Changelog

This changelog contains only changes in SAMSON SDK that concern developers.

0.8.3

Fixed known issues in the installer.

0.8.2

Support for older Linux distributions - compatibility with GLIBC version 2.17 and higher. See Compatibility with older Linux distributions.

SAMSON Facade :

Add new functionality to manage jobs in the cloud (more information and tutorials will follow later):

• SAMSON::createJob
• SAMSON::getJob
• SAMSON::getJobs
• SAMSON::getJobStatus
• SAMSON::startJob
• SAMSON::pauseJob
• SAMSON::stopJob
• SAMSON::eraseJob

Improvements in the installer.

Bugfix in the SAMSON Element generator: update in the generated CMakeLists.txt.

Other small bugfixes.

0.8.1

No changes in the public API.

Updates and bugfixes in the SAMSON Element generator.

Bugfixes in SBPath : SBPath::remove and a bug with animation crash in some cases.

Bugfix in SBDTypePhysicalIAVector3 with operator * and operator /.

0.8.0

The 0.8.0 release brings major changes in SAMSON and SAMSON SDK. It also improves stability and fixes known issues.

Below are listed the changes in the public API.

SAMSON Facade :

The SAMSON::getActiveModel function has been renamed to SAMSON::getActiveStructuralModel.

SBFolder (SBLayer before) :

SBLayer has been changed to a more general SBFolder. An SBFolder object can contain almost any node types, including other folders. Any usage of an active layer (SAMSON::getActiveLayer) should be modified to e.g. an active document (SAMSON::getActiveDocument()). Any other usages of an SBLayer should be modified to use either SBFolder or an active document.

The SAMSON::importFromFile function now receives a preferredFolder instead of a preferredLayer.

SBFolder has parts of the SBLayer's functionality and some new functionality e.g.: get lists of nodes of different types (see SBFolder).

SBStructuralRoot :

SBStructuralRoot is now hidden and implicit. When creating a structural model (SBStructuralModel) it is not necessary anymore to add it to the SBStructuralRoot of a document, it will be done implicitly.

New/updated functions:

• SAMSON::setActiveStructuralModel;
• get nodes at a particular (x, y) position (SAMSON::getAtom, SAMSON::getBond, SAMSON::getNode);
• get nodes in a rectangle SAMSON::getNodes.

SBNode :

New/updated functionality:

• SBNode::getNextNode
• SBNode::getPreviousNode
• SBNode::getDocument
• SBNode::canAddChild
• SBNode::canAddChildType
• SBNode::isOneOf
• SBNode::isType
• SBNode::isModel
• SBNode::isStructuralModel
• SBNode::isVisualModel
• SBNode::isDynamicalModel
• SBNode::isInteractionModel
• SBNode::isPropertyModel
• SBNode::isSimulator
• SBNode::isStructuralParticle.

These changes also affect all classes derived from the SBNode class i.e.: SBFolder, SBStructuralModel, SBStructuralGroup, SBMolecule, SBResidue, SBBackbone, SBSideChain, SBStructuralParticle, SBAtom, etc.

SBNodeIndexer :

New functionality:

• SBNodeIndexer::getRootNodes.

SBDocument :

New functionality:

• SBDocument::getActiveCamera
• SBDocument::setActiveCamera
• SBDocument::getActiveStructuralModel
• SBDocument::setActiveStructuralModel
• SBDocument::createGroup
• SBDocument::groupSelection
• SBDocument::selectGroupNodes
• SBDocument::addGroupNodesToSelection
• SBDocument::removeGroupNodesFromSelection
• SBDocument::intersectGroupNodesWithSelection

SBCamera :

New/updated functionality:

• SBCamera::transform ;
• SBCamera::center - centers the camera around nodes in the provided nodeIndexer.

SBPath :

Major changes in the SBMStructuralModelPath class:

Setter and getter functions for position, velocity, and force data have been changed from 1d arrays to 2d arrays; other functions have been updated accordingly. The according functions have been renamed:

• setPositionArray to SBPath::setPositionData, getPositionArray to SBPath::getPositionData
• setVelocityArray to SBPath::setVelocityData, getVelocityArray to SBPath::getVelocityData
• setForceArray to SBPath::setForceData, getForceArray to SBPath::getForceData
• setEnergyArray to SBPath::setEnergyData, getEnergyArray to SBPath::getEnergyData
• setTimeArray to SBPath::setTimeData, getTimeArray to SBPath::getTimeData

New functionality:

• add, insert, and remove SBStructuralParticle : SBPath::addStructuralParticle, SBPath::insertStructuralParticle, SBPath::removeStructuralParticle ;
• add, insert, remove, and copy frames: SBPath::add, SBPath::insert, SBPath::remove, SBPath::copy ;
• create SBConformation from SBPath : SBPath::createConformation, SBPath::createConformations ;
• create SBStructuralModel from the SBPath :SBPath::createStructuralModels ;
• change the stride of the SBPath animation: SBPath::getStride, SBPath::setStride .

SBConformation :

Functions renaming:

• getNumberOfPositions to SBConformation::getNumberOfStructuralParticles ;
• getAtomIndexer to SBConformation::getStructuralParticleIndexer .

New/updated functionality:

• SBConformation::createStructuralModels - create structural models from this conformation;
• getter and setter functions for position data: SBConformation::getPositionData and SBConformation::setPositionData ;
• getter and setter functions for velocity data: SBConformation::getVelocityData and SBConformation::setVelocityData ;
• getter and setter functions for force data: SBConformation::getForceData and SBConformation::setForceData ;
• getter and setter functions for energy: SBConformation::getEnergy and SBConformation::setEnergy ;
• getter and setter functions for time: SBConformation::getTime and SBConformation::setTime ;
• getter and setter functions for position of a structural particle: SBConformation::getPosition and SBConformation::setPosition ;
• getter and setter functions for velocity of a structural particle: SBConformation::getVelocity and SBConformation::setVelocity ;
• getter and setter functions for force of a structural particle: SBConformation::getForce and SBConformation::setForce .

SBResidue :

New functionality:

• SBResidue::setSecondaryStructureType - allows you to set the secondary structure type.

The SBDType Library :

Added more checks for operations with dimensionless quantities.