Serialization/Unserialization issues
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Hi Stephane,
Sorry for the late reply, my laptop broke and I couldn't test it.
The problem that I'm having is that when calling the parent functions the unserialize function crashes:
void MyStructuralModel::serialize(SBCSerializer * serializer, const SBNodeIndexer & nodeIndexer, const SBVersionNumber & sdkVersionNumber, const SBVersionNumber & classVersionNumber) { SBStructuralModel::serialize(serializer, nodeIndexer, sdkVersionNumber, classVersionNumber); serializer->writeIntElement("one_property", number1); serializer->writeIntElement("another_property", number2); }and:
void MyStructuralModel::unserialize(SBCSerializer * serializer, const SBNodeIndexer & nodeIndexer, const SBVersionNumber & sdkVersionNumber, const SBVersionNumber & classVersionNumber) { SBStructuralModel::unserialize(serializer, nodeIndexer, sdkVersionNumber, classVersionNumber); int p1 = serializer->readIntElement(); int p2 = serializer->readIntElement(); }After saving, I get the crash at
int p1 = serializer->readIntElement();as an overflow, like the serializer didn't move into the next value.I can avoid this crash if I don't call the parent functions, but then if I save more than one of my models, it will crash (again same error, probably because I'm reading something else from the .samx file)
I think this might be because I didn't implement serialize and unserialize functions for all elements of my model, I just re-used the code that we had for our internal saving (we are using json). I will try to set properly all serialize/unserialize functions.
Best regards,
Elisa
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Sorry for the double posting,
I have now done very basic serialization in my model, basically every element calls the parent function serialize or unserialize methods. I get all the nodes back, except for the atoms belonging to classes inheriting from SBBackbone and SBSideChain.
void MyBackbone::serialize(SBCSerializer * serializer, const SBNodeIndexer & nodeIndexer, const SBVersionNumber & sdkVersionNumber, const SBVersionNumber & classVersionNumber) const { SBBackbone::serialize(serializer, nodeIndexer, sdkVersionNumber, classVersionNumber); } void MyBackbone::unserialize(SBCSerializer * serializer, const SBNodeIndexer & nodeIndexer, const SBVersionNumber & sdkVersionNumber, const SBVersionNumber & classVersionNumber) { SBBackbone::unserialize(serializer, nodeIndexer, sdkVersionNumber, classVersionNumber); SB_FOR(SBNode* n, *getChildren()) { SBPointer<MyAtom> at = static_cast<MyAtom*>(n); //at->create(); } }I can check in this way that the atoms are correctly added as children to MyBackbone, but they are not created in the Datagraph. I don't have this problem with classes deriving from SBStructuralGroup, where atoms are correctly created in the data graph.
Thanks and best regards!
Elisa
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Hi Elisa,
if this is not confidential, could you please post the contents of the simplest .samx file that creates an issue with a backbone?
Stephane
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The file is quite long, so I will post the relevant parts:
<SAMSON> <majorVersionNumber> 0 </majorVersionNumber> <minorVersionNumber> 7 </minorVersionNumber> <patchVersionNumber> 0 </patchVersionNumber> <numberOfNodeTypes> 15 </numberOfNodeTypes> <nodeTypes> <nodeType> <nodeTypeIndex> 0 </nodeTypeIndex> <className> MySidechain </className> <elementUUID> DDA2A078-1AB6-96BA-0D14-EE1717632D7A </elementUUID> <sdkVersionNumber> 0.7.0 </sdkVersionNumber> <classVersionNumber> 1.0.0 </classVersionNumber> </nodeType> <nodeType> <nodeTypeIndex> 1 </nodeTypeIndex> <className> MyBackbone </className> <elementUUID> DDA2A078-1AB6-96BA-0D14-EE1717632D7A </elementUUID> <sdkVersionNumber> 0.7.0 </sdkVersionNumber> <classVersionNumber> 1.0.0 </classVersionNumber> </nodeType> ... <nodeType> <nodeTypeIndex> 4 </nodeTypeIndex> <className> MyStructuralGroup </className> <elementUUID> DDA2A078-1AB6-96BA-0D14-EE1717632D7A </elementUUID> <sdkVersionNumber> 0.7.0 </sdkVersionNumber> <classVersionNumber> 1.0.0 </classVersionNumber> </nodeType> ... <nodeType> <nodeTypeIndex> 11 </nodeTypeIndex> <className> SBMStructuralModelNodeRoot </className> <elementUUID> 5A3CE002-9368-1EAF-7DBA-66567958AB1F </elementUUID> <sdkVersionNumber> 0.7.0 </sdkVersionNumber> <classVersionNumber> 0.7.0 </classVersionNumber> </nodeType> <nodeType> <nodeTypeIndex> 12 </nodeTypeIndex> <className> SBDDocumentCamera </className> <elementUUID> 131D70CF-3B19-61A8-B67C-BBDA93776B38 </elementUUID> <sdkVersionNumber> 0.7.0 </sdkVersionNumber> <classVersionNumber> 0.7.0 </classVersionNumber> </nodeType> <nodeType> <nodeTypeIndex> 13 </nodeTypeIndex> <className> SBDDocumentLayer </className> <elementUUID> 131D70CF-3B19-61A8-B67C-BBDA93776B38 </elementUUID> <sdkVersionNumber> 0.7.0 </sdkVersionNumber> <classVersionNumber> 0.7.0 </classVersionNumber> </nodeType> <nodeType> <nodeTypeIndex> 14 </nodeTypeIndex> <className> SBDDocument </className> <elementUUID> 131D70CF-3B19-61A8-B67C-BBDA93776B38 </elementUUID> <sdkVersionNumber> 0.7.0 </sdkVersionNumber> <classVersionNumber> 0.7.0 </classVersionNumber> </nodeType> </nodeTypes> ... <nodeContents> <node> <index> 0 </index> <expandedFlag> 1 </expandedFlag> <visibilityFlag> 1 </visibilityFlag> <hasMaterial> 0 </hasMaterial> <numberOfCameras> 1 </numberOfCameras> <nodeIndex> 1 </nodeIndex> <numberOfLayers> 1 </numberOfLayers> <nodeIndex> 2 </nodeIndex> <numberOfGroups> 0 </numberOfGroups> <numberOfStoredConformations> 0 </numberOfStoredConformations> <numberOfStoredPaths> 0 </numberOfStoredPaths> <activeCameraIndex> 1 </activeCameraIndex> <activeLayerIndex> 2 </activeLayerIndex> </node> <node> <index> 1 </index> <expandedFlag> 0 </expandedFlag> <visibilityFlag> 1 </visibilityFlag> <hasMaterial> 0 </hasMaterial> <name> Camera 1 </name> <eyePosition> <v[0]> -49817.3 </v[0]> <v[1]> -37448.3 </v[1]> <v[2]> -27528.1 </v[2]> </eyePosition> <targetPosition> <v[0]> -2.47394 </v[0]> <v[1]> -0.57391 </v[1]> <v[2]> -5.94904 </v[2]> </targetPosition> <upVector> <v[0]> -0.569802 </v[0]> <v[1]> 0.166545 </v[1]> <v[2]> 0.804729 </v[2]> </upVector> <nearPlane> 100 </nearPlane> <farPlane> 2e+06 </farPlane> <aspectRatio> 1.41675 </aspectRatio> <fieldOfViewAngleY> 19 </fieldOfViewAngleY> <inertiaFlag> 0 </inertiaFlag> </node> <node> <index> 2 </index> <expandedFlag> 1 </expandedFlag> <visibilityFlag> 1 </visibilityFlag> <hasMaterial> 0 </hasMaterial> <name> Layer 1 </name> <numberOfModels> 1 </numberOfModels> <nodeIndex> 3 </nodeIndex> <numberOfSimulators> 0 </numberOfSimulators> <numberOfControllers> 0 </numberOfControllers> <numberOfLabels> 0 </numberOfLabels> <hasActiveModel> 0 </hasActiveModel> </node> <node> <index> 3 </index> <expandedFlag> 0 </expandedFlag> <visibilityFlag> 1 </visibilityFlag> <hasMaterial> 0 </hasMaterial> <name> 01_tetrahedron </name> <rootIndex> 4 </rootIndex> <propertyFlags> 0 </propertyFlags> <backboneNeighborGridInitialized> 0 </backboneNeighborGridInitialized> </node> <node> <index> 4 </index> <expandedFlag> 0 </expandedFlag> <visibilityFlag> 1 </visibilityFlag> <hasMaterial> 0 </hasMaterial> <mobilityFlag> 1 </mobilityFlag> <name> Nodes </name> <numberOfChildren> 26 </numberOfChildren> <nodeIndex> 5 </nodeIndex> <nodeIndex> 137 </nodeIndex> <nodeIndex> 269 </nodeIndex> <nodeIndex> 401 </nodeIndex> <nodeIndex> 533 </nodeIndex> <nodeIndex> 665 </nodeIndex> <nodeIndex> 797 </nodeIndex> <nodeIndex> 929 </nodeIndex> <nodeIndex> 1061 </nodeIndex> <nodeIndex> 1193 </nodeIndex> <nodeIndex> 1325 </nodeIndex> <nodeIndex> 1457 </nodeIndex> <nodeIndex> 1589 </nodeIndex> <nodeIndex> 4110 </nodeIndex> <nodeIndex> 4321 </nodeIndex> <nodeIndex> 4427 </nodeIndex> <nodeIndex> 4533 </nodeIndex> <nodeIndex> 4639 </nodeIndex> <nodeIndex> 4745 </nodeIndex> <nodeIndex> 4956 </nodeIndex> <nodeIndex> 5062 </nodeIndex> <nodeIndex> 5168 </nodeIndex> <nodeIndex> 5379 </nodeIndex> <nodeIndex> 5770 </nodeIndex> <nodeIndex> 6161 </nodeIndex> <nodeIndex> 6552 </nodeIndex> <propertyFlags> 0 </propertyFlags> </node> ... <node> <index> 6 </index> <expandedFlag> 0 </expandedFlag> <visibilityFlag> 1 </visibilityFlag> <hasMaterial> 0 </hasMaterial> <mobilityFlag> 1 </mobilityFlag> <name> My Structural Group </name> <numberOfChildren> 2 </numberOfChildren> <nodeIndex> 7 </nodeIndex> <nodeIndex> 8 </nodeIndex> <propertyFlags> 0 </propertyFlags> </node> ... <node> <index> 8 </index> <expandedFlag> 0 </expandedFlag> <visibilityFlag> 0 </visibilityFlag> <hasMaterial> 0 </hasMaterial> <mobilityFlag> 1 </mobilityFlag> <position> <v[0]> -1485.23 </v[0]> <v[1]> 172.5 </v[1]> <v[2]> 9081.48 </v[2]> </position> <element> 109 </element> <propertyFlags> 0 </propertyFlags> </node> ... <node> <index> 6552 </index> <expandedFlag> 0 </expandedFlag> <visibilityFlag> 1 </visibilityFlag> <hasMaterial> 0 </hasMaterial> <mobilityFlag> 1 </mobilityFlag> <name> Chain </name> <numberOfChildren> 78 </numberOfChildren> <nodeIndex> 6553 </nodeIndex> ... <propertyFlags> 0 </propertyFlags> </node> <node> <index> 6553 </index> <expandedFlag> 0 </expandedFlag> <visibilityFlag> 1 </visibilityFlag> <hasMaterial> 0 </hasMaterial> <mobilityFlag> 1 </mobilityFlag> <name> Nucleotide </name> <numberOfChildren> 2 </numberOfChildren> <nodeIndex> 6554 </nodeIndex> <nodeIndex> 6556 </nodeIndex> <propertyFlags> 0 </propertyFlags> <residueType> 34 </residueType> <residueTypeString> </residueTypeString> </node> <node> <index> 6554 </index> <expandedFlag> 0 </expandedFlag> <visibilityFlag> 1 </visibilityFlag> <hasMaterial> 0 </hasMaterial> <mobilityFlag> 1 </mobilityFlag> <name> Backbone </name> <numberOfChildren> 1 </numberOfChildren> <nodeIndex> 6555 </nodeIndex> <propertyFlags> 0 </propertyFlags> </node> <node> <index> 6555 </index> <expandedFlag> 0 </expandedFlag> <visibilityFlag> 0 </visibilityFlag> <hasMaterial> 0 </hasMaterial> <mobilityFlag> 1 </mobilityFlag> <position> <v[0]> 5569.81 </v[0]> <v[1]> 2913.26 </v[1]> <v[2]> -3182.39 </v[2]> </position> <element> 99 </element> <propertyFlags> 0 </propertyFlags> </node> <node> <index> 6556 </index> <expandedFlag> 0 </expandedFlag> <visibilityFlag> 1 </visibilityFlag> <hasMaterial> 0 </hasMaterial> <mobilityFlag> 1 </mobilityFlag> <name>Sidechain </name> <numberOfChildren> 1 </numberOfChildren> <nodeIndex> 6557 </nodeIndex> <propertyFlags> 0 </propertyFlags> </node> <node> <index> 6557 </index> <expandedFlag> 0 </expandedFlag> <visibilityFlag> 0 </visibilityFlag> <hasMaterial> 0 </hasMaterial> <mobilityFlag> 1 </mobilityFlag> <position> <v[0]> 5667.77 </v[0]> <v[1]> 2915.8 </v[1]> <v[2]> -2721.34 </v[2]> </position> <element> 100 </element> <propertyFlags> 0 </propertyFlags> </node> ... </nodeContents> </SAMSON>Everything is in the data graph except for the atoms belonging to the backbone and sidechain.
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I might need more information from the file but a quick check indicates that the visibility flag of the atoms is set to false:
<visibilityFlag> 0 </visibilityFlag>Is this normal? Also, do you have a
MyAtomclass or you use theSBAtomclass? There are also Einsteinium and Meitnerium atoms? -
It is normal, we hide them on purpose.
MyAtom class inherits from SBAtom, yes. I will try to produce a very small example so I can paste the entire file.
Edit: This is a small full sample
<SAMSON> <majorVersionNumber> 0 </majorVersionNumber> <minorVersionNumber> 7 </minorVersionNumber> <patchVersionNumber> 0 </patchVersionNumber> <numberOfNodeTypes> 13 </numberOfNodeTypes> <nodeTypes> <nodeType> <nodeTypeIndex> 0 </nodeTypeIndex> <className> MySidechain </className> <elementUUID> DDA2A078-1AB6-96BA-0D14-EE1717632D7A </elementUUID> <sdkVersionNumber> 0.7.0 </sdkVersionNumber> <classVersionNumber> 1.0.0 </classVersionNumber> </nodeType> <nodeType> <nodeTypeIndex> 1 </nodeTypeIndex> <className> MyBackbone </className> <elementUUID> DDA2A078-1AB6-96BA-0D14-EE1717632D7A </elementUUID> <sdkVersionNumber> 0.7.0 </sdkVersionNumber> <classVersionNumber> 1.0.0 </classVersionNumber> </nodeType> <nodeType> <nodeTypeIndex> 2 </nodeTypeIndex> <className> MyChain </className> <elementUUID> DDA2A078-1AB6-96BA-0D14-EE1717632D7A </elementUUID> <sdkVersionNumber> 0.7.0 </sdkVersionNumber> <classVersionNumber> 1.0.0 </classVersionNumber> </nodeType> <nodeType> <nodeTypeIndex> 3 </nodeTypeIndex> <className> MyStructuralModel </className> <elementUUID> DDA2A078-1AB6-96BA-0D14-EE1717632D7A </elementUUID> <sdkVersionNumber> 0.7.0 </sdkVersionNumber> <classVersionNumber> 1.0.0 </classVersionNumber> </nodeType> <nodeType> <nodeTypeIndex> 4 </nodeTypeIndex> <className> MyStructuralGroup </className> <elementUUID> DDA2A078-1AB6-96BA-0D14-EE1717632D7A </elementUUID> <sdkVersionNumber> 0.7.0 </sdkVersionNumber> <classVersionNumber> 1.0.0 </classVersionNumber> </nodeType> <nodeType> <nodeTypeIndex> 5 </nodeTypeIndex> <className> MyResidue </className> <elementUUID> DDA2A078-1AB6-96BA-0D14-EE1717632D7A </elementUUID> <sdkVersionNumber> 0.7.0 </sdkVersionNumber> <classVersionNumber> 1.0.0 </classVersionNumber> </nodeType> <nodeType> <nodeTypeIndex> 6 </nodeTypeIndex> <className> MyAtom </className> <elementUUID> DDA2A078-1AB6-96BA-0D14-EE1717632D7A </elementUUID> <sdkVersionNumber> 0.7.0 </sdkVersionNumber> <classVersionNumber> 1.0.0 </classVersionNumber> </nodeType> <nodeType> <nodeTypeIndex> 7 </nodeTypeIndex> <className> MyStructuralGroup2 </className> <elementUUID> DDA2A078-1AB6-96BA-0D14-EE1717632D7A </elementUUID> <sdkVersionNumber> 0.7.0 </sdkVersionNumber> <classVersionNumber> 1.0.0 </classVersionNumber> </nodeType> <nodeType> <nodeTypeIndex> 8 </nodeTypeIndex> <className> MyStructuralGroup3 </className> <elementUUID> DDA2A078-1AB6-96BA-0D14-EE1717632D7A </elementUUID> <sdkVersionNumber> 0.7.0 </sdkVersionNumber> <classVersionNumber> 1.0.0 </classVersionNumber> </nodeType> <nodeType> <nodeTypeIndex> 9 </nodeTypeIndex> <className> SBMStructuralModelNodeRoot </className> <elementUUID> 5A3CE002-9368-1EAF-7DBA-66567958AB1F </elementUUID> <sdkVersionNumber> 0.7.0 </sdkVersionNumber> <classVersionNumber> 0.7.0 </classVersionNumber> </nodeType> <nodeType> <nodeTypeIndex> 10 </nodeTypeIndex> <className> SBDDocumentCamera </className> <elementUUID> 131D70CF-3B19-61A8-B67C-BBDA93776B38 </elementUUID> <sdkVersionNumber> 0.7.0 </sdkVersionNumber> <classVersionNumber> 0.7.0 </classVersionNumber> </nodeType> <nodeType> <nodeTypeIndex> 11 </nodeTypeIndex> <className> SBDDocumentLayer </className> <elementUUID> 131D70CF-3B19-61A8-B67C-BBDA93776B38 </elementUUID> <sdkVersionNumber> 0.7.0 </sdkVersionNumber> <classVersionNumber> 0.7.0 </classVersionNumber> </nodeType> <nodeType> <nodeTypeIndex> 12 </nodeTypeIndex> <className> SBDDocument </className> <elementUUID> 131D70CF-3B19-61A8-B67C-BBDA93776B38 </elementUUID> <sdkVersionNumber> 0.7.0 </sdkVersionNumber> <classVersionNumber> 0.7.0 </classVersionNumber> </nodeType> </nodeTypes> <numberOfNodes> 21 </numberOfNodes> <nodes> <nodeTypeIndex> 12 </nodeTypeIndex> <nodeTypeIndex> 10 </nodeTypeIndex> <nodeTypeIndex> 11 </nodeTypeIndex> <nodeTypeIndex> 3 </nodeTypeIndex> <nodeTypeIndex> 9 </nodeTypeIndex> <nodeTypeIndex> 7 </nodeTypeIndex> <nodeTypeIndex> 4 </nodeTypeIndex> <nodeTypeIndex> 8 </nodeTypeIndex> <nodeTypeIndex> 6 </nodeTypeIndex> <nodeTypeIndex> 2 </nodeTypeIndex> <nodeTypeIndex> 5 </nodeTypeIndex> <nodeTypeIndex> 1 </nodeTypeIndex> <nodeTypeIndex> 6 </nodeTypeIndex> <nodeTypeIndex> 0 </nodeTypeIndex> <nodeTypeIndex> 6 </nodeTypeIndex> <nodeTypeIndex> 2 </nodeTypeIndex> <nodeTypeIndex> 5 </nodeTypeIndex> <nodeTypeIndex> 1 </nodeTypeIndex> <nodeTypeIndex> 6 </nodeTypeIndex> <nodeTypeIndex> 0 </nodeTypeIndex> <nodeTypeIndex> 6 </nodeTypeIndex> </nodes> <nodeContents> <node> <index> 0 </index> <expandedFlag> 1 </expandedFlag> <visibilityFlag> 1 </visibilityFlag> <hasMaterial> 0 </hasMaterial> <numberOfCameras> 1 </numberOfCameras> <nodeIndex> 1 </nodeIndex> <numberOfLayers> 1 </numberOfLayers> <nodeIndex> 2 </nodeIndex> <numberOfGroups> 0 </numberOfGroups> <numberOfStoredConformations> 0 </numberOfStoredConformations> <numberOfStoredPaths> 0 </numberOfStoredPaths> <activeCameraIndex> 1 </activeCameraIndex> <activeLayerIndex> 2 </activeLayerIndex> </node> <node> <index> 1 </index> <expandedFlag> 0 </expandedFlag> <visibilityFlag> 1 </visibilityFlag> <hasMaterial> 0 </hasMaterial> <name> Camera 1 </name> <eyePosition> <v[0]> 0 </v[0]> <v[1]> 0 </v[1]> <v[2]> 10000 </v[2]> </eyePosition> <targetPosition> <v[0]> 0 </v[0]> <v[1]> 0 </v[1]> <v[2]> 0 </v[2]> </targetPosition> <upVector> <v[0]> 0 </v[0]> <v[1]> 1 </v[1]> <v[2]> 0 </v[2]> </upVector> <nearPlane> 100 </nearPlane> <farPlane> 2e+06 </farPlane> <aspectRatio> 1.41675 </aspectRatio> <fieldOfViewAngleY> 19 </fieldOfViewAngleY> <inertiaFlag> 0 </inertiaFlag> </node> <node> <index> 2 </index> <expandedFlag> 1 </expandedFlag> <visibilityFlag> 1 </visibilityFlag> <hasMaterial> 0 </hasMaterial> <name> Layer 1 </name> <numberOfModels> 1 </numberOfModels> <nodeIndex> 3 </nodeIndex> <numberOfSimulators> 0 </numberOfSimulators> <numberOfControllers> 0 </numberOfControllers> <numberOfLabels> 0 </numberOfLabels> <hasActiveModel> 0 </hasActiveModel> </node> <node> <index> 3 </index> <expandedFlag> 1 </expandedFlag> <visibilityFlag> 1 </visibilityFlag> <hasMaterial> 0 </hasMaterial> <name> Structural model </name> <rootIndex> 4 </rootIndex> <propertyFlags> 0 </propertyFlags> <backboneNeighborGridInitialized> 0 </backboneNeighborGridInitialized> </node> <node> <index> 4 </index> <expandedFlag> 1 </expandedFlag> <visibilityFlag> 1 </visibilityFlag> <hasMaterial> 0 </hasMaterial> <mobilityFlag> 1 </mobilityFlag> <name> Nodes </name> <numberOfChildren> 3 </numberOfChildren> <nodeIndex> 5 </nodeIndex> <nodeIndex> 9 </nodeIndex> <nodeIndex> 15 </nodeIndex> <propertyFlags> 0 </propertyFlags> </node> <node> <index> 5 </index> <expandedFlag> 0 </expandedFlag> <visibilityFlag> 1 </visibilityFlag> <hasMaterial> 0 </hasMaterial> <mobilityFlag> 1 </mobilityFlag> <name> Double Strand 1 </name> <numberOfChildren> 1 </numberOfChildren> <nodeIndex> 6 </nodeIndex> <propertyFlags> 0 </propertyFlags> </node> <node> <index> 6 </index> <expandedFlag> 0 </expandedFlag> <visibilityFlag> 1 </visibilityFlag> <hasMaterial> 0 </hasMaterial> <mobilityFlag> 1 </mobilityFlag> <name> Base Segment 4099 </name> <numberOfChildren> 2 </numberOfChildren> <nodeIndex> 7 </nodeIndex> <nodeIndex> 8 </nodeIndex> <propertyFlags> 0 </propertyFlags> </node> <node> <index> 7 </index> <expandedFlag> 0 </expandedFlag> <visibilityFlag> 1 </visibilityFlag> <hasMaterial> 0 </hasMaterial> <mobilityFlag> 1 </mobilityFlag> <name> Base Pair 4100 </name> <numberOfChildren> 0 </numberOfChildren> <propertyFlags> 0 </propertyFlags> </node> <node> <index> 8 </index> <expandedFlag> 0 </expandedFlag> <visibilityFlag> 0 </visibilityFlag> <hasMaterial> 0 </hasMaterial> <mobilityFlag> 1 </mobilityFlag> <position> <v[0]> -877.886 </v[0]> <v[1]> 516.92 </v[1]> <v[2]> 0.0153761 </v[2]> </position> <element> 109 </element> <propertyFlags> 0 </propertyFlags> </node> <node> <index> 9 </index> <expandedFlag> 0 </expandedFlag> <visibilityFlag> 1 </visibilityFlag> <hasMaterial> 0 </hasMaterial> <mobilityFlag> 1 </mobilityFlag> <name> Single Strand 1 </name> <numberOfChildren> 1 </numberOfChildren> <nodeIndex> 10 </nodeIndex> <propertyFlags> 0 </propertyFlags> </node> <node> <index> 10 </index> <expandedFlag> 0 </expandedFlag> <visibilityFlag> 1 </visibilityFlag> <hasMaterial> 0 </hasMaterial> <mobilityFlag> 1 </mobilityFlag> <name> N4102 </name> <numberOfChildren> 2 </numberOfChildren> <nodeIndex> 11 </nodeIndex> <nodeIndex> 13 </nodeIndex> <propertyFlags> 0 </propertyFlags> <residueType> 36 </residueType> <residueTypeString> </residueTypeString> </node> <node> <index> 11 </index> <expandedFlag> 0 </expandedFlag> <visibilityFlag> 1 </visibilityFlag> <hasMaterial> 0 </hasMaterial> <mobilityFlag> 1 </mobilityFlag> <name> N4102 Backbone </name> <numberOfChildren> 1 </numberOfChildren> <nodeIndex> 12 </nodeIndex> <propertyFlags> 0 </propertyFlags> </node> <node> <index> 12 </index> <expandedFlag> 0 </expandedFlag> <visibilityFlag> 0 </visibilityFlag> <hasMaterial> 0 </hasMaterial> <mobilityFlag> 1 </mobilityFlag> <position> <v[0]> -970.453 </v[0]> <v[1]> -85.8914 </v[1]> <v[2]> 538.434 </v[2]> </position> <element> 99 </element> <propertyFlags> 0 </propertyFlags> </node> <node> <index> 13 </index> <expandedFlag> 0 </expandedFlag> <visibilityFlag> 1 </visibilityFlag> <hasMaterial> 0 </hasMaterial> <mobilityFlag> 1 </mobilityFlag> <name> N4102 Sidechain </name> <numberOfChildren> 1 </numberOfChildren> <nodeIndex> 14 </nodeIndex> <propertyFlags> 0 </propertyFlags> </node> <node> <index> 14 </index> <expandedFlag> 0 </expandedFlag> <visibilityFlag> 0 </visibilityFlag> <hasMaterial> 0 </hasMaterial> <mobilityFlag> 1 </mobilityFlag> <position> <v[0]> -880.731 </v[0]> <v[1]> 352.262 </v[1]> <v[2]> 220.392 </v[2]> </position> <element> 100 </element> <propertyFlags> 0 </propertyFlags> </node> <node> <index> 15 </index> <expandedFlag> 0 </expandedFlag> <visibilityFlag> 1 </visibilityFlag> <hasMaterial> 0 </hasMaterial> <mobilityFlag> 1 </mobilityFlag> <name> Single Strand 2 </name> <numberOfChildren> 1 </numberOfChildren> <nodeIndex> 16 </nodeIndex> <propertyFlags> 0 </propertyFlags> </node> <node> <index> 16 </index> <expandedFlag> 0 </expandedFlag> <visibilityFlag> 1 </visibilityFlag> <hasMaterial> 0 </hasMaterial> <mobilityFlag> 1 </mobilityFlag> <name> N4108 </name> <numberOfChildren> 2 </numberOfChildren> <nodeIndex> 17 </nodeIndex> <nodeIndex> 19 </nodeIndex> <propertyFlags> 0 </propertyFlags> <residueType> 36 </residueType> <residueTypeString> </residueTypeString> </node> <node> <index> 17 </index> <expandedFlag> 0 </expandedFlag> <visibilityFlag> 1 </visibilityFlag> <hasMaterial> 0 </hasMaterial> <mobilityFlag> 1 </mobilityFlag> <name> N4108 Backbone </name> <numberOfChildren> 1 </numberOfChildren> <nodeIndex> 18 </nodeIndex> <propertyFlags> 0 </propertyFlags> </node> <node> <index> 18 </index> <expandedFlag> 0 </expandedFlag> <visibilityFlag> 0 </visibilityFlag> <hasMaterial> 0 </hasMaterial> <mobilityFlag> 1 </mobilityFlag> <position> <v[0]> -788.488 </v[0]> <v[1]> 1018.95 </v[1]> <v[2]> -570.406 </v[2]> </position> <element> 99 </element> <propertyFlags> 0 </propertyFlags> </node> <node> <index> 19 </index> <expandedFlag> 0 </expandedFlag> <visibilityFlag> 1 </visibilityFlag> <hasMaterial> 0 </hasMaterial> <mobilityFlag> 1 </mobilityFlag> <name> N4108 Sidechain </name> <numberOfChildren> 1 </numberOfChildren> <nodeIndex> 20 </nodeIndex> <propertyFlags> 0 </propertyFlags> </node> <node> <index> 20 </index> <expandedFlag> 0 </expandedFlag> <visibilityFlag> 0 </visibilityFlag> <hasMaterial> 0 </hasMaterial> <mobilityFlag> 1 </mobilityFlag> <position> <v[0]> -874.781 </v[0]> <v[1]> 804.363 </v[1]> <v[2]> -159.697 </v[2]> </position> <element> 100 </element> <propertyFlags> 0 </propertyFlags> </node> </nodeContents> </SAMSON>The atoms below the Sidechain and Backbone are not created when reading the same, but the atom below the structural group is.
Thanks!
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This looks perfect. Could you please try the following things:
- load the short file above, and send me the log (Edit / Show log / Submit).
- in the document view, select a MyAtom in a MyBackbone, and press Ctrl+C, Ctrl+V. Do you see a copy of the MyAtom appear in the document view? Serialization is also used for copy/paste, so issues should appear at that moment too.
Thanks,
Stephane
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@stephane-redon
The log doesn't seem to show anything, I submitted it.
In the document view of the original system you can see the atoms in the document view. I attach two pictures showing the system I save and the system after loading the samx file.
Thanks!
PS: The element is now on the samson store, we are still debugging a lot but I could give you access if you want.
PS2: Copy and paste seems to work fine.
And another edit: I assumed the error would be on the atom, but I tried copy and pasting the Backbone or Sidechain and this time it didn't work. Could this be the problem?
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Could you please add developer [(at)] oneangstrom.com as a collaborator and send me a samx so I can test here?
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I did some checks in the code like:
void MyBackbone::unserialize(SBCSerializer * serializer, const SBNodeIndexer & nodeIndexer, const SBVersionNumber & sdkVersionNumber, const SBVersionNumber & classVersionNumber)
{
SBBackbone::unserialize(serializer, nodeIndexer, sdkVersionNumber, classVersionNumber);auto test = getNumberOfAtoms();
int here = 1;
}And the number of atoms there looks correct. I tried also with more than one atom, and all the number is still fine, but they are not produced in the data graph. I will try to create a mock project to test this, just in case.
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You can also check an updated Developer guide: Serialization.
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@Elisa could you please pack the debug version as well in your SAMSON Element ? (before using the packager, you would need to build both the debug and release version). Thanks!
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Hi,
I think I found the problem. Some initialization functions in the constructor of my class were overriding the unserialization. I tried to make a quick fix but when I do static casts in the unserialize function, SAMSON is crashing, so I will modify my constructor and check, it will take a bit though.
Thanks for your help!
