Re-design of MCS calculation functions

[mojaie]

mcismol, mcesmol methods would be integreted to the maxcommonsubstruct function that returns MCSresult object

Main method

maxcommonsubstruct(mol1, mol2, matchtype=:edgeinduced; kwargs...) -> MCSresult

Arguments:

• mol1, mol2(UndirectedGraph): molecules to compare
• matchtype(Symbol): :nodeinduced or :edgeinduced (default=:edgeinduced).

Keyword arguments:

• connected(Bool): if true, apply connected MCS constraint (default=false).
• topological(Bool): if true, apply topological constraint (default=false).
• diameter(Int): distance cutoff for topological constraint.
• tolerance(Int): distance mismatch tolerance for topological constraint.
• timeout(Int): abort calculation and return suboptimal results if the execution time has reached the given value (default=60, in seconds).
• targetsize(Int): abort calculation and return suboptimal result so far if the given mcs size achieved.

Result type

MCSresult would have a mapping between these molecular graphs and information how the calculation finished (:done, :timeout, :targetreached, etc.)

• mcssize(MCSresult) returns matched node/edge count

Convenient methods

There would be some convenient methods. The compatibility with version <=0.9 is as follows

• mcismol(mol1, mol2) -> disconnectedmcis(mol1, mol2)
• mcesmol(mol1, mol2) -> disconnectedmces(mol1, mol2)
• mcismol(mol1, mol2, connected=true) -> connectedmcis(mol1, mol2)
• mcesmol(mol1, mol2, connected=true) -> connectedmces(mol1, mol2)
• mcismol(mol1, mol2, topological=true) -> tcmcis(mol1, mol2)
• mcesmol(mol1, mol2, topological=true) -> tcmces(mol1, mol2)

[mojaie]

Redesign MCS methods: 6d0606c Use BitSet to improve MCS performance: d0d1107 fix MCS tests: ad34479 MCS result container type: bada8e0

MCS methods now returns MaxCommonSubgraphResult that have node (or edge if MCES) mappings and status (:done, :timeout, etc.) as fields. Tutorials would be updated soon.