- <init>
Constructor for the AtomPlacer object
- setMolecule
Sets the molecule the AtomPlacer currently works with
- placeLinearChain
Places the atoms in a linear chain.Expects the first atom to be placed and
places the next atom acco
- distributePartners
Distribute the bonded atoms (neighbours) of an atom such that they fill the
remaining space around a
- getInitialLongestChain
Search an aliphatic molecule for the longest chain. This is the method to be
used if there are no ri
- getLongestUnplacedChain
Search a molecule for the longest unplaced, aliphatic chain in it. If an
aliphatic chain encounters
- getNextBondVector
Returns the next bond vector needed for drawing an extended linear chain of
atoms. It assumes an ang
- populatePolygonCorners
Populates the corners of a polygon with atoms. Used to place atoms in a
geometrically regular way ar
- breadthFirstSearch
Performs a breadthFirstSearch in an AtomContainer starting with a particular
sphere, which usually c
- copyPlaced
Copy placed atoms/bonds from one container to another.
- doAngleSnap
- getDegreeSum
Sums up the degrees of atoms in an atomcontainer