firecode 1.3.0__tar.gz → 1.4.0__tar.gz

{firecode-1.3.0 → firecode-1.4.0}/CHANGELOG.md

@@ -3,6 +3,12 @@
 
 <!-- - ... mep_relax> BETA
 - ... IMAGES kw, also implement it for neb>-->
+## FIRECODE 1.4.0 🔥 (January 25 2026) - Big cleanup and reorganization!
+- Similarity pruning is now done via the standalone [PRISM](https://github.com/ntampellini/prism_pruner) library.
+- Removed dependencies: numba, cclib, periodictable.
+- Removed MOPAC, GAUSSIAN and OPENBABEL calculator interfaces completely.
+- Removed SADDLE, CSEARCH and NCI keywords, as well as the saddle> operator.
+- Bumped minimum Python version from 3.8 to 3.12.
 
 ## FIRECODE 1.3.0 🔥 (December 15 2025)
 - Added [UMA](https://fair-chem.github.io/core/uma.html) as a calculator with Meta MLIPs, via ASE and the fairchem-core library. The model path needs to be specified in the settings.py file.
@@ -12,7 +18,7 @@
 - Moved tests to their own folders.
 <!-- - Added free energy calculation via ASE vibrational analysis. -->
 
-## FIRECODE 1.2.0 🔥 (July X 2025)
+## FIRECODE 1.2.0 🔥 (July 2025)
 - Ignored KeyError exceptions from get_atom_type.
 - Implemented [tblite](https://github.com/tblite/tblite) as a calculator (yes, ready for g-xtb!).
 - Implemented multiplicity support for main calculators (XTB and TBLITE - AIMNET2 will raise a NotImplementedError, ORCA pending).

{firecode-1.3.0 → firecode-1.4.0}/MANIFEST.in

@@ -4,4 +4,5 @@ include LICENSE
 include firecode/*
 include firecode/tests/*
 include firecode/calculators/*
-include docs/*
+include docs/*
+exclude firecode/calculators/*.pt

{firecode-1.3.0/firecode.egg-info → firecode-1.4.0}/PKG-INFO

@@ -1,34 +1,32 @@
 Metadata-Version: 2.4
 Name: firecode
-Version: 1.3.0
+Version: 1.4.0
 Summary: Computational chemistry general purpose ensemble optimizer and molecular assemblies builder
 Home-page: https://www.github.com/ntampellini/firecode
 Author: Nicolò Tampellini
 Author-email: nicolo.tampellini@yale.edu
 Keywords: computational chemistry,ASE,transition state,xtb,AIMNET2,TBLITE
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.12
 Classifier: License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)
 Classifier: Operating System :: OS Independent
-Requires-Python: >=3.10
+Requires-Python: >=3.12
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: numpy==1.24
-Requires-Dist: scipy==1.13.1
-Requires-Dist: cclib==1.7
-Requires-Dist: periodictable==1.6.0
-Requires-Dist: matplotlib==3.4.2
-Requires-Dist: networkx==2.5.1
-Requires-Dist: ase==3.23
-Requires-Dist: numba==0.58.1
-Requires-Dist: prettytable==3.3.0
-Requires-Dist: typing-extensions==4.8.0
+Requires-Dist: numpy
+Requires-Dist: scipy
+Requires-Dist: matplotlib
+Requires-Dist: networkx
+Requires-Dist: ase
+Requires-Dist: prettytable
+Requires-Dist: typing-extensions
 Requires-Dist: llvmlite
 Requires-Dist: importlib-metadata
 Requires-Dist: psutil
-Requires-Dist: setuptools<60.0
+Requires-Dist: setuptools
 Requires-Dist: rich
 Requires-Dist: inquirerpy
+Requires-Dist: prism-pruner
 Dynamic: author
 Dynamic: author-email
 Dynamic: classifier
@@ -49,6 +47,12 @@ Ensemble optimizer. Systematic generation of multimolecular arrangements for mon
 
 <!-- - ... mep_relax> BETA
 - ... IMAGES kw, also implement it for neb>-->
+## FIRECODE 1.4.0 🔥 (January 25 2026) - Big cleanup and reorganization!
+- Similarity pruning is now done via the standalone [PRISM](https://github.com/ntampellini/prism_pruner) library.
+- Removed dependencies: numba, cclib, periodictable.
+- Removed MOPAC, GAUSSIAN and OPENBABEL calculator interfaces completely.
+- Removed SADDLE, CSEARCH and NCI keywords, as well as the saddle> operator.
+- Bumped minimum Python version from 3.8 to 3.12.
 
 ## FIRECODE 1.3.0 🔥 (December 15 2025)
 - Added [UMA](https://fair-chem.github.io/core/uma.html) as a calculator with Meta MLIPs, via ASE and the fairchem-core library. The model path needs to be specified in the settings.py file.
@@ -58,7 +62,7 @@ Ensemble optimizer. Systematic generation of multimolecular arrangements for mon
 - Moved tests to their own folders.
 <!-- - Added free energy calculation via ASE vibrational analysis. -->
 
-## FIRECODE 1.2.0 🔥 (July X 2025)
+## FIRECODE 1.2.0 🔥 (July 2025)
 - Ignored KeyError exceptions from get_atom_type.
 - Implemented [tblite](https://github.com/tblite/tblite) as a calculator (yes, ready for g-xtb!).
 - Implemented multiplicity support for main calculators (XTB and TBLITE - AIMNET2 will raise a NotImplementedError, ORCA pending).

{firecode-1.3.0 → firecode-1.4.0}/README.md

@@ -4,7 +4,7 @@
 <div align="center">
 
 [![License: GNU LGPL v3](https://img.shields.io/github/license/ntampellini/firecode)](https://opensource.org/licenses/LGPL-3.0)
-![Python Version](https://img.shields.io/badge/Python-3.8.10-blue)
+![Python Version](https://img.shields.io/badge/Python-3.12-blue)
 ![Size](https://img.shields.io/github/languages/code-size/ntampellini/firecode)
 ![Lines](https://sloc.xyz/github/ntampellini/firecode/)
 [![CodeFactor Grade](https://img.shields.io/codefactor/grade/github/ntampellini/firecode)](https://www.codefactor.io/repository/github/ntampellini/firecode)

{firecode-1.3.0 → firecode-1.4.0}/docs/conf.py

@@ -20,7 +20,7 @@ sys.path.insert(0, os.path.join(os.path.abspath('..'), 'firecode'))
 # -- Project information -----------------------------------------------------
 
 project = 'firecode'
-copyright = '2021-2025, Nicolò Tampellini'
+copyright = '2021-2026, Nicolò Tampellini'
 author = 'Nicolò Tampellini'
 
 # The full version, including alpha/beta/rc tags

{firecode-1.3.0 → firecode-1.4.0}/firecode/__main__.py

@@ -2,7 +2,7 @@
 '''
 
 FIRECODE: Filtering Refiner and Embedder for Conformationally Dense Ensembles
-Copyright (C) 2021-2025 Nicolò Tampellini
+Copyright (C) 2021-2026 Nicolò Tampellini
 
 This program is free software: you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by
@@ -25,7 +25,7 @@ import sys
 from rich.traceback import install
 install(show_locals=True)
 
-__version__ = '1.1.3'
+__version__ = '1.4.0'
 
 if __name__ == '__main__':
 

firecode-1.4.0/firecode/algebra.py

@@ -0,0 +1,115 @@
+'''
+
+FIRECODE: Filtering Refiner and Embedder for Conformationally Dense Ensembles
+Copyright (C) 2021-2026 Nicolò Tampellini
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+'''
+import numpy as np
+from prism_pruner.algebra import normalize
+
+norm_of = np.linalg.norm
+
+
+def point_angle(p1, p2, p3):
+    '''
+    Returns the planar angle between three points in space, in degrees.
+    '''
+    return np.arccos(np.clip(normalize(p1 - p2) @ normalize(p3 - p2), -1.0, 1.0))*180/np.pi
+
+
+def kronecker_delta(i, j) -> int:
+    if i == j:
+        return 1
+    return 0
+
+
+def align_vec_pair(ref, tgt):
+    '''
+    ref, tgt: iterables of two 3D vectors each
+    
+    return: rotation matrix that when applied to tgt,
+            optimally aligns it to ref
+    '''
+    
+    B = np.zeros((3,3))
+    for i in range(3):
+        for k in range(3):
+            tot = 0
+            for j in range(2):
+                tot += ref[j][i]*tgt[j][k]
+            B[i,k] = tot
+
+    u, s, vh = np.linalg.svd(B)
+
+    # Correct improper rotation if necessary (as in Kabsch algorithm)
+    if np.linalg.det(u @ vh) < 0:
+        s[-1] = -s[-1]
+        u[:, -1] = -u[:, -1]
+
+    return np.ascontiguousarray(np.dot(u, vh))
+
+
+def cart_prod_idx(sizes: np.ndarray):
+    """Generates ids tuples for a cartesian product"""
+    assert len(sizes) >= 2
+    tuples_count  = np.prod(sizes)
+    tuples = np.zeros((tuples_count, len(sizes)), dtype=np.int32)
+    tuple_idx = 0
+    # stores the current combination
+    current_tuple = np.zeros(len(sizes))
+    while tuple_idx < tuples_count:
+        tuples[tuple_idx] = current_tuple
+        current_tuple[0] += 1
+        # using a condition here instead of including this in the inner loop
+        # to gain a bit of speed: this is going to be tested each iteration,
+        # and starting a loop to have it end right away is a bit silly
+        if current_tuple[0] == sizes[0]:
+            # the reset to 0 and subsequent increment amount to carrying
+            # the number to the higher "power"
+            current_tuple[0] = 0
+            current_tuple[1] += 1
+            for i in range(1, len(sizes) - 1):
+                if current_tuple[i] == sizes[i]:
+                    # same as before, but in a loop, since this is going
+                    # to get run less often
+                    current_tuple[i + 1] += 1
+                    current_tuple[i] = 0
+                else:
+                    break
+        tuple_idx += 1
+    return tuples
+
+
+def vector_cartesian_product(x, y):
+    '''
+    Cartesian product, but with vectors instead of indices
+    '''
+    indices = cart_prod_idx(np.asarray((x.shape[0], y.shape[0]), dtype=np.int32))
+    dim = x.shape[-1] if len(x.shape) > 1 else 1
+    new_arr = np.zeros((*indices.shape, dim), dtype=x.dtype)
+    for i, (x_, y_) in enumerate(indices):
+        new_arr[i][0] = x[x_]
+        new_arr[i][1] = y[y_]
+    return np.ascontiguousarray(new_arr)
+
+
+def transform_coords(coords, rot, pos):
+    '''
+    Returns the rotated and tranlated
+    coordinates. Slightly faster than
+    Numpy, uses memory-contiguous arrays.
+    '''
+    t = np.transpose(coords)
+    m = rot @ t
+    f = np.transpose(m)
+    return f + pos