IMP Reference Guide
2.20.2
The Integrative Modeling Platform
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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>
Go to the source code of this file.
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:
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:
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 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) |