Action_Thermostats
Add_AtomRandomPerturbation
Add_FitFragmentPartialChargesAction
Add_RotateAroundBondAction
Add_SelectAtomByNameAction
Added_ParseSaveFragmentResults
AddingActions_SaveParseParticleParameters
Adding_Graph_to_ChangeBondActions
Adding_MD_integration_tests
Adding_ParticleName_to_Atom
Adding_StructOpt_integration_tests
AtomFragments
Automaking_mpqc_open
AutomationFragmentation_failures
Candidate_v1.5.4
Candidate_v1.6.0
Candidate_v1.6.1
ChangeBugEmailaddress
ChangingTestPorts
ChemicalSpaceEvaluator
CombiningParticlePotentialParsing
Combining_Subpackages
Debian_Package_split
Debian_package_split_molecuildergui_only
Disabling_MemDebug
Docu_Python_wait
EmpiricalPotential_contain_HomologyGraph
EmpiricalPotential_contain_HomologyGraph_documentation
Enable_parallel_make_install
Enhance_userguide
Enhanced_StructuralOptimization
Enhanced_StructuralOptimization_continued
Example_ManyWaysToTranslateAtom
Exclude_Hydrogens_annealWithBondGraph
FitPartialCharges_GlobalError
Fix_BoundInBox_CenterInBox_MoleculeActions
Fix_ChargeSampling_PBC
Fix_ChronosMutex
Fix_FitPartialCharges
Fix_FitPotential_needs_atomicnumbers
Fix_ForceAnnealing
Fix_IndependentFragmentGrids
Fix_ParseParticles
Fix_ParseParticles_split_forward_backward_Actions
Fix_PopActions
Fix_QtFragmentList_sorted_selection
Fix_Restrictedkeyset_FragmentMolecule
Fix_StatusMsg
Fix_StepWorldTime_single_argument
Fix_Verbose_Codepatterns
Fix_fitting_potentials
Fixes
ForceAnnealing_goodresults
ForceAnnealing_oldresults
ForceAnnealing_tocheck
ForceAnnealing_with_BondGraph
ForceAnnealing_with_BondGraph_continued
ForceAnnealing_with_BondGraph_continued_betteresults
ForceAnnealing_with_BondGraph_contraction-expansion
FragmentAction_writes_AtomFragments
FragmentMolecule_checks_bonddegrees
GeometryObjects
Gui_Fixes
Gui_displays_atomic_force_velocity
ImplicitCharges
IndependentFragmentGrids
IndependentFragmentGrids_IndividualZeroInstances
IndependentFragmentGrids_IntegrationTest
IndependentFragmentGrids_Sole_NN_Calculation
JobMarket_RobustOnKillsSegFaults
JobMarket_StableWorkerPool
JobMarket_unresolvable_hostname_fix
MoreRobust_FragmentAutomation
ODR_violation_mpqc_open
PartialCharges_OrthogonalSummation
PdbParser_setsAtomName
PythonUI_with_named_parameters
QtGui_reactivate_TimeChanged_changes
Recreated_GuiChecks
Rewrite_FitPartialCharges
RotateToPrincipalAxisSystem_UndoRedo
SaturateAtoms_findBestMatching
SaturateAtoms_singleDegree
StoppableMakroAction
Subpackage_CodePatterns
Subpackage_JobMarket
Subpackage_LinearAlgebra
Subpackage_levmar
Subpackage_mpqc_open
Subpackage_vmg
Switchable_LogView
ThirdParty_MPQC_rebuilt_buildsystem
TrajectoryDependenant_MaxOrder
TremoloParser_IncreasedPrecision
TremoloParser_MultipleTimesteps
TremoloParser_setsAtomName
Ubuntu_1604_changes
stable
Last change
on this file since ad011c was 16462f, checked in by Frederik Heber <heber@…>, 14 years ago |
PdbParser is now complete with respect to additionalAtomData.
- serial, name, resName, resSeq, element, and charge are updated if changed,
otherwise we use values from PdbAtomInfoContainer.
- PdbParser::saveLine() completely uses information from PdbAtomInfoContainer.
Testchanges:
- Simple_configuration/2/post/test.pdb updated as we are now closer to real
PDB format also concerning alignment and the resName changed again.
|
-
Property mode
set to
100644
|
File size:
1.9 KB
|
Rev | Line | |
---|
[4fbca9c] | 1 | /*
|
---|
| 2 | * PdbAtomInfoContainer.hpp
|
---|
| 3 | *
|
---|
| 4 | * Created on: Dec 4, 2010
|
---|
| 5 | * Author: heber
|
---|
| 6 | */
|
---|
| 7 |
|
---|
| 8 | #ifndef PDBATOMINFOCONTAINER_HPP_
|
---|
| 9 | #define PDBATOMINFOCONTAINER_HPP_
|
---|
| 10 |
|
---|
| 11 | #include "PdbKey.hpp"
|
---|
| 12 |
|
---|
[16462f] | 13 | class Vector;
|
---|
| 14 |
|
---|
[4fbca9c] | 15 | #include <string>
|
---|
[16462f] | 16 | #include <typeinfo>
|
---|
[4fbca9c] | 17 |
|
---|
| 18 | /**
|
---|
| 19 | * Holds tremolo-specific information which is not store in the atom class.
|
---|
| 20 | */
|
---|
| 21 | class PdbAtomInfoContainer {
|
---|
| 22 | public:
|
---|
| 23 | PdbAtomInfoContainer();
|
---|
| 24 | ~PdbAtomInfoContainer();
|
---|
| 25 |
|
---|
| 26 | // getter and setter
|
---|
[16462f] | 27 | template <class T> T get(const PdbKey::PdbDataKey key) const {
|
---|
| 28 | switch (key) {
|
---|
| 29 | default :
|
---|
| 30 | std::cout << "Unknown key or not representable as " << typeid(T).name() << ": " << key << std::endl;
|
---|
| 31 | break;
|
---|
| 32 | }
|
---|
| 33 | return (T)NULL;
|
---|
| 34 | }
|
---|
[4fbca9c] | 35 | void set(const PdbKey::PdbDataKey key, std::string value);
|
---|
| 36 |
|
---|
| 37 | /** Scans a value from a short string and checks whether its empty.
|
---|
| 38 | *
|
---|
| 39 | * @param value value to set
|
---|
| 40 | * @param _piece short string
|
---|
| 41 | */
|
---|
| 42 | template <class T> static void ScanKey(T& value, std::string _piece)
|
---|
| 43 | {
|
---|
| 44 | ConvertTo<T> toValue;
|
---|
| 45 | // scan all empty chars ' ' and skip
|
---|
| 46 | std::string::iterator iter = _piece.begin();
|
---|
| 47 | for (;iter != _piece.end();++iter)
|
---|
| 48 | if ((*iter != ' ') && (*iter != '\t'))
|
---|
| 49 | break;
|
---|
| 50 | // only set if there is something contained in the string
|
---|
| 51 | if (iter != _piece.end()) {
|
---|
| 52 | _piece.erase(_piece.begin(), iter);
|
---|
| 53 | value = toValue(_piece);
|
---|
| 54 | }
|
---|
| 55 | }
|
---|
| 56 |
|
---|
| 57 | private:
|
---|
[16462f] | 58 | std::string token;
|
---|
[4fbca9c] | 59 | int serial;
|
---|
| 60 | std::string name;
|
---|
[16462f] | 61 | char altLoc;
|
---|
[4fbca9c] | 62 | std::string resName;
|
---|
| 63 | char chainID;
|
---|
| 64 | int resSeq;
|
---|
| 65 | char iCode;
|
---|
[16462f] | 66 | Vector XYZ;
|
---|
[4fbca9c] | 67 | float occupancy;
|
---|
| 68 | float tempFactor;
|
---|
[16462f] | 69 | std::string element;
|
---|
[4fbca9c] | 70 | int charge;
|
---|
| 71 | };
|
---|
| 72 |
|
---|
[16462f] | 73 | template <>
|
---|
| 74 | std::string PdbAtomInfoContainer::get<std::string>(const PdbKey::PdbDataKey key) const;
|
---|
| 75 | template <>
|
---|
| 76 | int PdbAtomInfoContainer::get<int>(const PdbKey::PdbDataKey key) const;
|
---|
| 77 | template <>
|
---|
| 78 | double PdbAtomInfoContainer::get<double>(const PdbKey::PdbDataKey key) const;
|
---|
| 79 |
|
---|
[4fbca9c] | 80 | #endif /* PDBATOMINFOCONTAINER_HPP_ */
|
---|
Note:
See
TracBrowser
for help on using the repository browser.