From: toshinagata1964 Date: Thu, 21 Jul 2011 16:45:41 +0000 (+0000) Subject: Create New Atom menu command is being implemented (not tested at all yet) X-Git-Tag: v1.0.2~552 X-Git-Url: http://git.osdn.net/view?a=commitdiff_plain;h=3fba955cc2d5e71b0e818bc84978e022f394ec4b;p=molby%2FMolby.git Create New Atom menu command is being implemented (not tested at all yet) git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@78 a2be9bc6-48de-4e38-9406-05402d4bc13c --- diff --git a/Documents/etc/tutorial_5_01.png b/Documents/etc/tutorial_5_01.png new file mode 100644 index 0000000..955ea3d Binary files /dev/null and b/Documents/etc/tutorial_5_01.png differ diff --git a/Documents/src/doc_source.html b/Documents/src/doc_source.html index dd83497..25302b0 100644 --- a/Documents/src/doc_source.html +++ b/Documents/src/doc_source.html @@ -913,7 +913,7 @@ Molby の分子力学計算は、基本的な分子力場（結合の伸縮、

Step Five: Edit a Molecule: Using a Property Table

1. The Property Table of a Molecule

-A molecule has many properties. It has a set of atoms and bonds. An atom has a name, an atom type, an element, a weight (which can be derived from the element), a charge, coordinates, and so on. According to the custom in the biomolecular modeling, atoms are grouped in "residues." It also has a set of parameters used in molecular mechanics. Molby also has a limited support for quantum chemical calculations. For that purpose, a molecule in Molby can retain information such as MO coefficients. +A molecule has many properties. It has a set of atoms and bonds. An atom has a name, an atom type, an element, a weight (which can be derived from the element), a charge, coordinates, and so on. According to the custom in the biomolecular modeling, atoms are grouped in "residues." It also has a set of parameters used in molecular mechanics. Molby also has a limited support for quantum chemical calculations. In relation to that, a molecule in Molby can retain extra information such as MO coefficients.

Most of these information are accessible via the property table. The table is on the left side of the model window. diff --git a/MolLib/MainView.c b/MolLib/MainView.c index f0ffc24..6abda71 100755 --- a/MolLib/MainView.c +++ b/MolLib/MainView.c @@ -2987,6 +2987,26 @@ MainView_numberOfRowsInTable(MainView *mview) return IntGroupGetCount(mview->tableCache); } +int +MainView_indexToTableRow(MainView *mview, int idx) +{ + if (mview == NULL) + return -1; + if (mview->tableIndex == kMainViewParameterTableIndex) + return -1; /* Not supported yet */ + return IntGroupLookupPoint(mview->tableCache, idx); +} + +int +MainView_tableRowToIndex(MainView *mview, int row) +{ + if (mview == NULL) + return -1; + if (mview->tableIndex == kMainViewParameterTableIndex) + return -1; /* Not supported yet */ + return IntGroupGetNthPoint(mview->tableCache, row); +} + static char * sAtomDescription(Atom *ap, char *buf, int bufsize) { diff --git a/MolLib/MainView.h b/MolLib/MainView.h index ff0b5ce..3bdf663 100755 --- a/MolLib/MainView.h +++ b/MolLib/MainView.h @@ -190,6 +190,8 @@ void MainView_tableTitleForIndex(MainView *mview, int idx, char *buf, int bufsiz void MainView_createColumnsForTableAtIndex(MainView *mview, int idx); void MainView_refreshTable(MainView *mview); int MainView_numberOfRowsInTable(MainView *mview); +int MainView_indexToTableRow(MainView *mview, int idx); +int MainView_tableRowToIndex(MainView *mview, int row); void MainView_valueForTable(MainView *mview, int column, int row, char *buf, int bufsize); void MainView_setValueForTable(MainView *mview, int column, int row, const char *buf); int MainView_setColorForTable(MainView *mview, int column, int row, float *fg, float *bg); @@ -238,6 +240,7 @@ STUB void MainViewCallback_setTableSelection(MainView *mview, IntGroup *selectio STUB IntGroup *MainViewCallback_getTableSelection(MainView *mview); STUB void MainViewCallback_showTable(MainView *mview); STUB void MainViewCallback_hideTable(MainView *mview); +STUB void MainViewCallback_ensureVisible(MainView *mview, int row); /* Register the type definition */ //extern void MainView_register(PyObject *module); diff --git a/MolLib/Ruby_bind/ruby_bind.c b/MolLib/Ruby_bind/ruby_bind.c index de7d234..1b092d8 100644 --- a/MolLib/Ruby_bind/ruby_bind.c +++ b/MolLib/Ruby_bind/ruby_bind.c @@ -5622,14 +5622,22 @@ s_Molecule_CreateAnAtom(int argc, VALUE *argv, VALUE self) char *p, resName[6], atomName[6]; int resSeq; Data_Get_Struct(self, Molecule, mol); - rb_scan_args(argc, argv, "11", &name, &ival); + rb_scan_args(argc, argv, "02", &name, &ival); if (ival != Qnil) pos = NUM2INT(rb_Integer(ival)); else pos = -1; - p = StringValuePtr(name); - i = MoleculeAnalyzeAtomName(p, resName, &resSeq, atomName); - if (atomName[0] == 0) - rb_raise(rb_eMolbyError, "bad atom name specification: %s", p); + if (name != Qnil) { + p = StringValuePtr(name); + if (p[0] != 0) { + i = MoleculeAnalyzeAtomName(p, resName, &resSeq, atomName); + if (atomName[0] == 0) + rb_raise(rb_eMolbyError, "bad atom name specification: %s", p); + } + } else p = NULL; + if (p == NULL || p[0] == 0) { + memset(atomName, 0, 4); + resSeq = -1; + } memset(&arec, 0, sizeof(arec)); strncpy(arec.aname, atomName, 4); if (resSeq >= 0) { diff --git a/memo.txt b/memo.txt index fceb384..a0a145d 100755 --- a/memo.txt +++ b/memo.txt @@ -185,4 +185,5 @@ rdt: (only used in LES) sander -O -i min.in -o NAME.out -p NAME.prmtop -c NAME.inpcrd -x NAME.mdcrd -r NAME.restrt - +2011.7.8. +　MoleculeMerge(), MoleculeUnmerge() の仕様を見直した方がいい。undo サポート用に、bond/angle/dihedral/improper を指定した位置に入れる機能が欲しい。パラメータも、すべての種類のパラメータを指定した位置に入れる機能が必要。IntGroup の配列でパラメータを与えるか？ diff --git a/wxSources/MoleculeView.cpp b/wxSources/MoleculeView.cpp index 95e0ee0..6cf0201 100755 --- a/wxSources/MoleculeView.cpp +++ b/wxSources/MoleculeView.cpp @@ -1224,3 +1224,11 @@ MainViewCallback_hideTable(MainView *mview) // [doc hideTable: doc]; // } } + +void +MainViewCallback_ensureVisible(MainView *mview, int row) +{ + MyListCtrl *listctrl = s_MyListCtrlFromMainView(mview); + if (listctrl != NULL) + listctrl->EnsureVisible(row); +} diff --git a/wxSources/MyApp.cpp b/wxSources/MyApp.cpp index c2367d2..f4ef1f4 100755 --- a/wxSources/MyApp.cpp +++ b/wxSources/MyApp.cpp @@ -346,6 +346,17 @@ MyApp::CreateMenuBar(int kind, wxMenu **out_file_history_menu, wxMenu **out_edit edit_menu->Append(myMenuID_SelectFragment, _T("Select Fragment\tCtrl-F")); edit_menu->Append(myMenuID_SelectReverse, _T("Select Reverse")); edit_menu->AppendSeparator(); + wxMenu *create_parameter_menu = new wxMenu; + create_parameter_menu->Append(myMenuID_CreateNewVdwParameter, _T("Vdw")); + create_parameter_menu->Append(myMenuID_CreateNewBondParameter, _T("Bond")); + create_parameter_menu->Append(myMenuID_CreateNewAngleParameter, _T("Angle")); + create_parameter_menu->Append(myMenuID_CreateNewDihedralParameter, _T("Dihedral")); + create_parameter_menu->Append(myMenuID_CreateNewImproperParameter, _T("Improper")); + create_parameter_menu->Append(myMenuID_CreateNewVdwPairParameter, _T("Vdw Pair")); + create_parameter_menu->Append(myMenuID_CreateNewVdwOffsetParameter, _T("Vdw Offset")); + edit_menu->Append(myMenuID_CreateNewAtom, _T("Create New Atom\tCtrl-I")); + edit_menu->Append(myMenuID_CreateNewParameter, _T("Create New Parameter"), create_parameter_menu); + edit_menu->AppendSeparator(); wxMenu *add_hydrogen_menu = new wxMenu; add_hydrogen_menu->Append(myMenuID_AddHydrogenSp3, _T("Tetrahedral sp3")); add_hydrogen_menu->Append(myMenuID_AddHydrogenSp2, _T("Trigonal sp2")); diff --git a/wxSources/MyApp.h b/wxSources/MyApp.h index 1597a49..32cdb02 100755 --- a/wxSources/MyApp.h +++ b/wxSources/MyApp.h @@ -48,48 +48,57 @@ enum { myMenuID_Export = 102, myMenuID_SelectFragment = 103, myMenuID_SelectReverse = 104, - myMenuID_AddHydrogen = 105, - myMenuID_AddHydrogenSp3 = 106, - myMenuID_AddHydrogenSp2 = 107, - myMenuID_AddHydrogenLinear = 108, - myMenuID_AddHydrogenPyramidal = 109, - myMenuID_AddHydrogenBent = 110, - myMenuID_FitToScreen = 120, - myMenuID_CenterSelection = 121, - myMenuID_ShowUnitCell = 122, - myMenuID_ShowPeriodicBox = 123, - myMenuID_ShowHydrogens = 124, - myMenuID_ShowDummyAtoms = 125, - myMenuID_ShowExpandedAtoms = 126, - myMenuID_ShowEllipsoids = 127, - myMenuID_ShowRotationCenter = 128, - myMenuID_ShowGraphite = 129, - myMenuID_LineMode = 130, - myMenuID_ShowAllAtoms = 131, - myMenuID_HideSelected = 132, - myMenuID_HideUnselected = 133, - myMenuID_HideReverse = 134, - myMenuID_MolecularDynamics = 140, - myMenuID_Minimize = 141, - myMenuID_StopMDRun = 142, + myMenuID_CreateNewAtom = 105, + myMenuID_CreateNewParameter = 106, + myMenuID_CreateNewVdwParameter = 107, + myMenuID_CreateNewBondParameter = 108, + myMenuID_CreateNewAngleParameter = 109, + myMenuID_CreateNewDihedralParameter = 110, + myMenuID_CreateNewImproperParameter = 111, + myMenuID_CreateNewVdwPairParameter = 112, + myMenuID_CreateNewVdwOffsetParameter = 113, + myMenuID_AddHydrogen = 114, + myMenuID_AddHydrogenSp3 = 115, + myMenuID_AddHydrogenSp2 = 116, + myMenuID_AddHydrogenLinear = 117, + myMenuID_AddHydrogenPyramidal = 118, + myMenuID_AddHydrogenBent = 119, + myMenuID_FitToScreen = 150, + myMenuID_CenterSelection = 151, + myMenuID_ShowUnitCell = 152, + myMenuID_ShowPeriodicBox = 153, + myMenuID_ShowHydrogens = 154, + myMenuID_ShowDummyAtoms = 155, + myMenuID_ShowExpandedAtoms = 156, + myMenuID_ShowEllipsoids = 157, + myMenuID_ShowRotationCenter = 158, + myMenuID_ShowGraphite = 159, + myMenuID_LineMode = 160, + myMenuID_ShowAllAtoms = 161, + myMenuID_HideSelected = 162, + myMenuID_HideUnselected = 163, + myMenuID_HideReverse = 164, + myMenuID_MolecularDynamics = 200, + myMenuID_Minimize = 201, + myMenuID_StopMDRun = 202, // myMenuID_ReadParameters = 143, - myMenuID_ViewGlobalParameters = 144, - myMenuID_ViewParameterFilesList = 145, - myMenuID_DefinePeriodicBox = 146, - myMenuID_ShowPeriodicImage = 147, - myMenuID_PressureControl = 148, - myMenuID_DefineSymmetry = 149, - myMenuID_ExpandBySymmetry = 150, - myMenuID_MDTools = 151, - myMenuID_RunAntechamber = 152, - myMenuID_RunResp = 153, - myMenuID_CreateSanderInput = 154, - myMenuID_ImportAmberLib = 155, - myMenuID_CreateGamessInput = 160, - myMenuID_CreateMOCube = 161, - myMenuID_ExecuteScript = 200, - myMenuID_OpenConsoleWindow = 201, - myMenuID_CustomScript = 202, + myMenuID_ViewGlobalParameters = 204, + myMenuID_ViewParameterFilesList = 205, + myMenuID_DefinePeriodicBox = 206, + myMenuID_ShowPeriodicImage = 207, + myMenuID_PressureControl = 208, + myMenuID_DefineSymmetry = 209, + myMenuID_ExpandBySymmetry = 210, + myMenuID_MDTools = 211, + myMenuID_RunAntechamber = 212, + myMenuID_RunResp = 213, + myMenuID_CreateSanderInput = 214, + myMenuID_ImportAmberLib = 215, + myMenuID_CreateGamessInput = 250, + myMenuID_CreateMOCube = 251, + myMenuID_ExecuteScript = 300, + myMenuID_OpenConsoleWindow = 301, + myMenuID_CustomScript = 302, myMenuID_MyLastMenuItem = 499 }; diff --git a/wxSources/MyDocument.cpp b/wxSources/MyDocument.cpp index e6d446e..da11306 100755 --- a/wxSources/MyDocument.cpp +++ b/wxSources/MyDocument.cpp @@ -73,6 +73,8 @@ BEGIN_EVENT_TABLE(MyDocument, wxDocument) EVT_MENU(wxID_PASTE, MyDocument::OnPaste) EVT_MENU(wxID_CUT, MyDocument::OnCut) EVT_MENU(wxID_DELETE, MyDocument::OnDelete) + EVT_MENU(myMenuID_CreateNewAtom, MyDocument::OnCreateNewAtom) + EVT_MENU_RANGE(myMenuID_CreateNewVdwParameter, myMenuID_CreateNewVdwOffsetParameter, MyDocument::OnCreateNewParameter) EVT_MENU(wxID_SELECTALL, MyDocument::OnSelectAll) EVT_MENU(myMenuID_SelectFragment, MyDocument::OnSelectFragment) EVT_MENU(myMenuID_SelectReverse, MyDocument::OnSelectReverse) @@ -499,6 +501,46 @@ MyDocument::OnDelete(wxCommandEvent& event) } void +MyDocument::OnCreateNewAtom(wxCommandEvent &event) +{ + int idx; + IntGroup *ig = MoleculeGetSelection(mol); + MainView *mview = GetMainView(); + if (mview == NULL) + return; + MainViewCallback_selectTable(mview, kMainViewAtomTableIndex); + if (ig != NULL && IntGroupGetCount(ig) > 0) { + idx = IntGroupGetEndPoint(ig, IntGroupGetIntervalCount(ig) - 1); + } else { + idx = mol->natoms; + } + MolActionCreateAndPerform(mol, SCRIPT_ACTION("si"), "create_atom", "", idx); + ig = IntGroupNewWithPoints(idx, 1, -1); + MoleculeSetSelection(mol, ig); + IntGroupRelease(ig); + MainViewCallback_setNeedsDisplay(mview, 1); + MainViewCallback_reloadTableData(mview); + MainViewCallback_ensureVisible(mview, MainView_indexToTableRow(mview, idx)); +} + +void +MyDocument::OnCreateNewParameter(wxCommandEvent &event) +{ +/* int uid = event.GetId(); + const char *type; + IntGroup *ig; + switch (uid) { + case myMenuID_CreateNewVdwParameter: type = "td"; break; + case myMenuID_AddHydrogenSp2: type = "tr"; break; + case myMenuID_AddHydrogenLinear: type = "li"; break; + case myMenuID_AddHydrogenPyramidal: type = "py"; break; + case myMenuID_AddHydrogenBent: type = "be"; break; + default: return; + } + */ +} + +void MyDocument::OnSelectAll(wxCommandEvent& event) { if (wxWindow::FindFocus() == ((MoleculeView *)GetFirstView())->GetListCtrl() && mol->mview->tableIndex == kMainViewParameterTableIndex) { diff --git a/wxSources/MyDocument.h b/wxSources/MyDocument.h index 6d0cf9b..3004520 100755 --- a/wxSources/MyDocument.h +++ b/wxSources/MyDocument.h @@ -85,6 +85,9 @@ public: void OnPaste(wxCommandEvent& event); void OnDelete(wxCommandEvent& event); + void OnCreateNewAtom(wxCommandEvent &event); + void OnCreateNewParameter(wxCommandEvent &event); + void OnSelectAll(wxCommandEvent& event); void OnSelectFragment(wxCommandEvent& event); void OnSelectReverse(wxCommandEvent& event);