BALL
1.5.0
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#include <BALL/STRUCTURE/sideChainPlacementProcessor.h>
Classes | |
struct | Default |
Default values for options. More... | |
struct | Method |
struct | Option |
Option names. More... | |
Public Member Functions | |
Constant Definitions | |
BALL_CREATE (SideChainPlacementProcessor) | |
Constructors and Destructors | |
SideChainPlacementProcessor () | |
Default Constructor. More... | |
SideChainPlacementProcessor (const SideChainPlacementProcessor &scpp) | |
Copy Construcor. More... | |
virtual | ~SideChainPlacementProcessor () |
Destructor. More... | |
Processor-related methods | |
virtual bool | start () |
Processor method which is called before the operator()-call. More... | |
void | clear () |
virtual Processor::Result | operator() (AtomContainer &ac) |
virtual bool | finish () |
Processor method which is called after the operator()-call. More... | |
Accessors | |
void | setDefaultOptions () |
void | setMutations (String mutated_seq) |
const String & | getMutations () const |
String | getMutations () |
Assignment | |
SideChainPlacementProcessor & | operator= (const SideChainPlacementProcessor &scpp) |
assignment operator More... | |
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UnaryProcessor () | |
UnaryProcessor (const UnaryProcessor &) | |
virtual | ~UnaryProcessor () |
Public Attributes | |
Options | options |
options More... | |
String | mutated_sequence_ |
Sequence in OneLetterCode with mutated residues. More... | |
bool | valid_ |
bool | readOptions_ () |
Additional Inherited Members | |
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typedef ResultType | result_type |
typedef ArgumentType | argument_type |
typedef ArgumentType & | argument_reference |
typedef const ArgumentType & | const_argument_reference |
typedef ArgumentType * | argument_pointer |
typedef const ArgumentType * | const_argument_pointer |
Side Chain Placement Processor Placement of side chains.
Given the path to the SCWRL binary in the option Option::SCWRL_BINARY_PATH; the processor computes side chain conformations for the given side chains. If no selection is given all side chains are considered. The option Option::MUTATE_SELECTED_SIDE_CHAINS can be used to mutate selected amino acids as specified in the member mutated_sequence_.
Example code:
Definition at line 46 of file sideChainPlacementProcessor.h.
BALL::SideChainPlacementProcessor::SideChainPlacementProcessor | ( | ) |
Default Constructor.
BALL::SideChainPlacementProcessor::SideChainPlacementProcessor | ( | const SideChainPlacementProcessor & | scpp | ) |
Copy Construcor.
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virtual |
Destructor.
BALL::SideChainPlacementProcessor::BALL_CREATE | ( | SideChainPlacementProcessor | ) |
void BALL::SideChainPlacementProcessor::clear | ( | ) |
Clears the datastructures. NOTE: The options remain! Use setDefaultOptions() to clear the options.
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virtual |
Processor method which is called after the operator()-call.
Reimplemented from BALL::UnaryProcessor< AtomContainer >.
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inline |
Get the mutated sequence.
Definition at line 189 of file sideChainPlacementProcessor.h.
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inline |
Get the mutated sequence.
Definition at line 185 of file sideChainPlacementProcessor.h.
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virtual |
Operator () for the processor
Called with Default-options the processor assigns side chain torsion angles to residues.
The processor can be applied to a system, a protein, or a chain. The selection mechanism can be used to restrict the processor to certain residues. If no selection is given all side chains are considered. The option Option::MUTATE_SELECTED_SIDE_CHAINS can be used to mutate selected amino acids as specified in the member mutated_sequence_ (see setMutations(String mutationed_seq) .
ac | the AtomContainer to which the processor is applied. |
Reimplemented from BALL::UnaryProcessor< AtomContainer >.
SideChainPlacementProcessor& BALL::SideChainPlacementProcessor::operator= | ( | const SideChainPlacementProcessor & | scpp | ) |
assignment operator
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protected |
Reads, checks and stores the options.
void BALL::SideChainPlacementProcessor::setDefaultOptions | ( | ) |
Resets the options to default values.
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inline |
Set the mutation indicating sequence.
Definition at line 181 of file sideChainPlacementProcessor.h.
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virtual |
Processor method which is called before the operator()-call.
Reimplemented from BALL::UnaryProcessor< AtomContainer >.
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protected |
Sequence in OneLetterCode with mutated residues.
Definition at line 218 of file sideChainPlacementProcessor.h.
Options BALL::SideChainPlacementProcessor::options |
options
Definition at line 205 of file sideChainPlacementProcessor.h.
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protected |
Definition at line 221 of file sideChainPlacementProcessor.h.