Usage of virtual sites and better compatibility with MARTINI 3

.gitignore

@@ -0,0 +1,104 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*,cover
+.hypothesis/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# IPython Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# dotenv
+.env
+
+# virtualenv
+.venv/
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
+
+# IDEs
+.idea/
+.vscode/
+
+# Rope project settings
+.ropeproject
+
+# mypy
+.mypy_cache/
+
+# pytest
+.pytest_cache/
+
+# data
+/distributions.png
+/G1_DATA/.aa_traj.xtc_offsets.npz
+/G1_DATA/.cg_traj.xtc_offsets.npz

CODEOWNERS

@@ -0,0 +1,37 @@
+# This is a comment.
+# Each line is a file pattern followed by one or more owners.
+
+# These owners will be the default owners for everything in
+# the repo. Unless a later match takes precedence,
+# @global-owner1 and @global-owner2 will be requested for
+# review when someone opens a pull request.
+*       @CharlyEmpereurmot
+
+# Order is important; the last matching pattern takes the most
+# precedence. When someone opens a pull request that only
+# modifies JS files, only @js-owner and not the global
+# owner(s) will be requested for a review.
+*.py    @CharlyEmpereurmot @giovannidoni
+
+# You can also use email addresses if you prefer. They'll be
+# used to look up users just like we do for commit author
+# emails.
+# *.go [email protected]
+
+# In this example, @doctocat owns any files in the build/logs
+# directory at the root of the repository and any of its
+# subdirectories.
+# /build/logs/ @doctocat
+
+# The `docs/*` pattern will match files like
+# `docs/getting-started.md` but not further nested files like
+# `docs/build-app/troubleshooting.md`.
+# docs/*  [email protected]
+
+# In this example, @octocat owns any file in an apps directory
+# anywhere in your repository.
+# apps/ @octocat
+
+# In this example, @doctocat owns any file in the `/docs`
+# directory in the root of your repository.
+# /docs/ @doctocat

G1_DATA/cg_map.ndx

@@ -3,7 +3,7 @@
 [ N0 ]
 5 8 57 74
 [ Nda ]
-13 16 18 19 20 
+13 16 18 19 20
 [ N0 ]
 9 10 77 97
 [ Nda ]
@@ -15,7 +15,7 @@
 [ Qd ]
 110 113
 [ Nda ]
-30 33 35 36 37 
+30 33 35 36 37
 [ N0 ]
 26 27 117 137
 [ Nda ]

G1_DATA/cg_model.itp

@@ -7,35 +7,35 @@ G1               1
 ; id type resnr residue   atom  cgnr    charge
 
 1      N0     1      G1     A1  1      0.00000
-2      N0     2      G1     A2  2      0.00000
-3     Nda     3      G1     A3  3      0.00000
-4      N0     4      G1     A4  4      0.00000
-5     Nda     5      G1     A5  5      0.00000
-6      Qd     6      G1     A6  6      1.00000
-7     Nda     7      G1     A7  7      0.00000
-8      Qd     8      G1     A8  8      1.00000
-9     Nda     9      G1     A9  9      0.00000
-10     N0    10      G1    A10  10     0.00000
-11    Nda    11      G1    A11  11     0.00000
-12     Qd    12      G1    A12  12     1.00000
-13    Nda    13      G1    A13  13     0.00000
-14     Qd    14      G1    A14  14     1.00000
-15    Nda    15      G1    A15  15     0.00000
-16     N0    16      G1    A16  16     0.00000
-17    Nda    17      G1    A17  17     0.00000
-18     Qd    18      G1    A18  18     1.00000
-19    Nda    19      G1    A19  19     0.00000
-20     Qd    20      G1    A20  20     1.00000
-21    Nda    21      G1    A21  21     0.00000
-22     N0    22      G1    A22  22     0.00000
-23    Nda    23      G1    A23  23     0.00000
-24     Qd    24      G1    A24  24     1.00000
-25    Nda    25      G1    A25  25     0.00000
-26     Qd    26      G1    A26  26     1.00000
+2      N0     1      G1     A2  2      0.00000
+3     Nda     1      G1     A3  3      0.00000
+4      N0     1      G1     A4  4      0.00000
+5     Nda     1      G1     A5  5      0.00000
+6      Qd     1      G1     A6  6      1.00000
+7     Nda     1      G1     A7  7      0.00000
+8      Qd     1      G1     A8  8      1.00000
+9     Nda     1      G1     A9  9      0.00000
+10     N0     1      G1    A10  10     0.00000
+11    Nda     1      G1    A11  11     0.00000
+12     Qd     1      G1    A12  12     1.00000
+13    Nda     1      G1    A13  13     0.00000
+14     Qd     1      G1    A14  14     1.00000
+15    Nda     1      G1    A15  15     0.00000
+16     N0     1      G1    A16  16     0.00000
+17    Nda     1      G1    A17  17     0.00000
+18     Qd     1      G1    A18  18     1.00000
+19    Nda     1      G1    A19  19     0.00000
+20     Qd     1      G1    A20  20     1.00000
+21    Nda     1      G1    A21  21     0.00000
+22     N0     1      G1    A22  22     0.00000
+23    Nda     1      G1    A23  23     0.00000
+24     Qd     1      G1    A24  24     1.00000
+25    Nda     1      G1    A25  25     0.00000
+26     Qd     1      G1    A26  26     1.00000
 
 
 [ bonds ]
-;   i     j   funct   length   force.c.   
+;   i     j   funct   length   force.c.
 
 ; bond group 1
     1     2       1        0         0           ; B1
@@ -72,7 +72,7 @@ G1               1
 
 
 [ angles ]
-;   i     j     k   funct     angle   force.c.   
+;   i     j     k   funct     angle   force.c.
 
 ; angle group 1
     1     2    15       2       120         0           ; A1
@@ -114,3 +114,4 @@ G1               1
    22    23    24       2       180         0           ; A5
    22    25    26       2       180         0           ; A5
 
+

G1_DATA/start_conf.gro

@@ -1,5 +1,5 @@
 g1_GMX.gro created by acpype (Rev: 10101) on Thu Sep 12 17:34:03 2019 t=   0.00000 step= 0
- 1281
+ 1282
     1PG1     N1    1   2.936   2.913   2.508
     1PG1     C2    2   2.896   2.600   2.705
     1PG1     H7    3   3.134   3.247   2.318
@@ -26,6 +26,7 @@ g1_GMX.gro created by acpype (Rev: 10101) on Thu Sep 12 17:34:03 2019 t=   0.000
     1PG1     H9   24   2.384   3.105   3.680
     1PG1    H11   25   3.353   3.308   3.377
     1PG1     N7   26   3.705   3.490   3.432
+    1PG1     N7   26   3.705   3.490   3.432
     2W        W   27   0.084   3.595   3.359
     3W        W   28   0.460   2.488   2.882
     4W        W   29   3.165   2.218   0.652

G1_DATA/system.top

@@ -10,5 +10,5 @@ G1 (PAMAM) in water
 [ molecules ]
 ; Compound        #mols
 G1                1
-W                 1247
-CL-               8
+W                 1248
+CL-               8

README.md

@@ -1,16 +1,18 @@
 # Swarm-CG
 
-Swarm-CG is designed for automatically optimizing the bonded terms of a coarse-grained (CG) molecular model, in explicit or implicit solvent, with respect to a reference all-atom (AA) trajectory and starting from a preliminary CG model (topology and non-bonded parameters). The package is designed for usage with Gromacs and contains 3 modules for:
+Swarm-CG is designed for automatically optimizing the bonded terms of a MARTINI-based coarse-grained (CG) molecular model, in explicit or implicit solvent, with respect to a reference all-atom (AA) trajectory and starting from a preliminary CG model (topology and non-bonded parameters). The package is designed for usage with Gromacs and contains 3 modules for:
 
 1. Evaluating the bonded parametrization of a CG model
 2. Optimizing bonded terms of a CG model
 3. Monitoring an optimization procedure
 
 ![Swarm-CG](https://raw.githubusercontent.com/GMPavanLab/Swarm-CG/master/images/TOC_Swarm-CG_paper.png)
 
+Swarm-CG works with MARTINI version 2 or 3. Virtual sites are correctly handled and the AA-to-CG mapping can be interpreted as Center of Mass (COM) or Center of Geometry (COG).
+
 ### Publication
 
-> Empereur-mot, C.; Pesce, L.; Bochicchio, D.; Perego, C.; Pavan, G.M. (2020) Swarm-CG: Automatic Parametrization of Bonded Terms in Coarse-Grained Models of Simple to Complex Molecules via Fuzzy Self-Tuning Particle Swarm Optimization. [ChemRxiv. Preprint](https://doi.org/10.26434/chemrxiv.12613427)
+> Empereur-mot, C.; Pesce, L.; Bochicchio, D.; Perego, C.; Pavan, G.M. (2020) Swarm-CG: Automatic Parametrization of Bonded Terms in MARTINI-based Coarse-Grained Models of Simple to Complex Molecules via Fuzzy Self-Tuning Particle Swarm Optimization. [ChemRxiv. Preprint](https://doi.org/10.26434/chemrxiv.12613427)
 
 ### Installation & Usage
 
@@ -41,7 +43,7 @@ Here is an ITP file extract from the demonstration data of [PAMAM G1](https://gi
 
 The module `scg_evaluate` enables quick evaluation of the fit of bond, angle and dihedral distributions between a CG model trajectory and a reference AA model trajectory of an identical molecule, by producing a single comprehensive figure.
 
-	scg_evaluate -aa_tpr G1_DATA/aa_topol.tpr -aa_traj G1_DATA/aa_traj.xtc -cg_map G1_DATA/cg_map.ndx -cg_itp G1_DATA/cg_model.itp -cg_tpr your_cg.tpr -cg_traj your_cg.xtc
+	scg_evaluate -aa_tpr G1_DATA/aa_topol.tpr -aa_traj G1_DATA/aa_traj.xtc -cg_map G1_DATA/cg_map.ndx -cg_itp G1_DATA/cg_model.itp -cg_tpr G1_DATA/cg_topol.tpr -cg_traj G1_DATA/cg_traj.xtc
 
 It can also be used for inspecting AA-mapped distributions exclusively.
 

environment.yml

@@ -0,0 +1,24 @@
+name: swarmcg
+channels:
+  - conda-forge
+dependencies:
+  - cycler=0.10.0
+  - dscribe=0.4.0 # 0.3.5 available for linux
+  - matplotlib=3.2.0 # 3.2.1 available
+  - mdanalysis>=1.0.0
+  - mypy=0.770
+  - numpy=1.19.1
+  - pandas=1.0.1
+  - pip
+  - pybind11=2.4.3 # 2.5.0 available
+  - pyemd=0.5.1
+  - pylint=2.4.4
+  - pytest=5.4.1
+  - pytest-runner=5.2
+  - python=3.7.6
+  - scikit-learn=0.22.2.post1
+  - scipy=1.4.1
+  - setuptools
+  - wheel
+  - pip:
+      - fst-pso

setup.py

@@ -1,19 +1,21 @@
 from setuptools import setup, find_packages
 
+import swarmcg
+
 with open('README.md') as readme_file:
     README = readme_file.read()
 
 setup(
     name='swarm-cg',
-    version='v1.1.2',
+    version=swarmcg.__version__,
     description='Tools for automatic parametrization of bonded terms in coarse-grained molecular models, with respect to an all-atom trajectory',
-	author='Charly Empereur-mot',
-	author_email='[email protected]',
+    author='Charly Empereur-mot',
+    author_email='[email protected]',
     license='MIT',
-	url = 'https://github.com/GMPavanLab/Swarm-CG',
+    url = 'https://github.com/GMPavanLab/Swarm-CG',
     long_description=README,
     long_description_content_type="text/markdown",
-    keywords = ['gromacs', 'coarse-grain', 'molecular model', 'optimization', 'force field'],
+    keywords=['gromacs', 'coarse-grain', 'molecular model', 'optimization', 'force field'],
     packages=find_packages(include=['swarmcg', 'swarmcg.*']),
     install_requires=[
         'numpy>=1.16.4',
@@ -25,9 +27,9 @@
     ],
     entry_points={
         'console_scripts': [
-        	'scg_optimize=swarmcg.optimize_model:main',
-        	'scg_evaluate=swarmcg.evaluate_model:main',
-        	'scg_monitor=swarmcg.analyze_optimization:main'
+            'scg_optimize=swarmcg.optimize_model:main',
+            'scg_evaluate=swarmcg.evaluate_model:main',
+            'scg_monitor=swarmcg.analyze_optimization:main'
         ]
     }
 )

swarmcg/__init__.py

@@ -0,0 +1 @@
+__version__ = '1.1.3'