BondMaker (biojava 6.0.0 API)

java.lang.Object
- org.biojava.nbio.structure.io.BondMaker

```
public class BondMaker
extends Object
```
Adds polymer bonds for peptides and nucleotides based on distance cutoffs and intra-group (residue) bonds based on data from the Chemical Component Dictionary to the Structure object. TODO the current implementation adds bonds to the first model only. This should be sufficient for homogeneous models, but here are a few inhomogeneous models in the PDB. A better handling of models should be considered in the future.

Author:

Peter Rose, Ulysse Carion

Field Summary

Fields
Modifier and Type Field Description

static Set<String> BOND_TYPES_TO_PARSE
The types of bonds that are read from struct_conn (type specified in field conn_type_id)

Constructor Summary

Constructors
Constructor Description

BondMaker(Structure structure, FileParsingParameters params)

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`formBondsFromStructConn(org.rcsb.cif.schema.mm.StructConn conn)`
`void`	`formDisulfideBonds(List<SSBondImpl> disulfideBonds)`	Creates disulfide bond objects and references in the corresponding Atoms objects, given a list of `SSBondImpl`s parsed from a PDB file.
`void`	`formLinkRecordBond(PDBTemporaryStorageUtils.LinkRecord linkRecord)`	Creates bond objects from a LinkRecord as parsed from a PDB file
`void`	`makeBonds()`	Creates bond objects and corresponding references in Atom objects: peptide bonds: inferred from sequence and distances nucleotide bonds: inferred from sequence and distances intra-group (residue) bonds: read from the chemical component dictionary, via `ChemCompProvider`

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

- Field Detail
  - BOND_TYPES_TO_PARSE
```
public static final Set<String> BOND_TYPES_TO_PARSE
```
    The types of bonds that are read from struct_conn (type specified in field conn_type_id)
- Constructor Detail
  - BondMaker
```
public BondMaker(Structure structure,
                 FileParsingParameters params)
```
- Method Detail
  - makeBonds
```
public void makeBonds()
```
    Creates bond objects and corresponding references in Atom objects:
  - peptide bonds: inferred from sequence and distances
  - nucleotide bonds: inferred from sequence and distances
  - intra-group (residue) bonds: read from the chemical component dictionary, via ChemCompProvider

formDisulfideBonds
```
public void formDisulfideBonds(List<SSBondImpl> disulfideBonds)
```
Creates disulfide bond objects and references in the corresponding Atoms objects, given a list of SSBondImpls parsed from a PDB file.

Parameters:

disulfideBonds -

formLinkRecordBond
```
public void formLinkRecordBond(PDBTemporaryStorageUtils.LinkRecord linkRecord)
```
Creates bond objects from a LinkRecord as parsed from a PDB file

Parameters:

linkRecord - the PDB-format LINK record

formBondsFromStructConn

public void formBondsFromStructConn(org.rcsb.cif.schema.mm.StructConn conn)