SMILESes for CDK Depict

COP(=O)([O-])OCC P not seen as chiral
[C@](COP(=O)([O-])OCC[N+](C)(C)C)([H])(O)COC=O P seen as chiral
[C@](COP(=O)([O-])OCC[N+](C)(C)C)([H])(OC=O)COC=O P seen as chiral
[C@](COP(=O)([O-])OCC[N+](C)(C)C)([H])(OC(CCCCCCCCCCCCCCCCC)=O)COC(CCCCCCCCCCCCCCCCC)=O P seen as chiral

unittest.java

    @Test
    public void phosphate() throws Exception {
        none(     "COP(=O)([O-])OCC");
        none("[C@](COP(=O)([O-])OCC[N+](C)(C)C)([H])(O-)COC=O");
        none("[C@](COP(=O)([O-])OCC[N+](C)(C)C)([H])(OC=O)COC=O");
        // LMGP01010006 below
        none("[C@](COP(=O)([O-])OCC[N+](C)(C)C)([H])(OC(CCCCCCCCCCCCCCCCC)=O)COC(CCCCCCCCCCCCCCCCC)=O");
    }

Nvm found it just was lacking context, you're looking at Stereocenters right?

Yes, https://github.com/cdk/cdk/blob/master/base/test-standard/src/test/java/org/openscience/cdk/stereo/StereocentersTest.java#L811-L815

The thing seems to be this description: https://github.com/cdk/cdk/blob/master/base/standard/src/main/java/org/openscience/cdk/stereo/Stereocenters.java#L80-L83

Here it says that P's with two oxygens (along with some other elements) should not be tetra. The current code (and my none() examples as others in StereocentersTest) indeed finds *-P(=O)(O)-* groups not tetrahedral, but as soon as the hydroxyl group is deprotonated, the current CDK code make is tetrahedral. Is that a bug or a feature (of InChI)?

Ah, you wrote a patch. Thanks!