#include <BALL/DOCKING/COMMON/structurePreparer.h>
Definition at line 21 of file structurePreparer.h.
◆ StructurePreparer()
BALL::StructurePreparer::StructurePreparer |
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String | type = "", |
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bool | ignore = 0 ) |
◆ assignAtomTypes()
tries to assign the exact atom types, as defined in 'iniFile', to all atoms of 'at'
◆ assignCharges()
void BALL::StructurePreparer::assignCharges |
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AtomContainer * | at, |
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int | overwrite_mode ) |
assign all partial charges#
- Parameters
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overwrite_mode | 0 = no overwriting of charges, 1 = overwrite all charges, 2 = automatic (overwrite all charges only if most atoms do not have a charge yet) |
◆ assignMMFF94AtomTypes()
void BALL::StructurePreparer::assignMMFF94AtomTypes |
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AtomContainer * | at | ) |
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◆ assignPLPAtomTypes()
void BALL::StructurePreparer::assignPLPAtomTypes |
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AtomContainer * | at | ) |
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◆ assignProteinCharges()
bool BALL::StructurePreparer::assignProteinCharges |
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AtomContainer * | at, |
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String | parameterFile, |
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int | overwrite_mode ) |
assigns charges to a protein based on the charges template section of the specified parameter file
- Parameters
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overwrite_mode | 0 = no overwriting of charges, 1 = overwrite all charges, 2 = automatic (overwrite all charges only if most atoms do not have a charge yet) |
◆ assignSimpleAtomTypes()
tries to assign simplied atom types based mainly on element symbols.
- Parameters
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'iniFile' | is needed to obtain the corresponding IDs (force field dependend AtomType of type int) for each of these simple type names
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◆ buildBonds()
◆ getSimpleAtomTypes()
const std::set< String > * BALL::StructurePreparer::getSimpleAtomTypes |
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◆ prepare()
◆ saturate()
◆ selectHeavyAtoms()
void BALL::StructurePreparer::selectHeavyAtoms |
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AtomContainer * | at | ) |
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◆ setScoringType()
void BALL::StructurePreparer::setScoringType |
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String | type | ) |
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◆ setSimpleAtomTypes()
void BALL::StructurePreparer::setSimpleAtomTypes |
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std::set< String > & | new_types | ) |
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