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Actelion / openchemlib

Open source Java-based chemistry library
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IDCodeParser(true) and coordinates #66

Open lpatiny opened 2 years ago

lpatiny commented 2 years ago

@thsa When I create a molecule from IDCode using IDCodeParser(true); and I generate a molfile, the molfile does not contains atom coordinates.

It seems to me that the main difference between true and false in IDCodeParser is that you can recreate (or not) an idCode using 'getIDCode()' and that if you would like to have coordinates you need to inventCoordinates.

Maybe the comment in the following code could be more clear:

https://github.com/Actelion/openchemlib/blob/master/src/main/java/com/actelion/research/chem/IDCodeParser.java#L8-L15

thsa commented 2 years ago

System.out.println(new MolfileCreator(new IDCodeParser(true).getCompactMolecule("diTD@@qJZUkfFjjjbH@")).getMolfile());

produces this output, which includes coordinates. Can you show the source code you use?:

Actelion Java MolfileCreator 1.0

9 10 0 0 1 0 0 0 0 0999 V2000 -0.9659 -0.2588 -0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 -0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6730 0.4483 -0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.0000 -0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.2588 0.9659 -0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0000 -0.0000 -0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4142 1.4142 -0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0000 -1.0000 -0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4483 1.6730 -0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 1 0 0 0 1 3 1 0 0 0 0 2 4 1 0 0 0 0 2 5 1 0 0 0 0 2 6 1 0 0 0 0 3 7 1 0 0 0 0 4 8 1 0 0 0 0 5 9 1 0 0 0 0 6 8 1 0 0 0 0 7 9 1 0 0 0 0 M END

Von: Luc Patiny @.> Gesendet: Freitag, 1. Oktober 2021 10:00 An: Actelion/openchemlib @.> Cc: Thomas Sander @.>; Mention @.> Betreff: [Actelion/openchemlib] IDCodeParser(true) and coordinates (#66)

@thsahttps://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fthsa&data=04%7C01%7Cthomas.sander%40idorsia.com%7C7cf2190d6b404c2cc0d008d984b198d0%7Cbb9214bf0cb941fdbd55d0c1c3eda110%7C0%7C0%7C637686720570581693%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=dg%2FuW8NSun4SZ9kiKctg2RP6%2BpUlQs4zSWS8ND8saZk%3D&reserved=0 When I create a molecule from IDCode using IDCodeParser(true); and I generate a molfile, the molfile does not contains atom coordinates.

It seems to me that the main difference between true and false in IDCodeParser is that you can recreate (or not) an idCode using 'getIDCode()' and that if you would like to have coordinates you need to inventCoordinates.

Maybe the comment in the following code could be more clear:

https://github.com/Actelion/openchemlib/blob/master/src/main/java/com/actelion/research/chem/IDCodeParser.java#L8-L15https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FActelion%2Fopenchemlib%2Fblob%2Fmaster%2Fsrc%2Fmain%2Fjava%2Fcom%2Factelion%2Fresearch%2Fchem%2FIDCodeParser.java%23L8-L15&data=04%7C01%7Cthomas.sander%40idorsia.com%7C7cf2190d6b404c2cc0d008d984b198d0%7Cbb9214bf0cb941fdbd55d0c1c3eda110%7C0%7C0%7C637686720570581693%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=X%2FrJxuEpfS7JYAzjN72ODcW2H58QUL%2Blvx4x46Vx61c%3D&reserved=0

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