StructureTools (biojava 4.2.1 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 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 Atom[]`	`cloneAtomArray(Atom[] ca)` Provides an equivalent copy of Atoms in a new array.
`static Atom[]`	`cloneCAArray(Atom[] ca)` Deprecated. Use the better-named `cloneAtomArray(Atom[])` instead
`static Group[]`	`cloneGroups(Atom[] ca)` Clone a set of representative Atoms, but returns the parent groups
`static Character`	`convert_3code_1code(String code3)` Deprecated. Use `get1LetterCodeAmino(String)` instead
`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 (first model), including Hydrogens (if present) and all HETATOMs.
`static Atom[]`	`getAllAtomArray(Structure s)` Convert all atoms of the structure (first model) into an Atom array
`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[]`	`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.
`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.
`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.
`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 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)` Get the predominant `GroupType` for a given Chain, following these rules: if the ratio of number of residues of a certain `GroupType` to total non-water residues is above the threshold 0.95, then that `GroupType` is returned if there is no `GroupType` that is above the threshold then the `GroupType` with most members is chosen, logging it
`static Structure`	`getReducedStructure(Structure s, int chainNr)` Deprecated. Use `StructureIdentifier.reduce(Structure)` instead (v. 4.2.0)
`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.
`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 Structure`	`getSubRanges(Structure s, String ranges)` Deprecated. Use `StructureIdentifier` instead (4.2.0)
`static List<Group>`	`getUnalignedGroups(Atom[] ca)` List of groups from the structure not included in ca (e.g.
`static boolean`	`isChainPureNonPolymer(Chain c)` Returns true if the given chain is composed of non-polymeric groups only
`static boolean`	`isChainWaterOnly(Chain c)` Returns true if the given chain is composed of water molecules only
`static boolean`	`isNucleicAcid(Chain c)` Tell whether given chain is DNA or RNA
`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)` Tell whether given chain is a protein chain
`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
- 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 (first 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 (first model), 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:
  - 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(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:
  - 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
  - cloneCAArray
```
@Deprecated
public static final Atom[] cloneCAArray(Atom[] ca)
```
    Deprecated. Use the better-named cloneAtomArray(Atom[]) instead
    
    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
  - 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)}
  - convert_3code_1code
```
@Deprecated
public static final Character convert_3code_1code(String code3)
```
    Deprecated. Use get1LetterCodeAmino(String) instead
    
    Parameters:
    
    code3 -
    
    Returns:
  - 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 chainId 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
  - getReducedStructure
```
@Deprecated
public static final Structure getReducedStructure(Structure s,
                                                              int chainNr)
                                                       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 chainNr >=0 only takes the chain at that position into account.
    
    Parameters:
    
    s -
    
    chainNr - can be -1 to request all chains of model 0, otherwise will only add chain at this position
    
    Returns:
    
    Structure object
    
    Throws:
    
    StructureException
    
    Since:
    
    3.0
  - getSubRanges
```
@Deprecated
public static final Structure getSubRanges(Structure s,
                                                       String ranges)
                                                throws StructureException
```
    Deprecated. Use StructureIdentifier instead (4.2.0)
    
    In addition to the functionality provided by getReducedStructure(Structure, int) and getReducedStructure(Structure, String), also provides a way to specify sub-regions of a structure with the following specification:
  - ranges can be surrounded by ( and ). (but will be removed).
  - ranges are specified as PDBresnum1 : PDBresnum2
  - a list of ranges is separated by ,

Parameters:: s - The full structure; ranges - A comma-separated list of ranges, optionally surrounded by parentheses
Returns:: Substructure of s specified by ranges
Throws:: IllegalArgumentException - for malformed range strings; StructureException - for errors when reducing the Structure

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
```
public static boolean isProtein(Chain c)
```
Tell whether given chain is a protein chain

Parameters:

c -

Returns:

true if protein, false if nucleotide or ligand

See Also:

getPredominantGroupType(Chain)

isNucleicAcid
```
public static boolean isNucleicAcid(Chain c)
```
Tell whether given chain is DNA or RNA

Parameters:

c -

Returns:

true if nucleic acid, false if protein or ligand

See Also:

getPredominantGroupType(Chain)

getPredominantGroupType
```
public static GroupType getPredominantGroupType(Chain c)
```
Get the predominant GroupType for a given Chain, following these rules:
if the ratio of number of residues of a certain GroupType to total non-water residues is above the threshold 0.95, then that GroupType is returned
if there is no GroupType that is above the threshold then the GroupType with most members is chosen, logging it

See also ChemComp.getPolymerType() and ChemComp.getResidueType() which follow the PDB chemical component dictionary and provide a much more accurate description of groups and their linking.

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

Constructor Detail

StructureTools

Method Detail

getNrAtoms

getNrGroups

getAtomArray

getAtomArrayAllModels

getAllAtomArray

getAllAtomArray

getUnalignedGroups

getAllNonHAtomArray

getAllNonHAtomArray

getAtomArray

getAtomCAArray

getRepresentativeAtomArray

cloneCAArray

cloneAtomArray

cloneGroups

duplicateCA2

getAtomCAArray

getRepresentativeAtomArray

getBackboneAtomArray

get1LetterCodeAmino

convert_3code_1code

get1LetterCode

isNucleotide

getReducedStructure

getReducedStructure

getSubRanges

convertAtomsToSeq

getGroupByPDBResidueNumber

getAtomsInContact

getAtomsInContact

getAtomsCAInContact

getRepresentativeAtomsInContact

getAtomsInContact

getAtomsInContact

getGroupDistancesWithinShell

getGroupsWithinShell

getGroupsWithinShell

removeModels

filterLigands

getStructure

getStructure

isProtein

isNucleicAcid

getPredominantGroupType

isChainWaterOnly

isChainPureNonPolymer