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add pymol reference for selection string
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wujiewang committed Nov 20, 2023
1 parent 2f3f32a commit 8dde16c
Showing 1 changed file with 6 additions and 3 deletions.
9 changes: 6 additions & 3 deletions chroma/models/chroma.py
Original file line number Diff line number Diff line change
Expand Up @@ -172,13 +172,16 @@ def sample(
Can be `potts` and `autoregressive`. Default is `potts`.
design_selection (str, optional): Clamp selection for
conditioning on a subsequence during sequence sampling. Can be
either a PyMOl-like selection string
or a binary design mask indicating positions with shape `(num_batch,
1) a PyMOl-like selection string
(https://pymolwiki.org/index.php/Property_Selectors)
or
2) a binary design mask indicating positions with shape `(num_batch,
num_residues)`. 1. indicating the residue to be designed and
0. indicates the residue will be masked.
e.g.
design_selection = torch.Tensor([[0., 1. ,1., 0., 1. ... ]])
or position-specific valid amino acid choices with shape
or
3) position-specific valid amino acid choices with shape
`(num_batch, num_residues, num_alphabet)`.
design_t (float or torch.Tensor, optional): Diffusion time for models
trained with diffusion augmentation of input structures. Setting `t=0`
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