PROFASI  Version 1.5
Namespaces | Classes
ProFASi PDB handling module
Utilities
Collaboration diagram for ProFASi PDB handling module:

Namespaces

namespace  prf::prf_pdb_vars
 Constants describing the format of an atom record in PDB files.
 

Classes

class  prf::AtomDescriptor
 Minimal information that identifies one atom in a PDB file. More...
 
class  prf::AtomRecord
 Record corresponding to one atom in a PDB file. More...
 
class  prf::SimplePredicate< T >
 An extensible composite-capable simple predicate class. More...
 
class  prf::CompositePredicate< T >
 A composite predicate class. More...
 
class  prf::PDB_model
 An abstraction of one model in a PDB file. More...
 
class  prf::PDBReader
 A top level PDB file parser. More...
 
class  prf::isAtom
 A trivial predicate to select all atoms. More...
 
class  prf::isHeavyAtom
 A predicate that returns true if the atom is not Hydrogen. More...
 
class  prf::isBackboneAtom
 A predicate that returns true if the atom is on the backbone. More...
 
class  prf::AtomTypeSelector
 A predicate that returns true if the atom is of a certain species. More...
 
class  prf::ResSelector
 A predicate that returns true if the atom is in one kind of residue. More...
 
class  prf::LabelSelector
 A predicate that returns true if the atom has a certain label. More...
 
class  prf::RMSD_Utils
 The RMSD_Utils handler class. More...
 
class  prf::SelRes
 An abstraction for a residue selected for further processing. More...
 

Detailed Description

This is a collection of classes that implements reading and parsing of PDB files in ProFASi. The top level class, PDBReader is probably the only one most users are likely to encounter directly. It reads a PDB file. It can be told to select one area of the file, and apply certain filters on it, and then "export" the resulting list of AtomRecords, or AtomDescriptors.

At a lower level, this module contains a scheme for making arbitrary combination of filters, which have been used in this module to include or exclude atoms based on any property an atom record in a PDB file might have. But the filter composition methods here have potentially a wider applicability.

See Also
MimiqA : A swiss army knife for RMSD calculations

PROFASI: Protein Folding and Aggregation Simulator, Version 1.5
© (2005-2016) Anders Irbäck and Sandipan Mohanty
Documentation generated on Mon Jul 18 2016 using Doxygen version 1.8.2