Allow reading starting models in BinaryCIF format

pyext/src/topology/__init__.py

@@ -13,8 +13,8 @@
    like Molecule.get_atomic_residues() and Molecule.get_non_atomic_residues().
    These functions all return Python sets for easy set arithmetic using
    & (and), | (or), - (difference)
- * Molecule.add_structure() to add structural information from an mmCIF
-   or PDB file.
+ * Molecule.add_structure() to add structural information from an mmCIF,
+   BinaryCIF, or PDB file.
  * Molecule.add_representation() to create a representation unit - here you
    can choose bead resolutions as well as alternate representations like
    densities or ideal helices.
@@ -556,7 +556,7 @@ def add_structure(self, pdb_fn, chain_id, res_range=[],
                       soft_check=False):
         """Read a structure and store the coordinates.
         @return the atomic residues (as a set)
-        @param pdb_fn     The file to read (in PDB or mmCIF format)
+        @param pdb_fn     The file to read (in PDB, mmCIF or BinaryCIF format)
         @param chain_id   Chain ID to read
         @param res_range  Add only a specific set of residues from the PDB
                           file. res_range[0] is the starting and res_range[1]
@@ -1378,11 +1378,12 @@ class TopologyReader:
       of "cop9" and UniProt accession of "Q13098". If such an accession is
       present, it is added to the generated structure (and ultimately
       recorded in any output RMF file).
-    - `pdb_fn`: Name of PDB or mmCIF file with coordinates (if available).
-       If left empty, will set up as BEADS (you can also specify "BEADS")
-       Can also write "IDEAL_HELIX".
-    - `chain`: Chain ID of this domain in the PDB or mmCIF file. This is
-      the "author-provided" chain ID for mmCIF files, not the asym_id.
+    - `pdb_fn`: Name of PDB, mmCIF, or BinaryCIF file with coordinates
+      (if available). If left empty, will set up as BEADS (you can also
+      specify "BEADS") Can also write "IDEAL_HELIX".
+    - `chain`: Chain ID of this domain in the PDB, mmCIF or BinaryCIF file.
+      This is the "author-provided" chain ID for mmCIF or BinaryCIF files,
+      not the asym_id.
     - `residue_range`: Comma delimited pair defining range.
        Can leave empty or use 'all' for entire sequence from PDB file.
        The second item in the pair can be END to select the last residue in the

pyext/src/topology/system_tools.py

@@ -54,7 +54,7 @@ def get_structure(model, pdb_fn, chain_id, res_range=None, offset=0,
                   model_num=None, ca_only=False):
     """read a structure from a PDB file and return a list of residues
     @param model The IMP model
-    @param pdb_fn    The file to read (in traditional PDB or mmCIF format)
+    @param pdb_fn  The file to read (in mmCIF, BinaryCIF, or legacy PDB format)
     @param chain_id  Chain ID to read
     @param res_range Add only a specific set of residues.
            res_range[0] is the starting and res_range[1] is the ending
@@ -66,10 +66,13 @@ def get_structure(model, pdb_fn, chain_id, res_range=None, offset=0,
     @param model_num Read multi-model PDB and return that model (0-based index)
     @param ca_only Read only CA atoms (by default, all non-waters are read)
     """
-    # Read file in mmCIF format if requested
+    # Read file in mmCIF or BinaryCIF format if requested
     if pdb_fn.endswith('.cif'):
         read_file = IMP.atom.read_mmcif
         read_multi_file = IMP.atom.read_multimodel_mmcif
+    elif pdb_fn.endswith('.bcif'):
+        read_file = IMP.atom.read_bcif
+        read_multi_file = IMP.atom.read_multimodel_bcif
     else:
         read_file = IMP.atom.read_pdb
         read_multi_file = IMP.atom.read_multimodel_pdb

test/input/topology_bcif.txt

@@ -0,0 +1,2 @@
+|molecule_name | color | fasta_fn | fasta_id | pdb_fn | chain | residue_range | pdb_offset | bead_size | em_residues_per_gaussian | rigid_body | super_rigid_body | chain_of_super_rigid_bodies | 
+|Prot1   |blue  |seqs.fasta|Protein_1|prot.bcif   |A|55,65  |-54 |5|10|1|1,2| |

test/test_topology_input.py

@@ -363,8 +363,20 @@ def test_build_system_mmcif(self):
             import sklearn
         except ImportError:
             self.skipTest("no sklearn package")
-        mdl = IMP.Model()
         tfile = self.get_input_file_name('topology_mmcif.txt')
+        self._internal_test_build_system(tfile)
+
+    def test_build_system_binary_cif(self):
+        """Test BuildSystem macro with BinaryCIF input files"""
+        try:
+            import sklearn
+        except ImportError:
+            self.skipTest("no sklearn package")
+        tfile = self.get_input_file_name('topology_bcif.txt')
+        self._internal_test_build_system(tfile)
+
+    def _internal_test_build_system(self, tfile):
+        mdl = IMP.Model()
         input_dir = os.path.dirname(tfile)
         t = IMP.pmi.topology.TopologyReader(tfile,
                                             pdb_dir=input_dir,
@@ -381,6 +393,5 @@ def test_build_system_mmcif(self):
         self.assertEqual(len(sel1), 7  + 2 )
 
 
-
 if __name__=="__main__":
     IMP.test.main()