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authorBryan Bishop <kanzure@gmail.com>2012-09-17 15:55:38 -0500
committerBryan Bishop <kanzure@gmail.com>2012-09-17 15:55:38 -0500
commitabae3c8d869d9ad43d798b23a1e97473c03ebcf8 (patch)
treea1df3595aa0d6de0c018ce17ace8225ba1d9803e
parentf2d8861f28e235dcbcb13274771b072bd83205c2 (diff)
downloadnanoengineer-abae3c8d869d9ad43d798b23a1e97473c03ebcf8.tar.gz
nanoengineer-abae3c8d869d9ad43d798b23a1e97473c03ebcf8.zip
tab crusading (python files)
Diffstat
-rw-r--r--cad/plugins/NanoVision-1/src/Plugins/RenderingEngines/OpenGL/NXOpenGLRenderingEngine.cpp2178
-rw-r--r--cad/src/cnt/commands/InsertNanotube/InsertNanotube_EditCommand.py2
-rw-r--r--cad/src/command_support/DnaOrCnt_PropertyManager.py2
-rwxr-xr-xcad/src/commands/Fuse/FuseChunks_Command.py2
-rw-r--r--cad/src/commands/LightingScheme/LightingScheme_PropertyManager.py17
-rwxr-xr-xcad/src/commands/PlaneProperties/PlanePropertyManager.py14
-rw-r--r--cad/src/dna/commands/DnaStrand/DnaStrand_EditCommand.py2
-rw-r--r--cad/src/dna/commands/InsertDna/InsertDna_EditCommand.py2
-rw-r--r--cad/src/dna/generators/Dna_Generator.py26
-rwxr-xr-xcad/src/experimental/NH1_Integration/HDF5_SimResults/lib/NE1_Simulation/SimResultsDataStore.py872
-rwxr-xr-xcad/src/experimental/NH1_Integration/lib/NE1_CorePlugins/EnergyMinimizer.py38
-rwxr-xr-xcad/src/experimental/NH1_Integration/lib/NE1_JobManagement/NE1_Job.py226
-rwxr-xr-xcad/src/experimental/NH1_Integration/lib/NE1_Lib/NE1_Lib.py138
-rwxr-xr-xcad/src/experimental/NH1_Integration/lib/NE1_Simulation/Parameter.py238
-rwxr-xr-xcad/src/experimental/NH1_Integration/lib/NE1_Simulation/SimSpecification.py654
-rwxr-xr-xcad/src/experimental/basic-qt-app/ticker.py4
-rw-r--r--cad/src/graphics/drawables/DirectionArrow.py16
-rwxr-xr-xcad/src/graphics/drawing/ColorSorter.py26
-rwxr-xr-xcad/src/graphics/drawing/drawDnaLadder.py2
-rw-r--r--cad/src/graphics/drawing/drawNanotubeLadder.py2
-rw-r--r--cad/src/graphics/drawing/drawPeptideTrace.py2
-rwxr-xr-xcad/src/graphics/drawing/drawers.py6
-rwxr-xr-xcad/src/graphics/drawing/gl_lighting.py2
-rw-r--r--cad/src/graphics/drawing/gl_shaders.py12
-rw-r--r--cad/src/graphics/drawing/shader_objects_patch.py2
-rw-r--r--cad/src/graphics/drawing/vbo_patch.py10
-rwxr-xr-xcad/src/graphics/rendering/povray/povray.py2
-rw-r--r--cad/src/model/Chunk_Dna_methods.py6
-rwxr-xr-xcad/src/model/Plane.py2
-rwxr-xr-xcad/src/model/jigs.py4
-rw-r--r--cad/src/operations/ops_display.py4
-rw-r--r--cad/src/outtakes/PeptideGroup.py13
-rwxr-xr-xcad/src/outtakes/TreeView.py2
-rw-r--r--cad/src/protein/commands/InsertPeptide/InsertPeptide_EditCommand.py2
-rwxr-xr-xcad/src/protein/commands/InsertPeptide/PeptideGenerator.py4
-rwxr-xr-xcad/src/simulation/runSim.py20
-rwxr-xr-xcad/tests/nanotube.py6
-rwxr-xr-xsim/src/experimental/units.py68
38 files changed, 2314 insertions, 2314 deletions
diff --git a/cad/plugins/NanoVision-1/src/Plugins/RenderingEngines/OpenGL/NXOpenGLRenderingEngine.cpp b/cad/plugins/NanoVision-1/src/Plugins/RenderingEngines/OpenGL/NXOpenGLRenderingEngine.cpp
index 34b05d2f8..adfa656b5 100644
--- a/cad/plugins/NanoVision-1/src/Plugins/RenderingEngines/OpenGL/NXOpenGLRenderingEngine.cpp
+++ b/cad/plugins/NanoVision-1/src/Plugins/RenderingEngines/OpenGL/NXOpenGLRenderingEngine.cpp
@@ -25,38 +25,38 @@ using namespace OpenBabel;
/// Bypass OpenBabel's atom indexing
int get_nv1_atom_id(OBAtom *atomPtr)
{
- NXAtomData *atomData = static_cast<NXAtomData*>(atomPtr->GetData(NXAtomDataType));
- assert(atomData != NULL);
- int id = atomData->getIdx();
- return id;
+ NXAtomData *atomData = static_cast<NXAtomData*>(atomPtr->GetData(NXAtomDataType));
+ assert(atomData != NULL);
+ int id = atomData->getIdx();
+ return id;
}
/// Hack to bypass OpenBabel's atomicNum which is stored modulo 256 in a 'char'
int get_atomic_num(OBAtom *atomPtr)
{
- NXAtomData *atomData = static_cast<NXAtomData*>(atomPtr->GetData(NXAtomDataType));
- assert(atomData != NULL);
- int atomicNum = atomData->getAtomicNum();
- return atomicNum;
+ NXAtomData *atomData = static_cast<NXAtomData*>(atomPtr->GetData(NXAtomDataType));
+ assert(atomData != NULL);
+ int atomicNum = atomData->getAtomicNum();
+ return atomicNum;
}
#ifdef NX_DEBUG
string get_atom_scenegraph_name(OBAtom *const atomPtr)
{
- string name = "atom_";
- name += NXUtility::itos(get_nv1_atom_id(atomPtr));
- name += "_(" + NXUtility::itos(atomPtr->GetAtomicNum()) + ')';
- return name;
+ string name = "atom_";
+ name += NXUtility::itos(get_nv1_atom_id(atomPtr));
+ name += "_(" + NXUtility::itos(atomPtr->GetAtomicNum()) + ')';
+ return name;
}
string get_bond_scenegraph_name(OBBond *const bondPtr)
{
- return ("bond_" +
- NXUtility::itos(get_nv1_atom_id(bondPtr->GetBeginAtom())) +
- NXUtility::itos(get_nv1_atom_id(bondPtr->GetEndAtom()))
- );
+ return ("bond_" +
+ NXUtility::itos(get_nv1_atom_id(bondPtr->GetBeginAtom())) +
+ NXUtility::itos(get_nv1_atom_id(bondPtr->GetEndAtom()))
+ );
}
#endif
@@ -78,17 +78,17 @@ string get_bond_scenegraph_name(OBBond *const bondPtr)
NXOpenGLRenderingEngine::NXOpenGLRenderingEngine(QWidget *parent)
: QGLWidget(parent), NXRenderingEngine(), camera(this)
{
- initializeElementColorMap();
- initializeDefaultMaterials();
+ initializeElementColorMap();
+ initializeDefaultMaterials();
}
NXOpenGLRenderingEngine::~NXOpenGLRenderingEngine()
{
- // clear top-level scenegraph nodes
- NXRenderingEngine::deleteFrames();
- // clear lower-level scenegraph nodes
- cleanupPlugins();
+ // clear top-level scenegraph nodes
+ NXRenderingEngine::deleteFrames();
+ // clear lower-level scenegraph nodes
+ cleanupPlugins();
}
#if 0
@@ -137,77 +137,77 @@ bool NXOpenGLRenderingEngine::setRootMolecule(OpenBabel::OBMol *const molPtr)
bool NXOpenGLRenderingEngine::initializeElementColorMap(void)
{
- elementColorMap.clear();
- elementColorMap[0] = NXRGBColor(204,0,0,255);
- elementColorMap[1] = NXRGBColor(199,199,199,255);
- elementColorMap[2] = NXRGBColor(107,115,140,255);
- elementColorMap[3] = NXRGBColor(0,128,128,255);
- elementColorMap[4] = NXRGBColor(250,171,255,255);
- elementColorMap[5] = NXRGBColor(51,51,150,255);
- elementColorMap[6] = NXRGBColor(99,99,99,255);
- elementColorMap[7] = NXRGBColor(31,31,99,255);
- elementColorMap[8] = NXRGBColor(128,0,0,255);
- elementColorMap[9] = NXRGBColor(0,99,51,255);
- elementColorMap[10] = NXRGBColor(107,115,140,255);
- elementColorMap[11] = NXRGBColor(0,102,102,255);
- elementColorMap[12] = NXRGBColor(224,153,230,255);
- elementColorMap[13] = NXRGBColor(128,128,255,255);
- elementColorMap[14] = NXRGBColor(41,41,41,255);
- elementColorMap[15] = NXRGBColor(84,20,128,255);
- elementColorMap[16] = NXRGBColor(219,150,0,255);
- elementColorMap[17] = NXRGBColor(74,99,0,255);
- elementColorMap[18] = NXRGBColor(107,115,140,255);
- elementColorMap[19] = NXRGBColor(0,77,77,255);
- elementColorMap[20] = NXRGBColor(201,140,204,255);
- elementColorMap[21] = NXRGBColor(106,106,130,255);
- elementColorMap[22] = NXRGBColor(106,106,130,255);
- elementColorMap[23] = NXRGBColor(106,106,130,255);
- elementColorMap[24] = NXRGBColor(106,106,130,255);
- elementColorMap[25] = NXRGBColor(106,106,130,255);
- elementColorMap[26] = NXRGBColor(106,106,130,255);
- elementColorMap[27] = NXRGBColor(106,106,130,255);
- elementColorMap[28] = NXRGBColor(106,106,130,255);
- elementColorMap[29] = NXRGBColor(106,106,130,255);
- elementColorMap[30] = NXRGBColor(106,106,130,255);
- elementColorMap[31] = NXRGBColor(153,153,204,255);
- elementColorMap[32] = NXRGBColor(102,115,26,255);
- elementColorMap[33] = NXRGBColor(153,66,179,255);
- elementColorMap[34] = NXRGBColor(199,79,0,255);
- elementColorMap[35] = NXRGBColor(0,102,77,255);
- elementColorMap[36] = NXRGBColor(107,115,140,255);
- elementColorMap[51] = NXRGBColor(153,66,179,255);
- elementColorMap[52] = NXRGBColor(230,89,0,255);
- elementColorMap[53] = NXRGBColor(0,128,0,255);
- elementColorMap[54] = NXRGBColor(102,115,140,255);
-
- elementColorMap[200] = NXRGBColor(102,102,204,255); // Ax5
- elementColorMap[201] = NXRGBColor(102,204,102,255); // Ss5
- elementColorMap[202] = NXRGBColor(102, 26,128,255); // Pl5
- elementColorMap[203] = NXRGBColor(102,204,204,255); // Sj5
- elementColorMap[204] = NXRGBColor(102,102,204,255); // Ae5
- elementColorMap[205] = NXRGBColor(102, 26,128,255); // Pe5
- elementColorMap[206] = NXRGBColor(102,204,102,255); // Sh5
- elementColorMap[207] = NXRGBColor( 77,179, 77,255); // Hp5
- elementColorMap[208] = NXRGBColor(156, 83, 8,255); // Gv5
- elementColorMap[209] = NXRGBColor(156, 83, 8,255); // Gr5
- elementColorMap[210] = NXRGBColor(109,207,206,255); // Ub5
- elementColorMap[211] = NXRGBColor(109,207,206,255); // Ux5
- elementColorMap[212] = NXRGBColor(207,109,206,255); // Uy5
-
- elementColorMap[300] = NXRGBColor(102,102,204,255); // Ax3
- elementColorMap[301] = NXRGBColor(102,204,102,255); // Ss3
- elementColorMap[302] = NXRGBColor(102, 26,128,255); // Pl3
- elementColorMap[303] = NXRGBColor(102,204,204,255); // Sj3
- elementColorMap[304] = NXRGBColor( 26, 26,128,255); // Ae3
- elementColorMap[305] = NXRGBColor(102,204,102,255); // Se3
- elementColorMap[306] = NXRGBColor(153, 51,153,255); // Sh3
- elementColorMap[307] = NXRGBColor( 77,179, 77,255); // Hp3
- elementColorMap[310] = NXRGBColor(109,207,206,255); // Ub3
- elementColorMap[311] = NXRGBColor(109,207,206,255); // Ux3
- elementColorMap[312] = NXRGBColor(207,109,206,255); // Uy3
-
- return true;
-
+ elementColorMap.clear();
+ elementColorMap[0] = NXRGBColor(204,0,0,255);
+ elementColorMap[1] = NXRGBColor(199,199,199,255);
+ elementColorMap[2] = NXRGBColor(107,115,140,255);
+ elementColorMap[3] = NXRGBColor(0,128,128,255);
+ elementColorMap[4] = NXRGBColor(250,171,255,255);
+ elementColorMap[5] = NXRGBColor(51,51,150,255);
+ elementColorMap[6] = NXRGBColor(99,99,99,255);
+ elementColorMap[7] = NXRGBColor(31,31,99,255);
+ elementColorMap[8] = NXRGBColor(128,0,0,255);
+ elementColorMap[9] = NXRGBColor(0,99,51,255);
+ elementColorMap[10] = NXRGBColor(107,115,140,255);
+ elementColorMap[11] = NXRGBColor(0,102,102,255);
+ elementColorMap[12] = NXRGBColor(224,153,230,255);
+ elementColorMap[13] = NXRGBColor(128,128,255,255);
+ elementColorMap[14] = NXRGBColor(41,41,41,255);
+ elementColorMap[15] = NXRGBColor(84,20,128,255);
+ elementColorMap[16] = NXRGBColor(219,150,0,255);
+ elementColorMap[17] = NXRGBColor(74,99,0,255);
+ elementColorMap[18] = NXRGBColor(107,115,140,255);
+ elementColorMap[19] = NXRGBColor(0,77,77,255);
+ elementColorMap[20] = NXRGBColor(201,140,204,255);
+ elementColorMap[21] = NXRGBColor(106,106,130,255);
+ elementColorMap[22] = NXRGBColor(106,106,130,255);
+ elementColorMap[23] = NXRGBColor(106,106,130,255);
+ elementColorMap[24] = NXRGBColor(106,106,130,255);
+ elementColorMap[25] = NXRGBColor(106,106,130,255);
+ elementColorMap[26] = NXRGBColor(106,106,130,255);
+ elementColorMap[27] = NXRGBColor(106,106,130,255);
+ elementColorMap[28] = NXRGBColor(106,106,130,255);
+ elementColorMap[29] = NXRGBColor(106,106,130,255);
+ elementColorMap[30] = NXRGBColor(106,106,130,255);
+ elementColorMap[31] = NXRGBColor(153,153,204,255);
+ elementColorMap[32] = NXRGBColor(102,115,26,255);
+ elementColorMap[33] = NXRGBColor(153,66,179,255);
+ elementColorMap[34] = NXRGBColor(199,79,0,255);
+ elementColorMap[35] = NXRGBColor(0,102,77,255);
+ elementColorMap[36] = NXRGBColor(107,115,140,255);
+ elementColorMap[51] = NXRGBColor(153,66,179,255);
+ elementColorMap[52] = NXRGBColor(230,89,0,255);
+ elementColorMap[53] = NXRGBColor(0,128,0,255);
+ elementColorMap[54] = NXRGBColor(102,115,140,255);
+
+ elementColorMap[200] = NXRGBColor(102,102,204,255); // Ax5
+ elementColorMap[201] = NXRGBColor(102,204,102,255); // Ss5
+ elementColorMap[202] = NXRGBColor(102, 26,128,255); // Pl5
+ elementColorMap[203] = NXRGBColor(102,204,204,255); // Sj5
+ elementColorMap[204] = NXRGBColor(102,102,204,255); // Ae5
+ elementColorMap[205] = NXRGBColor(102, 26,128,255); // Pe5
+ elementColorMap[206] = NXRGBColor(102,204,102,255); // Sh5
+ elementColorMap[207] = NXRGBColor( 77,179, 77,255); // Hp5
+ elementColorMap[208] = NXRGBColor(156, 83, 8,255); // Gv5
+ elementColorMap[209] = NXRGBColor(156, 83, 8,255); // Gr5
+ elementColorMap[210] = NXRGBColor(109,207,206,255); // Ub5
+ elementColorMap[211] = NXRGBColor(109,207,206,255); // Ux5
+ elementColorMap[212] = NXRGBColor(207,109,206,255); // Uy5
+
+ elementColorMap[300] = NXRGBColor(102,102,204,255); // Ax3
+ elementColorMap[301] = NXRGBColor(102,204,102,255); // Ss3
+ elementColorMap[302] = NXRGBColor(102, 26,128,255); // Pl3
+ elementColorMap[303] = NXRGBColor(102,204,204,255); // Sj3
+ elementColorMap[304] = NXRGBColor( 26, 26,128,255); // Ae3
+ elementColorMap[305] = NXRGBColor(102,204,102,255); // Se3
+ elementColorMap[306] = NXRGBColor(153, 51,153,255); // Sh3
+ elementColorMap[307] = NXRGBColor( 77,179, 77,255); // Hp3
+ elementColorMap[310] = NXRGBColor(109,207,206,255); // Ub3
+ elementColorMap[311] = NXRGBColor(109,207,206,255); // Ux3
+ elementColorMap[312] = NXRGBColor(207,109,206,255); // Uy3
+
+ return true;
+
#if 0 // read from file - sensitive to location
/// @todo Remove filename hardcoding
ifstream elemColorMapFile("default-element-colors.txt", ios::in);
@@ -218,7 +218,7 @@ bool NXOpenGLRenderingEngine::initializeElementColorMap(void)
char linebuf[LINEBUF_SIZE];
elemColorMapFile.getline(linebuf, LINEBUF_SIZE);
assert((int)elemColorMapFile.gcount() < LINEBUF_SIZE);
-
+
istringstream line(linebuf);
// ignore comment lines
if(line.peek() == '#') continue;
@@ -236,273 +236,273 @@ bool NXOpenGLRenderingEngine::initializeElementColorMap(void)
void NXOpenGLRenderingEngine::initializeDefaultMaterials(void)
{
- defaultAtomMaterial.face = GL_FRONT;
- defaultAtomMaterial.ambient[0] = 1.0f;
- defaultAtomMaterial.ambient[1] = 1.0f;
- defaultAtomMaterial.ambient[2] = 1.0f;
- defaultAtomMaterial.ambient[3] = 1.0f;
-
- defaultAtomMaterial.diffuse[0] = 1.0f;
- defaultAtomMaterial.diffuse[1] = 1.0f;
- defaultAtomMaterial.diffuse[2] = 1.0f;
- defaultAtomMaterial.diffuse[3] = 1.0f;
-
- defaultAtomMaterial.specular[0] = 0.5f;
- defaultAtomMaterial.specular[1] = 0.5f;
- defaultAtomMaterial.specular[2] = 0.5f;
- defaultAtomMaterial.specular[3] = 1.0f;
-
- defaultAtomMaterial.shininess = 35.0;
-
- defaultAtomMaterial.emission[0] = 0.0f;
- defaultAtomMaterial.emission[1] = 0.0f;
- defaultAtomMaterial.emission[2] = 0.0f;
- defaultAtomMaterial.emission[3] = 1.0f;
-
- defaultBondMaterial.face = GL_FRONT;
- defaultBondMaterial.ambient[0] = 1.0f;
- defaultBondMaterial.ambient[1] = 1.0f;
- defaultBondMaterial.ambient[2] = 1.0f;
- defaultBondMaterial.ambient[3] = 1.0f;
-
- defaultBondMaterial.diffuse[0] = 1.0f;
- defaultBondMaterial.diffuse[1] = 1.0f;
- defaultBondMaterial.diffuse[2] = 1.0f;
- defaultBondMaterial.diffuse[3] = 1.0f;
-
- defaultBondMaterial.specular[0] = 0.5f;
- defaultBondMaterial.specular[1] = 0.5f;
- defaultBondMaterial.specular[2] = 0.5f;
- defaultBondMaterial.specular[3] = 1.0f;
-
- defaultBondMaterial.shininess = 35.0;
-
- defaultBondMaterial.emission[0] = 0.0f;
- defaultBondMaterial.emission[1] = 0.0f;
- defaultBondMaterial.emission[2] = 0.0f;
- defaultBondMaterial.emission[3] = 1.0f;
+ defaultAtomMaterial.face = GL_FRONT;
+ defaultAtomMaterial.ambient[0] = 1.0f;
+ defaultAtomMaterial.ambient[1] = 1.0f;
+ defaultAtomMaterial.ambient[2] = 1.0f;
+ defaultAtomMaterial.ambient[3] = 1.0f;
+
+ defaultAtomMaterial.diffuse[0] = 1.0f;
+ defaultAtomMaterial.diffuse[1] = 1.0f;
+ defaultAtomMaterial.diffuse[2] = 1.0f;
+ defaultAtomMaterial.diffuse[3] = 1.0f;
+
+ defaultAtomMaterial.specular[0] = 0.5f;
+ defaultAtomMaterial.specular[1] = 0.5f;
+ defaultAtomMaterial.specular[2] = 0.5f;
+ defaultAtomMaterial.specular[3] = 1.0f;
+
+ defaultAtomMaterial.shininess = 35.0;
+
+ defaultAtomMaterial.emission[0] = 0.0f;
+ defaultAtomMaterial.emission[1] = 0.0f;
+ defaultAtomMaterial.emission[2] = 0.0f;
+ defaultAtomMaterial.emission[3] = 1.0f;
+
+ defaultBondMaterial.face = GL_FRONT;
+ defaultBondMaterial.ambient[0] = 1.0f;
+ defaultBondMaterial.ambient[1] = 1.0f;
+ defaultBondMaterial.ambient[2] = 1.0f;
+ defaultBondMaterial.ambient[3] = 1.0f;
+
+ defaultBondMaterial.diffuse[0] = 1.0f;
+ defaultBondMaterial.diffuse[1] = 1.0f;
+ defaultBondMaterial.diffuse[2] = 1.0f;
+ defaultBondMaterial.diffuse[3] = 1.0f;
+
+ defaultBondMaterial.specular[0] = 0.5f;
+ defaultBondMaterial.specular[1] = 0.5f;
+ defaultBondMaterial.specular[2] = 0.5f;
+ defaultBondMaterial.specular[3] = 1.0f;
+
+ defaultBondMaterial.shininess = 35.0;
+
+ defaultBondMaterial.emission[0] = 0.0f;
+ defaultBondMaterial.emission[1] = 0.0f;
+ defaultBondMaterial.emission[2] = 0.0f;
+ defaultBondMaterial.emission[3] = 1.0f;
}
void NXOpenGLRenderingEngine::initializeGL(void)
{
- glClearColor(1.0, 1.0, 1.0, 1.0);
- glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT);
-
- glEnable(GL_LIGHTING);
- glEnable(GL_DEPTH_TEST);
-
- lightModel.setLocalViewer(1);
- lightModel.setTwoSide(0);
- lightModel.set();
- setupDefaultLights();
-
-// camera.gluLookAt(0.0, 0.0, 1.0,
-// 0.0, 0.0, 0.0,
-// 0.0, 1.0, 0.0);
-// camera.gluPerspective(55, (GLdouble)width()/(GLdouble)height(), 0.1, 50);
-
- NXNamedView defaultView("DefaultView",
- NXQuaternion<double>(1.0, 0.0, 0.0, 0.0),
- 10.0,
- NXVector3d(0.0, 0.0, 0.0),
- 1.0);
- camera.setNamedView(defaultView);
- camera.glViewport(0, 0, width(), height());
-
- (void) glGetError(); // clear errors
- // initializePlugins();
-
+ glClearColor(1.0, 1.0, 1.0, 1.0);
+ glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT);
+
+ glEnable(GL_LIGHTING);
+ glEnable(GL_DEPTH_TEST);
+
+ lightModel.setLocalViewer(1);
+ lightModel.setTwoSide(0);
+ lightModel.set();
+ setupDefaultLights();
+
+// camera.gluLookAt(0.0, 0.0, 1.0,
+// 0.0, 0.0, 0.0,
+// 0.0, 1.0, 0.0);
+// camera.gluPerspective(55, (GLdouble)width()/(GLdouble)height(), 0.1, 50);
+
+ NXNamedView defaultView("DefaultView",
+ NXQuaternion<double>(1.0, 0.0, 0.0, 0.0),
+ 10.0,
+ NXVector3d(0.0, 0.0, 0.0),
+ 1.0);
+ camera.setNamedView(defaultView);
+ camera.glViewport(0, 0, width(), height());
+
+ (void) glGetError(); // clear errors
+ // initializePlugins();
+
}
void NXOpenGLRenderingEngine::setupDefaultLights(void)
{
// light model
- lightModel.setLocalViewer(1);
- lightModel.setTwoSide(0);
- lightModel.set();
-
+ lightModel.setLocalViewer(1);
+ lightModel.setTwoSide(0);
+ lightModel.set();
+
// initialize light data
- GLint numSupportedOpenGLLights = 0;
- glGetIntegerv(GL_MAX_LIGHTS, &numSupportedOpenGLLights);
- lights.clear();
- for(GLint iLight=0; iLight<numSupportedOpenGLLights; ++iLight)
- {
- lights.push_back(GltLight(iLight+GL_LIGHT0));
- }
-
- GltColor const WHITE(1.0,1.0,1.0,1.0);
- lights[0].isEnabled() = true;
- lights[0].ambient() = 0.1 * WHITE;
- lights[0].diffuse() = 0.5 * WHITE;
- lights[0].specular() = 0.5 * WHITE;
- lights[0].position() = Vector(-50.0, 70.0, 30.0);
- lights[0].isDirectional() = true;
- lights[0].inEyeSpace() = true;
- lights[0].set();
-
- lights[1].isEnabled() = true;
- lights[1].ambient() = 0.1 * WHITE;
- lights[1].diffuse() = 0.5 * WHITE;
- lights[1].specular() = 0.5 * WHITE;
- lights[1].position() = Vector(-20.0, 20.0, 20.0);
- lights[1].isDirectional() = true;
- lights[1].inEyeSpace() = true;
- lights[1].set();
-
- for(GLint iLight=2; iLight<numSupportedOpenGLLights; ++iLight) {
- lights[iLight].isEnabled() = false;
- lights[iLight].ambient() = 0.1 * WHITE;
- lights[iLight].diffuse() = 0.5 * WHITE;
- lights[iLight].specular() = 0.5 * WHITE;
- lights[iLight].position() = Vector(0.0, 0.0, 100.0);
- lights[iLight].set();
- }
-
+ GLint numSupportedOpenGLLights = 0;
+ glGetIntegerv(GL_MAX_LIGHTS, &numSupportedOpenGLLights);
+ lights.clear();
+ for(GLint iLight=0; iLight<numSupportedOpenGLLights; ++iLight)
+ {
+ lights.push_back(GltLight(iLight+GL_LIGHT0));
+ }
+
+ GltColor const WHITE(1.0,1.0,1.0,1.0);
+ lights[0].isEnabled() = true;
+ lights[0].ambient() = 0.1 * WHITE;
+ lights[0].diffuse() = 0.5 * WHITE;
+ lights[0].specular() = 0.5 * WHITE;
+ lights[0].position() = Vector(-50.0, 70.0, 30.0);
+ lights[0].isDirectional() = true;
+ lights[0].inEyeSpace() = true;
+ lights[0].set();
+
+ lights[1].isEnabled() = true;
+ lights[1].ambient() = 0.1 * WHITE;
+ lights[1].diffuse() = 0.5 * WHITE;
+ lights[1].specular() = 0.5 * WHITE;
+ lights[1].position() = Vector(-20.0, 20.0, 20.0);
+ lights[1].isDirectional() = true;
+ lights[1].inEyeSpace() = true;
+ lights[1].set();
+
+ for(GLint iLight=2; iLight<numSupportedOpenGLLights; ++iLight) {
+ lights[iLight].isEnabled() = false;
+ lights[iLight].ambient() = 0.1 * WHITE;
+ lights[iLight].diffuse() = 0.5 * WHITE;
+ lights[iLight].specular() = 0.5 * WHITE;
+ lights[iLight].position() = Vector(0.0, 0.0, 100.0);
+ lights[iLight].set();
+ }
+
}
void NXOpenGLRenderingEngine::resizeGL(int width, int height)
{
- camera.resizeViewport(width, height);
- // camera.glSetViewport();
- // camera.glSetProjection();
+ camera.resizeViewport(width, height);
+ // camera.glSetViewport();
+ // camera.glSetProjection();
// glMatrixMode(GL_PROJECTION);
// glLoadIdentity();
// gluPerspective(55, (GLdouble)width/(GLdouble)height, 0.1, 50);
// camera.glGetProjection();
// camera.glGetViewport();
-
+
/* if(isOrthographicProjection)
orthographicProjection.set();
else
perspectiveProjection.set(); */
-
- // viewport.set((GLint) width, (GLint) height);*/
+
+ // viewport.set((GLint) width, (GLint) height);*/
}
void NXOpenGLRenderingEngine::paintGL(void)
{
- glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT);
- drawSkyBlueBackground();
- camera.glSetPosition();
- camera.glSetProjection();
- drawCompass();
-
- if(currentFrameIndex >= 0) {
- NXSGOpenGLNode *currentFrameSGNode =
- static_cast<NXSGOpenGLNode*>(frames[currentFrameIndex]);
- currentFrameSGNode->applyRecursive();
- }
- glFlush();
- swapBuffers();
+ glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT);
+ drawSkyBlueBackground();
+ camera.glSetPosition();
+ camera.glSetProjection();
+ drawCompass();
+
+ if(currentFrameIndex >= 0) {
+ NXSGOpenGLNode *currentFrameSGNode =
+ static_cast<NXSGOpenGLNode*>(frames[currentFrameIndex]);
+ currentFrameSGNode->applyRecursive();
+ }
+ glFlush();
+ swapBuffers();
}
void NXOpenGLRenderingEngine::drawSkyBlueBackground(void)
{
- glDisable(GL_LIGHTING);
- glMatrixMode(GL_MODELVIEW);
- glLoadIdentity();
- glMatrixMode(GL_PROJECTION);
- glLoadIdentity();
+ glDisable(GL_LIGHTING);
+ glMatrixMode(GL_MODELVIEW);
+ glLoadIdentity();
+ glMatrixMode(GL_PROJECTION);
+ glLoadIdentity();
// * GLPane.py::standard_repaint_0()
// * drawer.py::drawFullWindow()
- GltColor vtColors0(0.9, 0.9, 0.9, 1.0);
- GltColor vtColors1(0.9, 0.9, 0.9, 1.0);
- GltColor vtColors2(0.33, 0.73, 1.0, 1.0);
- GltColor vtColors3(0.33, 0.73, 1.0, 1.0);
- glBegin(GL_QUADS);
- vtColors0.glColor();
- glVertex3f(-1, -1, 0.999);
- vtColors1.glColor();
- glVertex3f(1, -1, 0.999);
- vtColors2.glColor();
- glVertex3f(1, 1, 0.999);
- vtColors3.glColor();
- glVertex3f(-1, 1, 0.999);
- glEnd();
- glEnable(GL_LIGHTING);
+ GltColor vtColors0(0.9, 0.9, 0.9, 1.0);
+ GltColor vtColors1(0.9, 0.9, 0.9, 1.0);
+ GltColor vtColors2(0.33, 0.73, 1.0, 1.0);
+ GltColor vtColors3(0.33, 0.73, 1.0, 1.0);
+ glBegin(GL_QUADS);
+ vtColors0.glColor();
+ glVertex3f(-1, -1, 0.999);
+ vtColors1.glColor();
+ glVertex3f(1, -1, 0.999);
+ vtColors2.glColor();
+ glVertex3f(1, 1, 0.999);
+ vtColors3.glColor();
+ glVertex3f(-1, 1, 0.999);
+ glEnd();
+ glEnable(GL_LIGHTING);
}
void NXOpenGLRenderingEngine::drawCompass(void)
{
- // Coordinate axis
- glBegin(GL_LINES);
- // x-axis
- glColor3f(1.0f, 0.0f, 0.0f);
- glVertex3f(0.0, 0.0, 0.0);
- glVertex3f(3.0, 0.0, 0.0);
-
- // y-axis
- glColor3f(0.0f, 1.0, 0.0f);
- glVertex3f(0.0, 0.0, 0.0);
- glVertex3f(0.0, 3.0, 0.0);
-
- // z-axis
- glColor3f(0.0f, 0.0, 1.0);
- glVertex3f(0.0, 0.0, 0.0);
- glVertex3f(0.0, 0.0, 3.0);
- glEnd();
+ // Coordinate axis
+ glBegin(GL_LINES);
+ // x-axis
+ glColor3f(1.0f, 0.0f, 0.0f);
+ glVertex3f(0.0, 0.0, 0.0);
+ glVertex3f(3.0, 0.0, 0.0);
+
+ // y-axis
+ glColor3f(0.0f, 1.0, 0.0f);
+ glVertex3f(0.0, 0.0, 0.0);
+ glVertex3f(0.0, 3.0, 0.0);
+
+ // z-axis
+ glColor3f(0.0f, 0.0, 1.0);
+ glVertex3f(0.0, 0.0, 0.0);
+ glVertex3f(0.0, 0.0, 3.0);
+ glEnd();
}
NXSGNode*
NXOpenGLRenderingEngine::createSceneGraph (NXMoleculeSet *const molSetPtr)
{
- ClearResult(commandResult);
- // Do nothing if no rendering plugins
- if(!pluginsInitialized) {
- SetResult(commandResult,
- NX_INTERNAL_ERROR,
- "Renderer-plugins not set/initialized");
- return NULL;
- }
-
- QCursor originalCursor = cursor();
- setCursor(QCursor(Qt::BusyCursor));
-
- renderedAtoms.clear();
- renderedBonds.clear();
- NXSGOpenGLNode *node = createOpenGLSceneGraph(molSetPtr);
-
- NXSGOpenGLRenderable *renderableNode = new NXSGOpenGLRenderable;
- makeCurrent();
- assert(renderableNode->beginRender());
- assert(node->applyRecursive());
- assert(renderableNode->endRender());
- delete node;
- node = NULL;
-
+ ClearResult(commandResult);
+ // Do nothing if no rendering plugins
+ if(!pluginsInitialized) {
+ SetResult(commandResult,
+ NX_INTERNAL_ERROR,
+ "Renderer-plugins not set/initialized");
+ return NULL;
+ }
+
+ QCursor originalCursor = cursor();
+ setCursor(QCursor(Qt::BusyCursor));
+
+ renderedAtoms.clear();
+ renderedBonds.clear();
+ NXSGOpenGLNode *node = createOpenGLSceneGraph(molSetPtr);
+
+ NXSGOpenGLRenderable *renderableNode = new NXSGOpenGLRenderable;
+ makeCurrent();
+ assert(renderableNode->beginRender());
+ assert(node->applyRecursive());
+ assert(renderableNode->endRender());
+ delete node;
+ node = NULL;
+
#ifdef NX_DEBUG
- NXSGNode const *const node1 = renderableNode;
- ofstream sgFile((molSetPtr->getTitle() + ".sg").c_str(), ios::out);
- sgFile << "digraph SG {" << endl;
- if(sgFile)
- node1->writeDotGraph(sgFile);
- sgFile << "}" << endl;
+ NXSGNode const *const node1 = renderableNode;
+ ofstream sgFile((molSetPtr->getTitle() + ".sg").c_str(), ios::out);
+ sgFile << "digraph SG {" << endl;
+ if(sgFile)
+ node1->writeDotGraph(sgFile);
+ sgFile << "}" << endl;
#endif
- setCursor(originalCursor);
-
- return static_cast<NXSGNode*>(renderableNode);
+ setCursor(originalCursor);
+
+ return static_cast<NXSGNode*>(renderableNode);
}
#if 0 // removed this method from NXRenderingEngine
NXSGNode* createSceneGraph (OpenBabel::OBMol *const molPtr) {
- // Do nothing if no rendering plugins
- if(!pluginsInitialized) {
- SetResult(commandResult, NX_INTERNAL_ERROR,
+ // Do nothing if no rendering plugins
+ if(!pluginsInitialized) {
+ SetResult(commandResult, NX_INTERNAL_ERROR,
"Rendering plugin not set/initialized");
- return NULL;
- }
- ClearResult(commandResult);
- NXSGOpenGLNode *node = createOpenGLSceneGraph(molPtr);
- return static_cast<NXSGNode*>(node);
+ return NULL;
+ }
+ ClearResult(commandResult);
+ NXSGOpenGLNode *node = createOpenGLSceneGraph(molPtr);
+ return static_cast<NXSGNode*>(node);
}
#endif
@@ -511,269 +511,269 @@ NXOpenGLRenderingEngine::createOpenGLSceneGraph(NXMoleculeSet *const molSetPtr)
{
/// @todo Trap soft-failure cases where pointer returned is non-NULL
/// but commandResult shows error
- NXSGOpenGLNode *moleculeSetNode = NULL;
- try {
- moleculeSetNode = new NXSGOpenGLNode;
- SET_SCENEGRAPH_NAME(moleculeSetNode,
- "Molecule_set_" + molSetPtr->getTitle());
- }
- catch(...) {
- SetResult(commandResult, NX_INTERNAL_ERROR,
- "Failed to initialize scenegraph node for molecule set " +
- molSetPtr->getTitle());
- return (NXSGOpenGLNode*) NULL;
- }
-
+ NXSGOpenGLNode *moleculeSetNode = NULL;
+ try {
+ moleculeSetNode = new NXSGOpenGLNode;
+ SET_SCENEGRAPH_NAME(moleculeSetNode,
+ "Molecule_set_" + molSetPtr->getTitle());
+ }
+ catch(...) {
+ SetResult(commandResult, NX_INTERNAL_ERROR,
+ "Failed to initialize scenegraph node for molecule set " +
+ molSetPtr->getTitle());
+ return (NXSGOpenGLNode*) NULL;
+ }
+
#if 0 /// @todo Post-FNANO08 (Dna rendering)
- /// @fixme r1.0.0 hacks
- // -- begin hacks --
- NXMoleculeSet::GroupClassification molSetClassification =
- molSetPtr->getGroupClassification();
- switch(molSetClassification) {
- case NXMoleculeSet::DNA_GROUP :
- inDnaGroup = true;
- // reset child-group flags
- inDnaSegment = false;
- inDnaStrand = false;
- break;
- case NXMoleculeSet::DNA_SEGMENT :
- assert(inDnaGroup);
- inDnaSegment = true;
- // force strand mol-sets to follow corresponding segment
- inDnaStrand = false;
- dnaSegmentMolSetPtr = molSetPtr;
- break;
- case NXMoleculeSet::DNA_STRAND :
- assert(inDnaGroup);
- inDnaStrand = true;
- inDnaSegment = false;
- dnaStrandMolSetPtr = molSetPtr;
- break;
- case NXMoleculeSet::NONE:
- inDnaGroup = false;
- inDnaSegment = false;
- inDnaStrand = false;
- break;
- default:
- NXLOG_WARNING("NXOpenGLRenderingEngine",
- string("Unknown group classification '") +
- molSetPtr->getGroupClassificationString() +
- "' - reverting to default");
- break;
- }
- // -- end hacks --
+ /// @fixme r1.0.0 hacks
+ // -- begin hacks --
+ NXMoleculeSet::GroupClassification molSetClassification =
+ molSetPtr->getGroupClassification();
+ switch(molSetClassification) {
+ case NXMoleculeSet::DNA_GROUP :
+ inDnaGroup = true;
+ // reset child-group flags
+ inDnaSegment = false;
+ inDnaStrand = false;
+ break;
+ case NXMoleculeSet::DNA_SEGMENT :
+ assert(inDnaGroup);
+ inDnaSegment = true;
+ // force strand mol-sets to follow corresponding segment
+ inDnaStrand = false;
+ dnaSegmentMolSetPtr = molSetPtr;
+ break;
+ case NXMoleculeSet::DNA_STRAND :
+ assert(inDnaGroup);
+ inDnaStrand = true;
+ inDnaSegment = false;
+ dnaStrandMolSetPtr = molSetPtr;
+ break;
+ case NXMoleculeSet::NONE:
+ inDnaGroup = false;
+ inDnaSegment = false;
+ inDnaStrand = false;
+ break;
+ default:
+ NXLOG_WARNING("NXOpenGLRenderingEngine",
+ string("Unknown group classification '") +
+ molSetPtr->getGroupClassificationString() +
+ "' - reverting to default");
+ break;
+ }
+ // -- end hacks --
#endif
-
- // cerr << "Creating OpenGL scenegraph for molecule-set " << molSetPtr->getTitle() << endl;
- OBMolIterator molIter;
- for(molIter = molSetPtr->moleculesBegin();
- molIter != molSetPtr->moleculesEnd();
- ++molIter)
- {
- if((*molIter)->Empty())
- continue;
- NXSGOpenGLNode* molNode = createOpenGLSceneGraph(*molIter);
- if(molNode != NULL &&
- commandResult.getResult() == (int) NX_CMD_SUCCESS)
- {
- bool childAdded = moleculeSetNode->addChild(molNode);
- if(!childAdded) {
- NX_DEBUG_FAIL;
- return moleculeSetNode;
- }
- }
- else {
- NX_DEBUG_FAIL;
- return moleculeSetNode;
- }
- /// @todo POST-FNANO: delete molNode upon failures?
- }
-
- NXMoleculeSetIterator childrenIter;
- for(childrenIter = molSetPtr->childrenBegin();
- childrenIter != molSetPtr->childrenEnd();
- ++childrenIter)
- {
- NXSGOpenGLNode *childMoleculeSetNode = createOpenGLSceneGraph(*childrenIter);
- if(childMoleculeSetNode != NULL &&
- commandResult.getResult() == (int) NX_CMD_SUCCESS)
- {
- bool childAdded = moleculeSetNode->addChild(childMoleculeSetNode);
- if(!childAdded) {
- NX_DEBUG_FAIL;
- return moleculeSetNode;
- }
- }
- else {
- NX_DEBUG_FAIL;
- return moleculeSetNode;
- }
- /// @todo POST-FNANO: delete childMoleculeSetNode upon failures?
- }
- return moleculeSetNode;
+
+ // cerr << "Creating OpenGL scenegraph for molecule-set " << molSetPtr->getTitle() << endl;
+ OBMolIterator molIter;
+ for(molIter = molSetPtr->moleculesBegin();
+ molIter != molSetPtr->moleculesEnd();
+ ++molIter)
+ {
+ if((*molIter)->Empty())
+ continue;
+ NXSGOpenGLNode* molNode = createOpenGLSceneGraph(*molIter);
+ if(molNode != NULL &&
+ commandResult.getResult() == (int) NX_CMD_SUCCESS)
+ {
+ bool childAdded = moleculeSetNode->addChild(molNode);
+ if(!childAdded) {
+ NX_DEBUG_FAIL;
+ return moleculeSetNode;
+ }
+ }
+ else {
+ NX_DEBUG_FAIL;
+ return moleculeSetNode;
+ }
+ /// @todo POST-FNANO: delete molNode upon failures?
+ }
+
+ NXMoleculeSetIterator childrenIter;
+ for(childrenIter = molSetPtr->childrenBegin();
+ childrenIter != molSetPtr->childrenEnd();
+ ++childrenIter)
+ {
+ NXSGOpenGLNode *childMoleculeSetNode = createOpenGLSceneGraph(*childrenIter);
+ if(childMoleculeSetNode != NULL &&
+ commandResult.getResult() == (int) NX_CMD_SUCCESS)
+ {
+ bool childAdded = moleculeSetNode->addChild(childMoleculeSetNode);
+ if(!childAdded) {
+ NX_DEBUG_FAIL;
+ return moleculeSetNode;
+ }
+ }
+ else {
+ NX_DEBUG_FAIL;
+ return moleculeSetNode;
+ }
+ /// @todo POST-FNANO: delete childMoleculeSetNode upon failures?
+ }
+ return moleculeSetNode;
}
NXSGOpenGLNode*
NXOpenGLRenderingEngine::createOpenGLSceneGraph(OBMol *const molPtr)
{
- assert(!molPtr->Empty());
-
+ assert(!molPtr->Empty());
+
#if 0 /// @todo Post-FNANO08 (Dna rendering)
- /// @fixme r1.0.0 hacks
- // -- begin hacks --
- if(inDnaGroup && inDnaSegment) {
- NXSGOpenGLNode *molSceneGraphNode =
- createOpenGLDnaSegmentSceneGraph(molPtr);
- if(molSceneGraphNode != NULL)
- return molSceneGraphNode;
- }
- else if(inDnaGroup && inDnaStrand) {
- NXSGOpenGLNode *molSceneGraphNode =
- createOpenGLDnaStrandSceneGraph(molPtr);
- if(molSceneGraphNode != NULL)
- return molSceneGraphNode;
- }
- // -- end hacks --
+ /// @fixme r1.0.0 hacks
+ // -- begin hacks --
+ if(inDnaGroup && inDnaSegment) {
+ NXSGOpenGLNode *molSceneGraphNode =
+ createOpenGLDnaSegmentSceneGraph(molPtr);
+ if(molSceneGraphNode != NULL)
+ return molSceneGraphNode;
+ }
+ else if(inDnaGroup && inDnaStrand) {
+ NXSGOpenGLNode *molSceneGraphNode =
+ createOpenGLDnaStrandSceneGraph(molPtr);
+ if(molSceneGraphNode != NULL)
+ return molSceneGraphNode;
+ }
+ // -- end hacks --
#endif
-
- Vector const canonicalZAxis(0.0, 0.0, 1.0);
- OBAtomIterator atomIter;
-
+
+ Vector const canonicalZAxis(0.0, 0.0, 1.0);
+ OBAtomIterator atomIter;
+
// Find first atom that is not already rendered
- // Necessary because bonds can bridge molecules and molecule-sets and in
- // the case of the second to last molecules rendered, their first atoms
- // may have been rendered while traversing the previous molecules.
-
- OBAtom *firstAtomPtr = molPtr->BeginAtom(atomIter);
-
- if(firstAtomPtr == (OBAtom*) NULL) {
- string const source("Molecule scenegraph creation");
- string const msg("empty molecule slipped past check");
- SetResult(commandResult, NX_INTERNAL_ERROR, source + " - " + msg);
- NX_DEBUG_FAIL;
- return (NXSGOpenGLNode*) NULL;
- }
-
- while(firstAtomPtr != (OBAtom*) NULL && isRendered(firstAtomPtr))
- firstAtomPtr = molPtr->NextAtom(atomIter);
-
- if(firstAtomPtr == (OBAtom*) NULL) {
- NXSGOpenGLNode *nullFirstAtomNode = new NXSGOpenGLNode;
- SET_SCENEGRAPH_NAME(nullFirstAtomNode, "Null_first_atom");
- return nullFirstAtomNode;
- }
-
- Vector const firstAtomPosition(firstAtomPtr->GetX(),
- firstAtomPtr->GetY(),
- firstAtomPtr->GetZ());
-
- NXSGOpenGLTranslate *rootMoleculeNode = NULL;
- try {
- rootMoleculeNode =
- new NXSGOpenGLTranslate(firstAtomPosition.x(),
- firstAtomPosition.y(),
- firstAtomPosition.z());
- SET_SCENEGRAPH_NAME(rootMoleculeNode, "First_atom_position");
- }
- catch(...) {
- if(rootMoleculeNode != NULL)
- delete rootMoleculeNode;
- rootMoleculeNode = NULL;
- SetResult(commandResult,
- NX_INTERNAL_ERROR,
- "Error translating to first atom position");
- NX_DEBUG_FAIL;
- return NULL;
- }
-
- NXSGOpenGLNode *firstAtomNode =
- createOpenGLSceneGraph(molPtr, firstAtomPtr, canonicalZAxis);
- if(firstAtomNode != NULL &&
- commandResult.getResult() == (int) NX_CMD_SUCCESS)
- {
+ // Necessary because bonds can bridge molecules and molecule-sets and in
+ // the case of the second to last molecules rendered, their first atoms
+ // may have been rendered while traversing the previous molecules.
+
+ OBAtom *firstAtomPtr = molPtr->BeginAtom(atomIter);
+
+ if(firstAtomPtr == (OBAtom*) NULL) {
+ string const source("Molecule scenegraph creation");
+ string const msg("empty molecule slipped past check");
+ SetResult(commandResult, NX_INTERNAL_ERROR, source + " - " + msg);
+ NX_DEBUG_FAIL;
+ return (NXSGOpenGLNode*) NULL;
+ }
+
+ while(firstAtomPtr != (OBAtom*) NULL && isRendered(firstAtomPtr))
+ firstAtomPtr = molPtr->NextAtom(atomIter);
+
+ if(firstAtomPtr == (OBAtom*) NULL) {
+ NXSGOpenGLNode *nullFirstAtomNode = new NXSGOpenGLNode;
+ SET_SCENEGRAPH_NAME(nullFirstAtomNode, "Null_first_atom");
+ return nullFirstAtomNode;
+ }
+
+ Vector const firstAtomPosition(firstAtomPtr->GetX(),
+ firstAtomPtr->GetY(),
+ firstAtomPtr->GetZ());
+
+ NXSGOpenGLTranslate *rootMoleculeNode = NULL;
+ try {
+ rootMoleculeNode =
+ new NXSGOpenGLTranslate(firstAtomPosition.x(),
+ firstAtomPosition.y(),
+ firstAtomPosition.z());
+ SET_SCENEGRAPH_NAME(rootMoleculeNode, "First_atom_position");
+ }
+ catch(...) {
+ if(rootMoleculeNode != NULL)
+ delete rootMoleculeNode;
+ rootMoleculeNode = NULL;
+ SetResult(commandResult,
+ NX_INTERNAL_ERROR,
+ "Error translating to first atom position");
+ NX_DEBUG_FAIL;
+ return NULL;
+ }
+
+ NXSGOpenGLNode *firstAtomNode =
+ createOpenGLSceneGraph(molPtr, firstAtomPtr, canonicalZAxis);
+ if(firstAtomNode != NULL &&
+ commandResult.getResult() == (int) NX_CMD_SUCCESS)
+ {
// submolecule scenegraph created completely and successfully
- bool childAdded = rootMoleculeNode->addChild(firstAtomNode);
- if(!childAdded) {
- SetResult(commandResult, NX_INTERNAL_ERROR,
- "Error adding child to first atom node");
- NX_DEBUG_FAIL;
- return rootMoleculeNode;
- }
- }
- else {
- NX_DEBUG_FAIL;
+ bool childAdded = rootMoleculeNode->addChild(firstAtomNode);
+ if(!childAdded) {
+ SetResult(commandResult, NX_INTERNAL_ERROR,
+ "Error adding child to first atom node");
+ NX_DEBUG_FAIL;
+ return rootMoleculeNode;
+ }
+ }
+ else {
+ NX_DEBUG_FAIL;
// either scenegraph could not be created or was created partially
// commandResult should hold the error
- return rootMoleculeNode;
- }
- /// @todo POST-FNANO delete firstAtomNode upon failures?
-
+ return rootMoleculeNode;
+ }
+ /// @todo POST-FNANO delete firstAtomNode upon failures?
+
// rest of the atoms
- OBAtom *atomPtr = molPtr->NextAtom(atomIter);
- for(; atomPtr != (OBAtom*) NULL;
- atomPtr = molPtr->NextAtom(atomIter))
- {
- if(isRendered(atomPtr)) // atom already rendered
- continue;
-
- Vector const atomPosition(atomPtr->GetX(),
- atomPtr->GetY(),
- atomPtr->GetZ());
- Vector const atomRelativePosition =
- (atomPosition - firstAtomPosition);
+ OBAtom *atomPtr = molPtr->NextAtom(atomIter);
+ for(; atomPtr != (OBAtom*) NULL;
+ atomPtr = molPtr->NextAtom(atomIter))
+ {
+ if(isRendered(atomPtr)) // atom already rendered
+ continue;
+
+ Vector const atomPosition(atomPtr->GetX(),
+ atomPtr->GetY(),
+ atomPtr->GetZ());
+ Vector const atomRelativePosition =
+ (atomPosition - firstAtomPosition);
// move scenegraph "cursor" to this atom
- NXSGOpenGLTranslate *translateToAtomNode = NULL;
- try {
- translateToAtomNode =
- new NXSGOpenGLTranslate(atomRelativePosition.x(),
- atomRelativePosition.y(),
- atomRelativePosition.z());
- SET_SCENEGRAPH_NAME(translateToAtomNode,
- "Translate_to_" + get_atom_scenegraph_name(atomPtr));
- }
- catch(...) {
- if(translateToAtomNode != NULL)
- delete translateToAtomNode;
- SetResult(commandResult, NX_INTERNAL_ERROR,
- "Error translating to atom");
- NX_DEBUG_FAIL;
- return rootMoleculeNode;
- }
-
- bool childAdded = rootMoleculeNode->addChild(translateToAtomNode);
- if(!childAdded) {
- SetResult(commandResult, NX_INTERNAL_ERROR,
- "Error adding translate-to-atom node to molecule root");
- NX_DEBUG_FAIL;
- return rootMoleculeNode;
- }
- /// @todo POST-FNANO delete translateToAtomNode upon failure?
-
+ NXSGOpenGLTranslate *translateToAtomNode = NULL;
+ try {
+ translateToAtomNode =
+ new NXSGOpenGLTranslate(atomRelativePosition.x(),
+ atomRelativePosition.y(),
+ atomRelativePosition.z());
+ SET_SCENEGRAPH_NAME(translateToAtomNode,
+ "Translate_to_" + get_atom_scenegraph_name(atomPtr));
+ }
+ catch(...) {
+ if(translateToAtomNode != NULL)
+ delete translateToAtomNode;
+ SetResult(commandResult, NX_INTERNAL_ERROR,
+ "Error translating to atom");
+ NX_DEBUG_FAIL;
+ return rootMoleculeNode;
+ }
+
+ bool childAdded = rootMoleculeNode->addChild(translateToAtomNode);
+ if(!childAdded) {
+ SetResult(commandResult, NX_INTERNAL_ERROR,
+ "Error adding translate-to-atom node to molecule root");
+ NX_DEBUG_FAIL;
+ return rootMoleculeNode;
+ }
+ /// @todo POST-FNANO delete translateToAtomNode upon failure?
+
// render subscenegraph rooted at this atom
- NXSGOpenGLNode *atomNode =
- createOpenGLSceneGraph(molPtr, atomPtr, canonicalZAxis);
-
- if(atomNode != NULL &&
- commandResult.getResult() == (int) NX_CMD_SUCCESS)
- {
- bool childAdded = translateToAtomNode->addChild(atomNode);
- if(!childAdded) {
- SetResult(commandResult, NX_INTERNAL_ERROR,
- "Error submolecule scenegraph as child of "
- "translation");
- NX_DEBUG_FAIL;
- return rootMoleculeNode;
- }
- }
- else {
- NX_DEBUG_FAIL;
- return rootMoleculeNode;
- }
- /// @todo POST-FNANO delete atomNode upon failures?
- } // loop over atoms
-
- return rootMoleculeNode;
+ NXSGOpenGLNode *atomNode =
+ createOpenGLSceneGraph(molPtr, atomPtr, canonicalZAxis);
+
+ if(atomNode != NULL &&
+ commandResult.getResult() == (int) NX_CMD_SUCCESS)
+ {
+ bool childAdded = translateToAtomNode->addChild(atomNode);
+ if(!childAdded) {
+ SetResult(commandResult, NX_INTERNAL_ERROR,
+ "Error submolecule scenegraph as child of "
+ "translation");
+ NX_DEBUG_FAIL;
+ return rootMoleculeNode;
+ }
+ }
+ else {
+ NX_DEBUG_FAIL;
+ return rootMoleculeNode;
+ }
+ /// @todo POST-FNANO delete atomNode upon failures?
+ } // loop over atoms
+
+ return rootMoleculeNode;
}
#if 0 /// @todo Post-FNANO08
@@ -782,19 +782,19 @@ NXOpenGLRenderingEngine::createOpenGLSceneGraph(OBMol *const molPtr)
NXSGOpenGLNode*
NXOpenGLRenderingEngine::createOpenGLDnaSegmentSceneGraph(OBMol *const molPtr)
{
- RenderStyleMap::const_iterator pluginIter = renderStyleMap.find("dna");
- if(pluginIter == renderStyleMap.end()) {
- NXLOG_WARNING("NXOpenGLRenderingEngine",
- "No plugin found to render DNA segment - "
- "reverting to default");
- return NULL;
- }
-
- NXOpenGLRendererPlugin *const dnaPlugin =
- static_cast<NXOpenGLRendererPlugin *const>(pluginIter->second);
-
- NXSGOpenGLNode *molSceneGraphNode = dnaPlugin->renderDnaSegment(molPtr);
- return molSceneGraphNode;
+ RenderStyleMap::const_iterator pluginIter = renderStyleMap.find("dna");
+ if(pluginIter == renderStyleMap.end()) {
+ NXLOG_WARNING("NXOpenGLRenderingEngine",
+ "No plugin found to render DNA segment - "
+ "reverting to default");
+ return NULL;
+ }
+
+ NXOpenGLRendererPlugin *const dnaPlugin =
+ static_cast<NXOpenGLRendererPlugin *const>(pluginIter->second);
+
+ NXSGOpenGLNode *molSceneGraphNode = dnaPlugin->renderDnaSegment(molPtr);
+ return molSceneGraphNode;
}
@@ -804,25 +804,25 @@ NXOpenGLRenderingEngine::createOpenGLDnaSegmentSceneGraph(OBMol *const molPtr)
NXSGOpenGLNode*
NXOpenGLRenderingEngine::createOpenGLDnaStrandSceneGraph(OBMol *const molPtr)
{
- RenderStyleMap::const_iterator pluginIter = renderStyleMap.find("dna");
- if(pluginIter == renderStyleMap.end()) {
- NXLOG_WARNING("NXOpenGLRenderingEngine",
- "No plugin found to render DNA strand - "
- "reverting to default");
- return NULL;
- }
-
- NXOpenGLRendererPlugin *const dnaPlugin =
- static_cast<NXOpenGLRendererPlugin *const>(pluginIter->second);
-
- assert(dnaSegmentMolSetPtr->moleculeCount() == 1);
- assert(dnaSegmentMolSetPtr->childCount() == 0);
-
- // locate segment molecule
- OBMol *const dnaSegmentMolPtr = *dnaSegmentMolSetPtr->moleculesBegin();
- NXSGOpenGLNode *molSceneGraphNode =
- dnaPlugin->renderDnaStrand(molPtr, dnaSegmentMolPtr);
- return molSceneGraphNode;
+ RenderStyleMap::const_iterator pluginIter = renderStyleMap.find("dna");
+ if(pluginIter == renderStyleMap.end()) {
+ NXLOG_WARNING("NXOpenGLRenderingEngine",
+ "No plugin found to render DNA strand - "
+ "reverting to default");
+ return NULL;
+ }
+
+ NXOpenGLRendererPlugin *const dnaPlugin =
+ static_cast<NXOpenGLRendererPlugin *const>(pluginIter->second);
+
+ assert(dnaSegmentMolSetPtr->moleculeCount() == 1);
+ assert(dnaSegmentMolSetPtr->childCount() == 0);
+
+ // locate segment molecule
+ OBMol *const dnaSegmentMolPtr = *dnaSegmentMolSetPtr->moleculesBegin();
+ NXSGOpenGLNode *molSceneGraphNode =
+ dnaPlugin->renderDnaStrand(molPtr, dnaSegmentMolPtr);
+ return molSceneGraphNode;
}
// -- end hacks --
#endif
@@ -832,44 +832,44 @@ NXSGOpenGLNode*
NXOpenGLRenderingEngine::getRotationNode(Vector const& zAxis,
Vector const& newZAxis)
{
- double const dotProduct = zAxis * newZAxis;
-
- if(dotProduct < 0.99999) {
- // Angle between both vectors is more than 0.25 degrees
- // therefore there is a well-defined rotation
- real const rotationAngleDeg =
- acos(dotProduct) * 180.0 / M_PI;
-
- Vector rotationAxis = xProduct(zAxis, newZAxis);
- rotationAxis.normalize();
-
- NXSGOpenGLRotate *rotateZAxisNode = NULL;
- try {
- rotateZAxisNode =
- new NXSGOpenGLRotate(rotationAngleDeg,
- rotationAxis.x(),
- rotationAxis.y(),
- rotationAxis.z());
- SET_SCENEGRAPH_NAME(rotateZAxisNode,
- "Rotate_Z_Axis");
- }
- catch(...) {
- SetResult(commandResult, NX_INTERNAL_ERROR,
- "Error creating axis rotation scenegraph node");
- NX_DEBUG_FAIL;
- return NULL;
- }
-
- return rotateZAxisNode;
- }
- else {
- // length of cross-product is below 1%
- // therefore the two z-axes are parallel to within numerical error
- // bypass creation of rotation scenegraph node
- return NULL;
-
- }
-
+ double const dotProduct = zAxis * newZAxis;
+
+ if(dotProduct < 0.99999) {
+ // Angle between both vectors is more than 0.25 degrees
+ // therefore there is a well-defined rotation
+ real const rotationAngleDeg =
+ acos(dotProduct) * 180.0 / M_PI;
+
+ Vector rotationAxis = xProduct(zAxis, newZAxis);
+ rotationAxis.normalize();
+
+ NXSGOpenGLRotate *rotateZAxisNode = NULL;
+ try {
+ rotateZAxisNode =
+ new NXSGOpenGLRotate(rotationAngleDeg,
+ rotationAxis.x(),
+ rotationAxis.y(),
+ rotationAxis.z());
+ SET_SCENEGRAPH_NAME(rotateZAxisNode,
+ "Rotate_Z_Axis");
+ }
+ catch(...) {
+ SetResult(commandResult, NX_INTERNAL_ERROR,
+ "Error creating axis rotation scenegraph node");
+ NX_DEBUG_FAIL;
+ return NULL;
+ }
+
+ return rotateZAxisNode;
+ }
+ else {
+ // length of cross-product is below 1%
+ // therefore the two z-axes are parallel to within numerical error
+ // bypass creation of rotation scenegraph node
+ return NULL;
+
+ }
+
}
/// Render given atom in the molecule in a depth-first manner
@@ -879,236 +879,236 @@ NXOpenGLRenderingEngine::createOpenGLSceneGraph(OBMol *const molPtr,
OBAtom *const atomPtr,
Vector const& zAxis)
{
- // Precondition: *atomPtr shouldn't have been rendered
- assert(renderedAtoms.find(atomPtr) == renderedAtoms.end());
- assert(atomPtr->GetParent() == molPtr);
-
+ // Precondition: *atomPtr shouldn't have been rendered
+ assert(renderedAtoms.find(atomPtr) == renderedAtoms.end());
+ assert(atomPtr->GetParent() == molPtr);
+
// Do nothing if no rendering plugins
- if(!pluginsInitialized) {
- SetResult(commandResult, NX_INTERNAL_ERROR,
- "Rendering plugin not set/initialized");
- NX_DEBUG_FAIL;
- return NULL;
- }
-
+ if(!pluginsInitialized) {
+ SetResult(commandResult, NX_INTERNAL_ERROR,
+ "Rendering plugin not set/initialized");
+ NX_DEBUG_FAIL;
+ return NULL;
+ }
+
// translate origin to atom center
- Vector atomPosition(atomPtr->GetX(), atomPtr->GetY(), atomPtr->GetZ());
-
-
+ Vector atomPosition(atomPtr->GetX(), atomPtr->GetY(), atomPtr->GetZ());
+
+
// create scenegraph node and mark atom as rendered
- // NXAtomRenderData atomRenderData(atomPtr->GetAtomicNum());
- // atomRenderData.addData(static_cast<void const *>(&defaultAtomMaterial));
- assert(atomPtr->HasData(NXAtomDataType));
- NXAtomData *atomData =
- static_cast<NXAtomData*>(atomPtr->GetData(NXAtomDataType));
- assert(atomData->GetDataType() == NXAtomDataType);
- assert(atomData != NULL);
-
- // default color
- NXRGBColor defaultElementColor(0.0, 0.0, 0.0);
- // Bypass OpenBabel's atomicNum because it is stored modulo 256 in a 'char'
- int atomicNum = get_atomic_num(atomPtr);
- map<uint, NXRGBColor>::iterator defaultElementColorIter =
- elementColorMap.find(atomicNum);
- if(defaultElementColorIter != elementColorMap.end()) {
- defaultElementColor = defaultElementColorIter->second;
- }
- else {
- cerr << "NXOpenGLRenderingEngine: no color found for atom with atomic num = "
- << atomicNum << endl;
- }
-
+ // NXAtomRenderData atomRenderData(atomPtr->GetAtomicNum());
+ // atomRenderData.addData(static_cast<void const *>(&defaultAtomMaterial));
+ assert(atomPtr->HasData(NXAtomDataType));
+ NXAtomData *atomData =
+ static_cast<NXAtomData*>(atomPtr->GetData(NXAtomDataType));
+ assert(atomData->GetDataType() == NXAtomDataType);
+ assert(atomData != NULL);
+
+ // default color
+ NXRGBColor defaultElementColor(0.0, 0.0, 0.0);
+ // Bypass OpenBabel's atomicNum because it is stored modulo 256 in a 'char'
+ int atomicNum = get_atomic_num(atomPtr);
+ map<uint, NXRGBColor>::iterator defaultElementColorIter =
+ elementColorMap.find(atomicNum);
+ if(defaultElementColorIter != elementColorMap.end()) {
+ defaultElementColor = defaultElementColorIter->second;
+ }
+ else {
+ cerr << "NXOpenGLRenderingEngine: no color found for atom with atomic num = "
+ << atomicNum << endl;
+ }
+
// set default material parameters
- defaultAtomMaterial.ambient[0] = defaultElementColor.r;
- defaultAtomMaterial.ambient[1] = defaultElementColor.g;
- defaultAtomMaterial.ambient[2] = defaultElementColor.b;
- defaultAtomMaterial.ambient[3] = 1.0;
- defaultAtomMaterial.diffuse[0] = defaultElementColor.r;
- defaultAtomMaterial.diffuse[1] = defaultElementColor.g;
- defaultAtomMaterial.diffuse[2] = defaultElementColor.b;
- defaultAtomMaterial.diffuse[3] = 1.0;
- defaultAtomMaterial.specular[0] = defaultElementColor.r;
- defaultAtomMaterial.specular[1] = defaultElementColor.g;
- defaultAtomMaterial.specular[2] = defaultElementColor.b;
- defaultAtomMaterial.specular[3] = 1.0;
-
-
- string const& atomRenderStyleCode = atomData->getRenderStyleCode();
- atomData->addSupplementalData(static_cast<void const*>(&defaultAtomMaterial));
- /// @todo consider if supplemental data can be added repeatedly and the
- /// corresponding vector grows needlessly
-
-
- // The following dynamic_cast is ok because plugins were type-checked at
- // initialization time
- /// @fixme Use qobject_cast instead of static_cast? dynamic_cast won't work
- NXOpenGLRendererPlugin *renderer =
- static_cast<NXOpenGLRendererPlugin*>(renderStyleMap[atomRenderStyleCode]);
- if(renderer == (NXOpenGLRendererPlugin*) NULL) {
- SetResult(commandResult,
- NX_PLUGIN_CAUSED_ERROR,
- "No renderer-plugin found for rendering-style-code '" +
- atomRenderStyleCode + "'");
- /// @todo POST-FNANO more descriptive error message - which atom# and moleculeSet
- NX_DEBUG_FAIL;
- return (NXSGOpenGLNode*) NULL;
- }
- NXSGOpenGLNode *const atomNode = renderer->renderAtom(*atomData);
- if(atomNode == NULL) {
- commandResult = renderer->getCommandResult();
- NX_DEBUG_FAIL;
- return NULL;
- }
- SET_ATOM_SCENEGRAPH_NAME(atomNode, atomPtr);
- renderedAtoms.insert(atomPtr); // mark as rendered
-
- // render outgoing bonds and neighbouring atoms (if applicable) as children
- OBBondIterator bondIter;
- OBBond *bondPtr(NULL);
- for(bondPtr = atomPtr->BeginBond(bondIter);
- bondPtr != NULL;
- bondPtr = atomPtr->NextBond(bondIter))
-
- {
- OBAtom *const nbrAtomPtr = bondPtr->GetNbrAtom(atomPtr);
- assert(nbrAtomPtr != atomPtr);
- Vector const nbrAtomPosition(nbrAtomPtr->GetX(),
- nbrAtomPtr->GetY(),
- nbrAtomPtr->GetZ());
- Vector const nbrAtomRelativePosition = (nbrAtomPosition - atomPosition);
- Vector newZAxis = nbrAtomRelativePosition;
- newZAxis.normalize();
-
- if(!isRendered(bondPtr)) {
+ defaultAtomMaterial.ambient[0] = defaultElementColor.r;
+ defaultAtomMaterial.ambient[1] = defaultElementColor.g;
+ defaultAtomMaterial.ambient[2] = defaultElementColor.b;
+ defaultAtomMaterial.ambient[3] = 1.0;
+ defaultAtomMaterial.diffuse[0] = defaultElementColor.r;
+ defaultAtomMaterial.diffuse[1] = defaultElementColor.g;
+ defaultAtomMaterial.diffuse[2] = defaultElementColor.b;
+ defaultAtomMaterial.diffuse[3] = 1.0;
+ defaultAtomMaterial.specular[0] = defaultElementColor.r;
+ defaultAtomMaterial.specular[1] = defaultElementColor.g;
+ defaultAtomMaterial.specular[2] = defaultElementColor.b;
+ defaultAtomMaterial.specular[3] = 1.0;
+
+
+ string const& atomRenderStyleCode = atomData->getRenderStyleCode();
+ atomData->addSupplementalData(static_cast<void const*>(&defaultAtomMaterial));
+ /// @todo consider if supplemental data can be added repeatedly and the
+ /// corresponding vector grows needlessly
+
+
+ // The following dynamic_cast is ok because plugins were type-checked at
+ // initialization time
+ /// @fixme Use qobject_cast instead of static_cast? dynamic_cast won't work
+ NXOpenGLRendererPlugin *renderer =
+ static_cast<NXOpenGLRendererPlugin*>(renderStyleMap[atomRenderStyleCode]);
+ if(renderer == (NXOpenGLRendererPlugin*) NULL) {
+ SetResult(commandResult,
+ NX_PLUGIN_CAUSED_ERROR,
+ "No renderer-plugin found for rendering-style-code '" +
+ atomRenderStyleCode + "'");
+ /// @todo POST-FNANO more descriptive error message - which atom# and moleculeSet
+ NX_DEBUG_FAIL;
+ return (NXSGOpenGLNode*) NULL;
+ }
+ NXSGOpenGLNode *const atomNode = renderer->renderAtom(*atomData);
+ if(atomNode == NULL) {
+ commandResult = renderer->getCommandResult();
+ NX_DEBUG_FAIL;
+ return NULL;
+ }
+ SET_ATOM_SCENEGRAPH_NAME(atomNode, atomPtr);
+ renderedAtoms.insert(atomPtr); // mark as rendered
+
+ // render outgoing bonds and neighbouring atoms (if applicable) as children
+ OBBondIterator bondIter;
+ OBBond *bondPtr(NULL);
+ for(bondPtr = atomPtr->BeginBond(bondIter);
+ bondPtr != NULL;
+ bondPtr = atomPtr->NextBond(bondIter))
+
+ {
+ OBAtom *const nbrAtomPtr = bondPtr->GetNbrAtom(atomPtr);
+ assert(nbrAtomPtr != atomPtr);
+ Vector const nbrAtomPosition(nbrAtomPtr->GetX(),
+ nbrAtomPtr->GetY(),
+ nbrAtomPtr->GetZ());
+ Vector const nbrAtomRelativePosition = (nbrAtomPosition - atomPosition);
+ Vector newZAxis = nbrAtomRelativePosition;
+ newZAxis.normalize();
+
+ if(!isRendered(bondPtr)) {
// compute bond orientation
-
- // Rotate z-axis to align with bond-direction if necessary
- NXSGOpenGLNode *rotateZAxisNode = getRotationNode(zAxis,newZAxis);
- if(rotateZAxisNode == NULL)
- rotateZAxisNode = atomNode;
-
- else {
- bool childAdded = atomNode->addChild(rotateZAxisNode);
- if(!childAdded) {
- SetResult(commandResult, NX_INTERNAL_ERROR,
- "Error adding rotation node as child to atom node");
- NX_DEBUG_FAIL;
- return atomNode;
- }
- }
-
- void const *const defBondMatPtr =
- static_cast<void const*>(&defaultBondMaterial);
- NXBondData bondRenderData((BondType)bondPtr->GetBondOrder(),
- bondPtr->GetLength());
- bondRenderData.addSupplementalData(defBondMatPtr);
- NXSGOpenGLNode *const bondNode = renderer->renderBond(bondRenderData);
- if(bondNode == NULL) {
- commandResult = renderer->getCommandResult();
- NX_DEBUG_FAIL;
- return atomNode;
- }
- SET_BOND_SCENEGRAPH_NAME(bondNode, bondPtr);
- bool const childAdded = rotateZAxisNode->addChild(bondNode);
- if(!childAdded) {
- SetResult(commandResult, NX_INTERNAL_ERROR,
- "Error adding bond node to z-axis rotation node");
- NX_DEBUG_FAIL;
- return atomNode;
- }
-
- markBondRendered(bondPtr);
-
- } // if bond not already rendered
-
-
- if(!isRendered(nbrAtomPtr) && nbrAtomPtr->GetParent() == molPtr) {
-
+
+ // Rotate z-axis to align with bond-direction if necessary
+ NXSGOpenGLNode *rotateZAxisNode = getRotationNode(zAxis,newZAxis);
+ if(rotateZAxisNode == NULL)
+ rotateZAxisNode = atomNode;
+
+ else {
+ bool childAdded = atomNode->addChild(rotateZAxisNode);
+ if(!childAdded) {
+ SetResult(commandResult, NX_INTERNAL_ERROR,
+ "Error adding rotation node as child to atom node");
+ NX_DEBUG_FAIL;
+ return atomNode;
+ }
+ }
+
+ void const *const defBondMatPtr =
+ static_cast<void const*>(&defaultBondMaterial);
+ NXBondData bondRenderData((BondType)bondPtr->GetBondOrder(),
+ bondPtr->GetLength());
+ bondRenderData.addSupplementalData(defBondMatPtr);
+ NXSGOpenGLNode *const bondNode = renderer->renderBond(bondRenderData);
+ if(bondNode == NULL) {
+ commandResult = renderer->getCommandResult();
+ NX_DEBUG_FAIL;
+ return atomNode;
+ }
+ SET_BOND_SCENEGRAPH_NAME(bondNode, bondPtr);
+ bool const childAdded = rotateZAxisNode->addChild(bondNode);
+ if(!childAdded) {
+ SetResult(commandResult, NX_INTERNAL_ERROR,
+ "Error adding bond node to z-axis rotation node");
+ NX_DEBUG_FAIL;
+ return atomNode;
+ }
+
+ markBondRendered(bondPtr);
+
+ } // if bond not already rendered
+
+
+ if(!isRendered(nbrAtomPtr) && nbrAtomPtr->GetParent() == molPtr) {
+
// translate to neighbouring atom center
- // double const bondLength = bondPtr->GetLength();
- NXSGOpenGLTranslate *translateToNbrAtomNode = NULL;
- try {
- translateToNbrAtomNode =
- new NXSGOpenGLTranslate(nbrAtomRelativePosition.x(),
- nbrAtomRelativePosition.y(),
- nbrAtomRelativePosition.z());
- SET_SCENEGRAPH_NAME(translateToNbrAtomNode,
- "Translate_to_" + get_atom_scenegraph_name(nbrAtomPtr));
- }
- catch(...) {
- SetResult(commandResult, NX_INTERNAL_ERROR,
- "Error creating trans-bond translation scenegraph node");
- NX_DEBUG_FAIL;
- return atomNode;
- }
- bool const childAdded = atomNode->addChild(translateToNbrAtomNode);
- if(!childAdded) {
- SetResult(commandResult, NX_INTERNAL_ERROR,
- "Error adding trans-bond translation node as child of"
- " bond-node");
- NX_DEBUG_FAIL;
- return atomNode;
- }
-
+ // double const bondLength = bondPtr->GetLength();
+ NXSGOpenGLTranslate *translateToNbrAtomNode = NULL;
+ try {
+ translateToNbrAtomNode =
+ new NXSGOpenGLTranslate(nbrAtomRelativePosition.x(),
+ nbrAtomRelativePosition.y(),
+ nbrAtomRelativePosition.z());
+ SET_SCENEGRAPH_NAME(translateToNbrAtomNode,
+ "Translate_to_" + get_atom_scenegraph_name(nbrAtomPtr));
+ }
+ catch(...) {
+ SetResult(commandResult, NX_INTERNAL_ERROR,
+ "Error creating trans-bond translation scenegraph node");
+ NX_DEBUG_FAIL;
+ return atomNode;
+ }
+ bool const childAdded = atomNode->addChild(translateToNbrAtomNode);
+ if(!childAdded) {
+ SetResult(commandResult, NX_INTERNAL_ERROR,
+ "Error adding trans-bond translation node as child of"
+ " bond-node");
+ NX_DEBUG_FAIL;
+ return atomNode;
+ }
+
// create scenegraph rooted at neighbouring atom
- NXSGOpenGLNode *nbrAtomNode =
- createOpenGLSceneGraph(molPtr, nbrAtomPtr, /*newZAxis*/ Vector(0.0, 0.0, 1.0));
- if(nbrAtomNode == NULL) {
- NX_DEBUG_FAIL;
- return atomNode;
- }
- else {
- bool const childAdded =
- translateToNbrAtomNode->addChild(nbrAtomNode);
- if(!childAdded) {
- SetResult(commandResult, NX_INTERNAL_ERROR,
- "Error adding neighboring-atom scenegraph subtree"
- " as child of trans-bond translation node");
- NX_DEBUG_FAIL;
- return atomNode;
- }
- }
- } // if neighbouring atom not already rendered
- }
-
- return atomNode;
+ NXSGOpenGLNode *nbrAtomNode =
+ createOpenGLSceneGraph(molPtr, nbrAtomPtr, /*newZAxis*/ Vector(0.0, 0.0, 1.0));
+ if(nbrAtomNode == NULL) {
+ NX_DEBUG_FAIL;
+ return atomNode;
+ }
+ else {
+ bool const childAdded =
+ translateToNbrAtomNode->addChild(nbrAtomNode);
+ if(!childAdded) {
+ SetResult(commandResult, NX_INTERNAL_ERROR,
+ "Error adding neighboring-atom scenegraph subtree"
+ " as child of trans-bond translation node");
+ NX_DEBUG_FAIL;
+ return atomNode;
+ }
+ }
+ } // if neighbouring atom not already rendered
+ }
+
+ return atomNode;
}
void NXOpenGLRenderingEngine::markBondRendered(OBBond *const bondPtr)
{
- OBAtom *const atom1 = bondPtr->GetBeginAtom();
- OBAtom *const atom2 = bondPtr->GetEndAtom();
-
- pair<OBAtom*,OBAtom*> atomPair = ( atom1 < atom2 ?
- make_pair(atom1, atom2) :
- make_pair(atom2, atom1) );
- renderedBonds.insert(atomPair);
+ OBAtom *const atom1 = bondPtr->GetBeginAtom();
+ OBAtom *const atom2 = bondPtr->GetEndAtom();
+
+ pair<OBAtom*,OBAtom*> atomPair = ( atom1 < atom2 ?
+ make_pair(atom1, atom2) :
+ make_pair(atom2, atom1) );
+ renderedBonds.insert(atomPair);
}
bool NXOpenGLRenderingEngine::isRendered(OBAtom *const atomPtr) const
{
- set<OBAtom*>::const_iterator memberIter = renderedAtoms.find(atomPtr);
- bool const result = (memberIter != renderedAtoms.end());
- return result;
+ set<OBAtom*>::const_iterator memberIter = renderedAtoms.find(atomPtr);
+ bool const result = (memberIter != renderedAtoms.end());
+ return result;
}
bool NXOpenGLRenderingEngine::isRendered(OBBond *const bondPtr) const
{
- OBAtom *atom1 = bondPtr->GetBeginAtom();
- OBAtom *atom2 = bondPtr->GetEndAtom();
-
- pair<OBAtom*,OBAtom*> atomPair = (atom1 < atom2 ?
- make_pair(atom1, atom2) :
- make_pair(atom2, atom1));
-
- RenderedBondsTableType::const_iterator memberIter =
- renderedBonds.find(atomPair);
-
- bool const result = (memberIter != renderedBonds.end());
- return result;
+ OBAtom *atom1 = bondPtr->GetBeginAtom();
+ OBAtom *atom2 = bondPtr->GetEndAtom();
+
+ pair<OBAtom*,OBAtom*> atomPair = (atom1 < atom2 ?
+ make_pair(atom1, atom2) :
+ make_pair(atom2, atom1));
+
+ RenderedBondsTableType::const_iterator memberIter =
+ renderedBonds.find(atomPair);
+
+ bool const result = (memberIter != renderedBonds.end());
+ return result;
}
@@ -1117,275 +1117,275 @@ static inline double sqr(double const&x) { return x*x; }
void NXOpenGLRenderingEngine::resetView(void)
{
// create axis-aligned bounding box
- if(currentFrameIndex < 0)
- return;
-
- NXMoleculeSet *molSetPtr = moleculeSets[currentFrameIndex];
- BoundingBox bbox = GetBoundingBox(molSetPtr);
- Vector bboxMin = bbox.min();
- Vector bboxMax = bbox.max();
-
- real const bboxXWidth = 1.0*(bboxMax.x() - bboxMin.x());
- real const bboxYWidth = 1.0*(bboxMax.y() - bboxMin.y());
- real const bboxZDepth = 1.0*(bboxMax.z() - bboxMin.z());
-
- real const projCubeWidth = max(bboxXWidth, max(bboxYWidth, bboxZDepth));
- real const circumSphereRad = sqrt(3.0*0.25*projCubeWidth*projCubeWidth);
-// sqrt(sqr(max(bboxMax.x(), bboxMin.x())) +
-// sqr(max(bboxMax.y(), bboxMin.y())) +
-// sqr(max(bboxMax.z(), bboxMin.z())) );
- real const circumSphereDia = 2.0 * circumSphereRad;
- Vector const bboxCenter = bbox.center();
-
- real l, r, b, t;
- real const n = 0.25 * circumSphereRad;
- real const f = 12.0 * circumSphereRad;
- real const aspect = real(width()) / real(height());
- if(aspect < 1.0) {
-// l = bboxCenter.x() - circumSphereDia;
-// r = bboxCenter.x() + circumSphereDia;
-// b = bboxCenter.y() - circumSphereDia / aspect;
-// t = bboxCenter.y() + circumSphereDia / aspect;
- l = -circumSphereRad;
- r = -l;
- b = -circumSphereRad / aspect;
- t = -b;
- }
- else {
-// l = bboxCenter.x() - aspect * circumSphereDia;
-// r = bboxCenter.x() + aspect * circumSphereDia;
-// b = bboxCenter.y() - circumSphereDia;
-// t = bboxCenter.y() + circumSphereDia;
- l = -aspect * circumSphereRad;
- r = -l;
- b = -circumSphereRad;
- t = -b;
- }
-
- // makeCurrent();
-// camera.gluLookAt(bboxCenter.x(), bboxCenter.y(),
-// bboxCenter.z()+circumSphereDia,
-// bboxCenter.x(), bboxCenter.y(), bboxCenter.z(),
-// 0.0, 1.0, 0.0);
+ if(currentFrameIndex < 0)
+ return;
+
+ NXMoleculeSet *molSetPtr = moleculeSets[currentFrameIndex];
+ BoundingBox bbox = GetBoundingBox(molSetPtr);
+ Vector bboxMin = bbox.min();
+ Vector bboxMax = bbox.max();
+
+ real const bboxXWidth = 1.0*(bboxMax.x() - bboxMin.x());
+ real const bboxYWidth = 1.0*(bboxMax.y() - bboxMin.y());
+ real const bboxZDepth = 1.0*(bboxMax.z() - bboxMin.z());
+
+ real const projCubeWidth = max(bboxXWidth, max(bboxYWidth, bboxZDepth));
+ real const circumSphereRad = sqrt(3.0*0.25*projCubeWidth*projCubeWidth);
+// sqrt(sqr(max(bboxMax.x(), bboxMin.x())) +
+// sqr(max(bboxMax.y(), bboxMin.y())) +
+// sqr(max(bboxMax.z(), bboxMin.z())) );
+ real const circumSphereDia = 2.0 * circumSphereRad;
+ Vector const bboxCenter = bbox.center();
+
+ real l, r, b, t;
+ real const n = 0.25 * circumSphereRad;
+ real const f = 12.0 * circumSphereRad;
+ real const aspect = real(width()) / real(height());
+ if(aspect < 1.0) {
+// l = bboxCenter.x() - circumSphereDia;
+// r = bboxCenter.x() + circumSphereDia;
+// b = bboxCenter.y() - circumSphereDia / aspect;
+// t = bboxCenter.y() + circumSphereDia / aspect;
+ l = -circumSphereRad;
+ r = -l;
+ b = -circumSphereRad / aspect;
+ t = -b;
+ }
+ else {
+// l = bboxCenter.x() - aspect * circumSphereDia;
+// r = bboxCenter.x() + aspect * circumSphereDia;
+// b = bboxCenter.y() - circumSphereDia;
+// t = bboxCenter.y() + circumSphereDia;
+ l = -aspect * circumSphereRad;
+ r = -l;
+ b = -circumSphereRad;
+ t = -b;
+ }
+
+ // makeCurrent();
+// camera.gluLookAt(bboxCenter.x(), bboxCenter.y(),
+// bboxCenter.z()+circumSphereDia,
+// bboxCenter.x(), bboxCenter.y(), bboxCenter.z(),
+// 0.0, 1.0, 0.0);
// camera.gluPerspective(60.0, double(width())/double(height()), n, f);
-
-// camera.gluLookAt(0.0, 0.0, circumSphereRad,
-// 0.0, 0.0, 0.0,
-// 0.0, 1.0, 0.0);
-// camera.glOrtho(l, r, b, t, n, f);
-
- NXNamedView defaultView("DefaultView",
- NXQuaternion<double>(1.0, 0.0, 0.0, 1.0),
- bboxYWidth,
- NXVector3d(-bboxCenter.x(),
- -bboxCenter.y(),
- -bboxCenter.z()),
- 1.0);
- cerr << defaultView << endl;
- camera.setNamedView(defaultView);
-
- // default HomeView: (1, 0, 0, 0) (10) (0, 0, 0) (1)
- // orthographic projection as in GLPane.py::_setup_projection()
-
-// double const SCALE = 10.0 * 1.0e-13;
-// double const VDIST = 6.0 * SCALE;
-// camera.gluLookAt(0.0, 0.0, VDIST,
-// 0.0, 0.0, 0.0,
-// 0.0, 1.0, 0.0);
-// double const NEAR = 0.25, FAR = 12.0;
-// camera.glOrtho(-SCALE * aspect, SCALE * aspect,
-// -SCALE , SCALE,
-// VDIST * NEAR , VDIST * FAR);
-
- updateGL();
+
+// camera.gluLookAt(0.0, 0.0, circumSphereRad,
+// 0.0, 0.0, 0.0,
+// 0.0, 1.0, 0.0);
+// camera.glOrtho(l, r, b, t, n, f);
+
+ NXNamedView defaultView("DefaultView",
+ NXQuaternion<double>(1.0, 0.0, 0.0, 1.0),
+ bboxYWidth,
+ NXVector3d(-bboxCenter.x(),
+ -bboxCenter.y(),
+ -bboxCenter.z()),
+ 1.0);
+ cerr << defaultView << endl;
+ camera.setNamedView(defaultView);
+
+ // default HomeView: (1, 0, 0, 0) (10) (0, 0, 0) (1)
+ // orthographic projection as in GLPane.py::_setup_projection()
+
+// double const SCALE = 10.0 * 1.0e-13;
+// double const VDIST = 6.0 * SCALE;
+// camera.gluLookAt(0.0, 0.0, VDIST,
+// 0.0, 0.0, 0.0,
+// 0.0, 1.0, 0.0);
+// double const NEAR = 0.25, FAR = 12.0;
+// camera.glOrtho(-SCALE * aspect, SCALE * aspect,
+// -SCALE , SCALE,
+// VDIST * NEAR , VDIST * FAR);
+
+ updateGL();
}
void NXOpenGLRenderingEngine::setNamedView(NXNamedView const& view)
{
- makeCurrent();
- camera.setNamedView(view);
- updateGL();
+ makeCurrent();
+ camera.setNamedView(view);
+ updateGL();
}
/* FUNCTION: mousePressEvent */
void NXOpenGLRenderingEngine::mousePressEvent(QMouseEvent *mouseEvent) {
-
- if (mouseEvent->button() == Qt::LeftButton) {
- if (mouseEvent->modifiers() == Qt::NoModifier) {
+
+ if (mouseEvent->button() == Qt::LeftButton) {
+ if (mouseEvent->modifiers() == Qt::NoModifier) {
printf("NXOpenGLRenderingEngine::mousePressEvent: rotate\n");
- camera.rotateStartEvent(mouseEvent->x(), mouseEvent->y());
- mouseEvent->accept();
-
- } else if (mouseEvent->modifiers() == Qt::ControlModifier) {
+ camera.rotateStartEvent(mouseEvent->x(), mouseEvent->y());
+ mouseEvent->accept();
+
+ } else if (mouseEvent->modifiers() == Qt::ControlModifier) {
printf("NXOpenGLRenderingEngine::mousePressEvent: pan\n");
- camera.panStartEvent(mouseEvent->x(), mouseEvent->y());
- mouseEvent->accept();
-
- } else if (mouseEvent->modifiers() == Qt::ShiftModifier) {
+ camera.panStartEvent(mouseEvent->x(), mouseEvent->y());
+ mouseEvent->accept();
+
+ } else if (mouseEvent->modifiers() == Qt::ShiftModifier) {
printf("NXOpenGLRenderingEngine::mousePressEvent: zoom\n");
- mouseEvent->accept();
- }
-
- } else {
- mouseEvent->ignore();
- }
- updateGL();
+ mouseEvent->accept();
+ }
+
+ } else {
+ mouseEvent->ignore();
+ }
+ updateGL();
}
/* FUNCTION: mouseMoveEvent */
void NXOpenGLRenderingEngine::mouseMoveEvent(QMouseEvent *mouseEvent) {
-
- Qt::MouseButtons buttons = mouseEvent->buttons();
- if (buttons & Qt::LeftButton) {
- if (mouseEvent->modifiers() == Qt::NoModifier) {
- camera.rotatingEvent(mouseEvent->x(), mouseEvent->y());
- mouseEvent->accept();
-
- } else if (mouseEvent->modifiers() == Qt::ControlModifier) {
- camera.panEvent(mouseEvent->x(), mouseEvent->y());
- mouseEvent->accept();
-
- } else if (mouseEvent->modifiers() == Qt::ShiftModifier) {
- mouseEvent->accept();
- }
-
- } else {
- mouseEvent->ignore();
- }
- updateGL();
+
+ Qt::MouseButtons buttons = mouseEvent->buttons();
+ if (buttons & Qt::LeftButton) {
+ if (mouseEvent->modifiers() == Qt::NoModifier) {
+ camera.rotatingEvent(mouseEvent->x(), mouseEvent->y());
+ mouseEvent->accept();
+
+ } else if (mouseEvent->modifiers() == Qt::ControlModifier) {
+ camera.panEvent(mouseEvent->x(), mouseEvent->y());
+ mouseEvent->accept();
+
+ } else if (mouseEvent->modifiers() == Qt::ShiftModifier) {
+ mouseEvent->accept();
+ }
+
+ } else {
+ mouseEvent->ignore();
+ }
+ updateGL();
}
/* FUNCTION: mouseReleaseEvent */
void NXOpenGLRenderingEngine::mouseReleaseEvent(QMouseEvent *mouseEvent) {
-
- if (mouseEvent->button() == Qt::LeftButton) {
- if (mouseEvent->modifiers() == Qt::NoModifier) {
- camera.rotateStopEvent(mouseEvent->x(), mouseEvent->y());
- mouseEvent->accept();
-
- } else if (mouseEvent->modifiers() == Qt::ControlModifier) {
- camera.panStopEvent(mouseEvent->x(), mouseEvent->y());
- mouseEvent->accept();
-
- } else if (mouseEvent->modifiers() == Qt::ShiftModifier) {
- mouseEvent->accept();
- }
-
- } else {
- mouseEvent->ignore();
- }
- updateGL();
+
+ if (mouseEvent->button() == Qt::LeftButton) {
+ if (mouseEvent->modifiers() == Qt::NoModifier) {
+ camera.rotateStopEvent(mouseEvent->x(), mouseEvent->y());
+ mouseEvent->accept();
+
+ } else if (mouseEvent->modifiers() == Qt::ControlModifier) {
+ camera.panStopEvent(mouseEvent->x(), mouseEvent->y());
+ mouseEvent->accept();
+
+ } else if (mouseEvent->modifiers() == Qt::ShiftModifier) {
+ mouseEvent->accept();
+ }
+
+ } else {
+ mouseEvent->ignore();
+ }
+ updateGL();
}
void NXOpenGLRenderingEngine::wheelEvent(QWheelEvent *event)
{
- int numDegrees = event->delta() / 8;
- int numSteps = numDegrees / 15;
- camera.advance(numSteps);
- updateGL();
+ int numDegrees = event->delta() / 8;
+ int numSteps = numDegrees / 15;
+ camera.advance(numSteps);
+ updateGL();
}
/// Meant to be called after all renderer-plugins have been set against
/// a render-style. This function initializes all plugins. Calling this
/// function, then including more plugins and then calling this function again
-/// will not initialize the newly
+/// will not initialize the newly
bool NXOpenGLRenderingEngine::initializePlugins(void)
{
- if(pluginsInitialized)
- return true;
-
- bool success = true;
- makeCurrent();
- map<string, NXRendererPlugin*>::iterator pluginIter;
- for(pluginIter = renderStyleMap.begin();
- pluginIter != renderStyleMap.end();
- ++pluginIter)
- {
- // since default rendering style must also appear independently
- // do not initialize
- string const& renderStyleCode = pluginIter->first;
- if(renderStyleCode == "def")
- continue;
-
- NXRendererPlugin *plugin = pluginIter->second;
- NXCommandResult const *const result = plugin->initialize();
-
- if(result->getResult() != (int) NX_CMD_SUCCESS) {
- success = false;
- ostringstream logMsgStream;
- logMsgStream << "Plugin for render-style " + pluginIter->first +
- " couldn't be initialized. ";
- vector<QString> const& msgs = result->getParamVector();
- vector<QString>::const_iterator msgIter;
- for(msgIter = msgs.begin(); msgIter != msgs.end(); ++msgIter) {
- logMsgStream << ' ' << qPrintable(*msgIter);
- }
- NXLOG_SEVERE("NXOpenGLRenderingEngine", logMsgStream.str());
- }
- else {
- NXLOG_INFO("NXOpenGLRenderingEngine",
- "Initialized plugin for render-style " +
- pluginIter->first);
- }
- }
-
- if(success)
- pluginsInitialized = true;
-
- return success;
+ if(pluginsInitialized)
+ return true;
+
+ bool success = true;
+ makeCurrent();
+ map<string, NXRendererPlugin*>::iterator pluginIter;
+ for(pluginIter = renderStyleMap.begin();
+ pluginIter != renderStyleMap.end();
+ ++pluginIter)
+ {
+ // since default rendering style must also appear independently
+ // do not initialize
+ string const& renderStyleCode = pluginIter->first;
+ if(renderStyleCode == "def")
+ continue;
+
+ NXRendererPlugin *plugin = pluginIter->second;
+ NXCommandResult const *const result = plugin->initialize();
+
+ if(result->getResult() != (int) NX_CMD_SUCCESS) {
+ success = false;
+ ostringstream logMsgStream;
+ logMsgStream << "Plugin for render-style " + pluginIter->first +
+ " couldn't be initialized. ";
+ vector<QString> const& msgs = result->getParamVector();
+ vector<QString>::const_iterator msgIter;
+ for(msgIter = msgs.begin(); msgIter != msgs.end(); ++msgIter) {
+ logMsgStream << ' ' << qPrintable(*msgIter);
+ }
+ NXLOG_SEVERE("NXOpenGLRenderingEngine", logMsgStream.str());
+ }
+ else {
+ NXLOG_INFO("NXOpenGLRenderingEngine",
+ "Initialized plugin for render-style " +
+ pluginIter->first);
+ }
+ }
+
+ if(success)
+ pluginsInitialized = true;
+
+ return success;
}
bool NXOpenGLRenderingEngine::cleanupPlugins(void)
{
- if(!pluginsInitialized)
- return true;
-
- bool success = true;
- makeCurrent();
-
- map<string, NXRendererPlugin*>::iterator pluginIter;
- for(pluginIter = renderStyleMap.begin();
- pluginIter != renderStyleMap.end();
- ++pluginIter)
- {
- // skip cleanup of default because it is an alias of another plugin
- string const& renderStyleCode = pluginIter->first;
- if(renderStyleCode == "def")
- continue;
-
- NXRendererPlugin *plugin = pluginIter->second;
- NXCommandResult const *const result = plugin->cleanup();
-
- if(result->getResult() != (int) NX_CMD_SUCCESS) {
- success = false;
- ostringstream logMsgStream;
- logMsgStream << "Plugin for render-style " + pluginIter->first +
- " could not cleanup. ";
- vector<QString> const& msgs = result->getParamVector();
- vector<QString>::const_iterator msgIter;
- for(msgIter = msgs.begin(); msgIter != msgs.end(); ++msgIter) {
- logMsgStream << ' ' << qPrintable(*msgIter);
- }
- NXLOG_SEVERE("NXOpenGLRenderingEngine", logMsgStream.str());
- success = false;
- }
- else {
- NXLOG_INFO("NXOpenGLRenderingEngine",
- "Cleaned up plugin for render-style " +
- pluginIter->first);
- }
- }
-
- pluginsInitialized = false;
- return success;
+ if(!pluginsInitialized)
+ return true;
+
+ bool success = true;
+ makeCurrent();
+
+ map<string, NXRendererPlugin*>::iterator pluginIter;
+ for(pluginIter = renderStyleMap.begin();
+ pluginIter != renderStyleMap.end();
+ ++pluginIter)
+ {
+ // skip cleanup of default because it is an alias of another plugin
+ string const& renderStyleCode = pluginIter->first;
+ if(renderStyleCode == "def")
+ continue;
+
+ NXRendererPlugin *plugin = pluginIter->second;
+ NXCommandResult const *const result = plugin->cleanup();
+
+ if(result->getResult() != (int) NX_CMD_SUCCESS) {
+ success = false;
+ ostringstream logMsgStream;
+ logMsgStream << "Plugin for render-style " + pluginIter->first +
+ " could not cleanup. ";
+ vector<QString> const& msgs = result->getParamVector();
+ vector<QString>::const_iterator msgIter;
+ for(msgIter = msgs.begin(); msgIter != msgs.end(); ++msgIter) {
+ logMsgStream << ' ' << qPrintable(*msgIter);
+ }
+ NXLOG_SEVERE("NXOpenGLRenderingEngine", logMsgStream.str());
+ success = false;
+ }
+ else {
+ NXLOG_INFO("NXOpenGLRenderingEngine",
+ "Cleaned up plugin for render-style " +
+ pluginIter->first);
+ }
+ }
+
+ pluginsInitialized = false;
+ return success;
}
@@ -1393,29 +1393,29 @@ BoundingBox
NXOpenGLRenderingEngine::
GetBoundingBox(NXMoleculeSet *const molSetPtr)
{
-
- BoundingBox bbox;
-
+
+ BoundingBox bbox;
+
// include all atoms
- OBMolIterator molIter;
- for(molIter = molSetPtr->moleculesBegin();
- molIter != molSetPtr->moleculesEnd();
- ++molIter)
- {
- OBMol *const molPtr = *molIter;
- bbox += GetBoundingBox(molPtr);
- }
-
+ OBMolIterator molIter;
+ for(molIter = molSetPtr->moleculesBegin();
+ molIter != molSetPtr->moleculesEnd();
+ ++molIter)
+ {
+ OBMol *const molPtr = *molIter;
+ bbox += GetBoundingBox(molPtr);
+ }
+
// include children molecule-sets
- NXMoleculeSetIterator molSetIter;
- for(molSetIter = molSetPtr->childrenBegin();
- molSetIter != molSetPtr->childrenEnd();
- ++molSetIter)
- {
- NXMoleculeSet *const molSetPtr = *molSetIter;
- bbox += GetBoundingBox(molSetPtr);
- }
- return bbox;
+ NXMoleculeSetIterator molSetIter;
+ for(molSetIter = molSetPtr->childrenBegin();
+ molSetIter != molSetPtr->childrenEnd();
+ ++molSetIter)
+ {
+ NXMoleculeSet *const molSetPtr = *molSetIter;
+ bbox += GetBoundingBox(molSetPtr);
+ }
+ return bbox;
}
//..............................................................................
@@ -1423,21 +1423,21 @@ GetBoundingBox(NXMoleculeSet *const molSetPtr)
BoundingBox
NXOpenGLRenderingEngine::GetBoundingBox(OBMol *const molPtr)
{
- BoundingBox bbox;
- OBAtomIterator atomIter;
- OBAtom *atomPtr = NULL;
-
- for(atomPtr = molPtr->BeginAtom(atomIter);
- atomPtr != NULL;
- atomPtr = molPtr->NextAtom(atomIter))
- {
- Vector atomPos(real(atomPtr->GetX()),
- real(atomPtr->GetY()),
- real(atomPtr->GetZ()));
- bbox += atomPos;
- }
-
- return bbox;
+ BoundingBox bbox;
+ OBAtomIterator atomIter;
+ OBAtom *atomPtr = NULL;
+
+ for(atomPtr = molPtr->BeginAtom(atomIter);
+ atomPtr != NULL;
+ atomPtr = molPtr->NextAtom(atomIter))
+ {
+ Vector atomPos(real(atomPtr->GetX()),
+ real(atomPtr->GetY()),
+ real(atomPtr->GetZ()));
+ bbox += atomPos;
+ }
+
+ return bbox;
}
//..............................................................................
diff --git a/cad/src/cnt/commands/InsertNanotube/InsertNanotube_EditCommand.py b/cad/src/cnt/commands/InsertNanotube/InsertNanotube_EditCommand.py
index 2f57a5554..be93e79d6 100644
--- a/cad/src/cnt/commands/InsertNanotube/InsertNanotube_EditCommand.py
+++ b/cad/src/cnt/commands/InsertNanotube/InsertNanotube_EditCommand.py
@@ -249,7 +249,7 @@ class InsertNanotube_EditCommand(EditCommand):
self._revertNumber()
- self._segmentList = []
+ self._segmentList = []
self.win.win_update()
def _createStructure(self):
diff --git a/cad/src/command_support/DnaOrCnt_PropertyManager.py b/cad/src/command_support/DnaOrCnt_PropertyManager.py
index 0d1549249..2ccc1236e 100644
--- a/cad/src/command_support/DnaOrCnt_PropertyManager.py
+++ b/cad/src/command_support/DnaOrCnt_PropertyManager.py
@@ -75,7 +75,7 @@ class DnaOrCnt_PropertyManager(EditCommand_PM):
def show(self):
"""
Show this PM
- """
+ """
_superclass.show(self)
if isinstance(self.showCursorTextCheckBox, PM_CheckBox):
diff --git a/cad/src/commands/Fuse/FuseChunks_Command.py b/cad/src/commands/Fuse/FuseChunks_Command.py
index 1e1dc394c..fe178b41b 100755
--- a/cad/src/commands/Fuse/FuseChunks_Command.py
+++ b/cad/src/commands/Fuse/FuseChunks_Command.py
@@ -359,7 +359,7 @@ class FuseChunks_Command(Move_Command, fusechunksBase):
original list will be appended to self.overlapping_atoms
(and will be eventually deleted)
- """
+ """
overlapping_atoms_to_delete = []
diff --git a/cad/src/commands/LightingScheme/LightingScheme_PropertyManager.py b/cad/src/commands/LightingScheme/LightingScheme_PropertyManager.py
index a05b7d086..a3e13e71b 100644
--- a/cad/src/commands/LightingScheme/LightingScheme_PropertyManager.py
+++ b/cad/src/commands/LightingScheme/LightingScheme_PropertyManager.py
@@ -563,12 +563,11 @@ class LightingScheme_PropertyManager(Command_PropertyManager):
def change_lighting(self, specularityValueJunk = None):
"""
- Updates win.glpane lighting using the current lighting parameters from
- the light checkboxes and sliders. This is also the slot for the light
- spin boxes.
- @param specularityValueJunk: This value from the spin box is not used
- We are interested in valueChanged signal
- only
+ Updates win.glpane lighting using the current lighting parameters from
+ the light checkboxes and sliders. This is also the slot for the light
+ spin boxes.
+ @param specularityValueJunk: This value from the spin box is not used
+ We are interested in valueChanged signal only
@type specularityValueJunk = int or None
"""
@@ -599,9 +598,9 @@ class LightingScheme_PropertyManager(Command_PropertyManager):
def change_active_light(self, currentIndexJunk = None):
"""
- Slot for the Light number combobox. This changes the current light.
- @param currentIndexJunk: This index value from the combobox is not used
- We are interested in 'activated' signal only
+ Slot for the Light number combobox. This changes the current light.
+ @param currentIndexJunk: This index value from the combobox is not used
+ We are interested in 'activated' signal only
@type currentIndexJunk = int or None
"""
self._updatePage_Lighting()
diff --git a/cad/src/commands/PlaneProperties/PlanePropertyManager.py b/cad/src/commands/PlaneProperties/PlanePropertyManager.py
index c3ca15ccd..54128565e 100755
--- a/cad/src/commands/PlaneProperties/PlanePropertyManager.py
+++ b/cad/src/commands/PlaneProperties/PlanePropertyManager.py
@@ -752,9 +752,9 @@ class PlanePropertyManager(EditCommand_PM):
# checkbox is set.
plane.glpane.gl_update()
- def update_spinboxes(self):
- """
- Update the width and height spinboxes.
+ def update_spinboxes(self):
+ """
+ Update the width and height spinboxes.
@see: Plane.resizeGeometry()
This typically gets called when the plane is resized from the
3D workspace (which marks assy as modified) .So, update the spinboxes
@@ -764,14 +764,14 @@ class PlanePropertyManager(EditCommand_PM):
@see: Plane.resizeGeometry()
@see: self._update_UI_do_updates()
@see: Plane_EditCommand.command_update_internal_state()
- """
- # blockSignals = True make sure that spinbox.valueChanged()
+ """
+ # blockSignals = True make sure that spinbox.valueChanged()
# signal is not emitted after calling spinbox.setValue(). This is done
#because the spinbox valu changes as a result of resizing the plane
#from the 3D workspace.
- if self.command.hasValidStructure():
+ if self.command.hasValidStructure():
self.heightDblSpinBox.setValue(self.command.struct.height,
- blockSignals = True)
+ blockSignals = True)
self.widthDblSpinBox.setValue(self.command.struct.width,
blockSignals = True)
diff --git a/cad/src/dna/commands/DnaStrand/DnaStrand_EditCommand.py b/cad/src/dna/commands/DnaStrand/DnaStrand_EditCommand.py
index ac32aeb09..2a9037b2b 100644
--- a/cad/src/dna/commands/DnaStrand/DnaStrand_EditCommand.py
+++ b/cad/src/dna/commands/DnaStrand/DnaStrand_EditCommand.py
@@ -1003,7 +1003,7 @@ class DnaStrand_EditCommand(State_preMixin, EditCommand):
item = (("Currently editing %r"%self.struct.name),
noop, 'disabled')
self.Menu_spec.append(item)
- return
+ return
#following should be self.struct.getDnaGroup or self.struct.getDnaGroup
#need to formalize method name and then make change.
dnaGroup = self.struct.parent_node_of_class(self.assy.DnaGroup)
diff --git a/cad/src/dna/commands/InsertDna/InsertDna_EditCommand.py b/cad/src/dna/commands/InsertDna/InsertDna_EditCommand.py
index 6952c6587..f8fbf316d 100644
--- a/cad/src/dna/commands/InsertDna/InsertDna_EditCommand.py
+++ b/cad/src/dna/commands/InsertDna/InsertDna_EditCommand.py
@@ -419,7 +419,7 @@ class InsertDna_EditCommand(EditCommand):
self._fallbackDnaGroup = None
- self._segmentList = []
+ self._segmentList = []
self.win.win_update()
def _createStructure(self):
diff --git a/cad/src/dna/generators/Dna_Generator.py b/cad/src/dna/generators/Dna_Generator.py
index 54bf3dd7f..020601ab5 100644
--- a/cad/src/dna/generators/Dna_Generator.py
+++ b/cad/src/dna/generators/Dna_Generator.py
@@ -800,20 +800,20 @@ class Dna_Generator:
if not atomsScheduledForDeletionDict.has_key(id(a)):
atomsScheduledForDeletionDict[id(a)] = a
- #Add the axis atom to the atoms scheduled for deletion only when
- #both the strand neighbors of this axis atom are scheduled for
- #deletion. But this is not true if its a sticky end i.e. the
- #axis atom has only one strand atom. To fix that problem
- #we also check (second condition) if all the strand neighbors
- #of an axis atom are scheduled for deletion... if so, ot also
- #adds that axis atom to the atom scheduled for deletion)
- #Axis atoms are explicitely deleted to fix part of memory
- #leak bug 2880 (and thus no longer depends on dna updater
- #to delete bare axis atoms .. which is good because there is a
- #debug pref that permits bare axis atoms for some other
- #uses -- Ninad 2008-05-15
+ #Add the axis atom to the atoms scheduled for deletion only when
+ #both the strand neighbors of this axis atom are scheduled for
+ #deletion. But this is not true if its a sticky end i.e. the
+ #axis atom has only one strand atom. To fix that problem
+ #we also check (second condition) if all the strand neighbors
+ #of an axis atom are scheduled for deletion... if so, ot also
+ #adds that axis atom to the atom scheduled for deletion)
+ #Axis atoms are explicitely deleted to fix part of memory
+ #leak bug 2880 (and thus no longer depends on dna updater
+ #to delete bare axis atoms .. which is good because there is a
+ #debug pref that permits bare axis atoms for some other
+ #uses -- Ninad 2008-05-15
if len(strand_neighbors_to_delete) == 2 or \
- len(atm.strand_neighbors()) == len(strand_neighbors_to_delete):
+ len(atm.strand_neighbors()) == len(strand_neighbors_to_delete):
if not atomsScheduledForDeletionDict.has_key(id(atm)):
atomsScheduledForDeletionDict[id(atm)] = atm
else:
diff --git a/cad/src/experimental/NH1_Integration/HDF5_SimResults/lib/NE1_Simulation/SimResultsDataStore.py b/cad/src/experimental/NH1_Integration/HDF5_SimResults/lib/NE1_Simulation/SimResultsDataStore.py
index 10d0e9d28..f5c29b5ce 100755
--- a/cad/src/experimental/NH1_Integration/HDF5_SimResults/lib/NE1_Simulation/SimResultsDataStore.py
+++ b/cad/src/experimental/NH1_Integration/HDF5_SimResults/lib/NE1_Simulation/SimResultsDataStore.py
@@ -8,445 +8,445 @@ class is really just a container for bond information.
class SimResultsBond:
- """
- A chemical bond. See L{SimResultsDataStore} for context.
- """
+ """
+ A chemical bond. See L{SimResultsDataStore} for context.
+ """
- def __init__(self, atomId_1, atomId_2, order):
- """
- Constructs a SimResultsBond with the given atom identifiers and order.
- """
- self.atomId_1 = atomId_1
- self.atomId_2 = atomId_2
- self.order = order
+ def __init__(self, atomId_1, atomId_2, order):
+ """
+ Constructs a SimResultsBond with the given atom identifiers and order.
+ """
+ self.atomId_1 = atomId_1
+ self.atomId_2 = atomId_2
+ self.order = order
class SimResultsDataStore:
- """
- Encapsulates a simulation results data store.
-
- B{Atom Records Alignment -}
- The arrays of atom identifiers, positions, and velocities within a given
- frame are aligned. So the contents at index X of all three arrays correspond
- to the same atom.
-
- B{Extension Data -}
- Extension data can be stored in each frame. Such data could be used to plot
- graphs, for example. Extension data exists as named floating point numbers,
- integers, floating point number arrays, and integer arrays inside a named
- data-set.
- """
-
-
- def openDataStore(self, directory):
- """
- Opens the simulation results data store, found in the given directory,
- for read/write access.
- @return: (0=successful or non-zero error code), (error description)
- """
- print 'directory=%s' % directory
- return 0
-
-
- def getNotes(self):
- """Returns the user's notes for these simulation results."""
- pass
- def setNotes(self, notes):
- """Sets the user's notes for these simulation results."""
- pass
-
-
- def getName(self):
- """Returns the simulation name."""
- pass
- def setName(self, name):
- """Sets the simulation name."""
- pass
-
-
- def getDescription(self):
- """Returns the simulation description."""
- pass
- def setDescription(self, description):
- """Sets the simulation description."""
- pass
-
-
- def getTimestep(self):
- """Returns the simulation timestep in seconds."""
- pass
- def setTimestep(self, timestep):
- """
- Sets the simulation timestep.
- @param timestep: duration in seconds
- """
- pass
-
-
- def getStartStep(self):
- """Returns the simulation starting step number."""
- pass
- def setStartStep(self, startStep):
- """Sets the simulation starting step number."""
- pass
-
-
- def getMaxSteps(self):
- """Returns the maximum number of steps to simulate."""
- pass
- def setMaxSteps(self, maxSteps):
- """Sets the maximum number of steps to simulate."""
- pass
-
-
- def getStepsPerFrame(self):
- """Returns the number of steps per frame."""
- pass
- def setStepsPerFrame(self, stepsPerFrame):
- """Sets the number of steps per frame."""
- pass
-
-
- def getEnvironmentTemperature(self):
- """Returns the simulation environment temperature in Kelvin."""
- pass
- def setEnvironmentTemperature(self, temperature):
- """
- Sets the simulation environment temperature.
- @param temperature: in Kelvin
- """
- pass
-
-
- def getEnvironmentPressure(self):
- """Returns the simulation environment pressure in Pascals."""
- pass
- def setEnvironmentPressure(self, pressure):
- """
- Sets the simulation environment pressure.
- @param pressure: in Pascals
- """
- pass
-
-
- def getFilePathKeys(self):
- """
- Returns an array of file path keys. These file paths are for simulation
- specification files, simulation workflow scripts, template files, etc.
- """
- pass
- def getFilePath(self, key):
- """Returns the file path associated with the given key."""
- pass
- def setFilePath(self, key, filePath):
- """Associates the given file path with the given key."""
- pass
-
-
- def getRunResult(self):
- """
- Returns the simulation run's result and failure message if the
- simulation failed.
- @return: (0=success, 1=still running, 2=failure, 3=aborted),
- (failure message)
- """
- pass
- def setRunResult(self, code, message):
- """
- Sets the simulation run's result and failure message.
- @param code: 0=success, 1=still running, 2=failure, 3=aborted
- @param message: description of a simulation failure
- """
- pass
-
-
- def getStepCount(self):
- """Returns the number of steps successfully simulated."""
- pass
- def setStepCount(self, count):
- """Sets the number of steps successfully simulated."""
- pass
-
-
- def getStartTime(self):
- """
- Returns the simulation start time.
- @return: a U{datetime<http://docs.python.org/lib/datetime-datetime.html>}
- object set to the simulation's start time
- """
- pass
- def setStartTime(self, startTime):
- """
- Sets the simulation start time.
- @param startTime: a U{datetime<http://docs.python.org/lib/datetime-datetime.html>}
- object set to the simulation's start time
- """
- pass
-
-
- def getCPU_RunningTime(self):
- """Returns the simulation CPU running time in seconds."""
- pass
- def setCPU_RunningTime(self, cpuRunningTime):
- """
- Set the simulation CPU running time.
- @param cpuRunningTime: in seconds
- """
- pass
-
-
- def getWallRunningTime(self):
- """Returns the simulation wall running time in seconds."""
- pass
- def setWallRunningTime(self, wallRunningTime):
- """
- Sets the simulation wall running time.
- @param wallRunningTime: in seconds
- """
- pass
-
-
- def getExtDataNames(self):
- """Returns an array of extension data-set names."""
- pass
- def getExtDataKeys(self, extDataSetName):
- """
- Returns an array of extension data-set keys for a given extension
- data-set.
- """
- pass
- def getExtDataFloat(self, extDataSetName, key):
- """
- Returns a floating point value stored in the extension data-set with the
- given key.
- """
- pass
- def getExtDataInt(self, extDataSetName, key):
- """
- Returns an integer value stored in the extension data-set with the
- given key.
- """
- pass
- def getExtDataFloatArray(self, extDataSetName, key):
- """
- Returns an array of floating point values stored in the extension
- data-set with the given key.
- """
- pass
- def getExtDataIntArray(self, extDataSetName, key):
- """
- Returns an array of integers stored in the extension data-set with the
- given key.
- """
- pass
- def setExtDataFloat(self, extDataSetName, key, value):
- """
- Sets a floating point value stored in the extension data-set with the
- given key.
- """
- pass
- def setExtDataInt(self, extDataSetName, key, value):
- """
- Sets an integer value stored in the extension data-set with the
- given key.
- """
- pass
- def setExtDataFloatArray(self, extDataSetName, key, floatArray):
- """
- Sets an array of floating point values stored in the extension data-set
- with the given key.
- """
- pass
- def setExtDataIntArray(self, extDataSetName, key, intArray):
- """
- Sets an array of integers stored in the extension data-set
- with the given key.
- """
- pass
-
-
- def getFrameSetNames(self):
- """
- Returns an array of frame-set names. These frame-set names are used to
- get/set frame data.
- """
- pass
- def addFrameSet(self, name, aggregationMode):
- """
- Adds a frame-set with the given name and aggregation mode.
- @param aggregationMode: 0=per-time-step values are averaged (default),
- 1=last per-time-step value is used
- """
- pass
- def removeFrameSet(self, name):
- """Removes the frame-set with the given name."""
- pass
-
-
- def getFrameCount(self, frameSetName):
- """Returns the number of frames in a frame-set."""
- pass
- def getFrameTimes(self, frameSetName):
- """Returns an array of frame times (in seconds) for a frame-set."""
- pass
- def getFrameTime(self, frameSetName, frameIndex):
- """Returns a specific frame time (in seconds) for a frame-set."""
- pass
- def addFrame(self, frameSetName, time):
- """
- Adds a frame to the specified frame-set.
- @param time: the frame's time in seconds
- """
- pass
- def removeFrame(self, frameSetName, frameIndex):
- """Removes a frame from the specified frame-set."""
- pass
-
-
- def getFrameAtomIds(self, frameSetName):
- """Returns an array of atom identifiers for a frame-set."""
- pass
- def setFrameAtomIds(self, frameSetName, atomIds):
- """Sets the array of atom identifiers for a frame-set."""
- pass
-
-
- def getFrameAtomPositions(self, frameSetName, frameIndex):
- """
- Returns an array of Cartesian atom positions for a specified frame. Each
- position is an array of length 3 corresponding to x, y, z coordinates in
- meters.
- """
- pass
- def setFrameAtomPositions(self, frameSetName, frameIndex, positions):
- """
- Sets the array of Cartesian atom positions for a specified frame.
- @param positions: an array of arrays of length 3 corresponding to
- x, y, z coordinates for each atom in meters
- """
- pass
-
-
- def getFrameAtomVelocities(self, frameSetName, frameIndex):
- """
- Returns an array of atom velocities for a specified frame. Each velocity
- is an array of length 3 corresponding to the x, y, z components of the
- atom's velocity in m/s.
- """
- pass
- def setFrameAtomVelocities(self, frameSetName, frameIndex, velocities):
- """
- Sets the array of atom velocities for a specified frame.
- @param velocities: an array of arrays of length 3 corresponding to the
- x, y, z components for each atom's velocity in m/s
- """
- pass
-
-
- def getFrameBonds(self, frameSetName, frameIndex):
- """Returns an array of SimResultsBond objects for a specified frame."""
- pass
- def setFrameBonds(self, frameSetName, frameIndex, bonds):
- """Sets the array of SimResultsBond objects for a specified frame."""
- pass
-
-
- def getFrameTotalEnergy(self, frameSetName, frameIndex):
- """Returns the total energy for the specified frame in Joules."""
- pass
- def setFrameTotalEnergy(self, frameSetName, frameIndex, totalEnergy):
- """
- Sets the total energy for the specified frame.
- @param totalEnergy: in Joules
- """
- pass
-
-
- def getFrameIdealTemperature(self, frameSetName, frameIndex):
- """Returns the ideal temperature for the specified frame in Kelvin."""
- pass
- def setFrameIdealTemperature(self, frameSetName, frameIndex, temperature):
- """
- Sets the ideal temperature for the specified frame.
- @param temperature: in Kelvin
- """
- pass
-
-
- def getFramePressure(self, frameSetName, frameIndex):
- """Returns the pressure for the specified frame in Pascals."""
- pass
- def setFramePressure(self, frameSetName, frameIndex, pressure):
- """
- Sets the pressure for the specified frame.
- @param pressure: in Pascals
- """
- pass
-
-
- def getFrameExtDataNames(self, frameSetName):
- """Returns an array of extension data-set names for a given frame-set."""
- pass
- def getFrameExtDataKeys(self, frameSetName, extDataSetName):
- """
- Returns an array of extension data-set keys for a given extension
- data-set.
- """
- pass
- def getFrameExtDataFloat(self, frameSetName, frameIndex, extDataSetName,
- key):
- """
- Returns a floating point value stored in the specified frame for the
- given key.
- """
- pass
- def getFrameExtDataInt(self, frameSetName, frameIndex, extDataSetName, key):
- """
- Returns an integer value stored in the specified frame for the given
- key.
- """
- pass
- def getFrameExtDataFloatArray(self, frameSetName, frameIndex,
- extDataSetName, key):
- """
- Returns an array of floating point values stored in the specified frame
- for the given key.
- """
- pass
- def getFrameExtDataIntArray(self, frameSetName, frameIndex, extDataSetName,
- key):
- """
- Returns an array of integers stored in the specified frame for the given
- key.
- """
- pass
- def setFrameExtDataFloat(self, frameSetName, frameIndex, extDataSetName,
- key, value):
- """
- Sets a floating point value stored in the specified frame for the given
- key.
- """
- pass
- def setFrameExtDataInt(self, frameSetName, frameIndex, extDataSetName, key,
- value):
- """
- Sets an integer value stored in the specified frame for the given
- key.
- """
- pass
- def setFrameExtDataFloatArray(self, frameSetName, frameIndex,
- extDataSetName, key, floatArray):
- """
- Sets an array of floating point values stored in the specified
- frame for the given key.
- """
- pass
- def setFrameExtDataIntArray(self, frameSetName, frameIndex, extDataSetName,
- key, intArray):
- """
- Sets an array of integers stored in the specified frame for the given
- key.
- """
- pass
+ """
+ Encapsulates a simulation results data store.
+
+ B{Atom Records Alignment -}
+ The arrays of atom identifiers, positions, and velocities within a given
+ frame are aligned. So the contents at index X of all three arrays correspond
+ to the same atom.
+
+ B{Extension Data -}
+ Extension data can be stored in each frame. Such data could be used to plot
+ graphs, for example. Extension data exists as named floating point numbers,
+ integers, floating point number arrays, and integer arrays inside a named
+ data-set.
+ """
+
+
+ def openDataStore(self, directory):
+ """
+ Opens the simulation results data store, found in the given directory,
+ for read/write access.
+ @return: (0=successful or non-zero error code), (error description)
+ """
+ print 'directory=%s' % directory
+ return 0
+
+
+ def getNotes(self):
+ """Returns the user's notes for these simulation results."""
+ pass
+ def setNotes(self, notes):
+ """Sets the user's notes for these simulation results."""
+ pass
+
+
+ def getName(self):
+ """Returns the simulation name."""
+ pass
+ def setName(self, name):
+ """Sets the simulation name."""
+ pass
+
+
+ def getDescription(self):
+ """Returns the simulation description."""
+ pass
+ def setDescription(self, description):
+ """Sets the simulation description."""
+ pass
+
+
+ def getTimestep(self):
+ """Returns the simulation timestep in seconds."""
+ pass
+ def setTimestep(self, timestep):
+ """
+ Sets the simulation timestep.
+ @param timestep: duration in seconds
+ """
+ pass
+
+
+ def getStartStep(self):
+ """Returns the simulation starting step number."""
+ pass
+ def setStartStep(self, startStep):
+ """Sets the simulation starting step number."""
+ pass
+
+
+ def getMaxSteps(self):
+ """Returns the maximum number of steps to simulate."""
+ pass
+ def setMaxSteps(self, maxSteps):
+ """Sets the maximum number of steps to simulate."""
+ pass
+
+
+ def getStepsPerFrame(self):
+ """Returns the number of steps per frame."""
+ pass
+ def setStepsPerFrame(self, stepsPerFrame):
+ """Sets the number of steps per frame."""
+ pass
+
+
+ def getEnvironmentTemperature(self):
+ """Returns the simulation environment temperature in Kelvin."""
+ pass
+ def setEnvironmentTemperature(self, temperature):
+ """
+ Sets the simulation environment temperature.
+ @param temperature: in Kelvin
+ """
+ pass
+
+
+ def getEnvironmentPressure(self):
+ """Returns the simulation environment pressure in Pascals."""
+ pass
+ def setEnvironmentPressure(self, pressure):
+ """
+ Sets the simulation environment pressure.
+ @param pressure: in Pascals
+ """
+ pass
+
+
+ def getFilePathKeys(self):
+ """
+ Returns an array of file path keys. These file paths are for simulation
+ specification files, simulation workflow scripts, template files, etc.
+ """
+ pass
+ def getFilePath(self, key):
+ """Returns the file path associated with the given key."""
+ pass
+ def setFilePath(self, key, filePath):
+ """Associates the given file path with the given key."""
+ pass
+
+
+ def getRunResult(self):
+ """
+ Returns the simulation run's result and failure message if the
+ simulation failed.
+ @return: (0=success, 1=still running, 2=failure, 3=aborted),
+ (failure message)
+ """
+ pass
+ def setRunResult(self, code, message):
+ """
+ Sets the simulation run's result and failure message.
+ @param code: 0=success, 1=still running, 2=failure, 3=aborted
+ @param message: description of a simulation failure
+ """
+ pass
+
+
+ def getStepCount(self):
+ """Returns the number of steps successfully simulated."""
+ pass
+ def setStepCount(self, count):
+ """Sets the number of steps successfully simulated."""
+ pass
+
+
+ def getStartTime(self):
+ """
+ Returns the simulation start time.
+ @return: a U{datetime<http://docs.python.org/lib/datetime-datetime.html>}
+ object set to the simulation's start time
+ """
+ pass
+ def setStartTime(self, startTime):
+ """
+ Sets the simulation start time.
+ @param startTime: a U{datetime<http://docs.python.org/lib/datetime-datetime.html>}
+ object set to the simulation's start time
+ """
+ pass
+
+
+ def getCPU_RunningTime(self):
+ """Returns the simulation CPU running time in seconds."""
+ pass
+ def setCPU_RunningTime(self, cpuRunningTime):
+ """
+ Set the simulation CPU running time.
+ @param cpuRunningTime: in seconds
+ """
+ pass
+
+
+ def getWallRunningTime(self):
+ """Returns the simulation wall running time in seconds."""
+ pass
+ def setWallRunningTime(self, wallRunningTime):
+ """
+ Sets the simulation wall running time.
+ @param wallRunningTime: in seconds
+ """
+ pass
+
+
+ def getExtDataNames(self):
+ """Returns an array of extension data-set names."""
+ pass
+ def getExtDataKeys(self, extDataSetName):
+ """
+ Returns an array of extension data-set keys for a given extension
+ data-set.
+ """
+ pass
+ def getExtDataFloat(self, extDataSetName, key):
+ """
+ Returns a floating point value stored in the extension data-set with the
+ given key.
+ """
+ pass
+ def getExtDataInt(self, extDataSetName, key):
+ """
+ Returns an integer value stored in the extension data-set with the
+ given key.
+ """
+ pass
+ def getExtDataFloatArray(self, extDataSetName, key):
+ """
+ Returns an array of floating point values stored in the extension
+ data-set with the given key.
+ """
+ pass
+ def getExtDataIntArray(self, extDataSetName, key):
+ """
+ Returns an array of integers stored in the extension data-set with the
+ given key.
+ """
+ pass
+ def setExtDataFloat(self, extDataSetName, key, value):
+ """
+ Sets a floating point value stored in the extension data-set with the
+ given key.
+ """
+ pass
+ def setExtDataInt(self, extDataSetName, key, value):
+ """
+ Sets an integer value stored in the extension data-set with the
+ given key.
+ """
+ pass
+ def setExtDataFloatArray(self, extDataSetName, key, floatArray):
+ """
+ Sets an array of floating point values stored in the extension data-set
+ with the given key.
+ """
+ pass
+ def setExtDataIntArray(self, extDataSetName, key, intArray):
+ """
+ Sets an array of integers stored in the extension data-set
+ with the given key.
+ """
+ pass
+
+
+ def getFrameSetNames(self):
+ """
+ Returns an array of frame-set names. These frame-set names are used to
+ get/set frame data.
+ """
+ pass
+ def addFrameSet(self, name, aggregationMode):
+ """
+ Adds a frame-set with the given name and aggregation mode.
+ @param aggregationMode: 0=per-time-step values are averaged (default),
+ 1=last per-time-step value is used
+ """
+ pass
+ def removeFrameSet(self, name):
+ """Removes the frame-set with the given name."""
+ pass
+
+
+ def getFrameCount(self, frameSetName):
+ """Returns the number of frames in a frame-set."""
+ pass
+ def getFrameTimes(self, frameSetName):
+ """Returns an array of frame times (in seconds) for a frame-set."""
+ pass
+ def getFrameTime(self, frameSetName, frameIndex):
+ """Returns a specific frame time (in seconds) for a frame-set."""
+ pass
+ def addFrame(self, frameSetName, time):
+ """
+ Adds a frame to the specified frame-set.
+ @param time: the frame's time in seconds
+ """
+ pass
+ def removeFrame(self, frameSetName, frameIndex):
+ """Removes a frame from the specified frame-set."""
+ pass
+
+
+ def getFrameAtomIds(self, frameSetName):
+ """Returns an array of atom identifiers for a frame-set."""
+ pass
+ def setFrameAtomIds(self, frameSetName, atomIds):
+ """Sets the array of atom identifiers for a frame-set."""
+ pass
+
+
+ def getFrameAtomPositions(self, frameSetName, frameIndex):
+ """
+ Returns an array of Cartesian atom positions for a specified frame. Each
+ position is an array of length 3 corresponding to x, y, z coordinates in
+ meters.
+ """
+ pass
+ def setFrameAtomPositions(self, frameSetName, frameIndex, positions):
+ """
+ Sets the array of Cartesian atom positions for a specified frame.
+ @param positions: an array of arrays of length 3 corresponding to
+ x, y, z coordinates for each atom in meters
+ """
+ pass
+
+
+ def getFrameAtomVelocities(self, frameSetName, frameIndex):
+ """
+ Returns an array of atom velocities for a specified frame. Each velocity
+ is an array of length 3 corresponding to the x, y, z components of the
+ atom's velocity in m/s.
+ """
+ pass
+ def setFrameAtomVelocities(self, frameSetName, frameIndex, velocities):
+ """
+ Sets the array of atom velocities for a specified frame.
+ @param velocities: an array of arrays of length 3 corresponding to the
+ x, y, z components for each atom's velocity in m/s
+ """
+ pass
+
+
+ def getFrameBonds(self, frameSetName, frameIndex):
+ """Returns an array of SimResultsBond objects for a specified frame."""
+ pass
+ def setFrameBonds(self, frameSetName, frameIndex, bonds):
+ """Sets the array of SimResultsBond objects for a specified frame."""
+ pass
+
+
+ def getFrameTotalEnergy(self, frameSetName, frameIndex):
+ """Returns the total energy for the specified frame in Joules."""
+ pass
+ def setFrameTotalEnergy(self, frameSetName, frameIndex, totalEnergy):
+ """
+ Sets the total energy for the specified frame.
+ @param totalEnergy: in Joules
+ """
+ pass
+
+
+ def getFrameIdealTemperature(self, frameSetName, frameIndex):
+ """Returns the ideal temperature for the specified frame in Kelvin."""
+ pass
+ def setFrameIdealTemperature(self, frameSetName, frameIndex, temperature):
+ """
+ Sets the ideal temperature for the specified frame.
+ @param temperature: in Kelvin
+ """
+ pass
+
+
+ def getFramePressure(self, frameSetName, frameIndex):
+ """Returns the pressure for the specified frame in Pascals."""
+ pass
+ def setFramePressure(self, frameSetName, frameIndex, pressure):
+ """
+ Sets the pressure for the specified frame.
+ @param pressure: in Pascals
+ """
+ pass
+
+
+ def getFrameExtDataNames(self, frameSetName):
+ """Returns an array of extension data-set names for a given frame-set."""
+ pass
+ def getFrameExtDataKeys(self, frameSetName, extDataSetName):
+ """
+ Returns an array of extension data-set keys for a given extension
+ data-set.
+ """
+ pass
+ def getFrameExtDataFloat(self, frameSetName, frameIndex, extDataSetName,
+ key):
+ """
+ Returns a floating point value stored in the specified frame for the
+ given key.
+ """
+ pass
+ def getFrameExtDataInt(self, frameSetName, frameIndex, extDataSetName, key):
+ """
+ Returns an integer value stored in the specified frame for the given
+ key.
+ """
+ pass
+ def getFrameExtDataFloatArray(self, frameSetName, frameIndex,
+ extDataSetName, key):
+ """
+ Returns an array of floating point values stored in the specified frame
+ for the given key.
+ """
+ pass
+ def getFrameExtDataIntArray(self, frameSetName, frameIndex, extDataSetName,
+ key):
+ """
+ Returns an array of integers stored in the specified frame for the given
+ key.
+ """
+ pass
+ def setFrameExtDataFloat(self, frameSetName, frameIndex, extDataSetName,
+ key, value):
+ """
+ Sets a floating point value stored in the specified frame for the given
+ key.
+ """
+ pass
+ def setFrameExtDataInt(self, frameSetName, frameIndex, extDataSetName, key,
+ value):
+ """
+ Sets an integer value stored in the specified frame for the given
+ key.
+ """
+ pass
+ def setFrameExtDataFloatArray(self, frameSetName, frameIndex,
+ extDataSetName, key, floatArray):
+ """
+ Sets an array of floating point values stored in the specified
+ frame for the given key.
+ """
+ pass
+ def setFrameExtDataIntArray(self, frameSetName, frameIndex, extDataSetName,
+ key, intArray):
+ """
+ Sets an array of integers stored in the specified frame for the given
+ key.
+ """
+ pass
diff --git a/cad/src/experimental/NH1_Integration/lib/NE1_CorePlugins/EnergyMinimizer.py b/cad/src/experimental/NH1_Integration/lib/NE1_CorePlugins/EnergyMinimizer.py
index 98ca80932..4bddcf495 100755
--- a/cad/src/experimental/NH1_Integration/lib/NE1_CorePlugins/EnergyMinimizer.py
+++ b/cad/src/experimental/NH1_Integration/lib/NE1_CorePlugins/EnergyMinimizer.py
@@ -9,23 +9,23 @@ from NE1_Simulation.Parameter import Parameter
class EnergyMinimizer:
- """
- Adjusts the positions of the given atoms so as to minimize the structure's
- total energy.
- """
-
-
- def minimize(self, structure, parameters):
- """
- Minimizes the given structure with the given parameters. When NE1 starts
- up, it reads some description of the EnergyMinimizer plugin to load
- which includes a list of Parameters to use for the minimizer
- configuration dialog.
-
- @param structure: whatever NE1 structure object
- @param parameters: an array of L{NE1_Simulation.Parameter.Parameter}
- objects
- @return: the minimized structure object
- """
- pass
+ """
+ Adjusts the positions of the given atoms so as to minimize the structure's
+ total energy.
+ """
+
+
+ def minimize(self, structure, parameters):
+ """
+ Minimizes the given structure with the given parameters. When NE1 starts
+ up, it reads some description of the EnergyMinimizer plugin to load
+ which includes a list of Parameters to use for the minimizer
+ configuration dialog.
+
+ @param structure: whatever NE1 structure object
+ @param parameters: an array of L{NE1_Simulation.Parameter.Parameter}
+ objects
+ @return: the minimized structure object
+ """
+ pass
diff --git a/cad/src/experimental/NH1_Integration/lib/NE1_JobManagement/NE1_Job.py b/cad/src/experimental/NH1_Integration/lib/NE1_JobManagement/NE1_Job.py
index 42ec84a29..a6c27f0ba 100755
--- a/cad/src/experimental/NH1_Integration/lib/NE1_JobManagement/NE1_Job.py
+++ b/cad/src/experimental/NH1_Integration/lib/NE1_JobManagement/NE1_Job.py
@@ -6,116 +6,116 @@ A job that the NE1 Job Manager schedules and monitors.
class NE1_Job:
- """
- A job that the NE1 Job Manager schedules and monitors. Subclasses know how
- to run themselves and can be polled.
-
- This is an abstract/interface class and should not be instantiated.
-
- The subclasses know how to run themselves and can be polled, etc.
- The NH1_Job, when run, would communicate with the NH1 instance to launch
- itself. The NE1 Job Manager could poll the NH1_Job for status. The NH1_Job
- could provide call-backs to indicate simulation completion, failures, etc.
-
- """
-
-
- def getPriority(self):
- """
- Returns the priority of this job.
- @return: (0=low, 1=normal, 2=high)
- """
- pass
-
-
- def setPriority(self, priority):
- """
- Sets the priority for this job.
- @param priority: 0=low, 1=normal, 2=high
- """
- pass
-
-
- def run(self):
- """
- Starts this job.
- """
- pass
-
-
- def pause(self, location):
- """
- Pauses this job in-, or out-of-, memory.
- @param location: 0=in-memory, 1=out-of-memory
- """
- pass
-
-
- def resume(self):
- """
- Resumes this job from the paused state.
- """
- pass
-
-
- def abort(self):
- """
- Abort this job.
- """
- pass
-
-
- def getStatus(self):
- """
- Returns the status of this job.
- @return: (0=idle, 1=running, 2=paused, 3=aborted, 4=failure),
- (% complete), (text message)
- """
- pass
-
-
- def getAlertEmailAddress(self):
- """
- Returns the email address to notify when this job completes or fails.
- """
- pass
- def setAlertEmailAddress(self, emailAddress):
- """
- Sets the email address to notify when this job completes or fails.
- """
- pass
-
-
- def getPopUpNE1_Alert(self):
- """
- Returns 1 if NE1 should pop up an alert when this job completes or
- fails, and 0 otherwise.
- """
- pass
- def setPopUpNE1_Alert(self, popUp):
- """
- Sets whether NE1 should pop up an alert when this job completes or
- fails.
- @param popUp: (1=do pop up an alert, 0=don't pop up an alert)
- """
- pass
-
-
- def getSchedule(self):
- """
- Returns the time this job is scheduled to run.
- @return: (0=later, 1=now),
- (the later
- U{datetime<http://docs.python.org/lib/datetime-datetime.html>}
- object)
- """
- pass
- def setSchedule(self, nowOrLater, laterDatetime):
- """
- Sets the time to run the job.
- @param nowOrLater: 0=later, 1=now
- @param laterDatetime: the later
- U{datetime<http://docs.python.org/lib/datetime-datetime.html>}
- object
- """
- pass
+ """
+ A job that the NE1 Job Manager schedules and monitors. Subclasses know how
+ to run themselves and can be polled.
+
+ This is an abstract/interface class and should not be instantiated.
+
+ The subclasses know how to run themselves and can be polled, etc.
+ The NH1_Job, when run, would communicate with the NH1 instance to launch
+ itself. The NE1 Job Manager could poll the NH1_Job for status. The NH1_Job
+ could provide call-backs to indicate simulation completion, failures, etc.
+
+ """
+
+
+ def getPriority(self):
+ """
+ Returns the priority of this job.
+ @return: (0=low, 1=normal, 2=high)
+ """
+ pass
+
+
+ def setPriority(self, priority):
+ """
+ Sets the priority for this job.
+ @param priority: 0=low, 1=normal, 2=high
+ """
+ pass
+
+
+ def run(self):
+ """
+ Starts this job.
+ """
+ pass
+
+
+ def pause(self, location):
+ """
+ Pauses this job in-, or out-of-, memory.
+ @param location: 0=in-memory, 1=out-of-memory
+ """
+ pass
+
+
+ def resume(self):
+ """
+ Resumes this job from the paused state.
+ """
+ pass
+
+
+ def abort(self):
+ """
+ Abort this job.
+ """
+ pass
+
+
+ def getStatus(self):
+ """
+ Returns the status of this job.
+ @return: (0=idle, 1=running, 2=paused, 3=aborted, 4=failure),
+ (% complete), (text message)
+ """
+ pass
+
+
+ def getAlertEmailAddress(self):
+ """
+ Returns the email address to notify when this job completes or fails.
+ """
+ pass
+ def setAlertEmailAddress(self, emailAddress):
+ """
+ Sets the email address to notify when this job completes or fails.
+ """
+ pass
+
+
+ def getPopUpNE1_Alert(self):
+ """
+ Returns 1 if NE1 should pop up an alert when this job completes or
+ fails, and 0 otherwise.
+ """
+ pass
+ def setPopUpNE1_Alert(self, popUp):
+ """
+ Sets whether NE1 should pop up an alert when this job completes or
+ fails.
+ @param popUp: (1=do pop up an alert, 0=don't pop up an alert)
+ """
+ pass
+
+
+ def getSchedule(self):
+ """
+ Returns the time this job is scheduled to run.
+ @return: (0=later, 1=now),
+ (the later
+ U{datetime<http://docs.python.org/lib/datetime-datetime.html>}
+ object)
+ """
+ pass
+ def setSchedule(self, nowOrLater, laterDatetime):
+ """
+ Sets the time to run the job.
+ @param nowOrLater: 0=later, 1=now
+ @param laterDatetime: the later
+ U{datetime<http://docs.python.org/lib/datetime-datetime.html>}
+ object
+ """
+ pass
diff --git a/cad/src/experimental/NH1_Integration/lib/NE1_Lib/NE1_Lib.py b/cad/src/experimental/NH1_Integration/lib/NE1_Lib/NE1_Lib.py
index c22889843..3fb00dbbb 100755
--- a/cad/src/experimental/NH1_Integration/lib/NE1_Lib/NE1_Lib.py
+++ b/cad/src/experimental/NH1_Integration/lib/NE1_Lib/NE1_Lib.py
@@ -6,72 +6,72 @@ NE1 core-library-related API.
class NE1_Lib:
- """
- Core NE1 methods (to support the NH1 wizard.) This API is just to give an
- idea - still needs to be thought through.
-
- The premise of the getXxxUI() methods is that NE1 shall provide a set of
- common UI for things for consistency, ie, so that the user only needs to
- learn one widget for model tree node selection, and the same widget for
- node selection is used everywhere.
- """
-
-
- def getConstraintsSelectorUI(self):
- """
- Returns the UI for selecting constraints.
- """
- pass
-
-
- def getMeasurementsSelectorUI(self):
- """
- Returns the UI for selecting measurements.
- """
- pass
-
-
- def getAtomSetSelectorUI(self):
- """
- Returns the UI for selecting atom set nodes from the model tree.
- """
- pass
-
-
- def detectUnMinized(self):
- """
- Detects and reports whether there are un-minimized structures in any of
- the simulation input files.
- """
- pass
-
-
- def checkJigSanity(self):
- """
- Checks whether there are any unreasonable jig parameters in the
- simulation.
- """
- pass
-
-
- def detectUnusedJigs(self):
- """
- Detects and reports whether there are any unused jigs in the input MMP
- files.
- """
- pass
-
-
- def detectReactionPoints(self):
- """
- Detects and reports reaction points found in the structures in the
- input files.
- """
- pass
-
-
- def checkSpinMultiplicity(self):
- """
- Reports on spin mulitiplicity.
- """
- pass
+ """
+ Core NE1 methods (to support the NH1 wizard.) This API is just to give an
+ idea - still needs to be thought through.
+
+ The premise of the getXxxUI() methods is that NE1 shall provide a set of
+ common UI for things for consistency, ie, so that the user only needs to
+ learn one widget for model tree node selection, and the same widget for
+ node selection is used everywhere.
+ """
+
+
+ def getConstraintsSelectorUI(self):
+ """
+ Returns the UI for selecting constraints.
+ """
+ pass
+
+
+ def getMeasurementsSelectorUI(self):
+ """
+ Returns the UI for selecting measurements.
+ """
+ pass
+
+
+ def getAtomSetSelectorUI(self):
+ """
+ Returns the UI for selecting atom set nodes from the model tree.
+ """
+ pass
+
+
+ def detectUnMinized(self):
+ """
+ Detects and reports whether there are un-minimized structures in any of
+ the simulation input files.
+ """
+ pass
+
+
+ def checkJigSanity(self):
+ """
+ Checks whether there are any unreasonable jig parameters in the
+ simulation.
+ """
+ pass
+
+
+ def detectUnusedJigs(self):
+ """
+ Detects and reports whether there are any unused jigs in the input MMP
+ files.
+ """
+ pass
+
+
+ def detectReactionPoints(self):
+ """
+ Detects and reports reaction points found in the structures in the
+ input files.
+ """
+ pass
+
+
+ def checkSpinMultiplicity(self):
+ """
+ Reports on spin mulitiplicity.
+ """
+ pass
diff --git a/cad/src/experimental/NH1_Integration/lib/NE1_Simulation/Parameter.py b/cad/src/experimental/NH1_Integration/lib/NE1_Simulation/Parameter.py
index 2ed772f50..b932bf7db 100755
--- a/cad/src/experimental/NH1_Integration/lib/NE1_Simulation/Parameter.py
+++ b/cad/src/experimental/NH1_Integration/lib/NE1_Simulation/Parameter.py
@@ -10,131 +10,131 @@ IMAGE_2
class Parameter:
- """
- A GUI editable key/value pair. When newly constructed, the value is
- officially un-set (see the L{getValue} method.)
-
- This is an abstract/interface class and should not be instantiated.
- """
-
-
- def __init__(self, key):
- """
- Constructs a Parameter object with the given key - should only be called
- by L{ParameterFactory}.
- """
- hasValue = 0;
-
-
- def getKey(self):
- """
- Returns the dotted descriptor of what this parameter is.
- """
- pass
-
-
- def getValue(self):
- """
- Returns whether this Parameter has a set value, and what that value is.
- @return: (0=no value set, 1=value set), (value)
- """
- pass
- def setValue(self, value):
- """
- Sets the value of this Parameter.
- """
- pass
- def unSetValue(self):
- """
- Un-sets this Parameter's value.
- """
- hasValue = 0;
-
+ """
+ A GUI editable key/value pair. When newly constructed, the value is
+ officially un-set (see the L{getValue} method.)
+
+ This is an abstract/interface class and should not be instantiated.
+ """
+
+
+ def __init__(self, key):
+ """
+ Constructs a Parameter object with the given key - should only be called
+ by L{ParameterFactory}.
+ """
+ hasValue = 0;
+
+
+ def getKey(self):
+ """
+ Returns the dotted descriptor of what this parameter is.
+ """
+ pass
+
+
+ def getValue(self):
+ """
+ Returns whether this Parameter has a set value, and what that value is.
+ @return: (0=no value set, 1=value set), (value)
+ """
+ pass
+ def setValue(self, value):
+ """
+ Sets the value of this Parameter.
+ """
+ pass
+ def unSetValue(self):
+ """
+ Un-sets this Parameter's value.
+ """
+ hasValue = 0;
+
class ParameterFactory:
- """
- Creates fully configured Parameter subclass objects.
-
- Key names are dot-separated based on the L{SimSpecification} object model.
- Here is the list of reserved key names:
-
- B{simSpec.timestep} [float seconds] - The amount of time
- between the calculations of a system's state. Widget: lineedit,
- min=0.05e-15, max=5.00e-15, default=0.1e-15, suffix=s
-
- B{simSpec.startStep} [integer] - The number of the first step -
- usually zero, but may be non-zero when a simulation is continuing on
- fromwhere a previous simulation stopped. Widget: lineedit,
- min=0, max=-1, default=0
-
- and etc. etc. for
-
- B{simSpec.}maxSteps, stepsPerFrame,
- environmentTemperature, environmentPressure, workingDirectory
-
- B{simSpec.input.}type, file
-
- B{simSpec.motionPath.interval.}start, end
-
- B{simSpec.motionPath.interval.velocity.}fixed, xyzComponents, etc.
-
- B{simSpec.operation.}action
-
- B{simSpec.operation.}engine, atomSet, method,
- basisSet, functional, multiplicity, integrator, energyAccuracy,
- maxConvergenceAttempts, unscripted, applyFrom, applyTo
-
- B{simSpec.operation.constraint.}motion, atomSet
-
- B{simSpec.operation.measurement.}measure, atomSet
-
- B{simSpec.preSimChecks.}all, detectUnMinimized, checkJigSanity,
- detectUnusedJigs, detectReactionPoints, checkSpinMultiplicity
- """
-
-
- def createParameter(self, key):
- """Returns a fully configured Parameter subclass for the given key."""
- pass
+ """
+ Creates fully configured Parameter subclass objects.
+
+ Key names are dot-separated based on the L{SimSpecification} object model.
+ Here is the list of reserved key names:
+
+ B{simSpec.timestep} [float seconds] - The amount of time
+ between the calculations of a system's state. Widget: lineedit,
+ min=0.05e-15, max=5.00e-15, default=0.1e-15, suffix=s
+
+ B{simSpec.startStep} [integer] - The number of the first step -
+ usually zero, but may be non-zero when a simulation is continuing on
+ fromwhere a previous simulation stopped. Widget: lineedit,
+ min=0, max=-1, default=0
+
+ and etc. etc. for
+
+ B{simSpec.}maxSteps, stepsPerFrame,
+ environmentTemperature, environmentPressure, workingDirectory
+
+ B{simSpec.input.}type, file
+
+ B{simSpec.motionPath.interval.}start, end
+
+ B{simSpec.motionPath.interval.velocity.}fixed, xyzComponents, etc.
+
+ B{simSpec.operation.}action
+
+ B{simSpec.operation.}engine, atomSet, method,
+ basisSet, functional, multiplicity, integrator, energyAccuracy,
+ maxConvergenceAttempts, unscripted, applyFrom, applyTo
+
+ B{simSpec.operation.constraint.}motion, atomSet
+
+ B{simSpec.operation.measurement.}measure, atomSet
+
+ B{simSpec.preSimChecks.}all, detectUnMinimized, checkJigSanity,
+ detectUnusedJigs, detectReactionPoints, checkSpinMultiplicity
+ """
+
+
+ def createParameter(self, key):
+ """Returns a fully configured Parameter subclass for the given key."""
+ pass
class ParameterSet:
- """A set of Parameters."""
-
-
- def getGroupName(self):
- """Returns this ParameterSet's group name for GUI use."""
- return self.groupName
-
-
- def getParameter(self, key):
- """
- Returns whether or not the Parameter with the given key is in this set,
- and the Parameter itself if it is.
- @return: (0=the Parameter for the given key is not in this set, 1=the
- Parameter is present), (the Parameter)
- """
- pass
- def getParameterArray(self):
- """
- Returns this object's Parameters in an array in the correct order. The
- correct order is determined by each Parameter's "order" attribute.
- """
- pass
- def setParameter(self, Parameter):
- """
- Sets the given parameter. Any existing Parameter with the same key will
- be clobbered.
- """
- # Insert the Parameter such that the array remains sorted by
- # Parameter.order
- pass
-
-
-
-
-
+ """A set of Parameters."""
+
+
+ def getGroupName(self):
+ """Returns this ParameterSet's group name for GUI use."""
+ return self.groupName
+
+
+ def getParameter(self, key):
+ """
+ Returns whether or not the Parameter with the given key is in this set,
+ and the Parameter itself if it is.
+ @return: (0=the Parameter for the given key is not in this set, 1=the
+ Parameter is present), (the Parameter)
+ """
+ pass
+ def getParameterArray(self):
+ """
+ Returns this object's Parameters in an array in the correct order. The
+ correct order is determined by each Parameter's "order" attribute.
+ """
+ pass
+ def setParameter(self, Parameter):
+ """
+ Sets the given parameter. Any existing Parameter with the same key will
+ be clobbered.
+ """
+ # Insert the Parameter such that the array remains sorted by
+ # Parameter.order
+ pass
+
+
+
+
+
diff --git a/cad/src/experimental/NH1_Integration/lib/NE1_Simulation/SimSpecification.py b/cad/src/experimental/NH1_Integration/lib/NE1_Simulation/SimSpecification.py
index 2a405de2b..7b43c499f 100755
--- a/cad/src/experimental/NH1_Integration/lib/NE1_Simulation/SimSpecification.py
+++ b/cad/src/experimental/NH1_Integration/lib/NE1_Simulation/SimSpecification.py
@@ -18,370 +18,370 @@ The following is the object model of the SimSpecification module:
IMAGE_1
The following is an example SimSpecification as it would appear in XML::
- <simSpecification name="Dual-H abstraction">
- <description>
- Abstraction of two hydrogens from the DC10 deposition tooltip.
- </description>
-
- <parameter key="timestep" value="0.1e-15" />
- <parameter key="startStep" value="0" />
- <parameter key="maxSteps" value="10000" />
- <parameter key="stepsPerFrame" value="10" />
- <parameter key="environmentTemperature" value="300.0" />
- <parameter key="environmentPressure" value="100000.0" />
-
- <input name="abstractor">
- <parameter key="file" value="abstractor.mmp" />
- </input>
- <input name="seed">
- <parameter key="file" value="diamond-fragment.mmp" />
- </input>
-
- <motionPath name="MotionPath1">
- <interval>
- <parameter key="start" value="0.0" />
- <parameter key="end" value="180.0e-15" />
- <velocity>
- <parameter key="fixed" value="true" />
- </velocity>
- </interval>
- <interval>
- <parameter key="start" value="180e-15" />
- <parameter key="end" value="2345e-15" />
- <linearforce>
- <parameter key="speed" value="200.0" />
- <parameter key="componentsXYZ" value="0.0 -5.0e-9 0.0" />
- </linearforce>
- </interval>
- </motionPath>
-
- <motionPath name="Anchor1">
- <interval>
- <parameter name="start" value="0.0" />
- <parameter name="end" value="3300.0e-15" />
- <velocity>
- <parameter key="fixed" value="true" />
- </velocity>
- </interval>
- </motionPath>
-
- <operation name="Force Field/Quantum Chemistry">
- <parameter key="action" value="dynamics" />
-
- <method name="ND-1">
- <parameter key="engine" value="NanoDynamics-1" />
- <parameter key="atomSet" value="BulkAtomSet1" />
- </method>
-
- <method name="GAMESS">
- <parameter key="engine" value="GAMESS" />
- <parameter key="atomSet" value="Tooltip1" />
- <parameter key="method" value="Hartree-Fock" />
- <parameter key="basisSet" value="3-21G" />
- <parameter key="functional" value="" />
- <parameter key="multiplicity" value="auto" />
- <parameter key="integrator" value="coarse" />
- <parameter key="energyAccuracty" value="1.0e-5" />
- <parameter key="maxConvergenceAttempts" value="10" />
- <parameter key="unscripted" value="no" />
- <parameter key="applyFrom" value="0.0" />
- <parameter key="applyTo" value="20.0e-12" />
- </method>
-
- <constraint>
- <parameter key="motion" value="MotionPath1" />
- <parameter key="atomSet" value="DC10" />
- </constraint>
- <constraint>
- <parameter key="motion" value="Anchor1" />
- <parameter key="atomSet" value="H-abstractor" />
- </constraint>
-
- <measurement>
- <parameter key="measure" value="Thermo1" />
- <parameter key="atomSet" value="H-abstractor" />
- </measurement>
- </operation>
-
- <preSimulationChecks>
- <parameter key="all" value="false" />
- <parameter key="detectUnMinimized" value="true" />
- <parameter key="checkJigSanity" value="true" />
- <parameter key="detectUnusedJigs" value="false" />
- <parameter key="detectReactionPoints" value="true" />
- <parameter key="checkSpinMultiplicity" value="true" />
- </preSimulationChecks>
- </simSpecification>
+ <simSpecification name="Dual-H abstraction">
+ <description>
+ Abstraction of two hydrogens from the DC10 deposition tooltip.
+ </description>
+
+ <parameter key="timestep" value="0.1e-15" />
+ <parameter key="startStep" value="0" />
+ <parameter key="maxSteps" value="10000" />
+ <parameter key="stepsPerFrame" value="10" />
+ <parameter key="environmentTemperature" value="300.0" />
+ <parameter key="environmentPressure" value="100000.0" />
+
+ <input name="abstractor">
+ <parameter key="file" value="abstractor.mmp" />
+ </input>
+ <input name="seed">
+ <parameter key="file" value="diamond-fragment.mmp" />
+ </input>
+
+ <motionPath name="MotionPath1">
+ <interval>
+ <parameter key="start" value="0.0" />
+ <parameter key="end" value="180.0e-15" />
+ <velocity>
+ <parameter key="fixed" value="true" />
+ </velocity>
+ </interval>
+ <interval>
+ <parameter key="start" value="180e-15" />
+ <parameter key="end" value="2345e-15" />
+ <linearforce>
+ <parameter key="speed" value="200.0" />
+ <parameter key="componentsXYZ" value="0.0 -5.0e-9 0.0" />
+ </linearforce>
+ </interval>
+ </motionPath>
+
+ <motionPath name="Anchor1">
+ <interval>
+ <parameter name="start" value="0.0" />
+ <parameter name="end" value="3300.0e-15" />
+ <velocity>
+ <parameter key="fixed" value="true" />
+ </velocity>
+ </interval>
+ </motionPath>
+
+ <operation name="Force Field/Quantum Chemistry">
+ <parameter key="action" value="dynamics" />
+
+ <method name="ND-1">
+ <parameter key="engine" value="NanoDynamics-1" />
+ <parameter key="atomSet" value="BulkAtomSet1" />
+ </method>
+
+ <method name="GAMESS">
+ <parameter key="engine" value="GAMESS" />
+ <parameter key="atomSet" value="Tooltip1" />
+ <parameter key="method" value="Hartree-Fock" />
+ <parameter key="basisSet" value="3-21G" />
+ <parameter key="functional" value="" />
+ <parameter key="multiplicity" value="auto" />
+ <parameter key="integrator" value="coarse" />
+ <parameter key="energyAccuracty" value="1.0e-5" />
+ <parameter key="maxConvergenceAttempts" value="10" />
+ <parameter key="unscripted" value="no" />
+ <parameter key="applyFrom" value="0.0" />
+ <parameter key="applyTo" value="20.0e-12" />
+ </method>
+
+ <constraint>
+ <parameter key="motion" value="MotionPath1" />
+ <parameter key="atomSet" value="DC10" />
+ </constraint>
+ <constraint>
+ <parameter key="motion" value="Anchor1" />
+ <parameter key="atomSet" value="H-abstractor" />
+ </constraint>
+
+ <measurement>
+ <parameter key="measure" value="Thermo1" />
+ <parameter key="atomSet" value="H-abstractor" />
+ </measurement>
+ </operation>
+
+ <preSimulationChecks>
+ <parameter key="all" value="false" />
+ <parameter key="detectUnMinimized" value="true" />
+ <parameter key="checkJigSanity" value="true" />
+ <parameter key="detectUnusedJigs" value="false" />
+ <parameter key="detectReactionPoints" value="true" />
+ <parameter key="checkSpinMultiplicity" value="true" />
+ </preSimulationChecks>
+ </simSpecification>
Packages may add their own custom parameters and they will be stored along
with the reserved-key parameters. Custom parameters can be specified with
the information necessary for viewing and editing them via some GUI. Here
is what a fully defined parameter would look like in XML::
- <parameter key="simFlowScript" value="/Users/bh/tooltip_action.tcl">
- <label>Workflow script</label>
- <widget>filechooser</widget>
- <extension>.tcl</extension>
- <tooltip>Simulation workflow script file</tooltip>
- </parameter>
+ <parameter key="simFlowScript" value="/Users/bh/tooltip_action.tcl">
+ <label>Workflow script</label>
+ <widget>filechooser</widget>
+ <extension>.tcl</extension>
+ <tooltip>Simulation workflow script file</tooltip>
+ </parameter>
"""
from Parameter import ParameterSet
class SimInput(ParameterSet):
- """Simulation input files. See L{SimSpecification} for context."""
-
-
- def __init__(self, name):
- """Constructs a SimInput with the given name."""
- groupName = "Input files"
-
-
- def getName(self):
- """Returns this SimInput's name."""
- pass
- def setName(self, name):
- """Sets this SimInput's name."""
- pass
+ """Simulation input files. See L{SimSpecification} for context."""
+
+
+ def __init__(self, name):
+ """Constructs a SimInput with the given name."""
+ groupName = "Input files"
+
+
+ def getName(self):
+ """Returns this SimInput's name."""
+ pass
+ def setName(self, name):
+ """Sets this SimInput's name."""
+ pass
class Action(ParameterSet):
- """
- An external effect applied to a set of atoms.
- See L{SimSpecification} for context.
-
- This is an abstract/interface class and should not be instantiated.
- """
- pass
+ """
+ An external effect applied to a set of atoms.
+ See L{SimSpecification} for context.
+
+ This is an abstract/interface class and should not be instantiated.
+ """
+ pass
class Velocity(Action):
- """
- A fixed velocity applied to a set of atoms.
- See L{SimSpecification} for context.
- """
-
-
- def __init__(self):
- """Constructs a Velocity object."""
- groupName = "Velocity"
+ """
+ A fixed velocity applied to a set of atoms.
+ See L{SimSpecification} for context.
+ """
+
+
+ def __init__(self):
+ """Constructs a Velocity object."""
+ groupName = "Velocity"
class LinearForce(Action):
- """
- A force applied to a set of atoms.
- See L{SimSpecification} for context.
- """
-
-
- def __init__(self):
- """Constructs a LinearForce object."""
- groupName = "Linear force"
+ """
+ A force applied to a set of atoms.
+ See L{SimSpecification} for context.
+ """
+
+
+ def __init__(self):
+ """Constructs a LinearForce object."""
+ groupName = "Linear force"
class Torque(Action):
- """
- A rotary force applied to a set of atoms.
- See L{SimSpecification} for context.
- """
-
-
- def __init__(self):
- """Constructs a Torque object."""
- groupName = "Torque"
-
+ """
+ A rotary force applied to a set of atoms.
+ See L{SimSpecification} for context.
+ """
+
+
+ def __init__(self):
+ """Constructs a Torque object."""
+ groupName = "Torque"
+
class Interval(ParameterSet):
- """
- A span of time and associated Action.
- See L{SimSpecification} for context.
- """
-
-
- def __init__(self):
- """Constructs an Interval object."""
- groupName = "Interval"
-
-
- def getAction(self):
- """Returns the Action subclass for this interval."""
- pass
- def setAction(self, Action):
- """
- Sets the Action subclass for this interval. Clobbers any existing
- Action.
- """
- pass
+ """
+ A span of time and associated Action.
+ See L{SimSpecification} for context.
+ """
+
+
+ def __init__(self):
+ """Constructs an Interval object."""
+ groupName = "Interval"
+
+
+ def getAction(self):
+ """Returns the Action subclass for this interval."""
+ pass
+ def setAction(self, Action):
+ """
+ Sets the Action subclass for this interval. Clobbers any existing
+ Action.
+ """
+ pass
class MotionPath(ParameterSet):
- """
- A description of motion during simulation.
- See L{SimSpecification} for context.
- """
-
-
- def __init__(self, name):
- """Constructs a MotionPath with the given name."""
- groupName = "Motion path"
-
-
- def getName(self):
- """Returns this MotionPath's name."""
- pass
- def setName(self, name):
- """Sets this MotionPath's name."""
- pass
-
-
- def getIntervalArray(self):
- """Returns this MotionPath's Interval as an array."""
- pass
- def addInterval(self, interval):
- """Adds the given Interval and returns an Interval index."""
- pass
- def deleteInterval(self, intervalIndex):
- """Deletes the Interval with the given index from this MotionPath."""
- pass
+ """
+ A description of motion during simulation.
+ See L{SimSpecification} for context.
+ """
+
+
+ def __init__(self, name):
+ """Constructs a MotionPath with the given name."""
+ groupName = "Motion path"
+
+
+ def getName(self):
+ """Returns this MotionPath's name."""
+ pass
+ def setName(self, name):
+ """Sets this MotionPath's name."""
+ pass
+
+
+ def getIntervalArray(self):
+ """Returns this MotionPath's Interval as an array."""
+ pass
+ def addInterval(self, interval):
+ """Adds the given Interval and returns an Interval index."""
+ pass
+ def deleteInterval(self, intervalIndex):
+ """Deletes the Interval with the given index from this MotionPath."""
+ pass
class Method(ParameterSet):
- """A simulation scheme. See L{SimSpecification} for context."""
-
-
- def __init__(self):
- """Constructs a Method object."""
- groupName = "Method"
+ """A simulation scheme. See L{SimSpecification} for context."""
+
+
+ def __init__(self):
+ """Constructs a Method object."""
+ groupName = "Method"
class Constraint(ParameterSet):
- """Application of a Motion path on an atom set."""
-
-
- def __init__(self):
- """Constructs a Constraint object."""
- groupName = "Constraint"
+ """Application of a Motion path on an atom set."""
+
+
+ def __init__(self):
+ """Constructs a Constraint object."""
+ groupName = "Constraint"
class Measurement(ParameterSet):
- """Application of a Measure on an atom set."""
-
-
- def __init__(self):
- """Constructs a Measurement object."""
- groupName = "Measurement"
+ """Application of a Measure on an atom set."""
+
+
+ def __init__(self):
+ """Constructs a Measurement object."""
+ groupName = "Measurement"
class Operation(ParameterSet):
- """Describes the components of the actual simulation process."""
-
-
- def __init__(self):
- """Constructs an Operation object."""
- groupName = "Operation"
-
-
+ """Describes the components of the actual simulation process."""
+
+
+ def __init__(self):
+ """Constructs an Operation object."""
+ groupName = "Operation"
+
+
class SimSpecification(ParameterSet):
- """
- Encapsulates all the particulars of a simulation such as input files,
- entity traversal, level of theory, calculation, motion, and results.
- """
-
-
- def __init__(self, name):
- """Constructs a SimSpecification with the given name."""
- groupName = "Simulation specification"
-
-
- def loadFromFile(self, filepath):
- """
- Loads this SimSpecification from the given filepath.
- @return: (0=successful or non-zero error code), (error description)
- """
- pass
-
-
- def writeToFile(self, filepath):
- """
- Writes this SimSpecification to the given filepath.
- @return: (0=successful or non-zero error code), (error description)
- """
- pass
-
-
- def getName(self):
- """Returns this SimSpecification's name."""
- pass
- def setName(self, name):
- """Sets this SimSpecification's name."""
- pass
-
-
- def getDescription(self):
- """Returns this SimSpecification's description."""
- pass
- def setDescription(self):
- """Sets this SimSpecification's description."""
- pass
-
-
- def getParameter(self, key):
- """
- Returns the Parameter with the given key. A blank Parameter is returned
- if no Parameter with the given key has been set.
- """
- pass
- def getParameterArray(self):
- """Returns this object's Parameters in an array."""
- pass
- def setParameter(self, Parameter):
- """
- Sets the given parameter. Any existing Parameter with the same key will
- be clobbered.
- """
- pass
-
-
- def getSimInputArray(self):
- """Returns this SimSpecification's SimInputs in an array."""
- pass
- def addSimInput(self, Input):
- """
- Adds the given SimInput. Any existing SimInput with the same
- name will be clobbered.
- """
- pass
-
-
- def getMotionPathArray(self):
- """Returns this SimSpecification's MotionPaths in an array."""
- pass
- def addMotionPath(self, MotionPath):
- """
- Adds the given MotionPath. Any existing MotionPath with the same
- name will be clobbered.
- """
- pass
-
-
- def getOperation(self):
- """Returns this SimSpecification's Operation."""
- pass
- def setOperation(self, Operation):
- """
- Sets the given Operation. Any existing Operation will be clobbered.
- """
- pass
-
-
- def getPreSimulationChecks(self):
- """
- Returns this SimSpecification's pre-simulation check Parameters in an
- array.
- """
- pass
- def addPreSimulationCheck(self, Parameter):
- """
- Adds the given pre-simulation check Parameter. Any existing pre-check
- with the same key will be clobbered.
- """
- pass
+ """
+ Encapsulates all the particulars of a simulation such as input files,
+ entity traversal, level of theory, calculation, motion, and results.
+ """
+
+
+ def __init__(self, name):
+ """Constructs a SimSpecification with the given name."""
+ groupName = "Simulation specification"
+
+
+ def loadFromFile(self, filepath):
+ """
+ Loads this SimSpecification from the given filepath.
+ @return: (0=successful or non-zero error code), (error description)
+ """
+ pass
+
+
+ def writeToFile(self, filepath):
+ """
+ Writes this SimSpecification to the given filepath.
+ @return: (0=successful or non-zero error code), (error description)
+ """
+ pass
+
+
+ def getName(self):
+ """Returns this SimSpecification's name."""
+ pass
+ def setName(self, name):
+ """Sets this SimSpecification's name."""
+ pass
+
+
+ def getDescription(self):
+ """Returns this SimSpecification's description."""
+ pass
+ def setDescription(self):
+ """Sets this SimSpecification's description."""
+ pass
+
+
+ def getParameter(self, key):
+ """
+ Returns the Parameter with the given key. A blank Parameter is returned
+ if no Parameter with the given key has been set.
+ """
+ pass
+ def getParameterArray(self):
+ """Returns this object's Parameters in an array."""
+ pass
+ def setParameter(self, Parameter):
+ """
+ Sets the given parameter. Any existing Parameter with the same key will
+ be clobbered.
+ """
+ pass
+
+
+ def getSimInputArray(self):
+ """Returns this SimSpecification's SimInputs in an array."""
+ pass
+ def addSimInput(self, Input):
+ """
+ Adds the given SimInput. Any existing SimInput with the same
+ name will be clobbered.
+ """
+ pass
+
+
+ def getMotionPathArray(self):
+ """Returns this SimSpecification's MotionPaths in an array."""
+ pass
+ def addMotionPath(self, MotionPath):
+ """
+ Adds the given MotionPath. Any existing MotionPath with the same
+ name will be clobbered.
+ """
+ pass
+
+
+ def getOperation(self):
+ """Returns this SimSpecification's Operation."""
+ pass
+ def setOperation(self, Operation):
+ """
+ Sets the given Operation. Any existing Operation will be clobbered.
+ """
+ pass
+
+
+ def getPreSimulationChecks(self):
+ """
+ Returns this SimSpecification's pre-simulation check Parameters in an
+ array.
+ """
+ pass
+ def addPreSimulationCheck(self, Parameter):
+ """
+ Adds the given pre-simulation check Parameter. Any existing pre-check
+ with the same key will be clobbered.
+ """
+ pass
diff --git a/cad/src/experimental/basic-qt-app/ticker.py b/cad/src/experimental/basic-qt-app/ticker.py
index f48d3b7b0..39e6f678b 100755
--- a/cad/src/experimental/basic-qt-app/ticker.py
+++ b/cad/src/experimental/basic-qt-app/ticker.py
@@ -10,11 +10,11 @@ class Ticker(QObject):
#timer.setSingleShot(True)
self.connect(self.timer, SIGNAL("timeout()"), self.hello)
timer.start(1000)
-
+
def hello(self):
print 'hi it works'
return 4
-
+
x=Ticker()
if __name__ == '__main__':
diff --git a/cad/src/graphics/drawables/DirectionArrow.py b/cad/src/graphics/drawables/DirectionArrow.py
index 87b9735f6..806aa2695 100644
--- a/cad/src/graphics/drawables/DirectionArrow.py
+++ b/cad/src/graphics/drawables/DirectionArrow.py
@@ -166,14 +166,14 @@ class DirectionArrow(DragHandler_API, Selobj_API):
@type glpane: L{GLPane}
@param color: Highlight color
"""
- q = self.parent.quat
- glPushMatrix()
- glTranslatef( self.parent.center[0],
- self.parent.center[1],
- self.parent.center[2])
- glRotatef( q.angle * ONE_RADIAN,
- q.x,
- q.y,
+ q = self.parent.quat
+ glPushMatrix()
+ glTranslatef( self.parent.center[0],
+ self.parent.center[1],
+ self.parent.center[2])
+ glRotatef( q.angle * ONE_RADIAN,
+ q.x,
+ q.y,
q.z)
if self.flipDirection:
diff --git a/cad/src/graphics/drawing/ColorSorter.py b/cad/src/graphics/drawing/ColorSorter.py
index 1db4de603..9e0016530 100755
--- a/cad/src/graphics/drawing/ColorSorter.py
+++ b/cad/src/graphics/drawing/ColorSorter.py
@@ -397,7 +397,7 @@ class ColorSorter:
else:
opacity = 1.0
- if opacity >= 0.0 and opacity != 1.0:
+ if opacity >= 0.0 and opacity != 1.0:
glDepthMask(GL_FALSE)
glEnable(GL_BLEND)
glBlendFunc(GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA)
@@ -463,10 +463,10 @@ class ColorSorter:
ColorSorter.glpane.glprefs.sphereShader_desired() and
drawing_globals.sphereShader_available()
)
- if len(color) == 3:
+ if len(color) == 3:
lcolor = (color[0], color[1], color[2], opacity)
else:
- lcolor = color
+ lcolor = color
pass
if sphereBatches and ColorSorter._parent_csdl: # Russ 080925: Added.
@@ -519,10 +519,10 @@ class ColorSorter:
ColorSorter._cur_shapelist.add_wiresphere(
lcolor, pos, radius, ColorSorter._gl_name_stack[-1])
else:
- if len(color) == 3:
+ if len(color) == 3:
lcolor = (color[0], color[1], color[2], 1.0)
else:
- lcolor = color
+ lcolor = color
ColorSorter.schedule(lcolor, drawwiresphere_worker,
# Use constant-color line drawing.
@@ -580,10 +580,10 @@ class ColorSorter:
lcolor, pos1, pos2, radius,
ColorSorter._gl_name_stack[-1], capped)
else:
- if len(color) == 3:
+ if len(color) == 3:
lcolor = (color[0], color[1], color[2], opacity)
else:
- lcolor = color
+ lcolor = color
# Russ 090119: Added.
cylinderBatches = ( ColorSorter._permit_shaders and
@@ -695,10 +695,10 @@ class ColorSorter:
lcolor, pos_array, rad_array,
ColorSorter._gl_name_stack[-1], capped)
else:
- if len(color) == 3:
+ if len(color) == 3:
lcolor = (color[0], color[1], color[2], opacity)
else:
- lcolor = color
+ lcolor = color
ColorSorter.schedule(lcolor, drawpolycone_worker,
(pos_array, rad_array))
@@ -729,10 +729,10 @@ class ColorSorter:
lcolor, pos_array, color_array, rad_array,
ColorSorter._gl_name_stack[-1], capped)
else:
- if len(color) == 3:
+ if len(color) == 3:
lcolor = (color[0], color[1], color[2], opacity)
else:
- lcolor = color
+ lcolor = color
ColorSorter.schedule(lcolor,
drawpolycone_multicolor_worker,
@@ -751,10 +751,10 @@ class ColorSorter:
if ColorSorter._relative_transforms():
ColorSorter._warn_transforms_nim("schedule_surface")
- if len(color) == 3:
+ if len(color) == 3:
lcolor = (color[0], color[1], color[2], 1.0)
else:
- lcolor = color
+ lcolor = color
ColorSorter.schedule(lcolor, drawsurface_worker, (pos, radius, tm, nm))
schedule_surface = staticmethod(schedule_surface)
diff --git a/cad/src/graphics/drawing/drawDnaLadder.py b/cad/src/graphics/drawing/drawDnaLadder.py
index 44819412d..c9d2e44be 100755
--- a/cad/src/graphics/drawing/drawDnaLadder.py
+++ b/cad/src/graphics/drawing/drawDnaLadder.py
@@ -120,7 +120,7 @@ def drawDnaLadder(endCenter1,
previousLadderBeam1Point = ladderBeam1Point
previousLadderBeam2Point = ladderBeam2Point
- pointOnAxis = pointOnAxis + unitVector*duplexRise
+ pointOnAxis = pointOnAxis + unitVector*duplexRise
x += duplexRise
ladderBeam1Point = previousPoint + \
diff --git a/cad/src/graphics/drawing/drawNanotubeLadder.py b/cad/src/graphics/drawing/drawNanotubeLadder.py
index ff70a32b0..70d7acfc1 100644
--- a/cad/src/graphics/drawing/drawNanotubeLadder.py
+++ b/cad/src/graphics/drawing/drawNanotubeLadder.py
@@ -118,7 +118,7 @@ def drawNanotubeLadder(endCenter1,
previousLadderBeam1Point = ladderBeam1Point
previousLadderBeam2Point = ladderBeam2Point
- pointOnAxis = pointOnAxis + unitVector * cntRise
+ pointOnAxis = pointOnAxis + unitVector * cntRise
x += cntRise
ladderBeam1Point = previousPoint + \
diff --git a/cad/src/graphics/drawing/drawPeptideTrace.py b/cad/src/graphics/drawing/drawPeptideTrace.py
index 1f5c4f061..cd7735d2a 100644
--- a/cad/src/graphics/drawing/drawPeptideTrace.py
+++ b/cad/src/graphics/drawing/drawPeptideTrace.py
@@ -163,7 +163,7 @@ def drawPeptideTrace_orig(endCenter1,
previousLadderBeam1Point = ladderBeam1Point
previousLadderBeam2Point = ladderBeam2Point
- pointOnAxis = pointOnAxis + unitVector * cntRise
+ pointOnAxis = pointOnAxis + unitVector * cntRise
x += cntRise
ladderBeam1Point = previousPoint + \
diff --git a/cad/src/graphics/drawing/drawers.py b/cad/src/graphics/drawing/drawers.py
index dd215cfe3..2ff9f137c 100755
--- a/cad/src/graphics/drawing/drawers.py
+++ b/cad/src/graphics/drawing/drawers.py
@@ -836,7 +836,7 @@ def drawbrick(color, center, axis, l, h, w, opacity = 1.0):
if len(color) == 3:
color = (color[0], color[1], color[2], opacity)
- if opacity != 1.0:
+ if opacity != 1.0:
glDepthMask(GL_FALSE)
glEnable(GL_BLEND)
glBlendFunc(GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA)
@@ -860,7 +860,7 @@ def drawbrick(color, center, axis, l, h, w, opacity = 1.0):
#bruce 060302 revised the contents of solidCubeList while fixing bug 1595
glCallList(drawing_globals.solidCubeList)
- if opacity != 1.0:
+ if opacity != 1.0:
glDisable(GL_BLEND)
glDepthMask(GL_TRUE)
@@ -1221,7 +1221,7 @@ def renderSurface(surfaceEntities, surfaceNormals):
onevert(entity[1])
onevert(entity[2])
glEnd()
- else:
+ else:
glBegin(GL_QUADS)
for entity in entityIndex:
onevert(entity[0])
diff --git a/cad/src/graphics/drawing/gl_lighting.py b/cad/src/graphics/drawing/gl_lighting.py
index b251c027a..05a24c2c3 100755
--- a/cad/src/graphics/drawing/gl_lighting.py
+++ b/cad/src/graphics/drawing/gl_lighting.py
@@ -53,7 +53,7 @@ try:
from OpenGL.GL import glFogv # piotr 080515
except:
# The installed version of OpenGL requires argument-typed glFog calls.
- from OpenGL.GL import glFogf as glFog
+ from OpenGL.GL import glFogf as glFog
from OpenGL.GL import glFogfv as glFogv
pass
diff --git a/cad/src/graphics/drawing/gl_shaders.py b/cad/src/graphics/drawing/gl_shaders.py
index 6bd96f841..d4980cc4c 100644
--- a/cad/src/graphics/drawing/gl_shaders.py
+++ b/cad/src/graphics/drawing/gl_shaders.py
@@ -101,13 +101,13 @@ CHECK_TEXTURE_XFORM_LOADING = False # True ## Never check in a True value.
# Exception Type: EXC_BAD_ACCESS (SIGSEGV)
# Exception Codes: KERN_INVALID_ADDRESS at 0x0000000013b88000
# Thread 0 Crashed:
-# 0 libSystem.B.dylib 0xffff08a0 __memcpy + 256
-# 1 libGLImage.dylib 0x913ea5e9 glgCopyRowsWithMemCopy(
+# 0 libSystem.B.dylib 0xffff08a0 __memcpy + 256
+# 1 libGLImage.dylib 0x913ea5e9 glgCopyRowsWithMemCopy(
# GLGOperation const*, unsigned long, GLDPixelMode const*) + 121
-# 2 libGLImage.dylib 0x913e8ac6 glgProcessPixelsWithProcessor + 326
-# 3 GLEngine 0x1ea16198 gleTextureImagePut + 1752
-# 4 GLEngine 0x1ea1f896 glTexSubImage2D_Exec + 1350
-# 5 libGL.dylib 0x91708cdb glTexSubImage2D + 155
+# 2 libGLImage.dylib 0x913e8ac6 glgProcessPixelsWithProcessor + 326
+# 3 GLEngine 0x1ea16198 gleTextureImagePut + 1752
+# 4 GLEngine 0x1ea1f896 glTexSubImage2D_Exec + 1350
+# 5 libGL.dylib 0x91708cdb glTexSubImage2D + 155
from geometry.VQT import A, norm
diff --git a/cad/src/graphics/drawing/shader_objects_patch.py b/cad/src/graphics/drawing/shader_objects_patch.py
index 4b92134a3..6c1703eab 100644
--- a/cad/src/graphics/drawing/shader_objects_patch.py
+++ b/cad/src/graphics/drawing/shader_objects_patch.py
@@ -123,7 +123,7 @@ glCompileShaderARB.errcheck = _afterCheck( GL_OBJECT_COMPILE_STATUS_ARB )
glLinkProgramARB.errcheck = _afterCheck( GL_OBJECT_LINK_STATUS_ARB )
## Not sure why, but these give invalid operation :(
##if glValidateProgramARB and OpenGL.ERROR_CHECKING:
-## glValidateProgramARB.errcheck = _afterCheck( GL_OBJECT_VALIDATE_STATUS_ARB )
+## glValidateProgramARB.errcheck = _afterCheck( GL_OBJECT_VALIDATE_STATUS_ARB )
base_glGetInfoLogARB = glGetInfoLogARB
def glGetInfoLogARB( obj ):
diff --git a/cad/src/graphics/drawing/vbo_patch.py b/cad/src/graphics/drawing/vbo_patch.py
index 44a71ad86..a2074f70c 100644
--- a/cad/src/graphics/drawing/vbo_patch.py
+++ b/cad/src/graphics/drawing/vbo_patch.py
@@ -43,11 +43,11 @@ glBufferSubDataARB = wrapper.wrapper( glBufferSubDataARB ).setPyConverter(
# Changed the "indices" argument type from ctypes.POINTER(ctypes.c_void_p) to
# arrays.GLintArray, like the "first" argument of glMultiDrawArrays.
glMultiDrawElementsVBO = platform.createExtensionFunction(
- 'glMultiDrawElementsEXT', dll=platform.GL,
- resultType=None,
- argTypes=(constants.GLenum, arrays.GLsizeiArray,
+ 'glMultiDrawElementsEXT', dll=platform.GL,
+ resultType=None,
+ argTypes=(constants.GLenum, arrays.GLsizeiArray,
constants.GLenum, arrays.GLintArray, constants.GLsizei,),
- doc = ('glMultiDrawElementsEXT( GLenum(mode), GLsizeiArray(count), '
+ doc = ('glMultiDrawElementsEXT( GLenum(mode), GLsizeiArray(count), '
'GLenum(type), GLintArray(indices), GLsizei(primcount) ) -> None'),
- argNames = ('mode', 'count', 'type', 'indices', 'primcount',),
+ argNames = ('mode', 'count', 'type', 'indices', 'primcount',),
)
diff --git a/cad/src/graphics/rendering/povray/povray.py b/cad/src/graphics/rendering/povray/povray.py
index e13eae233..47afeb30e 100755
--- a/cad/src/graphics/rendering/povray/povray.py
+++ b/cad/src/graphics/rendering/povray/povray.py
@@ -322,7 +322,7 @@ def launch_povray_or_megapov(win, info, povray_ini): #bruce 060707/11 revised th
# unless it matters that it reads and discards stdout/stderr
# (eg so large output would not block -- unlikely that this matters).
# It doesn't echo stdout/stderr. See also blabout/blaberr in other files. Maybe fix this? ###@@@
- p.setWorkingDirectory(workdir)
+ p.setWorkingDirectory(workdir)
p.start(program, arguments)
# Put up hourglass cursor to indicate we are busy. Restore the cursor below. Mark 060621.
diff --git a/cad/src/model/Chunk_Dna_methods.py b/cad/src/model/Chunk_Dna_methods.py
index ea069d96a..08219bbe2 100644
--- a/cad/src/model/Chunk_Dna_methods.py
+++ b/cad/src/model/Chunk_Dna_methods.py
@@ -144,11 +144,11 @@ class Chunk_Dna_methods: ## (NodeWithAtomContents):
else:
item = (("%s of [%s]" % (strand.name, dnaGroup.name)),
noop,
- 'disabled')
+ 'disabled')
contextMenuList.append(None) # adds a separator in the contextmenu
- contextMenuList.append(item)
+ contextMenuList.append(item)
item = (("Edit DnaStrand Properties..."),
- strand.edit)
+ strand.edit)
contextMenuList.append(item)
contextMenuList.append(None) # separator
diff --git a/cad/src/model/Plane.py b/cad/src/model/Plane.py
index 343d99531..c7a75547c 100755
--- a/cad/src/model/Plane.py
+++ b/cad/src/model/Plane.py
@@ -288,7 +288,7 @@ class Plane(ReferenceGeometry):
"""
if not previewing:
try:
- self.fill_color = self.default_fill_color
+ self.fill_color = self.default_fill_color
self.border_color = self.default_border_color
self.opacity = self.default_opacity
except:
diff --git a/cad/src/model/jigs.py b/cad/src/model/jigs.py
index 8283a74b9..1bf424d72 100755
--- a/cad/src/model/jigs.py
+++ b/cad/src/model/jigs.py
@@ -672,14 +672,14 @@ class Jig(NodeWith3DContents, Selobj_API):
so all they need to override is mmp_record_jigspecific_midpart.]
"""
if mapping is not None:
- ndix = mapping.atnums
+ ndix = mapping.atnums
name = mapping.encode_name(self.name)
# flags related to what we can do about atoms on this jig which have no encoding in mapping
permit_fwd_ref = not mapping.min #bruce 051031 (kluge, mapping should say this more directly)
permit_missing_jig_atoms = mapping.min #bruce 051031 (ditto on kluge)
assert not (permit_fwd_ref and permit_missing_jig_atoms) # otherwise wouldn't know which one to do with missing atoms!
else:
- ndix = None
+ ndix = None
name = self.name
permit_fwd_ref = False #bruce 051031
permit_missing_jig_atoms = False # guess [bruce 051031]
diff --git a/cad/src/operations/ops_display.py b/cad/src/operations/ops_display.py
index 5abec53f4..0c4f26c79 100644
--- a/cad/src/operations/ops_display.py
+++ b/cad/src/operations/ops_display.py
@@ -234,12 +234,12 @@ class displaySlotsMixin:
# it should be unpicked after changing its color.
# The user has most likely selected the chunk to change its color
# and won't like it still shown 'green'(the selection color)
- # even after changing the color. so deselect it.
+ # even after changing the color. so deselect it.
# The chunk is NOT unpicked IF the color is changed via chunk
# property dialog. see ChunkProp.change_chunk_color for details.
# This is intentional.
- for ob in list:
+ for ob in list:
ob.unpick()
self.win_update()
diff --git a/cad/src/outtakes/PeptideGroup.py b/cad/src/outtakes/PeptideGroup.py
index 38495d7c7..72207d11b 100644
--- a/cad/src/outtakes/PeptideGroup.py
+++ b/cad/src/outtakes/PeptideGroup.py
@@ -102,11 +102,11 @@ class PeptideGroup(Group):
def getProps(self):
"""
- Method to support Dna duplex editing. see Group.__init__ for
- a comment
+ Method to support Dna duplex editing. see Group.__init__ for
+ a comment
THIS IS THE DEFAULT IMPLEMENTATION. TO BE MODIFIED
- """
+ """
#Should it supply the Dna Segment list (children) and then add
#individual segments when setProps is called??
# [probably not; see B&N email discussion from when this comment was added]
@@ -116,10 +116,11 @@ class PeptideGroup(Group):
def setProps(self, props):
"""
- Method to support Dna duplex editing. see Group.__init__ for
- a comment
+ Method to support Dna duplex editing. see Group.__init__ for
+ a comment
+
THIS IS THE DEFAULT IMPLEMENTATION. TO BE MODIFIED
- """
+ """
#Should it accept the Dna Segment list and then add individual segments?
pass
diff --git a/cad/src/outtakes/TreeView.py b/cad/src/outtakes/TreeView.py
index c652d9177..ce457e578 100755
--- a/cad/src/outtakes/TreeView.py
+++ b/cad/src/outtakes/TreeView.py
@@ -235,7 +235,7 @@ class TreeView(QTreeView):
# try doing these first, but if that fails, do them after columns are made [as before]:
qt4skipit('self.setSorting(-1)')
-
+
self.setRootIsDecorated(1)
qt4skipit('self.setShowSortIndicator(0) # [this used to be done after setResizePolicy]')
diff --git a/cad/src/protein/commands/InsertPeptide/InsertPeptide_EditCommand.py b/cad/src/protein/commands/InsertPeptide/InsertPeptide_EditCommand.py
index c09f21b58..4e3472f0c 100644
--- a/cad/src/protein/commands/InsertPeptide/InsertPeptide_EditCommand.py
+++ b/cad/src/protein/commands/InsertPeptide/InsertPeptide_EditCommand.py
@@ -218,7 +218,7 @@ class InsertPeptide_EditCommand(EditCommand):
# peptide.kill_with_contents()
# self._revertNumber()
- self._peptideList = []
+ self._peptideList = []
self.win.win_update()
return
diff --git a/cad/src/protein/commands/InsertPeptide/PeptideGenerator.py b/cad/src/protein/commands/InsertPeptide/PeptideGenerator.py
index 6dd6b31ae..1b947ef54 100755
--- a/cad/src/protein/commands/InsertPeptide/PeptideGenerator.py
+++ b/cad/src/protein/commands/InsertPeptide/PeptideGenerator.py
@@ -969,8 +969,8 @@ class PeptideGenerator:
atom.set_atomtype_but_dont_revise_singlets(atom_type)
- ### debug - output in PDB format
- ### print "ATOM %5d %-3s %3s %c%4d %8.3f%8.3f%8.3f" % ( n, name, "ALA", ' ', res_num, xyz[0], xyz[1], xyz[2])
+ ### debug - output in PDB format
+ ### print "ATOM %5d %-3s %3s %c%4d %8.3f%8.3f%8.3f" % ( n, name, "ALA", ' ', res_num, xyz[0], xyz[1], xyz[2])
self.prev_psi = psi # Remember previous psi angle.
diff --git a/cad/src/simulation/runSim.py b/cad/src/simulation/runSim.py
index 8292d6cbd..c6847aa36 100755
--- a/cad/src/simulation/runSim.py
+++ b/cad/src/simulation/runSim.py
@@ -525,7 +525,7 @@ class SimRunner:
os.mkdir(hdf5DataStoreDir)
sleep(1) # Give GMX/HDF5 a chance to write basic info
-
+
# Determine the GMX process id (pid) for passing to nv1.
#
# (Py)QProcess.pid() doesn't return anything useable
@@ -560,7 +560,7 @@ class SimRunner:
all_atoms = {}
self.part.writemmpfile(inputFileName,
add_atomids_to_dict = all_atoms)
-
+
# Write a file that maps the ids of the atoms actually
# used for simulation to the atom ids of the complete
# structure stored in the MMP file above.
@@ -1039,7 +1039,7 @@ class SimRunner:
else:
electrostaticFlag = self.getElectrostaticPrefValueForMinimize()
-## electrostaticArg.append(str(electrostaticFlag))
+## electrostaticArg.append(str(electrostaticFlag))
electrostaticArg += str(electrostaticFlag) #bruce 070601 bugfix
if (self.useGromacs):
@@ -1068,9 +1068,9 @@ class SimRunner:
# THE TIMESTEP ARGUMENT IS MISSING ON PURPOSE.
# The timestep argument "-s + (movie.timestep)" is not supported for Alpha. #SIMOPT
- electrostaticArg = '--enable-electrostatic='
+ electrostaticArg = '--enable-electrostatic='
electrostaticFlag = self.getElectrostaticPrefValueForDynamics()
-## electrostaticArg.append(str(electrostaticFlag))
+## electrostaticArg.append(str(electrostaticFlag))
electrostaticArg += str(electrostaticFlag) #bruce 070601 bugfix
args = [program,
@@ -1129,7 +1129,7 @@ class SimRunner:
simopts.EnableElectrostatic = self.getElectrostaticPrefValueForDynamics()
if mflag:
self.set_minimize_threshhold_prefs(simopts)
- if self.cmd_type == 'Adjust' or self.cmd_type == 'Adjust Atoms':
+ if self.cmd_type == 'Adjust' or self.cmd_type == 'Adjust Atoms':
simopts.EnableElectrostatic = self.getElectrostaticPrefValueForAdjust()
simopts.NeighborSearching = 0
else:
@@ -1163,7 +1163,7 @@ class SimRunner:
if self.useGromacs and env.prefs[electrostaticsForDnaDuringAdjust_prefs_key]:
val = 1
else:
- val = 0
+ val = 0
return val
def getElectrostaticPrefValueForMinimize(self):
@@ -1173,14 +1173,14 @@ class SimRunner:
if self.useGromacs and env.prefs[electrostaticsForDnaDuringMinimize_prefs_key]:
val = 1
else:
- val = 0
+ val = 0
return val
def getNeighborSearchingPrefValue(self):
if env.prefs[neighborSearchingInGromacs_prefs_key]:
val = 1
else:
- val = 0
+ val = 0
return val
@@ -1191,7 +1191,7 @@ class SimRunner:
if env.prefs[electrostaticsForDnaDuringDynamics_prefs_key]:
val = 1
else:
- val = 0
+ val = 0
return val
def set_minimize_threshhold_prefs(self, simopts): #bruce 060628, revised 060705
diff --git a/cad/tests/nanotube.py b/cad/tests/nanotube.py
index 7c32fbe00..76452cf56 100755
--- a/cad/tests/nanotube.py
+++ b/cad/tests/nanotube.py
@@ -186,9 +186,9 @@ end molecular machine part Untitled
outf.close()
os.system("rasmol -xyz " + filename)
def test(self):
- mindist = None
- maxdist = None
- for a, b in self.bonds:
+ mindist = None
+ maxdist = None
+ for a, b in self.bonds:
a, b = self.atoms[a-1], self.atoms[b-1]
dist = ((a.x - b.x) ** 2 +
(a.y - b.y) ** 2 +
diff --git a/sim/src/experimental/units.py b/sim/src/experimental/units.py
index b1722e89a..e85f349f7 100755
--- a/sim/src/experimental/units.py
+++ b/sim/src/experimental/units.py
@@ -24,40 +24,40 @@ class UnitsMismatch(Exception):
class Quantity:
def __init__(self,stuff,units=None):
- if units == None:
- stuff = stuff.copy()
- c = stuff[coeff]
- del stuff[coeff]
- self.stuff = stuff
- else:
- c = 1. * stuff
- self.stuff = units.copy()
- for k in self.stuff.keys():
- if self.stuff[k] == 0:
- del self.stuff[k]
- self.stuff[coeff] = c
+ if units == None:
+ stuff = stuff.copy()
+ c = stuff[coeff]
+ del stuff[coeff]
+ self.stuff = stuff
+ else:
+ c = 1. * stuff
+ self.stuff = units.copy()
+ for k in self.stuff.keys():
+ if self.stuff[k] == 0:
+ del self.stuff[k]
+ self.stuff[coeff] = c
def __repr__(self):
- str = '<%g' % self.stuff[coeff]
- for k in self.stuff.keys():
- if k != coeff:
- str = str + ' ' + k
- if self.stuff[k] != 1:
- str = str + '^' + `self.stuff[k]`
- return str + '>'
+ str = '<%g' % self.stuff[coeff]
+ for k in self.stuff.keys():
+ if k != coeff:
+ str = str + ' ' + k
+ if self.stuff[k] != 1:
+ str = str + '^' + `self.stuff[k]`
+ return str + '>'
def __add__(self, other):
- self.testUnitsMatch(other)
- stuff = self.stuff.copy()
- stuff[coeff] += other.stuff[coeff]
- return Quantity(stuff)
+ self.testUnitsMatch(other)
+ stuff = self.stuff.copy()
+ stuff[coeff] += other.stuff[coeff]
+ return Quantity(stuff)
def __neg__(self):
- stuff = self.stuff.copy()
- stuff[coeff] = -stuff[coeff]
- return Quantity(stuff)
+ stuff = self.stuff.copy()
+ stuff[coeff] = -stuff[coeff]
+ return Quantity(stuff)
def __sub__(self, other):
return self + (-other)
def __cmp__(self, other):
- self.testUnitsMatch(other)
- return cmp(self.stuff[coeff], other.stuff[coeff])
+ self.testUnitsMatch(other)
+ return cmp(self.stuff[coeff], other.stuff[coeff])
def __mul__(self, other):
if type(other) in (types.IntType, types.FloatType, types.ComplexType):
stuff = self.stuff.copy()
@@ -97,12 +97,12 @@ class Quantity:
def unitsMatch(self, other):
if not isinstance(other, Quantity):
return False
- otherkeys = other.stuff.keys()
- for k in self.stuff.keys():
- if k not in otherkeys:
- return False
- if k != coeff and self.stuff[k] != other.stuff[k]:
- return False
+ otherkeys = other.stuff.keys()
+ for k in self.stuff.keys():
+ if k not in otherkeys:
+ return False
+ if k != coeff and self.stuff[k] != other.stuff[k]:
+ return False
return True
def testUnitsMatch(self, other):
if not self.unitsMatch(other):
generated by cgit v1.2.3 (git 2.39.1) at 2025-04-25 17:28:28 +0000