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/base/file.h>
#include "Selection.h"
#include <IMP/kernel/Model.h>
#include <IMP/kernel/Particle.h>
#include <IMP/kernel/OptimizerState.h>
#include <IMP/kernel/internal/utility.h>
#include <boost/format.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::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 HETATMrecords 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::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 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 selector. 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::WaterPDBSelector
	Select all non-water ATOM and HETATMrecords. More...
class	IMP::atom::WritePDBOptimizerState

Namespaces
	IMP
	All IMP::kernel code is brought into the IMP namespace.
	IMP::atom
	See IMP.atom for more information.

Typedefs
typedef IMP::base::Vector < IMP::base::Pointer < PDBSelector > >	IMP::atom::PDBSelectors
typedef IMP::base::Vector < IMP::base::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. 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 (base::TextInput input, kernel::Model *model, PDBSelector *selector=get_default_pdb_selector(), bool select_first_model=true)
void	IMP::atom::read_pdb (base::TextInput input, int model, Hierarchy h)
Hierarchies	IMP::atom::read_multimodel_pdb (base::TextInput input, kernel::Model *model, PDBSelector *selector=)

PDB Writing
The methods to write a PDBs 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, base::TextOutput out, unsigned int model=1)
void	IMP::atom::write_pdb_of_c_alphas (const Selection &mhd, base::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, base::TextOutput out)

Detailed Description

Copyright 2007-2013 IMP Inventors. All rights reserved.

Definition in file pdb.h.