Serialization/Unserialization issues



  • 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.



  • 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 MyAtom class or you use the SBAtom class? 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!



  • 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



  • @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.

    1_1553508805909_test_samx_before.PNG 0_1553508805908_test_samx_after.PNG

    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?



  • Could you please add developer [(at)] oneangstrom.com as a collaborator and send me a samx so I can test here?



  • 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.



  • You can also check an updated Developer guide: Serialization.



  • @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!



  • 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!


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