Merge pull request #547 from marrink-lab/issue522

Use MDTraj dssp
marrink-lab · Dec 6, 2023 · bae3e3b · bae3e3b
2 parents caa8f63 + a0bfe9a
commit bae3e3b
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diff --git a/README.md b/README.md
@@ -43,6 +43,9 @@ the following command:
 Note that vermouth and Martinize2, in particular development versions, may contain bugs that cause it to produce
 incorrect topologies. Check the produced output carefully!
 
+Martinize2 and vermouth have [mdtraj][mdtraj] as optional dependency as an 
+alternative to dssp.
+
 The behavior of the `pip` command can vary depending of the specificity of your
 python installation. See the [documentation on installing a python
 package][pipdoc] to learn more.
@@ -108,6 +111,7 @@ academic paper is left to our sole discretion.
 [Martini tutorials]: http://cgmartini.nl/index.php/tutorials-general-introduction-gmx5
 [Gromacs]: http://www.gromacs.org
 [pypi_vermouth]: https://pypi.org/project/vermouth/
+[mdtraj]: https://www.mdtraj.org/
 [pipdoc]: https://packaging.python.org/tutorials/installing-packages/#installing-packages
 [license]: https://github.com/marrink-lab/vermouth-martinize/blob/master/LICENSE
 [github]: https://github.com/marrink-lab/vermouth-martinize

diff --git a/bin/martinize2 b/bin/martinize2
@@ -226,7 +226,7 @@ def write_gmx_topology(system, top_path, defines=(), header=()):
             with deferred_open("{}.itp".format(moltype), "w") as outfile:
                 # here we format and merge all citations
                 header[-1] = header[-1] + "\n"
-                header.append("Pleas cite the following papers:")
+                header.append("Please cite the following papers:")
                 for citation in molecule.citations:
                     cite_string = citation_formatter(
                         molecule.force_field.citations[citation]
@@ -520,8 +520,10 @@ def entry():
     secstruct_exclusion.add_argument(
         "-dssp",
         nargs="?",
-        const="dssp",
-        help="DSSP executable for determining structure",
+        const=True,
+        help="DSSP executable for determining structure. If this flag is given"
+             "but no executable is specified, the mdtraj library will be used"
+             "to compute the secondary structure, if it can be imported.",
     )
     secstruct_exclusion.add_argument(
         "-ss",
@@ -890,8 +892,10 @@ def entry():
         LOGGER.debug("Read molecule {}.", molecule, type="step")
 
     target_ff = known_force_fields[args.to_ff]
-    if args.dssp is not None:
-        AnnotateDSSP(executable=args.dssp, savedir=".").run_system(system)
+    if args.dssp:
+        if not isinstance(args.dssp, str):
+            args.dssp = None
+        AnnotateDSSP(executable=args.dssp, savedir='.').run_system(system)
         AnnotateMartiniSecondaryStructures().run_system(system)
     elif args.ss is not None:
         AnnotateResidues(

diff --git a/requirements-tests.txt b/requirements-tests.txt
@@ -7,3 +7,4 @@ pylint
 hypothesis
 hypothesis-networkx
 codecov
+mdtraj
diff --git a/setup.cfg b/setup.cfg
@@ -37,6 +37,9 @@ install-requires =  # ?? requires-dist?
     scipy
 zip-safe = False
 
+[options.extras_require]
+mdtraj = mdtraj
+
 [build_sphinx]
 source-dir = doc/source
 build-dir = doc/build

diff --git a/vermouth/citation_parser.py b/vermouth/citation_parser.py
@@ -182,7 +182,7 @@ def citation_formatter(citation, title=False):
 
     <authors> [journal] <year>; [doi]
 
-    Note that the formatter cannot fromat latex
+    Note that the formatter cannot format latex
     like syntax (e.g. a{\"} for ae)
     """
     # first we split the author-list

diff --git a/vermouth/data/force_fields/elnedyn21/citations.bib b/vermouth/data/force_fields/elnedyn21/citations.bib
@@ -52,3 +52,13 @@ @article{M2polarizable
   year={2010},
   publisher={Public Library of Science}
 }
+@article{MDTraj,
+    title={MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories},
+    author={McGibbon, Robert T. and Beauchamp, Kyle A. and Harrigan, Matthew P. and Klein, Christoph and Swails, Jason M. and Hernández, Carlos X.  and Schwantes, Christian R. and Wang, Lee-Ping and Lane, Thomas J. and Pande, Vijay S.},
+    journal={Biophysical Journal},
+    volume={109},
+    number={8},
+    pages={1528 -- 1532},
+    year={2015},
+    doi={10.1016/j.bpj.2015.08.015}
+}
diff --git a/vermouth/data/force_fields/elnedyn22/citations.bib b/vermouth/data/force_fields/elnedyn22/citations.bib
@@ -52,3 +52,13 @@ @article{M2polarizable
   year={2010},
   publisher={Public Library of Science}
 }
+@article{MDTraj,
+    title={MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories},
+    author={McGibbon, Robert T. and Beauchamp, Kyle A. and Harrigan, Matthew P. and Klein, Christoph and Swails, Jason M. and Hernández, Carlos X.  and Schwantes, Christian R. and Wang, Lee-Ping and Lane, Thomas J. and Pande, Vijay S.},
+    journal={Biophysical Journal},
+    volume={109},
+    number={8},
+    pages={1528 -- 1532},
+    year={2015},
+    doi={10.1016/j.bpj.2015.08.015}
+}
diff --git a/vermouth/data/force_fields/elnedyn22p/citations.bib b/vermouth/data/force_fields/elnedyn22p/citations.bib
@@ -52,3 +52,13 @@ @article{M2polarizable
   year={2010},
   publisher={Public Library of Science}
 }
+@article{MDTraj,
+    title={MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories},
+    author={McGibbon, Robert T. and Beauchamp, Kyle A. and Harrigan, Matthew P. and Klein, Christoph and Swails, Jason M. and Hernández, Carlos X.  and Schwantes, Christian R. and Wang, Lee-Ping and Lane, Thomas J. and Pande, Vijay S.},
+    journal={Biophysical Journal},
+    volume={109},
+    number={8},
+    pages={1528 -- 1532},
+    year={2015},
+    doi={10.1016/j.bpj.2015.08.015}
+}
diff --git a/vermouth/data/force_fields/martini22/citations.bib b/vermouth/data/force_fields/martini22/citations.bib
@@ -52,3 +52,13 @@ @article{M2polarizable
   year={2010},
   publisher={Public Library of Science}
 }
+@article{MDTraj,
+    title={MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories},
+    author={McGibbon, Robert T. and Beauchamp, Kyle A. and Harrigan, Matthew P. and Klein, Christoph and Swails, Jason M. and Hernández, Carlos X.  and Schwantes, Christian R. and Wang, Lee-Ping and Lane, Thomas J. and Pande, Vijay S.},
+    journal={Biophysical Journal},
+    volume={109},
+    number={8},
+    pages={1528 -- 1532},
+    year={2015},
+    doi={10.1016/j.bpj.2015.08.015}
+}
diff --git a/vermouth/data/force_fields/martini22p/citations.bib b/vermouth/data/force_fields/martini22p/citations.bib
@@ -52,3 +52,13 @@ @article{M2polarizable
   year={2010},
   publisher={Public Library of Science}
 }
+@article{MDTraj,
+    title={MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories},
+    author={McGibbon, Robert T. and Beauchamp, Kyle A. and Harrigan, Matthew P. and Klein, Christoph and Swails, Jason M. and Hernández, Carlos X.  and Schwantes, Christian R. and Wang, Lee-Ping and Lane, Thomas J. and Pande, Vijay S.},
+    journal={Biophysical Journal},
+    volume={109},
+    number={8},
+    pages={1528 -- 1532},
+    year={2015},
+    doi={10.1016/j.bpj.2015.08.015}
+}
diff --git a/vermouth/data/force_fields/martini3001/citations.bib b/vermouth/data/force_fields/martini3001/citations.bib
@@ -18,3 +18,13 @@ @article{Martini3smallmolecules
   year={2022},
   publisher={Wiley Online Library}
 }
+@article{MDTraj,
+    title={MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories},
+    author={McGibbon, Robert T. and Beauchamp, Kyle A. and Harrigan, Matthew P. and Klein, Christoph and Swails, Jason M. and Hernández, Carlos X.  and Schwantes, Christian R. and Wang, Lee-Ping and Lane, Thomas J. and Pande, Vijay S.},
+    journal={Biophysical Journal},
+    volume={109},
+    number={8},
+    pages={1528 -- 1532},
+    year={2015},
+    doi={10.1016/j.bpj.2015.08.015}
+}
diff --git a/vermouth/data/force_fields/martini30b32/citations.bib b/vermouth/data/force_fields/martini30b32/citations.bib
@@ -3,3 +3,13 @@ @misc{Martini3Beta
   author={Souza, Paulo C T and Marrink, Siewert Jan},
   year={2020}
 }
+@article{MDTraj,
+    title={MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories},
+    author={McGibbon, Robert T. and Beauchamp, Kyle A. and Harrigan, Matthew P. and Klein, Christoph and Swails, Jason M. and Hernández, Carlos X.  and Schwantes, Christian R. and Wang, Lee-Ping and Lane, Thomas J. and Pande, Vijay S.},
+    journal={Biophysical Journal},
+    volume={109},
+    number={8},
+    pages={1528 -- 1532},
+    year={2015},
+    doi={10.1016/j.bpj.2015.08.015}
+}
diff --git a/vermouth/data/force_fields/martini30dev/citations.bib b/vermouth/data/force_fields/martini30dev/citations.bib
@@ -3,3 +3,13 @@ @misc{Martini3Beta
   author={Souza, Paulo C T and Marrink, Siewert Jan},
   year={2020}
 }
+@article{MDTraj,
+    title={MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories},
+    author={McGibbon, Robert T. and Beauchamp, Kyle A. and Harrigan, Matthew P. and Klein, Christoph and Swails, Jason M. and Hernández, Carlos X.  and Schwantes, Christian R. and Wang, Lee-Ping and Lane, Thomas J. and Pande, Vijay S.},
+    journal={Biophysical Journal},
+    volume={109},
+    number={8},
+    pages={1528 -- 1532},
+    year={2015},
+    doi={10.1016/j.bpj.2015.08.015}
+}