pyadmd 3.2.0__tar.gz → 3.2.2__tar.gz

{pyadmd-3.2.0/src/pyadmd.egg-info → pyadmd-3.2.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyadmd
-Version: 3.2.0
+Version: 3.2.2
 Summary: Adaptive Molecular Dynamics with Excited Normal Modes (aMDeNM) on OpenMM.
 Author-email: Pedro Túlio Resende-Lara <laraptr@unicamp.br>
 License-Expression: GPL-3.0-or-later
@@ -177,7 +177,7 @@ $$
 V = \frac{1}{2} \sum_{i < j} k_{ij} \left(r_{ij} - r_{ij}^0\right)^2
 $$
 
-where $`k_{ij}`$ is the spring constant between sites $`i`$ and $`j`$, $`r_{ij}`$ is the instantaneous distance between them, and $`r_{ij}^0`$ is their equilibrium distance. In the simplest ANM formulation, a **uniform spring constant** $`k_{ij} = k`$ is used for all connected pairs. This is a deliberate simplification: the spring constant encodes the stiffness of the local environment, and setting it uniformly to $`k`$ (with default $`k = 1.0 kcal/mol/Ų``$) means the model's predictions are expressed in units relative to $`k`$. More sophisticated variants assign distance-dependent spring constants (e.g., $`k_{ij} \propto (r_{ij}^0)^{-\alpha}`$), but the uniform model already captures the essential topology of collective motions.
+where $`k_{ij}`$ is the spring constant between sites $`i`$ and $`j`$, $`r_{ij}`$ is the instantaneous distance between them, and $`r_{ij}^0`$ is their equilibrium distance. In the simplest ANM formulation, a **uniform spring constant** $`k_{ij} = k`$ is used for all connected pairs. This is a deliberate simplification: the spring constant encodes the stiffness of the local environment, and setting it uniformly to $`k`$ (with default $`k = 1.0 kcal/mol/Ų`$) means the model's predictions are expressed in units relative to $`k`$. More sophisticated variants assign distance-dependent spring constants (e.g., $`k_{ij} \propto (r_{ij}^0)^{-\alpha}`$), but the uniform model already captures the essential topology of collective motions.
 
 ### The Hessian Matrix
 
@@ -663,7 +663,8 @@ fel/
 ├── fel_summary.html                        # HTML summary report
 └── centroids/
     └── centroid_frame[F]/                  # one directory per centroid, named by frame index
-        ├── prod.dcd                        # production trajectory (appended to on extension)
+        ├── centroid_[F].dcd                # production trajectory (appended to on extension)
+        ├── centroid_[F].log                # production logfile (appended to on extension)
         ├── prod_checkpoint.chk             # exact final state, for bit-identical extension
         └── checkpoint.chk                  # periodic (every 10 cycles) checkpoint
 ```

{pyadmd-3.2.0 → pyadmd-3.2.2}/README.md

@@ -149,7 +149,7 @@ $$
 V = \frac{1}{2} \sum_{i < j} k_{ij} \left(r_{ij} - r_{ij}^0\right)^2
 $$
 
-where $`k_{ij}`$ is the spring constant between sites $`i`$ and $`j`$, $`r_{ij}`$ is the instantaneous distance between them, and $`r_{ij}^0`$ is their equilibrium distance. In the simplest ANM formulation, a **uniform spring constant** $`k_{ij} = k`$ is used for all connected pairs. This is a deliberate simplification: the spring constant encodes the stiffness of the local environment, and setting it uniformly to $`k`$ (with default $`k = 1.0 kcal/mol/Ų``$) means the model's predictions are expressed in units relative to $`k`$. More sophisticated variants assign distance-dependent spring constants (e.g., $`k_{ij} \propto (r_{ij}^0)^{-\alpha}`$), but the uniform model already captures the essential topology of collective motions.
+where $`k_{ij}`$ is the spring constant between sites $`i`$ and $`j`$, $`r_{ij}`$ is the instantaneous distance between them, and $`r_{ij}^0`$ is their equilibrium distance. In the simplest ANM formulation, a **uniform spring constant** $`k_{ij} = k`$ is used for all connected pairs. This is a deliberate simplification: the spring constant encodes the stiffness of the local environment, and setting it uniformly to $`k`$ (with default $`k = 1.0 kcal/mol/Ų`$) means the model's predictions are expressed in units relative to $`k`$. More sophisticated variants assign distance-dependent spring constants (e.g., $`k_{ij} \propto (r_{ij}^0)^{-\alpha}`$), but the uniform model already captures the essential topology of collective motions.
 
 ### The Hessian Matrix
 
@@ -635,7 +635,8 @@ fel/
 ├── fel_summary.html                        # HTML summary report
 └── centroids/
     └── centroid_frame[F]/                  # one directory per centroid, named by frame index
-        ├── prod.dcd                        # production trajectory (appended to on extension)
+        ├── centroid_[F].dcd                # production trajectory (appended to on extension)
+        ├── centroid_[F].log                # production logfile (appended to on extension)
         ├── prod_checkpoint.chk             # exact final state, for bit-identical extension
         └── checkpoint.chk                  # periodic (every 10 cycles) checkpoint
 ```

{pyadmd-3.2.0 → pyadmd-3.2.2}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "pyadmd"
-version = "3.2.0"
+version = "3.2.2"
 description = "Adaptive Molecular Dynamics with Excited Normal Modes (aMDeNM) on OpenMM."
 readme = "README.md"
 license = "GPL-3.0-or-later"

{pyadmd-3.2.0 → pyadmd-3.2.2}/src/pyadmd/__init__.py

@@ -9,4 +9,4 @@ environmental resistance. Importantly, aMDeNM requires only an initial structure
 target states, distinguishing it from many biased sampling techniques that rely on predefined target conformations.
 """
 
-__version__ = "3.2.0"
+__version__ = "3.2.2"

{pyadmd-3.2.0 → pyadmd-3.2.2}/src/pyadmd/analysis/analyzer.py

@@ -507,7 +507,7 @@ class Analyzer:
         Analyze all fel centroid production trajectories and generate plots.
 
         Mirrors ``analyze_all_replicas``, but the analysis units are
-        fel centroids (``fel/centroids/centroid_frame{F}/prod.dcd``)
+        fel centroids (``fel/centroids/centroid_frame{F}/centroid_{F}.dcd``)
         instead of pyadmd replicas, and the shared (target) time axis is the
         ``production_ps`` value already recorded in
         ``fel/run_metadata.json`` (playing the role
@@ -585,7 +585,7 @@ class Analyzer:
         # Discover centroid production trajectories, sorted by frame index
         centroid_pattern = re.compile(r"centroid_frame(\d+)")
         centroid_dcds = sorted(
-            glob.glob(f"{cwd}/fel/centroids/centroid_frame*/prod.dcd"),
+            glob.glob(f"{cwd}/fel/centroids/centroid_frame*/centroid_*.dcd"),
             key=lambda p: int(centroid_pattern.search(p).group(1))
         )
 
@@ -708,7 +708,8 @@ class Analyzer:
         ``_analyze_replica_parallel``.
 
         Args:
-            dcd_file (str): Absolute path to the centroid's prod.dcd file.
+            dcd_file (str): Absolute path to the centroid's production DCD
+                file (``centroid_{F}.dcd``).
             psf_file (str): Absolute path to the shared PSF topology file.
             frame_idx (int): Centroid frame index, echoed in the return value.
             sim_time (float): Shared target production time in picoseconds

{pyadmd-3.2.0 → pyadmd-3.2.2}/src/pyadmd/console.py

@@ -53,7 +53,7 @@ class ConsoleConfig:
     ░░░░░       ░░░░░░
     '''
 
-    VERSION = '3.2.0'
+    VERSION = '3.2.2'
     CITATION = '''  Please cite:
 
     \tAdaptive Normal Mode Sampling (aMDeNM) Enhances Exploration of Protein Conformational Space

{pyadmd-3.2.0 → pyadmd-3.2.2/src/pyadmd.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyadmd
-Version: 3.2.0
+Version: 3.2.2
 Summary: Adaptive Molecular Dynamics with Excited Normal Modes (aMDeNM) on OpenMM.
 Author-email: Pedro Túlio Resende-Lara <laraptr@unicamp.br>
 License-Expression: GPL-3.0-or-later
@@ -177,7 +177,7 @@ $$
 V = \frac{1}{2} \sum_{i < j} k_{ij} \left(r_{ij} - r_{ij}^0\right)^2
 $$
 
-where $`k_{ij}`$ is the spring constant between sites $`i`$ and $`j`$, $`r_{ij}`$ is the instantaneous distance between them, and $`r_{ij}^0`$ is their equilibrium distance. In the simplest ANM formulation, a **uniform spring constant** $`k_{ij} = k`$ is used for all connected pairs. This is a deliberate simplification: the spring constant encodes the stiffness of the local environment, and setting it uniformly to $`k`$ (with default $`k = 1.0 kcal/mol/Ų``$) means the model's predictions are expressed in units relative to $`k`$. More sophisticated variants assign distance-dependent spring constants (e.g., $`k_{ij} \propto (r_{ij}^0)^{-\alpha}`$), but the uniform model already captures the essential topology of collective motions.
+where $`k_{ij}`$ is the spring constant between sites $`i`$ and $`j`$, $`r_{ij}`$ is the instantaneous distance between them, and $`r_{ij}^0`$ is their equilibrium distance. In the simplest ANM formulation, a **uniform spring constant** $`k_{ij} = k`$ is used for all connected pairs. This is a deliberate simplification: the spring constant encodes the stiffness of the local environment, and setting it uniformly to $`k`$ (with default $`k = 1.0 kcal/mol/Ų`$) means the model's predictions are expressed in units relative to $`k`$. More sophisticated variants assign distance-dependent spring constants (e.g., $`k_{ij} \propto (r_{ij}^0)^{-\alpha}`$), but the uniform model already captures the essential topology of collective motions.
 
 ### The Hessian Matrix
 
@@ -663,7 +663,8 @@ fel/
 ├── fel_summary.html                        # HTML summary report
 └── centroids/
     └── centroid_frame[F]/                  # one directory per centroid, named by frame index
-        ├── prod.dcd                        # production trajectory (appended to on extension)
+        ├── centroid_[F].dcd                # production trajectory (appended to on extension)
+        ├── centroid_[F].log                # production logfile (appended to on extension)
         ├── prod_checkpoint.chk             # exact final state, for bit-identical extension
         └── checkpoint.chk                  # periodic (every 10 cycles) checkpoint
 ```