examples/rosettafold_all_atom.md
... ...
@@ -75,3 +75,4 @@ python.rfaa -m rf2aa.run_inference \
75 75
database_params.hhdb=${ROSETTAFOLD_DB_PATH}/pdb100_2021Mar03/pdb100_2021Mar03
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```
78
+
examples/sbgrid_example.fasta
... ...
@@ -0,0 +1,2 @@
1
+>7U7W_1|Chain A|DNA polymerase eta|Homo sapiens (9606)
2
+GPHMATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGIIAVSYEARAFGVTRSMWADDAKKLCPDLLLAQVRESRGKANLTKYREASVEVMEIMSRFAVIERASIDEAYVDLTSAVQERLQKLQGQPISADLLPSTYIEGLPQGPTTAEETVQKEGMRKQGLFQWLDSLQIDNLTSPDLQLTVGAVIVEEMRAAIERETGFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMPIRKIRSLGGKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAMCRGIEHDPVKPRQLPKTIGCSKNFPGKTALATREQVQWWLLQLAQELEERLTKDRNDNDRVATQLVVSIRVQGDKRLSSLRRCCALTRYDAHKMSHDAFTVIKNCNTSGIQTEWSPPLTMLFLCATKFSAS
... ...
\ No newline at end of file
examples/sbgrid_example.yaml
... ...
@@ -0,0 +1,75 @@
1
+protein_inputs:
2
+ A:
3
+ fasta_file: sbgrid_example.fasta
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+
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+job_name: sbgrid_example
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+output_path: ${job_name}
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+
8
+checkpoint_path: RFAA_paper_weights.pt
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+database_params:
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+ sequencedb: ""
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+ hhdb: "pdb100_2021Mar03/pdb100_2021Mar03"
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+ command: make_msa.sh
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+ num_cpus: 4
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+ mem: 64
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+
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+na_inputs: null
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+sm_inputs: null
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+covale_inputs: null
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+residue_replacement: null
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+
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+chem_params:
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+ use_phospate_frames_for_NA: True
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+ use_cif_ordering_for_trp: True
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+
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+loader_params:
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+ n_templ: 4
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+ MAXLAT: 128
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+ MAXSEQ: 1024
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+ MAXCYCLE: 4
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+ BLACK_HOLE_INIT: False
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+ seqid: 150.0
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+
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+
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+legacy_model_param:
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+ n_extra_block: 4
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+ n_main_block: 32
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+ n_ref_block: 4
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+ n_finetune_block: 0
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+ d_msa: 256
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+ d_msa_full: 64
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+ d_pair: 192
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+ d_templ: 64
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+ n_head_msa: 8
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+ n_head_pair: 6
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+ n_head_templ: 4
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+ d_hidden_templ: 64
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+ p_drop: 0.0
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+ use_chiral_l1: True
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+ use_lj_l1: True
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+ use_atom_frames: True
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+ recycling_type: "all"
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+ use_same_chain: True
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+ lj_lin: 0.75
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+ SE3_param:
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+ num_layers: 1
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+ num_channels: 32
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+ num_degrees: 2
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+ l0_in_features: 64
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+ l0_out_features: 64
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+ l1_in_features: 3
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+ l1_out_features: 2
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+ num_edge_features: 64
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+ n_heads: 4
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+ div: 4
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+ SE3_ref_param:
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+ num_layers: 2
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+ num_channels: 32
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+ num_degrees: 2
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+ l0_in_features: 64
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+ l0_out_features: 64
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+ l1_in_features: 3
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+ l1_out_features: 2
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+ num_edge_features: 64
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+ n_heads: 4
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+ div: 4
... ...
\ No newline at end of file