Merge pull request #189 from fjclark/feature_rna_backbone

Add support for detecting nucleic acid backbone atoms for restraints.
OpenBioSim · Oct 24, 2023 · cb92227 · cb92227
2 parents 0095314 + 0ae9a3d
commit cb92227
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diff --git a/doc/source/changelog.rst b/doc/source/changelog.rst
@@ -39,6 +39,7 @@ within the biomolecular simulation community. Our software is hosted via the `Op
 `2023.3.0 <https://github.com/openbiosim/biosimspace/compare/2023.2.2...2023.3.0>`_ - Jun 30 2023
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+* Added support for restraining "backbone" atoms in nucleic acids (PR HERE).
 * Reinstate :data:`BioSimSpace.Stream <BioSimSpace.Stream>` sub-package (`#36 <https://github.com/OpenBioSim/biosimspace/pull/36>`__).
 * Fixed ``setup.py`` file to work correctly on Windows (`#72 <https://github.com/OpenBioSim/biosimspace/pull/72>`__).
 * Fixed bug with missing working directory when using ``rmsd_flex_align`` scoring function (`#75 <https://github.com/OpenBioSim/biosimspace/pull/75>`__).

diff --git a/python/BioSimSpace/Sandpit/Exscientia/Protocol/_config.py b/python/BioSimSpace/Sandpit/Exscientia/Protocol/_config.py
@@ -276,7 +276,19 @@ def generateAmberConfig(self, extra_options=None, extra_lines=None):
                         # "heavy" restraints using a non-interoperable name mask.
                         if type(restraint) is str:
                             if restraint == "backbone":
-                                restraint_mask = "@CA,C,O,N"
+                                # Determine wether the system contains protein, nucleic acid, or both.
+                                restraint_atom_names = []
+                                if self.system.nAminoAcids() > 0:
+                                    restraint_atom_names += ["N", "CA", "C", "O"]
+                                if self.system.nNucleotides() > 0:
+                                    restraint_atom_names += [
+                                        "P",
+                                        "C5'",
+                                        "C3'",
+                                        "O3'",
+                                        "O5'",
+                                    ]
+                                restraint_mask = "@" + ",".join(restraint_atom_names)
                             elif restraint == "heavy":
                                 restraint_mask = "!:WAT & !@H"
                             elif restraint == "all":