AMBER Archive (2002)

Subject: Re: "flags" in .lib files

From: Bill Ross (photoriot_at_yahoo.com)
Date: Wed Jan 23 2002 - 13:39:45 CST

> Can any one tell me what the number in the 5th
> column of the first section of the .lib files
> stands for.

This is a decimal rendition of a bitmap. The values in
hexadecimal are contained in atom.h, but the easiest
way to interpret them is to use the 'desc' command in
leap:

> desc DG.1.N2
 ...
Atom flags: (decimal 131072 hex 0x20000)
        posfxd n posblt n posdrwn n selected n
        pert n notdisp n touched n posknwn Y
        internal n needsmin n needsbuild n

In this case, the only flag set is 'posknwn' or
"position known." Not all the flags are necessarily
used or meaningful from a user's point of view, e.g.
I believe that 'touched' is used transiently when
identifying molecules (building a spanning tree).
Certainly one would never want to see 'notdisp'(layed)

set in a .lib file; in fact, it might make sense to
add this feature to 'saveOff'.

Bill Ross

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