diff --git a/biobb_dna/backbone/bipopulations.py b/biobb_dna/backbone/bipopulations.py index 89a1fac..d799be0 100755 --- a/biobb_dna/backbone/bipopulations.py +++ b/biobb_dna/backbone/bipopulations.py @@ -19,6 +19,7 @@ class BIPopulations(BiobbObject): """ | biobb_dna BIPopulations | Calculate BI/BII populations from epsilon and zeta parameters. + | Calculate BI/BII populations from epsilon and zeta parameters. Args: input_epsilC_path (str): Path to .ser file for helical parameter 'epsilC'. File type: input. `Sample file `_. Accepted formats: ser (edam:format_2330). diff --git a/biobb_dna/backbone/canonicalag.py b/biobb_dna/backbone/canonicalag.py index f0ca5a6..8fcf795 100755 --- a/biobb_dna/backbone/canonicalag.py +++ b/biobb_dna/backbone/canonicalag.py @@ -19,6 +19,7 @@ class CanonicalAG(BiobbObject): """ | biobb_dna CanonicalAG | Calculate Canonical Alpha/Gamma populations from alpha and gamma parameters. + | Calculate Canonical Alpha/Gamma populations from alpha and gamma parameters. Args: input_alphaC_path (str): Path to .ser file for helical parameter 'alphaC'. File type: input. File type: input. `Sample file `_. Accepted formats: ser (edam:format_2330). diff --git a/biobb_dna/backbone/puckering.py b/biobb_dna/backbone/puckering.py index f6c7c02..0e3237f 100755 --- a/biobb_dna/backbone/puckering.py +++ b/biobb_dna/backbone/puckering.py @@ -19,6 +19,7 @@ class Puckering(BiobbObject): """ | biobb_dna Puckering | Calculate Puckering from phase parameters. + | Calculate North/East/West/South distribution of sugar puckering backbone torsions. Args: input_phaseC_path (str): Path to .ser file for helical parameter 'phaseC'. File type: input. `Sample file `_. Accepted formats: ser (edam:format_2330). diff --git a/biobb_dna/curvesplus/biobb_canal.py b/biobb_dna/curvesplus/biobb_canal.py index 16b2bb2..f01c3f4 100755 --- a/biobb_dna/curvesplus/biobb_canal.py +++ b/biobb_dna/curvesplus/biobb_canal.py @@ -17,6 +17,7 @@ class Canal(BiobbObject): """ | biobb_dna Canal | Wrapper for the Canal executable that is part of the Curves+ software suite. + | The Canal program is used to analyze the curvature of DNA structures. Args: input_cda_file (str): Input cda file, from Cur+ output. File type: input. `Sample file `_. Accepted formats: cda (edam:format_2330). diff --git a/biobb_dna/curvesplus/biobb_canion.py b/biobb_dna/curvesplus/biobb_canion.py index ac8b1c2..3f560b0 100755 --- a/biobb_dna/curvesplus/biobb_canion.py +++ b/biobb_dna/curvesplus/biobb_canion.py @@ -16,6 +16,7 @@ class Canion(BiobbObject): """ | biobb_dna Canion | Wrapper for the Canion executable that is part of the Curves+ software suite. + | Analyzes the trajectory of ions around a DNA molecule. Args: input_cdi_path (str): Trajectory input file. File type: input. `Sample file `_. Accepted formats: cdi (edam:format_2330). diff --git a/biobb_dna/curvesplus/biobb_curves.py b/biobb_dna/curvesplus/biobb_curves.py index 333868c..1f09148 100755 --- a/biobb_dna/curvesplus/biobb_curves.py +++ b/biobb_dna/curvesplus/biobb_curves.py @@ -16,6 +16,7 @@ class Curves(BiobbObject): """ | biobb_dna Curves | Wrapper for the Cur+ executable that is part of the Curves+ software suite. + | The Cur+ program is used to analyze the structure of nucleic acids and their complexes. Args: input_struc_path (str): Trajectory or PDB input file. File type: input. `Sample file `_. Accepted formats: trj (edam:format_3910), pdb (edam:format_1476), netcdf (edam:format_3650), nc (edam:format_3650). diff --git a/biobb_dna/dna/dna_averages.py b/biobb_dna/dna/dna_averages.py index 3a973f3..c0d9bd0 100755 --- a/biobb_dna/dna/dna_averages.py +++ b/biobb_dna/dna/dna_averages.py @@ -19,6 +19,7 @@ class HelParAverages(BiobbObject): """ | biobb_dna HelParAverages | Load .ser file for a given helical parameter and read each column corresponding to a base calculating average over each one. + | Calculate average values for each base pair and save them in a .csv file. Args: input_ser_path (str): Path to .ser file for helical parameter. File is expected to be a table, with the first column being an index and the rest the helical parameter values for each base/basepair. File type: input. `Sample file `_. Accepted formats: ser (edam:format_2330). diff --git a/biobb_dna/dna/dna_bimodality.py b/biobb_dna/dna/dna_bimodality.py index 1e660fc..9ffa80b 100755 --- a/biobb_dna/dna/dna_bimodality.py +++ b/biobb_dna/dna/dna_bimodality.py @@ -24,6 +24,7 @@ class HelParBimodality(BiobbObject): """ | biobb_dna HelParBimodality | Determine binormality/bimodality from a helical parameter series dataset. + | Determine binormality/bimodality from a helical parameter series dataset. Args: input_csv_file (str): Path to .csv file with helical parameter series. If `input_zip_file` is passed, this should be just the filename of the .csv file inside .zip. File type: input. `Sample file `_. Accepted formats: csv (edam:format_3752). diff --git a/biobb_dna/dna/dna_timeseries.py b/biobb_dna/dna/dna_timeseries.py index 16ada3c..5e50928 100755 --- a/biobb_dna/dna/dna_timeseries.py +++ b/biobb_dna/dna/dna_timeseries.py @@ -20,6 +20,7 @@ class HelParTimeSeries(BiobbObject): """ | biobb_dna HelParTimeSeries | Created time series and histogram plots for each base pair from a helical parameter series file. + | The helical parameter series file is expected to be a table, with the first column being an index and the rest the helical parameter values for each base/basepair. Args: input_ser_path (str): Path to .ser file for helical parameter. File is expected to be a table, with the first column being an index and the rest the helical parameter values for each base/basepair. File type: input. `Sample file `_. Accepted formats: ser (edam:format_2330). diff --git a/biobb_dna/interbp_correlations/interbpcorr.py b/biobb_dna/interbp_correlations/interbpcorr.py index 19a6c25..9517a21 100755 --- a/biobb_dna/interbp_correlations/interbpcorr.py +++ b/biobb_dna/interbp_correlations/interbpcorr.py @@ -21,6 +21,7 @@ class InterBasePairCorrelation(BiobbObject): """ | biobb_dna InterBasePairCorrelation | Calculate correlation between all base pairs of a single sequence and for a single helical parameter. + | Calculate correlation between neighboring base pairs and pairs of helical parameters. Args: input_filename_shift (str): Path to .ser file with data for helical parameter 'shift'. File type: input. `Sample file `_. Accepted formats: ser (edam:format_2330). diff --git a/biobb_dna/interbp_correlations/interhpcorr.py b/biobb_dna/interbp_correlations/interhpcorr.py index f4ac0ef..4980b7b 100755 --- a/biobb_dna/interbp_correlations/interhpcorr.py +++ b/biobb_dna/interbp_correlations/interhpcorr.py @@ -18,6 +18,7 @@ class InterHelParCorrelation(BiobbObject): """ | biobb_dna InterHelParCorrelation | Calculate correlation between helical parameters for a single inter-base pair. + | Calculate correlation between helical parameters for a single inter-base pair. Args: input_filename_shift (str): Path to .csv file with data for helical parameter 'shift'. File type: input. `Sample file `_. Accepted formats: csv (edam:format_3752). diff --git a/biobb_dna/interbp_correlations/interseqcorr.py b/biobb_dna/interbp_correlations/interseqcorr.py index 9430ae6..a5cb27a 100755 --- a/biobb_dna/interbp_correlations/interseqcorr.py +++ b/biobb_dna/interbp_correlations/interseqcorr.py @@ -19,6 +19,7 @@ class InterSequenceCorrelation(BiobbObject): """ | biobb_dna InterSequenceCorrelation | Calculate correlation between all base pairs of a single sequence and for a single helical parameter. + | Calculate correlation between all base pairs of a single sequence and for a single helical parameter. Args: input_ser_path (str): Path to .ser file with data for single helical parameter. File type: input. `Sample file `_. Accepted formats: ser (edam:format_2330). diff --git a/biobb_dna/intrabp_correlations/intrabpcorr.py b/biobb_dna/intrabp_correlations/intrabpcorr.py index 0f8445c..8856939 100755 --- a/biobb_dna/intrabp_correlations/intrabpcorr.py +++ b/biobb_dna/intrabp_correlations/intrabpcorr.py @@ -21,6 +21,7 @@ class IntraBasePairCorrelation(BiobbObject): """ | biobb_dna IntraBasePairCorrelation | Calculate correlation between all intra-base pairs of a single sequence and for a single helical parameter. + | Calculate correlation between neighboring base pairs and pairs of helical parameters. Args: input_filename_shear (str): Path to .ser file with data for helical parameter 'shear'. File type: input. `Sample file `_. Accepted formats: ser (edam:format_2330). diff --git a/biobb_dna/intrabp_correlations/intrahpcorr.py b/biobb_dna/intrabp_correlations/intrahpcorr.py index 55d3ae3..bdf6cd7 100755 --- a/biobb_dna/intrabp_correlations/intrahpcorr.py +++ b/biobb_dna/intrabp_correlations/intrahpcorr.py @@ -18,6 +18,7 @@ class IntraHelParCorrelation(BiobbObject): """ | biobb_dna IntraHelParCorrelation | Calculate correlation between helical parameters for a single intra-base pair. + | Calculate correlation between helical parameters for a single intra-base pair. Args: input_filename_shear (str): Path to .csv file with data for helical parameter 'shear'. File type: input. `Sample file `_. Accepted formats: csv (edam:format_3752). diff --git a/biobb_dna/intrabp_correlations/intraseqcorr.py b/biobb_dna/intrabp_correlations/intraseqcorr.py index 8d13dfb..013d675 100755 --- a/biobb_dna/intrabp_correlations/intraseqcorr.py +++ b/biobb_dna/intrabp_correlations/intraseqcorr.py @@ -19,6 +19,7 @@ class IntraSequenceCorrelation(BiobbObject): """ | biobb_dna IntraSequenceCorrelation | Calculate correlation between all intra-base pairs of a single sequence and for a single helical parameter. + | Calculate correlation between all intra-base pairs of a single sequence and for a single helical parameter. Args: input_ser_path (str): Path to .ser file with data for single helical parameter. File type: input. `Sample file `_. Accepted formats: ser (edam:format_2330).