pdb.h File Reference

Functions to read PDBs. More...

#include <IMP/atom/atom_config.h>
#include "Hierarchy.h"
#include "Atom.h"
#include "element.h"
#include "internal/pdb.h"
#include "atom_macros.h"
#include <IMP/file.h>
#include "Selection.h"
#include <IMP/Model.h>
#include <IMP/Particle.h>
#include <IMP/OptimizerState.h>
#include <IMP/internal/utility.h>
#include <IMP/internal/pdb.h>
#include <boost/format.hpp>
#include <boost/algorithm/string.hpp>
#include <cereal/access.hpp>
#include <cereal/types/base_class.hpp>
#include <cereal/types/polymorphic.hpp>

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Classes
class	IMP::atom::AllPDBSelector
	Defines a selector that will pick every ATOM and HETATM record. More...
class	IMP::atom::AndPDBSelector
	Select atoms which are selected by both selectors. More...
class	IMP::atom::ATOMPDBSelector
	Select all non-alternative ATOM records. More...
class	IMP::atom::AtomTypePDBSelector
	Select all atoms of the given types. More...
class	IMP::atom::BackbonePDBSelector
	Select all backbone (N,CA,C,O) ATOM records. More...
class	IMP::atom::CAlphaPDBSelector
	Select all CA ATOM records. More...
class	IMP::atom::CBetaPDBSelector
	Select all CB ATOM records. More...
class	IMP::atom::ChainPDBSelector
	Select all ATOM and HETATM records with the given chain ids. More...
class	IMP::atom::CPDBSelector
	Select all C (not CA or CB) ATOM records. More...
class	IMP::atom::HydrogenPDBSelector
	Select all hydrogen ATOM and HETATM records. More...
class	IMP::atom::NonAlternativePDBSelector
	Select all ATOM and HETATM records which are not alternatives. More...
class	IMP::atom::NonHydrogenPDBSelector
	Select non hydrogen atoms. More...
class	IMP::atom::NonWaterNonHydrogenPDBSelector
	Select non water and non hydrogen atoms. More...
class	IMP::atom::NonWaterPDBSelector
	Select all non-water non-alternative ATOM and HETATM records. More...
class	IMP::atom::NotPDBSelector
	Select atoms which are not selected by a given selector. More...
class	IMP::atom::NPDBSelector
	Select all N ATOM records. More...
class	IMP::atom::OrPDBSelector
	Select atoms which are selected by either or both selectors. More...
class	IMP::atom::PDBRecord
	Represent a single ATOM/HETATM "line" in PDB or mmCIF format. More...
class	IMP::atom::PDBSelector
	Select which atoms to read from a PDB file. More...
class	IMP::atom::PPDBSelector
	Select all P (= phosphate) ATOM records. More...
class	IMP::atom::ResidueTypePDBSelector
	Select all atoms in residues of the given types. More...
class	IMP::atom::WaterPDBSelector
	Select all non-water ATOM and HETATM records. More...
class	IMP::atom::WritePDBOptimizerState
class	IMP::atom::XorPDBSelector
	Select atoms which are selected by either selector but not both. More...

Namespaces
	IMP
	Base functionality and abstract base classes for representation, scoring and sampling.
	IMP::atom
	Functionality for loading, creating, manipulating and scoring atomic structures.

Typedefs
typedef IMP::Vector< PDBRecord >	IMP::atom::PDBRecords
typedef IMP::Vector < IMP::Pointer< PDBSelector > >	IMP::atom::PDBSelectors
typedef IMP::Vector < IMP::WeakPointer < PDBSelector > >	IMP::atom::PDBSelectorsTemp

PDB Reading
The read PDB methods produce a hierarchy that looks as follows: One Atom per ATOM or HETATM record in the PDB. All Atom particles have a parent which is a Residue. All Residue particles have a parent which is a Chain. Waters are currently dropped if they are ATOM records. This can be fixed. The read_pdb() functions should successfully parse all valid PDB files. It can produce warnings on files which are not valid. It will attempt to read such files, but all bets are off. In order to track the provenance of IMP-generated models, the provenance of any PDB files read in here - for example, the PDB id, or detail about a comparative model - needs to also be tracked. This is done using the PDB headers: Structures stored in the PDB database should keep the standard HEADER record stating their PDB ID. Comparative models generated using MODELLER should include the MODELLER-generated EXPDTA and REMARK records. Structures that are trivial modifications of an existing PDB structure or comparative model should use the TITLE record to describe the nature of the modification (e.g. rotation and translation) and one of the two following custom EXPDTA record formats to point to the original structure: EXPDTA DERIVED FROM PDB:1XYZ EXPDTA DERIVED FROM COMPARATIVE MODEL, DOI:x.y/z Structures generated from multiple sources (e.g. two structures that have been docked and then concatenated into a single PDB file) are not allowed. Store each constituent structure in its own file and annotate each one with a suitable EXPDTA record, as above. Note that while provenance of PDB files is not currently enforced, it likely will be in future IMP releases. When reading PDBs, PDBSelector objects can be used to choose to only process certain record types. See the class documentation for more information. When no PDB selector is supplied for reading, the NonWaterPDBSelector is used. Set the IMP::LogLevel to VERBOSE to see details of parse errors.
PDBSelector *	IMP::atom::get_default_pdb_selector ()
Hierarchy	IMP::atom::read_pdb (TextInput input, Model *model, PDBSelector *selector=get_default_pdb_selector(), bool select_first_model=true)
	Read all the molecules in the first model of the PDB file. More...
void	IMP::atom::read_pdb (TextInput input, int model, Hierarchy h)
Hierarchies	IMP::atom::read_multimodel_pdb (TextInput input, Model *model, PDBSelector *selector=get_default_pdb_selector())

PDB Writing
The methods to write a PDB expects a Hierarchy that looks as follows: all leaves are Atom particles all Atom particles have Residue particles as parents All Residue particles that have a Chain particle as an ancestor are considered part of a protein, DNA or RNA, ones without are considered heterogens. The functions produce files that are not valid PDB files, eg only ATOM/HETATM lines are printed for all Atom particles in the hierarchy. Complain if your favorite program can't read them and we might fix it.
void	IMP::atom::write_pdb (const Selection &mhd, TextOutput out, unsigned int model=1)
void	IMP::atom::write_pdb_of_c_alphas (const Selection &mhd, TextOutput out, unsigned int model=1)
	Write a hierarchy to a PDB as C_alpha atoms. More...
void	IMP::atom::write_multimodel_pdb (const Hierarchies &mhd, TextOutput out)

Detailed Description

Functions to read PDBs.

Copyright 2007-2023 IMP Inventors. All rights reserved.

Definition in file pdb.h.