Merge pull request #3 from NostrumBioDiscovery/devel

Devel

MANIFEST.in

@@ -3,3 +3,5 @@ include pele_platform/Utilities/PlopRotTemp/param/*
 include pele_platform/AdaptivePELE/atomset/*
 include pele_platform/AdaptivePELE/freeEnergies/*
 recursive-include pele_platform/Utilities/PPP/Data/ *
+recursive-include pele_platform/Examples/ *
+recursive-include tests/data *

README.rst

@@ -1,18 +1,31 @@
 PELE_Platform
 ====================
 
-Wrap up Platform to launch all PELE features. [AdaptivePELE, MSM, LigandGrowing, Glide Rescoring]
+|MIT license| |GitHub release| |PyPI release| |Conda release|
+
+Pele platform is a python module to automatically launch PELE, AdaptivePELE, MSMPELE and FragPELE. It is built as a python layer on top of all PELE functionalities that can be used as a backend for a potential future GUI.
 
 PELE_Platform Fucntionalities
 =======================================
 
-1) Calculate absoluite free energies with [MSM_PELE](https://github.com/danielSoler93/MSM_PELE)
-2) Run Out-in | Kinase Rescoring | Induce-Fit | Free [Adaptive PELE](https://github.com/AdaptivePELE/AdaptivePELE)
-3) Grow your Ligand with [FRAG_PELE] (https://github.com/danielSoler93/LigandGrowing)
+Automatically prepare and launch PELE&AdaptivePELE input
 
 Install
 =====================
 
 pip install pele_platform
 
 
+.. |MIT license| image:: https://img.shields.io/badge/License-MIT-blue.svg
+   :target: https://lbesson.mit-license.org/
+
+
+.. |GitHub release| image:: https://img.shields.io/github/release/NostrumBioDiscovery/pele_platform.svg
+    :target: https://github.com/NostrumBioDiscovery/pele_platform/releases/
+
+.. |PyPI release| image:: https://img.shields.io/pypi/v/pele_platform.svg
+    :target: https://pypi.org/project/pele_platform/
+
+.. |Conda release| image:: https://anaconda.org/nostrumbiodiscovery/pele_platform/badges/version.svg
+    :target: https://anaconda.org/nostrumbiodiscovery/pele_platform
+

docs/_sources/changelog/index.rst.txt

@@ -1,2 +1,15 @@
-changelog
+What's new?
 ############
+
+Here we report the main changes for each version
+
+v1.0
+=====
+
+- Automatic Platform to automatically launch PELE&adaptivePELE. It creates the forcefield parameters, the control files, the PELE input.pdb and finally launch the simulation.
+
+- Flexibility to include MSM and Frag PELE
+
+- Flexibility to include analysis scripts
+
+- Flexibility to include PELE modes

docs/_sources/documentation/index.rst.txt

@@ -128,6 +128,10 @@ Parameters to set the exploration Box:
 PELE params
 ================
 
+- **seed**: Seed of the job for reproducibility. Default=12345
+
+- **log**: Retrieve PELE logfiles during simulation. Default=False
+
 - **anm_freq**: Every how many steps to perform anm. Default=4
 
 - **sidechain_freq**: Every how many steps to perform sidechain sampling. Default=2
@@ -148,6 +152,8 @@ PELE params
 
 ..  code-block:: yaml
 
+  seed: 312312
+  log: true
   anm_freq: 4
   sidechain_freq: 2
   min_freq: 1
@@ -215,6 +221,52 @@ This section allows the user to change the constraint values.
     water_constr: 5
 
 
+WaterPerturbation
+======================
+
+- Water modes:
+
+    - **water_exp**: Exploration of the hydratation sites of a binding site by perturbing and clusterizing a single water. More advance features will be later implemented to discriminate between "happy" and "unhappy" waters.
+
+    - **water_lig**: Perturb one or several water molecules while exploring the conformational space of the ligand.
+
+Example water exploration:
+
+..  code-block:: yaml
+
+  residue: HOH
+  water_exp: true
+
+Example water ligand:
+
+..  code-block:: yaml
+
+    residue: LIG
+    water_exp:
+    - M:1
+    - M:2
+
+- **box_water**: Center of the box for the waters
+
+- **water_radius**: Radius of the water box
+
+- **water_trials**: Numerical trials on water perturbation
+
+- **water_constr**: COM constraint applied to th water molecule after perturbation
+
+- **water_temp**: Temperature of the water perturbation step
+
+
+..  code-block:: yaml
+
+    box_water:
+    - 20
+    - 30
+    - 20
+    water_radius: 8
+    water_trials: 500
+    water_constr: 0.5
+    water_tamp: 2000
 
 
 Metrics

docs/_sources/installation/index.rst.txt

@@ -1,19 +1,42 @@
-installation
+Installation
 ###############
 
-Conda
---------
+Conda (recomended)
+--------------------
 
+on going
 
 
 Pypi
------
+------
+
+.. code-block:: bash
+
+    pip install numpy cython
+
+    pip install pele_platform
 
 
 Source Code
 -------------
 
+.. code-block:: bash
+
+    git clone https://github.com/NostrumBioDiscovery/pele_platform.git
+    
+    cd pele_platform
+    
+    vim pele_platform/constants/constants.py #(change paths under else statement)
+    
+    pip install pele_platform
+
+
+
+Test it works
+----------------
+
+.. code-block:: bash
 
+    cd pele_platform/tests
 
-Test
------
+    pytest

docs/_sources/tutorial/index.rst.txt

@@ -1,2 +1,36 @@
 Launch your first job
 ##########################
+
+0) Prepare the system with maestro (Protein Preparation Wizard, hydrogen optimization and posterior minimization)
+and output a complex.pdb
+
+1) Copy the text below into a file called input.yaml and change the path
+to your input pdb file, the residue name of the ligand to be perturb and its chain.
+
+..  code-block:: yaml
+
+    system: "complex.pdb"
+    residue: "LIG"
+    chain: "L"
+
+2)  Choose one of the modes below by copying its line to the input.yaml:
+
+..  code-block:: yaml
+
+    induced_fit: true
+    out_in: true
+    in_out: true
+    global: true   
+    
+3) Test your simulation (1min):
+
+First add the flag **test:true** into and launch the next command:
+
+``python -m pele_platform.main input.yaml``
+
+4) Run prodution
+
+If everything works change the flag **test: true** by **cpus: X** being X the number of cpus to use for the job. From 40-60 for induced fit simulation and exit paths, from 100-200 for local explorations and 250 for global. Finally run the python command again:
+
+``python -m pele_platform.main input.yaml``
+

docs/build_docs/source/changelog/index.rst

@@ -1,2 +1,15 @@
-changelog
+What's new?
 ############
+
+Here we report the main changes for each version
+
+v1.0
+=====
+
+- Automatic Platform to automatically launch PELE&adaptivePELE. It creates the forcefield parameters, the control files, the PELE input.pdb and finally launch the simulation.
+
+- Flexibility to include MSM and Frag PELE
+
+- Flexibility to include analysis scripts
+
+- Flexibility to include PELE modes

docs/build_docs/source/documentation/index.rst

@@ -128,6 +128,10 @@ Parameters to set the exploration Box:
 PELE params
 ================
 
+- **seed**: Seed of the job for reproducibility. Default=12345
+
+- **log**: Retrieve PELE logfiles during simulation. Default=False
+
 - **anm_freq**: Every how many steps to perform anm. Default=4
 
 - **sidechain_freq**: Every how many steps to perform sidechain sampling. Default=2
@@ -148,6 +152,8 @@ PELE params
 
 ..  code-block:: yaml
 
+  seed: 312312
+  log: true
   anm_freq: 4
   sidechain_freq: 2
   min_freq: 1
@@ -215,6 +221,52 @@ This section allows the user to change the constraint values.
     water_constr: 5
 
 
+WaterPerturbation
+======================
+
+- Water modes:
+
+    - **water_exp**: Exploration of the hydratation sites of a binding site by perturbing and clusterizing a single water. More advance features will be later implemented to discriminate between "happy" and "unhappy" waters.
+
+    - **water_lig**: Perturb one or several water molecules while exploring the conformational space of the ligand.
+
+Example water exploration:
+
+..  code-block:: yaml
+
+  residue: HOH
+  water_exp: true
+
+Example water ligand:
+
+..  code-block:: yaml
+
+    residue: LIG
+    water_exp:
+    - M:1
+    - M:2
+
+- **box_water**: Center of the box for the waters
+
+- **water_radius**: Radius of the water box
+
+- **water_trials**: Numerical trials on water perturbation
+
+- **water_constr**: COM constraint applied to th water molecule after perturbation
+
+- **water_temp**: Temperature of the water perturbation step
+
+
+..  code-block:: yaml
+
+    box_water:
+    - 20
+    - 30
+    - 20
+    water_radius: 8
+    water_trials: 500
+    water_constr: 0.5
+    water_tamp: 2000
 
 
 Metrics

docs/build_docs/source/installation/index.rst

@@ -1,19 +1,42 @@
-installation
+Installation
 ###############
 
-Conda
---------
+Conda (recomended)
+--------------------
 
+on going
 
 
 Pypi
------
+------
+
+.. code-block:: bash
+
+    pip install numpy cython
+
+    pip install pele_platform
 
 
 Source Code
 -------------
 
+.. code-block:: bash
+
+    git clone https://github.com/NostrumBioDiscovery/pele_platform.git
+    
+    cd pele_platform
+    
+    vim pele_platform/constants/constants.py #(change paths under else statement)
+    
+    pip install pele_platform
+
+
+
+Test it works
+----------------
+
+.. code-block:: bash
 
+    cd pele_platform/tests
 
-Test
------
+    pytest

docs/build_docs/source/tutorial/index.rst

@@ -1,2 +1,36 @@
 Launch your first job
 ##########################
+
+0) Prepare the system with maestro (Protein Preparation Wizard, hydrogen optimization and posterior minimization)
+and output a complex.pdb
+
+1) Copy the text below into a file called input.yaml and change the path
+to your input pdb file, the residue name of the ligand to be perturb and its chain.
+
+..  code-block:: yaml
+
+    system: "complex.pdb"
+    residue: "LIG"
+    chain: "L"
+
+2)  Choose one of the modes below by copying its line to the input.yaml:
+
+..  code-block:: yaml
+
+    induced_fit: true
+    out_in: true
+    in_out: true
+    global: true   
+    
+3) Test your simulation (1min):
+
+First add the flag **test:true** into and launch the next command:
+
+``python -m pele_platform.main input.yaml``
+
+4) Run prodution
+
+If everything works change the flag **test: true** by **cpus: X** being X the number of cpus to use for the job. From 40-60 for induced fit simulation and exit paths, from 100-200 for local explorations and 250 for global. Finally run the python command again:
+
+``python -m pele_platform.main input.yaml``
+