Merge branch 'bending' of https://github.com/marrink-lab/polyply_1.0 …

…into bending

.github/workflows/pypi_deploy.yml

@@ -36,7 +36,6 @@ jobs:
             token: ${{ secrets.CODECOV_TOKEN }}
             files: ./coverage.xml
             fail_ci_if_error: true
-            verbose: true
 
   deploy:
     needs: test

LIBRARY.md

@@ -21,7 +21,9 @@
 |Polystyrene sulfonate          |PSS                      |                                                                       |[martini2](polyply/data/martini2/PSS.martini.2.itp)   |
 |                               |                         |                                                                       |[martini3](polyply/data/martini3/PSS.martini3.ff)     |
 |Poly(para-phenylene ethynylene)|PPE                      |                                                                       |[martini3](polyply/data/martini3/PPE.martini3.ff)     |
-|Poly(TEMPO methacrylate)       |PTMA                     |[oplsaaLigParGen](polyply/data/oplsaaLigParGen/PTMA.oplsaa.LigParGen.ff)]|[martini3](polyply/data/martini3/PTMA.martini3.ff)  |
+|Poly(TEMPO methacrylate)       |PTMA                     |[oplsaaLigParGen](polyply/data/oplsaaLigParGen/PTMA.oplsaa.LigParGen.ff)|[martini3](polyply/data/martini3/PTMA.martini3.ff)   |
+|                               |                         |                                                                       |[ibi_cgm3](polyply/data/ibi_cmg3/PTMA.cgm3.ibi.ff)    |
+|                               |                         |                                                                       |[ibi_gbcg](polyply/data/ibi_gbcg/PTMA.gbno2.ibi.ff)   |
 |Dextran                        |DEX                      |                                                                       |[martini3](polyply/data/martini3/dextran.martini3.ff) |
 |DNA nucleobases                |Dx, Tx5, Dx3 w/ x=T,G,A,C|[parmbsc1](polyply/data/parmbsc1/dna_final.ff)                         |[martini2](polyply/data/martini2/DNA_M2.ff)           |
 |Aminoacids                     |3 letter code            |                                                                       |[martini3](polyply/data/martini3/aminoacids.ff)       |

README.md

@@ -39,6 +39,7 @@ force-field, molecule parameters and this program.
 - (Feb 8, 22') **Featured Research Article in Nature Communcations.** Our article on the polyply software suite is now featured on the [Editors' Highlights](https://www.nature.com/collections/hhfigaahch) for Structural biology, biochemistry and biophysics in Nature Communications. The Editors’ Highlights pages aims to showcase the 50 best papers recently published in an area. The development team is beyond happy to receive this honor.   
 - (May 23, 22') **Fighting Cancer with polyply.** Dane et al. used polyply to setup simulations of vesicles and lipid nanodiscs (LNDs) containing PEGylated lipids, which are used as nanocarriers for cancer therapeutics. They find that LNDs are more effective in delivery likely due to their higher flexibility.  Check it out in [Nature Materials](https://www.nature.com/articles/s41563-022-01251-z). 
 - (Jan 18, 23') **Towards whole cell simulations with polyply.** In [a perspective on whole-cell simulations](https://www.frontiersin.org/articles/10.3389/fchem.2023.1106495/full) using the Martini force field, Stevens *et al.* utilize polyply to construct the full 0.5 Mio bp chromosome of the Syn3A minimal cell. This impressive task is a good example of the power of the upcoming DNA implementation into polyply and the role of polyply in the Martini Ecosystem.
+- (May 11, 23') **Electronic coarse-grained models in polyply.** Curious about simulating non-conjugated radical-containing polymers for all-organic batteries? The models developed [in this work](https://doi.org/10.1021/acs.macromol.3c00141) for PTMA, or poly(TEMPO acrylamide), are avaiable in polyply. There is an all-atom model and different coarse-grained model (Martini 3, iterative Boltzmann inversion), all of which can be flexibly handled by polyply. 
 
 ## Contributions & Support
 We are happy to accept submissions of polymer parameters to the polyply library. To submit parameters simply 

bin/polyply

@@ -74,6 +74,9 @@ def main(): # pylint: disable=too-many-locals,too-many-statements
                            help='A linear sequence of residue names.')
     seq_group.add_argument('-seqf', dest='seq_file', type=Path,
                            help='A graph input file (JSON|TXT|FASTA|IG)')
+    dna_group = parser_gen_itp.add_argument_group('DNA specifc options')
+    dna_group.add_argument('-dsdna', dest='dsdna', action='store_true',
+                           help='complement single sequence to dsDNA sequence')
 
     parser_gen_itp.set_defaults(func=gen_itp)
 

polyply/__init__.py

@@ -19,16 +19,23 @@
 
 # Find the data directory once.
 try:
-    import pkg_resources
+    from importlib.resources import files, as_file
+    import atexit
+    from contextlib import ExitStack
 except ImportError:
-    import os
-    DATA_PATH = os.path.join(os.path.dirname(__file__), 'data')
-    TEST_DATA = os.path.join(os.path.dirname(__file__), 'tests/test_data')
-    del os
+    from pathlib import Path
+    DATA_PATH = Path(__file__).parent / 'data'
+    TEST_DATA = Path(__file__).parent / 'tests/test_data'
+    del Path
 else:
-    DATA_PATH = pkg_resources.resource_filename('polyply', 'data')
-    TEST_DATA = pkg_resources.resource_filename('polyply', 'tests/test_data')
-    del pkg_resources
+    ref_data = files('polyply') / 'data'
+    ref_test = files('polyply') / 'tests'/ 'test_data'
+    file_manager = ExitStack()
+    atexit.register(file_manager.close)
+    DATA_PATH = file_manager.enter_context(as_file(ref_data))
+    TEST_DATA = file_manager.enter_context(as_file(ref_test))
+
+    del files, as_file, atexit, ExitStack
 
 del pbr
 

polyply/data/ibi_cgm3/PTMA.cgm3.ibi.ff

@@ -0,0 +1,68 @@
+[ moleculetype ]
+; name nexcl.
+PTMA     2
+
+[ info ] 
+Nonbonded interaction potentials (and example run) can be found at: https://doi.org/10.5281/zenodo.8287521
+
+[ atoms ]
+; id  type  resnr  residu atom  cgnr  charge  mass
+   1   VNL    1    PTMA   VNL    1     0.0     54
+   2   EST    1    PTMA   EST    2     0.0     54
+   3    C1    1    PTMA    C1    3     0.0     54
+   4    C2    1    PTMA    C2    4     0.0     54
+   5    C2    1    PTMA    C3    5     0.0     54
+   6    N4    1    PTMA    N4    6     0.0     36
+
+[ bonds ]
+; i  j   funct   length
+  1  2      1     0.262   15000 { "comment": "M3 PMMA model [10.1038/s41467-021-27627-4] shortened"}
+  2  3      1     0.253   15000 { "comment": "PMMA-TEMPO connection"} 
+  3  4      1     0.326   25000 { "comment": "cog (TEMPO)"}
+  3  5      1     0.326   25000 { "comment": "cog (TEMPO)"}
+  3  6      1     0.310  100000 {"ifdef": "FLEXIBLE", "comment": "cog (TEMPO)"} 
+  4  6      1     0.238  100000 {"ifdef": "FLEXIBLE", "comment": "cog (TEMPO)"}
+  5  6      1     0.238  100000 {"ifdef": "FLEXIBLE", "comment": "cog (TEMPO)"}
+
+[constraints]
+; i  j   funct   length
+  3  6      1     0.310  {"ifndef": "FLEXIBLE", "comment": "cog (TEMPO)"} 
+  4  6      1     0.238  {"ifndef": "FLEXIBLE", "comment": "cog (TEMPO)"}
+  5  6      1     0.238  {"ifndef": "FLEXIBLE", "comment": "cog (TEMPO)"}
+
+[ angles ]
+; i  j  k  funct   length  force k
+  1  2  3    2      132.9    70 { "comment": "PMMA-TEMPO connection"} 
+  2  3  4    2      129.0    60 { "comment": "PMMA-TEMPO connection"} 
+  2  3  5    2      121.9    95 { "comment": "PMMA-TEMPO connection"} 
+
+[dihedrals]
+; i j k l  funct  ref.angle   force_k
+  3 4 5 6    2      140.00      20 { "comment": "cog (TEMPO)"}
+  2 4 5 6    2      150.00      80 { "comment": "PMMA-TEMPO connection"}
+
+[exclusions]
+  1 2 3 4 5 6
+  2 3 4 5 6 
+  3 4 5 6  
+  4 5 6  
+  5 6
+
+[ link ]
+resname "PTMA"
+[ bonds ]
+VNL     +VNL    1     0.315 4000  {"group": "vinyl backbone"}
+
+[ link ]
+resname "PTMA"
+[ angles ]
+VNL  +VNL  ++VNL   2  115  35  {"group": "vinyl backbone"}
+
+[ link ]
+resname "PTMA"
+[ angles ]
+EST  VNL  +VNL  2  70  20
+
+[ citation ]
+2023RAlessandri-Macromolecules
+polyply

polyply/data/ibi_cgm3/citations.bib

@@ -0,0 +1,22 @@
+
+@article{2023RAlessandri-Macromolecules,
+  title={Prediction of Electronic Properties of Radical-Containing Polymers at Coarse-Grained Resolutions},
+  author={Alessandri, Riccardo and de Pablo, Juan J},
+  journal={Macromolecules},
+  volume={56},
+  number={10},
+  pages={3574-3584},
+  doi={10.1021/acs.macromol.3c00141},
+  year={2023}
+}
+
+
+@article{polyply,
+  title={Polyply; a python suite for facilitating simulations of (bio-) macromolecules and nanomaterials},
+  author={Grunewald, Fabian and Alessandri, Riccardo and Kroon, Peter C and Monticelli, Luca and Souza, Paulo CT and Marrink, Siewert J},
+  journal={Nature Communications},
+  doi={10.1038/s41467-021-27627-4},
+  year={2022},
+  volume={13},
+  pages={68}
+}

polyply/data/ibi_gbcg/PTMA.gbno2.ibi.ff

@@ -0,0 +1,75 @@
+[ moleculetype ]
+; name nexcl.
+PTMA     2
+
+[ info ] 
+Nonbonded interaction potentials (and example run) can be found at: https://doi.org/10.5281/zenodo.8287521
+
+[ atoms ]
+; id  type  resnr  residu atom  cgnr  charge  mass
+   1   VNL    1     PTMA  VNL    1     0     71.099
+   2   EST    1     PTMA  EST    2     0     29.018
+   3    C1    1     PTMA   C1    3     0     56.108
+   4     U    1     PTMA   NN    4     0      0.000
+   5     U    1     PTMA   OO    5     0      0.000
+   6    C1    1     PTMA   C2    6     0     56.108 
+   7    NO    1     PTMA   NO    7     0     30.006
+
+[ bonds ]
+; i  j   funct   length
+  1  2      1     0.35337   12500 
+  2  3      1     0.32325   32000
+  2  6      1     0.32369   32000
+  3  6      1     0.38838   32000
+  3  7      1     0.23794 1000000 {"ifdef": "FLEXIBLE"}
+  6  7      1     0.23793 1000000 {"ifdef": "FLEXIBLE"}
+
+[constraints]
+; i  j   funct   length
+  3  7      1     0.23794  {"ifndef": "FLEXIBLE"}
+  6  7      1     0.23793  {"ifndef": "FLEXIBLE"}
+
+[ angles ]
+; i  j  k  funct   length  force k
+  1  2  3    2      130.000  90 
+  1  2  6    2      130.000  75 
+
+[dihedrals]
+; i j k l  funct  ref.angle   force_k
+  1 3 6 7    2      165.98      50
+  2 3 6 7    2      179.20      80
+  3 7 5 6    2      170.723     50 
+
+[virtual_sites3]
+; 3fd sites
+; site positioned as a linear combination of 3 atoms; the site is in the same plane
+; site  from      funct    a      b
+   4    3  2  7     2    0.834  0.210
+   5    3  2  7     2    1.180  0.276
+
+[exclusions]
+  1  2  3  4  5  6  7
+  2  3  4  5  6  7
+  3  4  5  6  7
+  4  5  6  7
+  5  6  7
+  6  7
+
+[ link ]
+resname "PTMA"
+[ bonds ]
+VNL     +VNL    1     0.305 12000  {"group": "vinyl backbone"}
+
+[ link ]
+resname "PTMA"
+[ angles ]
+VNL  +VNL  ++VNL   2  126  40  {"group": "vinyl backbone"}
+
+[ link ]
+resname "PTMA"
+[ angles ]
+EST  VNL  +VNL  2  90  20
+
+[ citation ]
+2023RAlessandri-Macromolecules
+polyply

polyply/data/ibi_gbcg/citations.bib

@@ -0,0 +1,22 @@
+
+@article{2023RAlessandri-Macromolecules,
+  title={Prediction of Electronic Properties of Radical-Containing Polymers at Coarse-Grained Resolutions},
+  author={Alessandri, Riccardo and de Pablo, Juan J},
+  journal={Macromolecules},
+  volume={56},
+  number={10},
+  pages={3574-3584},
+  doi={10.1021/acs.macromol.3c00141},
+  year={2023}
+}
+
+
+@article{polyply,
+  title={Polyply; a python suite for facilitating simulations of (bio-) macromolecules and nanomaterials},
+  author={Grunewald, Fabian and Alessandri, Riccardo and Kroon, Peter C and Monticelli, Luca and Souza, Paulo CT and Marrink, Siewert J},
+  journal={Nature Communications},
+  doi={10.1038/s41467-021-27627-4},
+  year={2022},
+  volume={13},
+  pages={68}
+}

polyply/data/martini2/DNA_M2.ff

@@ -566,3 +566,28 @@ BB3 +BB2
 BB2 BB3 +BB1 +BB2     1  180.00000     2     3 {"group": "link"}
 BB3 +BB1 +BB2 +BB3    9   85.00000     2     2 {"group": "link", "version": "1"}
 BB3 +BB1 +BB2 +BB3    9  160.00000     2     3 {"group": "link", "version": "2"}
+
+;
+; CIRCULAR MARTINI DNA
+;
+
+[ link ]
+resname "DT|DG|DA|DC"
+[ atoms ]
+BB3 { }
+>BB1 { }
+[ bonds ]
+BB3  >BB1 1  0.35300 10000 {"group": "link-circle", "edge": false}
+[ angles ]
+BB2 BB3  >BB1  2  102.00000   150 {"group": "backbone-circle", "edge": false}
+BB3 >BB1 >BB2  2  106.00000    75 {"group": "backbone-circle", "edge": false}
+[ exclusions ]
+#meta {"edge": false}
+BB2 >BB1
+BB3 >BB2
+[ dihedrals ]
+BB2 BB3 >BB1 >BB2     1  180.00000     2     3 {"group": "link-circle", "edge": false}
+BB3 >BB1 >BB2 >BB3    9   85.00000     2     2 {"group": "link-circle", "version": "1", "edge": false}
+BB3 >BB1 >BB2 >BB3    9  160.00000     2     3 {"group": "link-circle", "version": "2", "edge": false}
+[ edges ]
+BB3 >BB1 {"linktype": "circle"}

polyply/data/martini3/PTMA.martini3.ff

@@ -55,6 +55,6 @@ resname "PTMA"
 EST  VNL  +VNL  2  70  20
 
 [ citation ]
-2022RAlessandri-arXiv
+2023RAlessandri-Macromolecules
 Martini3
 polyply

polyply/data/martini3/citations.bib

@@ -31,14 +31,16 @@ @article{PPEs
   publisher={The Royal Society of Chemistry},
   url={http://dx.doi.org/10.1039/D1CP04237H},
 }
-@article{2022RAlessandri-arXiv,
-  title={Predicting Electronic Properties of Radical-Containing Polymers at Coarse-Grained Resolutions},
-  author={Alessandri, Riccardo and de Pablo, Juan J.},
-  journal={arXiv},
-  year={2022},
-  eprint={2209.02072},
-  primaryClass={cond-mat.soft},
-  doi={https://doi.org/10.48550/arXiv.2209.02072}}
+@article{2023RAlessandri-Macromolecules,
+  title={Prediction of Electronic Properties of Radical-Containing Polymers at Coarse-Grained Resolutions},
+  author={Alessandri, Riccardo and de Pablo, Juan J},
+  journal={Macromolecules},
+  volume={56},
+  number={10},
+  pages={3574-3584},
+  doi={10.1021/acs.macromol.3c00141},
+  year={2023}
+}
 @article{M3_sugars,
   title={Martini 3 Coarse-Grained Force Field for Carbohydrates},
   author={Fabian, Grünewald and Mats H., Punt and Elizabeth E., Jefferys and Petteri A., Vainikka and Melanie, König and Valtteri, Virtanen and Travis A., Meyer and Weria, Pezeshkian and Adam J., Gormley and Maarit, Karonen and Mark S. P., Sansom and Paulo C. T, Souza and Siewert J., Marrink},

polyply/src/apply_links.py

@@ -489,7 +489,12 @@ def run_molecule(self, meta_molecule):
 
         # take care to remove nodes if there are any scheduled for removal
         # we do this here becuase that's more efficent
-        molecule.remove_nodes_from(self.nodes_to_remove)
+        if self.nodes_to_remove:
+            molecule.remove_nodes_from(self.nodes_to_remove)
+            # make sure the residue graph is updated; this takes care that
+            # nodes are also removed from the fragment graphs in the
+            # meta_molecule.nodes['graph'] attribute
+            meta_molecule.relabel_and_redo_res_graph(mapping={})
         # now we add all interactions but not the ones that contain the removed
         # nodes
         for inter_type in self.applied_links:

polyply/src/gen_coords.py

@@ -236,6 +236,23 @@ def gen_coords(toppath,
         LOGGER.info("loading grid",  type="step")
         grid = np.loadtxt(grid)
 
+    # where to get the box size from
+    if box is not None and topology.box is not None\
+        and not np.array_equal(topology.box, box):
+        msg = ("A box is provided via the -box command line "
+               "and the starting coordinates. We consider the "
+               "the box of starting coordinates as correct. ")
+        LOGGER.warning(msg,  type="warning")
+        box = topology.box
+    elif topology.box is not None:
+        box = topology.box
+        if density is not None:
+            msg = ("A density is provided via the command line, "
+                   "but the starting coordinates define a box."
+                   "Will try to pack all molecules in the box "
+                   "provided with starting coordinates.")
+            LOGGER.warning(msg,  type="warning")
+
     # do a sanity check
     LOGGER.info("checking residue integrity",  type="step")
     check_residue_equivalence(topology)