| 21 |
|
HashMap<Integer,Double[]> atomser2coord; |
| 22 |
|
HashMap<Integer,Integer> atomser2resser; |
| 23 |
|
HashMap<String,ArrayList<String>> aas2atoms = AA.getaas2atoms(); |
| 24 |
< |
String sequence=""; |
| 25 |
< |
String accode=""; |
| 24 |
> |
public String sequence=""; |
| 25 |
> |
public String accode=""; |
| 26 |
|
// given "external" pdb chain code, i.e. the classic pdb code ("NULL" if it is blank in original pdb file) |
| 27 |
< |
String chaincode=""; |
| 28 |
< |
int model=DEFAULT_MODEL; |
| 27 |
> |
public String chaincode=""; |
| 28 |
> |
public int model=DEFAULT_MODEL; |
| 29 |
|
String db; |
| 30 |
|
|
| 31 |
|
// Our internal chain identifier (taken from dbs or pdb): |
| 65 |
|
this(pdbfile,DEFAULT_MODEL); |
| 66 |
|
} |
| 67 |
|
|
| 68 |
+ |
//TODO implement read of pdb file given model |
| 69 |
|
public Pdb (String pdbfile, int model_serial) throws FileNotFoundException, IOException { |
| 70 |
|
this.accode=""; |
| 71 |
|
this.model=model_serial; |
| 201 |
|
// finally we set accode and chaincode to unknown |
| 202 |
|
//TODO: we should parse accode and chaincode from appropriate fields in pdb file, |
| 203 |
|
// problem: in case of a non-original pdb file there won't be accession code |
| 204 |
< |
accode="?"; |
| 205 |
< |
chaincode="?"; |
| 204 |
> |
accode="Unknown"; |
| 205 |
> |
chaincode="Unknown"; |
| 206 |
|
} |
| 207 |
|
|
| 208 |
|
public void dump2pdbfile(String outfile) throws IOException { |
