StructureTools (biojava 5.0.0 API)

java.lang.Object
- org.biojava.nbio.structure.StructureTools

```
public class StructureTools
extends Object
```
A class that provides some tool methods.

Since:

1.0

Author:

Andreas Prlic, Jules Jacobsen

Field Summary

Fields
Modifier and Type	Field and Description
`static String`	`C_ATOM_NAME` The atom name for the backbone carbonyl
`static String`	`C1_ATOM_NAME` The atom name of the backbone C1' in RNA
`static String`	`C2_ATOM_NAME` The atom name of the backbone C2' in RNA
`static String`	`C3_ATOM_NAME` The atom name of the backbone C3' in RNA
`static String`	`C4_ATOM_NAME` The atom name of the backbone C4' in RNA
`static String`	`CA_ATOM_NAME` The atom name of the backbone C-alpha atom.
`static String`	`CB_ATOM_NAME` The atom name of the side-chain C-beta atom
`static double`	`DEFAULT_LIGAND_PROXIMITY_CUTOFF` Threshold for plausible binding of a ligand to the selected substructure
`static String`	`N_ATOM_NAME` The atom name for the backbone amide nitrogen
`static String`	`NUCLEOTIDE_REPRESENTATIVE` The atom used as representative for nucleotides, equivalent to `CA_ATOM_NAME` for proteins
`static String`	`O_ATOM_NAME` The atom name for the backbone carbonyl oxygen
`static String`	`O2_ATOM_NAME` The atom name of the backbone O2' in RNA
`static String`	`O3_ATOM_NAME` The atom name of the backbone O3' in RNA
`static String`	`O4_ATOM_NAME` The atom name of the backbone O4' in RNA
`static String`	`O5_ATOM_NAME` The atom name of the backbone O4' in RNA
`static String`	`OP1_ATOM_NAME` The atom name of the backbone O4' in RNA
`static String`	`OP2_ATOM_NAME` The atom name of the backbone O4' in RNA
`static String`	`P_ATOM_NAME` The atom name of the backbone phosphate in RNA
`static double`	`RATIO_RESIDUES_TO_TOTAL` 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)
`static char`	`UNKNOWN_GROUP_LABEL` The character to use for unknown compounds in sequence strings

Constructor Summary

Constructors
Constructor and Description

StructureTools()

Constructors
Constructor and Description
`StructureTools()`

Method Summary

All Methods Static Methods Concrete Methods Deprecated Methods
Modifier and Type	Method and Description
`static void`	`addGroupsToStructure(Structure s, Collection<Group> groups, int model, boolean clone)` Add a list of groups to a new structure.
`static Chain`	`addGroupToStructure(Structure s, Group g, int model, Chain chainGuess, boolean clone)` Adds a particular group to a structure.
`static void`	`cleanUpAltLocs(Structure structure)` Cleans up the structure's alternate location groups.
`static Atom[]`	`cloneAtomArray(Atom[] ca)` Provides an equivalent copy of Atoms in a new array.
`static Group[]`	`cloneGroups(Atom[] ca)` Clone a set of representative Atoms, but returns the parent groups
`static String`	`convertAtomsToSeq(Atom[] atoms)`
`static Atom[]`	`duplicateCA2(Atom[] ca2)` Utility method for working with circular permutations.
`static List<Group>`	`filterLigands(List<Group> allGroups)` Removes all polymeric and solvent groups from a list of groups
`static Character`	`get1LetterCode(String groupCode3)` Convert a three letter amino acid or nucleotide code into a single character code.
`static Character`	`get1LetterCodeAmino(String groupCode3)` Convert three character amino acid codes into single character e.g.
`static Atom[]`	`getAllAtomArray(Chain c)` Returns and array of all atoms of the chain, including Hydrogens (if present) and all HETATOMs.
`static Atom[]`	`getAllAtomArray(Structure s)` Convert all atoms of the structure (all models) into an Atom array
`static Atom[]`	`getAllAtomArray(Structure s, int model)` Convert all atoms of the structure (specified model) into an Atom array
`static Set<Group>`	`getAllGroupsFromSubset(Atom[] atoms)` Expand a set of atoms into all groups from the same structure.
`static Set<Group>`	`getAllGroupsFromSubset(Atom[] atoms, GroupType types)` Expand a set of atoms into all groups from the same structure.
`static Atom[]`	`getAllNonHAtomArray(Chain c, boolean hetAtoms)` Returns and array of all non-Hydrogen atoms in the given Chain, optionally including HET atoms or not Waters are not included.
`static Atom[]`	`getAllNonHAtomArray(Structure s, boolean hetAtoms)` Returns and array of all non-Hydrogen atoms in the given Structure, optionally including HET atoms or not.
`static Atom[]`	`getAllNonHAtomArray(Structure s, boolean hetAtoms, int modelNr)` Returns and array of all non-Hydrogen atoms in the given Structure, optionally including HET atoms or not.
`static javax.vecmath.Point3d[]`	`getAllNonHCoordsArray(Chain c, boolean hetAtoms)` Returns and array of all non-Hydrogen atoms coordinates in the given Chain, optionally including HET atoms or not Waters are not included.
`static Atom[]`	`getAtomArray(Chain c, String[] atomNames)` Returns an array of the requested Atoms from the Chain object.
`static Atom[]`	`getAtomArray(Structure s, String[] atomNames)` Returns an array of the requested Atoms from the Structure object.
`static Atom[]`	`getAtomArrayAllModels(Structure s, String[] atomNames)` Returns an array of the requested Atoms from the Structure object.
`static Atom[]`	`getAtomCAArray(Chain c)` Returns an Atom array of the C-alpha atoms.
`static Atom[]`	`getAtomCAArray(Structure s)` Return an Atom array of the C-alpha atoms.
`static AtomContactSet`	`getAtomsCAInContact(Chain chain, double cutoff)` Returns the set of intra-chain contacts for the given chain for C-alpha atoms (including non-standard aminoacids appearing as HETATM groups), i.e. the contact map.
`static AtomContactSet`	`getAtomsInContact(Chain chain1, Chain chain2, double cutoff, boolean hetAtoms)` Returns the set of inter-chain contacts between the two given chains for all non-H atoms.
`static AtomContactSet`	`getAtomsInContact(Chain chain1, Chain chain2, String[] atomNames, double cutoff, boolean hetAtoms)` Returns the set of inter-chain contacts between the two given chains for the given atom names.
`static AtomContactSet`	`getAtomsInContact(Chain chain, double cutoff)` Returns the set of intra-chain contacts for the given chain for all non-H atoms of non-hetatoms, i.e. the contact map.
`static AtomContactSet`	`getAtomsInContact(Chain chain, String[] atomNames, double cutoff)` Returns the set of intra-chain contacts for the given chain for given atom names, i.e. the contact map.
`static Atom[]`	`getBackboneAtomArray(Structure s)` Return an Atom array of the main chain atoms: CA, C, N, O Any group that contains those atoms will be included, be it a standard aminoacid or not
`static Group`	`getGroupByPDBResidueNumber(Structure struc, ResidueNumber pdbResNum)` Get a group represented by a ResidueNumber.
`static Map<Group,Double>`	`getGroupDistancesWithinShell(Structure structure, Atom centroid, Set<ResidueNumber> excludeResidues, double radius, boolean includeWater, boolean useAverageDistance)` Finds Groups in `structure` that contain at least one Atom that is within `radius` Angstroms of `centroid`.
`static Set<Group>`	`getGroupsWithinShell(Structure structure, Atom atom, Set<ResidueNumber> excludeResidues, double distance, boolean includeWater)`
`static Set<Group>`	`getGroupsWithinShell(Structure structure, Group group, double distance, boolean includeWater)` Returns a Set of Groups in a structure within the distance specified of a given group.
`static List<Group>`	`getLigandsByProximity(Collection<Group> target, Atom[] query, double cutoff)` Finds all ligand groups from the target which fall within the cutoff distance of some atom from the query set.
`static int`	`getNrAtoms(Structure s)` Count how many Atoms are contained within a Structure object.
`static int`	`getNrGroups(Structure s)` Count how many groups are contained within a structure object.
`static GroupType`	`getPredominantGroupType(Chain c)` Deprecated. use `Chain.getPredominantGroupType()` instead.
`static Structure`	`getReducedStructure(Structure s, String chainId)` Deprecated. Use `StructureIdentifier.reduce(Structure)` instead (v. 4.2.0)
`static Atom[]`	`getRepresentativeAtomArray(Chain c)` Gets a representative atom for each group that is part of the chain backbone.
`static Atom[]`	`getRepresentativeAtomArray(Structure s)` Gets a representative atom for each group that is part of the chain backbone.
`static AtomContactSet`	`getRepresentativeAtomsInContact(Chain chain, double cutoff)` Returns the set of intra-chain contacts for the given chain for C-alpha or C3' atoms (including non-standard aminoacids appearing as HETATM groups), i.e. the contact map.
`static Structure`	`getStructure(String name)` Short version of `getStructure(String, PDBFileParser, AtomCache)` which creates new parsers when needed
`static Structure`	`getStructure(String name, PDBFileParser parser, AtomCache cache)` Flexibly get a structure from an input String.
`static List<Group>`	`getUnalignedGroups(Atom[] ca)` List of groups from the structure not included in ca (e.g. ligands).
`static boolean`	`hasDeuteratedEquiv(Atom atom, Group currentGroup)` Check to see if a Hydorgen has a Deuterated brother in the group.
`static boolean`	`hasNonDeuteratedEquiv(Atom atom, Group currentGroup)` Check to see if an Deuterated atom has a non deuterated brother in the group.
`static boolean`	`isChainPureNonPolymer(Chain c)` Deprecated. use `Chain.isPureNonPolymer()` instead.
`static boolean`	`isChainWaterOnly(Chain c)` Deprecated. use `Chain.isWaterOnly()` instead.
`static boolean`	`isNucleicAcid(Chain c)` Deprecated. use `Chain.isNucleicAcid()` instead.
`static boolean`	`isNucleotide(String groupCode3)` Test if the three-letter code of an ATOM entry corresponds to a nucleotide or to an aminoacid.
`static boolean`	`isProtein(Chain c)` Deprecated. use `Chain.isProtein()` instead.
`static Structure`	`removeModels(Structure s)` Remove all models from a Structure and keep only the first

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - CA_ATOM_NAME
```
public static final String CA_ATOM_NAME
```
    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.
    
    See Also:
    
    Constant Field Values
  - N_ATOM_NAME
```
public static final String N_ATOM_NAME
```
    The atom name for the backbone amide nitrogen
    
    See Also:
    
    Constant Field Values
  - C_ATOM_NAME
```
public static final String C_ATOM_NAME
```
    The atom name for the backbone carbonyl
    
    See Also:
    
    Constant Field Values
  - O_ATOM_NAME
```
public static final String O_ATOM_NAME
```
    The atom name for the backbone carbonyl oxygen
    
    See Also:
    
    Constant Field Values
  - CB_ATOM_NAME
```
public static final String CB_ATOM_NAME
```
    The atom name of the side-chain C-beta atom
    
    See Also:
    
    Constant Field Values
  - C1_ATOM_NAME
```
public static final String C1_ATOM_NAME
```
    The atom name of the backbone C1' in RNA
    
    See Also:
    
    Constant Field Values
  - C2_ATOM_NAME
```
public static final String C2_ATOM_NAME
```
    The atom name of the backbone C2' in RNA
    
    See Also:
    
    Constant Field Values
  - C3_ATOM_NAME
```
public static final String C3_ATOM_NAME
```
    The atom name of the backbone C3' in RNA
    
    See Also:
    
    Constant Field Values
  - C4_ATOM_NAME
```
public static final String C4_ATOM_NAME
```
    The atom name of the backbone C4' in RNA
    
    See Also:
    
    Constant Field Values
  - O2_ATOM_NAME
```
public static final String O2_ATOM_NAME
```
    The atom name of the backbone O2' in RNA
    
    See Also:
    
    Constant Field Values
  - O3_ATOM_NAME
```
public static final String O3_ATOM_NAME
```
    The atom name of the backbone O3' in RNA
    
    See Also:
    
    Constant Field Values
  - O4_ATOM_NAME
```
public static final String O4_ATOM_NAME
```
    The atom name of the backbone O4' in RNA
    
    See Also:
    
    Constant Field Values
  - O5_ATOM_NAME
```
public static final String O5_ATOM_NAME
```
    The atom name of the backbone O4' in RNA
    
    See Also:
    
    Constant Field Values
  - OP1_ATOM_NAME
```
public static final String OP1_ATOM_NAME
```
    The atom name of the backbone O4' in RNA
    
    See Also:
    
    Constant Field Values
  - OP2_ATOM_NAME
```
public static final String OP2_ATOM_NAME
```
    The atom name of the backbone O4' in RNA
    
    See Also:
    
    Constant Field Values
  - P_ATOM_NAME
```
public static final String P_ATOM_NAME
```
    The atom name of the backbone phosphate in RNA
    
    See Also:
    
    Constant Field Values
  - NUCLEOTIDE_REPRESENTATIVE
```
public static final String NUCLEOTIDE_REPRESENTATIVE
```
    The atom used as representative for nucleotides, equivalent to CA_ATOM_NAME for proteins
    
    See Also:
    
    Constant Field Values
  - UNKNOWN_GROUP_LABEL
```
public static final char UNKNOWN_GROUP_LABEL
```
    The character to use for unknown compounds in sequence strings
    
    See Also:
    
    Constant Field Values
  - RATIO_RESIDUES_TO_TOTAL
```
public static final double RATIO_RESIDUES_TO_TOTAL
```
    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)
    
    See Also:
    
    Constant Field Values
  - DEFAULT_LIGAND_PROXIMITY_CUTOFF
```
public static final double DEFAULT_LIGAND_PROXIMITY_CUTOFF
```
    Threshold for plausible binding of a ligand to the selected substructure
    
    See Also:
    
    Constant Field Values
- Constructor Detail
  - StructureTools
```
public StructureTools()
```
- Method Detail
  - getNrAtoms
```
public static final int getNrAtoms(Structure s)
```
    Count how many Atoms are contained within a Structure object.
    
    Parameters:
    
    s - the structure object
    
    Returns:
    
    the number of Atoms in this Structure
  - getNrGroups
```
public static final int getNrGroups(Structure s)
```
    Count how many groups are contained within a structure object.
    
    Parameters:
    
    s - the structure object
    
    Returns:
    
    the number of groups in the structure
  - getAtomArray
```
public static final Atom[] getAtomArray(Structure s,
                                        String[] atomNames)
```
    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 AminoAcid or 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.
    
    Parameters:
    
    s - the structure to get the atoms from
    
    atomNames - contains the atom names to be used.
    
    Returns:
    
    an Atom[] array
  - getAtomArrayAllModels
```
public static final Atom[] getAtomArrayAllModels(Structure s,
                                                 String[] atomNames)
```
    Returns an array of the requested Atoms from the Structure object. In contrast to 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 AminoAcid or 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.
    
    Parameters:
    
    s - the structure to get the atoms from
    
    atomNames - contains the atom names to be used.
    
    Returns:
    
    an Atom[] array
  - getAllAtomArray
```
public static final Atom[] getAllAtomArray(Structure s)
```
    Convert all atoms of the structure (all models) into an Atom array
    
    Parameters:
    
    s - input structure
    
    Returns:
    
    all atom array
  - getAllAtomArray
```
public static final Atom[] getAllAtomArray(Structure s,
                                           int model)
```
    Convert all atoms of the structure (specified model) into an Atom array
    
    Parameters:
    
    s - input structure
    
    Returns:
    
    all atom array
  - getAllAtomArray
```
public static final Atom[] getAllAtomArray(Chain c)
```
    Returns and array of all atoms of the chain, including Hydrogens (if present) and all HETATOMs. Waters are not included.
    
    Parameters:
    
    c - input chain
    
    Returns:
    
    all atom array
  - getUnalignedGroups
```
public static List<Group> getUnalignedGroups(Atom[] ca)
```
    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.
    
    Parameters:
    
    ca - an array of atoms
    
    Returns:
  - getLigandsByProximity
```
public static List<Group> getLigandsByProximity(Collection<Group> target,
                                                Atom[] query,
                                                double cutoff)
```
    Finds all ligand groups from the target which fall within the cutoff distance of some atom from the query set.
    
    Parameters:
    
    target - Set of groups including the ligands
    
    query - Atom selection
    
    cutoff - Distance from query atoms to consider, in angstroms
    
    Returns:
    
    All groups from the target with at least one atom within cutoff of a query atom
    
    See Also:
    
    DEFAULT_LIGAND_PROXIMITY_CUTOFF
  - addGroupToStructure
```
public static Chain addGroupToStructure(Structure s,
                                        Group g,
                                        int model,
                                        Chain chainGuess,
                                        boolean clone)
```
    Adds a particular group to a structure. A new chain will be created if necessary.
    When adding multiple groups, pass the return value of one call as the chainGuess parameter of the next call for efficiency.
```
 Chain guess = null;
 for(Group g : groups) {
     guess = addGroupToStructure(s, g, guess );
 }
 
```
    Parameters:
    
    s - structure to receive the group
    
    g - group to add
    
    chainGuess - (optional) If not null, should be a chain from s. Used to improve performance when adding many groups from the same chain
    
    clone - Indicates whether the input group should be cloned before being added to the new chain
    
    Returns:
    
    the chain g was added to
  - addGroupsToStructure
```
public static void addGroupsToStructure(Structure s,
                                        Collection<Group> groups,
                                        int model,
                                        boolean clone)
```
    Add a list of groups to a new structure. Chains will be automatically created in the new structure as needed.
    
    Parameters:
    
    s - structure to receive the group
    
    g - group to add
    
    clone - Indicates whether the input groups should be cloned before being added to the new chain
  - getAllGroupsFromSubset
```
public static Set<Group> getAllGroupsFromSubset(Atom[] atoms)
```
    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.
    
    Parameters:
    
    atoms - Sample of atoms
    
    Returns:
    
    All groups from all chains accessible from the input atoms
  - getAllGroupsFromSubset
```
public static Set<Group> getAllGroupsFromSubset(Atom[] atoms,
                                                GroupType types)
```
    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.
    
    Parameters:
    
    atoms - Sample of atoms
    
    types - Type of groups to return (useful for getting only ligands, for instance). Null gets all groups.
    
    Returns:
    
    All groups from all chains accessible from the input atoms
  - getAllNonHAtomArray
```
public static final Atom[] getAllNonHAtomArray(Structure s,
                                               boolean hetAtoms)
```
    Returns and array of all non-Hydrogen atoms in the given Structure, optionally including HET atoms or not. Waters are not included.
    
    Parameters:
    
    s -
    
    hetAtoms - if true HET atoms are included in array, if false they are not
    
    Returns:
  - getAllNonHAtomArray
```
public static final Atom[] getAllNonHAtomArray(Structure s,
                                               boolean hetAtoms,
                                               int modelNr)
```
    Returns and array of all non-Hydrogen atoms in the given Structure, optionally including HET atoms or not. Waters are not included.
    
    Parameters:
    
    s -
    
    hetAtoms - if true HET atoms are included in array, if false they are not
    
    modelNr - Model number to draw atoms from
    
    Returns:
  - getAllNonHAtomArray
```
public static final Atom[] getAllNonHAtomArray(Chain c,
                                               boolean hetAtoms)
```
    Returns and array of all non-Hydrogen atoms in the given Chain, optionally including HET atoms or not Waters are not included.
    
    Parameters:
    
    c -
    
    hetAtoms - if true HET atoms are included in array, if false they are not
    
    Returns:
  - getAllNonHCoordsArray
```
public static final javax.vecmath.Point3d[] getAllNonHCoordsArray(Chain c,
                                                                  boolean hetAtoms)
```
    Returns and array of all non-Hydrogen atoms coordinates in the given Chain, optionally including HET atoms or not Waters are not included.
    
    Parameters:
    
    c -
    
    hetAtoms - if true HET atoms are included in array, if false they are not
    
    Returns:
  - getAtomArray
```
public static final Atom[] getAtomArray(Chain c,
                                        String[] atomNames)
```
    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.
    
    Parameters:
    
    c - the Chain to get the atoms from
    
    atomNames - contains the atom names to be used.
    
    Returns:
    
    an Atom[] array
  - getAtomCAArray
```
public static final Atom[] getAtomCAArray(Chain c)
```
    Returns an Atom array of the C-alpha atoms. Any atom that is a carbon and has CA name will be returned.
    
    Parameters:
    
    c - the structure object
    
    Returns:
    
    an Atom[] array
    
    See Also:
    
    getRepresentativeAtomArray(Chain)
  - getRepresentativeAtomArray
```
public static final Atom[] getRepresentativeAtomArray(Chain c)
```
    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 ReducedChemCompProvider was used to load the structure. For amino acids, the representative is a CA carbon. For nucleotides, the representative is the "P". Other group types will be ignored.
    
    Parameters:
    
    c -
    
    Returns:
    
    representative Atoms of the chain backbone
    
    Since:
    
    Biojava 4.1.0
  - cloneAtomArray
```
public static final Atom[] cloneAtomArray(Atom[] 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.
    
    Parameters:
    
    ca - array of representative atoms, e.g. CA atoms
    
    Returns:
    
    Atom array
    
    Since:
    
    Biojava 4.1.0
  - cloneGroups
```
public static Group[] cloneGroups(Atom[] ca)
```
    Clone a set of representative Atoms, but returns the parent groups
    
    Parameters:
    
    ca - Atom array
    
    Returns:
    
    Group array
  - duplicateCA2
```
public static Atom[] duplicateCA2(Atom[] ca2)
```
    Utility method for working with circular permutations. Creates a duplicated and cloned set of Calpha atoms from the input array.
    
    Parameters:
    
    ca2 - atom array
    
    Returns:
    
    cloned and duplicated set of input array
  - getAtomCAArray
```
public static Atom[] getAtomCAArray(Structure s)
```
    Return an Atom array of the C-alpha atoms. Any atom that is a carbon and has CA name will be returned.
    
    Parameters:
    
    s - the structure object
    
    Returns:
    
    an Atom[] array
    
    See Also:
    
    getRepresentativeAtomArray(Structure)
  - getRepresentativeAtomArray
```
public static Atom[] getRepresentativeAtomArray(Structure s)
```
    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 ReducedChemCompProvider was used to load the structure. For amino acids, the representative is a CA carbon. For nucleotides, the representative is the "P". Other group types will be ignored.
    
    Parameters:
    
    s - Input structure
    
    Returns:
    
    representative Atoms of the structure backbone
    
    Since:
    
    Biojava 4.1.0
  - getBackboneAtomArray
```
public static Atom[] getBackboneAtomArray(Structure s)
```
    Return an Atom array of the main chain atoms: CA, C, N, O Any group that contains those atoms will be included, be it a standard aminoacid or not
    
    Parameters:
    
    s - the structure object
    
    Returns:
    
    an Atom[] array
  - get1LetterCodeAmino
```
public static final Character get1LetterCodeAmino(String groupCode3)
```
    Convert three character amino acid codes into single character e.g. convert CYS to C. Valid 3-letter codes will be those of the standard 20 amino acids plus MSE, CSE, SEC, PYH, PYL (see the aminoAcids map)
    
    Parameters:
    
    groupCode3 - a three character amino acid representation String
    
    Returns:
    
    the 1 letter code, or null if the given 3 letter code does not correspond to an amino acid code
    
    See Also:
    
    #get1LetterCode(String)}
  - get1LetterCode
```
public static final Character get1LetterCode(String groupCode3)
```
    Convert a three letter amino acid or nucleotide code into a single character code. If the code does not correspond to an amino acid or nucleotide, returns UNKNOWN_GROUP_LABEL. Returned null for nucleotides prior to version 4.0.1.
    
    Parameters:
    
    groupCode3 - three letter representation
    
    Returns:
    
    The 1-letter abbreviation
  - isNucleotide
```
public static final boolean isNucleotide(String groupCode3)
```
    Test if the three-letter code of an ATOM entry corresponds to a nucleotide or to an aminoacid.
    
    Parameters:
    
    groupCode3 - 3-character code for a group.
  - getReducedStructure
```
@Deprecated
public static final Structure getReducedStructure(Structure s,
                                                              String chainId)
                                                       throws StructureException
```
    Deprecated. Use StructureIdentifier.reduce(Structure) instead (v. 4.2.0)
    
    Reduce a structure to provide a smaller representation . Only takes the first model of the structure. If chainName is provided only return a structure containing that Chain ID. Converts lower case chain IDs to upper case if structure does not contain a chain with that ID.
    
    Parameters:
    
    s -
    
    chainId -
    
    Returns:
    
    Structure
    
    Throws:
    
    StructureException
    
    Since:
    
    3.0
  - convertAtomsToSeq
```
public static final String convertAtomsToSeq(Atom[] atoms)
```
  - getGroupByPDBResidueNumber
```
public static final Group getGroupByPDBResidueNumber(Structure struc,
                                                     ResidueNumber pdbResNum)
                                              throws StructureException
```
    Get a group represented by a ResidueNumber.
    
    Parameters:
    
    struc - a Structure
    
    pdbResNum - a ResidueNumber
    
    Returns:
    
    a group in the structure that is represented by the pdbResNum.
    
    Throws:
    
    StructureException - if the group cannot be found.
  - getAtomsInContact
```
public static AtomContactSet getAtomsInContact(Chain chain,
                                               String[] atomNames,
                                               double cutoff)
```
    Returns the set of intra-chain contacts for the given chain for given atom names, i.e. the contact map. Uses a geometric hashing algorithm that speeds up the calculation without need of full distance matrix. The parsing mode FileParsingParameters.setAlignSeqRes(boolean) needs to be set to true for this to work.
    
    Parameters:
    
    chain -
    
    atomNames - the array with atom names to be used. Beware: CA will do both C-alphas an Calciums if null all non-H atoms of non-hetatoms will be used
    
    cutoff -
    
    Returns:
  - getAtomsInContact
```
public static AtomContactSet getAtomsInContact(Chain chain,
                                               double cutoff)
```
    Returns the set of intra-chain contacts for the given chain for all non-H atoms of non-hetatoms, i.e. the contact map. Uses a geometric hashing algorithm that speeds up the calculation without need of full distance matrix. The parsing mode FileParsingParameters.setAlignSeqRes(boolean) needs to be set to true for this to work.
    
    Parameters:
    
    chain -
    
    cutoff -
    
    Returns:
  - getAtomsCAInContact
```
public static AtomContactSet getAtomsCAInContact(Chain chain,
                                                 double cutoff)
```
    Returns the set of intra-chain contacts for the given chain for C-alpha atoms (including non-standard aminoacids appearing as HETATM groups), i.e. the contact map. Uses a geometric hashing algorithm that speeds up the calculation without need of full distance matrix. The parsing mode FileParsingParameters.setAlignSeqRes(boolean) needs to be set to true for this to work.
    
    Parameters:
    
    chain -
    
    cutoff -
    
    Returns:
    
    See Also:
    
    #getRepresentativeAtomsInContact(Chain, double)}
  - getRepresentativeAtomsInContact
```
public static AtomContactSet getRepresentativeAtomsInContact(Chain chain,
                                                             double cutoff)
```
    Returns the set of intra-chain contacts for the given chain for C-alpha or C3' atoms (including non-standard aminoacids appearing as HETATM groups), i.e. the contact map. Uses a geometric hashing algorithm that speeds up the calculation without need of full distance matrix.
    
    Parameters:
    
    chain -
    
    cutoff -
    
    Returns:
    
    Since:
    
    Biojava 4.1.0
  - getAtomsInContact
```
public static AtomContactSet getAtomsInContact(Chain chain1,
                                               Chain chain2,
                                               String[] atomNames,
                                               double cutoff,
                                               boolean hetAtoms)
```
    Returns the set of inter-chain contacts between the two given chains for the given atom names. Uses a geometric hashing algorithm that speeds up the calculation without need of full distance matrix. The parsing mode FileParsingParameters.setAlignSeqRes(boolean) needs to be set to true for this to work.
    
    Parameters:
    
    chain1 -
    
    chain2 -
    
    atomNames - the array with atom names to be used. For Calphas use {"CA"}, if null all non-H atoms will be used. Note HET atoms are ignored unless this parameter is null.
    
    cutoff -
    
    hetAtoms - if true HET atoms are included, if false they are not
    
    Returns:
  - getAtomsInContact
```
public static AtomContactSet getAtomsInContact(Chain chain1,
                                               Chain chain2,
                                               double cutoff,
                                               boolean hetAtoms)
```
    Returns the set of inter-chain contacts between the two given chains for all non-H atoms. Uses a geometric hashing algorithm that speeds up the calculation without need of full distance matrix. The parsing mode FileParsingParameters.setAlignSeqRes(boolean) needs to be set to true for this to work.
    
    Parameters:
    
    chain1 -
    
    chain2 -
    
    cutoff -
    
    hetAtoms - if true HET atoms are included, if false they are not
    
    Returns:
  - getGroupDistancesWithinShell
```
public static Map<Group,Double> getGroupDistancesWithinShell(Structure structure,
                                                             Atom centroid,
                                                             Set<ResidueNumber> excludeResidues,
                                                             double radius,
                                                             boolean includeWater,
                                                             boolean useAverageDistance)
```
    Finds Groups in structure that contain at least one Atom that is within radius Angstroms of centroid.
    
    Parameters:
    
    structure - The structure from which to find Groups
    
    centroid - The centroid of the shell
    
    excludeResidues - A list of ResidueNumbers to exclude
    
    radius - The radius from centroid, in Angstroms
    
    includeWater - Whether to include Groups whose only atoms are water
    
    useAverageDistance - When set to true, distances are the arithmetic mean (1-norm) of the distances of atoms that belong to the group and that are within the shell; otherwise, distances are the minimum of these values
    
    Returns:
    
    A map of Groups within (or partially within) the shell, to their distances in Angstroms
  - getGroupsWithinShell
```
public static Set<Group> getGroupsWithinShell(Structure structure,
                                              Atom atom,
                                              Set<ResidueNumber> excludeResidues,
                                              double distance,
                                              boolean includeWater)
```
  - getGroupsWithinShell
```
public static Set<Group> getGroupsWithinShell(Structure structure,
                                              Group group,
                                              double distance,
                                              boolean includeWater)
```
    Returns a Set of Groups in a structure within the distance specified of a given group.
    
    Updated 18-Sep-2015 sroughley to return a Set so only a unique set of Groups returned
    
    Parameters:
    
    structure - The structure to work with
    
    group - The 'query' group
    
    distance - The cutoff distance
    
    includeWater - Should water residues be included in the output?
    
    Returns:
    
    LinkedHashSet of Groups within at least one atom with distance of at least one atom in group
  - removeModels
```
public static Structure removeModels(Structure s)
```
    Remove all models from a Structure and keep only the first
    
    Parameters:
    
    s - original Structure
    
    Returns:
    
    a structure that contains only the first model
    
    Since:
    
    3.0.5
  - filterLigands
```
public static List<Group> filterLigands(List<Group> allGroups)
```
    Removes all polymeric and solvent groups from a list of groups
  - getStructure
```
public static Structure getStructure(String name)
                              throws IOException,
                                     StructureException
```
    Short version of getStructure(String, PDBFileParser, AtomCache) which creates new parsers when needed
    
    Parameters:
    
    name -
    
    Returns:
    
    Throws:
    
    IOException
    
    StructureException
  - getStructure
```
public static Structure getStructure(String name,
                                     PDBFileParser parser,
                                     AtomCache cache)
                              throws IOException,
                                     StructureException
```
    Flexibly get a structure from an input String. The intent of this method is to allow any reasonable string which could refer to a structure to be correctly parsed. The following are currently supported:
    1. Filename (if name refers to an existing file)
    2. PDB ID
    3. SCOP domains
    4. PDP domains
    5. Residue ranges
    6. Other formats supported by AtomCache
    Parameters:
    
    name - Some reference to the protein structure
    
    parser - A clean PDBFileParser to use if it is a file. If null, a PDBFileParser will be instantiated if needed.
    
    cache - An AtomCache to use if the structure can be fetched from the PDB. If null, a AtomCache will be instantiated if needed.
    
    Returns:
    
    A Structure object
    
    Throws:
    
    IOException - if name is an existing file, but doesn't parse correctly
    
    StructureException - if the format is unknown, or if AtomCache throws an exception.
  - isProtein
```
@Deprecated
public static boolean isProtein(Chain c)
```
    Deprecated. use Chain.isProtein() instead.
  - isNucleicAcid
```
@Deprecated
public static boolean isNucleicAcid(Chain c)
```
    Deprecated. use Chain.isNucleicAcid() instead.
  - getPredominantGroupType
```
@Deprecated
public static GroupType getPredominantGroupType(Chain c)
```
    Deprecated. use Chain.getPredominantGroupType() instead.
  - isChainWaterOnly
```
@Deprecated
public static boolean isChainWaterOnly(Chain c)
```
    Deprecated. use Chain.isWaterOnly() instead.
  - isChainPureNonPolymer
```
@Deprecated
public static boolean isChainPureNonPolymer(Chain c)
```
    Deprecated. use Chain.isPureNonPolymer() instead.
  - cleanUpAltLocs
```
public static void cleanUpAltLocs(Structure structure)
```
    Cleans up the structure's alternate location groups. All alternate location groups should have all atoms (except in the case of microheterogenity) or when a deuetuim exiss. Ensure that all the alt loc groups have all the atoms in the main group
    
    Parameters:
    
    structure - The Structure to be cleaned up
  - hasNonDeuteratedEquiv
```
public static boolean hasNonDeuteratedEquiv(Atom atom,
                                            Group currentGroup)
```
    Check to see if an Deuterated atom has a non deuterated brother in the group.
    
    Parameters:
    
    atom - the input atom that is putatively deuterium
    
    currentGroup - the group the atom is in
    
    Returns:
    
    true if the atom is deuterated and it's hydrogen equive exists.
  - hasDeuteratedEquiv
```
public static boolean hasDeuteratedEquiv(Atom atom,
                                         Group currentGroup)
```
    Check to see if a Hydorgen has a Deuterated brother in the group.
    
    Parameters:
    
    atom - the input atom that is putatively hydorgen
    
    currentGroup - the group the atom is in
    
    Returns:
    
    true if the atom is hydrogen and it's Deuterium equiv exists.

Class StructureTools

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

CA_ATOM_NAME

N_ATOM_NAME

C_ATOM_NAME

O_ATOM_NAME

CB_ATOM_NAME

C1_ATOM_NAME

C2_ATOM_NAME

C3_ATOM_NAME

C4_ATOM_NAME

O2_ATOM_NAME

O3_ATOM_NAME

O4_ATOM_NAME

O5_ATOM_NAME

OP1_ATOM_NAME

OP2_ATOM_NAME

P_ATOM_NAME

NUCLEOTIDE_REPRESENTATIVE

UNKNOWN_GROUP_LABEL

RATIO_RESIDUES_TO_TOTAL

DEFAULT_LIGAND_PROXIMITY_CUTOFF

Constructor Detail

StructureTools

Method Detail

getNrAtoms

getNrGroups

getAtomArray

getAtomArrayAllModels

getAllAtomArray

getAllAtomArray

getAllAtomArray

getUnalignedGroups

getLigandsByProximity

addGroupToStructure

addGroupsToStructure

getAllGroupsFromSubset

getAllGroupsFromSubset

getAllNonHAtomArray

getAllNonHAtomArray

getAllNonHAtomArray

getAllNonHCoordsArray

getAtomArray

getAtomCAArray

getRepresentativeAtomArray

cloneAtomArray

cloneGroups

duplicateCA2

getAtomCAArray

getRepresentativeAtomArray

getBackboneAtomArray

get1LetterCodeAmino

get1LetterCode

isNucleotide

getReducedStructure

convertAtomsToSeq

getGroupByPDBResidueNumber

getAtomsInContact

getAtomsInContact

getAtomsCAInContact

getRepresentativeAtomsInContact

getAtomsInContact

getAtomsInContact

getGroupDistancesWithinShell

getGroupsWithinShell

getGroupsWithinShell

removeModels

filterLigands

getStructure

getStructure

isProtein

isNucleicAcid

getPredominantGroupType

isChainWaterOnly

isChainPureNonPolymer

cleanUpAltLocs