update gorder documentation and rename references

Author: RubenChM

biobb_mem/docs/source/command_line.md

@@ -236,16 +236,16 @@ gorder_aa -h
       --input_top_path INPUT_TOP_PATH
                             Path to the input structure or topology file. Accepted formats: tpr.
       --input_traj_path INPUT_TRAJ_PATH
-                            Path to the input trajectory to be processed. Accepted formats: xtc, trr, cpt, gro, g96, pdb, tng.
+                            Path to the input trajectory to be processed. Accepted formats: xtc, trr, gro.
       -o OUTPUT_ORDER_PATH, --output_order_path OUTPUT_ORDER_PATH
                             Path to results of the order analysis. Accepted formats: yaml, xvg, csv.
 ### I / O Arguments
 Syntax: input_argument (datatype) : Definition
 
 Config input / output arguments for this building block:
-* **input_top_path** (*string*): Path to the input structure or topology file. File type: input. [Sample file](https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/data/ambertools/topology.tpr). Accepted formats: TPR
-* **input_traj_path** (*string*): Path to the input trajectory to be processed. File type: input. [Sample file](https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/data/ambertools/trajectory.xtc). Accepted formats: XTC, TRR, CPT, GRO, G96, PDB, TNG
-* **output_order_path** (*string*): Path to results of the order analysis. File type: output. [Sample file](https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/data/gromacs/order.xvg). Accepted formats: YAML, XVG, CSV
+* **input_top_path** (*string*): Path to the input structure or topology file. File type: input. [Sample file](https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/data/A01IP/A01IP.tpr). Accepted formats: TPR
+* **input_traj_path** (*string*): Path to the input trajectory to be processed. File type: input. [Sample file](https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/data/A01IP/A01IP.xtc). Accepted formats: XTC, TRR, GRO
+* **output_order_path** (*string*): Path to results of the order analysis. File type: output. [Sample file](https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/reference/gorder/order_aa.yaml). Accepted formats: YAML, XVG, CSV
 ### Config
 Syntax: input_parameter (datatype) - (default_value) Definition
 
@@ -266,7 +266,7 @@ properties:
 ```
 #### Command line
 ```python
-gorder_aa --config config_gorder_aa.yml --input_top_path topology.tpr --input_traj_path trajectory.xtc --output_order_path order.xvg
+gorder_aa --config config_gorder_aa.yml --input_top_path A01IP.tpr --input_traj_path A01IP.xtc --output_order_path order_aa.yaml
 ```
 ### JSON
 #### [Common config file](https://github.com/bioexcel/biobb_mem/blob/master/biobb_mem/test/data/config/config_gorder_aa.json)
@@ -280,7 +280,7 @@ gorder_aa --config config_gorder_aa.yml --input_top_path topology.tpr --input_tr
 ```
 #### Command line
 ```python
-gorder_aa --config config_gorder_aa.json --input_top_path topology.tpr --input_traj_path trajectory.xtc --output_order_path order.xvg
+gorder_aa --config config_gorder_aa.json --input_top_path A01IP.tpr --input_traj_path A01IP.xtc --output_order_path order_aa.yaml
 ```
 
 ## Gorder_cg
@@ -303,16 +303,16 @@ gorder_cg -h
       --input_top_path INPUT_TOP_PATH
                             Path to the input structure or topology file. Accepted formats: tpr.
       --input_traj_path INPUT_TRAJ_PATH
-                            Path to the input trajectory to be processed. Accepted formats: xtc, trr, cpt, gro, g96, pdb, tng.
+                            Path to the input trajectory to be processed. Accepted formats: xtc, trr, gro.
       -o OUTPUT_ORDER_PATH, --output_order_path OUTPUT_ORDER_PATH
                             Path to results of the order analysis. Accepted formats: yaml, xvg, csv.
 ### I / O Arguments
 Syntax: input_argument (datatype) : Definition
 
 Config input / output arguments for this building block:
-* **input_top_path** (*string*): Path to the input structure or topology file. File type: input. [Sample file](https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/data/ambertools/topology.tpr). Accepted formats: TPR
-* **input_traj_path** (*string*): Path to the input trajectory to be processed. File type: input. [Sample file](https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/data/ambertools/trajectory.xtc). Accepted formats: XTC, TRR, CPT, GRO, G96, PDB, TNG
-* **output_order_path** (*string*): Path to results of the order analysis. File type: output. [Sample file](https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/data/gromacs/order.xvg). Accepted formats: YAML, XVG, CSV
+* **input_top_path** (*string*): Path to the input structure or topology file. File type: input. [Sample file](https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/data/CG/cg_test.tpr). Accepted formats: TPR
+* **input_traj_path** (*string*): Path to the input trajectory to be processed. File type: input. [Sample file](https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/data/CG/cg_test.xtc). Accepted formats: XTC, TRR, GRO
+* **output_order_path** (*string*): Path to results of the order analysis. File type: output. [Sample file](https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/reference/gorder/order_cg.yaml). Accepted formats: YAML, XVG, CSV
 ### Config
 Syntax: input_parameter (datatype) - (default_value) Definition
 
@@ -332,7 +332,7 @@ properties:
 ```
 #### Command line
 ```python
-gorder_cg --config config_gorder_cg.yml --input_top_path topology.tpr --input_traj_path trajectory.xtc --output_order_path order.xvg
+gorder_cg --config config_gorder_cg.yml --input_top_path cg_test.tpr --input_traj_path cg_test.xtc --output_order_path order_cg.yaml
 ```
 ### JSON
 #### [Common config file](https://github.com/bioexcel/biobb_mem/blob/master/biobb_mem/test/data/config/config_gorder_cg.json)
@@ -346,7 +346,7 @@ gorder_cg --config config_gorder_cg.yml --input_top_path topology.tpr --input_tr
 ```
 #### Command line
 ```python
-gorder_cg --config config_gorder_cg.json --input_top_path topology.tpr --input_traj_path trajectory.xtc --output_order_path order.xvg
+gorder_cg --config config_gorder_cg.json --input_top_path cg_test.tpr --input_traj_path cg_test.xtc --output_order_path order_cg.yaml
 ```
 
 ## Gorder_ua
@@ -369,16 +369,16 @@ gorder_ua -h
       --input_top_path INPUT_TOP_PATH
                             Path to the input structure or topology file. Accepted formats: tpr.
       --input_traj_path INPUT_TRAJ_PATH
-                            Path to the input trajectory to be processed. Accepted formats: xtc, trr, cpt, gro, g96, pdb, tng.
+                            Path to the input trajectory to be processed. Accepted formats: xtc, trr, gro.
       -o OUTPUT_ORDER_PATH, --output_order_path OUTPUT_ORDER_PATH
                             Path to results of the order analysis. Accepted formats: yaml, xvg, csv.
 ### I / O Arguments
 Syntax: input_argument (datatype) : Definition
 
 Config input / output arguments for this building block:
-* **input_top_path** (*string*): Path to the input structure or topology file. File type: input. [Sample file](https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/data/ambertools/topology.tpr). Accepted formats: TPR
-* **input_traj_path** (*string*): Path to the input trajectory to be processed. File type: input. [Sample file](https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/data/ambertools/trajectory.xtc). Accepted formats: XTC, TRR, CPT, GRO, G96, PDB, TNG
-* **output_order_path** (*string*): Path to results of the order analysis. File type: output. [Sample file](https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/data/gromacs/order.xvg). Accepted formats: YAML, XVG, CSV
+* **input_top_path** (*string*): Path to the input structure or topology file. File type: input. [Sample file](https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/data/A01JP/A01JP.tpr). Accepted formats: TPR
+* **input_traj_path** (*string*): Path to the input trajectory to be processed. File type: input. [Sample file](https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/data/A01JP/A01JP.xtc). Accepted formats: XTC, TRR, GRO
+* **output_order_path** (*string*): Path to results of the order analysis. File type: output. [Sample file](https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/reference/gorder/order_ua.yaml). Accepted formats: YAML, XVG, CSV
 ### Config
 Syntax: input_parameter (datatype) - (default_value) Definition
 
@@ -398,7 +398,7 @@ properties:
 ```
 #### Command line
 ```python
-gorder_ua --config config_gorder_ua.yml --input_top_path topology.tpr --input_traj_path trajectory.xtc --output_order_path order.xvg
+gorder_ua --config config_gorder_ua.yml --input_top_path A01JP.tpr --input_traj_path A01JP.xtc --output_order_path order_ua.yaml
 ```
 ### JSON
 #### [Common config file](https://github.com/bioexcel/biobb_mem/blob/master/biobb_mem/test/data/config/config_gorder_ua.json)
@@ -411,7 +411,7 @@ gorder_ua --config config_gorder_ua.yml --input_top_path topology.tpr --input_tr
 ```
 #### Command line
 ```python
-gorder_ua --config config_gorder_ua.json --input_top_path topology.tpr --input_traj_path trajectory.xtc --output_order_path order.xvg
+gorder_ua --config config_gorder_ua.json --input_top_path A01JP.tpr --input_traj_path A01JP.xtc --output_order_path order_ua.yaml
 ```
 
 ## Lpp_assign_leaflets

biobb_mem/docs/source/gorder.rst

@@ -0,0 +1,29 @@
+gorder package
+=====================
+
+Submodules
+------------
+
+gorder.gorder_aa module
+-----------------------------------
+
+.. automodule:: gorder.gorder_aa
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+gorder.gorder_cg module
+-----------------------------------
+
+.. automodule:: gorder.gorder_cg
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+gorder.gorder_ua module
+-----------------------------------
+
+.. automodule:: gorder.gorder_ua
+    :members:
+    :undoc-members:
+    :show-inheritance:

biobb_mem/docs/source/gromacs.rst

@@ -6,6 +6,6 @@ biobb_mem
 
    ambertools
    fatslim
-   gromacs
+   gorder
    lipyphilic_biobb
    mdanalysis_biobb

biobb_mem/docs/source/modules.rst

@@ -1,2 +1,2 @@
-name = "gromacs"
+name = "gorder"
 __all__ = ["gorder_aa", "gorder_ua", "gorder_cg"]

biobb_mem/gorder/__init__.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 
-"""Module containing the GROMACS order class and the command line interface."""
+"""Module containing the gorder all atom class and the command line interface."""
 from biobb_common.generic.biobb_object import BiobbObject
 from biobb_common.tools.file_utils import launchlogger
 import gorder
@@ -13,9 +13,9 @@ class GorderAA(BiobbObject):
     | `gorder <https://ladme.github.io/gorder-manual/aaorder_basics.html>`_ uses `GSL <https://ladme.github.io/gsl-guide/>`_ for all its selections.
 
     Args:
-        input_top_path (str): Path to the input structure or topology file. File type: input. `Sample file <https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/data/ambertools/topology.tpr>`_. Accepted formats: tpr (edam:format_2333).
-        input_traj_path (str): Path to the input trajectory to be processed. File type: input. `Sample file <https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/data/ambertools/trajectory.xtc>`_. Accepted formats: xtc (edam:format_3875), trr (edam:format_3910), cpt (edam:format_2333), gro (edam:format_2033), g96 (edam:format_2033), pdb (edam:format_1476), tng (edam:format_3876)..
-        output_order_path (str): Path to results of the order analysis. File type: output. `Sample file <https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/data/gromacs/order.xvg>`_. Accepted formats: yaml (edam:format_3570), xvg (edam:format_2330), csv (edam:format_3752).
+        input_top_path (str): Path to the input structure or topology file. File type: input. `Sample file <https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/data/A01IP/A01IP.tpr>`_. Accepted formats: tpr (edam:format_2333).
+        input_traj_path (str): Path to the input trajectory to be processed. File type: input. `Sample file <https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/data/A01IP/A01IP.xtc>`_. Accepted formats: xtc (edam:format_3875), trr (edam:format_3910), gro (edam:format_2033).
+        output_order_path (str): Path to results of the order analysis. File type: output. `Sample file <https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/reference/gorder/order_aa.yaml>`_. Accepted formats: yaml (edam:format_3570), xvg (edam:format_2330), csv (edam:format_3752).
         properties (dic - Python dictionary object containing the tool parameters, not input/output files):
             * **heavy_atoms** (*str*) - ("@membrane and name r'C3.+|C2.+'") Selection query specifying the heavy atoms to be used in the analysis (typically carbon atoms in lipid tails).
             * **hydrogens** (*str*) - ("@membrane and element name hydrogen") Selection query specifiying the hydrogen atoms to be used in the analysis (only those bonded to heavy atoms will be considered).

biobb_mem/gorder/gorder_aa.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 
-"""Module containing the GROMACS order class and the command line interface."""
+"""Module containing the gorder coarse-grained class and the command line interface."""
 from biobb_common.generic.biobb_object import BiobbObject
 from biobb_common.tools.file_utils import launchlogger
 import gorder
@@ -13,9 +13,9 @@ class GorderCG(BiobbObject):
     | `gorder <https://ladme.github.io/gorder-manual/cgorder_basics.html>`_ uses `GSL <https://ladme.github.io/gsl-guide/>`_ for all its selections.
 
     Args:
-        input_top_path (str): Path to the input structure or topology file. File type: input. `Sample file <https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/data/ambertools/topology.tpr>`_. Accepted formats: tpr (edam:format_2333).
-        input_traj_path (str): Path to the input trajectory to be processed. File type: input. `Sample file <https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/data/ambertools/trajectory.xtc>`_. Accepted formats: xtc (edam:format_3875), trr (edam:format_3910), cpt (edam:format_2333), gro (edam:format_2033), g96 (edam:format_2033), pdb (edam:format_1476), tng (edam:format_3876)..
-        output_order_path (str): Path to results of the order analysis. File type: output. `Sample file <https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/data/gromacs/order.xvg>`_. Accepted formats: yaml (edam:format_3570), xvg (edam:format_2330), csv (edam:format_3752).
+        input_top_path (str): Path to the input structure or topology file. File type: input. `Sample file <https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/data/CG/cg_test.tpr>`_. Accepted formats: tpr (edam:format_2333).
+        input_traj_path (str): Path to the input trajectory to be processed. File type: input. `Sample file <https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/data/CG/cg_test.xtc>`_. Accepted formats: xtc (edam:format_3875), trr (edam:format_3910), gro (edam:format_2033).
+        output_order_path (str): Path to results of the order analysis. File type: output. `Sample file <https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/reference/gorder/order_cg.yaml>`_. Accepted formats: yaml (edam:format_3570), xvg (edam:format_2330), csv (edam:format_3752).
         properties (dic - Python dictionary object containing the tool parameters, not input/output files):
             * **beads** (*str*) - ("@membrane") Selection query specifying the beads to be used in the analysis.
             * **handle_pbc** (*bool*) - (True) If False, ignores periodic boundary conditions (PBC).

biobb_mem/gorder/gorder_cg.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 
-"""Module containing the GROMACS order class and the command line interface."""
+"""Module containing the gorder united atom class and the command line interface."""
 from biobb_common.generic.biobb_object import BiobbObject
 from biobb_common.tools.file_utils import launchlogger
 import gorder
@@ -13,9 +13,9 @@ class GorderUA(BiobbObject):
     | `gorder <https://ladme.github.io/gorder-manual/uaorder_basics.html>`_ uses `GSL <https://ladme.github.io/gsl-guide/>`_ for all its selections.
 
     Args:
-        input_top_path (str): Path to the input structure or topology file. File type: input. `Sample file <https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/data/ambertools/topology.tpr>`_. Accepted formats: tpr (edam:format_2333).
-        input_traj_path (str): Path to the input trajectory to be processed. File type: input. `Sample file <https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/data/ambertools/trajectory.xtc>`_. Accepted formats: xtc (edam:format_3875), trr (edam:format_3910), cpt (edam:format_2333), gro (edam:format_2033), g96 (edam:format_2033), pdb (edam:format_1476), tng (edam:format_3876)..
-        output_order_path (str): Path to results of the order analysis. File type: output. `Sample file <https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/data/gromacs/order.xvg>`_. Accepted formats: yaml (edam:format_3570), xvg (edam:format_2330), csv (edam:format_3752).
+        input_top_path (str): Path to the input structure or topology file. File type: input. `Sample file <https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/data/A01JP/A01JP.tpr>`_. Accepted formats: tpr (edam:format_2333).
+        input_traj_path (str): Path to the input trajectory to be processed. File type: input. `Sample file <https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/data/A01JP/A01JP.xtc>`_. Accepted formats: xtc (edam:format_3875), trr (edam:format_3910), gro (edam:format_2033).
+        output_order_path (str): Path to results of the order analysis. File type: output. `Sample file <https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/reference/gorder/order_ua.yaml>`_. Accepted formats: yaml (edam:format_3570), xvg (edam:format_2330), csv (edam:format_3752).
         properties (dic - Python dictionary object containing the tool parameters, not input/output files):
             * **saturated** (*str*) - ("@membrane") Selection query specifying the saturated carbons.
             * **unsaturated** (*str*) - (None) Selection query specifying the unsaturated carbons.