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testing

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This commit is contained in:
Joel Wallace 2025-11-28 21:27:34 +00:00
parent a37e07998c
commit 33c10efe62
1 changed files with 11 additions and 9 deletions
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src/test.py
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@ -1,6 +1,7 @@
from backbone.ramachandran import RamachandranSampler from backbone.ramachandran import RamachandranSampler
from rotamers.dunbrack import DunbrackRotamerLibrary from rotamers.dunbrack import DunbrackRotamerLibrary
from geometry.backbone import GEO, ORI from geometry.backbone import GEO as BACKBONE_GEO, ORI
from geometry.sidechain import GEO as SIDECHAIN_GEO
from geometry.nerf import nerf from geometry.nerf import nerf
from protein.residue import ResidueName, Residue from protein.residue import ResidueName, Residue
@ -25,8 +26,8 @@ for residue_index, residue_name in enumerate(primary_sequence[:2]):
residues[residue_index].backbone["atoms"]["N"], residues[residue_index].backbone["atoms"]["N"],
residues[residue_index].backbone["atoms"]["CA"], residues[residue_index].backbone["atoms"]["CA"],
residues[residue_index].backbone["atoms"]["C"], residues[residue_index].backbone["atoms"]["C"],
GEO["C_N_length"], BACKBONE_GEO["C_N_length"],
GEO["CA_C_N_angle"], BACKBONE_GEO["CA_C_N_angle"],
residues[residue_index].backbone["psi"], residues[residue_index].backbone["psi"],
) )
@ -34,8 +35,8 @@ for residue_index, residue_name in enumerate(primary_sequence[:2]):
residues[residue_index].backbone["atoms"]["CA"], residues[residue_index].backbone["atoms"]["CA"],
residues[residue_index].backbone["atoms"]["C"], residues[residue_index].backbone["atoms"]["C"],
residue.backbone["atoms"]["N"], residue.backbone["atoms"]["N"],
GEO["N_CA_length"], BACKBONE_GEO["N_CA_length"],
GEO["C_N_CA_angle"], BACKBONE_GEO["C_N_CA_angle"],
180, 180,
) )
@ -43,8 +44,8 @@ for residue_index, residue_name in enumerate(primary_sequence[:2]):
residues[residue_index].backbone["atoms"]["C"], residues[residue_index].backbone["atoms"]["C"],
residue.backbone["atoms"]["N"], residue.backbone["atoms"]["N"],
residue.backbone["atoms"]["CA"], residue.backbone["atoms"]["CA"],
GEO["CA_C_length"], BACKBONE_GEO["CA_C_length"],
GEO["N_CA_C_angle"], BACKBONE_GEO["N_CA_C_angle"],
residue.backbone["phi"], residue.backbone["phi"],
) )
@ -52,11 +53,12 @@ for residue_index, residue_name in enumerate(primary_sequence[:2]):
residue.backbone["atoms"]["N"], residue.backbone["atoms"]["N"],
residue.backbone["atoms"]["CA"], residue.backbone["atoms"]["CA"],
residue.backbone["atoms"]["C"], residue.backbone["atoms"]["C"],
GEO["C_O_length"], BACKBONE_GEO["C_O_length"],
GEO["CA_C_O_angle"], BACKBONE_GEO["CA_C_O_angle"],
residue.backbone["psi"] + 180, residue.backbone["psi"] + 180,
) )
residue.sidechain
residues.append(residue) residues.append(residue)
residue.sidechain["chis"] = rl.rotamer_params(residue.name.value, residue.backbone["phi"], residue.backbone["psi"]) residue.sidechain["chis"] = rl.rotamer_params(residue.name.value, residue.backbone["phi"], residue.backbone["psi"])