| 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 |
|
|
| 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; |
| 110 |
|
BufferedReader fpdb = new BufferedReader(new FileReader(new File(pdbfile))); |
| 111 |
|
int linecount=0; |
| 112 |
|
String line; |
| 113 |
< |
while ((line = fpdb.readLine() ) != null ) { |
| 114 |
< |
linecount++; |
| 113 |
> |
// read first line |
| 114 |
> |
if((line = fpdb.readLine()) != null ) { |
| 115 |
> |
linecount = 1; |
| 116 |
|
// HEADER |
| 117 |
< |
Pattern p = Pattern.compile("^HEADER"); |
| 118 |
< |
Matcher m = p.matcher(line); |
| 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 if (linecount==1) { // header not found and we are in line 1 |
| 126 |
< |
// 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 |
| 127 |
< |
throw new PdbfileFormatError("The pdb file "+pdbfile+" doesn't seem to have the right format"); |
| 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 |
| 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); |
| 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 |
|
} |
| 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); |
| 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 |
|
} |
| 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); |
| 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 |
|
} |
