Initial commit: RoseTTAFold-All-Atom configured for Wes with Harbor images and s3:// paths

rf2aa/config/inference/base.yaml

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+job_name: "structure_prediction"
+output_path: ""
+checkpoint_path: RFAA_paper_weights.pt
+database_params:
+  sequencedb: ""
+  hhdb: "pdb100_2021Mar03/pdb100_2021Mar03"
+  command: make_msa.sh
+  num_cpus: 4
+  mem: 64
+protein_inputs: null
+na_inputs: null
+sm_inputs: null
+covale_inputs:  null
+residue_replacement: null
+
+chem_params:
+  use_phospate_frames_for_NA: True
+  use_cif_ordering_for_trp: True
+
+loader_params:
+  n_templ: 4
+  MAXLAT: 128
+  MAXSEQ: 1024
+  MAXCYCLE: 4
+  BLACK_HOLE_INIT: False
+  seqid: 150.0
+
+
+legacy_model_param:
+  n_extra_block: 4
+  n_main_block: 32
+  n_ref_block: 4
+  n_finetune_block: 0
+  d_msa: 256
+  d_msa_full: 64
+  d_pair: 192
+  d_templ: 64
+  n_head_msa: 8
+  n_head_pair: 6
+  n_head_templ: 4
+  d_hidden_templ: 64
+  p_drop: 0.0
+  use_chiral_l1: True
+  use_lj_l1: True
+  use_atom_frames: True
+  recycling_type: "all"
+  use_same_chain: True
+  lj_lin: 0.75
+  SE3_param: 
+    num_layers: 1
+    num_channels: 32
+    num_degrees: 2
+    l0_in_features: 64
+    l0_out_features: 64
+    l1_in_features: 3
+    l1_out_features: 2
+    num_edge_features: 64
+    n_heads: 4
+    div: 4
+  SE3_ref_param:
+    num_layers: 2
+    num_channels: 32
+    num_degrees: 2
+    l0_in_features: 64
+    l0_out_features: 64
+    l1_in_features: 3
+    l1_out_features: 2
+    num_edge_features: 64
+    n_heads: 4
+    div: 4

rf2aa/config/inference/covalent.yaml

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+defaults:
+  - base
+
+job_name: 7s69_A
+
+protein_inputs: 
+  A: 
+    fasta_file: examples/protein/7s69_A.fasta
+
+sm_inputs:
+  B: 
+    input: examples/small_molecule/7s69_glycan.sdf
+    input_type: sdf
+
+covale_inputs: "[((\"A\", \"74\", \"ND2\"), (\"B\", \"1\"), (\"CW\", \"null\"))]"
+
+loader_params:
+  MAXCYCLE: 10

rf2aa/config/inference/nucleic_acid.yaml

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+defaults:
+  - base
+
+job_name: "7u7w_protein_nucleic"
+protein_inputs: 
+  A: 
+    fasta_file: examples/protein/7u7w_A.fasta
+na_inputs: 
+  B: 
+    fasta: examples/nucleic_acid/7u7w_B.fasta
+    input_type: "dna"
+  C: 
+    fasta: examples/nucleic_acid/7u7w_C.fasta
+    input_type: "dna"

rf2aa/config/inference/protein.yaml

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+defaults:
+  - base
+
+job_name: "7u7w_protein"
+protein_inputs: 
+  A:
+    fasta_file: examples/protein/7u7w_A.fasta

rf2aa/config/inference/protein_complex_sm.yaml

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+defaults:
+  - base
+job_name: "3fap"
+
+protein_inputs:
+  A:
+    fasta_file: examples/protein/3fap_A.fasta
+  B: 
+    fasta_file: examples/protein/3fap_B.fasta
+
+sm_inputs:
+  C:
+    input: examples/small_molecule/ARD_ideal.sdf
+    input_type: "sdf"

rf2aa/config/inference/protein_na_sm.yaml

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+defaults:
+  - base
+
+job_name: "7u7w_protein_nucleic_sm"
+protein_inputs: 
+  A: 
+    fasta_file: examples/protein/7u7w_A.fasta
+na_inputs: 
+  B: 
+    fasta: examples/nucleic_acid/7u7w_B.fasta
+    input_type: "dna"
+  C: 
+    fasta: examples/nucleic_acid/7u7w_C.fasta
+    input_type: "dna"
+sm_inputs: 
+  D:
+    input: examples/small_molecule/XG4.sdf
+    input_type: "sdf"

rf2aa/config/inference/protein_sm.yaml

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+defaults:
+  - base
+
+job_name: 7qxr
+
+protein_inputs:
+  A: 
+    fasta_file: examples/protein/7qxr.fasta
+
+sm_inputs:
+  B:
+    input: examples/small_molecule/NSW_ideal.sdf
+    input_type: "sdf"