/*
public Atom getAtom(byte specialAtomID) {
return (specialAtomID == JmolConstants.ATOMID_NUCLEIC_PHOSPHORUS
? getLeadAtom()
: null);
}
public Point3f getAtomPoint(byte specialAtomID) {
return (specialAtomID == JmolConstants.ATOMID_NUCLEIC_PHOSPHORUS
? getLeadAtomPoint()
: null);
}
*/
boolean isConnectedAfter(Monomer possiblyPreviousMonomer) {
if (possiblyPreviousMonomer == null) return true;
if (!(possiblyPreviousMonomer instanceof PhosphorusMonomer)) return false;
// 1PN8 73:d and 74:d are 7.001 angstroms apart
// but some P atoms are up to 7.4 angstroms apart
float distance = getLeadAtomPoint().distance(possiblyPreviousMonomer.getLeadAtomPoint());
return distance <= MAX_ADJACENT_PHOSPHORUS_DISTANCE;
}
/**
* Updatetes the matrix by linking the parameter monomer to the corresponding cell if it is empty.
* If the matrix is two small it is created again with larger size.
*
* @param monomer
* @return true upon success and false upon failur, that is in case the cell was already occupied.
*/
public boolean update(Monomer monomer) {
protein = monomer.protein;
int x = monomer.getX();
int y = monomer.getY();
int z = monomer.getZ();
boolean modified = false;
if (x < minX) {
minX = x;
modified = true;
} else if (x > maxX) {
maxX = x + 1;
modified = true;
}
if (y < minY) {
minY = y;
modified = true;
} else if (y > maxY) {
maxY = y + 1;
modified = true;
}
if (z < minZ) {
minZ = z;
modified = true;
} else if (z > maxZ) {
maxZ = z + 1;
modified = true;
}
if (modified) {
grid = new Monomer[maxX - minX + 1][maxY - minY + 1][maxZ - minZ + 1];
for (Monomer CurrentMonomer : protein) {
if (CurrentMonomer == monomer) break;
if (!setCell(
CurrentMonomer.getX(), CurrentMonomer.getY(), CurrentMonomer.getZ(), CurrentMonomer))
throw new RuntimeException(
"Overlaping monomers "
+ getCell(CurrentMonomer.getX(), CurrentMonomer.getY(), CurrentMonomer.getZ())
+ " and "
+ CurrentMonomer);
}
}
return (setCell(x, y, z, monomer)); // true if the (x,y,z) cell was empty and false otherwis.
}
/**
* Counts the number of HH contacts between the
*
* @param monomer and its neighbors with higher spetial indeces. The other contacts will be taken
* care of by the other monomers.
* @return the number of contacts
*/
public int countContacts(Monomer monomer) {
Monomer monomer1;
Vector3f pos = monomer.getR();
if (monomer.type != MonomerType.H) return 0;
int count = 0;
int x = monomer.getX();
int y = monomer.getY();
int z = monomer.getZ();
if (!xEdge(x)) {
monomer1 = getCell(x + 1, y, z);
if ((GARun.debug) && (monomer1 != null) && (monomer.protein != monomer1.protein))
throw new RuntimeException(
"Two proteins on the grid\n" + monomer.protein + "\n" + monomer1.protein);
if ((monomer1 != null)
&& (monomer1 != monomer.getPrev())
&& (monomer1 != monomer.getNext())
&& (monomer1.type == MonomerType.H)) count++;
}
if (!yEdge(y)) {
monomer1 = getCell(x, y + 1, z);
if ((GARun.debug) && (monomer1 != null) && (monomer.protein != monomer1.protein))
throw new RuntimeException(
"Two proteins on the grid\n" + monomer.protein + "\n" + monomer1.protein);
if ((monomer1 != null)
&& (monomer1 != monomer.getPrev())
&& (monomer1 != monomer.getNext())
&& (monomer1.type == MonomerType.H)) count++;
}
if (!zEdge(z)) {
monomer1 = getCell(x, y, z + 1);
if ((GARun.debug) && (monomer1 != null) && (monomer.protein != monomer1.protein))
throw new RuntimeException(
"Two proteins on the grid\n" + monomer.protein + "\n" + monomer1.protein);
if ((monomer1 != null)
&& (monomer1 != monomer.getPrev())
&& (monomer1 != monomer.getNext())
&& (monomer1.type == MonomerType.H)) count++;
}
return count;
}
public void reset(Monomer monomer) {
grid[monomer.getX() - minX][monomer.getY() - minY][monomer.getZ() - minZ] = null;
}