Update to work with latest python-modelcif

We now need to provide the UniProt sequence
of the target and give an explicit alignment
between it and the model. This should quiet
the warnings from the latest python-modelcif
and populate the struct_ref table in the
mmCIF output.

README.md

@@ -13,5 +13,5 @@ This should preserve all information in the PDB file.
 This utility requires a local mirror of PDB in compressed mmCIF format.
 Use the `-r` command line option to point to the location of this mirror.
 It also needs the [python-modelcif](https://github.com/ihmwg/python-modelcif)
-library, to read the mmCIF files for any template structures and to write
-the final mmCIF or BinaryCIF ModBase file.
+library, version 1.1 or later, to read the mmCIF files for any template
+structures and to write the final mmCIF or BinaryCIF ModBase file.

modbase_pdb_to_cif.py

@@ -299,7 +299,8 @@ def get_system(self, align):
             target_e.description = "Target and template"
         else:
             target_e = modelcif.Entity(tgt_primary, description="Target")
-        target_e.references.extend(self.get_target_refs(tgtbeg, tgtend))
+        target_e.references.extend(self.get_target_refs(tgt_primary,
+                                                        tgtbeg, tgtend))
         chain_id = self.chain_id.strip() or 'A'
         asym = modelcif.AsymUnit(target_e, details='Model subunit',
                                  id=chain_id, auth_seq_id_map=tgtbeg-1)
@@ -352,16 +353,22 @@ class OurAlignment(modelcif.alignment.Global,
 
         return s
 
-    def get_target_refs(self, tgtbeg, tgtend):
+    def get_target_refs(self, tgtprimary, tgtbeg, tgtend):
         refmap = {'UniProt': modelcif.reference.UniProt,
                   'RefSeq': RefSeq,
                   'PlasmoDB': PlasmoDB}
         for db in self.seqdb:
             cls = refmap.get(db.name)
             if cls:
-                yield cls(code=db.code, accession=db.accession,
-                          align_begin=tgtbeg, align_end=tgtend,
-                          isoform=ihm.unknown)
+                # We only know the modeled sequence, not the full database
+                # sequence, so pad it with gaps as necessary
+                r = cls(code=db.code, accession=db.accession,
+                        isoform=ihm.unknown,
+                        sequence="-" * (tgtbeg - 1) + "".join(tgtprimary))
+                aln = modelcif.reference.Alignment(db_begin=tgtbeg,
+                                                   db_end=tgtend)
+                r.alignments.append(aln)
+                yield r
 
     def get_model_class(self, asym, atoms):
         class MyModel(modelcif.model.HomologyModel):

test/input/output.cif

@@ -4,9 +4,9 @@ _struct.entry_id model_66b8fbc891f519c1ba8d8ad2e62c6caa
 _struct.pdbx_model_details .
 _struct.pdbx_structure_determination_methodology computational
 _struct.title 'Model of S54091 hypothetical protein YPR070w - yeast (Saccha'
-_audit_conform.dict_location https://raw.githubusercontent.com/ihmwg/ModelCIF/ba728c4/base/mmcif_ma-core.dic
+_audit_conform.dict_location https://raw.githubusercontent.com/ihmwg/ModelCIF/d18ba38/base/mmcif_ma-core.dic
 _audit_conform.dict_name mmcif_ma.dic
-_audit_conform.dict_version 1.4.5
+_audit_conform.dict_version 1.4.6
 _database_2.database_code 66b8fbc891f519c1ba8d8ad2e62c6caa
 _database_2.database_id MODBASE
 #
@@ -126,6 +126,48 @@ _entity.details
 #
 #
 loop_
+_struct_ref.id
+_struct_ref.entity_id
+_struct_ref.db_name
+_struct_ref.db_code
+_struct_ref.pdbx_db_accession
+_struct_ref.pdbx_align_begin
+_struct_ref.pdbx_seq_one_letter_code
+_struct_ref.details
+1 1 UNP B5VTL7_YEAS6 B5VTL7 9
+;ETLDSMIELFKDYKPGSITLENITRLCQTLGLESFTEELSNELSRLSTASKIIVIDVDYNKKQDRIQDVK
+LVLASNFDNFDYFNQRDGEHEKSNILLNSLTKYPDLKAFHNNLKFLYLLDAYSHIESDSTSHNNGSSDKS
+LDSSNASFNNQGKLDLFKYFTELSHYIRQCFQDNCCDFKVRTNLNDKFGIYILTQGINGKEVPLAKIYLE
+ENKSDSQYRFYEYIYSQETKSWINESAENFSNGISLVMEIVANAKESNYTDLIWFPEDFISPELIIDKVT
+CSSNSSSSPPIIDLFSNNNYNSRIQLMNDFTTKLINIKKFDISNDNLDLISEILKWVQWSRIVLQNVFKL
+VSTPSSNSNSSELEPDYQAPFSTSTKDKNSSTSNTEPIPRSNRHGSVVEASRRRRSSTNKSKRPSITEAM
+MLKEEGLQQFNLHEILSEPAIEEE
+;
+.
+2 1 Other NP_015395.1 NP_015395 9
+;ETLDSMIELFKDYKPGSITLENITRLCQTLGLESFTEELSNELSRLSTASKIIVIDVDYNKKQDRIQDVK
+LVLASNFDNFDYFNQRDGEHEKSNILLNSLTKYPDLKAFHNNLKFLYLLDAYSHIESDSTSHNNGSSDKS
+LDSSNASFNNQGKLDLFKYFTELSHYIRQCFQDNCCDFKVRTNLNDKFGIYILTQGINGKEVPLAKIYLE
+ENKSDSQYRFYEYIYSQETKSWINESAENFSNGISLVMEIVANAKESNYTDLIWFPEDFISPELIIDKVT
+CSSNSSSSPPIIDLFSNNNYNSRIQLMNDFTTKLINIKKFDISNDNLDLISEILKWVQWSRIVLQNVFKL
+VSTPSSNSNSSELEPDYQAPFSTSTKDKNSSTSNTEPIPRSNRHGSVVEASRRRRSSTNKSKRPSITEAM
+MLKEEGLQQFNLHEILSEPAIEEE
+;
+.
+#
+#
+loop_
+_struct_ref_seq.align_id
+_struct_ref_seq.ref_id
+_struct_ref_seq.seq_align_beg
+_struct_ref_seq.seq_align_end
+_struct_ref_seq.db_align_beg
+_struct_ref_seq.db_align_end
+1 1 1 444 9 452
+2 2 1 444 9 452
+#
+#
+loop_
 _ma_target_ref_db_details.target_entity_id
 _ma_target_ref_db_details.db_name
 _ma_target_ref_db_details.db_name_other_details

test/input/output_with_align.cif

@@ -4,9 +4,9 @@ _struct.entry_id model_66b8fbc891f519c1ba8d8ad2e62c6caa
 _struct.pdbx_model_details .
 _struct.pdbx_structure_determination_methodology computational
 _struct.title 'Model of S54091 hypothetical protein YPR070w - yeast (Saccha'
-_audit_conform.dict_location https://raw.githubusercontent.com/ihmwg/ModelCIF/ba728c4/base/mmcif_ma-core.dic
+_audit_conform.dict_location https://raw.githubusercontent.com/ihmwg/ModelCIF/d18ba38/base/mmcif_ma-core.dic
 _audit_conform.dict_name mmcif_ma.dic
-_audit_conform.dict_version 1.4.5
+_audit_conform.dict_version 1.4.6
 _database_2.database_code 66b8fbc891f519c1ba8d8ad2e62c6caa
 _database_2.database_id MODBASE
 #
@@ -129,6 +129,48 @@ _entity.details
 #
 #
 loop_
+_struct_ref.id
+_struct_ref.entity_id
+_struct_ref.db_name
+_struct_ref.db_code
+_struct_ref.pdbx_db_accession
+_struct_ref.pdbx_align_begin
+_struct_ref.pdbx_seq_one_letter_code
+_struct_ref.details
+1 1 UNP B5VTL7_YEAS6 B5VTL7 9
+;ETLDSMIELFKDYKPGSITLENITRLCQTLGLESFTEELSNELSRLSTASKIIVIDVDYNKKQDRIQDVK
+LVLASNFDNFDYFNQRDGEHEKSNILLNSLTKYPDLKAFHNNLKFLYLLDAYSHIESDSTSHNNGSSDKS
+LDSSNASFNNQGKLDLFKYFTELSHYIRQCFQDNCCDFKVRTNLNDKFGIYILTQGINGKEVPLAKIYLE
+ENKSDSQYRFYEYIYSQETKSWINESAENFSNGISLVMEIVANAKESNYTDLIWFPEDFISPELIIDKVT
+CSSNSSSSPPIIDLFSNNNYNSRIQLMNDFTTKLINIKKFDISNDNLDLISEILKWVQWSRIVLQNVFKL
+VSTPSSNSNSSELEPDYQAPFSTSTKDKNSSTSNTEPIPRSNRHGSVVEASRRRRSSTNKSKRPSITEAM
+MLKEEGLQQFNLHEILSEPAIEEE
+;
+.
+2 1 Other NP_015395.1 NP_015395 9
+;ETLDSMIELFKDYKPGSITLENITRLCQTLGLESFTEELSNELSRLSTASKIIVIDVDYNKKQDRIQDVK
+LVLASNFDNFDYFNQRDGEHEKSNILLNSLTKYPDLKAFHNNLKFLYLLDAYSHIESDSTSHNNGSSDKS
+LDSSNASFNNQGKLDLFKYFTELSHYIRQCFQDNCCDFKVRTNLNDKFGIYILTQGINGKEVPLAKIYLE
+ENKSDSQYRFYEYIYSQETKSWINESAENFSNGISLVMEIVANAKESNYTDLIWFPEDFISPELIIDKVT
+CSSNSSSSPPIIDLFSNNNYNSRIQLMNDFTTKLINIKKFDISNDNLDLISEILKWVQWSRIVLQNVFKL
+VSTPSSNSNSSELEPDYQAPFSTSTKDKNSSTSNTEPIPRSNRHGSVVEASRRRRSSTNKSKRPSITEAM
+MLKEEGLQQFNLHEILSEPAIEEE
+;
+.
+#
+#
+loop_
+_struct_ref_seq.align_id
+_struct_ref_seq.ref_id
+_struct_ref_seq.seq_align_beg
+_struct_ref_seq.seq_align_end
+_struct_ref_seq.db_align_beg
+_struct_ref_seq.db_align_end
+1 1 1 444 9 452
+2 2 1 444 9 452
+#
+#
+loop_
 _ma_target_ref_db_details.target_entity_id
 _ma_target_ref_db_details.db_name
 _ma_target_ref_db_details.db_name_other_details

test/input/test_multi_expdta.cif

@@ -4,9 +4,9 @@ _struct.entry_id model_66b8fbc891f519c1ba8d8ad2e62c6caa
 _struct.pdbx_model_details .
 _struct.pdbx_structure_determination_methodology computational
 _struct.title 'Model of S54091 hypothetical protein YPR070w - yeast (Saccharomyces cerevisiae)'
-_audit_conform.dict_location https://raw.githubusercontent.com/ihmwg/ModelCIF/ba728c4/base/mmcif_ma-core.dic
+_audit_conform.dict_location https://raw.githubusercontent.com/ihmwg/ModelCIF/d18ba38/base/mmcif_ma-core.dic
 _audit_conform.dict_name mmcif_ma.dic
-_audit_conform.dict_version 1.4.5
+_audit_conform.dict_version 1.4.6
 _database_2.database_code 66b8fbc891f519c1ba8d8ad2e62c6caa
 _database_2.database_id MODBASE
 #
@@ -108,6 +108,30 @@ _entity.details
 #
 #
 loop_
+_struct_ref.id
+_struct_ref.entity_id
+_struct_ref.db_name
+_struct_ref.db_code
+_struct_ref.pdbx_db_accession
+_struct_ref.pdbx_align_begin
+_struct_ref.pdbx_seq_one_letter_code
+_struct_ref.details
+1 1 UNP B5VTL7_YEAS6 B5VTL7 9 ET .
+2 1 Other NP_015395.1 NP_015395 9 ET .
+#
+#
+loop_
+_struct_ref_seq.align_id
+_struct_ref_seq.ref_id
+_struct_ref_seq.seq_align_beg
+_struct_ref_seq.seq_align_end
+_struct_ref_seq.db_align_beg
+_struct_ref_seq.db_align_end
+1 1 1 2 9 10
+2 2 1 2 9 10
+#
+#
+loop_
 _ma_target_ref_db_details.target_entity_id
 _ma_target_ref_db_details.db_name
 _ma_target_ref_db_details.db_name_other_details

test/input/test_no_chain.cif

@@ -4,9 +4,9 @@ _struct.entry_id model_66b8fbc891f519c1ba8d8ad2e62c6caa
 _struct.pdbx_model_details .
 _struct.pdbx_structure_determination_methodology computational
 _struct.title 'Model of S54091 hypothetical protein YPR070w - yeast (Saccha'
-_audit_conform.dict_location https://raw.githubusercontent.com/ihmwg/ModelCIF/ba728c4/base/mmcif_ma-core.dic
+_audit_conform.dict_location https://raw.githubusercontent.com/ihmwg/ModelCIF/d18ba38/base/mmcif_ma-core.dic
 _audit_conform.dict_name mmcif_ma.dic
-_audit_conform.dict_version 1.4.5
+_audit_conform.dict_version 1.4.6
 _database_2.database_code 66b8fbc891f519c1ba8d8ad2e62c6caa
 _database_2.database_id MODBASE
 #
@@ -108,6 +108,30 @@ _entity.details
 #
 #
 loop_
+_struct_ref.id
+_struct_ref.entity_id
+_struct_ref.db_name
+_struct_ref.db_code
+_struct_ref.pdbx_db_accession
+_struct_ref.pdbx_align_begin
+_struct_ref.pdbx_seq_one_letter_code
+_struct_ref.details
+1 1 UNP B5VTL7_YEAS6 B5VTL7 9 ET .
+2 1 Other NP_015395.1 NP_015395 9 ET .
+#
+#
+loop_
+_struct_ref_seq.align_id
+_struct_ref_seq.ref_id
+_struct_ref_seq.seq_align_beg
+_struct_ref_seq.seq_align_end
+_struct_ref_seq.db_align_beg
+_struct_ref_seq.db_align_end
+1 1 1 2 9 10
+2 2 1 2 9 10
+#
+#
+loop_
 _ma_target_ref_db_details.target_entity_id
 _ma_target_ref_db_details.db_name
 _ma_target_ref_db_details.db_name_other_details

test/input/test_old_model.cif

@@ -4,9 +4,9 @@ _struct.entry_id model_9abae378d2aa2c1a5b21c65c98564dc0
 _struct.pdbx_model_details .
 _struct.pdbx_structure_determination_methodology computational
 _struct.title 'Model of'
-_audit_conform.dict_location https://raw.githubusercontent.com/ihmwg/ModelCIF/ba728c4/base/mmcif_ma-core.dic
+_audit_conform.dict_location https://raw.githubusercontent.com/ihmwg/ModelCIF/d18ba38/base/mmcif_ma-core.dic
 _audit_conform.dict_name mmcif_ma.dic
-_audit_conform.dict_version 1.4.5
+_audit_conform.dict_version 1.4.6
 _database_2.database_code 9abae378d2aa2c1a5b21c65c98564dc0
 _database_2.database_id MODBASE
 #