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3. General issues

3.1 Command line interface

A consistent interface is used, at least for the main program suite. The order for command parameters is generally given in this form:

program [conformation-file | conformation-pair-file | conformation-file-list | conformation-pair-file-list | input-file | input-file-list]
        [scoring-function-file | parameter-file]
        [output-file | output-file-prefix | output-file-suffix]


is generally a PDB format file; sometimes a DSSP format file is used. If containing the extension .pdb, then a single file is assumed; else multiple conformations are assumed (in some cases)

is a file containing a list of multiple conformation files (in general, a file-list is a file containing a list of files)

contains the relevant scoring function

is any other parameter-file

is the name of the output-file; if omitted and there is no requirement for multiple output files, then stdout will be used to generate a new conformation-file

is the prefix used when multiple output files are generated

is the suffix used when multiple output files are generated

any other arguments.

In addition, each program may have its own options and parameters. Typing the name of the program will give some help. The common interface options are:

-c conformation-file-list|conformation-file
-i input-file
-o output-file

In cases where the above options are irrelevant, the program will make an attempt to adhere to the philosophy of the above approach as much as possible. For example, plot_scores will take a file containing a list of pairs of group names, or just two group names. In general, an attempt will be made to be able to specify the output file in an optional manner (i.e., explicit vs. redirection to stdout). Similarly, if there is only one input argument, or for programs for which such a function would be useful, an attempt will be made to read from stdin. All errors and informational messages will be sent to stderr (these can be redefined in ramp/src/common/common.h).

Reading multiple input files is not possible unless a single output file is generated for the entire set of input files, or when multiple output files are generated for a single input file.

Typing the name of the program without any arguments or with an excess number of arguments (in cases where standard input is expected) will give you the usage information, including the set of parametres used during compilation. The display of parametres, and reporting of progress as a program does its job, can be disabled or enabled (default) by turning off or on the VERBOSE flag in ramp/src/common/defines.h and recompiling the entire suite. Additional debugging can be enabled or disabled (default) by turning on the DEBUG flag in ramp/src/common/defines.h and recompiling the entire suite.

3.2 Terminology

The following terms are used interchangeably at times:

score - energy - probability

3.3 Directory structure

ramp/bin/scripts           - architecture-independent executables
ramp/bin/architecture      - architecture dependent executables; four
                             architectures are supported: linux_alpha,
                             linux_ix86, irix_mips, and osf1_alpha.
ramp/doc                   - documentation
ramp/src                   - source
ramp/src/common            - common routines used by several programs
ramp/src/mc_commom         - common main chain routines used by
                             several programs
ramp/src/mcgen             - main chain generation programs
ramp/src/music             - music related programs
ramp/src/obsolete          - obsolete source; this directory contains
                             code for stuff that is incomplete, being
                             worked on, or ideas that didn't pan out.
ramp/src/potentials        - scoring functions
ramp/src/scores            - scoring function related programs
ramp/src/sc_common         - common side chain routines used by
                             several programs
ramp/src/scgen             - side chain generation programs
ramp/lib                   - parameter files
ramp/lib/folds             - fold libraries
ramp/lib/scoring_functions - parametres for scoring functions

3.4 Environment variables

BINDIR_EXTENSION - architecture dependent binary directory names.
HDRS             - list of paths for includes for compilation purposes
RAMP_ROOT        - top level directory for the RAMP source/executable directory tree

3.5 Test sets

I have a test set that will verify a program in the RAMP suite against previously obtained results. Unfortunately it's not ready for distribution yet.

To test the scoring functions generally, the Decoys 'R Us decoy database may prove useful.

3.6 Caveats

Most, but not all, programs in the suite require residues to be numbered consecutively starting from 1. Behaviour is unpredictable otherwise. PDB files do not come like this always. So the solution is to normally use clean_pdb first on the PDB file and then have it used by the other software.

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