PROFASI  Version 1.5
Public Member Functions | List of all members
prf::PopBase Class Reference

Base class for a population of representations of proteins. More...

#include <PopBase.hh>

Inheritance diagram for prf::PopBase:
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Public Member Functions

int num_chains () const
 Number of chains.
 
int get_model () const
 Currently selected model.
 
virtual void set_model (int i)
 Select model i (makes sense only for PDB files)
 
virtual std::string chain_name (int i) const
 Label of the i'th chain.
 
virtual int chain_number (std::string chnm) const
 Integer index (starting from 0) of the chain labeled chnm.
 
virtual int num_grp (int ich) const
 Number of groups (residues and capping groups)
 
virtual int index_of_grp (std::string ires, int ich)
 Natural index of group labeled "ires" in the chain ich.
 
virtual std::string str_index (int ires, int ich)
 String index of the chain with natural index ires.
 
virtual std::string grp_name (int ires, int ich)
 Label of the group with natural index ires.
 
virtual int descriptors (std::list< SelRes > &slc, std::list< AtomDescriptor > &des)
 Return a list of all atom descriptors for a given selection.
 
virtual int export_shape (std::vector< int > &vct, Shape &shp)
 Export a pure set of 3D coordinates for particular atoms indicated by integer labels.
 
int mk_selection (std::string slcstr, std::list< SelRes > &slc)
 Create a selected list of residues using a selection string slcstr.
 

Detailed Description

Two kinds of representations of proteins and their populations occur inside PROFASI. One is the regular Protein and Population classes, with real Atom objects whose energy can be evaluated, and which can be affected by conformational Updates. But when parsing PDB files, we deal frequently with the same kinds of relations between similar concepts. This file is meant to represent the common features. It facilitates in comparing structures between an "internal" protein object with one in a PDB file. The comparison program only needs to deal with the common properties.

Member Function Documentation

int prf::PopBase::mk_selection ( std::string  slcstr,
std::list< SelRes > &  slc 
)

The string is translated into a selection criteria using ProFASi PDB handling: Selections and Filters


The documentation for this class was generated from the following files:

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