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DSilva27DSilva27
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Merge pull request #77 from flatironinstitute/71-cleaning-up-for-publication
71 cleaning up for publication
2 parents 1c5f9cb + 0f6cfd4 commit 5590857

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lines changed

15 files changed

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lines changed

‎.gitignore‎

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.vscode/
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uv.lock
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*_version.py
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‎src/cryojax_eo/simulator/_dilated_mask.py‎

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@@ -17,7 +17,9 @@ def __init__(
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self.volume = cxs.FourierVoxelGridVolume.from_real_voxel_grid(real_voxel_grid)
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def project(self, pose: cxs.AbstractPose):
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mask2d = cxs.make_image_model(self.volume, self.image_config, pose).simulate()
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mask2d = cxs.make_image_model(
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self.volume, self.image_config, pose.to_inverse_rotation()
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).simulate()
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mask2d /= mask2d.max()
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mask2d = jnp.where(jnp.abs(mask2d) > 0.2, 1.0, 0.0)
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return mask2d

‎src/cryojax_eo/simulator/_image_simulation.py‎

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from typing import Dict, Tuple
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from typing import Tuple
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import cryojax.simulator as cxs
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import jax
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import jax.numpy as jnp
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from cryojax.dataset import ParticleParameterInfo
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from cryojax.ndimage.transforms import CircularCosineMask
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from jaxtyping import Array, Float, Int, PRNGKeyArray
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@@ -13,7 +14,7 @@ def _select_potential(volumes, idx):
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def simulate_image_with_white_gaussian_noise(
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particle_parameters: Dict,
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particle_parameters: ParticleParameterInfo,
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constant_args: Tuple[
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Tuple[cxs.AbstractVolumeRepresentation],
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CircularCosineMask,
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volumes, mask, data_sign = constant_args
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volume = _select_potential(volumes, potential_idx)
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pose = jax.lax.cond(
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isinstance(volume, cxs.FourierVoxelGridVolume),
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lambda p: p.to_inverse_rotation(),
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lambda p: p,
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particle_parameters["pose"],
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)
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image_model = cxs.make_image_model(
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volume,
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particle_parameters["image_config"],
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particle_parameters["pose"],
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pose,
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particle_parameters["transfer_theory"],
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signal_region=(mask.array == 1),
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normalizes_signal=True,

‎tutorial/atomic_models/ala_A.pdb‎

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ATOM 1 H1 ACE X 1 -3.667 5.352 -2.257 1.00 0.00 SYST H
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ATOM 2 CH3 ACE X 1 -3.268 4.481 -2.776 1.00 0.00 SYST C
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ATOM 3 H2 ACE X 1 -3.295 4.764 -3.828 1.00 0.00 SYST H
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ATOM 4 H3 ACE X 1 -3.895 3.622 -2.536 1.00 0.00 SYST H
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ATOM 5 C ACE X 1 -1.820 4.273 -2.320 1.00 0.00 SYST C
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ATOM 6 O ACE X 1 -0.989 5.056 -2.661 1.00 0.00 SYST O
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ATOM 7 N ALA X 2 -1.584 3.221 -1.515 1.00 0.00 SYST N
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ATOM 8 H ALA X 2 -2.396 2.744 -1.153 1.00 0.00 SYST H
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ATOM 9 CA ALA X 2 -0.309 2.995 -0.866 1.00 0.00 SYST C
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ATOM 10 HA ALA X 2 0.508 3.505 -1.377 1.00 0.00 SYST H
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ATOM 11 CB ALA X 2 -0.367 3.557 0.538 1.00 0.00 SYST C
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ATOM 12 HB1 ALA X 2 0.623 3.651 0.985 1.00 0.00 SYST H
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ATOM 13 HB2 ALA X 2 -0.694 4.595 0.469 1.00 0.00 SYST H
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ATOM 14 HB3 ALA X 2 -1.083 3.016 1.157 1.00 0.00 SYST H
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ATOM 15 C ALA X 2 0.098 1.510 -0.776 1.00 0.00 SYST C
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ATOM 16 O ALA X 2 -0.697 0.618 -0.827 1.00 0.00 SYST O
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ATOM 17 N ALA X 3 1.438 1.189 -0.726 1.00 0.00 SYST N
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ATOM 18 H ALA X 3 2.141 1.914 -0.753 1.00 0.00 SYST H
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ATOM 19 CA ALA X 3 2.103 -0.189 -0.737 1.00 0.00 SYST C
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ATOM 20 HA ALA X 3 1.463 -0.756 -1.413 1.00 0.00 SYST H
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ATOM 21 CB ALA X 3 3.538 -0.142 -1.164 1.00 0.00 SYST C
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ATOM 22 HB1 ALA X 3 4.127 0.377 -0.408 1.00 0.00 SYST H
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ATOM 23 HB2 ALA X 3 3.993 -1.114 -1.354 1.00 0.00 SYST H
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ATOM 24 HB3 ALA X 3 3.597 0.348 -2.136 1.00 0.00 SYST H
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ATOM 25 C ALA X 3 1.911 -0.977 0.617 1.00 0.00 SYST C
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ATOM 26 O ALA X 3 2.931 -1.321 1.242 1.00 0.00 SYST O
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ATOM 27 N ALA X 4 0.679 -1.288 0.905 1.00 0.00 SYST N
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ATOM 28 H ALA X 4 -0.109 -0.779 0.529 1.00 0.00 SYST H
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ATOM 29 CA ALA X 4 0.355 -2.265 1.980 1.00 0.00 SYST C
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ATOM 30 HA ALA X 4 1.233 -2.404 2.611 1.00 0.00 SYST H
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ATOM 31 CB ALA X 4 -0.699 -1.644 2.824 1.00 0.00 SYST C
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ATOM 32 HB1 ALA X 4 -0.931 -2.279 3.679 1.00 0.00 SYST H
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ATOM 33 HB2 ALA X 4 -0.260 -0.741 3.248 1.00 0.00 SYST H
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ATOM 34 HB3 ALA X 4 -1.542 -1.403 2.175 1.00 0.00 SYST H
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ATOM 35 C ALA X 4 -0.011 -3.727 1.516 1.00 0.00 SYST C
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ATOM 36 O ALA X 4 -0.181 -4.709 2.209 1.00 0.00 SYST O
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ATOM 37 N NME X 5 -0.217 -3.873 0.193 1.00 0.00 SYST N
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ATOM 38 H NME X 5 -0.029 -3.037 -0.342 1.00 0.00 SYST H
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ATOM 39 C NME X 5 -0.952 -5.007 -0.409 1.00 0.00 SYST C
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ATOM 40 H1 NME X 5 -0.462 -5.965 -0.234 1.00 0.00 SYST H
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ATOM 41 H2 NME X 5 -2.021 -4.966 -0.200 1.00 0.00 SYST H
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ATOM 42 H3 NME X 5 -0.841 -4.927 -1.490 1.00 0.00 SYST H
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TER 43 NME X 5
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CONECT 1 2
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CONECT 2 5 1 3 4
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CONECT 3 2
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CONECT 4 2
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CONECT 5 2 6 7
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CONECT 6 5
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CONECT 7 5
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CONECT 35 37
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CONECT 37 35 39 38
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CONECT 38 37
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CONECT 39 40 41 42 37
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CONECT 40 39
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CONECT 41 39
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CONECT 42 39
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END

‎tutorial/atomic_models/ala_B.pdb‎

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ATOM 1 H1 ACE X 1 -3.143 1.934 -3.243 1.00 0.00 SYST H
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ATOM 2 CH3 ACE X 1 -3.032 2.997 -3.028 1.00 0.00 SYST C
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ATOM 3 H2 ACE X 1 -3.905 3.366 -2.490 1.00 0.00 SYST H
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ATOM 4 H3 ACE X 1 -3.102 3.623 -3.918 1.00 0.00 SYST H
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ATOM 5 C ACE X 1 -1.763 3.253 -2.279 1.00 0.00 SYST C
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ATOM 6 O ACE X 1 -0.870 3.949 -2.756 1.00 0.00 SYST O
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ATOM 7 N ALA X 2 -1.712 2.761 -1.019 1.00 0.00 SYST N
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ATOM 8 H ALA X 2 -2.496 2.281 -0.601 1.00 0.00 SYST H
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ATOM 9 CA ALA X 2 -0.429 2.679 -0.380 1.00 0.00 SYST C
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ATOM 10 HA ALA X 2 0.312 3.337 -0.835 1.00 0.00 SYST H
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ATOM 11 CB ALA X 2 -0.651 3.078 1.060 1.00 0.00 SYST C
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ATOM 12 HB1 ALA X 2 -1.395 2.431 1.524 1.00 0.00 SYST H
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ATOM 13 HB2 ALA X 2 0.275 2.983 1.627 1.00 0.00 SYST H
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ATOM 14 HB3 ALA X 2 -1.006 4.097 1.211 1.00 0.00 SYST H
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ATOM 15 C ALA X 2 0.156 1.231 -0.526 1.00 0.00 SYST C
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ATOM 16 O ALA X 2 -0.553 0.242 -0.641 1.00 0.00 SYST O
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ATOM 17 N ALA X 3 1.513 1.288 -0.536 1.00 0.00 SYST N
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ATOM 18 H ALA X 3 1.926 2.205 -0.448 1.00 0.00 SYST H
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ATOM 19 CA ALA X 3 2.476 0.207 -0.624 1.00 0.00 SYST C
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ATOM 20 HA ALA X 3 2.409 -0.087 -1.672 1.00 0.00 SYST H
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ATOM 21 CB ALA X 3 3.915 0.736 -0.354 1.00 0.00 SYST C
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ATOM 22 HB1 ALA X 3 4.597 -0.112 -0.284 1.00 0.00 SYST H
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ATOM 23 HB2 ALA X 3 4.333 1.488 -1.023 1.00 0.00 SYST H
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ATOM 24 HB3 ALA X 3 3.935 1.217 0.623 1.00 0.00 SYST H
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ATOM 25 C ALA X 3 2.102 -1.112 0.152 1.00 0.00 SYST C
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ATOM 26 O ALA X 3 2.505 -2.205 -0.248 1.00 0.00 SYST O
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ATOM 27 N ALA X 4 1.404 -0.986 1.293 1.00 0.00 SYST N
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ATOM 28 H ALA X 4 1.059 -0.058 1.497 1.00 0.00 SYST H
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ATOM 29 CA ALA X 4 0.668 -2.122 1.947 1.00 0.00 SYST C
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ATOM 30 HA ALA X 4 1.302 -2.992 2.118 1.00 0.00 SYST H
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ATOM 31 CB ALA X 4 0.346 -1.715 3.391 1.00 0.00 SYST C
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ATOM 32 HB1 ALA X 4 -0.298 -2.541 3.692 1.00 0.00 SYST H
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ATOM 33 HB2 ALA X 4 1.196 -1.787 4.070 1.00 0.00 SYST H
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ATOM 34 HB3 ALA X 4 -0.012 -0.685 3.382 1.00 0.00 SYST H
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ATOM 35 C ALA X 4 -0.631 -2.656 1.115 1.00 0.00 SYST C
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ATOM 36 O ALA X 4 -1.793 -2.548 1.545 1.00 0.00 SYST O
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ATOM 37 N NME X 5 -0.345 -3.280 -0.066 1.00 0.00 SYST N
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ATOM 38 H NME X 5 0.627 -3.334 -0.334 1.00 0.00 SYST H
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ATOM 39 C NME X 5 -1.346 -4.036 -0.795 1.00 0.00 SYST C
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ATOM 40 H1 NME X 5 -0.825 -4.704 -1.482 1.00 0.00 SYST H
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ATOM 41 H2 NME X 5 -2.064 -4.495 -0.115 1.00 0.00 SYST H
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ATOM 42 H3 NME X 5 -1.965 -3.314 -1.328 1.00 0.00 SYST H
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TER 43 NME X 5
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CONECT 1 2
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CONECT 2 5 1 3 4
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CONECT 3 2
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CONECT 4 2
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CONECT 5 2 6 7
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CONECT 6 5
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CONECT 7 5
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CONECT 35 37
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CONECT 37 35 39 38
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CONECT 38 37
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CONECT 39 40 41 42 37
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CONECT 40 39
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CONECT 41 39
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CONECT 42 39
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END

tutorial/ensemble_optimization/atomic_models/initial_model_0.pdb renamed to tutorial/atomic_models/ala_C.pdb

File renamed without changes.

‎tutorial/data_simulation/config_data_simulation.yaml‎

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atomic_models_params:
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path_to_atomic_models:
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- ./atomic_models/ala_model_0.pdb
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- ./atomic_models/ala_model_1.pdb
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- ../atomic_models/ala_A.pdb
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- ../atomic_models/ala_B.pdb
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atomic_models_probabilities:
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- 0.7
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- 0.3

‎tutorial/data_simulation/simulate_and_visualize_data.ipynb‎

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],
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"metadata": {
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"kernelspec": {
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"display_name": "cryojax_ensemble_refinement (3.11.11)",
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"display_name": "ens_opt_cuda_forge",
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"language": "python",
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"name": "python3"
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},
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.11.11"
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"version": "3.12.0"
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}
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},
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"nbformat": 4,

‎tutorial/ensemble_optimization/atomic_models/initial_model_1.pdb‎

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‎tutorial/ensemble_optimization/atomic_models/initial_state_0.xml‎

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