Molecules
Source
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Target
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Parameters
Atom modificationAllow atom type changes
Cap ring with carbonClose open rings with C
Cap ring with hydrogenClose open rings with H
No backward searchForward-only intermediate search
Use MCS seedSeed BFS with MCS substructure
IonizeFilter by formal charge match
Max intermediatesUpper limit on generated intermediates
Max optimal path lengthMax hops in optimal path
Rough score thresholdCutoff for rough search pass
0.50
Min score thresholdMinimum edge score to include
0.20
Cycle link thresholdScore below this triggers cycle links
0.60
Optimal path modeOutput only optimal path, no full map
Squared sum scoringPenalize low-score edges quadratically
Result
Source
Target
Intermediate
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Input
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Multi-molecule SDF for perturbation map generation
Molecules (0)
Parameters
Similarity thresholdMin score for edges in the network
0.60
Max intermediates-1 = unlimited
Max degreeMax edges per node
Max dist from actives
Max path length
Allow tree
Radial layout mode
IonizeFilter by formal charge match
Max optimal path length
Rough score threshold
0.50
Min score threshold
0.20
Optimal path mode
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Map —
Active
Intermediate
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