Merge pull request #48 from martimunicoy/output_names_fix

Default output names fix

docs/releasehistory.rst

@@ -8,8 +8,18 @@ Releases follow the ``major.minor.micro`` scheme recommended by `PEP440 <https:/
 * ``micro`` increments represent bugfix releases or improvements in documentation
 
 
-0.3.0 - Current development
--------------------------
+0.3.1 - Current development
+---------------------------
+
+This is a micro release that includes general bug fixes and stability improvements. It is still a preliminary version of the Open Force Field to PELE package which is under development.
+
+Bugfixes
+""""""""
+- `PR #48 <https://github.com/martimunicoy/offpele/pull/48>`_: Fixes CLI's default output paths.
+
+
+0.3.0 - Rotamers, OPLS2005, SMILES and stability improvements
+-------------------------------------------------------------
 
 This is a minor release that includes a refactoring of the classes and methods that involve the rotamer library builder. Besides, now it is possible to combine parameters from OPLS2005 and OFF. This release also contains a new method to define a molecule through a SMILES tag. It is still a preliminary version of the Open Force Field to PELE package which is under development.
 
@@ -26,7 +36,7 @@ Bugfixes
 """"""""
 - `PR #22 <https://github.com/martimunicoy/offpele/pull/22>`_: Fixes many bugs. For example, the default output name of the solvent parameters template is changed to `ligandParams.txt`, which is the name that PELE expects.
 - `PR #32 <https://github.com/martimunicoy/offpele/pull/32>`_: Minor fixes in ToolkitWrapper classes.
-- `PR #34 <https://github.com/martimunicoy/offpele/pull/34:>`_: Improves the translation of dihedrals coming from the Open Force Fielf Toolkit and corrects the lack of exclusions in PELE 1-4 list that result from Impact's dihedral definitions.
+- `PR #34 <https://github.com/martimunicoy/offpele/pull/34>`_: Improves the translation of dihedrals coming from the Open Force Fielf Toolkit and corrects the lack of exclusions in PELE 1-4 list that result from Impact's dihedral definitions.
 - `PR #46 <https://github.com/martimunicoy/offpele/pull/46>`_: Prevents molecule to be untagged when loading it from a SMILES tag.
 
 Tests added

docs/usage.rst

@@ -104,8 +104,8 @@ PDB file
 It is a mandatory positional argument that points to the PDB file which
 contains ligand to parameterize.
 
-- Flag: PDB FILE
-- Type: string
+- Flag: ``PDB FILE``
+- Type: ``string``
 - Example: the code below will run `offpele` to parameterize the ligand at `path/to/my_ligand.pdb`
 
   .. code-block:: bash
@@ -116,9 +116,9 @@ Force field
 -----------
 It defines the Open Force Field force field to employ to parameterize the ligand.
 
-- Flag: -f NAME, --forcefield NAME
-- Type: string
-- Default: 'openff_unconstrained-1.2.0.offxml'
+- Flag: ``-f NAME``, ``--forcefield NAME``
+- Type: ``string``
+- Default: ``openff_unconstrained-1.2.0.offxml``
 - Example: the code below will run offpele using the forcefield named as 'openff_unconstrained-1.0.0.offxml'
 
   .. code-block:: bash
@@ -129,9 +129,9 @@ Rotamer library resolution
 --------------------------
 It defines the resolution, in degrees, to use in the rotamer library.
 
-- Flag: -r INT, --resolution INT
-- Type: int
-- Default: 30
+- Flag: ``-r INT``, ``--resolution INT``
+- Type: ``int``
+- Default: ``30``
 - Example: the code below will run offpele using a resolution of 60 for the rotamer library
 
   .. code-block:: bash
@@ -142,9 +142,9 @@ Output path
 -----------
 It defines the output path where the resulting files will be saved.
 
-- Flag: -o PATH, --output PATH
-- Type: string
-- Default: '.', the current working directory
+- Flag: ``-o PATH``, ``--output PATH``
+- Type: ``string``
+- Default: ``.``, the current working directory
 - Example: the code below will save the results into my_custom_folder/
 
   .. code-block:: bash
@@ -155,8 +155,8 @@ Include solvent parameters
 --------------------------
 It also generates the OBC solvent parameters and saves them into the output location.
 
-- Flag: --with_solvent
-- Default: False, not include
+- Flag: ``--with_solvent``
+- Default: ``False``, do not include
 - Example: the code below will generate and save the OBC solvent parameters
 
   .. code-block:: bash
@@ -167,8 +167,8 @@ Save output as DataLocal
 ------------------------
 It saves the output files following the DataLocal hierarchy expected by PELE.
 
-- Flag: --as_DataLocal
-- Default: False, not save output files as DataLocal
+- Flag: ``--as_DataLocal``
+- Default: ``False``, do not save output files as DataLocal
 - Example: the code below will generate and save output files following the DataLocal hierarcy of PELE
 
   .. code-block:: bash
@@ -179,10 +179,10 @@ Charges method
 --------------
 It sets the method to compute the partial charges.
 
-- Flag: -c NAME, --charges_method NAME
-- Type: string
-- Choices: one of ['gasteiger', 'am1bcc', 'OPLS']
-- Default: 'am1bcc'
+- Flag: ``-c NAME``, ``--charges_method NAME``
+- Type: ``string``
+- Choices: one of [``gasteiger``, ``am1bcc``, ``OPLS``]
+- Default: ``am1bcc``
 - Example: the code below will calculate partial charges using 'gasteiger' method
 
   .. code-block:: bash
@@ -193,8 +193,8 @@ Include terminal rotamers
 -------------------------
 It always includes terminal rotamers, even if they belong to a terminal methyl group whose rotation is trivial in PELE.
 
-- Flag: --include_terminal_rotamers
-- Default: False, exclude terminal rotamers
+- Flag: ``--include_terminal_rotamers``
+- Default: ``False``, exclude terminal rotamers
 - Example: the code below will generate a rotamer library including all terminal rotamers
 
   .. code-block:: bash
@@ -208,8 +208,8 @@ Parameterize non-bonding terms with OPLS2005
 
 It uses `OPLS2005` to parameterize the non-bonding terms of the ligand. It also assigns the atom types according to this force field.
 
-- Flag: --use_OPLS_nonbonding_param
-- Default: False, exclude terminal rotamers
+- Flag: ``--use_OPLS_nonbonding_param``
+- Default: ``False``, exclude terminal rotamers
 - Example: the code below will parameterize the non-bonding terms with OPLS2005
 
   .. code-block:: bash
@@ -223,8 +223,8 @@ Parameterize bonding and angular terms with OPLS2005
 
 It uses `OPLS2005` to parameterize the bonds and angle terms of the ligand.
 
-- Flag: --use_OPLS_bonds_and_angles
-- Default: False, exclude terminal rotamers
+- Flag: ``--use_OPLS_bonds_and_angles``
+- Default: ``False``, exclude terminal rotamers
 - Example: the code below will parameterize the non-bonding, bonding and angular terms with OPLS2005
 
   .. code-block:: bash

offpele/main.py

@@ -109,16 +109,16 @@ def handle_output_paths(molecule, output, as_datalocal):
         The output path for the solvent template
     """
     from pathlib import Path
-    name = molecule.name
+    tag = molecule.tag
     output_path = Path(output)
     check_if_path_exists(output_path)
 
     rotlib_path = output_path
     impact_path = output_path
     solvent_path = output_path
 
-    rotlib_name = name.upper() + '.rot.assign'
-    impact_name = name.lower() + 'z'
+    rotlib_name = tag.upper() + '.rot.assign'
+    impact_name = tag.lower() + 'z'
     solvent_name = 'ligandParams.txt'
 
     if as_datalocal:

offpele/tests/test_main.py

@@ -4,9 +4,11 @@
 
 import pytest
 
+import os
 import tempfile
-from offpele.main import run_offpele
+from offpele.main import run_offpele, handle_output_paths
 from offpele.utils import get_data_file_path, temporary_cd
+from offpele.topology import Molecule
 
 
 FORCEFIELD_NAME = 'openff_unconstrained-1.2.0.offxml'
@@ -18,6 +20,9 @@ class TestMain(object):
     """
 
     def test_offpele_default_call(self):
+        """
+        It checks the default call of offpele's main function.
+        """
         LIGAND_PATH = 'ligands/BNZ.pdb'
         ligand_path = get_data_file_path(LIGAND_PATH)
 
@@ -26,6 +31,9 @@ def test_offpele_default_call(self):
                 run_offpele(ligand_path, output=tmpdir)
 
     def test_offpele_custom_call(self):
+        """
+        It checks the custom call of offpele's main function.
+        """
         LIGAND_PATH = 'ligands/BNZ.pdb'
         ligand_path = get_data_file_path(LIGAND_PATH)
 
@@ -38,3 +46,81 @@ def test_offpele_custom_call(self):
                             output=tmpdir,
                             with_solvent=True,
                             as_datalocal=True)
+
+    def test_default_output_paths(self):
+        """
+        It checks the default output paths that are used for each parameter
+        file from offpele.
+        """
+
+        def from_PosixPath_to_string(paths):
+            """
+            Convert PosixPaths to strings
+            """
+            return map(str, paths)
+
+        molecule = Molecule(smiles='c1ccccc1', name='benzene', tag='BNZ')
+
+        rotlib_path, impact_path, solvent_path = \
+            handle_output_paths(molecule, '', False)
+
+        # Convert PosixPaths to strings
+        rotlib_path, impact_path, solvent_path = map(
+            str, [rotlib_path, impact_path, solvent_path])
+
+        assert rotlib_path == 'BNZ.rot.assign', 'Unexpected default ' \
+            + 'rotamer library path'
+        assert impact_path == 'bnzz', 'Unexpected default Impact ' \
+            + 'template path'
+        assert solvent_path == 'ligandParams.txt', 'Unexpected default ' \
+            + 'solvent parameters path'
+
+        with tempfile.TemporaryDirectory() as tmpdir:
+            with temporary_cd(tmpdir):
+                # To avoid the complain about unexistent folder
+                os.mkdir('output')
+                rotlib_path, impact_path, solvent_path = \
+                    handle_output_paths(molecule, 'output', False)
+
+        # Convert PosixPaths to strings
+        rotlib_path, impact_path, solvent_path = map(
+            str, [rotlib_path, impact_path, solvent_path])
+
+        assert rotlib_path == 'output/BNZ.rot.assign', 'Unexpected default ' \
+            + 'rotamer library path'
+        assert impact_path == 'output/bnzz', 'Unexpected default Impact ' \
+            + 'template path'
+        assert solvent_path == 'output/ligandParams.txt', 'Unexpected ' \
+            + 'default solvent parameters path'
+
+        rotlib_path, impact_path, solvent_path = \
+            handle_output_paths(molecule, '', True)
+
+        # Convert PosixPaths to strings
+        rotlib_path, impact_path, solvent_path = map(
+            str, [rotlib_path, impact_path, solvent_path])
+
+        assert rotlib_path == 'DataLocal/LigandRotamerLibs/' \
+            + 'BNZ.rot.assign', 'Unexpected default rotamer library path'
+        assert impact_path == 'DataLocal/Templates/OFF/Parsley/' \
+            + 'HeteroAtoms/bnzz', 'Unexpected default Impact template'
+        assert solvent_path == 'DataLocal/OBC/ligandParams.txt', \
+            'Unexpected default solvent parameters path'
+
+        with tempfile.TemporaryDirectory() as tmpdir:
+            with temporary_cd(tmpdir):
+                # To avoid the complain about unexistent folder
+                os.mkdir('output')
+                rotlib_path, impact_path, solvent_path = \
+                    handle_output_paths(molecule, 'output', True)
+
+        # Convert PosixPaths to strings
+        rotlib_path, impact_path, solvent_path = map(
+            str, [rotlib_path, impact_path, solvent_path])
+
+        assert rotlib_path == 'output/DataLocal/LigandRotamerLibs/' \
+            + 'BNZ.rot.assign', 'Unexpected default rotamer library path'
+        assert impact_path == 'output/DataLocal/Templates/OFF/Parsley/' \
+            + 'HeteroAtoms/bnzz', 'Unexpected default Impact template path'
+        assert solvent_path == 'output/DataLocal/OBC/ligandParams.txt', \
+            'Unexpected default solvent parameters path'