Hydra-Powered YAML Configuration and Enhanced File Support in HelixFold3

apps/protein_folding/helixfold3/data/7s69_glycan.sdf

@@ -0,0 +1,155 @@
+
+ OpenBabel03042416223D
+
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+M  END
+$$$$

apps/protein_folding/helixfold3/data/demo_3fap_protein_sm.json

@@ -0,0 +1,20 @@
+{
+    "entities": [
+        {
+            "type": "protein",
+            "sequence": "GVQVETISPGDGRTFPKRGQTCVVHYTGMLEDGKKFDSSRDRNKPFKFMLGKQEVIRGWEEGVAQMSVGQRAKLTISPDYAYGATGHPGIIPPHATLVFDVELLKLE",
+            "count": 1
+        },
+        {
+            "type": "protein",
+            "sequence": "VAILWHEMWHEGLEEASRLYFGERNVKGMFEVLEPLHAMMERGPQTLKETSFNQAYGRDLMEAQEWCRKYMKSGNVKDLTQAWDLYYHVFRRIS",
+            "count": 1
+        },
+        {
+            "type": "ligand",
+            "sdf": "/mnt/data/yinying/tests/helixfold/ligands/ARD_ideal.sdf",
+            "use_3d": false,
+            "count": 1
+        }
+    ]
+}

apps/protein_folding/helixfold3/data/demo_4Fe-4S.json

@@ -0,0 +1,45 @@
+{
+    "entities": [
+        {
+            "type": "protein",
+            "sequence": "MKLNVDGLLVYFPYDYIYPEQFSYMRELKRTLDAKGHGVLEMPSGTGKTVSLLALIMAYQRAYPLEVTKLIYCSRTVPEIEKVIEELRKLLNFYEKQEGEKLPFLGLALSSRKNLCIHPEVTPLRFGKDVDGKCHSLTASYVRAQYQHDTSLPHCRFYEEFDAHGREVPLPAGIYNLDDLKALGRRQGWCPYFLARYSILHANVVVYSYHYLLDPKIADLVSKELARKAVVVFDEAHNIDNVCIDSMSVNLTRRTLDRCQGNLETLQKTVLRIKETDEQRLRDEYRRLVEGLREASAARETDAHLANPVLPDEVLQEAVPGSIRTAEHFLGFLRRLLEYVKWRLRVQHVVQESPPAFLSGLAQRVCIQRKPLRFCAERLRSLLHTLEITDLADFSPLTLLANFATLVSTYAKGFTIIIEPFDDRTPTIANPILHFSCMDASLAIKPVFERFQSVIITSGTLSPLDIYPKILDFHPVTMATFTMTLARVCLCPMIIGRGNDQVAISSKFETREDIAVIRNYGNLLLEMSAVVPDGIVAFFTSYQYMESTVASWYEQGILENIQRNKLLFIETQDGAETSVALEKYQEACENGRGAILLSVARGKVSEGIDFVHHYGRAVIMFGVPYVYTQSRILKARLEYLRDQFQIRENDFLTFDAMRHAAQCVGRAIRGKTDYGLMVFADKRFARGDKRGKLPRWIQEHLTDANLNLTVDEGVQVAKYFLRQMAQPFHREDQLGLSLLSLEQLESEETLKRIEQIAQQL",
+            "count": 1
+        },
+        {
+            "type": "ligand",
+            "ccd": "SF4",
+            "count": 1,
+            "_note": "5T5I"
+        },
+        {
+            "type": "bond",
+            "bond": "A,CYS,116,SG,B,SF4,1,FE1,metalc,2.2;A,CYS,134,SG,B,SF4,1,FE2,metalc,2.2;A,CYS,155,SG,B,SF4,1,FE3,metalc,2.2;A,CYS,190,SG,B,SF4,1,FE4,metalc,2.2",
+            "_case_from": "https://www.uniprot.org/uniprotkb/P18074/entry",
+            "_note":"ALL_CYS-ALL_FE"
+        },
+        {
+            "type": "bond",
+            "bond": "B,SF4,1,FE1,B,SF4,1,S2,metalc,2.2;B,SF4,1,FE1,B,SF4,1,S3,metalc,2.2;B,SF4,1,FE1,B,SF4,1,S4,metalc,2.2",
+            "_case_from": "https://www.uniprot.org/uniprotkb/P18074/entry",
+            "_note":"FE1-S234"
+        },
+        {
+            "type": "bond",
+            "bond": "B,SF4,1,FE2,B,SF4,1,S1,metalc,2.2;B,SF4,1,FE2,B,SF4,1,S3,metalc,2.2;B,SF4,1,FE2,B,SF4,1,S4,metalc,2.2",
+            "_case_from": "https://www.uniprot.org/uniprotkb/P18074/entry",
+            "_note":"FE2-S134"
+        },
+        {
+            "type": "bond",
+            "bond": "B,SF4,1,FE3,B,SF4,1,S1,metalc,2.2;B,SF4,1,FE3,B,SF4,1,S2,metalc,2.2;B,SF4,1,FE3,B,SF4,1,S4,metalc,2.2",
+            "_case_from": "https://www.uniprot.org/uniprotkb/P18074/entry",
+            "_note":"FE3-S124"
+        },
+        {
+            "type": "bond",
+            "bond": "B,SF4,1,FE4,B,SF4,1,S1,metalc,2.2;B,SF4,1,FE14,B,SF4,1,S2,metalc,2.2;B,SF4,1,FE4,B,SF4,1,S3,metalc,2.2",
+            "_case_from": "https://www.uniprot.org/uniprotkb/P18074/entry",
+            "_note":"FE4-S123"
+        }
+    ]
+}

apps/protein_folding/helixfold3/data/demo_7s69_coval.json

@@ -0,0 +1,20 @@
+{
+    "entities": [
+        {
+            "type": "protein",
+            "sequence": "DRHHHHHHKLGKMKIVEEPNSFGLNNPFLSQTNKLQPRVQPSPVSGPSHLFRLAGKCFNLVESTYKYELCPFHNVTQHEQTFRWNAYSGILGIWQEWDIENNTFSGMWMREGDSCGNKNRQTKVLLVCGKANKLSSVSEPSTCLYSLTFETPLVCHPHSLLVYPTLSEGLQEKWNEAEQALYDELITEQGHGKILKEIFREAGYLKTTKPDGEGKETQDKPKEFDSLEKCNKGYTELTSEIQRLKKMLNEHGISYVTNGTSRSEGQPAEVNTTFARGEDKVHLRGDTGIRDGQ",
+            "count": 1
+        },
+        {
+            "type": "ligand",
+            "sdf": "/repo/PaddleHelix/apps/protein_folding/helixfold3/data/7s69_glycan.sdf",
+            "count": 1
+        },
+        {
+            "type": "bond",
+            "bond": "A,ASN,74,ND2,B,UNK-1,1,C16,covale,2.3",
+            "_comment": "'A,74,ND2:B,1:CW,null' from RF2AA.",
+            "_also_comment": "For ccd input, use CCD key as residue name; for smiles and file input, use `UNK-<index>` where index is the chain order you input"
+        }
+    ]
+}

apps/protein_folding/helixfold3/data/demo_7u7w_protein_nucleic.json

@@ -0,0 +1,19 @@
+{
+    "entities": [
+        {
+            "type": "protein",
+            "sequence": "GPHMATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGIIAVSYEARAFGVTRSMWADDAKKLCPDLLLAQVRESRGKANLTKYREASVEVMEIMSRFAVIERASIDEAYVDLTSAVQERLQKLQGQPISADLLPSTYIEGLPQGPTTAEETVQKEGMRKQGLFQWLDSLQIDNLTSPDLQLTVGAVIVEEMRAAIERETGFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMPIRKIRSLGGKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAMCRGIEHDPVKPRQLPKTIGCSKNFPGKTALATREQVQWWLLQLAQELEERLTKDRNDNDRVATQLVVSIRVQGDKRLSSLRRCCALTRYDAHKMSHDAFTVIKNCNTSGIQTEWSPPLTMLFLCATKFSAS",
+            "count": 1
+        },
+        {
+            "type": "dna",
+            "sequence": "CATTATGACGCT",
+            "count": 1
+        },
+        {
+            "type": "dna",
+            "sequence": "AGCGTCAT",
+            "count": 1
+        }
+    ]
+}

apps/protein_folding/helixfold3/data/demo_7u7w_protein_nucleic_sm.json

@@ -0,0 +1,24 @@
+{
+    "entities": [
+        {
+            "type": "protein",
+            "sequence": "GPHMATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGIIAVSYEARAFGVTRSMWADDAKKLCPDLLLAQVRESRGKANLTKYREASVEVMEIMSRFAVIERASIDEAYVDLTSAVQERLQKLQGQPISADLLPSTYIEGLPQGPTTAEETVQKEGMRKQGLFQWLDSLQIDNLTSPDLQLTVGAVIVEEMRAAIERETGFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMPIRKIRSLGGKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAMCRGIEHDPVKPRQLPKTIGCSKNFPGKTALATREQVQWWLLQLAQELEERLTKDRNDNDRVATQLVVSIRVQGDKRLSSLRRCCALTRYDAHKMSHDAFTVIKNCNTSGIQTEWSPPLTMLFLCATKFSAS",
+            "count": 1
+        },
+        {
+            "type": "dna",
+            "sequence": "CATTATGACGCT",
+            "count": 1
+        },
+        {
+            "type": "dna",
+            "sequence": "AGCGTCAT",
+            "count": 1
+        },
+        {
+            "type": "ligand",
+            "ccd": "XG4",
+            "count": 1
+        }
+    ]
+}

apps/protein_folding/helixfold3/data/demo_disulf.json

@@ -0,0 +1,14 @@
+{
+    "entities": [
+        {
+            "type": "protein",
+            "sequence": "MASVKSSSSSSSSSFISLLLLILLVIVLQSQVIECQPQQSCTASLTGLNVCAPFLVPGSPTASTECCNAVQSINHDCMCNTMRIAAQIPAQCNLPPLSCSAN",
+            "count": 1
+        },
+        {
+            "type": "bond",
+            "bond": "A,CYS,41,SG,A,CYS,77,SG,disulf,2.2;A,CYS,51,SG,A,CYS,66,SG,disulf,2.2;A,CYS,67,SG,A,CYS,92,SG,disulf,2.2;A,CYS,79,SG,A,CYS,99,SG,disulf,2.2",
+            "_case_from": "https://www.uniprot.org/uniprotkb/Q43495/entry#ptm_processing"
+        }
+    ]
+}

apps/protein_folding/helixfold3/data/demo_disulf_homodimer.json

@@ -0,0 +1,33 @@
+{
+    "entities": [
+        {
+            "type": "protein",
+            "sequence": "NSVHPCCDPVICEPREGEHCISGPCCENCYFLNSGTICKRARGDGNQDYCTGITPDCPRNRYNV",
+            "count": 2
+        },
+        {
+            "type": "bond",
+            "bond": "A,CYS,6,SG,A,CYS,29,SG,disulf,2.3;A,CYS,20,SG,A,CYS,26,SG,disulf,2.3;A,CYS,25,SG,A,CYS,50,SG,disulf,2.3;A,CYS,38,SG,A,CYS,57,SG,disulf,2.3",
+            "_case_from": "https://www.uniprot.org/uniprotkb/P83658/entry#ptm_processing",
+            "_note": "Intrachain, A"
+        },
+        {
+            "type": "bond",
+            "bond": "B,CYS,6,SG,B,CYS,29,SG,disulf,2.3;B,CYS,20,SG,B,CYS,26,SG,disulf,2.3;B,CYS,25,SG,B,CYS,50,SG,disulf,2.3;B,CYS,38,SG,B,CYS,57,SG,disulf,2.3",
+            "_case_from": "https://www.uniprot.org/uniprotkb/P83658/entry#ptm_processing",
+            "_note": "Intrachain, B"
+        },
+        {
+            "type": "bond",
+            "bond": "A,CYS,7,SG,B,CYS,12,SG,disulf,2.3",
+            "_case_from": "https://www.uniprot.org/uniprotkb/P83658/entry#ptm_processing",
+            "_note": "Interchain, AB"
+        },
+        {
+            "type": "bond",
+            "bond": "B,CYS,7,SG,A,CYS,12,SG,disulf,2.3",
+            "_case_from": "https://www.uniprot.org/uniprotkb/P83658/entry#ptm_processing",
+            "_note": "Interchain, BA"
+        }
+    ]
+}

apps/protein_folding/helixfold3/data/demo_p450_heme.json

@@ -0,0 +1,19 @@
+{
+    "entities": [
+        {
+            "type": "protein",
+            "sequence": "MDALYKSTVAKFNEVIQLDCSTEFFSIALSSIAGILLLLLLFRSKRHSSLKLPPGKLGIPFIGESFIFLRALRSNSLEQFFDERVKKFGLVFKTSLIGHPTVVLCGPAGNRLILSNEEKLVQMSWPAQFMKLMGENSVATRRGEDHIVMRSALAGFFGPGALQSYIGKMNTEIQSHINEKWKGKDEVNVLPLVRELVFNISAILFFNIYDKQEQDRLHKLLETILVGSFALPIDLPGFGFHRALQGRAKLNKIMLSLIKKRKEDLQSGSATATQDLLSVLLTFRDDKGTPLTNDEILDNFSSLLHASYDTTTSPMALIFKLLSSNPECYQKVVQEQLEILSNKEEGEEITWKDLKAMKYTWQVAQETLRMFPPVFGTFRKAITDIQYDGYTIPKGWKLLWTTYSTHPKDLYFNEPEKFMPSRFDQEGKHVAPYTFLPFGGGQRSCVGWEFSKMEILLFVHHFVKTFSSYTPVDPDEKISGDPLPPLPSKGFSIKLFPRP",
+            "count": 1
+        },
+        {
+            "type": "ligand",
+            "ccd": "HEM",
+            "count": 1
+        },
+        {
+            "type": "ligand",
+            "smiles": "CC1=C2CC[C@@]3(CCCC(=C)[C@H]3C[C@@H](C2(C)C)CC1)C",
+            "count": 1
+        }
+    ]
+}

apps/protein_folding/helixfold3/data/demo_p450_heme_coval.json

@@ -0,0 +1,25 @@
+{
+    "entities": [
+        {
+            "type": "protein",
+            "sequence": "MDALYKSTVAKFNEVIQLDCSTEFFSIALSSIAGILLLLLLFRSKRHSSLKLPPGKLGIPFIGESFIFLRALRSNSLEQFFDERVKKFGLVFKTSLIGHPTVVLCGPAGNRLILSNEEKLVQMSWPAQFMKLMGENSVATRRGEDHIVMRSALAGFFGPGALQSYIGKMNTEIQSHINEKWKGKDEVNVLPLVRELVFNISAILFFNIYDKQEQDRLHKLLETILVGSFALPIDLPGFGFHRALQGRAKLNKIMLSLIKKRKEDLQSGSATATQDLLSVLLTFRDDKGTPLTNDEILDNFSSLLHASYDTTTSPMALIFKLLSSNPECYQKVVQEQLEILSNKEEGEEITWKDLKAMKYTWQVAQETLRMFPPVFGTFRKAITDIQYDGYTIPKGWKLLWTTYSTHPKDLYFNEPEKFMPSRFDQEGKHVAPYTFLPFGGGQRSCVGWEFSKMEILLFVHHFVKTFSSYTPVDPDEKISGDPLPPLPSKGFSIKLFPRP",
+            "count": 1
+        },
+        {
+            "type": "ligand",
+            "ccd": "HEM",
+            "count": 1
+        },
+        {
+            "type": "ligand",
+            "smiles": "CC1=C2CC[C@@]3(CCCC(=C)[C@H]3C[C@@H](C2(C)C)CC1)C",
+            "count": 1
+        },
+        {
+            "type": "bond",
+            "bond": "A,CYS,445,SG,B,HEM,1,FE,covale,2.3",
+            "_comment": "<chain-id>,<residue name>,<residue index>,<atom id>,<chain-id>,<residue name>,<residue index>,<atom id>,<bond type>,<bond length>",
+            "_also_comment": "For ccd input, use CCD key as residue name; for smiles and file input, use `UNK-<index>` where index is the chain order you input"
+        }
+    ]
+}