trunk/proteinstructure/PdbfilePdb.java

package proteinstructure;

import java.io.BufferedReader;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.TreeMap;
import java.util.regex.Matcher;
import java.util.regex.Pattern;

import javax.vecmath.Point3d;

public class PdbfilePdb extends Pdb {
        
        private static final String UNKNOWN_STRING ="Unknown";
        private static final String NULL_chainCode = "A";
        
        private String pdbfile;

        /**
         * Constructs Pdb object reading from pdb file given pdb chain code. Model will be DEFAULT_MODEL
         * @param pdbfile
         * @param pdbChainCode
         * @throws FileNotFoundException
         * @throws IOException
         * @throws PdbfileFormatError
         * @throws PdbChainCodeNotFoundError 
         */
        public PdbfilePdb (String pdbfile, String pdbChainCode) throws FileNotFoundException, IOException, PdbfileFormatError, PdbChainCodeNotFoundError {
                this(pdbfile,pdbChainCode,DEFAULT_MODEL);
        }
        
        /**
         * Constructs Pdb object reading from pdb file given pdb chain code and model serial
         * @param pdbfile
         * @param pdbChainCode
         * @param model_serial
         * @throws FileNotFoundException
         * @throws IOException
         * @throws PdbfileFormatError
         * @throws PdbChainCodeNotFoundError 
         */
        public PdbfilePdb (String pdbfile, String pdbChainCode, int model_serial) throws FileNotFoundException, IOException, PdbfileFormatError, PdbChainCodeNotFoundError {
                this.pdbfile = pdbfile;
                this.model=model_serial;
                this.pdbCode=UNKNOWN_STRING; // we initialise to unknown in case we don't find it in pdb file 
                this.pdbChainCode=pdbChainCode.toUpperCase();   // our convention: chain codes are upper case
                // we set chainCode to pdbChainCode except for case NULL where we use "A"
                this.chainCode=pdbChainCode;
                if (pdbChainCode.equals("NULL")) this.chainCode=NULL_chainCode;
                
                this.sequence=""; // we initialise it to empty string, then is set inread_pdb_data_from_file 
                
                // we initialise the resser2secstruct and secstruct2resinterval Maps to empty, if no sec structure info is found then it remains empty
                this.resser2secstruct = new HashMap<Integer, String>();
                this.secstruct2resinterval = new TreeMap<String, Interval>();
                
                read_pdb_data_from_file();
                
                // when reading from pdb file we have no information of residue numbers or author's (original) pdb residue number, so we fill the mapping with the residue numbers we know
                //TODO eventually we could assign our own internal residue numbers when reading from pdb and thus this map would be used
                this.resser2pdbresser = new HashMap<Integer, String>();
                this.pdbresser2resser = new HashMap<String, Integer>();
                for (int resser:resser2restype.keySet()){
                        resser2pdbresser.put(resser, String.valueOf(resser));
                        pdbresser2resser.put(String.valueOf(resser), resser);
                }
                
                // initialising atomser2atom from resser_atom2atomserial
                atomser2atom = new HashMap<Integer, String>();
                for (String resser_atom:resser_atom2atomserial.keySet()){
                        int atomserial = resser_atom2atomserial.get(resser_atom);
                        String atom = resser_atom.split("_")[1];
                        atomser2atom.put(atomserial,atom);
                }
        }

        
        
        /**
         * To read the pdb data (atom coordinates, residue serials, atom serials) from file.
         * chainCode gets set to same as pdbChainCode, except if input chain code NULL then chainCode will be 'A'
         * pdbCode 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)
         * No insertion codes are parsed or taken into account at the moment. Thus files with 
         * insertion codes will be incorrectly read
         * @param pdbfile
         * @throws FileNotFoundException
         * @throws IOException
         * @throws PdbfileFormatError
         * @throws PdbChainCodeNotFoundError  
         */
        private void read_pdb_data_from_file() throws FileNotFoundException, IOException, PdbfileFormatError, PdbChainCodeNotFoundError {
                resser_atom2atomserial = new HashMap<String,Integer>();
                resser2restype = new HashMap<Integer,String>();
                atomser2coord = new HashMap<Integer,Point3d>();
                atomser2resser = new HashMap<Integer,Integer>();
                Pattern p;
                Matcher m;
                boolean empty = true; // controls whether we don't find any atom line for given pdbChainCode and model
                // we set chainCodeStr (for regex) to pdbChainCode except for case NULL where we use " " (NULL is a blank chain code in pdb files)
                String chainCodeStr=pdbChainCode;
                if (pdbChainCode.equals("NULL")) chainCodeStr=" ";
                
                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)));
                int linecount=0;
                String line;
                // read first line
                if((line = fpdb.readLine()) != null ) {
                        linecount = 1;
                        // HEADER
                        p = Pattern.compile("^HEADER");
                        m = p.matcher(line);
                        if (m.find()){
                                Pattern ph = Pattern.compile("^HEADER.{56}(\\d\\w{3})");
                                Matcher mh = ph.matcher(line);
                                if (mh.find()) {
                                        pdbCode=mh.group(1).toLowerCase();
                                }
                        } else { // header not found
                                // check whether this is a Casp prediction file
                                p = Pattern.compile("^PFRMAT TS");
                                m = p.matcher(line);
                                if(m.find()) {
                                        // ok, it is
                                        pdbCode = "CASP";
                                } else {
                                        // a HEADER is the minimum we ask at the moment for a pdb file to have, if we don't find it in line 1 we throw an exception
                                        throw new PdbfileFormatError("The pdb file "+pdbfile+" doesn't seem to have the right format");
                                }
                        }
                } else {
                        throw new PdbfileFormatError("The file "+pdbfile+" is empty.");
                }
                // read further lines
                while ((line = fpdb.readLine() ) != null ) {
                        linecount++;
                        // SECONDARY STRUCTURE
                        // helix
                        //HELIX    1   1 LYS A   17  LEU A   26  1
                        //                                                      helix ser                               beg res ser                                     end res ser
                        p = Pattern.compile("^HELIX..(...).{9}"+chainCodeStr+".(....).{6}"+chainCodeStr+".(....)");
                        m = p.matcher(line);
                        if (m.find()){
                                int serial = Integer.valueOf(m.group(1).trim());
                                int beg = Integer.valueOf(m.group(2).trim());
                                int end = Integer.valueOf(m.group(3).trim());
                                String ssId = "H"+serial;
                                secstruct2resinterval.put(ssId, new Interval(beg,end));
                                for (int i=beg;i<=end;i++){
                                        if (resser2secstruct.containsKey(i)){// if already assigned we print a warning and then assign it
                                                //System.err.println("Inconsistency in secondary structure assignment. " +
                                                //              "Residue "+i+" is getting reassigned from "+resser2secstruct.get(i)+" to "+ssId);
                                        }
                                        resser2secstruct.put(i,ssId);
                                }
                        }
                        // sheet
                        //SHEET    2   A 5 ILE A  96  THR A  99 -1  N  LYS A  98   O  THR A 107
                        //                       strand ser sheet id                     beg res ser                 end res ser
                        p = Pattern.compile("^SHEET..(...).(...).{7}"+chainCodeStr+"(....).{6}"+chainCodeStr+"(....)");
                        m = p.matcher(line);
                        if (m.find()){
                                int strandSerial = Integer.valueOf(m.group(1).trim());
                                String sheetId = m.group(2).trim();
                                int beg = Integer.valueOf(m.group(3).trim());
                                int end = Integer.valueOf(m.group(4).trim());
                                String ssId = "S"+sheetId+strandSerial;
                                secstruct2resinterval.put(ssId, new Interval(beg,end));
                                for (int i=beg;i<=end;i++){
                                        if (resser2secstruct.containsKey(i)){// if already assigned we print a warning and then assign it
                                                //System.err.println("Inconsistency in secondary structure assignment. " +
                                                //              "Residue "+i+" is getting reassigned from "+resser2secstruct.get(i)+" to "+ssId);
                                        }
                                        resser2secstruct.put(i,ssId);
                                }
                        }
                        // we've stored the sec structure info in the strands2begEnd and sheets2strands maps.
                        // the assignment to resser2secstruct is done when we reach the ATOM lines, see below
                        // turn
                        //TURN     1 S1A GLY A  16  GLN A  18     SURFACE
                        //                                                      turn ser                                beg res ser                                     end res ser
                        p = Pattern.compile("^TURN...(...).{9}"+chainCodeStr+"(....).{6}"+chainCodeStr+"(....)");
                        m = p.matcher(line);
                        if (m.find()){
                                int serial = Integer.valueOf(m.group(1).trim());
                                int beg = Integer.valueOf(m.group(2).trim());
                                int end = Integer.valueOf(m.group(3).trim());
                                String ssId = "T"+serial;
                                secstruct2resinterval.put(ssId, new Interval(beg,end));
                                for (int i=beg;i<=end;i++){
                                        if (resser2secstruct.containsKey(i)){// if already assigned we print a warning and then assign it
                                                //System.err.println("Inconsistency in secondary structure assignment. " +
                                                //              "Residue "+i+" is getting reassigned from "+resser2secstruct.get(i)+" to "+ssId);
                                        }
                                        resser2secstruct.put(i,ssId);
                                }
                        }                       
                        // MODEL
                        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
                        // ATOM
                        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}"+chainCodeStr+"(.{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());
                                        Point3d coords = new Point3d(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 pdbChainCode: "+pdbChainCode+", model: "+model);
                        throw new PdbChainCodeNotFoundError("Couldn't find any ATOM line for given pdbChainCode: "+pdbChainCode+", 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);
                for (int resser:ressers){
                        String oneletter = AA.threeletter2oneletter(resser2restype.get(resser));
                        sequence += oneletter;
                }
        }
        
}
Revision:	255
Committed:	Thu Aug 9 13:45:10 2007 UTC (17 years, 2 months ago) by stehr
File size:	10852 byte(s)
Log Message:	PdbfilePdb now also accepts Casp prediction files ('PFRMAT TS' instead of 'HEADER')
Line	File contents
1	package proteinstructure;
2
3	import java.io.BufferedReader;
4	import java.io.File;
5	import java.io.FileNotFoundException;
6	import java.io.FileReader;
7	import java.io.IOException;
8	import java.util.ArrayList;
9	import java.util.Collections;
10	import java.util.HashMap;
11	import java.util.TreeMap;
12	import java.util.regex.Matcher;
13	import java.util.regex.Pattern;
14
15	import javax.vecmath.Point3d;
16
17	public class PdbfilePdb extends Pdb {
18
19	private static final String UNKNOWN_STRING ="Unknown";
20	private static final String NULL_chainCode = "A";
21
22	private String pdbfile;
23
24	/**
25	* Constructs Pdb object reading from pdb file given pdb chain code. Model will be DEFAULT_MODEL
26	* @param pdbfile
27	* @param pdbChainCode
28	* @throws FileNotFoundException
29	* @throws IOException
30	* @throws PdbfileFormatError
31	* @throws PdbChainCodeNotFoundError
32	*/
33	public PdbfilePdb (String pdbfile, String pdbChainCode) throws FileNotFoundException, IOException, PdbfileFormatError, PdbChainCodeNotFoundError {
34	this(pdbfile,pdbChainCode,DEFAULT_MODEL);
35	}
36
37	/**
38	* Constructs Pdb object reading from pdb file given pdb chain code and model serial
39	* @param pdbfile
40	* @param pdbChainCode
41	* @param model_serial
42	* @throws FileNotFoundException
43	* @throws IOException
44	* @throws PdbfileFormatError
45	* @throws PdbChainCodeNotFoundError
46	*/
47	public PdbfilePdb (String pdbfile, String pdbChainCode, int model_serial) throws FileNotFoundException, IOException, PdbfileFormatError, PdbChainCodeNotFoundError {
48	this.pdbfile = pdbfile;
49	this.model=model_serial;
50	this.pdbCode=UNKNOWN_STRING; // we initialise to unknown in case we don't find it in pdb file
51	this.pdbChainCode=pdbChainCode.toUpperCase(); // our convention: chain codes are upper case
52	// we set chainCode to pdbChainCode except for case NULL where we use "A"
53	this.chainCode=pdbChainCode;
54	if (pdbChainCode.equals("NULL")) this.chainCode=NULL_chainCode;
55
56	this.sequence=""; // we initialise it to empty string, then is set inread_pdb_data_from_file
57
58	// we initialise the resser2secstruct and secstruct2resinterval Maps to empty, if no sec structure info is found then it remains empty
59	this.resser2secstruct = new HashMap<Integer, String>();
60	this.secstruct2resinterval = new TreeMap<String, Interval>();
61
62	read_pdb_data_from_file();
63
64	// when reading from pdb file we have no information of residue numbers or author's (original) pdb residue number, so we fill the mapping with the residue numbers we know
65	//TODO eventually we could assign our own internal residue numbers when reading from pdb and thus this map would be used
66	this.resser2pdbresser = new HashMap<Integer, String>();
67	this.pdbresser2resser = new HashMap<String, Integer>();
68	for (int resser:resser2restype.keySet()){
69	resser2pdbresser.put(resser, String.valueOf(resser));
70	pdbresser2resser.put(String.valueOf(resser), resser);
71	}
72
73	// initialising atomser2atom from resser_atom2atomserial
74	atomser2atom = new HashMap<Integer, String>();
75	for (String resser_atom:resser_atom2atomserial.keySet()){
76	int atomserial = resser_atom2atomserial.get(resser_atom);
77	String atom = resser_atom.split("_")[1];
78	atomser2atom.put(atomserial,atom);
79	}
80	}
81
82
83
84	/**
85	* To read the pdb data (atom coordinates, residue serials, atom serials) from file.
86	* chainCode gets set to same as pdbChainCode, except if input chain code NULL then chainCode will be 'A'
87	* pdbCode gets set to the one parsed in HEADER or to 'Unknown' if not found
88	* sequence gets set to the sequence read from ATOM lines (i.e. observed resdiues only)
89	* No insertion codes are parsed or taken into account at the moment. Thus files with
90	* insertion codes will be incorrectly read
91	* @param pdbfile
92	* @throws FileNotFoundException
93	* @throws IOException
94	* @throws PdbfileFormatError
95	* @throws PdbChainCodeNotFoundError
96	*/
97	private void read_pdb_data_from_file() throws FileNotFoundException, IOException, PdbfileFormatError, PdbChainCodeNotFoundError {
98	resser_atom2atomserial = new HashMap<String,Integer>();
99	resser2restype = new HashMap<Integer,String>();
100	atomser2coord = new HashMap<Integer,Point3d>();
101	atomser2resser = new HashMap<Integer,Integer>();
102	Pattern p;
103	Matcher m;
104	boolean empty = true; // controls whether we don't find any atom line for given pdbChainCode and model
105	// we set chainCodeStr (for regex) to pdbChainCode except for case NULL where we use " " (NULL is a blank chain code in pdb files)
106	String chainCodeStr=pdbChainCode;
107	if (pdbChainCode.equals("NULL")) chainCodeStr=" ";
108
109	int thismodel=DEFAULT_MODEL; // we initialise to DEFAULT_MODEL, in case file doesn't have MODEL lines
110	BufferedReader fpdb = new BufferedReader(new FileReader(new File(pdbfile)));
111	int linecount=0;
112	String line;
113	// read first line
114	if((line = fpdb.readLine()) != null ) {
115	linecount = 1;
116	// HEADER
117	p = Pattern.compile("^HEADER");
118	m = p.matcher(line);
119	if (m.find()){
120	Pattern ph = Pattern.compile("^HEADER.{56}(\\d\\w{3})");
121	Matcher mh = ph.matcher(line);
122	if (mh.find()) {
123	pdbCode=mh.group(1).toLowerCase();
124	}
125	} else { // header not found
126	// check whether this is a Casp prediction file
127	p = Pattern.compile("^PFRMAT TS");
128	m = p.matcher(line);
129	if(m.find()) {
130	// ok, it is
131	pdbCode = "CASP";
132	} else {
133	// a HEADER is the minimum we ask at the moment for a pdb file to have, if we don't find it in line 1 we throw an exception
134	throw new PdbfileFormatError("The pdb file "+pdbfile+" doesn't seem to have the right format");
135	}
136	}
137	} else {
138	throw new PdbfileFormatError("The file "+pdbfile+" is empty.");
139	}
140	// read further lines
141	while ((line = fpdb.readLine() ) != null ) {
142	linecount++;
143	// SECONDARY STRUCTURE
144	// helix
145	//HELIX 1 1 LYS A 17 LEU A 26 1
146	// helix ser beg res ser end res ser
147	p = Pattern.compile("^HELIX..(...).{9}"+chainCodeStr+".(....).{6}"+chainCodeStr+".(....)");
148	m = p.matcher(line);
149	if (m.find()){
150	int serial = Integer.valueOf(m.group(1).trim());
151	int beg = Integer.valueOf(m.group(2).trim());
152	int end = Integer.valueOf(m.group(3).trim());
153	String ssId = "H"+serial;
154	secstruct2resinterval.put(ssId, new Interval(beg,end));
155	for (int i=beg;i<=end;i++){
156	if (resser2secstruct.containsKey(i)){// if already assigned we print a warning and then assign it
157	//System.err.println("Inconsistency in secondary structure assignment. " +
158	// "Residue "+i+" is getting reassigned from "+resser2secstruct.get(i)+" to "+ssId);
159	}
160	resser2secstruct.put(i,ssId);
161	}
162	}
163	// sheet
164	//SHEET 2 A 5 ILE A 96 THR A 99 -1 N LYS A 98 O THR A 107
165	// strand ser sheet id beg res ser end res ser
166	p = Pattern.compile("^SHEET..(...).(...).{7}"+chainCodeStr+"(....).{6}"+chainCodeStr+"(....)");
167	m = p.matcher(line);
168	if (m.find()){
169	int strandSerial = Integer.valueOf(m.group(1).trim());
170	String sheetId = m.group(2).trim();
171	int beg = Integer.valueOf(m.group(3).trim());
172	int end = Integer.valueOf(m.group(4).trim());
173	String ssId = "S"+sheetId+strandSerial;
174	secstruct2resinterval.put(ssId, new Interval(beg,end));
175	for (int i=beg;i<=end;i++){
176	if (resser2secstruct.containsKey(i)){// if already assigned we print a warning and then assign it
177	//System.err.println("Inconsistency in secondary structure assignment. " +
178	// "Residue "+i+" is getting reassigned from "+resser2secstruct.get(i)+" to "+ssId);
179	}
180	resser2secstruct.put(i,ssId);
181	}
182	}
183	// we've stored the sec structure info in the strands2begEnd and sheets2strands maps.
184	// the assignment to resser2secstruct is done when we reach the ATOM lines, see below
185	// turn
186	//TURN 1 S1A GLY A 16 GLN A 18 SURFACE
187	// turn ser beg res ser end res ser
188	p = Pattern.compile("^TURN...(...).{9}"+chainCodeStr+"(....).{6}"+chainCodeStr+"(....)");
189	m = p.matcher(line);
190	if (m.find()){
191	int serial = Integer.valueOf(m.group(1).trim());
192	int beg = Integer.valueOf(m.group(2).trim());
193	int end = Integer.valueOf(m.group(3).trim());
194	String ssId = "T"+serial;
195	secstruct2resinterval.put(ssId, new Interval(beg,end));
196	for (int i=beg;i<=end;i++){
197	if (resser2secstruct.containsKey(i)){// if already assigned we print a warning and then assign it
198	//System.err.println("Inconsistency in secondary structure assignment. " +
199	// "Residue "+i+" is getting reassigned from "+resser2secstruct.get(i)+" to "+ssId);
200	}
201	resser2secstruct.put(i,ssId);
202	}
203	}
204	// MODEL
205	p = Pattern.compile("^MODEL\\s+(\\d+)");
206	m = p.matcher(line);
207	if (m.find()){
208	thismodel=Integer.parseInt(m.group(1));
209	}
210	if (thismodel!=model) continue; // we skip reading of atom lines if we are not in the desired model
211	// ATOM
212	p = Pattern.compile("^ATOM");
213	m = p.matcher(line);
214	if (m.find()){
215	// serial atom res_type chain res_ser x y z
216	Pattern pl = Pattern.compile(".{6}(.....).{2}(...).{1}(...).{1}"+chainCodeStr+"(.{4}).{4}(.{8})(.{8})(.{8})",Pattern.CASE_INSENSITIVE);
217	Matcher ml = pl.matcher(line);
218	if (ml.find()) {
219	empty=false;
220	int atomserial=Integer.parseInt(ml.group(1).trim());
221	String atom = ml.group(2).trim();
222	String res_type = ml.group(3).trim();
223	int res_serial = Integer.parseInt(ml.group(4).trim());
224	double x = Double.parseDouble(ml.group(5).trim());
225	double y = Double.parseDouble(ml.group(6).trim());
226	double z = Double.parseDouble(ml.group(7).trim());
227	Point3d coords = new Point3d(x,y,z);
228	ArrayList<String> aalist=AA.aas();
229	if (aalist.contains(res_type)) {
230	atomser2coord.put(atomserial, coords);
231	atomser2resser.put(atomserial, res_serial);
232	resser2restype.put(res_serial, res_type);
233	ArrayList<String> atomlist = aas2atoms.get(res_type);
234	if (atomlist.contains(atom)){
235	resser_atom2atomserial.put(res_serial+"_"+atom, atomserial);
236	}
237	}
238	}
239	}
240	}
241	fpdb.close();
242	if (empty) {
243	//System.err.println("Couldn't find any atom line for given pdbChainCode: "+pdbChainCode+", model: "+model);
244	throw new PdbChainCodeNotFoundError("Couldn't find any ATOM line for given pdbChainCode: "+pdbChainCode+", model: "+model);
245	}
246	// now we read the sequence from the resser2restype HashMap
247	// NOTE: we must make sure elsewhere that there are no unobserved residues, we can't check that here!
248	ArrayList<Integer> ressers = new ArrayList<Integer>();
249	for (int resser:resser2restype.keySet()) {
250	ressers.add(resser);
251	}
252	Collections.sort(ressers);
253	for (int resser:ressers){
254	String oneletter = AA.threeletter2oneletter(resser2restype.get(resser));
255	sequence += oneletter;
256	}
257	}
258
259	}