| 219 |
|
return dist_matrix; |
| 220 |
|
} |
| 221 |
|
|
| 222 |
+ |
/** |
| 223 |
+ |
* Get the contacts for given contact type and cutoff for this Pdb object. |
| 224 |
+ |
* Returns a Graph object with the contacts |
| 225 |
+ |
* The graph is always directional, i.e. in crossed cases xx/yy: i corresponds to xx and j to yy |
| 226 |
+ |
* ct here can be single contact type (e.g. Ca, BB) or crossed (e.g. BB/SC or Ca/Cb) |
| 227 |
+ |
* @param ct |
| 228 |
+ |
* @param cutoff |
| 229 |
+ |
* @return |
| 230 |
+ |
*/ |
| 231 |
|
public Graph get_graph(String ct, double cutoff){ |
| 232 |
|
TreeMap<Contact,Double> dist_matrix = calculate_dist_matrix(ct); |
| 233 |
|
ArrayList<Contact> contacts = new ArrayList<Contact>(); |
| 234 |
+ |
// we loop here over all indices of dist_matrix, |
| 235 |
+ |
// we took care already that in symmetric cases (i.e. single contact type, not crossed) we have only one side of the matrix and |
| 236 |
+ |
// in asymmetrical cases (i.e. crossed cases) we have both sides of the matrix |
| 237 |
|
for (Contact pair:dist_matrix.keySet()){ |
| 238 |
|
int i_atomser=pair.i; |
| 239 |
|
int j_atomser=pair.j; |
| 241 |
|
int i_resser = atomser2resser.get(i_atomser); |
| 242 |
|
int j_resser = atomser2resser.get(j_atomser); |
| 243 |
|
Contact resser_pair = new Contact(i_resser,j_resser); |
| 244 |
+ |
// for multi-atom models (BB, SC, ALL or BB/SC) we need to make sure that we don't have contacts from residue to itself or that we don't have duplicates |
| 245 |
|
if (i_resser!=j_resser && (! contacts.contains(resser_pair))){ |
| 246 |
|
contacts.add(resser_pair); |
| 247 |
|
} |
| 248 |
|
} |
| 249 |
|
} |
| 250 |
|
Collections.sort(contacts); |
| 251 |
< |
Graph graph = new Graph (contacts,cutoff,ct); |
| 251 |
> |
TreeMap<Integer,String> nodes = new TreeMap<Integer,String>(); |
| 252 |
> |
for (int resser:resser2restype.keySet()){ |
| 253 |
> |
nodes.put(resser,resser2restype.get(resser)); |
| 254 |
> |
} |
| 255 |
> |
// NOTE: we pass to the graph object the chain (internal pdbase id) not the pdb chain code! |
| 256 |
> |
Graph graph = new Graph (contacts,nodes,sequence,cutoff,ct,accode,chain); |
| 257 |
|
return graph; |
| 258 |
|
} |
| 259 |
|
|
