Domain_label_traits Class Reference

Model of MolecularSystemLabelTraits for molecular complexes defined in a file. More...

#include <Domain_label_traits.hpp>

Static Public Member Functions
static unsigned	get_number_of_labels (void)
	Total number of system's labels. More...
static unsigned	get_number_of_primitive_labels (void)
	Number of primitive system's labels. More...
static Label	get_parent_of (Label label)
	Return the parent label of the input label. More...
static std::string	to_string (Label label)
	Return the string representation of the label. More...
static int	get_current_set_of_labels_index (void)
	Return the current index of set of labels to be used. More...
static void	set_current_set_of_labels_index (unsigned i)
	Set the current index of set of labels to be used. More...

Detailed Description

Model of MolecularSystemLabelTraits for molecular complexes defined in a file.

The specification follows these rules:

• template of domains: when several chains share the same set of domains, it is natural to define only once the domains as a template, and use this template for each chain. A template starts with the command domains-template-begin <template-name> and terminates with the command end. To add a domain to the template, use the following syntax: <domain-name> [resid-resid|resid|*] [...] . The first argument is the name of the domain, while all the following arguments define the residues in the domain: resid for a specific residue, resid-resid for a range of residues, and * for all residues that were not included in any other domain of the template. Note that * can be used only for one domain in the template and without any other residue's id specification for this domain.

• chains enumeration: enumerating the chains consist on specifying which chains have an associated label, and possibly associating a template of domains to the chains. A enumeration starts with the command chains-enumeration-begin and terminates with the command end. To specify a chain, use the following syntax: <chains> [like <template-name>] . The first argument is a list of chains to specify in the same way : each chain is represented by its id, that is one character. The second optional argument allows to specify a template of domains to all the specified chains. If no template of domains is given, the entire chains are considered. As a result, one primitive label will be created for each specified chain with no template of domains, and one hierarchical label for each specified chain with a template of domains. Each such label has the name of the chain. Furthermore, for each chain decomposed into domains, there is one primitive label per domain with name the concatenation of the name of the chain with the name of the domain.

• chains' hierarchy: the chains' hierarchy defines a way to group hierarchically the chains. A hierarchy starts with the command chains-hierarchy-begin and terminates with the command end. To specify a hierarchy, use the following syntax: <label-name> chain|<label-name> [...] . The first argument is the name of hierarchical label, while all the following arguments are the name of specified chains or other existing hierarchical labels to be grouped under the first hierarchical label.

The next example shows a configuration file for representing the contacts within the domains within a homo-trimer (EFF-1):

#example with secret-C_elegans-EFF-1
 
#define a template of residues
 
#the first line starts the template and give it a name
domains-template-begin EFF1
 
#the following lines contain: the name of the label, then the ranges
#of residues corresponding to this label (including the bounds)
 
D1      23-110  211-262  382-392 
D2      111-210 263-381
D3      409-509
LINKER  393-408
STEM    510-560
 
#the star denotes the complementary, i.e all residues not
#mentionned before in the template
COIL    **
 
#terminates the template
end
 
 
 
#define the partners
 
#the first line starts the enumeration and give a name to the enum
chains-enumeration-begin
 
#For decomposing the chains A, B and C like the template EFF1:
ABC like EFF1
 
#For creating one label per chain, but not decomposing (commented)
#ABC
 
#terminates the enumeration
end
 
#Grouping the chains 
chains-hierarchy-begin
ALL A B C
end
 
 

Member Function Documentation

get_current_set_of_labels_index()

static int get_current_set_of_labels_index ( void  )

inlinestaticinherited

Return the current index of set of labels to be used.

get_number_of_labels()

static unsigned get_number_of_labels ( void  )

inlinestaticinherited

Total number of system's labels.

get_number_of_primitive_labels()

static unsigned get_number_of_primitive_labels ( void  )

inlinestaticinherited

Number of primitive system's labels.

get_parent_of()

static Label get_parent_of ( Label  label )

inlinestaticinherited

Return the parent label of the input label.

set_current_set_of_labels_index()

static void set_current_set_of_labels_index ( unsigned  i )

inlinestaticinherited

Set the current index of set of labels to be used.

to_string()

static std::string to_string ( Label  label )

inlinestaticinherited

Return the string representation of the label.