Handle UNK/X in template sequence

If the template sequence contains any X residues (ModBase never generates models containing X) assume these map to UNK and populate the relevant tables. Closes #5.
salilab · Dec 2, 2021 · f2f8907 · f2f8907
1 parent 38e58bf
commit f2f8907
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Showing 3 changed files with 32 additions and 16 deletions.
diff --git a/modbase_pdb_to_cif.py b/modbase_pdb_to_cif.py
@@ -12,7 +12,8 @@
 
 # Single sequence in a Modeller alignment
 Sequence = collections.namedtuple(
-    "Sequence", ["seqtyp", "chain", "method", "gapped", "primary"])
+    "Sequence", ["seqtyp", "chain", "method", "gapped", "primary",
+                 "primary_can", "primary_print"])
 
 
 # Reference sequence database
@@ -30,6 +31,7 @@
 }
 
 one_to_three = {val: key for key, val in three_to_one.items()}
+one_to_three['UNK'] = 'UNK'
 
 
 def split_resnum(resnum):
@@ -71,9 +73,20 @@ def _read_seq(self, fh):
             if seqlines[-1].endswith('*'):
                 break
         gapped = "".join(seqlines)[:-1]
+        # "Canonical" primary sequence is always a sequence of one-letter
+        # codes; regular primary sequence is 1-letter for standard amino
+        # acids, but can be longer for any non-standard residues (currently
+        # only UNK is handled here, assuming X always means UNK in the
+        # template).
+        primary_can = gapped.replace('-', '')
+        primary = ['UNK' if x == 'X' else x for x in primary_can]
+        # Primary sequence suitable for printing, e.g. "ACG(UNK)"
+        primary_print = "".join('(%s)' % x if len(x) > 1 else x
+                                for x in primary)
         return Sequence(
             seqtyp=header[0], chain=header[3], method=header[7],
-            gapped=gapped, primary=gapped.replace('-', ''))
+            gapped=gapped, primary=primary, primary_can=primary_can,
+            primary_print=primary_print)
 
 
 class CifWriter:
@@ -201,16 +214,17 @@ def write_entity_details(self, sequence3):
                  "pdbx_seq_one_letter_code",
                  "pdbx_seq_one_letter_code_can"]) as lp:
             if self.align:
-                if self.align.target.primary != target_primary:
+                if self.align.target.primary_can != target_primary:
                     raise ValueError(
                         "Model sequence does not match target "
-                        "sequence in alignment:",
-                        target_primary, self.align.target.primary)
-                p = self.align.template.primary
+                        "canonical sequence in alignment:",
+                        target_primary, self.align.target.primary_can)
+                p = self.align.template.primary_print
+                p_can = self.align.template.primary_can
                 lp.write(entity_id=self.template.entity_id,
                          type="polypeptide(L)", nstd_linkage="no",
                          pdbx_seq_one_letter_code=p,
-                         pdbx_seq_one_letter_code_can=p)
+                         pdbx_seq_one_letter_code_can=p_can)
             lp.write(entity_id=self.target.entity_id,
                      type="polypeptide(L)", nstd_linkage="no",
                      pdbx_seq_one_letter_code=target_primary,
@@ -269,9 +283,10 @@ def write_template_details(self, chain_id, tmpbeg, tmpend, tmpasym,
                 "_ma_template_poly",
                 ["template_id", "seq_one_letter_code",
                  "seq_one_letter_code_can"]) as lp:
-            p = self.align.template.primary
+            p = self.align.template.primary_print
+            p_can = self.align.template.primary_can
             lp.write(template_id=1, seq_one_letter_code=p,
-                     seq_one_letter_code_can=p)
+                     seq_one_letter_code_can=p_can)
 
         if self.align:
             # template_id makes no sense if we have no alignment

diff --git a/test/input/align.ali b/test/input/align.ali
@@ -9,7 +9,7 @@ STSTKDKNSSTSNTEPIPRSNRHGSVVEASRRRRSSTNKSKRPSITEAMMLKEEGLQQFNLHEILSEPAIEEE*
 
 >P1;3icqT
 structureX:3icq:401:T:835:T:3icqT:Seq-Prf (0001):-1.00:-1.00
-PDSEEEAEFQEMRKKLKIFQDTINSIDSSLFSSYMYSAITSSLSTAATLSPENSWQLIEFALYETYIFGEGLRGP
+PDSEEEAEFQEMRKKLKIFQDTINSIDSSLFSSYMYSAITSSLSTAATLSPENSWQLIEFALYETYIFXEGLRGP
 D----AFFNEVDKSPTVLSQILALVTTSQVCRHPHPLVQLLYMEILVRYASFFDYESAAIPALIEYFVGPRGIHN
 TNERVRPRAWY--LFYRFVKSIKKVNYTE-SSLAMLGDLLNISVSPVTDMDAPVPTLNSSIRNSDFNSQLYLFET
 VGVLISSGNLTPEEQALYCDSLINALIGKANAALSSDLSAL------ENIISVYCSLMAIGNFAKGFPAREEVAW

diff --git a/test/input/output_with_align.cif b/test/input/output_with_align.cif
@@ -83,6 +83,7 @@ SER 'L-peptide linking' SERINE 'C3 H7 N O3' 105.093
 THR 'L-peptide linking' THREONINE 'C4 H9 N O3' 119.120
 TRP 'L-peptide linking' TRYPTOPHAN 'C11 H12 N2 O2' 204.229
 TYR 'L-peptide linking' TYROSINE 'C9 H11 N O3' 181.191
+UNK 'L-peptide linking' UNKNOWN 'C4 H9 N O2' 103.121
 VAL 'L-peptide linking' VALINE 'C5 H11 N O2' 117.148
 #
 #
@@ -102,8 +103,8 @@ _entity_poly.nstd_linkage
 _entity_poly.pdbx_seq_one_letter_code
 _entity_poly.pdbx_seq_one_letter_code_can
 1 polypeptide(L) no
-PDSEEEAEFQEMRKKLKIFQDTINSIDSSLFSSYMYSAITSSLSTAATLSPENSWQLIEFALYETYIFGEGLRGPDAFFNEVDKSPTVLSQILALVTTSQVCRHPHPLVQLLYMEILVRYASFFDYESAAIPALIEYFVGPRGIHNTNERVRPRAWYLFYRFVKSIKKVNYTESSLAMLGDLLNISVSPVTDMDAPVPTLNSSIRNSDFNSQLYLFETVGVLISSGNLTPEEQALYCDSLINALIGKANAALSSDLSALENIISVYCSLMAIGNFAKGFPAREEVAWLASFNKASDEIFLILDRMGFNEDIRGAVRFTSGRIINVVGPDMLPKVPQLISILLNSIDMNELVDVLSFISQLIHIYKDNMMEITNRMLPTLLMRIFSSLSAAPQGTDDAVKQNDLRKSYISFILQLLNKGFGSILFTEENQVY
-PDSEEEAEFQEMRKKLKIFQDTINSIDSSLFSSYMYSAITSSLSTAATLSPENSWQLIEFALYETYIFGEGLRGPDAFFNEVDKSPTVLSQILALVTTSQVCRHPHPLVQLLYMEILVRYASFFDYESAAIPALIEYFVGPRGIHNTNERVRPRAWYLFYRFVKSIKKVNYTESSLAMLGDLLNISVSPVTDMDAPVPTLNSSIRNSDFNSQLYLFETVGVLISSGNLTPEEQALYCDSLINALIGKANAALSSDLSALENIISVYCSLMAIGNFAKGFPAREEVAWLASFNKASDEIFLILDRMGFNEDIRGAVRFTSGRIINVVGPDMLPKVPQLISILLNSIDMNELVDVLSFISQLIHIYKDNMMEITNRMLPTLLMRIFSSLSAAPQGTDDAVKQNDLRKSYISFILQLLNKGFGSILFTEENQVY
+PDSEEEAEFQEMRKKLKIFQDTINSIDSSLFSSYMYSAITSSLSTAATLSPENSWQLIEFALYETYIF(UNK)EGLRGPDAFFNEVDKSPTVLSQILALVTTSQVCRHPHPLVQLLYMEILVRYASFFDYESAAIPALIEYFVGPRGIHNTNERVRPRAWYLFYRFVKSIKKVNYTESSLAMLGDLLNISVSPVTDMDAPVPTLNSSIRNSDFNSQLYLFETVGVLISSGNLTPEEQALYCDSLINALIGKANAALSSDLSALENIISVYCSLMAIGNFAKGFPAREEVAWLASFNKASDEIFLILDRMGFNEDIRGAVRFTSGRIINVVGPDMLPKVPQLISILLNSIDMNELVDVLSFISQLIHIYKDNMMEITNRMLPTLLMRIFSSLSAAPQGTDDAVKQNDLRKSYISFILQLLNKGFGSILFTEENQVY
+PDSEEEAEFQEMRKKLKIFQDTINSIDSSLFSSYMYSAITSSLSTAATLSPENSWQLIEFALYETYIFXEGLRGPDAFFNEVDKSPTVLSQILALVTTSQVCRHPHPLVQLLYMEILVRYASFFDYESAAIPALIEYFVGPRGIHNTNERVRPRAWYLFYRFVKSIKKVNYTESSLAMLGDLLNISVSPVTDMDAPVPTLNSSIRNSDFNSQLYLFETVGVLISSGNLTPEEQALYCDSLINALIGKANAALSSDLSALENIISVYCSLMAIGNFAKGFPAREEVAWLASFNKASDEIFLILDRMGFNEDIRGAVRFTSGRIINVVGPDMLPKVPQLISILLNSIDMNELVDVLSFISQLIHIYKDNMMEITNRMLPTLLMRIFSSLSAAPQGTDDAVKQNDLRKSYISFILQLLNKGFGSILFTEENQVY
 2 polypeptide(L) no
 ETLDSMIELFKDYKPGSITLENITRLCQTLGLESFTEELSNELSRLSTASKIIVIDVDYNKKQDRIQDVKLVLASNFDNFDYFNQRDGEHEKSNILLNSLTKYPDLKAFHNNLKFLYLLDAYSHIESDSTSHNNGSSDKSLDSSNASFNNQGKLDLFKYFTELSHYIRQCFQDNCCDFKVRTNLNDKFGIYILTQGINGKEVPLAKIYLEENKSDSQYRFYEYIYSQETKSWINESAENFSNGISLVMEIVANAKESNYTDLIWFPEDFISPELIIDKVTCSSNSSSSPPIIDLFSNNNYNSRIQLMNDFTTKLINIKKFDISNDNLDLISEILKWVQWSRIVLQNVFKLVSTPSSNSNSSELEPDYQAPFSTSTKDKNSSTSNTEPIPRSNRHGSVVEASRRRRSSTNKSKRPSITEAMMLKEEGLQQFNLHEILSEPAIEEE
 ETLDSMIELFKDYKPGSITLENITRLCQTLGLESFTEELSNELSRLSTASKIIVIDVDYNKKQDRIQDVKLVLASNFDNFDYFNQRDGEHEKSNILLNSLTKYPDLKAFHNNLKFLYLLDAYSHIESDSTSHNNGSSDKSLDSSNASFNNQGKLDLFKYFTELSHYIRQCFQDNCCDFKVRTNLNDKFGIYILTQGINGKEVPLAKIYLEENKSDSQYRFYEYIYSQETKSWINESAENFSNGISLVMEIVANAKESNYTDLIWFPEDFISPELIIDKVTCSSNSSSSPPIIDLFSNNNYNSRIQLMNDFTTKLINIKKFDISNDNLDLISEILKWVQWSRIVLQNVFKLVSTPSSNSNSSELEPDYQAPFSTSTKDKNSSTSNTEPIPRSNRHGSVVEASRRRRSSTNKSKRPSITEAMMLKEEGLQQFNLHEILSEPAIEEE
@@ -182,7 +183,7 @@ _entity_poly_seq.hetero
 1 66 TYR .
 1 67 ILE .
 1 68 PHE .
-1 69 GLY .
+1 69 UNK .
 1 70 GLU .
 1 71 GLY .
 1 72 LEU .
@@ -1027,8 +1028,8 @@ _ma_template_poly.template_id
 _ma_template_poly.seq_one_letter_code
 _ma_template_poly.seq_one_letter_code_can
 1
-PDSEEEAEFQEMRKKLKIFQDTINSIDSSLFSSYMYSAITSSLSTAATLSPENSWQLIEFALYETYIFGEGLRGPDAFFNEVDKSPTVLSQILALVTTSQVCRHPHPLVQLLYMEILVRYASFFDYESAAIPALIEYFVGPRGIHNTNERVRPRAWYLFYRFVKSIKKVNYTESSLAMLGDLLNISVSPVTDMDAPVPTLNSSIRNSDFNSQLYLFETVGVLISSGNLTPEEQALYCDSLINALIGKANAALSSDLSALENIISVYCSLMAIGNFAKGFPAREEVAWLASFNKASDEIFLILDRMGFNEDIRGAVRFTSGRIINVVGPDMLPKVPQLISILLNSIDMNELVDVLSFISQLIHIYKDNMMEITNRMLPTLLMRIFSSLSAAPQGTDDAVKQNDLRKSYISFILQLLNKGFGSILFTEENQVY
-PDSEEEAEFQEMRKKLKIFQDTINSIDSSLFSSYMYSAITSSLSTAATLSPENSWQLIEFALYETYIFGEGLRGPDAFFNEVDKSPTVLSQILALVTTSQVCRHPHPLVQLLYMEILVRYASFFDYESAAIPALIEYFVGPRGIHNTNERVRPRAWYLFYRFVKSIKKVNYTESSLAMLGDLLNISVSPVTDMDAPVPTLNSSIRNSDFNSQLYLFETVGVLISSGNLTPEEQALYCDSLINALIGKANAALSSDLSALENIISVYCSLMAIGNFAKGFPAREEVAWLASFNKASDEIFLILDRMGFNEDIRGAVRFTSGRIINVVGPDMLPKVPQLISILLNSIDMNELVDVLSFISQLIHIYKDNMMEITNRMLPTLLMRIFSSLSAAPQGTDDAVKQNDLRKSYISFILQLLNKGFGSILFTEENQVY
+PDSEEEAEFQEMRKKLKIFQDTINSIDSSLFSSYMYSAITSSLSTAATLSPENSWQLIEFALYETYIF(UNK)EGLRGPDAFFNEVDKSPTVLSQILALVTTSQVCRHPHPLVQLLYMEILVRYASFFDYESAAIPALIEYFVGPRGIHNTNERVRPRAWYLFYRFVKSIKKVNYTESSLAMLGDLLNISVSPVTDMDAPVPTLNSSIRNSDFNSQLYLFETVGVLISSGNLTPEEQALYCDSLINALIGKANAALSSDLSALENIISVYCSLMAIGNFAKGFPAREEVAWLASFNKASDEIFLILDRMGFNEDIRGAVRFTSGRIINVVGPDMLPKVPQLISILLNSIDMNELVDVLSFISQLIHIYKDNMMEITNRMLPTLLMRIFSSLSAAPQGTDDAVKQNDLRKSYISFILQLLNKGFGSILFTEENQVY
+PDSEEEAEFQEMRKKLKIFQDTINSIDSSLFSSYMYSAITSSLSTAATLSPENSWQLIEFALYETYIFXEGLRGPDAFFNEVDKSPTVLSQILALVTTSQVCRHPHPLVQLLYMEILVRYASFFDYESAAIPALIEYFVGPRGIHNTNERVRPRAWYLFYRFVKSIKKVNYTESSLAMLGDLLNISVSPVTDMDAPVPTLNSSIRNSDFNSQLYLFETVGVLISSGNLTPEEQALYCDSLINALIGKANAALSSDLSALENIISVYCSLMAIGNFAKGFPAREEVAWLASFNKASDEIFLILDRMGFNEDIRGAVRFTSGRIINVVGPDMLPKVPQLISILLNSIDMNELVDVLSFISQLIHIYKDNMMEITNRMLPTLLMRIFSSLSAAPQGTDDAVKQNDLRKSYISFILQLLNKGFGSILFTEENQVY
 #
 #
 loop_
@@ -1108,7 +1109,7 @@ _ma_alignment.alignment_id
 _ma_alignment.target_template_flag
 _ma_alignment.sequence
 1 1 2
-PDSEEEAEFQEMRKKLKIFQDTINSIDSSLFSSYMYSAITSSLSTAATLSPENSWQLIEFALYETYIFGEGLRGPD----AFFNEVDKSPTVLSQILALVTTSQVCRHPHPLVQLLYMEILVRYASFFDYESAAIPALIEYFVGPRGIHNTNERVRPRAWY--LFYRFVKSIKKVNYTE-SSLAMLGDLLNISVSPVTDMDAPVPTLNSSIRNSDFNSQLYLFETVGVLISSGNLTPEEQALYCDSLINALIGKANAALSSDLSAL------ENIISVYCSLMAIGNFAKGFPAREEVAWLASFNKASDEIFLILDRMGFN--EDIRGAVRFTSGRIIN--VVGPDMLPKVPQLISILLNSIDMNELVDVLSFISQLIHIYKDNMMEITNRMLPTLLMRIFSSLSAAPQGTDDAVKQNDLRKSYISFILQLLNKGFGSILFTEENQVY
+PDSEEEAEFQEMRKKLKIFQDTINSIDSSLFSSYMYSAITSSLSTAATLSPENSWQLIEFALYETYIFXEGLRGPD----AFFNEVDKSPTVLSQILALVTTSQVCRHPHPLVQLLYMEILVRYASFFDYESAAIPALIEYFVGPRGIHNTNERVRPRAWY--LFYRFVKSIKKVNYTE-SSLAMLGDLLNISVSPVTDMDAPVPTLNSSIRNSDFNSQLYLFETVGVLISSGNLTPEEQALYCDSLINALIGKANAALSSDLSAL------ENIISVYCSLMAIGNFAKGFPAREEVAWLASFNKASDEIFLILDRMGFN--EDIRGAVRFTSGRIIN--VVGPDMLPKVPQLISILLNSIDMNELVDVLSFISQLIHIYKDNMMEITNRMLPTLLMRIFSSLSAAPQGTDDAVKQNDLRKSYISFILQLLNKGFGSILFTEENQVY
 2 1 1
 ETLDSMIELFKDYKPGSITLENITRLCQTLGLESFTEELSNELSRLSTASKIIVIDVDYNKKQDRIQDVKLVLASNFDNFDYFNQRDGEHEKSNILLNSLTKYPDLKAFHNNLK--FLYLLDAYSHIESDSTSHNNGSSDKSLDSSNASFNNQGKLDLFKYFTELSHYIRQCFQDNCCDFKVRTNLNDKFGIYILTQGINGKEVPLAKIYLEENKSDSQYRFYEYIYS--QETKSWINESAENFSNGISLVMEIVANAKESNYTDLIWFPEDFISPELIIDKVTCSSNSSSSPPIIDLFSNNNYNSRIQLMNDFTTKLINIKKFDISNDNLDLISEILKWVQWSRIVLQNVFKLVSTPSSNSNSSELEPDYQAPFSTSTKDKNSSTSNTEPIPRSNRHGSVVEASRRRRSSTNKSKRPSITEAMMLKEEGLQQFNLHEILSEPAIEEE
 #