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Patch/mdlv3000 updates#824

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egonw merged 7 commits intomasterfrom
patch/mdlv3000-updates
Feb 7, 2022
Merged

Patch/mdlv3000 updates#824
egonw merged 7 commits intomasterfrom
patch/mdlv3000-updates

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@johnmay
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@johnmay johnmay commented Feb 7, 2022

Fixes #603.

Unifies the options between V2000 and V3000 and updates V3000 to handle these options including a new Stereo 0d option.

…o add a new option allow us to turn on/off 0d stereo perception.
…oth. After the molecule is parsed we determine how many dimensions we have based on the header and avaliable data.
…3000 to be more consistent with V2000. This is a corner case and I may change to off by default.
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sonarqubecloud bot commented Feb 7, 2022

Kudos, SonarCloud Quality Gate passed!    Quality Gate passed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 5 Code Smells

0.0% 0.0% Coverage
0.0% 0.0% Duplication

Elements e = Elements.ofString(element);
if (e != Elements.Unknown) {
atom.setAtomicNumber(e.number());
} else if ("D".equals(element) && optHydIso.isSet()) {
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I was thinking that the String comparison must be slower than the bool matching, but then I realize that the former is pretty rare, and overall this order must be more efficient...

@egonw egonw merged commit 23cec7e into master Feb 7, 2022
@johnmay johnmay deleted the patch/mdlv3000-updates branch February 9, 2022 15:33
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SDF parsing - V3000 mol - CFG ignored in atom block warning

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