Changes in src/Actions/MapOfActions.cpp [83f176:446bc1]

File:

• src/Actions/MapOfActions.cpp (modified) (30 diffs)

src/Actions/MapOfActions.cpp

@@ -1 @@
-/*
- * Project: MoleCuilder
- * Description: creates and alters molecular systems
- * Copyright (C)  2010 University of Bonn. All rights reserved.
- * Please see the LICENSE file or "Copyright notice" in builder.cpp for details.
- */
-
 /*
  * MapOfActions.cpp
@@ -12 +5 @@
  *      Author: heber
  */
-
-// include config.h
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
 
 #include "Helpers/MemDebug.hpp"
@@ -79 +67 @@
 #include "Actions/ParserAction/SaveXyzAction.hpp"
 #include "Actions/SelectionAction/AllAtomsAction.hpp"
-#include "Actions/SelectionAction/AllAtomsInsideCuboidAction.hpp"
-#include "Actions/SelectionAction/AllAtomsInsideSphereAction.hpp"
 #include "Actions/SelectionAction/AllAtomsOfMoleculeAction.hpp"
 #include "Actions/SelectionAction/AllMoleculesAction.hpp"
-#include "Actions/SelectionAction/AtomByElementAction.hpp"
 #include "Actions/SelectionAction/AtomByIdAction.hpp"
 #include "Actions/SelectionAction/ClearAllAtomsAction.hpp"
 #include "Actions/SelectionAction/ClearAllMoleculesAction.hpp"
-#include "Actions/SelectionAction/MoleculeByFormulaAction.hpp"
 #include "Actions/SelectionAction/MoleculeByIdAction.hpp"
 #include "Actions/SelectionAction/MoleculeOfAtomAction.hpp"
 #include "Actions/SelectionAction/NotAllAtomsAction.hpp"
-#include "Actions/SelectionAction/NotAllAtomsInsideCuboidAction.hpp"
-#include "Actions/SelectionAction/NotAllAtomsInsideSphereAction.hpp"
 #include "Actions/SelectionAction/NotAllAtomsOfMoleculeAction.hpp"
 #include "Actions/SelectionAction/NotAllMoleculesAction.hpp"
-#include "Actions/SelectionAction/NotAtomByElementAction.hpp"
 #include "Actions/SelectionAction/NotAtomByIdAction.hpp"
-#include "Actions/SelectionAction/NotMoleculeByFormulaAction.hpp"
 #include "Actions/SelectionAction/NotMoleculeByIdAction.hpp"
 #include "Actions/SelectionAction/NotMoleculeOfAtomAction.hpp"
@@ -109 +89 @@
 #include "Actions/WorldAction/InputAction.hpp"
 #include "Actions/WorldAction/OutputAction.hpp"
+#include "Actions/WorldAction/RemoveSphereOfAtomsAction.hpp"
 #include "Actions/WorldAction/RepeatBoxAction.hpp"
 #include "Actions/WorldAction/ScaleBoxAction.hpp"
@@ -231 +212 @@
   DescriptionMap["redo"] = "redo last action";
   DescriptionMap["remove-atom"] = "remove a specified atom";
+  DescriptionMap["remove-sphere"] = "remove sphere of atoms of around a specified atom";
   DescriptionMap["repeat-box"] = "create periodic copies of the simulation box per axis";
   DescriptionMap["rotate-origin"] = "rotate selected atoms by a specific angle around origin";
@@ -242 +224 @@
   DescriptionMap["select-all-atoms"] = "select all atoms";
   DescriptionMap["select-all-molecules"] = "select all molecules";
-  DescriptionMap["select-atom-by-element"] = "select an atom by element";
   DescriptionMap["select-atom-by-id"] = "select an atom by index";
-  DescriptionMap["select-atoms-inside-cuboid"] = "select all atoms inside a cuboid";
-  DescriptionMap["select-atoms-inside-sphere"] = "select all atoms inside a sphere";
   DescriptionMap["select-molecule-by-id"] = "select a molecule by index";
-  DescriptionMap["select-molecule-by-formula"] = "select a molecule by chemical formula";
   DescriptionMap["select-molecule-of-atom"] = "select a molecule to which a given atom belongs";
   DescriptionMap["select-molecules-atoms"] = "select all atoms of a molecule";
@@ -259 +237 @@
   DescriptionMap["unselect-all-atoms"] = "unselect all atoms";
   DescriptionMap["unselect-all-molecules"] = "unselect all molecules";
-  DescriptionMap["unselect-atom-by-element"] = "unselect an atom by element";
   DescriptionMap["unselect-atom-by-id"] = "unselect an atom by index";
-  DescriptionMap["unselect-atoms-inside-cuboid"] = "unselect all atoms inside a cuboid";
-  DescriptionMap["unselect-atoms-inside-sphere"] = "unselect all atoms inside a sphere";
-  DescriptionMap["unselect-molecule-by-formula"] = "unselect a molecule by chemical formula";
   DescriptionMap["unselect-molecule-by-id"] = "unselect a molecule by index";
   DescriptionMap["unselect-molecule-of-atom"] = "unselect a molecule to which a given atom belongs";
@@ -271 +245 @@
   DescriptionMap["version"] = "show version";
   // keys for values
-  DescriptionMap["angle-x"] = "angle of a rotation around x axis";
-  DescriptionMap["angle-y"] = "angle of a rotation around y axis";
-  DescriptionMap["angle-z"] = "angle of a rotation around z axis";
   DescriptionMap["bin-output-file"] = "name of the bin output file";
   DescriptionMap["bin-end"] = "start of the last bin";
@@ -322 +293 @@
   ShortFormMap["parse-xyz"] = "p";
   ShortFormMap["remove-atom"] = "r";
+  ShortFormMap["remove-sphere"] = "R";
   ShortFormMap["repeat-box"] = "d";
   ShortFormMap["rotate-to-pas"] = "m";
@@ -338 +310 @@
 
   // value types for the actions
-  TypeMap["add-atom"] = &typeid(const element);
+  TypeMap["add-atom"] = &typeid(element);
   TypeMap["bond-file"] = &typeid(std::string);
   TypeMap["bond-table"] = &typeid(std::string);
@@ -344 +316 @@
   TypeMap["center-in-box"] = &typeid(BoxValue);
   TypeMap["change-box"] = &typeid(BoxValue);
-  TypeMap["change-element"] = &typeid(const element);
+  TypeMap["change-element"] = &typeid(element);
   TypeMap["change-molname"] = &typeid(std::string);
   TypeMap["clear-atom-selection"] = &typeid(void);
@@ -366 +338 @@
   TypeMap["redo"] = &typeid(void);
   TypeMap["remove-atom"] = &typeid(void);
+  TypeMap["remove-sphere"] = &typeid(double);
   TypeMap["repeat-box"] = &typeid(VectorValue);
   TypeMap["rotate-origin"] = &typeid(double);
@@ -376 +349 @@
   TypeMap["select-all-atoms"] = &typeid(void);
   TypeMap["select-all-molecules"] = &typeid(void);
-  TypeMap["select-atom-by-element"] = &typeid(const element);
   TypeMap["select-atom-by-id"] = &typeid(atom);
-  TypeMap["select-atoms-inside-cuboid"] = &typeid(VectorValue);
-  TypeMap["select-atoms-inside-sphere"] = &typeid(double);
-  TypeMap["select-molecule-by-formula"] = &typeid(std::string);
   TypeMap["select-molecule-by-id"] = &typeid(molecule);
   TypeMap["select-molecule-of-atom"] = &typeid(atom);
@@ -393 +362 @@
   TypeMap["unselect-all-atoms"] = &typeid(void);
   TypeMap["unselect-all-molecules"] = &typeid(void);
-  TypeMap["unselect-atom-by-element"] = &typeid(const element);
   TypeMap["unselect-atom-by-id"] = &typeid(atom);
-  TypeMap["unselect-atoms-inside-cuboid"] = &typeid(VectorValue);
-  TypeMap["unselect-atoms-inside-sphere"] = &typeid(double);
-  TypeMap["unselect-molecule-by-formula"] = &typeid(std::string);
   TypeMap["unselect-molecule-by-id"] = &typeid(molecule);
   TypeMap["unselect-molecule-of-atom"] = &typeid(atom);
@@ -405 +370 @@
 
   // value types for the values
-  TypeMap["angle-x"] = &typeid(double);
-  TypeMap["angle-y"] = &typeid(double);
-  TypeMap["angle-z"] = &typeid(double);
   TypeMap["bin-output-file"] = &typeid(std::string);
   TypeMap["bin-end"] = &typeid(double);
@@ -416 +378 @@
   TypeMap["distances"] = &typeid(VectorValue);
   TypeMap["DoRotate"] = &typeid(bool);
-  TypeMap["element"] = &typeid(const element);
-  TypeMap["elements"] = &typeid(std::vector<const element *>);
+  TypeMap["element"] = &typeid(element);
+  TypeMap["elements"] = &typeid(std::vector<element *>);
   TypeMap["end-step"] = &typeid(int);
   TypeMap["id-mapping"] = &typeid(bool);
@@ -446 +408 @@
   TypeEnumMap[&typeid(atom)] = Atom;
   TypeEnumMap[&typeid(std::vector<atom *>)] = ListOfAtoms;
-  TypeEnumMap[&typeid(const element)] = Element;
-  TypeEnumMap[&typeid(std::vector<const element *>)] = ListOfElements;
+  TypeEnumMap[&typeid(element)] = Element;
+  TypeEnumMap[&typeid(std::vector<element *>)] = ListOfElements;
 
   // default values for any action that needs one (always string!)
@@ -506 +468 @@
   MenuContainsActionMap.insert( pair<std::string, std::string> ("selection", "select-all-atoms") );
   MenuContainsActionMap.insert( pair<std::string, std::string> ("selection", "select-all-molecules") );
-  MenuContainsActionMap.insert( pair<std::string, std::string> ("selection", "select-atom-by-element") );
   MenuContainsActionMap.insert( pair<std::string, std::string> ("selection", "select-atom-by-id") );
-  MenuContainsActionMap.insert( pair<std::string, std::string> ("selection", "select-atoms-inside-cuboid") );
-  MenuContainsActionMap.insert( pair<std::string, std::string> ("selection", "select-atoms-inside-sphere") );
   MenuContainsActionMap.insert( pair<std::string, std::string> ("selection", "select-molecule-by-id") );
-  MenuContainsActionMap.insert( pair<std::string, std::string> ("selection", "select-molecule-by-formula") );
   MenuContainsActionMap.insert( pair<std::string, std::string> ("selection", "select-molecule-of-atom") );
   MenuContainsActionMap.insert( pair<std::string, std::string> ("selection", "select-molecules-atoms") );
   MenuContainsActionMap.insert( pair<std::string, std::string> ("selection", "unselect-all-atoms") );
   MenuContainsActionMap.insert( pair<std::string, std::string> ("selection", "unselect-all-molecules") );
-  MenuContainsActionMap.insert( pair<std::string, std::string> ("selection", "unselect-atom-by-element") );
   MenuContainsActionMap.insert( pair<std::string, std::string> ("selection", "unselect-atom-by-id") );
-  MenuContainsActionMap.insert( pair<std::string, std::string> ("selection", "unselect-atoms-inside-cuboid") );
-  MenuContainsActionMap.insert( pair<std::string, std::string> ("selection", "unselect-atoms-inside-sphere") );
-  MenuContainsActionMap.insert( pair<std::string, std::string> ("selection", "unselect-molecule-by-formula") );
   MenuContainsActionMap.insert( pair<std::string, std::string> ("selection", "unselect-molecule-by-id") );
   MenuContainsActionMap.insert( pair<std::string, std::string> ("selection", "unselect-molecule-of-atom") );
@@ -535 +489 @@
   MenuContainsActionMap.insert( pair<std::string, std::string> ("world", "input") );
   MenuContainsActionMap.insert( pair<std::string, std::string> ("world", "output") );
+  MenuContainsActionMap.insert( pair<std::string, std::string> ("world", "remove-sphere") );
   MenuContainsActionMap.insert( pair<std::string, std::string> ("world", "repeat-box") );
   MenuContainsActionMap.insert( pair<std::string, std::string> ("world", "scale-box") );
@@ -573 +528 @@
   generic.insert("redo");
   generic.insert("remove-atom");
+  generic.insert("remove-sphere");
   generic.insert("repeat-box");
   generic.insert("rotate-origin");
@@ -583 +539 @@
   generic.insert("select-all-atoms");
   generic.insert("select-all-molecules");
-  generic.insert("select-atom-by-element");
   generic.insert("select-atom-by-id");
-  generic.insert("select-atoms-inside-cuboid");
-  generic.insert("select-atoms-inside-sphere");
   generic.insert("select-molecule-by-id");
-  generic.insert("select-molecule-by-formula");
   generic.insert("select-molecule-of-atom");
   generic.insert("select-molecules-atoms");
@@ -600 +552 @@
   generic.insert("unselect-all-atoms");
   generic.insert("unselect-all-molecules");
-  generic.insert("unselect-atom-by-element");
   generic.insert("unselect-atom-by-id");
-  generic.insert("unselect-atoms-inside-cuboid");
-  generic.insert("unselect-atoms-inside-sphere");
-  generic.insert("unselect-molecule-by-formula");
   generic.insert("unselect-molecule-by-id");
   generic.insert("unselect-molecule-of-atom");
@@ -616 +564 @@
 
     // hidden arguments
-  hidden.insert("angle-x");
-  hidden.insert("angle-y");
-  hidden.insert("angle-z");
   hidden.insert("bin-end");
   hidden.insert("bin-output-file");
@@ -650 +595 @@
 }
 
-bool MapOfActions::isCurrentValuePresent(const char *name) const
-{
-  return (CurrentValue.find(name) != CurrentValue.end());
-}
-
 void MapOfActions::queryCurrentValue(const char * name, class atom * &_T)
 {
@@ -668 +608 @@
 }
 
-void MapOfActions::queryCurrentValue(const char * name, const element * &_T)  {
+void MapOfActions::queryCurrentValue(const char * name, class element * &_T)  {
   int Z = -1;
-  if (typeid(const element ) == *TypeMap[name]) {
+  if (typeid( element ) == *TypeMap[name]) {
     if (CurrentValue.find(name) == CurrentValue.end())
       throw MissingValueException(__FILE__, __LINE__);
@@ -752 +692 @@
 }
 
-void MapOfActions::queryCurrentValue(const char * name, std::vector<const element *>&_T)
+void MapOfActions::queryCurrentValue(const char * name, std::vector<element *>&_T)
 {
   int Z = -1;
-  const element *elemental = NULL;
-  if (typeid( std::vector<const element *> ) == *TypeMap[name]) {
+  element *elemental = NULL;
+  if (typeid( std::vector<element *> ) == *TypeMap[name]) {
     if (CurrentValue.find(name) == CurrentValue.end())
       throw MissingValueException(__FILE__, __LINE__);
@@ -804 +744 @@
 }
 
-void MapOfActions::setCurrentValue(const char * name, const element * &_T)
-{
-  if (typeid(const element ) == *TypeMap[name]) {
+void MapOfActions::setCurrentValue(const char * name, class element * &_T)
+{
+  if (typeid( element ) == *TypeMap[name]) {
     std::ostringstream stream;
-    stream << _T->getAtomicNumber();
+    stream << _T->Z;
     CurrentValue[name] = stream.str();
   } else
@@ -864 +804 @@
 }
 
-void MapOfActions::setCurrentValue(const char * name, std::vector<const element *>&_T)
-{
-  if (typeid( std::vector<const element *> ) == *TypeMap[name]) {
+void MapOfActions::setCurrentValue(const char * name, std::vector<element *>&_T)
+{
+  if (typeid( std::vector<element *> ) == *TypeMap[name]) {
     std::ostringstream stream;
-    for (std::vector<const element *>::iterator iter = _T.begin(); iter != _T.end(); ++iter) {
-      stream << (*iter)->getAtomicNumber() << " ";
+    for (std::vector<element *>::iterator iter = _T.begin(); iter != _T.end(); ++iter) {
+      stream << (*iter)->Z << " ";
     }
     CurrentValue[name] = stream.str();
@@ -933 +873 @@
   new SelectionClearAllMoleculesAction();
   new SelectionAllAtomsAction();
-  new SelectionAllAtomsInsideCuboidAction();
-  new SelectionAllAtomsInsideSphereAction();
   new SelectionAllAtomsOfMoleculeAction();
   new SelectionAllMoleculesAction();
-  new SelectionAtomByElementAction();
   new SelectionAtomByIdAction();
   new SelectionMoleculeByIdAction();
-  new SelectionMoleculeByFormulaAction();
   new SelectionMoleculeOfAtomAction();
   new SelectionNotAllAtomsAction();
-  new SelectionNotAllAtomsInsideCuboidAction();
-  new SelectionNotAllAtomsInsideSphereAction();
   new SelectionNotAllAtomsOfMoleculeAction();
   new SelectionNotAllMoleculesAction();
-  new SelectionNotAtomByElementAction();
   new SelectionNotAtomByIdAction();
-  new SelectionNotMoleculeByFormulaAction();
   new SelectionNotMoleculeByIdAction();
   new SelectionNotMoleculeOfAtomAction();
@@ -963 +895 @@
   new WorldInputAction();
   new WorldOutputAction();
+  new WorldRemoveSphereOfAtomsAction();
   new WorldRepeatBoxAction();
   new WorldScaleBoxAction();