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

bioexcel · Jul 25, 2023 · fa2fc48 · fa2fc48
2 parents 1344ae0 + ed522a2
commit fa2fc48
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diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -5,13 +5,17 @@
 # Required
 version: 2
 
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.7"
+
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
    configuration: biobb_analysis/docs/source/conf.py
 
 # Optionally set the version of Python and requirements required to build your docs
 python:
-   version: "3.7"
    install:
       - requirements: biobb_analysis/docs/requirements.txt
       - method: pip

diff --git a/README.md b/README.md
@@ -3,7 +3,7 @@
 [![](https://img.shields.io/conda/vn/bioconda/biobb_analysis?label=Conda)](https://anaconda.org/bioconda/biobb_analysis)
 [![](https://img.shields.io/conda/dn/bioconda/biobb_analysis?label=Conda%20Downloads)](https://anaconda.org/bioconda/biobb_analysis)
 [![](https://img.shields.io/badge/Docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_analysis?tab=tags)
-[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_analysis:4.0.0--pyhdfd78af_1)
+[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_analysis:4.0.1--pyhdfd78af_0)
 
 [![](https://img.shields.io/badge/OS-Unix%20%7C%20MacOS-blue)](https://github.com/bioexcel/biobb_analysis)
 [![](https://img.shields.io/pypi/pyversions/biobb-analysis.svg?label=Python%20Versions)](https://pypi.org/project/biobb-analysis/)
@@ -34,7 +34,7 @@ The latest documentation of this package can be found in our readthedocs site:
 [latest API documentation](http://biobb_analysis.readthedocs.io/en/latest/).
 
 ### Version
-v4.0.0 2023.1
+v4.0.1 2023.1
 
 ### Installation
 Using PIP:
@@ -44,7 +44,7 @@ Using PIP:
 * Installation:
 
 
-        pip install "biobb_analysis>=4.0.0"
+        pip install "biobb_analysis>=4.0.1"
 
 
 * Usage: [Python API documentation](https://biobb-analysis.readthedocs.io/en/latest/modules.html)
@@ -54,7 +54,7 @@ Using ANACONDA:
 * Installation:
 
 
-        conda install -c bioconda "biobb_analysis>=4.0.0"
+        conda install -c bioconda "biobb_analysis>=4.0.1"
 
 
 * Usage: With conda installation BioBBs can be used with the [Python API documentation](https://biobb-analysis.readthedocs.io/en/latest/modules.html) and the [Command Line documentation](https://biobb-analysis.readthedocs.io/en/latest/command_line.html)
@@ -64,13 +64,13 @@ Using DOCKER:
 * Installation:
 
 
-        docker pull quay.io/biocontainers/biobb_analysis:4.0.0--pyhdfd78af_1
+        docker pull quay.io/biocontainers/biobb_analysis:4.0.1--pyhdfd78af_0
 
 
 * Usage:
 
 
-        docker run quay.io/biocontainers/biobb_analysis:4.0.0--pyhdfd78af_1 <command>
+        docker run quay.io/biocontainers/biobb_analysis:4.0.1--pyhdfd78af_0 <command>
 
 
 Using SINGULARITY:
@@ -80,7 +80,7 @@ Using SINGULARITY:
 * Installation:
 
 
-        singularity pull --name biobb_analysis.sif https://depot.galaxyproject.org/singularity/biobb_analysis:4.0.0--pyhdfd78af_1
+        singularity pull --name biobb_analysis.sif https://depot.galaxyproject.org/singularity/biobb_analysis:4.0.1--pyhdfd78af_0
 
 
 * Usage:

diff --git a/biobb_analysis/__init__.py b/biobb_analysis/__init__.py
@@ -1,3 +1,3 @@
 name = "biobb_analysis"
 __all__ = ["ambertools", "gromacs"]
-__version__ = "4.0.0"
+__version__ = "4.0.1"
diff --git a/biobb_analysis/docs/source/command_line.md b/biobb_analysis/docs/source/command_line.md
@@ -1352,7 +1352,7 @@ Command:
 ```python
 gmx_cluster -h
 ```
-    usage: gmx_cluster [-h] [--config CONFIG] --input_structure_path INPUT_STRUCTURE_PATH --input_traj_path INPUT_TRAJ_PATH [--input_index_path INPUT_INDEX_PATH] --output_pdb_path OUTPUT_PDB_PATH
+    usage: gmx_cluster [-h] [--config CONFIG] --input_structure_path INPUT_STRUCTURE_PATH --input_traj_path INPUT_TRAJ_PATH [--input_index_path INPUT_INDEX_PATH] --output_pdb_path OUTPUT_PDB_PATH [--output_cluster_log_path OUTPUT_CLUSTER_LOG_PATH] [--output_rmsd_cluster_xpm_path OUTPUT_RMSD_CLUSTER_XPM_PATH] [--output_rmsd_dist_xvg_path OUTPUT_RMSD_DIST_XVG_PATH]
 
     Creates cluster structures from a given GROMACS compatible trajectory.
 
@@ -1361,6 +1361,12 @@ gmx_cluster -h
       --config CONFIG       Configuration file
       --input_index_path INPUT_INDEX_PATH
                             Path to the GROMACS index file. Accepted formats: ndx.
+      --output_cluster_log_path OUTPUT_CLUSTER_LOG_PATH
+                            Path to the output log file. Accepted formats: log.
+      --output_rmsd_cluster_xpm_path OUTPUT_RMSD_CLUSTER_XPM_PATH
+                            Path to the output xpm file. Accepted formats: xpm.
+      --output_rmsd_dist_xvg_path OUTPUT_RMSD_DIST_XVG_PATH
+                            Path to the output xvg file. Accepted formats: xvg.
 
     required arguments:
       --input_structure_path INPUT_STRUCTURE_PATH
@@ -1377,13 +1383,17 @@ Config input / output arguments for this building block:
 * **input_traj_path** (*string*): Path to the GROMACS trajectory file. File type: input. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/gromacs/trajectory.trr). Accepted formats: XTC, TRR, CPT, GRO, G96, PDB, TNG
 * **input_index_path** (*string*): Path to the GROMACS index file. File type: input. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/gromacs/index.ndx). Accepted formats: NDX
 * **output_pdb_path** (*string*): Path to the output cluster file. File type: output. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/reference/gromacs/ref_cluster.pdb). Accepted formats: XTC, TRR, CPT, GRO, G96, PDB, TNG
+* **output_cluster_log_path** (*string*): Path to the output log file. File type: output. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/reference/gmx_cluster_cluster.log). Accepted formats: LOG
+* **output_rmsd_cluster_xpm_path** (*string*): Path to the output X PixMap compatible matrix file. File type: output. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/reference/gmx_cluster_rmsd-clust.xpm). Accepted formats: XPM
+* **output_rmsd_dist_xvg_path** (*string*): Path to xvgr/xmgr file. File type: output. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/reference/gmx_cluster_rmsd-dist.xvg). Accepted formats: XVG
 ### Config
 Syntax: input_parameter (datatype) - (default_value) Definition
 
 Config parameters for this building block:
 * **fit_selection** (*string*): (System) Group where the fitting will be performed. If **input_index_path** provided, check the file for the accepted values. .
 * **output_selection** (*string*): (System) Group that is going to be written in the output trajectory. If **input_index_path** provided, check the file for the accepted values. .
 * **dista** (*boolean*): (False) Use RMSD of distances instead of RMS deviation..
+* **nofit** (*boolean*): (False) Do not use least squares fitting before RMSD calculation..
 * **method** (*string*): (linkage) Method for cluster determination. .
 * **cutoff** (*number*): (0.1) RMSD cut-off (nm) for two structures to be neighbor..
 * **binary_path** (*string*): (gmx) Path to the GROMACS executable binary..
@@ -1435,7 +1445,7 @@ properties:
 ```
 #### Command line
 ```python
-gmx_cluster --config config_gmx_cluster.yml --input_structure_path topology.tpr --input_traj_path trajectory.trr --input_index_path index.ndx --output_pdb_path ref_cluster.pdb
+gmx_cluster --config config_gmx_cluster.yml --input_structure_path topology.tpr --input_traj_path trajectory.trr --input_index_path index.ndx --output_pdb_path ref_cluster.pdb --output_cluster_log_path gmx_cluster_cluster.log --output_rmsd_cluster_xpm_path gmx_cluster_rmsd-clust.xpm --output_rmsd_dist_xvg_path gmx_cluster_rmsd-dist.xvg
 ```
 ### JSON
 #### [Common config file](https://github.com/bioexcel/biobb_analysis/blob/master/biobb_analysis/test/data/config/config_gmx_cluster.json)
@@ -1483,7 +1493,7 @@ gmx_cluster --config config_gmx_cluster.yml --input_structure_path topology.tpr
 ```
 #### Command line
 ```python
-gmx_cluster --config config_gmx_cluster.json --input_structure_path topology.tpr --input_traj_path trajectory.trr --input_index_path index.ndx --output_pdb_path ref_cluster.pdb
+gmx_cluster --config config_gmx_cluster.json --input_structure_path topology.tpr --input_traj_path trajectory.trr --input_index_path index.ndx --output_pdb_path ref_cluster.pdb --output_cluster_log_path gmx_cluster_cluster.log --output_rmsd_cluster_xpm_path gmx_cluster_rmsd-clust.xpm --output_rmsd_dist_xvg_path gmx_cluster_rmsd-dist.xvg
 ```
 
 ## Cpptraj_rgyr

diff --git a/biobb_analysis/docs/source/conf.py b/biobb_analysis/docs/source/conf.py
@@ -74,9 +74,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = u'4.0.0'
+version = u'4.0.1'
 # The full version, including alpha/beta/rc tags.
-release = u'4.0.0'
+release = u'4.0.1'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

diff --git a/biobb_analysis/docs/source/readme.md b/biobb_analysis/docs/source/readme.md
@@ -3,7 +3,7 @@
 [![](https://img.shields.io/conda/vn/bioconda/biobb_analysis?label=Conda)](https://anaconda.org/bioconda/biobb_analysis)
 [![](https://img.shields.io/conda/dn/bioconda/biobb_analysis?label=Conda%20Downloads)](https://anaconda.org/bioconda/biobb_analysis)
 [![](https://img.shields.io/badge/Docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_analysis?tab=tags)
-[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_analysis:4.0.0--pyhdfd78af_1)
+[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_analysis:4.0.1--pyhdfd78af_0)
 
 [![](https://img.shields.io/badge/OS-Unix%20%7C%20MacOS-blue)](https://github.com/bioexcel/biobb_analysis)
 [![](https://img.shields.io/pypi/pyversions/biobb-analysis.svg?label=Python%20Versions)](https://pypi.org/project/biobb-analysis/)
@@ -34,7 +34,7 @@ The latest documentation of this package can be found in our readthedocs site:
 [latest API documentation](http://biobb_analysis.readthedocs.io/en/latest/).
 
 ### Version
-v4.0.0 2023.1
+v4.0.1 2023.1
 
 ### Installation
 Using PIP:
@@ -44,7 +44,7 @@ Using PIP:
 * Installation:
 
 
-        pip install "biobb_analysis>=4.0.0"
+        pip install "biobb_analysis>=4.0.1"
 
 
 * Usage: [Python API documentation](https://biobb-analysis.readthedocs.io/en/latest/modules.html)
@@ -54,7 +54,7 @@ Using ANACONDA:
 * Installation:
 
 
-        conda install -c bioconda "biobb_analysis>=4.0.0"
+        conda install -c bioconda "biobb_analysis>=4.0.1"
 
 
 * Usage: With conda installation BioBBs can be used with the [Python API documentation](https://biobb-analysis.readthedocs.io/en/latest/modules.html) and the [Command Line documentation](https://biobb-analysis.readthedocs.io/en/latest/command_line.html)
@@ -64,13 +64,13 @@ Using DOCKER:
 * Installation:
 
 
-        docker pull quay.io/biocontainers/biobb_analysis:4.0.0--pyhdfd78af_1
+        docker pull quay.io/biocontainers/biobb_analysis:4.0.1--pyhdfd78af_0
 
 
 * Usage:
 
 
-        docker run quay.io/biocontainers/biobb_analysis:4.0.0--pyhdfd78af_1 <command>
+        docker run quay.io/biocontainers/biobb_analysis:4.0.1--pyhdfd78af_0 <command>
 
 
 Using SINGULARITY:
@@ -80,7 +80,7 @@ Using SINGULARITY:
 * Installation:
 
 
-        singularity pull --name biobb_analysis.sif https://depot.galaxyproject.org/singularity/biobb_analysis:4.0.0--pyhdfd78af_1
+        singularity pull --name biobb_analysis.sif https://depot.galaxyproject.org/singularity/biobb_analysis:4.0.1--pyhdfd78af_0
 
 
 * Usage:

diff --git a/biobb_analysis/docs/source/schema.html b/biobb_analysis/docs/source/schema.html
@@ -10,7 +10,7 @@
   "applicationSubCategory": "http://www.edamontology.org/topic_3892",
   "citation": "https://www.nature.com/articles/s41597-019-0177-4",
   "license": "https://www.apache.org/licenses/LICENSE-2.0",
-  "softwareVersion": "4.0.0",
+  "softwareVersion": "4.0.1",
   "applicationSuite": "BioBB BioExcel Building Blocks",
   "codeRepository": "https://github.com/bioexcel/biobb_analysis",
   "isAccessibleForFree": "True",