| 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 |
| 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 |
| 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 resdiues only) |
| 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 |
| 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 |
+ |
sequence+= AA.threeletter2oneletter(line.substring(i, i+3)); |
| 155 |
+ |
} |
| 156 |
+ |
} |
| 157 |
+ |
} |
| 158 |
|
// SECONDARY STRUCTURE |
| 159 |
|
// helix |
| 160 |
|
//HELIX 1 1 LYS A 17 LEU A 26 1 |
| 258 |
|
//System.err.println("Couldn't find any atom line for given pdbChainCode: "+pdbChainCode+", model: "+model); |
| 259 |
|
throw new PdbChainCodeNotFoundError("Couldn't find any ATOM line for given pdbChainCode: "+pdbChainCode+", model: "+model); |
| 260 |
|
} |
| 261 |
< |
// now we read the sequence from the resser2restype HashMap |
| 262 |
< |
// NOTE: we must make sure elsewhere that there are no unobserved residues, we can't check that here! |
| 263 |
< |
ArrayList<Integer> ressers = new ArrayList<Integer>(); |
| 264 |
< |
for (int resser:resser2restype.keySet()) { |
| 265 |
< |
ressers.add(resser); |
| 266 |
< |
} |
| 267 |
< |
Collections.sort(ressers); |
| 268 |
< |
for (int resser:ressers){ |
| 269 |
< |
String oneletter = AA.threeletter2oneletter(resser2restype.get(resser)); |
| 270 |
< |
sequence += oneletter; |
| 261 |
> |
if (sequence.equals("")){ |
| 262 |
> |
// if we couldn't read anything from SEQRES then we read it from the resser2restype HashMap |
| 263 |
> |
// NOTE: we must make sure elsewhere that there are no unobserved residues, we can't check that here! |
| 264 |
> |
ArrayList<Integer> ressers = new ArrayList<Integer>(); |
| 265 |
> |
for (int resser:resser2restype.keySet()) { |
| 266 |
> |
ressers.add(resser); |
| 267 |
> |
} |
| 268 |
> |
Collections.sort(ressers); |
| 269 |
> |
for (int resser:ressers){ |
| 270 |
> |
String oneletter = AA.threeletter2oneletter(resser2restype.get(resser)); |
| 271 |
> |
sequence += oneletter; |
| 272 |
> |
} |
| 273 |
|
} |
| 274 |
|
} |
| 275 |
|
|
