Incorrect phosphorus valence

[jblack-mestre]

Summary
When generating an .svg image with indigo-depict phosphorus_valence.cml, the phosphorus is incorrectly depicted as having a wrong valence of 5. It should have a valence of 3, with no added hydrogens.

Steps to Reproduce

1. indigo-depict.exe phosphorus_valence.cml phosphorus_valence.svg

Actual behavior
The phosphorus is depicted as having a valence of 5 with two added hydrogens.

Expected behavior
The phosphorus should be depicted as having a valence of 3 with no added hydrogens.

Environment details:

• windows 11
• indigo 4960b8e

Attachments
phosphorus_valence.cml.txt

Additional context
When adding sgroup bonds, indigo recalculates the valence and implicit hydrogens before it has removed the bond to the atom connecting to the sgroup. So P initially has a valence of 3, then this is raised to 4 when adding the bond to the new sgroup. Once the valence is recalculated, this is increased to 5.

[AliaksandrDziarkach]

Looks like issue reproduced when abbreviation contracted and all valence connection used:

[jblack-mestre]

Could you send me the file for this picture so I can reproduce the issue? The problem is that the molecules at the top should have the same oxidation state as the ones at the bottom?

[AliaksandrDziarkach]

Just add correspondig count of C, then make one of them Superatom S-Group and contract it.

{
    "root": {
        "nodes": [
            {
                "$ref": "mol0"
            },
            {
                "$ref": "mol1"
            }
        ],
        "connections": [],
        "templates": []
    },
    "mol0": {
        "type": "molecule",
        "atoms": [
            {
                "label": "P",
                "location": [
                    9.850000000000001,
                    -4.575,
                    0
                ]
            },
            {
                "label": "C",
                "location": [
                    10.850000000000001,
                    -4.575,
                    0
                ]
            },
            {
                "label": "C",
                "location": [
                    9.350000000000001,
                    -3.7089745962155614,
                    0
                ]
            },
            {
                "label": "C",
                "location": [
                    9.350000000000001,
                    -5.4410254037844386,
                    0
                ]
            }
        ],
        "bonds": [
            {
                "type": 1,
                "atoms": [
                    0,
                    1
                ]
            },
            {
                "type": 1,
                "atoms": [
                    0,
                    2
                ]
            },
            {
                "type": 1,
                "atoms": [
                    0,
                    3
                ]
            }
        ],
        "sgroups": [
            {
                "type": "SUP",
                "atoms": [
                    1
                ],
                "name": "Sub",
                "expanded": false,
                "id": 0
            }
        ]
    },
    "mol1": {
        "type": "molecule",
        "atoms": [
            {
                "label": "P",
                "location": [
                    14.25,
                    -4.675,
                    0
                ]
            },
            {
                "label": "C",
                "location": [
                    15.25,
                    -4.675,
                    0
                ]
            },
            {
                "label": "C",
                "location": [
                    13.75,
                    -3.808974596215561,
                    0
                ]
            },
            {
                "label": "C",
                "location": [
                    13.75,
                    -5.541025403784438,
                    0
                ]
            }
        ],
        "bonds": [
            {
                "type": 1,
                "atoms": [
                    0,
                    1
                ]
            },
            {
                "type": 1,
                "atoms": [
                    0,
                    2
                ]
            },
            {
                "type": 1,
                "atoms": [
                    0,
                    3
                ]
            }
        ],
        "sgroups": [
            {
                "type": "SUP",
                "atoms": [
                    1
                ],
                "name": "Sub",
                "expanded": true,
                "id": 0
            }
        ]
    }
}

[jblack-mestre]

I'm having trouble reproducing your test. I have taken your ket file - modified it in ketcher and then put it through indigo-depict. But my svg looks very bad

Instead, if I save to a cdxml file and use with indigo depict, I lose the bracketed [CH3]Sub group, however all the oxidation states are correct