Package org.jmol.api

Examples of org.jmol.api.AtomIndexIterator.release()


              ptXyzTemp.set(ptY0);
              ptXyzTemp.add(volumetricVectors[0]);
            }
          }
        }
      iter.release();
      iter = null;
    }
    if (params.thePlane == null) {
      for (int x = 0; x < nPointsX; ++x)
        for (int y = 0; y < nPointsY; ++y)
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          }
          setIteratorForAtom(iter, -1, i, distance);
          iter.addAtoms(bsResult);
        }
    }
    iter.release();
    return bsResult;
  }

  public BitSet getGroupsWithin(int nResidues, BitSet bs) {
    BitSet bsCheck = getIterativeModels(false);
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        continue;
      setIteratorForAtom(iter, -1, models[iModel].firstAtomIndex, -1);
      iter.set(coord, distance);
      iter.addAtoms(bsResult);
    }
    iter.release();
    return bsResult;
  }
  private String getBasePairInfo(BitSet bs) {
    StringBuffer info = new StringBuffer();
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        if (order > 0) {
          if (checkValencesAndBond(atom, atomNear, order, mad, bsBonds))
            nNew++;
        }
      }
      iter.release();
    }
    if (showRebondTimes)//&& Logger.debugging)
      Logger.checkTimer("Time to autoBond");
    return nNew;
  }
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        }
        bsHBondsRasmol.set(addHBond(atom, atomNear, bo, energy));
        nNew++;
      }
    }
    iter.release();
    shapeManager.setShapeSize(JmolConstants.SHAPE_STICKS, Integer.MIN_VALUE, null,
        bsHBondsRasmol);
    if (showRebondTimes && Logger.debugging)
      Logger.checkTimer("Time to hbond");
    return (haveHAtoms ? nNew : -nNew);
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      if (bsIgnore == null || !bsIgnore.get(i)) {
        setAtomI(i);
        getNeighbors(iter);
        calcConvexMap(isSurface);
      }
    iter.release();
    currentPoints = null;
    setDotsConvexMax();
  }
 
  public float getRadius(int atomIndex) {
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        polyhedrons[polyhedronCount++] = p;
      }
      if (haveBitSetVertices)
        break;
    }
    iter.release();
  }

  private Polyhedron constructBondsPolyhedron(int atomIndex) {
    Atom atom = atoms[atomIndex];
    Bond[] bonds = atom.getBonds();
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