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 in read_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 |
if(!resser2secstruct.isEmpty()) { |
64 |
hasSecondaryStructure = true; |
65 |
secondaryStructureSource = "Author"; |
66 |
} |
67 |
|
68 |
// 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 |
69 |
//TODO eventually we could assign our own internal residue numbers when reading from pdb and thus this map would be used |
70 |
this.resser2pdbresser = new HashMap<Integer, String>(); |
71 |
this.pdbresser2resser = new HashMap<String, Integer>(); |
72 |
for (int resser:resser2restype.keySet()){ |
73 |
resser2pdbresser.put(resser, String.valueOf(resser)); |
74 |
pdbresser2resser.put(String.valueOf(resser), resser); |
75 |
} |
76 |
|
77 |
// initialising atomser2atom from resser_atom2atomserial |
78 |
atomser2atom = new HashMap<Integer, String>(); |
79 |
for (String resser_atom:resser_atom2atomserial.keySet()){ |
80 |
int atomserial = resser_atom2atomserial.get(resser_atom); |
81 |
String atom = resser_atom.split("_")[1]; |
82 |
atomser2atom.put(atomserial,atom); |
83 |
} |
84 |
} |
85 |
|
86 |
|
87 |
|
88 |
/** |
89 |
* To read the pdb data (atom coordinates, residue serials, atom serials) from file. |
90 |
* chainCode gets set to same as pdbChainCode, except if input chain code NULL then chainCode will be 'A' |
91 |
* pdbCode gets set to the one parsed in HEADER or to 'Unknown' if not found |
92 |
* sequence gets set to the sequence read from ATOM lines (i.e. observed residues only) |
93 |
* No insertion codes are parsed or taken into account at the moment. Thus files with |
94 |
* insertion codes will be incorrectly read |
95 |
* @param pdbfile |
96 |
* @throws FileNotFoundException |
97 |
* @throws IOException |
98 |
* @throws PdbfileFormatError |
99 |
* @throws PdbChainCodeNotFoundError |
100 |
*/ |
101 |
private void read_pdb_data_from_file() throws FileNotFoundException, IOException, PdbfileFormatError, PdbChainCodeNotFoundError { |
102 |
resser_atom2atomserial = new HashMap<String,Integer>(); |
103 |
resser2restype = new HashMap<Integer,String>(); |
104 |
atomser2coord = new HashMap<Integer,Point3d>(); |
105 |
atomser2resser = new HashMap<Integer,Integer>(); |
106 |
Pattern p; |
107 |
Matcher m; |
108 |
boolean empty = true; // controls whether we don't find any atom line for given pdbChainCode and model |
109 |
// we set chainCodeStr (for regex) to pdbChainCode except for case NULL where we use " " (NULL is a blank chain code in pdb files) |
110 |
String chainCodeStr=pdbChainCode; |
111 |
if (pdbChainCode.equals("NULL")) chainCodeStr=" "; |
112 |
|
113 |
int thismodel=DEFAULT_MODEL; // we initialise to DEFAULT_MODEL, in case file doesn't have MODEL lines |
114 |
BufferedReader fpdb = new BufferedReader(new FileReader(new File(pdbfile))); |
115 |
int linecount=0; |
116 |
String line; |
117 |
// read first line |
118 |
if((line = fpdb.readLine()) != null ) { |
119 |
linecount = 1; |
120 |
// HEADER |
121 |
p = Pattern.compile("^HEADER"); |
122 |
m = p.matcher(line); |
123 |
if (m.find()){ |
124 |
Pattern ph = Pattern.compile("^HEADER.{56}(\\d\\w{3})"); |
125 |
Matcher mh = ph.matcher(line); |
126 |
if (mh.find()) { |
127 |
pdbCode=mh.group(1).toLowerCase(); |
128 |
} |
129 |
} else { // header not found |
130 |
// check whether this is a Casp prediction file |
131 |
p = Pattern.compile("^PFRMAT TS"); |
132 |
m = p.matcher(line); |
133 |
if(m.find()) { |
134 |
// ok, it is |
135 |
pdbCode = "CASP"; |
136 |
} else { |
137 |
// 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 |
138 |
throw new PdbfileFormatError("The pdb file "+pdbfile+" doesn't seem to have the right format"); |
139 |
} |
140 |
} |
141 |
} else { |
142 |
throw new PdbfileFormatError("The file "+pdbfile+" is empty."); |
143 |
} |
144 |
// read further lines |
145 |
while ((line = fpdb.readLine() ) != null ) { |
146 |
linecount++; |
147 |
// SEQRES |
148 |
//SEQRES 1 A 348 VAL ASN ILE LYS THR ASN PRO PHE LYS ALA VAL SER PHE |
149 |
p = Pattern.compile("^SEQRES.{5}"+chainCodeStr); |
150 |
m = p.matcher(line); |
151 |
if (m.find()){ |
152 |
for (int i=19;i<=67;i+=4) { |
153 |
if (!line.substring(i, i+3).equals(" ")) { |
154 |
if (AA.threeletter2oneletter(line.substring(i, i+3))!=null) { // for non-standard aas |
155 |
sequence+= AA.threeletter2oneletter(line.substring(i, i+3)); |
156 |
} |
157 |
} |
158 |
} |
159 |
} |
160 |
// SECONDARY STRUCTURE |
161 |
// helix |
162 |
//HELIX 1 1 LYS A 17 LEU A 26 1 |
163 |
// helix ser beg res ser end res ser |
164 |
p = Pattern.compile("^HELIX..(...).{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 = "H"+serial; |
171 |
secstruct2resinterval.put(ssId, new Interval(beg,end)); |
172 |
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 |
// sheet |
181 |
//SHEET 2 A 5 ILE A 96 THR A 99 -1 N LYS A 98 O THR A 107 |
182 |
// strand ser sheet id beg res ser end res ser |
183 |
p = Pattern.compile("^SHEET..(...).(...).{7}"+chainCodeStr+"(....).{6}"+chainCodeStr+"(....)"); |
184 |
m = p.matcher(line); |
185 |
if (m.find()){ |
186 |
int strandSerial = Integer.valueOf(m.group(1).trim()); |
187 |
String sheetId = m.group(2).trim(); |
188 |
int beg = Integer.valueOf(m.group(3).trim()); |
189 |
int end = Integer.valueOf(m.group(4).trim()); |
190 |
String ssId = "S"+sheetId+strandSerial; |
191 |
secstruct2resinterval.put(ssId, new Interval(beg,end)); |
192 |
for (int i=beg;i<=end;i++){ |
193 |
if (resser2secstruct.containsKey(i)){// if already assigned we print a warning and then assign it |
194 |
//System.err.println("Inconsistency in secondary structure assignment. " + |
195 |
// "Residue "+i+" is getting reassigned from "+resser2secstruct.get(i)+" to "+ssId); |
196 |
} |
197 |
resser2secstruct.put(i,ssId); |
198 |
} |
199 |
} |
200 |
// we've stored the sec structure info in the strands2begEnd and sheets2strands maps. |
201 |
// the assignment to resser2secstruct is done when we reach the ATOM lines, see below |
202 |
// turn |
203 |
//TURN 1 S1A GLY A 16 GLN A 18 SURFACE |
204 |
// turn ser beg res ser end res ser |
205 |
p = Pattern.compile("^TURN...(...).{9}"+chainCodeStr+"(....).{6}"+chainCodeStr+"(....)"); |
206 |
m = p.matcher(line); |
207 |
if (m.find()){ |
208 |
int serial = Integer.valueOf(m.group(1).trim()); |
209 |
int beg = Integer.valueOf(m.group(2).trim()); |
210 |
int end = Integer.valueOf(m.group(3).trim()); |
211 |
String ssId = "T"+serial; |
212 |
secstruct2resinterval.put(ssId, new Interval(beg,end)); |
213 |
for (int i=beg;i<=end;i++){ |
214 |
if (resser2secstruct.containsKey(i)){// if already assigned we print a warning and then assign it |
215 |
//System.err.println("Inconsistency in secondary structure assignment. " + |
216 |
// "Residue "+i+" is getting reassigned from "+resser2secstruct.get(i)+" to "+ssId); |
217 |
} |
218 |
resser2secstruct.put(i,ssId); |
219 |
} |
220 |
} |
221 |
// MODEL |
222 |
p = Pattern.compile("^MODEL\\s+(\\d+)"); |
223 |
m = p.matcher(line); |
224 |
if (m.find()){ |
225 |
thismodel=Integer.parseInt(m.group(1)); |
226 |
} |
227 |
if (thismodel!=model) continue; // we skip reading of atom lines if we are not in the desired model |
228 |
// ATOM |
229 |
p = Pattern.compile("^ATOM"); |
230 |
m = p.matcher(line); |
231 |
if (m.find()){ |
232 |
// serial atom res_type chain res_ser x y z |
233 |
Pattern pl = Pattern.compile(".{6}(.....).{2}(...).{1}(...).{1}"+chainCodeStr+"(.{4}).{4}(.{8})(.{8})(.{8})",Pattern.CASE_INSENSITIVE); |
234 |
Matcher ml = pl.matcher(line); |
235 |
if (ml.find()) { |
236 |
empty=false; |
237 |
int atomserial=Integer.parseInt(ml.group(1).trim()); |
238 |
String atom = ml.group(2).trim(); |
239 |
String res_type = ml.group(3).trim(); |
240 |
int res_serial = Integer.parseInt(ml.group(4).trim()); |
241 |
double x = Double.parseDouble(ml.group(5).trim()); |
242 |
double y = Double.parseDouble(ml.group(6).trim()); |
243 |
double z = Double.parseDouble(ml.group(7).trim()); |
244 |
Point3d coords = new Point3d(x,y,z); |
245 |
ArrayList<String> aalist=AA.aas(); |
246 |
if (aalist.contains(res_type)) { |
247 |
atomser2coord.put(atomserial, coords); |
248 |
atomser2resser.put(atomserial, res_serial); |
249 |
resser2restype.put(res_serial, res_type); |
250 |
ArrayList<String> atomlist = aas2atoms.get(res_type); |
251 |
if (atomlist.contains(atom)){ |
252 |
resser_atom2atomserial.put(res_serial+"_"+atom, atomserial); |
253 |
} |
254 |
} |
255 |
} |
256 |
} |
257 |
} |
258 |
fpdb.close(); |
259 |
if (empty) { |
260 |
//System.err.println("Couldn't find any atom line for given pdbChainCode: "+pdbChainCode+", model: "+model); |
261 |
throw new PdbChainCodeNotFoundError("Couldn't find any ATOM line for given pdbChainCode: "+pdbChainCode+", model: "+model); |
262 |
} |
263 |
if (sequence.equals("")){ |
264 |
// if we couldn't read anything from SEQRES then we read it from the resser2restype HashMap |
265 |
// NOTE: we must make sure elsewhere that there are no unobserved residues, we can't check that here! |
266 |
ArrayList<Integer> ressers = new ArrayList<Integer>(); |
267 |
for (int resser:resser2restype.keySet()) { |
268 |
ressers.add(resser); |
269 |
} |
270 |
Collections.sort(ressers); |
271 |
for (int resser:ressers){ |
272 |
String oneletter = AA.threeletter2oneletter(resser2restype.get(resser)); |
273 |
sequence += oneletter; |
274 |
} |
275 |
} |
276 |
} |
277 |
|
278 |
} |