/**
* Gets the radius for given nucleotide atom
*
* @param atom
* @return
*/
private static double getRadiusForNucl(NucleotideImpl nuc, Atom atom) {
if (atom.getElement().equals(Element.H)) return Element.H.getVDWRadius();
if (atom.getElement().equals(Element.D)) return Element.D.getVDWRadius();
if (atom.getElement() == Element.C) return NUC_CARBON_VDW;
if (atom.getElement() == Element.N) return NUC_NITROGEN_VDW;
if (atom.getElement() == Element.P) return PHOSPHOROUS_VDW;
if (atom.getElement() == Element.O) return OXIGEN_VDW;
System.err.println(
"Warning: unexpected atom "
+ atom.getName()
+ " for nucleotide "
+ nuc.getPDBName()
+ ", assigning its standard vdw radius");
return atom.getElement().getVDWRadius();
}
/**
* Gets the radius for given amino acid and atom
*
* @param aa
* @param atom
* @return
*/
private static double getRadiusForAmino(AminoAcid amino, Atom atom) {
if (atom.getElement().equals(Element.H)) return Element.H.getVDWRadius();
// some unusual entries (e.g. 1tes) contain Deuterium atoms in standard aminoacids
if (atom.getElement().equals(Element.D)) return Element.D.getVDWRadius();
String atomCode = atom.getName();
char aa = amino.getAminoType();
// here we use the values that Chothia gives in his paper (as NACCESS does)
if (atom.getElement() == Element.O) {
return OXIGEN_VDW;
} else if (atom.getElement() == Element.S) {
return SULFUR_VDW;
} else if (atom.getElement() == Element.N) {
if (atomCode.equals("NZ")) return TETRAHEDRAL_NITROGEN_VDW; // tetrahedral Nitrogen
return TRIGONAL_NITROGEN_VDW; // trigonal Nitrogen
} else if (atom.getElement() == Element.C) { // it must be a carbon
if (atomCode.equals("C")
|| atomCode.equals("CE1")
|| atomCode.equals("CE2")
|| atomCode.equals("CE3")
|| atomCode.equals("CH2")
|| atomCode.equals("CZ")
|| atomCode.equals("CZ2")
|| atomCode.equals("CZ3")) {
return TRIGONAL_CARBON_VDW; // trigonal Carbon
} else if (atomCode.equals("CA")
|| atomCode.equals("CB")
|| atomCode.equals("CE")
|| atomCode.equals("CG1")
|| atomCode.equals("CG2")) {
return TETRAHEDRAL_CARBON_VDW; // tetrahedral Carbon
}
// the rest of the cases (CD, CD1, CD2, CG) depend on amino acid
else {
switch (aa) {
case 'F':
case 'W':
case 'Y':
case 'H':
case 'D':
case 'N':
return TRIGONAL_CARBON_VDW;
case 'P':
case 'K':
case 'R':
case 'M':
case 'I':
case 'L':
return TETRAHEDRAL_CARBON_VDW;
case 'Q':
case 'E':
if (atomCode.equals("CD")) return TRIGONAL_CARBON_VDW;
else if (atomCode.equals("CG")) return TETRAHEDRAL_CARBON_VDW;
default:
System.err.println(
"Warning: unexpected carbon atom "
+ atomCode
+ " for aminoacid "
+ aa
+ ", assigning its standard vdw radius");
return Element.C.getVDWRadius();
}
}
// not any of the expected atoms
} else {
System.err.println(
"Warning: unexpected atom "
+ atomCode
+ " for aminoacid "
+ aa
+ ", assigning its standard vdw radius");
return atom.getElement().getVDWRadius();
}
}