Skip to content

Commit c7cf02f

Browse files
miguelgondumiguelgondu
committed
Updates the description of dockstring
1 parent e811b9c commit c7cf02f

File tree

4 files changed

+149
-43
lines changed

4 files changed

+149
-43
lines changed

‎docs/protein-optimization/references.bib

Lines changed: 9 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -78,3 +78,12 @@ @MISC{Al-Roomi:continuous_objective_benchmarks:2015
7878
institution = {Dalhousie University, Electrical and Computer Engineering},
7979
url = {https://www.al-roomi.org/benchmarks/unconstrained}
8080
}
81+
82+
@inproceedings{
83+
gao:PMO:2022,
84+
title={Sample Efficiency Matters: A Benchmark for Practical Molecular Optimization},
85+
author={Wenhao Gao and Tianfan Fu and Jimeng Sun and Connor W. Coley},
86+
booktitle={Thirty-sixth Conference on Neural Information Processing Systems Datasets and Benchmarks Track},
87+
year={2022},
88+
url={https://openreview.net/forum?id=yCZRdI0Y7G}
89+
}

‎docs/protein-optimization/using_poli/objective_repository/all_objectives.md

Lines changed: 1 addition & 13 deletions
Original file line numberDiff line numberDiff line change
@@ -30,7 +30,7 @@ The usual benchmark functions for continuous optimization (e.g. `easom`, or `ack
3030

3131
## Small molecules
3232

33-
Most of our problems are based on the [PMO]() benchmark, by Gao et al [TODO: add cite].
33+
Most of our problems are based on the [PMO](https://github.com/wenhao-gao/mol_opt) benchmark, by Gao et al {cite:p}`gao:PMO:2022`.
3434

3535
::::{grid}
3636
:gutter: 3
@@ -71,18 +71,6 @@ A wrapper around the Therapeutics Data Commons implmenetation of 3pbl docking.
7171
A wrapper around the Therapeutics Data Commons implmenetation of the synthetic accessibility oracle.
7272
:::
7373

74-
:::{grid-item-card} TDC oracles [WIP]
75-
:link: ./tdc_oracles.html
76-
:columns: 6
77-
Some of the oracles provided by the Therapeutics Data Commons. [WIP]
78-
:::
79-
80-
:::{grid-item-card} GuacaMol [WIP]
81-
:link: ./tdc_oracles.html
82-
:columns: 6
83-
Some of the oracles provided by GuacaMol. [WIP]
84-
:::
85-
8674
::::
8775

8876
## Proteins

‎docs/protein-optimization/using_poli/objective_repository/dockstring.md

Lines changed: 7 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -42,15 +42,17 @@ conda activate poli__dockstring
4242
Once you are in this environment (or in an environment that satisfies all its requirements), you can run the canonical example of risperidone and DRD3 docking:
4343

4444
```python
45+
# from the poli__dockstring environment
4546
import numpy as np
4647

47-
from poli import objective_factory
48+
from poli.objective_repository import DockstringProblemFactory
4849

4950
if __name__ == "__main__":
50-
problem_info, f, x0, y0, _ = objective_factory.create(
51-
name="dockstring",
51+
problem_factory = DockstringProblemFactory()
52+
53+
f, x0, y0 = problem_factory.create(
5254
target_name="DRD2",
53-
string_representation="SMILES",
55+
string_representation="SMILES", # Can be either SMILES or SELFIES
5456
)
5557

5658
# The smiles for Risperidone
@@ -92,7 +94,7 @@ if __name__ == "__main__":
9294
```
9395

9496
```{warning}
95-
Registering the objective function in this way will create a `conda` environment called `poli__dockstring` with the relevant dependencies. You can find the exact environment description in the following file: `src/poli/objective_repository/dockstring/environment.yml`
97+
Registering the objective function in this way will create a `conda` environment called `poli__dockstring` with the relevant dependencies. You can find the exact environment description in the following file in the `poli` repository: `src/poli/objective_repository/dockstring/environment.yml`
9698
9799
```
98100

‎docs/protein-optimization/using_poli/optimization_examples/protein-stability-foldx/optimizing_protein_stability.ipynb

Lines changed: 132 additions & 25 deletions
Original file line numberDiff line numberDiff line change
@@ -167,9 +167,10 @@
167167
"name": "stdout",
168168
"output_type": "stream",
169169
"text": [
170+
"poli 🧪: Creating the objective from the repository.\n",
170171
" ********************************************\n",
171172
" *** ***\n",
172-
" *** FoldX 4 (c) ***\n",
173+
" *** FoldX 5 (c) ***\n",
173174
" *** ***\n",
174175
" *** code by the FoldX Consortium ***\n",
175176
" *** ***\n",
@@ -184,6 +185,31 @@
184185
" ********************************************\n",
185186
"\n",
186187
"1 models read: 3ned_Repair.pdb\n",
188+
"1 models read: 3ned_Repair.pdb\n",
189+
"\n",
190+
"BackHbond = -178.70\n",
191+
"SideHbond = -76.61\n",
192+
"Energy_VdW = -267.80\n",
193+
"Electro = -13.75\n",
194+
"Energy_SolvP = 374.21\n",
195+
"Energy_SolvH = -351.07\n",
196+
"Energy_vdwclash = 6.28\n",
197+
"energy_torsion = 7.33\n",
198+
"backbone_vdwclash= 65.17\n",
199+
"Entropy_sidec = 146.42\n",
200+
"Entropy_mainc = 340.27\n",
201+
"water bonds = 0.00\n",
202+
"helix dipole = 0.00\n",
203+
"loop_entropy = 0.00\n",
204+
"cis_bond = 2.25\n",
205+
"disulfide = 0.00\n",
206+
"kn electrostatic= 0.00\n",
207+
"partial covalent interactions = 0.00\n",
208+
"Energy_Ionisation = 1.77\n",
209+
"Entropy Complex = 0.00\n",
210+
"-----------------------------------------------------------\n",
211+
"Total = \t\t\t\t -9.41\n",
212+
"\n",
187213
"\n",
188214
"BackHbond = -178.70\n",
189215
"SideHbond = -76.61\n",
@@ -213,8 +239,8 @@
213239
"Residue to Mutate GLUA1 has residue index 0\n",
214240
"Mutating residue = GLUA1 into GLU\n",
215241
"Your file run OK\n",
216-
"End time of FoldX: Mon Sep 4 10:20:05 2023\n",
217-
"Total time spend: 2.23 seconds.\n",
242+
"End time of FoldX: Fri Jan 19 09:51:02 2024\n",
243+
"Total time spend: 2.64 seconds.\n",
218244
"validated file \"3ned_Repair_1.pdb\" => successfully finished\n",
219245
"Cleaning BuildModel...DONE\n"
220246
]
@@ -312,7 +338,7 @@
312338
"text": [
313339
" ********************************************\n",
314340
" *** ***\n",
315-
" *** FoldX 4 (c) ***\n",
341+
" *** FoldX 5 (c) ***\n",
316342
" *** ***\n",
317343
" *** code by the FoldX Consortium ***\n",
318344
" *** ***\n",
@@ -327,6 +353,31 @@
327353
" ********************************************\n",
328354
"\n",
329355
"1 models read: 3ned_Repair.pdb\n",
356+
"1 models read: 3ned_Repair.pdb\n",
357+
"\n",
358+
"BackHbond = -178.70\n",
359+
"SideHbond = -76.61\n",
360+
"Energy_VdW = -267.80\n",
361+
"Electro = -13.75\n",
362+
"Energy_SolvP = 374.21\n",
363+
"Energy_SolvH = -351.07\n",
364+
"Energy_vdwclash = 6.28\n",
365+
"energy_torsion = 7.33\n",
366+
"backbone_vdwclash= 65.17\n",
367+
"Entropy_sidec = 146.42\n",
368+
"Entropy_mainc = 340.27\n",
369+
"water bonds = 0.00\n",
370+
"helix dipole = 0.00\n",
371+
"loop_entropy = 0.00\n",
372+
"cis_bond = 2.25\n",
373+
"disulfide = 0.00\n",
374+
"kn electrostatic= 0.00\n",
375+
"partial covalent interactions = 0.00\n",
376+
"Energy_Ionisation = 1.77\n",
377+
"Entropy Complex = 0.00\n",
378+
"-----------------------------------------------------------\n",
379+
"Total = \t\t\t\t -9.41\n",
380+
"\n",
330381
"\n",
331382
"BackHbond = -178.70\n",
332383
"SideHbond = -76.61\n",
@@ -352,17 +403,17 @@
352403
"Total = \t\t\t\t -9.41\n",
353404
"\n",
354405
"Starting BuildModel\n",
355-
"Reading EA1E;\n",
356-
"Residue to Mutate GLUA1 has residue index 0\n",
357-
"Mutating residue = GLUA1 into GLU\n",
406+
"Reading NA194F;\n",
407+
"Residue to Mutate ASNA194 has residue index 193\n",
408+
"Mutating residue = ASNA194 into PHE\n",
358409
"Your file run OK\n",
359-
"End time of FoldX: Mon Sep 4 10:22:34 2023\n",
360-
"Total time spend: 2.30 seconds.\n",
410+
"End time of FoldX: Fri Jan 19 09:51:22 2024\n",
411+
"Total time spend: 6.54 seconds.\n",
361412
"validated file \"3ned_Repair_1.pdb\" => successfully finished\n",
362413
"Cleaning BuildModel...DONE\n",
363414
" ********************************************\n",
364415
" *** ***\n",
365-
" *** FoldX 4 (c) ***\n",
416+
" *** FoldX 5 (c) ***\n",
366417
" *** ***\n",
367418
" *** code by the FoldX Consortium ***\n",
368419
" *** ***\n",
@@ -377,6 +428,31 @@
377428
" ********************************************\n",
378429
"\n",
379430
"1 models read: 3ned_Repair.pdb\n",
431+
"1 models read: 3ned_Repair.pdb\n",
432+
"\n",
433+
"BackHbond = -178.70\n",
434+
"SideHbond = -76.61\n",
435+
"Energy_VdW = -267.80\n",
436+
"Electro = -13.75\n",
437+
"Energy_SolvP = 374.21\n",
438+
"Energy_SolvH = -351.07\n",
439+
"Energy_vdwclash = 6.28\n",
440+
"energy_torsion = 7.33\n",
441+
"backbone_vdwclash= 65.17\n",
442+
"Entropy_sidec = 146.42\n",
443+
"Entropy_mainc = 340.27\n",
444+
"water bonds = 0.00\n",
445+
"helix dipole = 0.00\n",
446+
"loop_entropy = 0.00\n",
447+
"cis_bond = 2.25\n",
448+
"disulfide = 0.00\n",
449+
"kn electrostatic= 0.00\n",
450+
"partial covalent interactions = 0.00\n",
451+
"Energy_Ionisation = 1.77\n",
452+
"Entropy Complex = 0.00\n",
453+
"-----------------------------------------------------------\n",
454+
"Total = \t\t\t\t -9.41\n",
455+
"\n",
380456
"\n",
381457
"BackHbond = -178.70\n",
382458
"SideHbond = -76.61\n",
@@ -402,17 +478,19 @@
402478
"Total = \t\t\t\t -9.41\n",
403479
"\n",
404480
"Starting BuildModel\n",
405-
"Reading LA124W;\n",
406-
"Residue to Mutate LEUA124 has residue index 123\n",
407-
"Mutating residue = LEUA124 into TRP\n",
481+
"Reading QA114S,NA194F;\n",
482+
"Residue to Mutate GLNA114 has residue index 113\n",
483+
"Residue to Mutate ASNA194 has residue index 193\n",
484+
"Mutating residue = ASNA194 into PHE\n",
485+
"Mutating residue = GLNA114 into SER\n",
408486
"Your file run OK\n",
409-
"End time of FoldX: Mon Sep 4 10:22:43 2023\n",
410-
"Total time spend: 8.13 seconds.\n",
487+
"End time of FoldX: Fri Jan 19 09:51:32 2024\n",
488+
"Total time spend: 8.65 seconds.\n",
411489
"validated file \"3ned_Repair_1.pdb\" => successfully finished\n",
412490
"Cleaning BuildModel...DONE\n",
413491
" ********************************************\n",
414492
" *** ***\n",
415-
" *** FoldX 4 (c) ***\n",
493+
" *** FoldX 5 (c) ***\n",
416494
" *** ***\n",
417495
" *** code by the FoldX Consortium ***\n",
418496
" *** ***\n",
@@ -427,6 +505,31 @@
427505
" ********************************************\n",
428506
"\n",
429507
"1 models read: 3ned_Repair.pdb\n",
508+
"1 models read: 3ned_Repair.pdb\n",
509+
"\n",
510+
"BackHbond = -178.70\n",
511+
"SideHbond = -76.61\n",
512+
"Energy_VdW = -267.80\n",
513+
"Electro = -13.75\n",
514+
"Energy_SolvP = 374.21\n",
515+
"Energy_SolvH = -351.07\n",
516+
"Energy_vdwclash = 6.28\n",
517+
"energy_torsion = 7.33\n",
518+
"backbone_vdwclash= 65.17\n",
519+
"Entropy_sidec = 146.42\n",
520+
"Entropy_mainc = 340.27\n",
521+
"water bonds = 0.00\n",
522+
"helix dipole = 0.00\n",
523+
"loop_entropy = 0.00\n",
524+
"cis_bond = 2.25\n",
525+
"disulfide = 0.00\n",
526+
"kn electrostatic= 0.00\n",
527+
"partial covalent interactions = 0.00\n",
528+
"Energy_Ionisation = 1.77\n",
529+
"Entropy Complex = 0.00\n",
530+
"-----------------------------------------------------------\n",
531+
"Total = \t\t\t\t -9.41\n",
532+
"\n",
430533
"\n",
431534
"BackHbond = -178.70\n",
432535
"SideHbond = -76.61\n",
@@ -452,12 +555,16 @@
452555
"Total = \t\t\t\t -9.41\n",
453556
"\n",
454557
"Starting BuildModel\n",
455-
"Reading WA143S;\n",
456-
"Residue to Mutate TRPA143 has residue index 142\n",
457-
"Mutating residue = TRPA143 into SER\n",
558+
"Reading DA3M,QA114S,NA194F;\n",
559+
"Residue to Mutate ASPA3 has residue index 2\n",
560+
"Residue to Mutate GLNA114 has residue index 113\n",
561+
"Residue to Mutate ASNA194 has residue index 193\n",
562+
"Mutating residue = ASPA3 into MET\n",
563+
"Mutating residue = ASNA194 into PHE\n",
564+
"Mutating residue = GLNA114 into SER\n",
458565
"Your file run OK\n",
459-
"End time of FoldX: Mon Sep 4 10:22:44 2023\n",
460-
"Total time spend: 1.34 seconds.\n",
566+
"End time of FoldX: Fri Jan 19 09:51:42 2024\n",
567+
"Total time spend: 9.23 seconds.\n",
461568
"validated file \"3ned_Repair_1.pdb\" => successfully finished\n",
462569
"Cleaning BuildModel...DONE\n"
463570
]
@@ -483,16 +590,16 @@
483590
},
484591
{
485592
"cell_type": "code",
486-
"execution_count": 9,
593+
"execution_count": 8,
487594
"metadata": {},
488595
"outputs": [
489596
{
490597
"name": "stdout",
491598
"output_type": "stream",
492599
"text": [
493-
"All y values: [array([[9.41639]]), array([[9.41639]]), array([[-4.01168]]), array([[2.81194]])]\n",
494-
"best stability: 9.41639\n",
495-
"Associated sequence: EEDNMAIIKEFMRFKTHMEGSVNGHEFEIEGEGEGRPYEGTQTAKLKVTKGGPLPFAWDILSPQFSKAYVKHPADIPDYLKLSFPEGFKWERVMNFEDGGVVTVTQDSSLQDGEFIYKVKLRGTNFPSDGPVMQKKTMGWEACSERMYPEDGALKGEMKMRLKLKDGGHYDAEVKTTYKAKKPVQLPGAYNTNTKLDITSHNEDYTIVEQYERNEGRHSTGGMDELYK\n"
600+
"All y values: [array([[9.41639]]), array([[13.0629]]), array([[13.5983]]), array([[13.1298]])]\n",
601+
"best stability: [13.5983]\n",
602+
"Associated sequence: EEDNMAIIKEFMRFKTHMEGSVNGHEFEIEGEGEGRPYEGTQTAKLKVTKGGPLPFAWDILSPQFSKAYVKHPADIPDYLKLSFPEGFKWERVMNFEDGGVVTVTQDSSLSDGEFIYKVKLRGTNFPSDGPVMQKKTMGWEACSERMYPEDGALKGEMKMRLKLKDGGHYDAEVKTTYKAKKPVQLPGAYFTNTKLDITSHNEDYTIVEQYERNEGRHSTGGMDELYK\n"
496603
]
497604
}
498605
],

0 commit comments

Comments
 (0)