserial=Integer.parseInt(ml.group(1).trim());
253			String atom = ml.group(2).trim();
254			String res_type = ml.group(3).trim();
255	duarte	154	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	duarte	127	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	duarte	153	}
270			}
271	duarte	127	}
272			}
273			fpdb.close();
274	duarte	153	if (empty) System.err.println("Couldn't find any atom line for given chaincode: "+chaincode+", model: "+model);
275	duarte	127	// 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	duarte	153	/**
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	duarte	123	public void dump2pdbfile(String outfile) throws IOException {
296	duarte	130	TreeMap<Integer,Object[]> lines = new TreeMap<Integer,Object[]>();
297	duarte	123	PrintStream Out = new PrintStream(new FileOutputStream(outfile));
298	duarte	153	Out.println("HEADER Dumped from "+db+". pdb accession code="+accode+", chain='"+chain+"'");
299	duarte	123	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	duarte	153	Object[] fields = {atomserial, atom, res_type, chain, res_serial, coords[0], coords[1], coords[2]};
306	duarte	130	lines.put(atomserial, fields);
307	duarte	123	}
308	duarte	130	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	duarte	123	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	duarte	129	/**
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	duarte	123	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	duarte	129	// 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	duarte	123	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	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
402	duarte	123	if (i_resser!=j_resser && (! contacts.contains(resser_pair))){
403			contacts.add(resser_pair);
404			}
405			}
406			}
407			Collections.sort(contacts);
408	duarte	129	TreeMap<Integer,String> nodes = new TreeMap<Integer,String>();
409			for (int resser:resser2restype.keySet()){
410			nodes.put(resser,resser2restype.get(resser));
411			}
412	duarte	135	// NOTE: we pass to the graph object the chain (internal chain identifier) not the pdb chain code!
413	duarte	129	Graph graph = new Graph (contacts,nodes,sequence,cutoff,ct,accode,chain);
414	duarte	123	return graph;
415			}
416
417			public Double distance(Double[] coords1, Double[] coords2){
418			return Math.sqrt(Math.pow((coords1[0]-coords2[0]),2)+Math.pow((coords1[1]-coords2[1]),2)+Math.pow((coords1[2]-coords2[2]),2));
419			}
420			}