Merge branch 'master' of github.com:bioexcel/biobb_dna

bioexcel · May 24, 2024 · a75db9b · a75db9b
2 parents 16b78f3 + 0bec217
commit a75db9b
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diff --git 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 <https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/backbone/canal_output_epsilC.ser>`_. Accepted formats: ser (edam:format_2330).

diff --git 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 <https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/backbone/canal_output_alphaC.ser>`_. Accepted formats: ser (edam:format_2330).

diff --git 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 <https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/backbone/canal_output_phaseC.ser>`_. Accepted formats: ser (edam:format_2330).

diff --git 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 <https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/curvesplus/curves_output.cda>`_. Accepted formats: cda (edam:format_2330).

diff --git 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 <https://mmb.irbbarcelona.org/biobb-dev/biobb-api/public/samples/THGA_K.cdi>`_. Accepted formats: cdi (edam:format_2330).

diff --git 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 <https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/curvesplus/structure.stripped.trj>`_. 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
@@ -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 <https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/dna/canal_output_shift.ser>`_. Accepted formats: ser (edam:format_2330).

diff --git 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 <https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/dna/series_shift_AT.csv>`_. Accepted formats: csv (edam:format_3752).

diff --git 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 <https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/dna/canal_output_shift.ser>`_. Accepted formats: ser (edam:format_2330).

diff --git 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 <https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/correlation/canal_output_shift.ser>`_. Accepted formats: ser (edam:format_2330).

diff --git 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 <https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/stiffness/series_shift_AA.csv>`_. Accepted formats: csv (edam:format_3752).

diff --git 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 <https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/correlation/canal_output_roll.ser>`_. Accepted formats: ser (edam:format_2330).

diff --git 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 <https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/correlation/canal_output_shear.ser>`_. Accepted formats: ser (edam:format_2330).

diff --git 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 <https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/correlation/series_shear_A.csv>`_. Accepted formats: csv (edam:format_3752).

diff --git 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 <https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/correlation/canal_output_buckle.ser>`_. Accepted formats: ser (edam:format_2330).

diff --git a/biobb_dna/json_schemas/average_stiffness.json b/biobb_dna/json_schemas/average_stiffness.json
@@ -3,7 +3,7 @@
     "$id": "http://bioexcel.eu/biobb_dna/json_schemas/1.0/average_stiffness",
     "name": "biobb_dna AverageStiffness",
     "title": "Calculate average stiffness constants for each base pair of a trajectory's series.",
-    "description": null,
+    "description": "Calculate the average stiffness constants for each base pair of a trajectory's series. The input is a .ser file with the helical parameter values for each base/basepair. The output is a .csv file with the average stiffness constants for each base pair and a .jpg file with a plot of the average stiffness constants for each base pair.",
     "type": "object",
     "info": {
         "wrapped_software": {

diff --git a/biobb_dna/json_schemas/basepair_stiffness.json b/biobb_dna/json_schemas/basepair_stiffness.json
@@ -3,7 +3,7 @@
     "$id": "http://bioexcel.eu/biobb_dna/json_schemas/1.0/basepair_stiffness",
     "name": "biobb_dna BPStiffness",
     "title": "Calculate stiffness constants matrix between all six helical parameters for a single base pair step.",
-    "description": null,
+    "description": "Calculate stiffness constants matrix between all six helical parameters for a single base pair step.",
     "type": "object",
     "info": {
         "wrapped_software": {

diff --git a/biobb_dna/json_schemas/biobb_canal.json b/biobb_dna/json_schemas/biobb_canal.json
@@ -3,7 +3,7 @@
     "$id": "http://bioexcel.eu/biobb_dna/json_schemas/1.0/biobb_canal",
     "name": "biobb_dna Canal",
     "title": "Wrapper for the Canal executable that is part of the Curves+ software suite.",
-    "description": null,
+    "description": "The Canal program is used to analyze the curvature of DNA structures.",
     "type": "object",
     "info": {
         "wrapped_software": {

diff --git a/biobb_dna/json_schemas/biobb_canion.json b/biobb_dna/json_schemas/biobb_canion.json
@@ -3,7 +3,7 @@
     "$id": "http://bioexcel.eu/biobb_dna/json_schemas/1.0/biobb_canion",
     "name": "biobb_dna Canion",
     "title": "Wrapper for the Canion executable  that is part of the Curves+ software suite.",
-    "description": null,
+    "description": "Analyzes the trajectory of ions around a DNA molecule.",
     "type": "object",
     "info": {
         "wrapped_software": {

diff --git a/biobb_dna/json_schemas/biobb_curves.json b/biobb_dna/json_schemas/biobb_curves.json
@@ -3,7 +3,7 @@
     "$id": "http://bioexcel.eu/biobb_dna/json_schemas/1.0/biobb_curves",
     "name": "biobb_dna Curves",
     "title": "Wrapper for the Cur+ executable  that is part of the Curves+ software suite.",
-    "description": null,
+    "description": "The Cur+ program is used to analyze the structure of nucleic acids and their complexes.",
     "type": "object",
     "info": {
         "wrapped_software": {

diff --git a/biobb_dna/json_schemas/bipopulations.json b/biobb_dna/json_schemas/bipopulations.json
@@ -3,7 +3,7 @@
     "$id": "http://bioexcel.eu/biobb_dna/json_schemas/1.0/bipopulations",
     "name": "biobb_dna BIPopulations",
     "title": "Calculate BI/BII populations from epsilon and zeta parameters.",
-    "description": null,
+    "description": "Calculate BI/BII populations from epsilon and zeta parameters.",
     "type": "object",
     "info": {
         "wrapped_software": {

diff --git a/biobb_dna/json_schemas/canonicalag.json b/biobb_dna/json_schemas/canonicalag.json
@@ -3,7 +3,7 @@
     "$id": "http://bioexcel.eu/biobb_dna/json_schemas/1.0/canonicalag",
     "name": "biobb_dna CanonicalAG",
     "title": "Calculate Canonical Alpha/Gamma populations from alpha and gamma parameters.",
-    "description": null,
+    "description": "Calculate Canonical Alpha/Gamma populations from alpha and gamma parameters.",
     "type": "object",
     "info": {
         "wrapped_software": {

diff --git a/biobb_dna/json_schemas/dna_averages.json b/biobb_dna/json_schemas/dna_averages.json
@@ -3,7 +3,7 @@
     "$id": "http://bioexcel.eu/biobb_dna/json_schemas/1.0/dna_averages",
     "name": "biobb_dna HelParAverages",
     "title": "Load .ser file for a given helical parameter and read each column corresponding to a base calculating average over each one.",
-    "description": null,
+    "description": "Calculate average values for each base pair and save them in a .csv file.",
     "type": "object",
     "info": {
         "wrapped_software": {

diff --git a/biobb_dna/json_schemas/dna_bimodality.json b/biobb_dna/json_schemas/dna_bimodality.json
@@ -3,7 +3,7 @@
     "$id": "http://bioexcel.eu/biobb_dna/json_schemas/1.0/dna_bimodality",
     "name": "biobb_dna HelParBimodality",
     "title": "Determine binormality/bimodality from a helical parameter series dataset.",
-    "description": null,
+    "description": "Determine binormality/bimodality from a helical parameter series dataset.",
     "type": "object",
     "info": {
         "wrapped_software": {

diff --git a/biobb_dna/json_schemas/dna_timeseries.json b/biobb_dna/json_schemas/dna_timeseries.json
@@ -3,7 +3,7 @@
     "$id": "http://bioexcel.eu/biobb_dna/json_schemas/1.0/dna_timeseries",
     "name": "biobb_dna HelParTimeSeries",
     "title": "Created time series and histogram plots for each base pair from a helical parameter series file.",
-    "description": null,
+    "description": "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.",
     "type": "object",
     "info": {
         "wrapped_software": {

diff --git a/biobb_dna/json_schemas/interbpcorr.json b/biobb_dna/json_schemas/interbpcorr.json
@@ -3,7 +3,7 @@
     "$id": "http://bioexcel.eu/biobb_dna/json_schemas/1.0/interbpcorr",
     "name": "biobb_dna InterBasePairCorrelation",
     "title": "Calculate correlation between all base pairs of a single sequence and for a single helical parameter.",
-    "description": null,
+    "description": "Calculate correlation between neighboring base pairs and pairs of helical parameters.",
     "type": "object",
     "info": {
         "wrapped_software": {

diff --git a/biobb_dna/json_schemas/interhpcorr.json b/biobb_dna/json_schemas/interhpcorr.json
@@ -3,7 +3,7 @@
     "$id": "http://bioexcel.eu/biobb_dna/json_schemas/1.0/interhpcorr",
     "name": "biobb_dna InterHelParCorrelation",
     "title": "Calculate correlation between helical parameters for a single inter-base pair.",
-    "description": null,
+    "description": "Calculate correlation between helical parameters for a single inter-base pair.",
     "type": "object",
     "info": {
         "wrapped_software": {

diff --git a/biobb_dna/json_schemas/interseqcorr.json b/biobb_dna/json_schemas/interseqcorr.json
@@ -3,7 +3,7 @@
     "$id": "http://bioexcel.eu/biobb_dna/json_schemas/1.0/interseqcorr",
     "name": "biobb_dna InterSequenceCorrelation",
     "title": "Calculate correlation between all base pairs of a single sequence and for a single helical parameter.",
-    "description": null,
+    "description": "Calculate correlation between all base pairs of a single sequence and for a single helical parameter.",
     "type": "object",
     "info": {
         "wrapped_software": {

diff --git a/biobb_dna/json_schemas/intrabpcorr.json b/biobb_dna/json_schemas/intrabpcorr.json
@@ -3,7 +3,7 @@
     "$id": "http://bioexcel.eu/biobb_dna/json_schemas/1.0/intrabpcorr",
     "name": "biobb_dna IntraBasePairCorrelation",
     "title": "Calculate correlation between all intra-base pairs of a single sequence and for a single helical parameter.",
-    "description": null,
+    "description": "Calculate correlation between neighboring base pairs and pairs of helical parameters.",
     "type": "object",
     "info": {
         "wrapped_software": {

diff --git a/biobb_dna/json_schemas/intrahpcorr.json b/biobb_dna/json_schemas/intrahpcorr.json
@@ -3,7 +3,7 @@
     "$id": "http://bioexcel.eu/biobb_dna/json_schemas/1.0/intrahpcorr",
     "name": "biobb_dna IntraHelParCorrelation",
     "title": "Calculate correlation between helical parameters for a single intra-base pair.",
-    "description": null,
+    "description": "Calculate correlation between helical parameters for a single intra-base pair.",
     "type": "object",
     "info": {
         "wrapped_software": {

diff --git a/biobb_dna/json_schemas/intraseqcorr.json b/biobb_dna/json_schemas/intraseqcorr.json
@@ -3,7 +3,7 @@
     "$id": "http://bioexcel.eu/biobb_dna/json_schemas/1.0/intraseqcorr",
     "name": "biobb_dna IntraSequenceCorrelation",
     "title": "Calculate correlation between all intra-base pairs of a single sequence and for a single helical parameter.",
-    "description": null,
+    "description": "Calculate correlation between all intra-base pairs of a single sequence and for a single helical parameter.",
     "type": "object",
     "info": {
         "wrapped_software": {

diff --git a/biobb_dna/json_schemas/puckering.json b/biobb_dna/json_schemas/puckering.json
@@ -3,7 +3,7 @@
     "$id": "http://bioexcel.eu/biobb_dna/json_schemas/1.0/puckering",
     "name": "biobb_dna Puckering",
     "title": "Calculate Puckering from phase parameters.",
-    "description": null,
+    "description": "Calculate North/East/West/South distribution of sugar puckering backbone torsions.",
     "type": "object",
     "info": {
         "wrapped_software": {

diff --git a/biobb_dna/stiffness/average_stiffness.py b/biobb_dna/stiffness/average_stiffness.py
@@ -20,6 +20,7 @@ class AverageStiffness(BiobbObject):
     """
     | biobb_dna AverageStiffness
     | Calculate average stiffness constants for each base pair of a trajectory's series.
+    | Calculate the average stiffness constants for each base pair of a trajectory's series. The input is a .ser file with the helical parameter values for each base/basepair. The output is a .csv file with the average stiffness constants for each base pair and a .jpg file with a plot of the average stiffness constants for each base pair.
 
     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 <https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/stiffness/canal_output_roll.ser>`_. Accepted formats: ser (edam:format_2330).

diff --git a/biobb_dna/stiffness/basepair_stiffness.py b/biobb_dna/stiffness/basepair_stiffness.py
@@ -19,6 +19,7 @@ class BPStiffness(BiobbObject):
     """
     | biobb_dna BPStiffness
     | Calculate stiffness constants matrix between all six helical parameters for a single base pair step.
+    | Calculate stiffness constants matrix between all six helical parameters for a single base pair step.
 
     Args:
         input_filename_shift (str): Path to csv file with data for helical parameter 'shift'. File type: input. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/stiffness/series_shift_AA.csv>`_. Accepted formats: csv (edam:format_3752)