Dear rdkit, I am wondering whether after reading a molecule from an sdf file, it is possible to keep the original 3d coordinates that were in that sdf file? I will modify the molecules (fragment bonds and saturate with hydrogen) but as much as possible I want to keep the original coordinates. For example, if I had H3C-CH=CH2 and I break the first bond to remove H3C (to saturate to CH4) leaving CH=CH2 (to saturate to H2C=CH2), would it be possible to keep the original C coordinates rather than generate conformations and so on?
I appreciate the assistance. Best regards, -- *Puck van Gerwen* Doktorandin / PhD candidate Departement Chemie Klingelbergstrasse 80 CH-4056 Basel https://www.chemspacelab.org/
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