pdbx

Documentation

Overview

Package pdbx provides types and functions for reading PDBx/mmCIF formatted files conveniently.

Index

• type Atom
• type Chain
• type Entity
• type Entry
  • func Read(r io.Reader) (*Entry, error)
  • func ReadAll(r io.Reader) ([]*Entry, error)
  • func ReadCIFDataBlock(b *cif.DataBlock) (*Entry, error)
• type Model
• type Site

Types

type Atom

type Atom struct {
	Name string
	Het  bool
	structure.Coords
}

Atom represents a single ATOM record.

type Chain

type Chain struct {
	// A pointer back to its corresponding entity.
	Entity *Entity

	// A single character that uniquely identifies this structure in an entry.
	Id byte

	// All models corresponding to this structure. There may be zero models,
	// although in the vast majority of cases, there is precisely one (but
	// there may be more, particularly for NMR structures).
	Models []*Model
}

Chain corresponds to a single unique unit of structure within this PDB file.

type Entity

type Entity struct {
	// A pointer back to its corresponding PDB entry.
	Entry *Entry

	// The identifier for this entity.
	// (CIF: entity.id)
	Id byte

	// The type of entity.
	// Must be either "macrolide", "non-polymer", "polymer" or "water".
	// (CIF: entity.type)
	Type string

	// The formula weight of this entity in daltons.
	// (CIF: entity.formula_weight)
	FormulaWeight float64

	// The number of molecules for this entity in the entry.
	// (CIF: entity.pdbx_number_of_molecules)
	NumOfMolecules float64

	// The sequence as specified in the _entity_poly_seq category (NOT the
	// _entity_poly.pdbx_seq_one_letter_code data item).
	Seq []seq.Residue

	// A list of all structures (chains) in this entry.
	// Note that each structure may contain multiple models.
	// Note that identifiers are stored as characters, so that a "1" is the
	// character '1' and not the integer 1.
	Chains map[byte]*Chain
}

type Entry

type Entry struct {
	// The underlying CIF file. This provides raw access to attributes of a
	// PDBx file that are not captured by the types in this package.
	CIF *cif.DataBlock

	// The four letter PDB identifier corresponding to this entry.
	// It is stored in lowercase.
	Id string

	// Corresponds to the "struct.title" and "struct.pdbx_descriptor" items.
	Title, Descriptor string

	// A list of all entities in this entry.
	// Each entity may contain multiple structures (chains).
	// Note that identifiers are stored as characters, so that a "1" is the
	// character '1' and not the integer 1.
	Entities map[byte]*Entity
}

Entry corresponds to a single data block inside a PDBx/mmCIF formatted file. Usually, a file contains only one data block.

Note that an Entry does *not* encapsulate all information in a PDBx/mmCIF file. In fact, it's only a small subset of the information mostly related to the structures and sequences in the file. For this reason, access to the raw CIF data block from the file is exposed in this type.

func Read

func Read(r io.Reader) (*Entry, error)

Read reads exactly one PDB entry from the reader given. If there are 0 entries or more than 1 entry, an error is returned.

An error is also returned if the reader could not be interpreted as a valid PDBx/mmCIF file (which must be a valid CIF file).

This function is useful for reading standard PDBx/mmCIF files obtained from the PDB. (But in general, a PDBx/mmCIF file may contain more than one entry.)

func ReadAll

func ReadAll(r io.Reader) ([]*Entry, error)

ReadAll reads all PDB entries from the reader provided. If you're reading PDBx/mmCIF files from the PDB, then use the Read function which guarantees the reader given only has a single entry.

An error is returned if the reader could not be interpreted as a valid PDBx/mmCIF file (which must be a valid CIF file).

func ReadCIFDataBlock

func ReadCIFDataBlock(b *cif.DataBlock) (*Entry, error)

ReadCIFDataBlock converts a PDBx/mmCIF data block to a PDB entry. It is exposed in the public interface so that clients can freely mix Entry objects and their corresponding underlying data blocks.

An error is returned if the data block given does not correspond to a valid PDBx/mmCIF entry.

type Model

type Model struct {
	// A pointer back to its corresponding chain.
	Chain *Chain

	// The model number (usually starting at 1).
	Num int

	// The ATOM records grouped by sequence residue.
	// Note that this slice has exactly the same size as Chain.Seq.
	// Since not every residue has a corresponding ATOM record, some
	// values in this slice may be nil.
	Sites []Site

	// For convenience, the coordinates of each alpha-carbon atom found in
	// the ATOM records for this structure are stored here. Like Sites, this
	// is also guaranteed to have the same length as Chain.Seq, and since
	// not every reside has an ATOM record, some values may be nil.
	//
	// Note that if more than one alpha-carbon ATOM record exists for a
	// single residue, the first set of coordinates is used. (However, it is
	// not omitted from the set of atoms in each value in Sites.)
	//
	// Finally, this slice omits HETATM records.
	AlphaCarbonsSeq []*structure.Coords

	// This is the same as AlphaCarbonsSeq, except it is not in correspondence
	// with the sequence for this chain. In particular, it is constructed by
	// simply appending the coordinates from the first alpha-carbon ATOM record
	// in each ATOM site.
	AlphaCarbons []structure.Coords
}

Model corresponds to a single structural model in a PDB file. There may be more than one model for each chain, although in practice, there is usually only one.

type Site

type Site struct {
	// The index corresponding to the residue for this ATOM site.
	// (Starting from 0.)
	SeqIndex int

	// The component identifier for this site. (For amino acid sequences,
	// it is usually the codon.)
	Comp string

	// The set of atoms (in no particular order) for this site.
	Atoms []Atom
}

Site corresponds to the set of ATOM records for a particular residue in a structure's sequence.