Dependency file generators

BMERC : needle tools : Programs : Dependency generators

This page gives detailed descriptions of the needle tools dependency file generator scripts. General documentation is provided on the Dependency files for make page.

Table of contents

1. Dependency file generators
   1. Table of contents
   2. make-core-depends.pl
      1. make-core-depends.pl file types
      2. Macros used by make-core-depends.pl
   3. make-mrf-depends.pl
      1. make-mrf-depends.pl file types
   4. Known bugs in the dependency file generators

If core files are desired, make-core-depends.pl will also generate smoothed DSSP secondary structure definitions if necessary from abbreviated DSSP files, which in turn will be generated if necessary from the PDB file.

Additional arguments:

-make-exposure-files

generate exposure file targets for Eisenberg "fat alanine" exposure, which are not made by default.

-no-core-files

suppress generating core and segment file targets, which are otherwise made by default.

-no-seq-files

suppress generating sequence file targets, which are otherwise made by default.

File Type	File name prefix/suffix/macro/make state args & defaults	Description (with file format)
	Invocation macro name and default(s)
abbrev-dssp	-abbrev-dssp-file-prefix '' -abbrev-dssp-file-suffix '.ent.out' -abbrev-dssp-macro abbrev-dssp-files -path-abbrev-dssp-files	Abbreviated DSSP file; file naming is based on the PDB entry.
	GENERATE-DSSP = generate-dssp
core	-core-file-prefix '' -core-file-suffix '.core' -core-macro core-files -make-core-files	Core file.
	MAKE-CORE = make-core.pl MAKE-CORE = make-domain-core.pl
exposure	-exposure-file-prefix '' -exposure-file-suffix '.nexp' -exposure-macro exposure-files -local-exposure-files	Eisenberg "fat ALA" exposure (.nexp) file.
	GENERATE-EXPOSURE = efa.pl GENERATE-EXPOSURE = generate-exposure
gmt-env	-gmt-env-file-prefix 'singleton_environments_MRF_' -gmt-env-file-suffix '.dat' -gmt-env-macro gmt-environments -local-gmt-env-files	GMT environment file (singleton environment format).
	MRF-GMT-ENVS = mrf-envs
pdb	-pdb-file-prefix '' -pdb-file-suffix '.ent' -pdb-macro pdb-files -path-pdb-files	PDB file.
seg	-seg-file-prefix '' -seg-file-suffix '.dssp' -seg-macro segment-files -local-seg-files	Segment definition file.
	MAKE-SS-DESIGNATIONS = make-ss-designations
seq	-seq-file-prefix '' -seq-file-suffix '.seq' -seq-macro sequence-files -make-seq-files	Sequence (IG) file.
	MAKE-SEQ-FILE = make-seq-file.pl MAKE-SEQ-FILE = pdb-domain-seq.pl

Macros used by make-core-depends.pl

    GENERATE-DSSP = generate-dssp
    DSSP4 = dssp4.pl -dont-fill-e-gaps
    MAKE-SS-DESIGNATIONS = make-ss-designations
    GENERATE-EXPOSURE = generate-exposure
    MAKE-CORE = make-core.pl
    MAKE-SEQ-FILE = pdb-to-seq.pl

Name	Usage	Compatible program
Unless core files were suppressed via -no-core-files:
GENERATE-DSSP	Invokes a program that makes abbreviated DSSP file format from a PDB file.	generate-dssp
DSSP4	Invokes a program that produces filtered "ss" format from abbreviated DSSP file format.	dssp4.pl
MAKE-SS-DESIGNATIONS	Invokes a program that produces segment file format from "ss" format from abbreviated DSSP file format.	make-ss-designations
MAKE-CORE	Invokes a program that makes a core file from a PDB file and its corresponding segment file.	make-core.pl
Unless sequence files were suppressed via -no-seq-files:
MAKE-SEQ-FILE	Invokes a program that makes a sequence file from a PDB file.	pdb-to-seq.pl
If exposure files were requested via -make-exposure-files:
GENERATE-EXPOSURE	Invokes a program that makes an Eisenberg "fat alanine" exposure file from a PDB file.	generate-exposure

[the cross-validation discussion in the "Types of cross-validation" section belongs in mrf.html instead. -- rgr, 24-Apr-98.]

The make-mrf-depends.pl script takes a list of core names and produces on the standard output the appropriate rules that tell the Unix make utility how to create the MRF score and environment files.

make-mrf-depends.pl overflows with options, so that every aspect of score/environment file generation can be customized, but using the defaults works well for the simplest case of producing scores for a new core library. See elsewhere for a simple example of usage. The important arguments are -core-list-file, which is required to identify the model set; and -search-path, which allows make-mrf-depends.pl to find files in other directories. For more complicated cases, one can either (a) modify one of the examples [give link]; (b) pipe the output of make-mrf-depends.pl through (e.g.) a sed or awk script that makes the required changes; or (c) hand-edit the results of running with default parameters (though this does make it more difficult to change the model set).

Arguments:

See the "Dependency file generator arguments" and "MRF-specific dependency generator arguments" sections for details of common arguments.

Note that GMT environment files are independent of the singleton and pairwise environment files. GMT environments do not depend on anything except the length of the core, and are used only for threading and not counting or score generation, so they are completely orthogonal to the rest of the MRF process. (Indeed, the fact that they are still generated by the mrf-envs program is something of a historical accident.)

make-mrf-depends.pl file types

1. *** There is no (user-accessible) way to define how to make secondary structure definitions other than smoothed DSSP, though the dependency generators will use files created with the -seg-file-suffix if they already exist on the search path. -- rgr, 20-Feb-97.
2. *** If you specify an -exposure-file-suffix other than ".nexp", any locus.nexp files that happen to be in that directory get overwritten anyway. This is a limitation of the generate-exposure program. -- rgr, 27-Mar-97. [which is why this should be rewritten to use efa.pl instead. -- rgr, 6-Nov-98.]