Discussion: cleaning up master branch

Issue #112 resolved
Xinqiu Yao created an issue

Following files are subject to deletion or moving. Let me know what you think:

  1. unlist2.R -> delete. Find alternative way to do the same task.
  2. dccm.mean.R -> merge to filter.dccm.R

Comments (9)

  1. Lars Skjærven

    atom2ele is in use in atom2mass. usage is:

    > atom.names <- c("CA", "O", "N", "OXT")
    > atom2ele(atom.names)
    [1] "C" "O" "N" "O"
    

    We could in principle to try to hide it under atom2mass, but I would rather have it open and available

  2. Barry Grant

    unlist2() can be removed - see comment although not yet tested/committed.

    atom2ele() should be kept.

    cmap.filter() can probably just be kept for now - I am agnostic about this.

  3. Xinqiu Yao reporter

    Right. I misunderstood the purpose of cmap.filter. We can probably merge dccm.mean with filter.dccm, which basically do very similar task. The contents of this issue will be updated

  4. Barry Grant

    Sounds good, should we call it dccm.filter() then to math the others? I know you don't like [dots] and we have S3 concerns but this does make sense to me.

  5. Xinqiu Yao reporter

    I have no problem to change the name but I concern it will affect the CNA vignette we just submitted. Is it better to change the name at some later stage?

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