boltz-api 0.30.4 → 0.35.2

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (218) hide show
  1. package/CHANGELOG.md +67 -0
  2. package/api-promise.d.mts +1 -0
  3. package/api-promise.d.mts.map +1 -1
  4. package/api-promise.d.ts +1 -0
  5. package/api-promise.d.ts.map +1 -1
  6. package/api-promise.mjs +1 -0
  7. package/api-promise.mjs.map +1 -1
  8. package/client.d.mts.map +1 -1
  9. package/client.d.ts.map +1 -1
  10. package/client.mjs.map +1 -1
  11. package/core/api-promise.d.mts.map +1 -1
  12. package/core/api-promise.d.ts.map +1 -1
  13. package/core/api-promise.mjs.map +1 -1
  14. package/core/error.mjs.map +1 -1
  15. package/core/pagination.d.mts.map +1 -1
  16. package/core/pagination.d.ts.map +1 -1
  17. package/core/pagination.mjs.map +1 -1
  18. package/core/resource.d.mts.map +1 -1
  19. package/core/resource.d.ts.map +1 -1
  20. package/core/uploads.d.mts.map +1 -1
  21. package/core/uploads.d.ts.map +1 -1
  22. package/core/uploads.mjs.map +1 -1
  23. package/error.d.mts +1 -0
  24. package/error.d.mts.map +1 -1
  25. package/error.d.ts +1 -0
  26. package/error.d.ts.map +1 -1
  27. package/error.mjs +1 -0
  28. package/error.mjs.map +1 -1
  29. package/index.d.mts.map +1 -1
  30. package/index.d.ts.map +1 -1
  31. package/index.mjs.map +1 -1
  32. package/internal/detect-platform.mjs.map +1 -1
  33. package/internal/headers.mjs.map +1 -1
  34. package/internal/parse.d.mts.map +1 -1
  35. package/internal/parse.d.ts.map +1 -1
  36. package/internal/parse.mjs.map +1 -1
  37. package/internal/qs/formats.d.mts.map +1 -1
  38. package/internal/qs/formats.d.ts.map +1 -1
  39. package/internal/qs/index.d.mts +2 -2
  40. package/internal/qs/index.d.mts.map +1 -1
  41. package/internal/qs/index.d.ts +2 -2
  42. package/internal/qs/index.d.ts.map +1 -1
  43. package/internal/qs/index.mjs.map +1 -1
  44. package/internal/qs/stringify.d.mts.map +1 -1
  45. package/internal/qs/stringify.d.ts.map +1 -1
  46. package/internal/qs/stringify.mjs.map +1 -1
  47. package/internal/qs/utils.d.mts.map +1 -1
  48. package/internal/qs/utils.d.ts.map +1 -1
  49. package/internal/qs/utils.mjs.map +1 -1
  50. package/internal/request-options.d.mts.map +1 -1
  51. package/internal/request-options.d.ts.map +1 -1
  52. package/internal/shims.d.mts +6 -0
  53. package/internal/shims.d.mts.map +1 -1
  54. package/internal/shims.d.ts +6 -0
  55. package/internal/shims.d.ts.map +1 -1
  56. package/internal/to-file.d.mts.map +1 -1
  57. package/internal/to-file.d.ts.map +1 -1
  58. package/internal/to-file.mjs.map +1 -1
  59. package/internal/types.d.mts +4 -4
  60. package/internal/types.d.mts.map +1 -1
  61. package/internal/types.d.ts +4 -4
  62. package/internal/types.d.ts.map +1 -1
  63. package/internal/uploads.d.mts.map +1 -1
  64. package/internal/uploads.d.ts.map +1 -1
  65. package/internal/uploads.mjs.map +1 -1
  66. package/internal/utils/base64.mjs.map +1 -1
  67. package/internal/utils/log.d.mts.map +1 -1
  68. package/internal/utils/log.d.ts.map +1 -1
  69. package/internal/utils/log.mjs.map +1 -1
  70. package/internal/utils/path.mjs.map +1 -1
  71. package/internal/utils/query.mjs.map +1 -1
  72. package/internal/utils/values.mjs.map +1 -1
  73. package/internal/utils.d.mts.map +1 -1
  74. package/internal/utils.d.ts.map +1 -1
  75. package/internal/utils.mjs.map +1 -1
  76. package/package.json +1 -1
  77. package/pagination.d.mts +1 -0
  78. package/pagination.d.mts.map +1 -1
  79. package/pagination.d.ts +1 -0
  80. package/pagination.d.ts.map +1 -1
  81. package/pagination.mjs +1 -0
  82. package/pagination.mjs.map +1 -1
  83. package/resource.d.mts +1 -0
  84. package/resource.d.mts.map +1 -1
  85. package/resource.d.ts +1 -0
  86. package/resource.d.ts.map +1 -1
  87. package/resource.mjs +1 -0
  88. package/resource.mjs.map +1 -1
  89. package/resources/admin/admin.d.mts +2 -2
  90. package/resources/admin/admin.d.mts.map +1 -1
  91. package/resources/admin/admin.d.ts +2 -2
  92. package/resources/admin/admin.d.ts.map +1 -1
  93. package/resources/admin/admin.js.map +1 -1
  94. package/resources/admin/admin.mjs.map +1 -1
  95. package/resources/admin/api-keys.d.mts.map +1 -1
  96. package/resources/admin/api-keys.d.ts.map +1 -1
  97. package/resources/admin/api-keys.mjs.map +1 -1
  98. package/resources/admin/index.d.mts +1 -1
  99. package/resources/admin/index.d.mts.map +1 -1
  100. package/resources/admin/index.d.ts +1 -1
  101. package/resources/admin/index.d.ts.map +1 -1
  102. package/resources/admin/index.js.map +1 -1
  103. package/resources/admin/index.mjs.map +1 -1
  104. package/resources/admin/usage.d.mts.map +1 -1
  105. package/resources/admin/usage.d.ts.map +1 -1
  106. package/resources/admin/usage.mjs.map +1 -1
  107. package/resources/admin/workspaces.d.mts +94 -1
  108. package/resources/admin/workspaces.d.mts.map +1 -1
  109. package/resources/admin/workspaces.d.ts +94 -1
  110. package/resources/admin/workspaces.d.ts.map +1 -1
  111. package/resources/admin/workspaces.js +15 -0
  112. package/resources/admin/workspaces.js.map +1 -1
  113. package/resources/admin/workspaces.mjs +15 -0
  114. package/resources/admin/workspaces.mjs.map +1 -1
  115. package/resources/admin.d.mts.map +1 -1
  116. package/resources/admin.d.ts.map +1 -1
  117. package/resources/admin.mjs.map +1 -1
  118. package/resources/auth.d.mts.map +1 -1
  119. package/resources/auth.d.ts.map +1 -1
  120. package/resources/auth.mjs.map +1 -1
  121. package/resources/cli.d.mts.map +1 -1
  122. package/resources/cli.d.ts.map +1 -1
  123. package/resources/cli.mjs.map +1 -1
  124. package/resources/index.d.mts.map +1 -1
  125. package/resources/index.d.ts.map +1 -1
  126. package/resources/index.mjs.map +1 -1
  127. package/resources/predictions/adme.d.mts +539 -0
  128. package/resources/predictions/adme.d.mts.map +1 -0
  129. package/resources/predictions/adme.d.ts +539 -0
  130. package/resources/predictions/adme.d.ts.map +1 -0
  131. package/resources/predictions/adme.js +72 -0
  132. package/resources/predictions/adme.js.map +1 -0
  133. package/resources/predictions/adme.mjs +68 -0
  134. package/resources/predictions/adme.mjs.map +1 -0
  135. package/resources/predictions/index.d.mts +1 -0
  136. package/resources/predictions/index.d.mts.map +1 -1
  137. package/resources/predictions/index.d.ts +1 -0
  138. package/resources/predictions/index.d.ts.map +1 -1
  139. package/resources/predictions/index.js +3 -1
  140. package/resources/predictions/index.js.map +1 -1
  141. package/resources/predictions/index.mjs +1 -0
  142. package/resources/predictions/index.mjs.map +1 -1
  143. package/resources/predictions/predictions.d.mts +4 -0
  144. package/resources/predictions/predictions.d.mts.map +1 -1
  145. package/resources/predictions/predictions.d.ts +4 -0
  146. package/resources/predictions/predictions.d.ts.map +1 -1
  147. package/resources/predictions/predictions.js +4 -0
  148. package/resources/predictions/predictions.js.map +1 -1
  149. package/resources/predictions/predictions.mjs +4 -0
  150. package/resources/predictions/predictions.mjs.map +1 -1
  151. package/resources/predictions/structure-and-binding.d.mts.map +1 -1
  152. package/resources/predictions/structure-and-binding.d.ts.map +1 -1
  153. package/resources/predictions/structure-and-binding.mjs.map +1 -1
  154. package/resources/predictions.d.mts.map +1 -1
  155. package/resources/predictions.d.ts.map +1 -1
  156. package/resources/predictions.mjs.map +1 -1
  157. package/resources/protein/design.d.mts +85 -15
  158. package/resources/protein/design.d.mts.map +1 -1
  159. package/resources/protein/design.d.ts +85 -15
  160. package/resources/protein/design.d.ts.map +1 -1
  161. package/resources/protein/design.mjs.map +1 -1
  162. package/resources/protein/index.d.mts.map +1 -1
  163. package/resources/protein/index.d.ts.map +1 -1
  164. package/resources/protein/index.mjs.map +1 -1
  165. package/resources/protein/library-screen.d.mts +85 -15
  166. package/resources/protein/library-screen.d.mts.map +1 -1
  167. package/resources/protein/library-screen.d.ts +85 -15
  168. package/resources/protein/library-screen.d.ts.map +1 -1
  169. package/resources/protein/library-screen.mjs.map +1 -1
  170. package/resources/protein/protein.d.mts.map +1 -1
  171. package/resources/protein/protein.d.ts.map +1 -1
  172. package/resources/protein/protein.mjs.map +1 -1
  173. package/resources/protein.d.mts.map +1 -1
  174. package/resources/protein.d.ts.map +1 -1
  175. package/resources/protein.mjs.map +1 -1
  176. package/resources/small-molecule/design.d.mts +21 -0
  177. package/resources/small-molecule/design.d.mts.map +1 -1
  178. package/resources/small-molecule/design.d.ts +21 -0
  179. package/resources/small-molecule/design.d.ts.map +1 -1
  180. package/resources/small-molecule/design.mjs.map +1 -1
  181. package/resources/small-molecule/index.d.mts.map +1 -1
  182. package/resources/small-molecule/index.d.ts.map +1 -1
  183. package/resources/small-molecule/index.mjs.map +1 -1
  184. package/resources/small-molecule/library-screen.d.mts +21 -0
  185. package/resources/small-molecule/library-screen.d.mts.map +1 -1
  186. package/resources/small-molecule/library-screen.d.ts +21 -0
  187. package/resources/small-molecule/library-screen.d.ts.map +1 -1
  188. package/resources/small-molecule/library-screen.mjs.map +1 -1
  189. package/resources/small-molecule/small-molecule.d.mts.map +1 -1
  190. package/resources/small-molecule/small-molecule.d.ts.map +1 -1
  191. package/resources/small-molecule/small-molecule.mjs.map +1 -1
  192. package/resources/small-molecule.d.mts.map +1 -1
  193. package/resources/small-molecule.d.ts.map +1 -1
  194. package/resources/small-molecule.mjs.map +1 -1
  195. package/resources.d.mts.map +1 -1
  196. package/resources.d.ts.map +1 -1
  197. package/resources.mjs.map +1 -1
  198. package/src/resources/admin/admin.ts +6 -0
  199. package/src/resources/admin/index.ts +3 -0
  200. package/src/resources/admin/workspaces.ts +131 -1
  201. package/src/resources/predictions/adme.ts +682 -0
  202. package/src/resources/predictions/index.ts +11 -0
  203. package/src/resources/predictions/predictions.ts +26 -0
  204. package/src/resources/protein/design.ts +85 -15
  205. package/src/resources/protein/library-screen.ts +85 -15
  206. package/src/resources/small-molecule/design.ts +25 -0
  207. package/src/resources/small-molecule/library-screen.ts +25 -0
  208. package/src/version.ts +1 -1
  209. package/uploads.d.mts +1 -0
  210. package/uploads.d.mts.map +1 -1
  211. package/uploads.d.ts +1 -0
  212. package/uploads.d.ts.map +1 -1
  213. package/uploads.mjs +1 -0
  214. package/uploads.mjs.map +1 -1
  215. package/version.d.mts +1 -1
  216. package/version.d.ts +1 -1
  217. package/version.js +1 -1
  218. package/version.mjs +1 -1
@@ -1,6 +1,18 @@
1
1
  // File generated from our OpenAPI spec by Stainless. See CONTRIBUTING.md for details.
2
2
 
3
3
  import { APIResource } from '../../core/resource';
4
+ import * as AdmeAPI from './adme';
5
+ import {
6
+ Adme,
7
+ AdmeDeleteDataResponse,
8
+ AdmeListParams,
9
+ AdmeListResponse,
10
+ AdmeListResponsesCursorPage,
11
+ AdmeRetrieveParams,
12
+ AdmeRetrieveResponse,
13
+ AdmeStartParams,
14
+ AdmeStartResponse,
15
+ } from './adme';
4
16
  import * as StructureAndBindingAPI from './structure-and-binding';
5
17
  import {
6
18
  StructureAndBinding,
@@ -22,9 +34,11 @@ import {
22
34
  export class Predictions extends APIResource {
23
35
  structureAndBinding: StructureAndBindingAPI.StructureAndBinding =
24
36
  new StructureAndBindingAPI.StructureAndBinding(this._client);
37
+ adme: AdmeAPI.Adme = new AdmeAPI.Adme(this._client);
25
38
  }
26
39
 
27
40
  Predictions.StructureAndBinding = StructureAndBinding;
41
+ Predictions.Adme = Adme;
28
42
 
29
43
  export declare namespace Predictions {
30
44
  export {
@@ -40,4 +54,16 @@ export declare namespace Predictions {
40
54
  type StructureAndBindingEstimateCostParams as StructureAndBindingEstimateCostParams,
41
55
  type StructureAndBindingStartParams as StructureAndBindingStartParams,
42
56
  };
57
+
58
+ export {
59
+ Adme as Adme,
60
+ type AdmeRetrieveResponse as AdmeRetrieveResponse,
61
+ type AdmeListResponse as AdmeListResponse,
62
+ type AdmeDeleteDataResponse as AdmeDeleteDataResponse,
63
+ type AdmeStartResponse as AdmeStartResponse,
64
+ type AdmeListResponsesCursorPage as AdmeListResponsesCursorPage,
65
+ type AdmeRetrieveParams as AdmeRetrieveParams,
66
+ type AdmeListParams as AdmeListParams,
67
+ type AdmeStartParams as AdmeStartParams,
68
+ };
43
69
  }
@@ -962,7 +962,7 @@ export namespace DesignRetrieveResponse {
962
962
  * Chains selected from the uploaded structure, keyed by chain ID. Only chains
963
963
  * listed here are included in the engine run — any chains omitted from this
964
964
  * mapping are ignored. Each value defines which residues to keep, which are
965
- * epitope residues, and which are flexible.
965
+ * epitope residues, which are non-binding residues, and which are flexible.
966
966
  */
967
967
  chain_selection: {
968
968
  [key: string]:
@@ -991,7 +991,8 @@ export namespace DesignRetrieveResponse {
991
991
 
992
992
  /**
993
993
  * 0-indexed residue indices where binder contact is desired (the epitope). All
994
- * indices must be present in crop_residues.
994
+ * indices must be present in crop_residues and must not overlap
995
+ * non_binding_residues.
995
996
  */
996
997
  epitope_residues?: Array<number>;
997
998
 
@@ -1000,6 +1001,12 @@ export namespace DesignRetrieveResponse {
1000
1001
  * regions). All indices must be present in crop_residues.
1001
1002
  */
1002
1003
  flexible_residues?: Array<number>;
1004
+
1005
+ /**
1006
+ * 0-indexed residue indices where binder contact should be discouraged. All
1007
+ * indices must be present in crop_residues and must not overlap epitope_residues.
1008
+ */
1009
+ non_binding_residues?: Array<number>;
1003
1010
  }
1004
1011
 
1005
1012
  /**
@@ -1063,9 +1070,16 @@ export namespace DesignRetrieveResponse {
1063
1070
  /**
1064
1071
  * Polymer chain residues where binder contact is desired (the epitope). Each key
1065
1072
  * is a chain ID of a polymer entity, each value is an array of 0-indexed residue
1066
- * indices.
1073
+ * indices. Residues must not overlap non_binding_residues on the same chain.
1067
1074
  */
1068
1075
  epitope_residues?: { [key: string]: Array<number> };
1076
+
1077
+ /**
1078
+ * Polymer chain residues where binder contact should be discouraged. Each key is a
1079
+ * chain ID of a polymer entity, each value is an array of 0-indexed residue
1080
+ * indices. Residues must not overlap epitope_residues on the same chain.
1081
+ */
1082
+ non_binding_residues?: { [key: string]: Array<number> };
1069
1083
  }
1070
1084
 
1071
1085
  export namespace NoTemplateTargetResponse {
@@ -2769,7 +2783,7 @@ export namespace DesignStartResponse {
2769
2783
  * Chains selected from the uploaded structure, keyed by chain ID. Only chains
2770
2784
  * listed here are included in the engine run — any chains omitted from this
2771
2785
  * mapping are ignored. Each value defines which residues to keep, which are
2772
- * epitope residues, and which are flexible.
2786
+ * epitope residues, which are non-binding residues, and which are flexible.
2773
2787
  */
2774
2788
  chain_selection: {
2775
2789
  [key: string]:
@@ -2798,7 +2812,8 @@ export namespace DesignStartResponse {
2798
2812
 
2799
2813
  /**
2800
2814
  * 0-indexed residue indices where binder contact is desired (the epitope). All
2801
- * indices must be present in crop_residues.
2815
+ * indices must be present in crop_residues and must not overlap
2816
+ * non_binding_residues.
2802
2817
  */
2803
2818
  epitope_residues?: Array<number>;
2804
2819
 
@@ -2807,6 +2822,12 @@ export namespace DesignStartResponse {
2807
2822
  * regions). All indices must be present in crop_residues.
2808
2823
  */
2809
2824
  flexible_residues?: Array<number>;
2825
+
2826
+ /**
2827
+ * 0-indexed residue indices where binder contact should be discouraged. All
2828
+ * indices must be present in crop_residues and must not overlap epitope_residues.
2829
+ */
2830
+ non_binding_residues?: Array<number>;
2810
2831
  }
2811
2832
 
2812
2833
  /**
@@ -2870,9 +2891,16 @@ export namespace DesignStartResponse {
2870
2891
  /**
2871
2892
  * Polymer chain residues where binder contact is desired (the epitope). Each key
2872
2893
  * is a chain ID of a polymer entity, each value is an array of 0-indexed residue
2873
- * indices.
2894
+ * indices. Residues must not overlap non_binding_residues on the same chain.
2874
2895
  */
2875
2896
  epitope_residues?: { [key: string]: Array<number> };
2897
+
2898
+ /**
2899
+ * Polymer chain residues where binder contact should be discouraged. Each key is a
2900
+ * chain ID of a polymer entity, each value is an array of 0-indexed residue
2901
+ * indices. Residues must not overlap epitope_residues on the same chain.
2902
+ */
2903
+ non_binding_residues?: { [key: string]: Array<number> };
2876
2904
  }
2877
2905
 
2878
2906
  export namespace NoTemplateTargetResponse {
@@ -4103,7 +4131,7 @@ export namespace DesignStopResponse {
4103
4131
  * Chains selected from the uploaded structure, keyed by chain ID. Only chains
4104
4132
  * listed here are included in the engine run — any chains omitted from this
4105
4133
  * mapping are ignored. Each value defines which residues to keep, which are
4106
- * epitope residues, and which are flexible.
4134
+ * epitope residues, which are non-binding residues, and which are flexible.
4107
4135
  */
4108
4136
  chain_selection: {
4109
4137
  [key: string]:
@@ -4132,7 +4160,8 @@ export namespace DesignStopResponse {
4132
4160
 
4133
4161
  /**
4134
4162
  * 0-indexed residue indices where binder contact is desired (the epitope). All
4135
- * indices must be present in crop_residues.
4163
+ * indices must be present in crop_residues and must not overlap
4164
+ * non_binding_residues.
4136
4165
  */
4137
4166
  epitope_residues?: Array<number>;
4138
4167
 
@@ -4141,6 +4170,12 @@ export namespace DesignStopResponse {
4141
4170
  * regions). All indices must be present in crop_residues.
4142
4171
  */
4143
4172
  flexible_residues?: Array<number>;
4173
+
4174
+ /**
4175
+ * 0-indexed residue indices where binder contact should be discouraged. All
4176
+ * indices must be present in crop_residues and must not overlap epitope_residues.
4177
+ */
4178
+ non_binding_residues?: Array<number>;
4144
4179
  }
4145
4180
 
4146
4181
  /**
@@ -4204,9 +4239,16 @@ export namespace DesignStopResponse {
4204
4239
  /**
4205
4240
  * Polymer chain residues where binder contact is desired (the epitope). Each key
4206
4241
  * is a chain ID of a polymer entity, each value is an array of 0-indexed residue
4207
- * indices.
4242
+ * indices. Residues must not overlap non_binding_residues on the same chain.
4208
4243
  */
4209
4244
  epitope_residues?: { [key: string]: Array<number> };
4245
+
4246
+ /**
4247
+ * Polymer chain residues where binder contact should be discouraged. Each key is a
4248
+ * chain ID of a polymer entity, each value is an array of 0-indexed residue
4249
+ * indices. Residues must not overlap epitope_residues on the same chain.
4250
+ */
4251
+ non_binding_residues?: { [key: string]: Array<number> };
4210
4252
  }
4211
4253
 
4212
4254
  export namespace NoTemplateTargetResponse {
@@ -5374,7 +5416,7 @@ export namespace DesignEstimateCostParams {
5374
5416
  * Chains selected from the uploaded structure, keyed by chain ID. Only chains
5375
5417
  * listed here are included in the engine run — any chains omitted from this
5376
5418
  * mapping are ignored. Each value defines which residues to keep, which are
5377
- * epitope residues, and which are flexible.
5419
+ * epitope residues, which are non-binding residues, and which are flexible.
5378
5420
  */
5379
5421
  chain_selection: {
5380
5422
  [key: string]:
@@ -5407,7 +5449,8 @@ export namespace DesignEstimateCostParams {
5407
5449
 
5408
5450
  /**
5409
5451
  * 0-indexed residue indices where binder contact is desired (the epitope). All
5410
- * indices must be present in crop_residues.
5452
+ * indices must be present in crop_residues and must not overlap
5453
+ * non_binding_residues.
5411
5454
  */
5412
5455
  epitope_residues?: Array<number>;
5413
5456
 
@@ -5416,6 +5459,12 @@ export namespace DesignEstimateCostParams {
5416
5459
  * regions). All indices must be present in crop_residues.
5417
5460
  */
5418
5461
  flexible_residues?: Array<number>;
5462
+
5463
+ /**
5464
+ * 0-indexed residue indices where binder contact should be discouraged. All
5465
+ * indices must be present in crop_residues and must not overlap epitope_residues.
5466
+ */
5467
+ non_binding_residues?: Array<number>;
5419
5468
  }
5420
5469
 
5421
5470
  /**
@@ -5485,9 +5534,16 @@ export namespace DesignEstimateCostParams {
5485
5534
  /**
5486
5535
  * Polymer chain residues where binder contact is desired (the epitope). Each key
5487
5536
  * is a chain ID of a polymer entity, each value is an array of 0-indexed residue
5488
- * indices.
5537
+ * indices. Residues must not overlap non_binding_residues on the same chain.
5489
5538
  */
5490
5539
  epitope_residues?: { [key: string]: Array<number> };
5540
+
5541
+ /**
5542
+ * Polymer chain residues where binder contact should be discouraged. Each key is a
5543
+ * chain ID of a polymer entity, each value is an array of 0-indexed residue
5544
+ * indices. Residues must not overlap epitope_residues on the same chain.
5545
+ */
5546
+ non_binding_residues?: { [key: string]: Array<number> };
5491
5547
  }
5492
5548
 
5493
5549
  export namespace NoTemplateTarget {
@@ -6618,7 +6674,7 @@ export namespace DesignStartParams {
6618
6674
  * Chains selected from the uploaded structure, keyed by chain ID. Only chains
6619
6675
  * listed here are included in the engine run — any chains omitted from this
6620
6676
  * mapping are ignored. Each value defines which residues to keep, which are
6621
- * epitope residues, and which are flexible.
6677
+ * epitope residues, which are non-binding residues, and which are flexible.
6622
6678
  */
6623
6679
  chain_selection: {
6624
6680
  [key: string]:
@@ -6651,7 +6707,8 @@ export namespace DesignStartParams {
6651
6707
 
6652
6708
  /**
6653
6709
  * 0-indexed residue indices where binder contact is desired (the epitope). All
6654
- * indices must be present in crop_residues.
6710
+ * indices must be present in crop_residues and must not overlap
6711
+ * non_binding_residues.
6655
6712
  */
6656
6713
  epitope_residues?: Array<number>;
6657
6714
 
@@ -6660,6 +6717,12 @@ export namespace DesignStartParams {
6660
6717
  * regions). All indices must be present in crop_residues.
6661
6718
  */
6662
6719
  flexible_residues?: Array<number>;
6720
+
6721
+ /**
6722
+ * 0-indexed residue indices where binder contact should be discouraged. All
6723
+ * indices must be present in crop_residues and must not overlap epitope_residues.
6724
+ */
6725
+ non_binding_residues?: Array<number>;
6663
6726
  }
6664
6727
 
6665
6728
  /**
@@ -6729,9 +6792,16 @@ export namespace DesignStartParams {
6729
6792
  /**
6730
6793
  * Polymer chain residues where binder contact is desired (the epitope). Each key
6731
6794
  * is a chain ID of a polymer entity, each value is an array of 0-indexed residue
6732
- * indices.
6795
+ * indices. Residues must not overlap non_binding_residues on the same chain.
6733
6796
  */
6734
6797
  epitope_residues?: { [key: string]: Array<number> };
6798
+
6799
+ /**
6800
+ * Polymer chain residues where binder contact should be discouraged. Each key is a
6801
+ * chain ID of a polymer entity, each value is an array of 0-indexed residue
6802
+ * indices. Residues must not overlap epitope_residues on the same chain.
6803
+ */
6804
+ non_binding_residues?: { [key: string]: Array<number> };
6735
6805
  }
6736
6806
 
6737
6807
  export namespace NoTemplateTarget {
@@ -300,7 +300,7 @@ export namespace LibraryScreenRetrieveResponse {
300
300
  * Chains selected from the uploaded structure, keyed by chain ID. Only chains
301
301
  * listed here are included in the engine run — any chains omitted from this
302
302
  * mapping are ignored. Each value defines which residues to keep, which are
303
- * epitope residues, and which are flexible.
303
+ * epitope residues, which are non-binding residues, and which are flexible.
304
304
  */
305
305
  chain_selection: {
306
306
  [key: string]:
@@ -329,7 +329,8 @@ export namespace LibraryScreenRetrieveResponse {
329
329
 
330
330
  /**
331
331
  * 0-indexed residue indices where binder contact is desired (the epitope). All
332
- * indices must be present in crop_residues.
332
+ * indices must be present in crop_residues and must not overlap
333
+ * non_binding_residues.
333
334
  */
334
335
  epitope_residues?: Array<number>;
335
336
 
@@ -338,6 +339,12 @@ export namespace LibraryScreenRetrieveResponse {
338
339
  * regions). All indices must be present in crop_residues.
339
340
  */
340
341
  flexible_residues?: Array<number>;
342
+
343
+ /**
344
+ * 0-indexed residue indices where binder contact should be discouraged. All
345
+ * indices must be present in crop_residues and must not overlap epitope_residues.
346
+ */
347
+ non_binding_residues?: Array<number>;
341
348
  }
342
349
 
343
350
  /**
@@ -401,9 +408,16 @@ export namespace LibraryScreenRetrieveResponse {
401
408
  /**
402
409
  * Polymer chain residues where binder contact is desired (the epitope). Each key
403
410
  * is a chain ID of a polymer entity, each value is an array of 0-indexed residue
404
- * indices.
411
+ * indices. Residues must not overlap non_binding_residues on the same chain.
405
412
  */
406
413
  epitope_residues?: { [key: string]: Array<number> };
414
+
415
+ /**
416
+ * Polymer chain residues where binder contact should be discouraged. Each key is a
417
+ * chain ID of a polymer entity, each value is an array of 0-indexed residue
418
+ * indices. Residues must not overlap epitope_residues on the same chain.
419
+ */
420
+ non_binding_residues?: { [key: string]: Array<number> };
407
421
  }
408
422
 
409
423
  export namespace NoTemplateTargetResponse {
@@ -1455,7 +1469,7 @@ export namespace LibraryScreenStartResponse {
1455
1469
  * Chains selected from the uploaded structure, keyed by chain ID. Only chains
1456
1470
  * listed here are included in the engine run — any chains omitted from this
1457
1471
  * mapping are ignored. Each value defines which residues to keep, which are
1458
- * epitope residues, and which are flexible.
1472
+ * epitope residues, which are non-binding residues, and which are flexible.
1459
1473
  */
1460
1474
  chain_selection: {
1461
1475
  [key: string]:
@@ -1484,7 +1498,8 @@ export namespace LibraryScreenStartResponse {
1484
1498
 
1485
1499
  /**
1486
1500
  * 0-indexed residue indices where binder contact is desired (the epitope). All
1487
- * indices must be present in crop_residues.
1501
+ * indices must be present in crop_residues and must not overlap
1502
+ * non_binding_residues.
1488
1503
  */
1489
1504
  epitope_residues?: Array<number>;
1490
1505
 
@@ -1493,6 +1508,12 @@ export namespace LibraryScreenStartResponse {
1493
1508
  * regions). All indices must be present in crop_residues.
1494
1509
  */
1495
1510
  flexible_residues?: Array<number>;
1511
+
1512
+ /**
1513
+ * 0-indexed residue indices where binder contact should be discouraged. All
1514
+ * indices must be present in crop_residues and must not overlap epitope_residues.
1515
+ */
1516
+ non_binding_residues?: Array<number>;
1496
1517
  }
1497
1518
 
1498
1519
  /**
@@ -1556,9 +1577,16 @@ export namespace LibraryScreenStartResponse {
1556
1577
  /**
1557
1578
  * Polymer chain residues where binder contact is desired (the epitope). Each key
1558
1579
  * is a chain ID of a polymer entity, each value is an array of 0-indexed residue
1559
- * indices.
1580
+ * indices. Residues must not overlap non_binding_residues on the same chain.
1560
1581
  */
1561
1582
  epitope_residues?: { [key: string]: Array<number> };
1583
+
1584
+ /**
1585
+ * Polymer chain residues where binder contact should be discouraged. Each key is a
1586
+ * chain ID of a polymer entity, each value is an array of 0-indexed residue
1587
+ * indices. Residues must not overlap epitope_residues on the same chain.
1588
+ */
1589
+ non_binding_residues?: { [key: string]: Array<number> };
1562
1590
  }
1563
1591
 
1564
1592
  export namespace NoTemplateTargetResponse {
@@ -2127,7 +2155,7 @@ export namespace LibraryScreenStopResponse {
2127
2155
  * Chains selected from the uploaded structure, keyed by chain ID. Only chains
2128
2156
  * listed here are included in the engine run — any chains omitted from this
2129
2157
  * mapping are ignored. Each value defines which residues to keep, which are
2130
- * epitope residues, and which are flexible.
2158
+ * epitope residues, which are non-binding residues, and which are flexible.
2131
2159
  */
2132
2160
  chain_selection: {
2133
2161
  [key: string]:
@@ -2156,7 +2184,8 @@ export namespace LibraryScreenStopResponse {
2156
2184
 
2157
2185
  /**
2158
2186
  * 0-indexed residue indices where binder contact is desired (the epitope). All
2159
- * indices must be present in crop_residues.
2187
+ * indices must be present in crop_residues and must not overlap
2188
+ * non_binding_residues.
2160
2189
  */
2161
2190
  epitope_residues?: Array<number>;
2162
2191
 
@@ -2165,6 +2194,12 @@ export namespace LibraryScreenStopResponse {
2165
2194
  * regions). All indices must be present in crop_residues.
2166
2195
  */
2167
2196
  flexible_residues?: Array<number>;
2197
+
2198
+ /**
2199
+ * 0-indexed residue indices where binder contact should be discouraged. All
2200
+ * indices must be present in crop_residues and must not overlap epitope_residues.
2201
+ */
2202
+ non_binding_residues?: Array<number>;
2168
2203
  }
2169
2204
 
2170
2205
  /**
@@ -2228,9 +2263,16 @@ export namespace LibraryScreenStopResponse {
2228
2263
  /**
2229
2264
  * Polymer chain residues where binder contact is desired (the epitope). Each key
2230
2265
  * is a chain ID of a polymer entity, each value is an array of 0-indexed residue
2231
- * indices.
2266
+ * indices. Residues must not overlap non_binding_residues on the same chain.
2232
2267
  */
2233
2268
  epitope_residues?: { [key: string]: Array<number> };
2269
+
2270
+ /**
2271
+ * Polymer chain residues where binder contact should be discouraged. Each key is a
2272
+ * chain ID of a polymer entity, each value is an array of 0-indexed residue
2273
+ * indices. Residues must not overlap epitope_residues on the same chain.
2274
+ */
2275
+ non_binding_residues?: { [key: string]: Array<number> };
2234
2276
  }
2235
2277
 
2236
2278
  export namespace NoTemplateTargetResponse {
@@ -2955,7 +2997,7 @@ export namespace LibraryScreenEstimateCostParams {
2955
2997
  * Chains selected from the uploaded structure, keyed by chain ID. Only chains
2956
2998
  * listed here are included in the engine run — any chains omitted from this
2957
2999
  * mapping are ignored. Each value defines which residues to keep, which are
2958
- * epitope residues, and which are flexible.
3000
+ * epitope residues, which are non-binding residues, and which are flexible.
2959
3001
  */
2960
3002
  chain_selection: {
2961
3003
  [key: string]:
@@ -2988,7 +3030,8 @@ export namespace LibraryScreenEstimateCostParams {
2988
3030
 
2989
3031
  /**
2990
3032
  * 0-indexed residue indices where binder contact is desired (the epitope). All
2991
- * indices must be present in crop_residues.
3033
+ * indices must be present in crop_residues and must not overlap
3034
+ * non_binding_residues.
2992
3035
  */
2993
3036
  epitope_residues?: Array<number>;
2994
3037
 
@@ -2997,6 +3040,12 @@ export namespace LibraryScreenEstimateCostParams {
2997
3040
  * regions). All indices must be present in crop_residues.
2998
3041
  */
2999
3042
  flexible_residues?: Array<number>;
3043
+
3044
+ /**
3045
+ * 0-indexed residue indices where binder contact should be discouraged. All
3046
+ * indices must be present in crop_residues and must not overlap epitope_residues.
3047
+ */
3048
+ non_binding_residues?: Array<number>;
3000
3049
  }
3001
3050
 
3002
3051
  /**
@@ -3066,9 +3115,16 @@ export namespace LibraryScreenEstimateCostParams {
3066
3115
  /**
3067
3116
  * Polymer chain residues where binder contact is desired (the epitope). Each key
3068
3117
  * is a chain ID of a polymer entity, each value is an array of 0-indexed residue
3069
- * indices.
3118
+ * indices. Residues must not overlap non_binding_residues on the same chain.
3070
3119
  */
3071
3120
  epitope_residues?: { [key: string]: Array<number> };
3121
+
3122
+ /**
3123
+ * Polymer chain residues where binder contact should be discouraged. Each key is a
3124
+ * chain ID of a polymer entity, each value is an array of 0-indexed residue
3125
+ * indices. Residues must not overlap epitope_residues on the same chain.
3126
+ */
3127
+ non_binding_residues?: { [key: string]: Array<number> };
3072
3128
  }
3073
3129
 
3074
3130
  export namespace NoTemplateTarget {
@@ -3749,7 +3805,7 @@ export namespace LibraryScreenStartParams {
3749
3805
  * Chains selected from the uploaded structure, keyed by chain ID. Only chains
3750
3806
  * listed here are included in the engine run — any chains omitted from this
3751
3807
  * mapping are ignored. Each value defines which residues to keep, which are
3752
- * epitope residues, and which are flexible.
3808
+ * epitope residues, which are non-binding residues, and which are flexible.
3753
3809
  */
3754
3810
  chain_selection: {
3755
3811
  [key: string]:
@@ -3782,7 +3838,8 @@ export namespace LibraryScreenStartParams {
3782
3838
 
3783
3839
  /**
3784
3840
  * 0-indexed residue indices where binder contact is desired (the epitope). All
3785
- * indices must be present in crop_residues.
3841
+ * indices must be present in crop_residues and must not overlap
3842
+ * non_binding_residues.
3786
3843
  */
3787
3844
  epitope_residues?: Array<number>;
3788
3845
 
@@ -3791,6 +3848,12 @@ export namespace LibraryScreenStartParams {
3791
3848
  * regions). All indices must be present in crop_residues.
3792
3849
  */
3793
3850
  flexible_residues?: Array<number>;
3851
+
3852
+ /**
3853
+ * 0-indexed residue indices where binder contact should be discouraged. All
3854
+ * indices must be present in crop_residues and must not overlap epitope_residues.
3855
+ */
3856
+ non_binding_residues?: Array<number>;
3794
3857
  }
3795
3858
 
3796
3859
  /**
@@ -3860,9 +3923,16 @@ export namespace LibraryScreenStartParams {
3860
3923
  /**
3861
3924
  * Polymer chain residues where binder contact is desired (the epitope). Each key
3862
3925
  * is a chain ID of a polymer entity, each value is an array of 0-indexed residue
3863
- * indices.
3926
+ * indices. Residues must not overlap non_binding_residues on the same chain.
3864
3927
  */
3865
3928
  epitope_residues?: { [key: string]: Array<number> };
3929
+
3930
+ /**
3931
+ * Polymer chain residues where binder contact should be discouraged. Each key is a
3932
+ * chain ID of a polymer entity, each value is an array of 0-indexed residue
3933
+ * indices. Residues must not overlap epitope_residues on the same chain.
3934
+ */
3935
+ non_binding_residues?: { [key: string]: Array<number> };
3866
3936
  }
3867
3937
 
3868
3938
  export namespace NoTemplateTarget {
@@ -1127,6 +1127,11 @@ export interface DesignListResultsResponse {
1127
1127
  */
1128
1128
  smiles: string;
1129
1129
 
1130
+ /**
1131
+ * Tier 1 ADME summary values for this molecule.
1132
+ */
1133
+ adme?: DesignListResultsResponse.Adme;
1134
+
1130
1135
  /**
1131
1136
  * Warnings about potential quality issues with this result.
1132
1137
  */
@@ -1210,6 +1215,26 @@ export namespace DesignListResultsResponse {
1210
1215
  structure_confidence: number;
1211
1216
  }
1212
1217
 
1218
+ /**
1219
+ * Tier 1 ADME summary values for this molecule.
1220
+ */
1221
+ export interface Adme {
1222
+ /**
1223
+ * Lipophilicity score from the internal LogD prediction.
1224
+ */
1225
+ lipophilicity: number;
1226
+
1227
+ /**
1228
+ * Permeability score for this molecule.
1229
+ */
1230
+ permeability: number;
1231
+
1232
+ /**
1233
+ * Solubility judgement for this molecule.
1234
+ */
1235
+ solubility: 'high-confidence' | 'medium-confidence' | 'high-risk';
1236
+ }
1237
+
1213
1238
  /**
1214
1239
  * A warning about a potential quality issue with a result
1215
1240
  */
@@ -1161,6 +1161,11 @@ export interface LibraryScreenListResultsResponse {
1161
1161
  */
1162
1162
  smiles: string;
1163
1163
 
1164
+ /**
1165
+ * Tier 1 ADME summary values for this molecule.
1166
+ */
1167
+ adme?: LibraryScreenListResultsResponse.Adme;
1168
+
1164
1169
  /**
1165
1170
  * Client-provided identifier for this molecule, if provided
1166
1171
  */
@@ -1249,6 +1254,26 @@ export namespace LibraryScreenListResultsResponse {
1249
1254
  structure_confidence: number;
1250
1255
  }
1251
1256
 
1257
+ /**
1258
+ * Tier 1 ADME summary values for this molecule.
1259
+ */
1260
+ export interface Adme {
1261
+ /**
1262
+ * Lipophilicity score from the internal LogD prediction.
1263
+ */
1264
+ lipophilicity: number;
1265
+
1266
+ /**
1267
+ * Permeability score for this molecule.
1268
+ */
1269
+ permeability: number;
1270
+
1271
+ /**
1272
+ * Solubility judgement for this molecule.
1273
+ */
1274
+ solubility: 'high-confidence' | 'medium-confidence' | 'high-risk';
1275
+ }
1276
+
1252
1277
  /**
1253
1278
  * A warning about a potential quality issue with a result
1254
1279
  */
package/src/version.ts CHANGED
@@ -1 +1 @@
1
- export const VERSION = '0.30.4'; // x-release-please-version
1
+ export const VERSION = '0.35.2'; // x-release-please-version
package/uploads.d.mts CHANGED
@@ -1,2 +1,3 @@
1
+ /** @deprecated Import from ./core/uploads instead */
1
2
  export * from "./core/uploads.mjs";
2
3
  //# sourceMappingURL=uploads.d.mts.map
package/uploads.d.mts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"uploads.d.mts","sourceRoot":"","sources":["src/uploads.ts"],"names":[],"mappings":""}
1
+ {"version":3,"file":"uploads.d.mts","sourceRoot":"","sources":["src/uploads.ts"],"names":[],"mappings":"AAAA,qDAAqD;AACrD,mCAA+B"}
package/uploads.d.ts CHANGED
@@ -1,2 +1,3 @@
1
+ /** @deprecated Import from ./core/uploads instead */
1
2
  export * from "./core/uploads.js";
2
3
  //# sourceMappingURL=uploads.d.ts.map
package/uploads.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"uploads.d.ts","sourceRoot":"","sources":["src/uploads.ts"],"names":[],"mappings":""}
1
+ {"version":3,"file":"uploads.d.ts","sourceRoot":"","sources":["src/uploads.ts"],"names":[],"mappings":"AAAA,qDAAqD;AACrD,kCAA+B"}
package/uploads.mjs CHANGED
@@ -1,2 +1,3 @@
1
+ /** @deprecated Import from ./core/uploads instead */
1
2
  export * from "./core/uploads.mjs";
2
3
  //# sourceMappingURL=uploads.mjs.map
package/uploads.mjs.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"uploads.mjs","sourceRoot":"","sources":["src/uploads.ts"],"names":[],"mappings":""}
1
+ {"version":3,"file":"uploads.mjs","sourceRoot":"","sources":["src/uploads.ts"],"names":[],"mappings":"AAAA,qDAAqD;AACrD,mCAA+B"}
package/version.d.mts CHANGED
@@ -1,2 +1,2 @@
1
- export declare const VERSION = "0.30.4";
1
+ export declare const VERSION = "0.35.2";
2
2
  //# sourceMappingURL=version.d.mts.map
package/version.d.ts CHANGED
@@ -1,2 +1,2 @@
1
- export declare const VERSION = "0.30.4";
1
+ export declare const VERSION = "0.35.2";
2
2
  //# sourceMappingURL=version.d.ts.map
package/version.js CHANGED
@@ -1,5 +1,5 @@
1
1
  "use strict";
2
2
  Object.defineProperty(exports, "__esModule", { value: true });
3
3
  exports.VERSION = void 0;
4
- exports.VERSION = '0.30.4'; // x-release-please-version
4
+ exports.VERSION = '0.35.2'; // x-release-please-version
5
5
  //# sourceMappingURL=version.js.map
package/version.mjs CHANGED
@@ -1,2 +1,2 @@
1
- export const VERSION = '0.30.4'; // x-release-please-version
1
+ export const VERSION = '0.35.2'; // x-release-please-version
2
2
  //# sourceMappingURL=version.mjs.map