amina-cli 0.2.8__tar.gz → 0.2.9__tar.gz

{amina_cli-0.2.8 → amina_cli-0.2.9}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: amina-cli
-Version: 0.2.8
+Version: 0.2.9
 Summary: CLI for AminoAnalytica protein engineering platform
 Project-URL: Homepage, https://aminoanalytica.com
 Project-URL: Documentation, https://docs.aminoanalytica.com

{amina_cli-0.2.8 → amina_cli-0.2.9}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "amina-cli"
-version = "0.2.8"
+version = "0.2.9"
 description = "CLI for AminoAnalytica protein engineering platform"
 readme = "README.md"
 license = {text = "Apache-2.0"}

{amina_cli-0.2.8 → amina_cli-0.2.9}/src/amina_cli/__init__.py

@@ -9,4 +9,4 @@ Quick start:
     amina run esmfold --sequence "MKFLILLFNILCLFPVLAADNH"
 """
 
-__version__ = "0.2.8"
+__version__ = "0.2.9"

{amina_cli-0.2.8 → amina_cli-0.2.9}/src/amina_cli/commands/tools/folding/docs/openfold3.yaml

@@ -238,15 +238,12 @@ output_metrics:
   ipsae:
     display_name: ipSAE
     description: |
-      **ipSAE** (Interface Predicted Symmetrized Alignment Error) scores
-      protein-protein interfaces using the Dunbrack Lab algorithm. Unlike
-      ipTM, it uses only interchain residue pairs with low PAE (< 10 A
-      cutoff), normalizing by the number of confident interface residues
-      rather than total sequence length. This makes it insensitive to
-      disordered regions and non-interacting domains. Returns a dictionary
-      with six variants: d0res_max/min, d0chn_max/min, d0dom_max/min.
-      The primary metric for binder screening is **d0res_min** (worst
-      direction's best residue normalization).
+      **ipSAE** (Interaction prediction Score from Aligned Errors) scores
+      protein-protein interfaces using only interchain residue pairs with
+      low PAE, normalizing by the number of confident interface residues
+      rather than total sequence length. Unlike ipTM, it is insensitive
+      to disordered regions and non-interacting domains. Computed directly
+      from the PAE matrix output by the structure prediction model.
     range: [0, 1]
     interpretation: |
       - d0res_min > 0.5: Confident interface — strong predicted contacts

{amina_cli-0.2.8 → amina_cli-0.2.9}/src/amina_cli/commands/tools/folding/docs/protenix.yaml

@@ -304,9 +304,9 @@ output_metrics:
       non-protein entities (ligands, DNA, RNA, ions) are excluded.
     range: [0, 1]
     interpretation: |
-      - >0.5: Confident interface — strong predicted contacts
-      - 0.3-0.5: Moderate interface confidence
-      - <0.3: Weak or uncertain interface
+      - >0.7: Confident interface — strong predicted contacts
+      - 0.5-0.7: Moderate interface confidence
+      - <0.5: Weak or uncertain interface
 
   ipsae_per_chain_pair:
     display_name: ipSAE per Chain Pair