firecode 1.1.1__tar.gz → 1.1.3__tar.gz

{firecode-1.1.1 → firecode-1.1.3}/CHANGELOG.md

@@ -4,6 +4,15 @@
 <!-- - ... mep_relax> BETA
 - ... IMAGES kw, also implement it for neb>-->
 
+## FIRECODE 1.1.3 🔥 (June 3 2025)
+- The CREST MTD operator checks that CREST 2 is installed before trying to run a search. For now, only CREST 2 is supported, as CREST 3 needs some updated interface
+- Solved CRETSLEVEL bug.
+
+## FIRECODE 1.1.2 🔥 (April 29 2025)
+- Added CRESTLEVEL keyword to specify CREST theory level (i.e. "CRESTLEVEL=GFN2").
+- Updated aimnet2 bindings to only useunderscore in the module name calls and not hyphens.
+- Fixed bug with the default value for the attribute "charge".
+
 ## FIRECODE 1.1.1 🔥 (January 2025)
 - Added pretty error traceback with rich.
 <!-- SMARTS Constraint class -->

{firecode-1.1.1/firecode.egg-info → firecode-1.1.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: firecode
-Version: 1.1.1
+Version: 1.1.3
 Summary: Computational chemistry general purpose ensemble optimizer and transition state builder
 Home-page: https://www.github.com/ntampellini/firecode
 Author: Nicolò Tampellini
@@ -41,6 +41,15 @@ Ensemble optimizer. Systematic generation of multimolecular arrangements for mon
 <!-- - ... mep_relax> BETA
 - ... IMAGES kw, also implement it for neb>-->
 
+## FIRECODE 1.1.3 🔥 (June 3 2025)
+- The CREST MTD operator checks that CREST 2 is installed before trying to run a search. For now, only CREST 2 is supported, as CREST 3 needs some updated interface
+- Solved CRETSLEVEL bug.
+
+## FIRECODE 1.1.2 🔥 (April 29 2025)
+- Added CRESTLEVEL keyword to specify CREST theory level (i.e. "CRESTLEVEL=GFN2").
+- Updated aimnet2 bindings to only useunderscore in the module name calls and not hyphens.
+- Fixed bug with the default value for the attribute "charge".
+
 ## FIRECODE 1.1.1 🔥 (January 2025)
 - Added pretty error traceback with rich.
 <!-- SMARTS Constraint class -->

{firecode-1.1.1 → firecode-1.1.3}/firecode/__main__.py

@@ -25,7 +25,7 @@ import sys
 from rich.traceback import install
 install(show_locals=True)
 
-__version__ = '1.1.0'
+__version__ = '1.1.3'
 
 if __name__ == '__main__':
 

{firecode-1.1.1 → firecode-1.1.3}/firecode/embedder.py

@@ -748,7 +748,7 @@ class Embedder:
             self.embed = 'refine'
 
             # in a refine run, the global charge must be the one of the single molecule
-            self.options.charge = self.objects[0].charge
+            self.options.charge = getattr(self.objects[0], "charge", 0)
 
             # If the run is a refine>/REFINE one, the self.embed
             # attribute is set in advance by the self._set_options

{firecode-1.1.1 → firecode-1.1.3}/firecode/embedder_options.py

@@ -48,6 +48,8 @@ keywords_dict = {
             
             'CRESTNCI' : 1,     # passes the "--nci" flag to CREST metadynamic conformational searches.
 
+            'CRESTLEVEL' : 1,   # level of the CREST run
+
             'DEEP' : 1,           # Performs a deeper search, retaining more starting points
                                 # for calculations and smaller turning angles.
 
@@ -562,6 +564,10 @@ class OptionSetter:
     def csearch(self, options, *args):
         options.csearch_aug = True
 
+    def crestlevel(self, options, *args):
+        kw = self.keywords_simple[self.keywords.index('CRESTLEVEL')]
+        options.crestlevel = kw.split('=')[1]
+
     def set_options(self):
 
         # self.keywords = sorted(self.keywords, key=lambda x: __keywords__.index(x))

{firecode-1.1.1 → firecode-1.1.3}/firecode/graph_manipulations.py

@@ -32,8 +32,8 @@ from firecode.algebra import all_dists, dihedral, norm_of
 from firecode.pt import pt
 
 
-def d_min_bond(e1, e2):
-    return 1.2 * (pt[e1].covalent_radius + pt[e2].covalent_radius)
+def d_min_bond(e1, e2, factor=1.2):
+    return factor * (pt[e1].covalent_radius + pt[e2].covalent_radius)
     # return 0.2 + (pt[e1].covalent_radius + pt[e2].covalent_radius)
 # if this is somewhat prone to bugs, this might help https://cccbdb.nist.gov/calcbondcomp1x.asp
 

{firecode-1.1.1 → firecode-1.1.3}/firecode/hypermolecule_class.py

@@ -108,6 +108,7 @@ class Hypermolecule:
             try:
                 filename = smi_to_3d(filename, "generated_3D_coords")
                 print(f"--> Embedded SMILES string to 3D structure, saved as {filename}")
+                
             except Exception:
                 raise SyntaxError((f'The program is trying to read something that is not a valid molecule input ({filename}). ' +
                             'If this looks like a keyword, it is probably faulted by a syntax error.'))

{firecode-1.1.1 → firecode-1.1.3}/firecode/operators.py

@@ -23,6 +23,7 @@ https://www.gnu.org/licenses/lgpl-3.0.en.html#license-text.
 
 # import pickle
 import time
+from shutil import which
 from subprocess import CalledProcessError
 
 import numpy as np
@@ -39,10 +40,11 @@ from firecode.optimization_methods import _refine_structures, optimize
 from firecode.pka import pka_routine
 from firecode.pruning import prune_by_rmsd, prune_by_rmsd_rot_corr
 from firecode.settings import (CALCULATOR, DEFAULT_FF_LEVELS, DEFAULT_LEVELS,
-                             FF_CALC, FF_OPT_BOOL, PROCS)
+                               FF_CALC, FF_OPT_BOOL, PROCS)
 from firecode.torsion_module import _get_quadruplets, csearch
 from firecode.utils import (align_structures, get_scan_peak_index,
-                          molecule_check, read_xyz, time_to_string, write_xyz)
+                            molecule_check, read_xyz, time_to_string,
+                            write_xyz)
 
 
 def operate(input_string, embedder):
@@ -430,6 +432,9 @@ def mtd_search_operator(filename, embedder):
     '''
     Run a CREST metadynamic conformational search and return the output filename.
     '''
+
+    assert crest_is_installed(), 'CREST 2 does not seem to be installed. Install it with: conda install -c conda-forge crest==2.*'
+
     mol = next((mol for mol in embedder.objects if mol.filename == filename))
     # load molecule to be optimized from embedder
 
@@ -539,6 +544,7 @@ def mtd_search_operator(filename, embedder):
 
                                             solvent=embedder.options.solvent,
                                             charge=mol.charge,
+                                            method=getattr(embedder.options, "crestlevel", 'GFN2-XTB//GFN-FF'),
                                             kcal=embedder.options.kcal_thresh,
                                             ncimode=embedder.options.crestnci,
                                             title=mol.rootname+"_mtd_csearch",
@@ -797,6 +803,14 @@ def distance_scan(embedder):
     # Log data to the embedder class
     mol.scan_data = (dists, energies)
 
+def crest_is_installed() -> bool:
+    '''
+    Returns True if a CREST installation is found.
+    For now, only CREST 2 is supported.
+
+    '''
+    return (which('crest') is not None)
+
 def _get_lowest_calc(embedder=None):
     '''
     Returns the values for calculator,

{firecode-1.1.1 → firecode-1.1.3}/firecode/optimization_methods.py

@@ -57,7 +57,7 @@ class Opt_func_dispatcher:
 
         except ImportError:
             raise Exception(('Cannot import AIMNet2 python bindings for FIRECODE. Install them with:\n'
-                            '>>> pip install aimnet2-firecode'))
+                            '>>> pip install aimnet2_firecode'))
             
         self.opt_funcs_dict['AIMNET2'] = aimnet2_opt
         self.aimnet2_calc = get_aimnet2_calc(theory_level, logfunction=logfunction)

{firecode-1.1.1 → firecode-1.1.3}/firecode/torsion_module.py

@@ -270,7 +270,7 @@ def _get_hydrogen_bonds(coords, atomnos, graph, d_min=2.5, d_max=3.3, max_angle=
     # initializing output list
 
     if elements is None:
-        elements = ((7, 8), (7, 8))
+        elements = ((7, 8), (7, 8, 9))
 
     het_idx_from = np.array([i for i, a in enumerate(atomnos) if a in elements[0]], dtype=int)
     het_idx_to = np.array([i for i, a in enumerate(atomnos) if a in elements[1]], dtype=int)

{firecode-1.1.1 → firecode-1.1.3}/firecode/utils.py

@@ -74,22 +74,22 @@ class Constraint:
         
         if self.type == 'B':
             a, b = self.indices
-            deltas = [round(abs(norm_of(coords[match[a]]-coords[match[b]])-self.value), 3) for match in match_indices_list]
+            deltas = [abs(norm_of(coords[match[a]]-coords[match[b]])-self.value) for match in match_indices_list]
             best_match_indices = match_indices_list[deltas.index(min(deltas))]
 
         if self.type == 'A':
             a, b, c = self.indices
-            deltas = [round(abs(point_angle(coords[match[a]], 
+            deltas = [abs(point_angle(coords[match[a]], 
                                       coords[match[b]],
-                                      coords[match[c]])-self.value), 3) for match in match_indices_list]
+                                      coords[match[c]])-self.value) for match in match_indices_list]
             best_match_indices = match_indices_list[deltas.index(min(deltas))]
 
         if self.type == 'D':
             a, b, c, d = self.indices
-            deltas = [round(abs(dihedral((coords[match[a]],
+            deltas = [abs(dihedral((coords[match[a]],
                                     coords[match[b]],
                                     coords[match[c]],
-                                    coords[match[d]]))-self.value), 3) for match in match_indices_list]
+                                    coords[match[d]]))-self.value) for match in match_indices_list]
             best_match_indices = match_indices_list[deltas.index(min(deltas))]
 
         old_indices = self.indices[:]

{firecode-1.1.1 → firecode-1.1.3/firecode.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: firecode
-Version: 1.1.1
+Version: 1.1.3
 Summary: Computational chemistry general purpose ensemble optimizer and transition state builder
 Home-page: https://www.github.com/ntampellini/firecode
 Author: Nicolò Tampellini
@@ -41,6 +41,15 @@ Ensemble optimizer. Systematic generation of multimolecular arrangements for mon
 <!-- - ... mep_relax> BETA
 - ... IMAGES kw, also implement it for neb>-->
 
+## FIRECODE 1.1.3 🔥 (June 3 2025)
+- The CREST MTD operator checks that CREST 2 is installed before trying to run a search. For now, only CREST 2 is supported, as CREST 3 needs some updated interface
+- Solved CRETSLEVEL bug.
+
+## FIRECODE 1.1.2 🔥 (April 29 2025)
+- Added CRESTLEVEL keyword to specify CREST theory level (i.e. "CRESTLEVEL=GFN2").
+- Updated aimnet2 bindings to only useunderscore in the module name calls and not hyphens.
+- Fixed bug with the default value for the attribute "charge".
+
 ## FIRECODE 1.1.1 🔥 (January 2025)
 - Added pretty error traceback with rich.
 <!-- SMARTS Constraint class -->

{firecode-1.1.1 → firecode-1.1.3}/setup.py

@@ -20,7 +20,7 @@ along with this program. If not, see
 https://www.gnu.org/licenses/lgpl-3.0.en.html#license-text.
 
 '''
-__version__ = '1.1.1'
+__version__ = '1.1.3'
 from setuptools import setup, find_packages
 
 long_description = ('## FIRECODE: Filtering Refiner and Embedder for Conformationally Dense Ensembles.\nEnsemble optimizer. Systematic generation of multimolecular arrangements for ' +