/**
* Gets the van der Waals radius of the given atom following the values defined by Chothia (1976)
* J.Mol.Biol.105,1-14 NOTE: the vdw values defined by the paper assume no Hydrogens and thus
* "inflates" slightly the heavy atoms to account for Hydrogens. Thus this method cannot be used
* in a structure that contains Hydrogens!
*
* <p>If atom is neither part of a nucleotide nor of a standard aminoacid, the default vdw radius
* for the element is returned. If atom is of unknown type (element) the vdw radius of {@link
* #Element().N} is returned
*
* @param atom
* @return
*/
public static double getRadius(Atom atom) {
if (atom.getElement() == null) {
System.err.println(
"Warning: unrecognised atom "
+ atom.getName()
+ " with serial "
+ atom.getPDBserial()
+ ", assigning the default vdw radius (Nitrogen vdw radius).");
return Element.N.getVDWRadius();
}
Group res = atom.getGroup();
if (res == null) {
System.err.println(
"Warning: unknown parent residue for atom "
+ atom.getName()
+ " with serial "
+ atom.getPDBserial()
+ ", assigning its default vdw radius");
return atom.getElement().getVDWRadius();
}
String type = res.getType();
if (type.equals(GroupType.AMINOACID)) return getRadiusForAmino(((AminoAcid) res), atom);
if (type.equals(GroupType.NUCLEOTIDE)) return getRadiusForNucl((NucleotideImpl) res, atom);
return atom.getElement().getVDWRadius();
}
private void checkRange(Structure s, String range) {
GroupIterator iter = new GroupIterator(s);
Group g1 = iter.next();
Group g2 = null;
while (iter.hasNext()) {
g2 = iter.next();
}
assertNotNull(g1);
assertNotNull(g2);
String chainId = g1.getChain().getChainID();
String rangeTest =
chainId + ":" + g1.getResidueNumber().toString() + "-" + g2.getResidueNumber().toString();
assertEquals("The expected range and the detected range don;t match!", rangeTest, range);
}
private void recordUnidentifiableModifiedResidues(List<ModifiedCompound> modComps) {
Set<StructureGroup> identifiedComps = new HashSet<StructureGroup>();
for (ModifiedCompound mc : modComps) {
identifiedComps.addAll(mc.getGroups(true));
}
// TODO: use the ModifiedAminoAcid after Andreas add that.
for (Group group : residues) {
if (group.getType().equals(GroupType.HETATM)) {
StructureGroup strucGroup = StructureUtil.getStructureGroup(group, true);
if (!identifiedComps.contains(strucGroup)) {
unidentifiableModifiedResidues.add(strucGroup);
}
}
}
}
/**
* Record unidentifiable atom linkages in a chain. Only linkages between two residues or one
* residue and one ligand will be recorded.
*/
private void recordUnidentifiableAtomLinkages(
List<ModifiedCompound> modComps, List<Group> ligands) {
// first put identified linkages in a map for fast query
Set<StructureAtomLinkage> identifiedLinkages = new HashSet<StructureAtomLinkage>();
for (ModifiedCompound mc : modComps) {
identifiedLinkages.addAll(mc.getAtomLinkages());
}
// record
// cross link
int nRes = residues.size();
for (int i = 0; i < nRes - 1; i++) {
Group group1 = residues.get(i);
for (int j = i + 1; j < nRes; j++) {
Group group2 = residues.get(j);
List<Atom[]> linkages =
StructureUtil.findAtomLinkages(group1, group2, true, bondLengthTolerance);
for (Atom[] atoms : linkages) {
StructureAtomLinkage link =
StructureUtil.getStructureAtomLinkage(atoms[0], true, atoms[1], true);
unidentifiableAtomLinkages.add(link);
}
}
}
// attachment
int nLig = ligands.size();
for (int i = 0; i < nRes; i++) {
Group group1 = residues.get(i);
for (int j = 0; j < nLig; j++) {
Group group2 = ligands.get(j);
if (group1.equals(group2)) { // overlap between residues and ligands
continue;
}
List<Atom[]> linkages =
StructureUtil.findAtomLinkages(group1, group2, false, bondLengthTolerance);
for (Atom[] atoms : linkages) {
StructureAtomLinkage link =
StructureUtil.getStructureAtomLinkage(atoms[0], true, atoms[1], false);
unidentifiableAtomLinkages.add(link);
}
}
}
}
private static char getOneLetter(Group g) {
try {
Character c = StructureTools.get1LetterCode(g.getPDBName());
return c;
} catch (Exception e) {
return 'X';
}
}
/**
* Calculates ASA for all atoms and return them as a GroupAsa array (one element per residue in
* structure) containing ASAs per residue and per atom. The sorting of Groups in returned array is
* as specified by {@link org.biojava.bio.structure.ResidueNumber}
*
* @return
*/
public GroupAsa[] getGroupAsas() {
TreeMap<ResidueNumber, GroupAsa> asas = new TreeMap<ResidueNumber, GroupAsa>();
double[] asasPerAtom = calculateAsas();
for (int i = 0; i < atoms.length; i++) {
Group g = atoms[i].getGroup();
if (!asas.containsKey(g.getResidueNumber())) {
GroupAsa groupAsa = new GroupAsa(g);
groupAsa.addAtomAsaU(asasPerAtom[i]);
asas.put(g.getResidueNumber(), groupAsa);
} else {
GroupAsa groupAsa = asas.get(g.getResidueNumber());
groupAsa.addAtomAsaU(asasPerAtom[i]);
}
}
return (GroupAsa[]) asas.values().toArray(new GroupAsa[asas.size()]);
}
public static void main(String[] args) {
try {
FileParsingParameters params = new FileParsingParameters();
params.setParseSecStruc(true);
AtomCache cache = new AtomCache();
cache.setFileParsingParams(params);
Structure s = cache.getStructure("4hhb");
for (Chain c : s.getChains()) {
for (Group g : c.getAtomGroups()) {
if (g instanceof AminoAcid) {
AminoAcid aa = (AminoAcid) g;
Map<String, String> sec = aa.getSecStruc();
System.out.println(
c.getChainID()
+ " "
+ g.getResidueNumber()
+ " "
+ g.getPDBName()
+ " "
+ " "
+ sec);
}
}
}
} catch (Exception e) {
e.printStackTrace();
}
}
public static Structure createArtificalStructure(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
throws Exception {
if (afpChain.getNrEQR() < 1) {
return GuiWrapper.getAlignedStructure(ca1, ca2);
}
Group[] twistedGroups = GuiWrapper.prepareGroupsForDisplay(afpChain, ca1, ca2);
List<Atom> twistedAs = new ArrayList<Atom>();
for (Group g : twistedGroups) {
if (g == null) continue;
if (g.size() < 1) continue;
Atom a = g.getAtom(0);
twistedAs.add(a);
}
Atom[] twistedAtoms = (Atom[]) twistedAs.toArray(new Atom[twistedAs.size()]);
List<Group> hetatms = new ArrayList<Group>();
List<Group> nucs1 = new ArrayList<Group>();
Group g1 = ca1[0].getParent();
Chain c1 = null;
if (g1 != null) {
c1 = g1.getParent();
if (c1 != null) {
hetatms = c1.getAtomGroups("hetatm");
;
nucs1 = c1.getAtomGroups("nucleotide");
}
}
List<Group> hetatms2 = new ArrayList<Group>();
List<Group> nucs2 = new ArrayList<Group>();
Group g2 = ca2[0].getParent();
Chain c2 = null;
if (g2 != null) {
c2 = g2.getParent();
if (c2 != null) {
hetatms2 = c2.getAtomGroups("hetatm");
nucs2 = c2.getAtomGroups("nucleotide");
}
}
Atom[] arr1 = GuiWrapper.getAtomArray(ca1, hetatms, nucs1);
Atom[] arr2 = GuiWrapper.getAtomArray(twistedAtoms, hetatms2, nucs2);
Structure artificial = GuiWrapper.getAlignedStructure(arr1, arr2);
return artificial;
}
/** Get matched atoms for all linkages. */
private List<List<Atom[]>> getMatchedAtomsOfLinkages(
ModificationCondition condition, Map<Component, Set<Group>> mapCompGroups) {
List<ModificationLinkage> linkages = condition.getLinkages();
int nLink = linkages.size();
List<List<Atom[]>> matchedAtomsOfLinkages = new ArrayList<List<Atom[]>>(nLink);
for (int iLink = 0; iLink < nLink; iLink++) {
ModificationLinkage linkage = linkages.get(iLink);
Component comp1 = linkage.getComponent1();
Component comp2 = linkage.getComponent2();
// boolean isAA1 = comp1.;
// boolean isAA2 = comp2.getType()==true;
Set<Group> groups1 = mapCompGroups.get(comp1);
Set<Group> groups2 = mapCompGroups.get(comp2);
List<Atom[]> list = new ArrayList<Atom[]>();
List<String> potentialNamesOfAtomOnGroup1 = linkage.getPDBNameOfPotentialAtomsOnComponent1();
for (String name : potentialNamesOfAtomOnGroup1) {
if (name.equals("*")) {
// wildcard
potentialNamesOfAtomOnGroup1 = null; // search all atoms
break;
}
}
List<String> potentialNamesOfAtomOnGroup2 = linkage.getPDBNameOfPotentialAtomsOnComponent2();
for (String name : potentialNamesOfAtomOnGroup2) {
if (name.equals("*")) {
// wildcard
potentialNamesOfAtomOnGroup2 = null; // search all atoms
break;
}
}
for (Group g1 : groups1) {
for (Group g2 : groups2) {
if (g1.equals(g2)) {
continue;
}
// only for wildcard match of two residues
boolean ignoreNCLinkage =
potentialNamesOfAtomOnGroup1 == null
&& potentialNamesOfAtomOnGroup2 == null
&& residues.contains(g1)
&& residues.contains(g2);
Atom[] atoms =
StructureUtil.findNearestAtomLinkage(
g1,
g2,
potentialNamesOfAtomOnGroup1,
potentialNamesOfAtomOnGroup2,
ignoreNCLinkage,
bondLengthTolerance);
if (atoms != null) {
list.add(atoms);
}
}
}
if (list.isEmpty()) {
// broken linkage
break;
}
matchedAtomsOfLinkages.add(list);
}
return matchedAtomsOfLinkages;
}
/**
* @param modifications a set of {@link ProteinModification}s.
* @param residues
* @param ligands
* @param saveTo save result to
* @return map from component to list of corresponding residues in the chain.
*/
private void addModificationGroups(
final Set<ProteinModification> modifications,
final List<Group> residues,
final List<Group> ligands,
final Map<Component, Set<Group>> saveTo) {
if (residues == null || ligands == null || modifications == null) {
throw new IllegalArgumentException("Null argument(s).");
}
Map<Component, Set<Component>> mapSingleMultiComps = new HashMap<Component, Set<Component>>();
for (ProteinModification mod : modifications) {
ModificationCondition condition = mod.getCondition();
for (Component comp : condition.getComponents()) {
for (String pdbccId : comp.getPdbccIds()) {
Component single =
Component.of(Collections.singleton(pdbccId), comp.isNTerminal(), comp.isCTerminal());
Set<Component> mult = mapSingleMultiComps.get(single);
if (mult == null) {
mult = new HashSet<Component>();
mapSingleMultiComps.put(single, mult);
}
mult.add(comp);
}
}
}
{
// ligands
Set<Component> ligandsWildCard = mapSingleMultiComps.get(Component.of("*"));
for (Group group : ligands) {
String pdbccId = group.getPDBName().trim();
Set<Component> comps = mapSingleMultiComps.get(Component.of(pdbccId));
for (Component comp : unionComponentSet(ligandsWildCard, comps)) {
Set<Group> gs = saveTo.get(comp);
if (gs == null) {
gs = new LinkedHashSet<Group>();
saveTo.put(comp, gs);
}
gs.add(group);
}
}
}
{
// residues
if (residues.isEmpty()) {
return;
}
Set<Component> residuesWildCard = mapSingleMultiComps.get(Component.of("*"));
// for all residues
for (Group group : residues) {
String pdbccId = group.getPDBName().trim();
Set<Component> comps = mapSingleMultiComps.get(Component.of(pdbccId));
for (Component comp : unionComponentSet(residuesWildCard, comps)) {
Set<Group> gs = saveTo.get(comp);
if (gs == null) {
gs = new LinkedHashSet<Group>();
saveTo.put(comp, gs);
}
gs.add(group);
}
}
// for N-terminal
int nRes = residues.size();
int iRes = 0;
Group res;
do {
// for all ligands on N terminal and the first residue
res = residues.get(iRes++);
Set<Component> nTermWildCard = mapSingleMultiComps.get(Component.of("*", true, false));
Set<Component> comps = mapSingleMultiComps.get(Component.of(res.getPDBName(), true, false));
for (Component comp : unionComponentSet(nTermWildCard, comps)) {
Set<Group> gs = saveTo.get(comp);
if (gs == null) {
gs = new LinkedHashSet<Group>();
saveTo.put(comp, gs);
}
gs.add(res);
}
} while (iRes < nRes && ligands.contains(res));
// for C-terminal
iRes = residues.size() - 1;
do {
// for all ligands on C terminal and the last residue
res = residues.get(iRes--);
Set<Component> cTermWildCard = mapSingleMultiComps.get(Component.of("*", false, true));
Set<Component> comps = mapSingleMultiComps.get(Component.of(res.getPDBName(), false, true));
for (Component comp : unionComponentSet(cTermWildCard, comps)) {
Set<Group> gs = saveTo.get(comp);
if (gs == null) {
gs = new LinkedHashSet<Group>();
saveTo.put(comp, gs);
}
gs.add(res);
}
} while (iRes >= 0 && ligands.contains(res));
}
}