read.pdb
Issue #182
resolved
proposing to change default value of multi in read.pdb() to TRUE. I guess the only reason for having this FALSE is speed (?), but you dont save too much anyway:
> get.pdb("1d1d")
> system.time(read.pdb("1d1d.pdb", multi=FALSE))
user system elapsed
0.539 0.003 0.544
> system.time(read.pdb("1d1d.pdb", multi=TRUE))
user system elapsed
0.680 0.000 0.683
Also, I exchange calls to print with message (or cat). ok?
Comments (4)
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reporter neh.. pdbsplit() would be affected, so that we would need to include a multi argument there as well. thats a hassle, so I take it back. the other functions would be ok though.
there are calls to print in read.pdb so that the messaging gets a bit ugly:
> read.pdb("2RSC", multi=TRUE) Note: Accessing on-line PDB file [1] "PDB has multiple END/ENDMDL records" [1] "multi=TRUE: 'read.dcd/read.ncdf' will be quicker!" HEADER HYDROLASE 19-DEC-11 2RSC
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reporter - changed status to resolved
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I agree, pdbsplit() changes could get painful.
Also changing the print() call would be good.
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How wold this effect regular pdbaln() - pdbfit() - etc workflows? Also I am sure what your print() to cat() change is about?