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2102 lines (1850 loc) · 59.6 KB
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/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
* Created on Jan 4, 2006
*
*/
package org.biojava.nbio.structure;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.LinkedHashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import javax.vecmath.Matrix4d;
import javax.vecmath.Point3d;
import org.biojava.nbio.structure.align.util.AtomCache;
import org.biojava.nbio.structure.contact.AtomContactSet;
import org.biojava.nbio.structure.contact.Grid;
import org.biojava.nbio.structure.io.FileParsingParameters;
import org.biojava.nbio.structure.io.PDBFileParser;
import org.biojava.nbio.structure.io.util.FileDownloadUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
* A class that provides some tool methods.
*
* @author Andreas Prlic, Jules Jacobsen
* @since 1.0
*/
public class StructureTools {
private static final Logger logger = LoggerFactory
.getLogger(StructureTools.class);
// Amino Acid backbone
/**
* The atom name of the backbone C-alpha atom. Note that this can be
* ambiguous depending on the context since Calcium atoms use the same name
* in PDB.
*/
public static final String CA_ATOM_NAME = "CA";
/**
* The atom name for the backbone amide nitrogen
*/
public static final String N_ATOM_NAME = "N";
/**
* The atom name for the backbone carbonyl
*/
public static final String C_ATOM_NAME = "C";
/**
* The atom name for the backbone carbonyl oxygen
*/
public static final String O_ATOM_NAME = "O";
/**
* The atom name of the side-chain C-beta atom
*/
public static final String CB_ATOM_NAME = "CB";
// Nucleotide backbone
/**
* The atom name of the backbone C1' in RNA
*/
public static final String C1_ATOM_NAME = "C1'";
/**
* The atom name of the backbone C2' in RNA
*/
public static final String C2_ATOM_NAME = "C2'";
/**
* The atom name of the backbone C3' in RNA
*/
public static final String C3_ATOM_NAME = "C3'";
/**
* The atom name of the backbone C4' in RNA
*/
public static final String C4_ATOM_NAME = "C4'";
/**
* The atom name of the backbone O2' in RNA
*/
public static final String O2_ATOM_NAME = "O2'";
/**
* The atom name of the backbone O3' in RNA
*/
public static final String O3_ATOM_NAME = "O3'";
/**
* The atom name of the backbone O4' in RNA
*/
public static final String O4_ATOM_NAME = "O4'";
/**
* The atom name of the backbone O4' in RNA
*/
public static final String O5_ATOM_NAME = "O5'";
/**
* The atom name of the backbone O4' in RNA
*/
public static final String OP1_ATOM_NAME = "OP1";
/**
* The atom name of the backbone O4' in RNA
*/
public static final String OP2_ATOM_NAME = "OP2";
/**
* The atom name of the backbone phosphate in RNA
*/
public static final String P_ATOM_NAME = "P";
/**
* The atom used as representative for nucleotides, equivalent to
* {@link #CA_ATOM_NAME} for proteins
*/
public static final String NUCLEOTIDE_REPRESENTATIVE = P_ATOM_NAME;
/**
* The character to use for unknown compounds in sequence strings
*/
public static final char UNKNOWN_GROUP_LABEL = 'X';
/**
* Below this ratio of aminoacid/nucleotide residues to the sequence total,
* we use simple majority of aminoacid/nucleotide residues to decide the
* character of the chain (protein/nucleotide)
*/
public static final double RATIO_RESIDUES_TO_TOTAL = 0.95;
/**
* Threshold for plausible binding of a ligand to the selected substructure
*/
public static final double DEFAULT_LIGAND_PROXIMITY_CUTOFF = 5;
// there is a file format change in PDB 3.0 and nucleotides are being
// renamed
private static final Map<String, Character> nucleotides30;
private static final Map<String, Character> nucleotides23;
// amino acid 3 and 1 letter code definitions
private static final Map<String, Character> aminoAcids;
private static final Set<Element> hBondDonorAcceptors;
static {
nucleotides30 = new HashMap<String, Character>();
nucleotides30.put("DA", 'A');
nucleotides30.put("DC", 'C');
nucleotides30.put("DG", 'G');
nucleotides30.put("DT", 'T');
nucleotides30.put("DI", 'I');
nucleotides30.put("A", 'A');
nucleotides30.put("G", 'G');
nucleotides30.put("C", 'C');
nucleotides30.put("U", 'U');
nucleotides30.put("I", 'I');
// the DNA linkers - the +C , +G, +A +T +U and +I have been replaced
// with these:
nucleotides30.put("TAF", UNKNOWN_GROUP_LABEL); // Fluorinated Thymine
nucleotides30.put("TC1", UNKNOWN_GROUP_LABEL); // Furanosyl
nucleotides30.put("TFE", UNKNOWN_GROUP_LABEL); // Fluorinated Thymine
nucleotides30.put("TFO", UNKNOWN_GROUP_LABEL); // Tenofovir (3'
// terminator)
nucleotides30.put("TGP", UNKNOWN_GROUP_LABEL); // Guanine variant
nucleotides30.put("THX", UNKNOWN_GROUP_LABEL); // 5' terminator
nucleotides30.put("TLC", UNKNOWN_GROUP_LABEL); // Thymine with dicyclic
// sugar
nucleotides30.put("TLN", UNKNOWN_GROUP_LABEL); // locked Thymine
nucleotides30.put("LCG", UNKNOWN_GROUP_LABEL); // locked Guanine
nucleotides30.put("TP1", UNKNOWN_GROUP_LABEL); // Thymine peptide
// nucleic acid, with
// added methyl
nucleotides30.put("CP1", UNKNOWN_GROUP_LABEL); // Cytidine peptide
// nucleic acid, with
// added methyl
nucleotides30.put("TPN", UNKNOWN_GROUP_LABEL); // Thymine peptide
// nucleic acid
nucleotides30.put("CPN", UNKNOWN_GROUP_LABEL); // Cytidine peptide
// nucleic acid
nucleotides30.put("GPN", UNKNOWN_GROUP_LABEL); // Guanine peptide
// nucleic acid
nucleotides30.put("APN", UNKNOWN_GROUP_LABEL); // Adenosine peptide
// nucleic acid
nucleotides30.put("TPC", UNKNOWN_GROUP_LABEL); // Thymine variant
// store nucleic acids (C, G, A, T, U, and I), and
// the modified versions of nucleic acids (+C, +G, +A, +T, +U, and +I),
// and
nucleotides23 = new HashMap<String, Character>();
String[] names = { "C", "G", "A", "T", "U", "I", "+C", "+G", "+A",
"+T", "+U", "+I" };
for (String n : names) {
nucleotides23.put(n, n.charAt(n.length() - 1));
}
aminoAcids = new HashMap<String, Character>();
aminoAcids.put("GLY", 'G');
aminoAcids.put("ALA", 'A');
aminoAcids.put("VAL", 'V');
aminoAcids.put("LEU", 'L');
aminoAcids.put("ILE", 'I');
aminoAcids.put("PHE", 'F');
aminoAcids.put("TYR", 'Y');
aminoAcids.put("TRP", 'W');
aminoAcids.put("PRO", 'P');
aminoAcids.put("HIS", 'H');
aminoAcids.put("LYS", 'K');
aminoAcids.put("ARG", 'R');
aminoAcids.put("SER", 'S');
aminoAcids.put("THR", 'T');
aminoAcids.put("GLU", 'E');
aminoAcids.put("GLN", 'Q');
aminoAcids.put("ASP", 'D');
aminoAcids.put("ASN", 'N');
aminoAcids.put("CYS", 'C');
aminoAcids.put("MET", 'M');
// MSE is only found as a molecular replacement for MET
aminoAcids.put("MSE", 'M');
// 'non-standard', genetically encoded
// http://www.chem.qmul.ac.uk/iubmb/newsletter/1999/item3.html
// IUBMB recommended name is 'SEC' but the wwPDB currently use 'CSE'
// likewise 'PYL' (IUBMB) and 'PYH' (PDB)
aminoAcids.put("CSE", 'U');
aminoAcids.put("SEC", 'U');
aminoAcids.put("PYH", 'O');
aminoAcids.put("PYL", 'O');
hBondDonorAcceptors = new HashSet<Element>();
hBondDonorAcceptors.add(Element.N);
hBondDonorAcceptors.add(Element.O);
hBondDonorAcceptors.add(Element.S);
}
/**
* Count how many Atoms are contained within a Structure object.
*
* @param s
* the structure object
* @return the number of Atoms in this Structure
*/
public static final int getNrAtoms(Structure s) {
int nrAtoms = 0;
Iterator<Group> iter = new GroupIterator(s);
while (iter.hasNext()) {
Group g = iter.next();
nrAtoms += g.size();
}
return nrAtoms;
}
/**
* Count how many groups are contained within a structure object.
*
* @param s
* the structure object
* @return the number of groups in the structure
*/
public static final int getNrGroups(Structure s) {
int nrGroups = 0;
List<Chain> chains = s.getChains(0);
for (Chain c : chains) {
nrGroups += c.getAtomLength();
}
return nrGroups;
}
/**
* Returns an array of the requested Atoms from the Structure object.
* Iterates over all groups and checks if the requested atoms are in this
* group, no matter if this is a {@link AminoAcid} or {@link HetatomImpl}
* group. If the group does not contain all requested atoms then no atoms
* are added for that group. For structures with more than one model, only
* model 0 will be used.
*
* @param s
* the structure to get the atoms from
*
* @param atomNames
* contains the atom names to be used.
* @return an Atom[] array
*/
public static final Atom[] getAtomArray(Structure s, String[] atomNames) {
List<Chain> chains = s.getModel(0);
List<Atom> atoms = new ArrayList<Atom>();
extractAtoms(atomNames, chains, atoms);
return atoms.toArray(new Atom[atoms.size()]);
}
/**
* Returns an array of the requested Atoms from the Structure object. In
* contrast to {@link #getAtomArray(Structure, String[])} this method
* iterates over all chains. Iterates over all chains and groups and checks
* if the requested atoms are in this group, no matter if this is a
* {@link AminoAcid} or {@link HetatomImpl} group. If the group does not
* contain all requested atoms then no atoms are added for that group. For
* structures with more than one model, only model 0 will be used.
*
* @param s
* the structure to get the atoms from
*
* @param atomNames
* contains the atom names to be used.
* @return an Atom[] array
*/
public static final Atom[] getAtomArrayAllModels(Structure s,
String[] atomNames) {
List<Atom> atoms = new ArrayList<Atom>();
for (int i = 0; i < s.nrModels(); i++) {
List<Chain> chains = s.getModel(i);
extractAtoms(atomNames, chains, atoms);
}
return atoms.toArray(new Atom[atoms.size()]);
}
/**
* Convert all atoms of the structure (all models) into an Atom array
*
* @param s
* input structure
* @return all atom array
*/
public static final Atom[] getAllAtomArray(Structure s) {
List<Atom> atoms = new ArrayList<Atom>();
AtomIterator iter = new AtomIterator(s);
while (iter.hasNext()) {
Atom a = iter.next();
atoms.add(a);
}
return atoms.toArray(new Atom[atoms.size()]);
}
/**
* Convert all atoms of the structure (specified model) into an Atom array
*
* @param s
* input structure
* @return all atom array
*/
public static final Atom[] getAllAtomArray(Structure s, int model) {
List<Atom> atoms = new ArrayList<Atom>();
AtomIterator iter = new AtomIterator(s,model);
while (iter.hasNext()) {
Atom a = iter.next();
atoms.add(a);
}
return atoms.toArray(new Atom[atoms.size()]);
}
/**
* Returns and array of all atoms of the chain, including
* Hydrogens (if present) and all HETATOMs. Waters are not included.
*
* @param c
* input chain
* @return all atom array
*/
public static final Atom[] getAllAtomArray(Chain c) {
List<Atom> atoms = new ArrayList<Atom>();
for (Group g : c.getAtomGroups()) {
if (g.isWater())
continue;
for (Atom a : g.getAtoms()) {
atoms.add(a);
}
}
return atoms.toArray(new Atom[atoms.size()]);
}
/**
* List of groups from the structure not included in ca (e.g. ligands).
*
* Unaligned groups are searched from all chains referenced in ca, as well
* as any chains in the first model of the structure from ca[0], if any.
*
* @param ca an array of atoms
* @return
*/
public static List<Group> getUnalignedGroups(Atom[] ca) {
Set<Chain> chains = new HashSet<Chain>();
Set<Group> caGroups = new HashSet<Group>();
// Create list of all chains in this structure
Structure s = null;
if (ca.length > 0) {
Group g = ca[0].getGroup();
if (g != null) {
Chain c = g.getChain();
if (c != null) {
s = c.getStructure();
}
}
}
if (s != null) {
// Add all chains from the structure
for (Chain c : s.getChains(0)) {
chains.add(c);
}
}
// Add groups and chains from ca
for (Atom a : ca) {
Group g = a.getGroup();
if (g != null) {
caGroups.add(g);
Chain c = g.getChain();
if (c != null) {
chains.add(c);
}
}
}
// Iterate through all chains, finding groups not in ca
List<Group> unadded = new ArrayList<Group>();
for (Chain c : chains) {
for (Group g : c.getAtomGroups()) {
if (!caGroups.contains(g)) {
unadded.add(g);
}
}
}
return unadded;
}
/**
* Finds all ligand groups from the target which fall within the cutoff distance
* of some atom from the query set.
*
* @param target Set of groups including the ligands
* @param query Atom selection
* @param cutoff Distance from query atoms to consider, in angstroms
* @return All groups from the target with at least one atom within cutoff of a query atom
* @see StructureTools#DEFAULT_LIGAND_PROXIMITY_CUTOFF
*/
public static List<Group> getLigandsByProximity(Collection<Group> target, Atom[] query, double cutoff) {
// Geometric hashing of the reduced structure
Grid grid = new Grid(cutoff);
grid.addAtoms(query);
List<Group> ligands = new ArrayList<>();
for(Group g :target ) {
// don't worry about waters
if(g.isWater()) {
continue;
}
if(g.isPolymeric() ) {
// Polymers aren't ligands
continue;
}
// It is a ligand!
// Check that it's within cutoff of something in reduced
List<Atom> groupAtoms = g.getAtoms();
if( ! grid.hasAnyContact(Calc.atomsToPoints(groupAtoms))) {
continue;
}
ligands.add(g);
}
return ligands;
}
/**
* Adds a particular group to a structure. A new chain will be created if necessary.
*
* <p>When adding multiple groups, pass the return value of one call as the
* chainGuess parameter of the next call for efficiency.
* <pre>
* Chain guess = null;
* for(Group g : groups) {
* guess = addGroupToStructure(s, g, guess );
* }
* </pre>
* @param s structure to receive the group
* @param g group to add
* @param chainGuess (optional) If not null, should be a chain from s. Used
* to improve performance when adding many groups from the same chain
* @param clone Indicates whether the input group should be cloned before
* being added to the new chain
* @return the chain g was added to
*/
public static Chain addGroupToStructure(Structure s, Group g, int model, Chain chainGuess, boolean clone ) {
synchronized(s) {
// Find or create the chain
String chainId = g.getChainId();
assert !chainId.isEmpty();
Chain chain;
if(chainGuess != null && chainGuess.getId() == chainId) {
// previously guessed chain
chain = chainGuess;
} else {
// Try to guess
chain = s.getChain(chainId, model);
if(chain == null) {
// no chain found
chain = new ChainImpl();
chain.setId(chainId);
Chain oldChain = g.getChain();
chain.setName(oldChain.getName());
EntityInfo oldEntityInfo = oldChain.getEntityInfo();
EntityInfo newEntityInfo = s.getEntityById(oldEntityInfo.getMolId());
if( newEntityInfo == null ) {
newEntityInfo = new EntityInfo(oldEntityInfo);
s.addEntityInfo(newEntityInfo);
}
newEntityInfo.addChain(chain);
chain.setEntityInfo(newEntityInfo);
// TODO Do the seqres need to be cloned too? -SB 2016-10-7
chain.setSeqResGroups(oldChain.getSeqResGroups());
chain.setSeqMisMatches(oldChain.getSeqMisMatches());
s.addChain(chain,model);
}
}
// Add cloned group
if(clone) {
g = (Group)g.clone();
}
chain.addGroup(g);
return chain;
}
}
/**
* Add a list of groups to a new structure. Chains will be automatically
* created in the new structure as needed.
* @param s structure to receive the group
* @param g group to add
* @param clone Indicates whether the input groups should be cloned before
* being added to the new chain
*/
public static void addGroupsToStructure(Structure s, Collection<Group> groups, int model, boolean clone) {
Chain chainGuess = null;
for(Group g : groups) {
chainGuess = addGroupToStructure(s, g, model, chainGuess, clone);
}
}
/**
* Expand a set of atoms into all groups from the same structure.
*
* If the structure is set, only the first atom is used (assuming all
* atoms come from the same original structure).
* If the atoms aren't linked to a structure (for instance, for cloned atoms),
* searches all chains of all atoms for groups.
* @param atoms Sample of atoms
* @return All groups from all chains accessible from the input atoms
*/
public static Set<Group> getAllGroupsFromSubset(Atom[] atoms) {
return getAllGroupsFromSubset(atoms,null);
}
/**
* Expand a set of atoms into all groups from the same structure.
*
* If the structure is set, only the first atom is used (assuming all
* atoms come from the same original structure).
* If the atoms aren't linked to a structure (for instance, for cloned atoms),
* searches all chains of all atoms for groups.
* @param atoms Sample of atoms
* @param types Type of groups to return (useful for getting only ligands, for instance).
* Null gets all groups.
* @return All groups from all chains accessible from the input atoms
*/
public static Set<Group> getAllGroupsFromSubset(Atom[] atoms,GroupType types) {
// Get the full structure
Structure s = null;
if (atoms.length > 0) {
Group g = atoms[0].getGroup();
if (g != null) {
Chain c = g.getChain();
if (c != null) {
s = c.getStructure();
}
}
}
// Collect all groups from the structure
Set<Chain> allChains = new HashSet<>();
if( s != null ) {
allChains.addAll(s.getChains());
}
// In case the structure wasn't set, need to use ca chains too
for(Atom a : atoms) {
Group g = a.getGroup();
if(g != null) {
Chain c = g.getChain();
if( c != null ) {
allChains.add(c);
}
}
}
if(allChains.isEmpty() ) {
return Collections.emptySet();
}
// Extract all ligand groups
Set<Group> full = new HashSet<>();
for(Chain c : allChains) {
if(types == null) {
full.addAll(c.getAtomGroups());
} else {
full.addAll(c.getAtomGroups(types));
}
}
return full;
}
/**
* Returns and array of all non-Hydrogen atoms in the given Structure,
* optionally including HET atoms or not. Waters are not included.
*
* @param s
* @param hetAtoms
* if true HET atoms are included in array, if false they are not
* @return
*/
public static final Atom[] getAllNonHAtomArray(Structure s, boolean hetAtoms) {
AtomIterator iter = new AtomIterator(s);
return getAllNonHAtomArray(s, hetAtoms, iter);
}
/**
* Returns and array of all non-Hydrogen atoms in the given Structure,
* optionally including HET atoms or not. Waters are not included.
*
* @param s
* @param hetAtoms
* if true HET atoms are included in array, if false they are not
* @param modelNr Model number to draw atoms from
* @return
*/
public static final Atom[] getAllNonHAtomArray(Structure s, boolean hetAtoms, int modelNr) {
AtomIterator iter = new AtomIterator(s,modelNr);
return getAllNonHAtomArray(s, hetAtoms, iter);
}
private static final Atom[] getAllNonHAtomArray(Structure s, boolean hetAtoms, AtomIterator iter) {
List<Atom> atoms = new ArrayList<Atom>();
while (iter.hasNext()) {
Atom a = iter.next();
if (a.getElement() == Element.H)
continue;
Group g = a.getGroup();
if (g.isWater())
continue;
if (!hetAtoms && g.getType().equals(GroupType.HETATM))
continue;
atoms.add(a);
}
return atoms.toArray(new Atom[atoms.size()]);
}
/**
* Returns and array of all non-Hydrogen atoms in the given Chain,
* optionally including HET atoms or not Waters are not included.
*
* @param c
* @param hetAtoms
* if true HET atoms are included in array, if false they are not
* @return
*/
public static final Atom[] getAllNonHAtomArray(Chain c, boolean hetAtoms) {
List<Atom> atoms = new ArrayList<Atom>();
for (Group g : c.getAtomGroups()) {
if (g.isWater())
continue;
for (Atom a : g.getAtoms()) {
if (a.getElement() == Element.H)
continue;
if (!hetAtoms && g.getType().equals(GroupType.HETATM))
continue;
atoms.add(a);
}
}
return atoms.toArray(new Atom[atoms.size()]);
}
/**
* Returns and array of all non-Hydrogen atoms coordinates in the given Chain,
* optionally including HET atoms or not Waters are not included.
*
* @param c
* @param hetAtoms
* if true HET atoms are included in array, if false they are not
* @return
*/
public static final Point3d[] getAllNonHCoordsArray(Chain c, boolean hetAtoms) {
List<Point3d> atoms = new ArrayList<Point3d>();
for (Group g : c.getAtomGroups()) {
if (g.isWater())
continue;
for (Atom a : g.getAtoms()) {
if (a.getElement() == Element.H)
continue;
if (!hetAtoms && g.getType().equals(GroupType.HETATM))
continue;
atoms.add(a.getCoordsAsPoint3d());
}
}
return atoms.toArray(new Point3d[atoms.size()]);
}
/**
* Adds to the given atoms list, all atoms of groups that contained all
* requested atomNames, i.e. if a group does not contain all of the
* requested atom names, its atoms won't be added.
*
* @param atomNames
* @param chains
* @param atoms
*/
private static void extractAtoms(String[] atomNames, List<Chain> chains,
List<Atom> atoms) {
for (Chain c : chains) {
for (Group g : c.getAtomGroups()) {
// a temp container for the atoms of this group
List<Atom> thisGroupAtoms = new ArrayList<Atom>();
// flag to check if this group contains all the requested atoms.
boolean thisGroupAllAtoms = true;
for (String atomName : atomNames) {
Atom a = g.getAtom(atomName);
if (a == null) {
// this group does not have a required atom, skip it...
thisGroupAllAtoms = false;
break;
}
thisGroupAtoms.add(a);
}
if (thisGroupAllAtoms) {
// add the atoms of this group to the array.
for (Atom a : thisGroupAtoms) {
atoms.add(a);
}
}
}
}
}
/**
* Returns an array of the requested Atoms from the Chain object. Iterates
* over all groups and checks if the requested atoms are in this group, no
* matter if this is a AminoAcid or Hetatom group. If the group does not
* contain all requested atoms then no atoms are added for that group.
*
* @param c
* the Chain to get the atoms from
*
* @param atomNames
* contains the atom names to be used.
* @return an Atom[] array
*/
public static final Atom[] getAtomArray(Chain c, String[] atomNames) {
List<Atom> atoms = new ArrayList<Atom>();
for (Group g : c.getAtomGroups()) {
// a temp container for the atoms of this group
List<Atom> thisGroupAtoms = new ArrayList<Atom>();
// flag to check if this group contains all the requested atoms.
boolean thisGroupAllAtoms = true;
for (String atomName : atomNames) {
Atom a = g.getAtom(atomName);
if (a == null) {
logger.debug("Group " + g.getResidueNumber() + " ("
+ g.getPDBName()
+ ") does not have the required atom '" + atomName
+ "'");
// this group does not have a required atom, skip it...
thisGroupAllAtoms = false;
break;
}
thisGroupAtoms.add(a);
}
if (thisGroupAllAtoms) {
// add the atoms of this group to the array.
for (Atom a : thisGroupAtoms) {
atoms.add(a);
}
}
}
return atoms.toArray(new Atom[atoms.size()]);
}
/**
* Returns an Atom array of the C-alpha atoms. Any atom that is a carbon and
* has CA name will be returned.
*
* @param c
* the structure object
* @return an Atom[] array
* @see #getRepresentativeAtomArray(Chain)
*/
public static final Atom[] getAtomCAArray(Chain c) {
List<Atom> atoms = new ArrayList<Atom>();
for (Group g : c.getAtomGroups()) {
if (g.hasAtom(CA_ATOM_NAME)
&& g.getAtom(CA_ATOM_NAME).getElement() == Element.C) {
atoms.add(g.getAtom(CA_ATOM_NAME));
}
}
return atoms.toArray(new Atom[atoms.size()]);
}
/**
* Gets a representative atom for each group that is part of the chain
* backbone. Note that modified aminoacids won't be returned as part of the
* backbone if the {@link org.biojava.nbio.structure.io.mmcif.ReducedChemCompProvider} was used to load the
* structure.
*
* For amino acids, the representative is a CA carbon. For nucleotides, the
* representative is the {@value #NUCLEOTIDE_REPRESENTATIVE}. Other group
* types will be ignored.
*
* @param c
* @return representative Atoms of the chain backbone
* @since Biojava 4.1.0
*/
public static final Atom[] getRepresentativeAtomArray(Chain c) {
List<Atom> atoms = new ArrayList<Atom>();
for (Group g : c.getAtomGroups()) {
switch (g.getType()) {
case AMINOACID:
if (g.hasAtom(CA_ATOM_NAME)
&& g.getAtom(CA_ATOM_NAME).getElement() == Element.C) {
atoms.add(g.getAtom(CA_ATOM_NAME));
}
break;
case NUCLEOTIDE:
if (g.hasAtom(NUCLEOTIDE_REPRESENTATIVE)) {
atoms.add(g.getAtom(NUCLEOTIDE_REPRESENTATIVE));
}
break;
default:
// don't add
}
}
return atoms.toArray(new Atom[atoms.size()]);
}
/**
* Provides an equivalent copy of Atoms in a new array. Clones everything,
* starting with parent groups and chains. The chain will only contain
* groups that are part of the input array.
*
* @param ca
* array of representative atoms, e.g. CA atoms
* @return Atom array
* @deprecated Use the better-named {@link #cloneAtomArray(Atom[])} instead
*/
@Deprecated
public static final Atom[] cloneCAArray(Atom[] ca) {
return cloneAtomArray(ca);
}
/**
* Provides an equivalent copy of Atoms in a new array. Clones everything,
* starting with parent groups and chains. The chain will only contain
* groups that are part of the input array.
*
* @param ca
* array of representative atoms, e.g. CA atoms
* @return Atom array
* @since Biojava 4.1.0
*/
public static final Atom[] cloneAtomArray(Atom[] ca) {
Atom[] newCA = new Atom[ca.length];
List<Chain> model = new ArrayList<Chain>();
int apos = -1;
for (Atom a : ca) {
apos++;
Group parentG = a.getGroup();
Chain parentC = parentG.getChain();
Chain newChain = null;
for (Chain c : model) {
if (c.getName().equals(parentC.getName())) {
newChain = c;
break;
}
}
if (newChain == null) {
newChain = new ChainImpl();
newChain.setId(parentC.getId());
newChain.setName(parentC.getName());
model.add(newChain);
}
Group parentN = (Group) parentG.clone();
newCA[apos] = parentN.getAtom(a.getName());
try {
// if the group doesn't exist yet, this produces a StructureException
newChain.getGroupByPDB(parentN.getResidueNumber());
} catch (StructureException e) {
// the group doesn't exist yet in the newChain, let's add it
newChain.addGroup(parentN);
}
}
return newCA;
}
/**
* Clone a set of representative Atoms, but returns the parent groups
*
* @param ca
* Atom array
* @return Group array
*/
public static Group[] cloneGroups(Atom[] ca) {
Group[] newGroup = new Group[ca.length];
List<Chain> model = new ArrayList<Chain>();
int apos = -1;
for (Atom a : ca) {
apos++;
Group parentG = a.getGroup();
Chain parentC = parentG.getChain();
Chain newChain = null;
for (Chain c : model) {
if (c.getName().equals(parentC.getName())) {