Glossary of AutoPeak Scripts and Programs

apply_shifting.pl - adjusts peaks chemical shifts using the given shifting.
average_duplicates.pl - create a set of average peaks from groups of duplicate peaks.
bmrb2cmap.pl - converts bmrb format to cmap format.
bmrbACS2pks.pl - converts BMRB assigned chemical shifts frame to an AutoAssign peak list.
bmrbACS2SparkyPks.pl - converts bmrb assigned chemical shift save frame to Assigned Sparky Peak List format.
bmrb2AutoStructure.pl - converts bmrb format to AutoStructure Resonance List format.
bmrbSPL2pks.pl - converts BMRB spectral peak list frames to an AutoAssign peak lists.
bmrbSPL2SparkyPks.pl - converts BMRB spectral peak list frames to Sparky peak lists.
bmrb2SparkyRL.pl - converts bmrb format to Sparky Resonance List format.
bmrb_apply_shifting.pl - apply atom type shifting to the shifts of a bmrb file.
bmrb_assign_spl.pl - assigns the spectral_peak_lists in a BMRB file.
bmrb_calculate_shifting.pl - calculate difference in same shifts between two bmrb files.
bmrb_extract_shifts.pl - extract a list of shifts from a bmrb file.
calc_rdc.pl - calculates RDCs from peak lists with the peak splittings for the free and aligned protein.
calc_resonance_splitting.pl - converts assigned peak doublets into pseudo-central peaks with splittings dimension in Hz.
calculate_registration - calculates the registration (shifting) of one peak list against another.
change_phase.pl - changes the sign of the peak intensities.
cmap2bmrb.pl - converts a cmap file into a BMRB file.
compare_bmrb.pl   - compares two bmrb files and returns how well they match.
compare_cmap.pl - compares two CMap files and returns how well they match.
concat_bmrb_shifts.pl   - combine a set of bmrb files.
concatenate.pl - concatenates multiple peak files.
create_bmrb.pl   - converts a list of shift assignments in 3 column format into a BMRB file.
create_peak_list.pl - creates a peak list given peak information in separate columns.
create_split_doublet.pl - create split doublet from central peak with splittings dimension.
createSparkyNOESYPks.pl - creates hypothetical NOESY peak list from an assignment list.
dyanaUPL2cmap.pl - converts the backbone NOEs from a DYANA UPL constraint file to the CMap format.
examine_spin_systems.pl - groups peaks into spin systems and examines them for completeness and overlap.
extract_columns.pl - extracts columns from text files.
extract_dims.pl - extracts and rearranges peak dimensions of a peak file.
extract_dup_assignments.pl - extracts groups of peaks that have duplicate assignments in 'Notes' column.
extract_duplicates.pl - extracts duplicate or nonduplicate peaks.
extract_by_dup_count.pl - extract peak duplicates with a certain peak count.
extract_by_filter.pl - extracts peaks that match (or don't match) a filter list.
extract_by_intensity.pl - extract a certain fraction of strong peaks.
extract_by_intensity2.pl - extract peaks above a fraction of the average/top peak.
extract_by_intensity3.pl - extract peaks above a threshhold.
extract_by_phase.pl - extract positive or negative intensity peaks.
extract_by_shift.pl - extract peaks with chemical shifts above or below certain values.
extract_by_shift_range.pl - extract peaks with chemical shifts within a range of values.
file_history.pl - print File History of a peak file.
jval2bmrb.pl - converts AutoStructure Input J HNHA values into BMRB coupling constants save frame.
manage_bmrb.pl - manage save frames inside a BMRB file.
manage_cmap.pl - manage the sections and columns in a cmap file.
match_recombine.pl - create new peaks from parts of other peaks.
missing_shifts.pl - reports the missing AtomTypes in a given BMRB file.
pales2cns.pl - converts data from pales output table format to cns input format for RDCs.
pks2bmrb.pl - converts AutoAssign peak list into BMRB spectral peak list save frame.
pks2SparkyPks.pl - converts an AutoAssign peak list file to a Sparky peak list file.
rdc2cns.pl - converts RDCs from peak list format to cns format.
rdc2pales.pl - converts RDCs from peak list format to PALES input table.
remove_peaks.pl - removes peaks from a peak list with the given indeces.
sec2bmrb.pl - converts AutoStructure output .sec file into BMRB secondary_structure save frame.
sparkyPks2bmrb.pl - converts a sparky peaklist into a BMRB assigned peak list save frame.
sparkyPks2pks.pl - create a peak list given the shift values and intensity in separate columns. It also tries to assert a HN, N15, HX, CX, CO and X dimension ordering.
sparkyRL2bmrb.pl - converts Sparky resonance list into a BMRB file. 
tag_peaks.pl - extract a group of peaks using a set of filter peaks and tag them.
typing_degeneracy.pl - calculates the typing degeneracy for a given sequence.
validate_assignments.pl - validates assignments in bmrb format.

apply_shifting.pl -- Adjust peak shifts using the given shifting.
usage: apply_shifting.pl in_peak_file new_workbook_name out_peak_file shift1 shift2 ...

peak_file  - name of peak file or "-" for standard input/output.
workbook_name - string to use as workbook name or "-" to use old name.
shift1 shift2 ...   - dimension shifts to apply.


average_duplicates.pl -- Average duplicate peaks on given dimensions.

  usage: average_duplicates.pl in_peak_file new_workbook_name out_peak_file [options] tol1 tol2 ...

        peak_file - name of peak file or "-" for standard input/output.
        workbook_name - string to use as workbook name or "-" to use old name.
        tol1 tol2 ...  - dimension tolerances for comparing peaks.  Must have a value for every dimension.

        options (requires either -min or -max)
             -min  count  - minimum number of peaks needed to average.
             -max count  - maximum number of peaks needed to average.
             -abs  - take the absolute value of the intensities


bmrb2cmap.pl -- Converts bmrb format to cmap format.

    usage: bmrb2cmap.pl input_bmrb_file output_cmap_file [options]

                input_bmrb_file - bmrb file to read ("-" to read from standard input).
                output_cmap_file - output file to write to ("-" to write to standard output).
                options:
                        -entity id_num - id of entity to use from bmrb file.
                        -interpret atom_list - add following atom_list using assigned chemical shifts if no assigned peak is available.
                                atom_list - comma separated list of atoms in cmap format (i.e. CA, CA-1, HN, N15, CO, etc.)
                        -restrict saveframe_list - restrict conversion to the given list of saveframes.
                                saveframe_list - comma separated list of save frame types (i.e. spectral_peak_list, coupling_constants, secondary_structure).


  bmrbACS2pks.pl -- Converts BMRB assigned chemical shifts frame to an AutoAssign peak list.
 
  usage: bmrbACS2pks.pl input_bmrb_file output_peak_file intensity workbook dim1 dim2 ...
 
                input_bmrb_file - bmrb file to read ("-" to read from standard input).
                output_peak_file - output file to write to ("-" to write to standard output).
                intensity - intensity value to use for the peaks
                workbook - workbook name for the peaks (residue name and peak definition are added by script)
                dim1 dim2 ...

                        dim - quoted list of atom names (in CMap convention) for a dimension.

  bmrbACS2SparkyPks.pl -- Converts bmrb assigned chemical shift save frame to Assigned Sparky Peak List format.
 
  usage: bmrbACS2SparkyPks.pl input_bmrb_file output_peak_file dim1 dim2 ...
 
                input_bmrb_file - bmrb file to read ("-" to read from standard input).
                output_peak_file - output file to write to ("-" to write to standard output).
                dim1 dim2 ...
                        dim - quoted list of atom names for a dimension.
 
  Hint: Sparky reads them in using the rp command.

bmrb2AutoStructure.pl -- Converts bmrb format to AutoStructure Resonance List format.

  usage: bmrb2AutoStructure.pl input_bmrb_file autostructure_rl [options]

                bmrb_file - name of bmrb file or "-" to read from standard input.
                autostructure_rl - name of AutoStructure resonance list file or "-" to write to standard output.
                options:
                        -restrict shift_list - restrict conversion to the given quoted list of shift names.
                        -entity idnum - entity to use.

bmrbSPL2pks.pl -- Converts BMRB spectral peak list frames to AutoAssign peak lists.
 
  usage: bmrbSPL2pks.pl input_bmrb_file [options]
 
                input_bmrb_file - bmrb file to read ("-" to read from standard input).
                options:
                        -id peak_list_id output_peak_list - use only the spectral peak list with given ID.


bmrbSPL2SparkyPks.pl -- Converts BMRB spectral peak list frames to Sparky peak lists.
 
  usage: bmrbSPL2SparkyPks.pl input_bmrb_file [options]
 
                input_bmrb_file - bmrb file to read ("-" to read from standard input).
                options:
                        -id peak_list_id output_peak_list - use only the spectral peak list with given ID.
                        -add_intensity - add the intensity to the outputted sparky peak lists.

bmrb2SparkyRL.pl -- Converts bmrb format to Sparky Resonance List format.

    usage: bmrb2SparkyRL.pl input_bmrb_file output_sparky_rl [options]

                bmrb_file - name of bmrb file or "-" to read from standard input.
                sparky_rl - name of sparky RL file or "-" to write to standard output.
                options:
                        -restrict shift_list - restrict conversion to the given quoted list of shift names.
                        -entity idnum - entity to use.


bmrb_assign_spl.pl -- Assigns the spectral_peak_lists in a BMRB file.

  usage: bmrb_assign_spl.pl in_bmrb_file out_bmrb_file [options]

                in_bmrb_file  - current assignments in bmrb format
                out_bmrb_file  - current assignments in bmrb format
                options:
                        -ambiguity num - level of ambiguity assignment to allow; 0 is none; 1 is everything within tolerance; default is 0.25 which equates to 1/4 the tolerance.
                        -override - let given atom_type tolerances override tolerances (shift_error) given in the peak lists.
                        -atolerance tol_pair ... - list of tolerances by atom_type.
                                tol_pair - atom_type tolerance (where atom_type can be H, N, HA, CA,...).
                        -ntolerance tol_pair ... - list of tolerances by nuclei_type.
                                tol_pair - nuclei_type tolerance (where nuclei_type can be H, N, C).


bmrb_apply_shifting.pl -- Apply atom type shifting to the shifts of a bmrb file.

  usage: bmrb_apply_shifting.pl input_filename output_filename shift_pair shift_pair ...

        filename - bmrb filename or "-" for standard input/output.
        shift_pair - (atom_type shift_value).
                atom_type - type of atom (ie. C, N, H).
                shift_value - amount to shift by.


bmrb_calculate_shifting.pl -- Calculate difference in same shifts between two bmrb files.

  usage: bmrb_calculate_shifting.pl input_bmrb_file1 input_bmrb_file2 [options]

        bmrb_file - name of bmrb file or "-" for standard input/output.
        options:
                -verbose - give extra information during calculation.
                -degeneracy - treat shift degenerately.
                -cutoff - inclusion cutoff in units of standard deviation.


bmrb_extract_shifts.pl -- Extract a list of shifts from a bmrb file.

  usage: bmrb_extract_shifts.pl input_bmrb_file output_bmrb_file inclusion_toggle shift_name shift_name ...

        bmrb_file - name of bmrb file or "-" for standard input/output.
        inclusion_toggle:
                inc(lusive) - include those shift names that match list.
                exc(lusive) - exclude those shift names that match list.
        shift_name - name of a shift in bmrb naming convention.


calc_rdc.pl -- Calculates RDCs from peak lists with the peak splittings for the free and aligned protein.

  usage: calc_rdc.pl free_splits_peaklist aligned_splits_peaklist out_rdc_peaklist out_unused_peaklist workbook_name

       free_splits_peaklist - peak list with splittings from free (i.e. unaligned) sample in last dimension.
    aligned_splits_peaklist - peak list with splitting from aligned sample in last dimension.
    out_rdc_peaklist - peak list with RDCs in last dimension.
    out_unused_peaklist -  peaklist of used peaks because they are not present in both input lists.
    workbook_name - string to use as workbook name.
  Assumptions: The peak list for free and aligned proteins have the same number and order of dimensions columns
               (splittings in ppm in the 2nd from last *Dim, and in Hz in the last *Dim column)
               and the sets of peaks have the same registration.

  Hint: Use 'calc_resonance_splitting.pl' first to generate the list of splittings for each peak list (for each sample).


calc_resonance_splitting.pl -- Converts assigned peak doublets into pseudo-central peaks with splittings dimension in Hz.

 usage: calc_resonance_splitting.pl in_peaklist out_peaklist unused_peaklist workbook_name split_dim conversion_factor

     peaklist - name of peak file or "-" for standard input/output.
    unused_peaklist -  name of peak file for unpaired split peaks.
    workbook_name - string to use as workbook name.
    split_dim - dimension in which peaks are split.
    conversion_factor - ppm to Hz conversion factor (dependent on spectrometer field strength).
 Hint: In case you want to deal with splittings from IPAP, concatenate the assigned peak lists first.

calculate_registration -- Calculates the registration that will make in_file match root_file.

  usage: calculate_registration in_file root_file [options]

    in_file     - the peak list you wish to register and filter
    root_file   - the reference peak list
    options:
        -dimension idim1 idim2 ... : rdim1 rdim2 ... - description of matching dimensions in input and root files.
        -tolerance num_units - number of stds to use as the match tolerance (default 4).
        -nobounds - do not perform bounds checking
        -map filename - save list of input peaks and their mapping to the root peaks.
        -verbose  - print verbose information.
        -restricted - use restricted std instead of weighted std for iteration.
        -H init_std - set starting std to try for H dimensions (default 0.0075).
        -C init_std - set starting std to try for C dimensions (default 0.075).
        -N init_std - set starting std to try for N dimensions (default 0.075).
        -i max - maximum number of iteration to perform (default 20).

Guidelines for use:

  The raw robustness should be around the number of peaks in the input file that should match peaks in the root file.
  The weighted registration should be used for aligning peak files.
  Values between weighted and full STD's should be used in determining tolerances for AutoAssign.
  The weighted STD is normally used in iterative determination of STD's and registration.
    This is because it has the best properties for an iterative algorithm.


change_phase.pl -- Change the sign of the peak intensities.
usage: change_phase.pl in_peak_file toggle_sign new_workbook_name out_peak_file
peak_file  - name of peak file or "-" for standard input/output.
toggle_sign:
       invert    - invert the sign of the peak intensity.
       pos(itive) - make all peak intensities positive.
       neg(ative) - make all peak intensities negative.
workbook_name - string to use as workbook name or "-" to keep old name.

cmap2bmrb.pl -- Converts a cmap file into a BMRB file.

  usage: cmap2bmrb.pl input_cmap_file output_bmrb_file sequence_start sequence

     input_cmap_file - name of cmap file or "-" for standard input.
    output_bmrb_file - name of the output BMRB file or  "-" for standard output.
    sequence_start - the starting residue number of the sequence.
    sequence - the protein sequence using single letter codes.

compare_bmrb.pl -- Compares two bmrb files and returns how well they match.

  usage: compare_bmrb.pl input_bmrb_file input_bmrb_file [options]

        bmrb_file - name of bmrb file or "-" for standard input/output.
        options:
                -verbose - print information verbosely.
                -master - work as if the first input_file contains master verified results.
                -Ctol value, -Ntol value, -Htol value - set identity tolerances to value for carbons, nitrogens, or hydrogens (default values are 0.1, 0.1, and 0.01 respectively).
                -Cshift value, -Nshift value, Hshift value - shift the second input_file shifts before comparison.
                -nodegenerate - do not compare shifts degenerately.


compare_cmap.pl -- Compares two CMap files and returns how well they match.

  usage: compare_cmap.pl old_cmap_file new_cmap_file [options]
cmap_file - name of CMap file.
    options:
        -Ctol value, -Ntol value, -Htol value - set match tolerances to value for
                carbons, nitrogens, or hydrogens (default values are 0.1, 0.1, and 0.01
                respectively).
        -tol resonance_type value - set match tolerance to value for specific resonance_type.
        -resonance_only - test resonance differences only.
        -output output_cmap_file - output cmap file with differences graphics row.
        -master - treat old_cmap_file as the master file.

concat_bmrb_shifts.pl -- Combine a set of bmrb files.

    usage: concat_bmrb_shifts.pl [options] -input filename ...

        -Ctol value, -Ntol value, -Htol value - set identity tolerances to value forcarbons, nitrogens, or hydrogens (default values are 0.1, 0.1, and 0.01 respectively).
        -output filename - output file ("-" for stdout).
        -master filename - master input file to add to ("-" for stdin).
        -input filename... - input files ("-" for stdin).
        -inclusive - include all shifts (include only unique or consistent is default).
        -keep_sequence - keep current sequence.
        -limit - limit to number of possible shifts for each type.


concatenate.pl -- Concatenates multiple peak files into new peak file.
usage: concatenate.pl out_peak_file new_workbook_name [options] in_peak_file1 in_peak_file2 ...

peak_file  - name of peak file or "-" for standard input/output.
workbook_name - string to use as workbook name  or "-" to use old name.
options:
        -old_index - use old peak indexes.


create_bmrb.pl -- Converts a list of shift assignments in 3 column format into a BMRB file.

    usage: create_bmrb.pl input_assignment_file output_bmrb_file sequence_start sequence [options]

        input_assignment_file - name of assignment file or "-" for standard input.
                assignment file format:  ResidueName   AtomType    ShiftValue    [AmbiguityCode]
                        ResidueName - Residue followed by its position in the sequence  (ie. A32, G53).
                        AtomType - Type of Atom using BMRB conventions (ie. CA, CB, CG, HA1, HB3, HG22).
                        ShiftValue - The chemical shift value   (ie. 120.6 4.43, 3.84, 3.21).
                        AmbiguityCode - (optional) The ambiguity code (ie. 1 2 3 4 5 9).
        output_bmrb_file - name of the output BMRB file or  "-" for standard output.
        sequence_start - the starting residue number of the sequence.
        sequence - the protein sequence using single letter codes.
        options:
                -diasterio - give diasteriomer resonancess an ambiguity code of 2.
                -index index - assignment file uses the following indexing.


create_peak_list.pl -- Create a peak list given the shift values and intensity in separate columns. The script adds an index column to the front and destroys note columns and appends them to the workbook_name.
usage: create_peak_list.pl in_peak_file new_workbook_name out_peak_file note1 note2 ...

peak_file  - name of peak file or "-" for standard input/output.
workbook_name - string to use as workbook name.
note1 note2 ... - columns that should be appended to the workbook_name as notes and then deleted; range [1..].


create_split_doublet.pl -- Create split doublet from central peak with splittings dimension.

 usage: create_split_doublet.pl central_peaklist split_peaklist workbook_name split_dim

     central_peaklist - peak list of central peaks with splittings in last dimension.
    split_peaklist - peak list with split doublet.
    workbook_name - string to use as workbook name.
    split_dim - dimension to split.
 Hint: Useful to create peaklist to load into Sparky for assigning split doublets.

createSparkyNOESYPks.pl -- Create a variety of virtual Sparky NOESY peak lists from resonance assignments in bmrb format.
 
usage: createSparkyNOESYPks.pl input_bmrb_file output_peak_file [options]
 
                input_bmrb_file - bmrb file to read ("-" to read from standard input).
                output_peak_file - output file to write to ("-" to write to standard output).
                options:
                        -n15 - generate peak list for N15-edited NOESY.
                        -c13 - generate peak list for C13-edited NOESY.
                        -both - generate peak list for combined N15-C13-edited NOESY.
                        -4D - generate 4D peak list.
                        -local_connectivity - limit peaks to 2- and 3-bond local connectivity peaks.
                        -aromatic - include aromatic resonances.
                        -diagonal - include diagonal peaks.
                        -degenerate - include peaks with degenerate resonances.
 
  Hint: Sparky reads them in using the rp command.


dyanaUPL2cmap.pl -- Converts the backbone NOEs from a DYANA UPL constraint file to the CMap format.

  usage: dyanaUPL2cmap.pl [options] input_dyana_file output_cmap_file 

input_dyana_file  - NOE distance constraints in DYANA UPL format
output_cmap_file  - NOE information in CMap format
options:
             -append                     - append CMap file
             -intra                         - include intraresidue NOEs.
             -convert strong medium weak - the NOEs with distance < strong are +++ (default 3.5)
                                                      < medium are ++ (default 4.5)
                                                      < weak are + (default 8.5).
                                                     NOEs with distance >= weak are disregarded   - .


 examine_spin_systems.pl -- Groups peaks into spin systems and examines them for completeness and overlap.

 usage: examine_spin_systems.pl in_peak_file out_peak_file [options] Htol Ntol CACBtol HAtol Ctol

        peak_file       - name of peak file or "-" for standard input/output.  The dimensions of the peaks are Hdim Ndim Xdim.
        Htol Ntol       - Amide H and N dimension tolerances for comparing peaks.
        CACBtol       - CA/CB dimension tolerances for comparing peaks.
        HAtol           - HA dimension tolerance for comparing peaks.
        Ctol             - C dimension tolerance for comparing peaks.
        options:
                -deuteration fraction - set the amount of deuteration to the given fraction (default is 0).
                -skip_matching_overlap - ignore overlap spin systems when determining nearest neighbors.
                -skip_peak_overrides - ignore peak based assignment constraints.
                -ignore peak_list - type of peak list to ignore in analysis.
                -noroot - do not require HSQC or HNCO peak in evaluating ESS Scores.
                -error_only - only list spin systems with errors.
                -html filename - print a comprehensive report in html.
                -sequence sequence - use given sequence to produce peak list based summary.
                -phase workbookname - given peak list has intensity sign that distinguishing resonance type (i.e. CA+/CB- for HNCACB).
                -gly_phase workbookname - given peak list has negative intensity sign indicate a glycine residue (i.e. CA+/GlyCA- for HNcoCA).

   Hint:  First use concatenate.pl to create a peak list from all the other peak lists.
           Use a "-" for the workbookname and the "-old_index" option in the concatenation.
           List HSQC and HNCO peaklists first in the concatenation.
           Use standard workbooknames in the individual peak lists.
           Recognized workbooknames are: HNHAHB, HNcoHB, HNcoCACACB, hCCcoNH, HNCACACB, HNHA, HNcoCACB, HNcoCA, HNHB, HNcaCOintra, HNCB, hCCcoNH_ILV, HNcoHAHB, HNCO, HNCACB, HNcoCB, HNCA, HNcaCO, HNcoHA, HSQC


extract_columns.pl -- Extract whitespace-delimited columns in the given order.
usage: extract_columns.pl col1 col2 col3 ...

col1 col2 ... - column number; range [1..].


extract_dims.pl -- Generate new peak file by extracting/reorganizing specific dimensions from another peak file.
usage: extract_dims.pl in_peak_file new_workbook_name out_peak_file dim1 dim2 ...

peak_file  - name of peak file or "-" for standard input/output.
workbook_name - string to use as workbook name.
dim1 dim2 ...  - column numbers for dimensions to extract in the order they should appear; range [1..].


extract_dup_assignments.pl -- Extracts groups of peaks that have duplicate assignments in 'Notes' column.
 usage: find_duplicate_assignments.pl in_peak_file workbook_name out_peak_file inclusion_toggle

 peak_file        - name of peak file or "-" for standard input.
 workbook_name        - name of workbook.
 inclusion_toggle:
            inc(lusive)    - include only peaks with duplicates.
            exc(lusive)    - exclude peaks with duplicates.


extract_duplicates.pl -- Extract a group of peaks that have duplicate chemical shifts.
usage: extract_duplicates.pl in_peak_file inclusion_toggle new_workbook_name out_peak_file to11 tol2 ...

peak_file  - name of peak file or "-" for standard input/output.
inclusion_toggle:
      inc(lusive) - include only peaks with duplicates.
      exc(lusive) - exclude peaks with duplicates.
      low      - include only the low intensity representative of each set of duplicates.
      high      - include only the high intensity representative of each set of duplicates.
workbook_name - string to use as workbook name  or "-" to use old name.
tol1 tol2 ...  - dimension tolerances for comparison or "0" not to use specific dimension.


extract_by_dup_count.pl -- Extract certain groups of peaks with matching chemical shifts and a certain peak count.
usage: extract_by_dup_count.pl in_peak_file count_qualifier new_workbook_name out_peak_file to11 tol2 ...

peak_file  - name of peak file or "-" for standard input/output.
count_qualifier  - (comparison_operator peak_count).
      comparison_operator  - "equal","less","greater","less_equal","greater_equal".
      peak_count  - number of peaks in the glob.
workbook_name  - string to use as workbook name or "-" to use old name.
tol1 tol2 ...  - dimension tolerances for comparison or "0" not to use specific dimension


extract_by_filter.pl -- Extract a group of peaks using a set of filter peaks.
usage: extract_by_filter.pl in_peak_file filter_peak_file inclusion_toggle new_workbook_name out_peak_file tol1 tol2 ...

peak_file  - name of peak file or "-" for standard input/output.
filter_peak_file - name of peak file.
inclusion_toggle:
      inc(lusive) - include peaks that match filter.
      exc(lusive) - exclude peak that match filter.
workbook_name  - string to use as workbook name or "-" to use old name.
tol1 tol2 ...  - dimension tolerances for comparison or "0" not to use specific dimension


extract_by_intensity.pl -- Extract the top intensity peaks based on a fraction of the file to include.
usage: extract_by_intensity.pl in_peak_file include_fraction new_workbook_name out_peak_file

peak_file   - name of peak file or "-" for standard input/output.
include_fraction - the fraction of strongest intensity peaks to include.
workbook_name  - string to use as workbook name or "-" to use old name.


extract_by_intensity2.pl -- Extract the top intensity peaks based upon the top or average intensity.
usage: extract_by_intensity2.pl in_peak_file paragon_intensity include_fraction new_workbook_name out_peak_file

peak_file    - name of peak file or "-" for standard input/output.
paragon_intensity:
      top/high  - use highest intensity.
      ave(rage) - use average intensity.
include_fraction  - fraction of paragon_intensity to use as the include threshold.
workbook_name   - string to use as workbook name or "-" to use old name.


extract_by_intensity3.pl -- Extract peaks with an abs(intensity) greater than a threshhold.
usage: extract_by_intensity3.pl in_peak_file threshhold new_workbook_name out_peak_file

peak_file   - name of peak file or "-" for standard input/output.
threshhold  - minimum absolute value for an included peak.
workbook_name  - string to use as workbook name or "-" to use old name.


extract_by_phase.pl -- Extract phase-labelled peaks into separate peaks file.
usage: extract_by_phase.pl in_peak_file toggle_sign new_workbook_name out_peak_file

peak_file  - name of peak file or "-" for standard input/output.
toggle_sign:
      pos(itive) - for positive intensity peaks.
      neg(ative) - for negative intensity peaks.
workbook_name - string to use as workbook name or "-" to use old name.


extract_by_shift.pl -- Extract peaks with chemical shifts above or below certain values.
usage: extract_by_shift.pl in_peak_file new_workbook_name out_peak_file shift_comparison1 \
                                                 shift_comparison2 ...

peak_file   - name of peak file or "-" for standard input/output.
workbook_name  - string to use as workbook name.
shift_comparison - (comparison_operator shift_value) for each dimension.
comparison_operator - "none","equal","less","greater","less_equal","greater_equal".
shift_value         - value to compare to.


extract_by_shift_range.pl -- Extract peaks with chemical shifts within a range of values.
  usage: extract_by_shift_range.pl in_peak_file new_workbook_name out_peak_file shift_range1 shift_range2 ...

    peak_file  - name of peak file or "-" for standard input/output.
    workbook_name  - string to use as workbook name.
    shift_range  - (lower_bound upper_bound) or (N N) for none.

file_history.pl -- Print File History of a peak file.
usage: file_history.pl in_peak_file.

    peak_file - name of peak file or "-" for standard input.


jval2bmrb.pl -- Converts AutoStructure Input J HNHA values into BMRB coupling constants save frame
usage: jval2bmrb.pl in_j_file in_bmrb_file out_bmrb_file [options]

  j_file           - name of j file or "-" for standard input/output.
 bmrb_file   - name of BMRB file.


manage_bmrb.pl -- manage the save frames in a bmrb file
 usage: manage_bmrb.pl input_bmrb_file [options]

        input_bmrb_file - bmrb file to read ("-" to read from standard input).
        options:
               -add bmrb_file save_frame_list - add list of comma-seperated save frames from the bmrb_file.
               -delete save_frame_list - delete the list of comma-separated save frames.
               -extract save_frame_alist - extract comma-separated list of save frames in the given order.
               -output bmrb_file - bmrb_file to save changes to ("-" to write to standard output).


  manage_cmap.pl -- manage the sections and columns in a cmap file.
  usage: manage_cmap.pl input_cmap_file [options]

        input_cmap_file - cmap file to read ("-" to read from standard input).
        no options: lists sections of the input_cmap_file.
        options:
                -add cmap_file "column_list1 column_list2 ..." - add quoted list of sections from another cmap file.
                        column_list - list of comma-separated columns (use "all" for all remaining columns).
                -delete column_list - delete the list of comma-separated columns.
                -force - force the changes.
                -nocollapse - make all sections full (no collapse).
                -collapse - collapse all sections.
                -resort - resort row order.
                -trim range_list - remove rows in the given comma-separated index ranges (i.e. 4-7,9-12).
                -output cmap_file - cmap_file to save changes to ("-" to write to standard output).
                -extract "column_list1 column_list2 ..." - extract quoted list of sections in the given order.
                        column_list - list of comma-separated columns (use "all" for all remaining columns).


match_recombine.pl -- Generate new peaks from the parts of other peaks that match along certain dimensions.
usage: match_recombine.pl in_peak_file1 in_peak_file2 new_workbook_name out_peak_file intensity_source triple1 triple2 ...

peak_file   - name of peak file or "-" for standard input/output.
in_peak_file2   - name of peak file.
workbook_name  - string to use as workbook name.
intensity_source - [1,2] = which peak_file to use for intensity.
triple1 ...   - (tolerance toggle1_include toggle2_include) for each dimension.
      tolerance      - tolerance for comparison or "0" not to use dimension.
      toggle_include - "1" to include dimension from file or "0" not to include.


missing_shifts.pl --  Reports the missing AtomTypes in a given BMRB file.

   usage: missing_shifts.pl [ options ] input_bmrb_file

        input_bmrb_file - the BMRB file to check.
        options:

            -noaromatics - will not check for ring atoms.
        -expected - print expected values for shifts.
        -std - print standard deviations for shifts.
        -long - print each shift on a separate line.
        -printstats - print percent missing data for all AtomTypes.
        -nonreleavant - print info on all shifts and not just NMR relevant shifts.
        -count - print a count of missing shifts.
        -Conly - print carbon shifts only.
        -Nonly - print nitrogen shifts only.
        -Honly - print hydrogen shifts only.
        -Cgreater value - print carbons with average carbons shifts greater than value.
        -Ngreater value - print carbons with average nitrogen shifts greater than value.
        -Hgreater value - print carbons with average hydrogren shifts greater than value.
        -Cless value - print carbons with average carbons shifts less than value.
        -Nless value - print carbons with average nitrogen shifts less than value.
        -Hless value - print carbons with average hydrogren shifts less than value.

pales2cns.pl -- Converts data from pales output table format to cns input format for RDCs.
usage: pales2cns.pl input_file output_file extract_toggle [option]

        input_file        - PALES output table of measured and predicted RDCs.
        output_file        - CNS formatted file for RDCs.
        extract_toggle:
               meas(ured)    - measured RDCs.
               pred(icted)    - RDCs predicted by PALES.
        options:
               -margin n - n is the error margin to use in CNS calculations.

pks2bmrb.pl -- Converts AutoAssign peak list into BMRB spectral peak list save frame.

   usage: pks2bmrb.pl in_bmrb_file in_peak_file out_bmrb_file [options] [-dim descrip1 descrip2 ...]

       peak_file      - name of peak file or "-" for standard input/output.
    bmrb_file      - name of BMRB file or "-" for standard input/output.
    options:
           -label experiment_label - experiment label (default is workbook name of first peak).
        -dim descrip1 ... - list of dimension descriptions.
             nuclei_type - type of nuclei in dimension (i.e. 1H, 13C, etc.).
            spectral_region - spectral region for dimension (i.e. CA, H-C, CA/CB, etc.).
            shift_error - shift error.

 pks2SparkyPks.pl -- Converts an AutoAssign peak list file to a Sparky peak list file.
 
   usage: pks2SparkyPks.pl in_peak_file out_peak_file
peak_file     - name of peak file or "-" for standard input/output.

rdc2cns.pl -- Converts RDCs from peak list format to cns format.
 usage: rdc2cns.pl in_peak_file cns_out_file dim1_atom_type dim2_atom_type [option]

    in_peak_file  - name of peak file or "-" for standard input/output.
    cns_out_file  - name of CNS-formatted output file.
    dim1_atom_type  - Atom type for the 1Dim column.
    dim2_atom_type  - Atom type for the 2Dim column.
    options:
           -margin n  - n is the error margin to use in CNS calculations.

 Assumption: Residue name and numbers are stored in the Notes column.
                          RDCs in Hz are stored in the last *Dim column.
                          CNS convention is used for naming atom types for the each dimension.
                          RDCs are only for intra-residue atoms.

rdc2pales.pl -- Converts RDCs from peak list format to PALES input table.
 usage: rdc2pales.pl in_peak_file pales_inp_tab_file dim1_atom_type dim2_atom_type [option]

    in_peak_file        - name of peak file or "-" for standard input.
    pales_inp_tab_file    - name of PALES input-format table file.
    dim1_atom_type        - Atom type for the 1Dim column.
    dim2_atom_type        - Atom type for the 2Dim column.
    option:
            -seq sequence_file: sequence of ENTIRE, in 1-letter format.

 Assumption: Residue name and numbers are stored in the Notes column.
                          RDCs in Hz are stored in the last *Dim column.
                          PALES convention is used for naming atom types for the each dimension.
                          RDCs are only for intra-residue atoms.


remove_peaks.pl -- Removes peaks from a peak list with the given indeces.
 
   usage: remove_peaks.pl in_peak_file out_peak_file index1 index2 ...
     peak_file      - name of peak file or "-" for standard input/output.
     index1 index2 ... - list of peak indeces to remove.

sec2bmrb.pl -- Converts AutoStructure output .sec file into BMRB secondary_structure save frame.

usage: sec2bmrb.pl in_sec_file  in_bmrb_file out_bmrb_file

 
 sec_file   - name of sec file or "-" for standard input/output.
 bmrb_file   - name of BMRB file or "-" for standard input/output.

 sparkyPks2bmrb.pl -- Converts a sparky peaklist into a BMRB assigned peak list save frame.

   usage: sparkyPks2bmrb.pl in_bmrb_file out_bmrb_file [options] sparky_peak_files

        sparky_peak_file - name of sparky peak file.
        bmrb_file        - name of the bmrb file.
        options:
                -no_intensity    - sparky peak lists do not have intensities.
                -no_error        - do not put a shift_error into the bmrb file.


sparkyPks2pks.pl -- Create a peak list given the shift values and intensity in separate columns.  It also tries to assert a HN, N15, HX, CX, CO and X dimension ordering.

usage:  sparkyPks2pks.pl in_peak_file new_workbook_name out_peak_file

  peak_file  - name of peak file or "-" for standard input/output.
 workbook_name - string to use as workbook name.

sparkyRL2bmrb.pl -- Converts Sparky resonance list into a BMRB file.
usage: same as create_bmrb.pl

tag_peaks.pl   -- Extract a group of peaks using a set of filter peaks and tag them.

  usage: tag_peaks.pl in_peak_file  filter_peak_file   new_workbook_name  out_peak_file  tol1 tol2 ...

        peak_file        - name of peak file or "-" for standard input/output.
        filter_peak_file - name of peak file.
        workbook_name    - string to use as workbook name.
        tol1 tol2 ...    - dimension tolerances for comparison or "0" not to use specific dimension.


typing_degeneracy.pl -- Calculates the typing degeneracy for a given sequence.

  usage:  typing_degeneracy.pl [options]

        options:
            -cmap cmap_file - input cmap file to analyze (overrides -sequence).
            -bmrb bmrb_file - input bmrb file to analyze (overrides -sequence).
            -entity id_num  - which entity to analyze in the input bmrb file.
            -sequence sequence - sequence to analyze.

            -output cmap_file - output file to write bar graphs in.
            -length min_length - minimum length of degenerate sequences to print (default 4).
            -similarity min - minimum segment similarity to consider degenerate (default 0.5).
            -CG - use a residue similarity matrix which reflects CG's being used in the amino acid typing.
            -linkage - create linkage strength row only.
            -strength min_strength - minimum linkage strength for defining assigned segments (default 2).
            -typing - create typing degeneracy bar graph only.
            -aromatic - use aromatics in typing for evaluation of mapping uniqueness.
            -deuteration fraction - set the amount of deuteration to the given fraction (default is 0).
            -unique ratio - minimum probability ratio for a uniquely mapped segment (default 1000).
            -noesy strength - strength of a noesy link (default 1).
          -dangerous color - graphic color to represent dangerous (highly suspicious) segments in type degeneracy BarGraph Row (default A).
            -suspicious color - graphic color to represent suspicious segments in type degeneracy BarGraph Row (default B).
            -tolerance atom1 tol1 atom2 tol2 ... - tolerances for matching intra and sequential shifts.
                    atom - name of atom.
                    tol - maximum tolerance to accept when comparing chemical shift values.


validate_assignments.pl -- Validates assignments in bmrb format.

  usage: validate_assignments.pl [options] input_bmrb_file

        bmrb_file  - current assignments in bmrb format
        options:
                        -aromatic - consider aromatic carbons in typing.
                        -Ctolerance Cequiv - sets the tolerence for resolving equivalent carbons when analyzing a hCCcoNH TOCSY.
                        -clean - remove unknown atom and convert ambiguous atoms (i.e. HB converted to ambiguous HB2 and HB3).
                        -deuteration fraction - set the amount of deuteration to the given fraction (default is 0).
                        -fmean - force the printing of mean values.
                        -fixCACB - fix CA,CB shifts during suspicious typing.
                        -limit n - limit tocsy typing analysis to n peaks per residue.
                        -nitrogen - test the nitrogen shifts too.
                        -nosidechain - don't type considering CG, CD, etc.
                        -notocsy - don't type considering the tocsy data.
                        -output bmrb_file - output bmrb file.
                        -rules consistency - check shift order rules of given/better consistency; range [0.5-1] (default 0.99).
                        -shift min - minimum probability considered consistent (default 0.001).
                        -std - print standard deviation info with mean.
                        -sterilize - remove missassigned atoms
                        -tocsy peak_file - hCCcoNH TOCSY peak list file to analyze.
                        -tolerance Hmax Nratio - tolerance for detecting amide overlap (default 0.04 7 respectively).
                        -type sum  - sum of top typing probabilities used as a cutoff in type checking (default 0.999).
                        -verbose - print out extra info while cleaning or sterilizing.
                        -anomalous - only display items with an overall_status of Anomalous.
                        -anno_ltr - generate output to be used for BMRB annotators to send back to the author.  Generally a very short output.
                        -notconsistent - Only print out information that does not have an overal_status value of Consistent.
                        -star_output - output in NMR-STAR 3.0 format.
                        -suspicious - only display items with an overall_status of Suspicious.