Correct the judgment of hydrogen bonds #370
Conversation
Corrected the error of not distinguishing between hydrogen receptors and donors, distinguishing OE as OE1 and OE2
for more information, see https://pre-commit.ci
|
Thanks for the PR @Linsastar! Could you clarify why the atoms are different to those specified in the existing Hbond acceptors and donors |
for more information, see https://pre-commit.ci
for more information, see https://pre-commit.ci
for more information, see https://pre-commit.ci
|
|
Hi Chenyang, thanks for clarifying, that all makes sense to me. Appreciate it! To cover your points:
|
|
Hi Arian, Thanks for your feedback! (1) It makes sense to me that users have three hbond options, sc-sc, bb-sc, bb-bb, according to the locations of donors and acceptors. (2) Indeed, Sulfur involved hydrogen bonds are typically weak when compared with others and thus can be discarded. |
… chain can be identified Corrected hydrogen bond determination, now hydrogen bonds on the main chain can be identified
for more information, see https://pre-commit.ci
|
| if rgroup_df is None: | ||
| rgroup_df = G.graph["rgroup_df"] | ||
| # if rgroup_df is None: | ||
| # rgroup_df = G.graph["rgroup_df"] |
There was a problem hiding this comment.
What is the purpose of not using the supplied rgroup_df?
There was a problem hiding this comment.
Yes, you're right. I commented out the code like that just to facilitate debugging and determine the hydrogen bonds on the main chain.
Errors of adding the essential hydrogen bond interaction have been corrected. In particular, OE was divided into OE1 and OE2.
Besides, OE1, OE2, OD1, OD2 and O were defined as the hydrogen acceptors and the rest hydrogen donors.