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

README.md

@@ -3,7 +3,7 @@
 [![](https://img.shields.io/conda/vn/bioconda/biobb_chemistry?label=Conda)](https://anaconda.org/bioconda/biobb_chemistry)
 [![](https://img.shields.io/conda/dn/bioconda/biobb_chemistry?label=Conda%20Downloads)](https://anaconda.org/bioconda/biobb_chemistry)
 [![](https://img.shields.io/badge/Docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_chemistry?tab=tags)
-[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_chemistry:5.0.1--pyhdfd78af_0)
+[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_chemistry:5.0.2--pyhdfd78af_1)
 
 [![](https://img.shields.io/badge/OS-Unix%20%7C%20MacOS-blue)](https://github.com/bioexcel/biobb_chemistry)
 [![](https://img.shields.io/pypi/pyversions/biobb-chemistry.svg?label=Python%20Versions)](https://pypi.org/project/biobb-chemistry/)
@@ -40,7 +40,7 @@ The latest documentation of this package can be found in our readthedocs site:
 [latest API documentation](http://biobb-chemistry.readthedocs.io/en/latest/).
 
 ### Version
-v5.0.1 2024.2
+v5.0.2 2024.2
 
 ### Installation
 Using PIP:
@@ -50,7 +50,7 @@ Using PIP:
 * Installation:
 
 
-        pip install "biobb_chemistry>=5.0.1"
+        pip install "biobb_chemistry>=5.0.2"
 
 
 * Usage: [Python API documentation](https://biobb-chemistry.readthedocs.io/en/latest/modules.html)
@@ -60,7 +60,7 @@ Using ANACONDA:
 * Installation:
 
 
-        conda install -c bioconda "biobb_chemistry>=5.0.1"
+        conda install -c bioconda "biobb_chemistry>=5.0.2"
 
 
 * Usage: With conda installation BioBBs can be used with the [Python API documentation](https://biobb-chemistry.readthedocs.io/en/latest/modules.html) and the [Command Line documentation](https://biobb-chemistry.readthedocs.io/en/latest/command_line.html)
@@ -70,13 +70,13 @@ Using DOCKER:
 * Installation:
 
 
-        docker pull quay.io/biocontainers/biobb_chemistry:5.0.1--pyhdfd78af_0
+        docker pull quay.io/biocontainers/biobb_chemistry:5.0.2--pyhdfd78af_1
 
 
 * Usage:
 
 
-        docker run quay.io/biocontainers/biobb_chemistry:5.0.1--pyhdfd78af_0 <command>
+        docker run quay.io/biocontainers/biobb_chemistry:5.0.2--pyhdfd78af_1 <command>
 
 Using SINGULARITY:
 
@@ -85,7 +85,7 @@ Using SINGULARITY:
 * Installation:
 
 
-        singularity pull --name biobb_chemistry.sif https://depot.galaxyproject.org/singularity/biobb_chemistry:5.0.1--pyhdfd78af_0
+        singularity pull --name biobb_chemistry.sif https://depot.galaxyproject.org/singularity/biobb_chemistry:5.0.2--pyhdfd78af_1
 
 
 * Usage:

biobb_chemistry/__init__.py

@@ -4,4 +4,4 @@
 
 name = "biobb_chemistry"
 __all__ = ["acpype", "ambertools", "babelm"]
-__version__ = "5.0.1"
+__version__ = "5.0.2"

biobb_chemistry/acpype/__init__.py

@@ -2,5 +2,6 @@
 from . import acpype_params_cns
 from . import acpype_params_gmx
 from . import acpype_params_gmx_opls
+from . import acpype_convert_amber_to_gmx
 name = "acpype"
-__all__ = ["acpype_params_ac", "acpype_params_cns", "acpype_params_gmx", "acpype_params_gmx_opls"]
+__all__ = ["acpype_params_ac", "acpype_params_cns", "acpype_params_gmx", "acpype_params_gmx_opls", "acpype_convert_amber_to_gmx"]

biobb_chemistry/acpype/acpype_convert_amber_to_gmx.py

@@ -16,10 +16,10 @@ class AcpypeConvertAMBERtoGMX(BiobbObject):
     | Acpype is a tool based in Python to use Antechamber to generate topologies for chemical compounds and to interface with others python applications like CCPN or ARIA. `Visit the official page <https://github.com/alanwilter/acpype>`_.
 
     Args:
-        input_crd_path (str): Path to the input coordinates file (AMBER crd). File type: input. `Sample file <https://github.com/bioexcel/biobb_chemistry/raw/master/biobb_chemistry/test/reference/acpype/ref_acpype.ac.container.inpcrd>`_. Accepted formats: inpcrd (edam:format_3878).
-        input_top_path (str): Path to the input topology file (AMBER ParmTop). File type: input. `Sample file <https://github.com/bioexcel/biobb_chemistry/raw/master/biobb_chemistry/test/reference/acpype/ref_acpype.ac.container.prmtop>`_. Accepted formats: top (edam:format_3881), parmtop (edam:format_3881), prmtop (edam:format_3881).
-        output_path_gro (str): Path to the GRO output file. File type: output. `Sample file <https://github.com/bioexcel/biobb_chemistry/raw/master/biobb_chemistry/test/reference/acpype/ref_acpype.gmx.gro>`_. Accepted formats: gro (edam:format_2033).
-        output_path_top (str): Path to the TOP output file. File type: output. `Sample file <https://github.com/bioexcel/biobb_chemistry/raw/master/biobb_chemistry/test/reference/acpype/ref_acpype.gmx.top>`_. Accepted formats: top (edam:format_3880).
+        input_crd_path (str): Path to the input coordinates file (AMBER crd). File type: input. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_chemistry/master/biobb_chemistry/test/data/acpype/acpype.coords.inpcrd>`_. Accepted formats: inpcrd (edam:format_3878).
+        input_top_path (str): Path to the input topology file (AMBER ParmTop). File type: input. `Sample file <https://github.com/bioexcel/biobb_chemistry/raw/master/biobb_chemistry/test/data/acpype/acpype.top.prmtop>`_. Accepted formats: top (edam:format_3881), parmtop (edam:format_3881), prmtop (edam:format_3881).
+        output_path_gro (str): Path to the GRO output file. File type: output. `Sample file <https://github.com/bioexcel/biobb_chemistry/raw/master/biobb_chemistry/test/reference/acpype/ref_acpype.amber2gmx.gro>`_. Accepted formats: gro (edam:format_2033).
+        output_path_top (str): Path to the TOP output file. File type: output. `Sample file <https://github.com/bioexcel/biobb_chemistry/raw/master/biobb_chemistry/test/reference/acpype/ref_acpype.amber2gmx.top>`_. Accepted formats: top (edam:format_3880).
         properties (dic - Python dictionary object containing the tool parameters, not input/output files):
             * **basename** (*str*) - ("BBB") A basename for the project (folder and output files).
             * **binary_path** (*str*) - ("acpype") Path to the acpype executable binary.

biobb_chemistry/acpype/common.py

@@ -144,7 +144,7 @@ def process_output_gmx(unique_name, files_folder, remove_tmp, basename, class_pa
             for line in file:
                 print(line.replace(basename + '.' + unique_name, basename), end='')
 
-        if (Path(file_name).is_file()):  
+        if (Path(file_name).is_file()):
             file_extension = PurePath(file_name).suffix
             # in top files for gromacs, replace file.itp by name given by user
             if (file_extension[1:] == 'top') and ('itp' in output_files):

biobb_chemistry/docs/source/acpype.rst

@@ -33,6 +33,14 @@ acpype.acpype_params_gmx_opls module
 -------------------------------------
 
 .. automodule:: acpype.acpype_params_gmx_opls
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+acpype.acpype_convert_amber_to_gmx module
+------------------------------------------
+
+.. automodule:: acpype.acpype_convert_amber_to_gmx
     :members:
     :undoc-members:
     :show-inheritance:

biobb_chemistry/docs/source/change_log.md

@@ -1,6 +1,6 @@
 # Biobb Chemistry changelog
 
-## What's new in version [5.0.1](https://github.com/bioexcel/biobb_chemistry/releases/tag/v5.0.1)?
+## What's new in version [5.0.2](https://github.com/bioexcel/biobb_chemistry/releases/tag/v5.0.2)?
 
 ### Changes
 * [FEATURE](all): AcpypeConvertAMBERtoGMX module

biobb_chemistry/docs/source/command_line.md

@@ -1148,6 +1148,77 @@ acpype_params_gmx --config config_acpype_params_gmx.yml --input_path acpype.para
 acpype_params_gmx --config config_acpype_params_gmx.json --input_path acpype.params.mol2 --output_path_gro ref_acpype.gmx.gro --output_path_itp ref_acpype.gmx.itp --output_path_top ref_acpype.gmx.top
 ```
 
+## Acpype_convert_amber_to_gmx
+This class is a wrapper of Acpype tool for the conversion of AMBER topologies to GROMACS.
+### Get help
+Command:
+```python
+acpype_convert_amber_to_gmx -h
+```
+    usage: acpype_convert_amber_to_gmx [-h] [--config CONFIG] --input_crd_path INPUT_CRD_PATH --input_top_path INPUT_TOP_PATH --output_path_gro OUTPUT_PATH_GRO --output_path_top OUTPUT_PATH_TOP
+
+    Small molecule parameterization for GROMACS MD package.
+
+    optional arguments:
+      -h, --help            show this help message and exit
+      --config CONFIG       Configuration file
+
+    required arguments:
+      --input_crd_path INPUT_CRD_PATH
+                            Path to the input coordinates file (AMBER crd). Accepted formats: inpcrd.
+      --input_top_path INPUT_TOP_PATH
+                            Path to the input topology file (AMBER ParmTop). Accepted formats: top, parmtop, prmtop.
+      --output_path_gro OUTPUT_PATH_GRO
+                            Path to the GRO output file. Accepted formats: gro.
+      --output_path_top OUTPUT_PATH_TOP
+                            Path to the TOP output file. Accepted formats: top.
+### I / O Arguments
+Syntax: input_argument (datatype) : Definition
+
+Config input / output arguments for this building block:
+* **input_crd_path** (*string*): Path to the input coordinates file (AMBER crd). File type: input. [Sample file](https://raw.githubusercontent.com/bioexcel/biobb_chemistry/master/biobb_chemistry/test/data/acpype/acpype.coords.inpcrd). Accepted formats: INPCRD
+* **input_top_path** (*string*): Path to the input topology file (AMBER ParmTop). File type: input. [Sample file](https://github.com/bioexcel/biobb_chemistry/raw/master/biobb_chemistry/test/data/acpype/acpype.top.prmtop). Accepted formats: TOP, PARMTOP, PRMTOP
+* **output_path_gro** (*string*): Path to the GRO output file. File type: output. [Sample file](https://github.com/bioexcel/biobb_chemistry/raw/master/biobb_chemistry/test/reference/acpype/ref_acpype.amber2gmx.gro). Accepted formats: GRO
+* **output_path_top** (*string*): Path to the TOP output file. File type: output. [Sample file](https://github.com/bioexcel/biobb_chemistry/raw/master/biobb_chemistry/test/reference/acpype/ref_acpype.amber2gmx.top). Accepted formats: TOP
+### Config
+Syntax: input_parameter (datatype) - (default_value) Definition
+
+Config parameters for this building block:
+* **basename** (*string*): (BBB) A basename for the project (folder and output files)..
+* **binary_path** (*string*): (acpype) Path to the acpype executable binary..
+* **remove_tmp** (*boolean*): (True) Remove temporal files..
+* **restart** (*boolean*): (False) Do not execute if output files exist..
+* **container_path** (*string*): (None) Container path definition..
+* **container_image** (*string*): (acpype/acpype:2022.7.21) Container image definition..
+* **container_volume_path** (*string*): (/tmp) Container volume path definition..
+* **container_working_dir** (*string*): (None) Container working directory definition..
+* **container_user_id** (*string*): (None) Container user_id definition..
+* **container_shell_path** (*string*): (/bin/bash) Path to default shell inside the container..
+### YAML
+#### [Common config file](https://github.com/bioexcel/biobb_chemistry/blob/master/biobb_chemistry/test/data/config/config_acpype_convert_amber_to_gmx.yml)
+```python
+properties:
+  basename: BBB
+
+```
+#### Command line
+```python
+acpype_convert_amber_to_gmx --config config_acpype_convert_amber_to_gmx.yml --input_crd_path acpype.coords.inpcrd --input_top_path acpype.top.prmtop --output_path_gro ref_acpype.amber2gmx.gro --output_path_top ref_acpype.amber2gmx.top
+```
+### JSON
+#### [Common config file](https://github.com/bioexcel/biobb_chemistry/blob/master/biobb_chemistry/test/data/config/config_acpype_convert_amber_to_gmx.json)
+```python
+{
+  "properties": {
+    "basename": "BBB"
+  }
+}
+```
+#### Command line
+```python
+acpype_convert_amber_to_gmx --config config_acpype_convert_amber_to_gmx.json --input_crd_path acpype.coords.inpcrd --input_top_path acpype.top.prmtop --output_path_gro ref_acpype.amber2gmx.gro --output_path_top ref_acpype.amber2gmx.top
+```
+
 ## Babel_convert
 This class is a wrapper of the Open Babel tool.
 ### Get help

biobb_chemistry/docs/source/conf.py

@@ -74,9 +74,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = "5.0.1"
+version = "5.0.2"
 # The full version, including alpha/beta/rc tags.
-release = "5.0.1"
+release = "5.0.2"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

biobb_chemistry/docs/source/readme.md

@@ -3,7 +3,7 @@
 [![](https://img.shields.io/conda/vn/bioconda/biobb_chemistry?label=Conda)](https://anaconda.org/bioconda/biobb_chemistry)
 [![](https://img.shields.io/conda/dn/bioconda/biobb_chemistry?label=Conda%20Downloads)](https://anaconda.org/bioconda/biobb_chemistry)
 [![](https://img.shields.io/badge/Docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_chemistry?tab=tags)
-[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_chemistry:5.0.1--pyhdfd78af_0)
+[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_chemistry:5.0.2--pyhdfd78af_1)
 
 [![](https://img.shields.io/badge/OS-Unix%20%7C%20MacOS-blue)](https://github.com/bioexcel/biobb_chemistry)
 [![](https://img.shields.io/pypi/pyversions/biobb-chemistry.svg?label=Python%20Versions)](https://pypi.org/project/biobb-chemistry/)
@@ -40,7 +40,7 @@ The latest documentation of this package can be found in our readthedocs site:
 [latest API documentation](http://biobb-chemistry.readthedocs.io/en/latest/).
 
 ### Version
-v5.0.1 2024.2
+v5.0.2 2024.2
 
 ### Installation
 Using PIP:
@@ -50,7 +50,7 @@ Using PIP:
 * Installation:
 
 
-        pip install "biobb_chemistry>=5.0.1"
+        pip install "biobb_chemistry>=5.0.2"
 
 
 * Usage: [Python API documentation](https://biobb-chemistry.readthedocs.io/en/latest/modules.html)
@@ -60,7 +60,7 @@ Using ANACONDA:
 * Installation:
 
 
-        conda install -c bioconda "biobb_chemistry>=5.0.1"
+        conda install -c bioconda "biobb_chemistry>=5.0.2"
 
 
 * Usage: With conda installation BioBBs can be used with the [Python API documentation](https://biobb-chemistry.readthedocs.io/en/latest/modules.html) and the [Command Line documentation](https://biobb-chemistry.readthedocs.io/en/latest/command_line.html)
@@ -70,13 +70,13 @@ Using DOCKER:
 * Installation:
 
 
-        docker pull quay.io/biocontainers/biobb_chemistry:5.0.1--pyhdfd78af_0
+        docker pull quay.io/biocontainers/biobb_chemistry:5.0.2--pyhdfd78af_1
 
 
 * Usage:
 
 
-        docker run quay.io/biocontainers/biobb_chemistry:5.0.1--pyhdfd78af_0 <command>
+        docker run quay.io/biocontainers/biobb_chemistry:5.0.2--pyhdfd78af_1 <command>
 
 Using SINGULARITY:
 
@@ -85,7 +85,7 @@ Using SINGULARITY:
 * Installation:
 
 
-        singularity pull --name biobb_chemistry.sif https://depot.galaxyproject.org/singularity/biobb_chemistry:5.0.1--pyhdfd78af_0
+        singularity pull --name biobb_chemistry.sif https://depot.galaxyproject.org/singularity/biobb_chemistry:5.0.2--pyhdfd78af_1
 
 
 * Usage:

biobb_chemistry/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": "5.0.1",
+  "softwareVersion": "5.0.2",
   "applicationSuite": "BioBB BioExcel Building Blocks",
   "codeRepository": "https://github.com/bioexcel/biobb_chemistry",
   "isAccessibleForFree": "True",