you can use bash or perl script to extract information from one or more files..

If your protein of interest is NMR structure, it can be done from http://pacsy.nmrfam.wisc.edu/ by submitting simple SQL line.

For example, PDB 1D3Z,

select A_DB.*,A_STRC_DB.* from A_DB,A_STRC_DB,SEQ_DB where SEQ_DB.PDB_ID="1D3Z" and A_STRC_DB.MODEL_NO=1 and A_DB.KEY_ID=A_STRC_DB.KEY_ID and A_DB.FIRSTKEY_ID=SEQ_DB.KEY_ID

will retrieve all 2' structures, PHI, PSI angles, SASs, hydrophobicities from Alanine. You can simple conjugate A into other amino acid types.

If you are interested in analyzing coordinates, especially for CA,

select A_COORD_DB.*,A_DB.* from A_COORD_DB,A_DB,SEQ_DB,A_STRC_DB where SEQ_DB.PDB_ID="1D3Z" and A_STRC_DB.MODEL_NO=1 and A_COORD_DB.ATOM_NAME="CA" and A_COORD_DB.KEY_ID=A_DB.KEY_ID and A_COORD_DB.FIRSTKEY_ID=SEQ_DB.KEY_ID and A_COORD_DB.KEY_ID=A_STRC_DB.KEY_ID

will provide you coordinates. You can simply calculate distances with them.

If you want to create a tool for yourself and are not afraid of learning a little python (or if you know already, it will be quite easy), I would suppose to use MDAnalysis (https://pypi.python.org/pypi/MDAnalysis). It is quite flexbile, not limited to one file format and has built-in routines for distance and angle calculation. Yet, it is not a "point and click" tool, you have to write some lines of (python script) code to get results.

@Woonghee Lee:  Presently, I need to compare small molecule data from computation and X-ray structures. But thanks for the tip, it could be useful in future.

@Matthias Ernst: I asked the question because I have would have preferred avoiding  programming (moreso testing and debugging), but I can write python, and this library seems to fit the bill perfectly for my needs. Thanks.

The same can be done in JavaScript with Ascalaph.

Scripting is the same as in http://www.biomolecular-modeling.com/Abalone/Manual.html

http://www.biomolecular-modeling.com/Products.html

Yes, use Platon or  Ortep.