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);
                }
                
        }

        
        
        /**
         * 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>();
                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;
                while ((line = fpdb.readLine() ) != null ) {
                        linecount++;
                        // HEADER
                        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()) {
                                        pdbCode=mh.group(1).toLowerCase();
                                }
                        } else if (linecount==1) { // header not found and we are in line 1
                                // 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");
                        }
                        // 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:	226
Committed:	Fri Jul 6 13:43:30 2007 UTC (17 years, 2 months ago) by duarte
File size:	10170 byte(s)
Log Message:	First geometric hashing implementation for calculating graph (with new class Box). Only does non-crossed cts Geometrich hashing graph calculation kept in a separate method than normal get_graph. Still either of the methods can be used. Using javax.vectormath objects for the vectors (distance method also from that) Using TreeMap for get_coords_for_ct
Line	User	Rev	File contents
1	duarte	207	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	duarte	222	import java.util.TreeMap;
12	duarte	207	import java.util.regex.Matcher;
13			import java.util.regex.Pattern;
14
15	duarte	226	import javax.vecmath.Point3d;
16
17	duarte	207	public class PdbfilePdb extends Pdb {
18
19	duarte	208	private static final String UNKNOWN_STRING ="Unknown";
20			private static final String NULL_chainCode = "A";
21
22	duarte	207	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	duarte	208	* @throws PdbfileFormatError
31	stehr	215	* @throws PdbChainCodeNotFoundError
32	duarte	207	*/
33	stehr	215	public PdbfilePdb (String pdbfile, String pdbChainCode) throws FileNotFoundException, IOException, PdbfileFormatError, PdbChainCodeNotFoundError {
34	duarte	207	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	duarte	208	* @throws PdbfileFormatError
45	stehr	215	* @throws PdbChainCodeNotFoundError
46	duarte	207	*/
47	stehr	215	public PdbfilePdb (String pdbfile, String pdbChainCode, int model_serial) throws FileNotFoundException, IOException, PdbfileFormatError, PdbChainCodeNotFoundError {
48	duarte	207	this.pdbfile = pdbfile;
49			this.model=model_serial;
50	duarte	208	this.pdbCode=UNKNOWN_STRING; // we initialise to unknown in case we don't find it in pdb file
51	stehr	217	this.pdbChainCode=pdbChainCode.toUpperCase(); // our convention: chain codes are upper case
52	duarte	208	// 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	duarte	222	// we initialise the resser2secstruct and secstruct2resinterval Maps to empty, if no sec structure info is found then it remains empty
59	duarte	219	this.resser2secstruct = new HashMap<Integer, String>();
60	duarte	222	this.secstruct2resinterval = new TreeMap<String, Interval>();
61	duarte	219
62	duarte	207	read_pdb_data_from_file();
63	duarte	208
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	duarte	219
73	duarte	207	}
74
75
76
77			/**
78	duarte	219	* To read the pdb data (atom coordinates, residue serials, atom serials) from file.
79			* chainCode gets set to same as pdbChainCode, except if input chain code NULL then chainCode will be 'A'
80	duarte	207	* pdbCode gets set to the one parsed in HEADER or to 'Unknown' if not found
81			* sequence gets set to the sequence read from ATOM lines (i.e. observed resdiues only)
82	duarte	219	* No insertion codes are parsed or taken into account at the moment. Thus files with
83			* insertion codes will be incorrectly read
84	duarte	207	* @param pdbfile
85			* @throws FileNotFoundException
86			* @throws IOException
87	duarte	208	* @throws PdbfileFormatError
88	stehr	215	* @throws PdbChainCodeNotFoundError
89	duarte	207	*/
90	stehr	215	private void read_pdb_data_from_file() throws FileNotFoundException, IOException, PdbfileFormatError, PdbChainCodeNotFoundError {
91	duarte	207	resser_atom2atomserial = new HashMap<String,Integer>();
92			resser2restype = new HashMap<Integer,String>();
93	duarte	226	atomser2coord = new HashMap<Integer,Point3d>();
94	duarte	207	atomser2resser = new HashMap<Integer,Integer>();
95			boolean empty = true; // controls whether we don't find any atom line for given pdbChainCode and model
96	duarte	208	// we set chainCodeStr (for regex) to pdbChainCode except for case NULL where we use " " (NULL is a blank chain code in pdb files)
97			String chainCodeStr=pdbChainCode;
98			if (pdbChainCode.equals("NULL")) chainCodeStr=" ";
99
100	duarte	207	int thismodel=DEFAULT_MODEL; // we initialise to DEFAULT_MODEL, in case file doesn't have MODEL lines
101			BufferedReader fpdb = new BufferedReader(new FileReader(new File(pdbfile)));
102	duarte	208	int linecount=0;
103	duarte	207	String line;
104			while ((line = fpdb.readLine() ) != null ) {
105	duarte	208	linecount++;
106	duarte	219	// HEADER
107	duarte	207	Pattern p = Pattern.compile("^HEADER");
108			Matcher m = p.matcher(line);
109			if (m.find()){
110			Pattern ph = Pattern.compile("^HEADER.{56}(\\d\\w{3})");
111			Matcher mh = ph.matcher(line);
112			if (mh.find()) {
113			pdbCode=mh.group(1).toLowerCase();
114			}
115	duarte	208	} else if (linecount==1) { // header not found and we are in line 1
116			// 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
117			throw new PdbfileFormatError("The pdb file "+pdbfile+" doesn't seem to have the right format");
118	duarte	207	}
119	duarte	219	// SECONDARY STRUCTURE
120			// helix
121			//HELIX 1 1 LYS A 17 LEU A 26 1
122			// helix ser beg res ser end res ser
123			p = Pattern.compile("^HELIX..(...).{9}"+chainCodeStr+".(....).{6}"+chainCodeStr+".(....)");
124			m = p.matcher(line);
125			if (m.find()){
126			int serial = Integer.valueOf(m.group(1).trim());
127			int beg = Integer.valueOf(m.group(2).trim());
128			int end = Integer.valueOf(m.group(3).trim());
129			String ssId = "H"+serial;
130	duarte	222	secstruct2resinterval.put(ssId, new Interval(beg,end));
131	duarte	219	for (int i=beg;i<=end;i++){
132			if (resser2secstruct.containsKey(i)){// if already assigned we print a warning and then assign it
133			System.err.println("Inconsistency in secondary structure assignment. " +
134			"Residue "+i+" is getting reassigned from "+resser2secstruct.get(i)+" to "+ssId);
135			}
136			resser2secstruct.put(i,ssId);
137			}
138			}
139			// sheet
140			//SHEET 2 A 5 ILE A 96 THR A 99 -1 N LYS A 98 O THR A 107
141			// strand ser sheet id beg res ser end res ser
142			p = Pattern.compile("^SHEET..(...).(...).{7}"+chainCodeStr+"(....).{6}"+chainCodeStr+"(....)");
143			m = p.matcher(line);
144			if (m.find()){
145			int strandSerial = Integer.valueOf(m.group(1).trim());
146			String sheetId = m.group(2).trim();
147			int beg = Integer.valueOf(m.group(3).trim());
148			int end = Integer.valueOf(m.group(4).trim());
149			String ssId = "S"+sheetId+strandSerial;
150	duarte	222	secstruct2resinterval.put(ssId, new Interval(beg,end));
151	duarte	219	for (int i=beg;i<=end;i++){
152			if (resser2secstruct.containsKey(i)){// if already assigned we print a warning and then assign it
153			System.err.println("Inconsistency in secondary structure assignment. " +
154			"Residue "+i+" is getting reassigned from "+resser2secstruct.get(i)+" to "+ssId);
155			}
156			resser2secstruct.put(i,ssId);
157			}
158			}
159			// we've stored the sec structure info in the strands2begEnd and sheets2strands maps.
160			// the assignment to resser2secstruct is done when we reach the ATOM lines, see below
161			// turn
162			//TURN 1 S1A GLY A 16 GLN A 18 SURFACE
163			// turn ser beg res ser end res ser
164			p = Pattern.compile("^TURN...(...).{9}"+chainCodeStr+"(....).{6}"+chainCodeStr+"(....)");
165			m = p.matcher(line);
166			if (m.find()){
167			int serial = Integer.valueOf(m.group(1).trim());
168			int beg = Integer.valueOf(m.group(2).trim());
169			int end = Integer.valueOf(m.group(3).trim());
170			String ssId = "T"+serial;
171	duarte	222	secstruct2resinterval.put(ssId, new Interval(beg,end));
172	duarte	219	for (int i=beg;i<=end;i++){
173			if (resser2secstruct.containsKey(i)){// if already assigned we print a warning and then assign it
174			System.err.println("Inconsistency in secondary structure assignment. " +
175			"Residue "+i+" is getting reassigned from "+resser2secstruct.get(i)+" to "+ssId);
176			}
177			resser2secstruct.put(i,ssId);
178			}
179			}
180			// MODEL
181	duarte	207	p = Pattern.compile("^MODEL\\s+(\\d+)");
182			m = p.matcher(line);
183			if (m.find()){
184			thismodel=Integer.parseInt(m.group(1));
185			}
186			if (thismodel!=model) continue; // we skip reading of atom lines if we are not in the desired model
187	duarte	219	// ATOM
188	duarte	207	p = Pattern.compile("^ATOM");
189			m = p.matcher(line);
190			if (m.find()){
191	duarte	208	// serial atom res_type chain res_ser x y z
192			Pattern pl = Pattern.compile(".{6}(.....).{2}(...).{1}(...).{1}"+chainCodeStr+"(.{4}).{4}(.{8})(.{8})(.{8})",Pattern.CASE_INSENSITIVE);
193	duarte	207	Matcher ml = pl.matcher(line);
194			if (ml.find()) {
195			empty=false;
196			int atomserial=Integer.parseInt(ml.group(1).trim());
197			String atom = ml.group(2).trim();
198			String res_type = ml.group(3).trim();
199			int res_serial = Integer.parseInt(ml.group(4).trim());
200			double x = Double.parseDouble(ml.group(5).trim());
201			double y = Double.parseDouble(ml.group(6).trim());
202			double z = Double.parseDouble(ml.group(7).trim());
203	duarte	226	Point3d coords = new Point3d(x,y,z);
204	duarte	207	ArrayList<String> aalist=AA.aas();
205			if (aalist.contains(res_type)) {
206			atomser2coord.put(atomserial, coords);
207			atomser2resser.put(atomserial, res_serial);
208			resser2restype.put(res_serial, res_type);
209			ArrayList<String> atomlist = aas2atoms.get(res_type);
210			if (atomlist.contains(atom)){
211			resser_atom2atomserial.put(res_serial+"_"+atom, atomserial);
212			}
213			}
214			}
215			}
216			}
217			fpdb.close();
218	stehr	215	if (empty) {
219			//System.err.println("Couldn't find any atom line for given pdbChainCode: "+pdbChainCode+", model: "+model);
220			throw new PdbChainCodeNotFoundError("Couldn't find any ATOM line for given pdbChainCode: "+pdbChainCode+", model: "+model);
221			}
222	duarte	207	// now we read the sequence from the resser2restype HashMap
223			// NOTE: we must make sure elsewhere that there are no unobserved residues, we can't check that here!
224			ArrayList<Integer> ressers = new ArrayList<Integer>();
225			for (int resser:resser2restype.keySet()) {
226			ressers.add(resser);
227			}
228			Collections.sort(ressers);
229			for (int resser:ressers){
230			String oneletter = AA.threeletter2oneletter(resser2restype.get(resser));
231			sequence += oneletter;
232			}
233			}
234	duarte	219
235	duarte	207	}