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extracting the substructure patterns of CircularFingerprint. #224
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Signed-off-by: Egon Willighagen <egon.willighagen@gmail.com>
Signed-off-by: Egon Willighagen <egon.willighagen@gmail.com>
…Here we simply store a visit map and only bend/stretch a bond if it's the first pair it's seen in. Signed-off-by: Egon Willighagen <egon.willighagen@gmail.com>
Signed-off-by: Egon Willighagen <egon.willighagen@gmail.com>
Signed-off-by: Egon Willighagen <egon.willighagen@gmail.com>
…epresentation, for example (H2O)8. Signed-off-by: Egon Willighagen <egon.willighagen@gmail.com>
…error handling. Signed-off-by: Egon Willighagen <egon.willighagen@gmail.com>
…imple adaption to existing parser.
…easily implement matching.
…s connected (even if they are ionic).
…t everything into one class with local access modifier
…ash wedges) as we also use it to assign wiggly bonds.
…;' in the atom label field.
…erwrite aromaticity information of the configured atom (see bug #1322)
…m type (closes #1322)
@@ -1258,6 +1262,14 @@ private int findBond(int a1, int a2) { | |||
if (atomAdj[a1][n] == a2) return bondAdj[a1][n]; | |||
return -1; | |||
} | |||
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// convecience: find value within array | |||
private int findArrayIndex(int value, int array[]){ |
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Can use Ints.indexOf()
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agree
I need to rebase this but looks like interesting functionality. Late here but the only things that stick out a little at the moment is the SMARTS generation in the fingerprint, okay for now but I would prefer to centralise this but obviously would need to write that/use AMBITs one. Also wondering how you get rings in a circular fingerprint? Shouldn't all the subgraphs be trees, will probably become clear once I look more in depth. |
ECFP6 ( :1 means count , it's not part of the SMARTS)
ECFP4 (no ring structures)
our code generates these fragments for benzene (default CLASS_ECFP6)
and for CLASS_ECFP4
|
Rebased - #231 |
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