Fix cell2mol version

environment-minimal.yml

@@ -13,4 +13,4 @@ dependencies:
   - pip:
       - pyscf==2.11.0
       - metatensor-core==0.1.17
-      - git+https://github.com/lcmd-epfl/cell2mol.git@40b3237
+      - git+https://github.com/lcmd-epfl/cell2mol.git@283c965

environment.yml

@@ -92,4 +92,4 @@ dependencies:
       - typing-extensions==4.15.0
       - typing-inspection==0.4.2
       - tzdata==2025.2
-      - git+https://github.com/lcmd-epfl/cell2mol.git@40b3237
+      - git+https://github.com/lcmd-epfl/cell2mol.git@283c965

pyproject.toml

@@ -47,7 +47,7 @@ pyscf = ['pyscf >= 2.1.0, < 2.12']
 qml = ['ase >= 3.22, < 3.27']
 regression = ["scikit-learn >= 0.24.2, < 1.8"]
 wigner = ["sympy >= 1.5, < 1.15"]
-cell2mol-itself = ["cell2mol @ git+https://github.com/lcmd-epfl/cell2mol.git@40b3237"]
+cell2mol-itself = ["cell2mol @ git+https://github.com/lcmd-epfl/cell2mol.git@283c965"]
 cell2mol = ["qstack[pyscf,cell2mol-itself]"]
 equio-itself = ["metatensor-core >= 0.1.8, == 0.1.*"]
 equio = ["qstack[pyscf,equio-itself]"]

qstack/io/cell2mol.py

@@ -1,10 +1,10 @@
 """Converter from cell2mol Cell objects to PySCF Mole."""
 
-import sys
 import os
 import io
-from cell2mol.read_write import load_binary
-from cell2mol.unitcell import process_unitcell
+from contextlib import redirect_stdout
+import numpy as np
+from cell2mol.process_unitcell import interpret_unitcell
 from qstack.compound import xyz_to_mol
 
 
@@ -21,10 +21,9 @@ def get_cell2mol_xyz(mol):
         - spin (int): Number of unpaired electrons of the molecule (multiplicity - 1)
         for molecules and None for ligands.
     """
-    f = io.StringIO()
-    sys.stdout, stdout = f, sys.stdout
-    mol.print_xyz()
-    xyz, sys.stdout = f.getvalue(), stdout
+    with redirect_stdout(io.StringIO()) as f:
+        mol.print_xyz()
+    xyz = f.getvalue()
     f.close()
     return xyz, mol.totcharge, (mol.get_spin()-1 if hasattr(mol, 'get_spin') else None)
 
@@ -49,14 +48,14 @@ def get_cell(fpath, workdir='.'):
     """
     ext = os.path.splitext(fpath)[-1]
     if ext=='.cell':
-        cell = load_binary(fpath)
+        cell = np.load(fpath, allow_pickle=True)
     elif ext=='.cif':
         name = os.path.basename(os.path.splitext(fpath)[0])
         cell_path = f'{workdir}/Cell_{name}.cell'
         if os.path.isfile(cell_path):
-            cell = load_binary(cell_path)
+            cell = np.load(cell_path, allow_pickle=True)
         else:
-            cell = process_unitcell(fpath, name, workdir, cif_bond_info=True, debug=0)
+            cell = interpret_unitcell(input_path=fpath, name=name, current_dir=workdir)
     else:
         raise NotImplementedError(f'{ext} input is not supported')
     return cell

requirements.py3.11.txt

@@ -14,4 +14,4 @@ scikit-learn==1.7.2
 ase==3.26
 tqdm==4.67
 metatensor-core==0.1.17
-cell2mol @ git+https://github.com/lcmd-epfl/cell2mol.git@40b3237
+cell2mol @ git+https://github.com/lcmd-epfl/cell2mol.git@283c965

requirements.py3.13.txt

@@ -11,4 +11,4 @@ scikit-learn==1.7.2
 ase==3.26
 tqdm==4.67
 metatensor-core==0.1.17
-cell2mol @ git+https://github.com/lcmd-epfl/cell2mol.git@40b3237
+cell2mol @ git+https://github.com/lcmd-epfl/cell2mol.git@283c965

tests/data/cell2mol/reference_summary.txt

@@ -0,0 +1,89 @@
+YOXKUS
+Total charge comparison result: True
+Metal oxidation state comparison result: True
+  - Reported:   [('carbonyl-diiodo-rhenium', 3)]
+  - Matched:    ['Re_3']
+  - Confidence: 1.00
+
+Molecules in reference:
+Molecule 0: H24-C23-O-P-I2-Re (TM Complex) totcharge=0 totcharge_cif=0 totcharge_agree=True spin_multiplicity=1 smiles=C[c]12->[Re+3]3456(<-[I-])(<-[I-])(<-[C-]#[O+])<-[c]1(C)[c]->3(C)[c-]->4(C[P]->5(c1ccccc1)c1ccccc1)[c]->62C
+	Re (metal) atom_site_label=Re1 metal_OS=3 metal_spin=1
+	|--coord_sphere_formula=C6-P-I2
+	|--coord_nr=5 coord_geometry=Trigonal bipyramidal geom_deviation=3.348
+	|--(group) ['C'] atom_site_labels=['C23'] denticity=1
+	|--(group) ['C', 'C', 'C', 'C', 'C'] atom_site_labels=['C1', 'C2', 'C3', 'C4', 'C5'] denticity=5 haptic_type=eta5(Cp)
+	|--(group) ['P'] atom_site_labels=['P1'] denticity=1
+	|--(group) ['I'] atom_site_labels=['I2'] denticity=1
+	|--(group) ['I'] atom_site_labels=['I1'] denticity=1
+	C-O (ligand) smiles=[C-]#[O+] denticity=1 totcharge=0
+	|--(group) ['C'] atom_site_labels=['C23'] denticity=1 connected_metals=['Re1']
+	H24-C22-P (ligand) smiles=[H]c1c([H])c([H])c(P(c2c([H])c([H])c([H])c([H])c2[H])C([H])([H])[c-]2c(C([H])([H])[H])c(C([H])([H])[H])c(C([H])([H])[H])c2C([H])([H])[H])c([H])c1[H] denticity=6 totcharge=-1
+	|--(group) ['C', 'C', 'C', 'C', 'C'] atom_site_labels=['C1', 'C2', 'C3', 'C4', 'C5'] denticity=5 haptic_type=eta5(Cp) connected_metals=['Re1']
+	|--(group) ['P'] atom_site_labels=['P1'] denticity=1 connected_metals=['Re1']
+	I (ligand) smiles=[I-] denticity=1 totcharge=-1
+	|--(group) ['I'] atom_site_labels=['I2'] denticity=1 connected_metals=['Re1']
+	I (ligand) smiles=[I-] denticity=1 totcharge=-1
+	|--(group) ['I'] atom_site_labels=['I1'] denticity=1 connected_metals=['Re1']
+
+Unique Species in reference:
+	unique_index=0 C-O (ligand) denticity=1 smiles=[C-]#[O+] totcharge=0 groups=['C']
+	unique_index=1 H24-C22-P (ligand) denticity=6 haptic_type=['eta5(Cp)'] smiles=[H]c1c([H])c([H])c(P(c2c([H])c([H])c([H])c([H])c2[H])C([H])([H])[c-]2c(C([H])([H])[H])c(C([H])([H])[H])c(C([H])([H])[H])c2C([H])([H])[H])c([H])c1[H] totcharge=-1 groups=['C5', 'P']
+	unique_index=2 I (ligand) denticity=1 smiles=[I-] totcharge=-1 groups=['I']
+	unique_index=3 Re (metal) coord_sphere_formula=C6-P-I2 charge=3
+
+Possible charges of species in reference:
+	unique_index=0 C-O (ligand)
+	possible_cs=[------------- Cell2mol Charge State ---------------
+ Status                          = True
+ Smiles                          = [C-]#[O+]
+ Number of Protons Added         = 0
+ Charge Tried                    = 0
+ Uncorrected Total Charge        = 0
+ Corrected Total Charge          = 0
+ Corrected Absolute Total Charge = 2
+ Corrected Is Zwitterion?        = True
+---------------------------------------------------
+]
+	unique_index=1 H24-C22-P (ligand)
+	possible_cs=[------------- Cell2mol Charge State ---------------
+ Status                          = True
+ Smiles                          = [H]c1c([H])c([H])c(P(c2c([H])c([H])c([H])c([H])c2[H])C([H])([H])C2([H])C(C([H])([H])[H])=C(C([H])([H])[H])C(C([H])([H])[H])=C2C([H])([H])[H])c([H])c1[H]
+ Number of Protons Added         = 1
+ Charge Tried                    = 0
+ Uncorrected Total Charge        = 0
+ Corrected Total Charge          = -1
+ Corrected Absolute Total Charge = 1
+ Corrected Is Zwitterion?        = False
+---------------------------------------------------
+]
+	unique_index=2 I (ligand)
+	possible_cs=[------------- Cell2mol Charge State ---------------
+ Status                          = True
+ Smiles                          = [I-]
+ Number of Protons Added         = 0
+ Charge Tried                    = -1
+ Uncorrected Total Charge        = -1
+ Corrected Total Charge          = -1
+ Corrected Absolute Total Charge = 1
+ Corrected Is Zwitterion?        = False
+---------------------------------------------------
+]
+	unique_index=2 I (ligand)
+	possible_cs=[------------- Cell2mol Charge State ---------------
+ Status                          = True
+ Smiles                          = [I-]
+ Number of Protons Added         = 0
+ Charge Tried                    = -1
+ Uncorrected Total Charge        = -1
+ Corrected Total Charge          = -1
+ Corrected Absolute Total Charge = 1
+ Corrected Is Zwitterion?        = False
+---------------------------------------------------
+]
+	unique_index=3 Re (metal) coord_sphere_formula=C6-P-I2 possible_cs=[1, 2, 3, 4, 5, 7]
+
+Reference Error (mode=ref_molecules): No errors found
+Reference Error (mode=hydrogens): No errors found
+Reference Error (mode=possible_charges): No errors found
+Reference Error (mode=charge_assignment): No errors found
+Reference Error (mode=spin_assignment): No errors found

tests/data/cell2mol/unitcell_summary.txt

@@ -0,0 +1,81 @@
+YOXKUS
+Total charge comparison result: True
+Metal oxidation state comparison result: True
+
+Molecules in unitcell:
+Molecule 0: H24-C23-O-P-I2-Re (TM Complex) totcharge=0 spin_multiplicity=1 smiles=C[c]12->[Re+3]3456(<-[I-])(<-[I-])(<-[C-]#[O+])<-[c]1(C)[c]->3(C)[c-]->4(C[P]->5(c1ccccc1)c1ccccc1)[c]->62C
+	Re (metal) atom_site_label=Re1 metal_OS=3 metal_spin=1
+	|--coord_sphere_formula=C6-P-I2
+	|--coord_nr=5 coord_geometry=Trigonal bipyramidal geom_deviation=3.348
+	|--(group) ['C'] atom_site_labels=['C23'] denticity=1
+	|--(group) ['C', 'C', 'C', 'C', 'C'] atom_site_labels=['C1', 'C5', 'C2', 'C3', 'C4'] denticity=5 haptic_type=eta5(Cp)
+	|--(group) ['P'] atom_site_labels=['P1'] denticity=1
+	|--(group) ['I'] atom_site_labels=['I2'] denticity=1
+	|--(group) ['I'] atom_site_labels=['I1'] denticity=1
+	C-O (ligand) smiles=[C-]#[O+] denticity=1 totcharge=0
+	|--(group) ['C'] atom_site_labels=['C23'] denticity=1 connected_metals=['Re1']
+	H24-C22-P (ligand) smiles=[H]c1c([H])c([H])c(P(c2c([H])c([H])c([H])c([H])c2[H])C([H])([H])[c-]2c(C([H])([H])[H])c(C([H])([H])[H])c(C([H])([H])[H])c2C([H])([H])[H])c([H])c1[H] denticity=6 totcharge=-1
+	|--(group) ['C', 'C', 'C', 'C', 'C'] atom_site_labels=['C1', 'C5', 'C2', 'C3', 'C4'] denticity=5 haptic_type=eta5(Cp) connected_metals=['Re1']
+	|--(group) ['P'] atom_site_labels=['P1'] denticity=1 connected_metals=['Re1']
+	I (ligand) smiles=[I-] denticity=1 totcharge=-1
+	|--(group) ['I'] atom_site_labels=['I2'] denticity=1 connected_metals=['Re1']
+	I (ligand) smiles=[I-] denticity=1 totcharge=-1
+	|--(group) ['I'] atom_site_labels=['I1'] denticity=1 connected_metals=['Re1']
+Molecule 1: H24-C23-O-P-I2-Re (TM Complex) totcharge=0 spin_multiplicity=1 smiles=C[c]12->[Re+3]3456(<-[I-])(<-[I-])(<-[C-]#[O+])<-[c]1(C)[c]->3(C)[c-]->4(C[P]->5(c1ccccc1)c1ccccc1)[c]->62C
+	Re (metal) atom_site_label=Re1 metal_OS=3 metal_spin=1
+	|--coord_sphere_formula=C6-P-I2
+	|--coord_nr=5 coord_geometry=Trigonal bipyramidal geom_deviation=3.348
+	|--(group) ['C'] atom_site_labels=['C23'] denticity=1
+	|--(group) ['C', 'C', 'C', 'C', 'C'] atom_site_labels=['C1', 'C2', 'C3', 'C4', 'C5'] denticity=5 haptic_type=eta5(Cp)
+	|--(group) ['P'] atom_site_labels=['P1'] denticity=1
+	|--(group) ['I'] atom_site_labels=['I2'] denticity=1
+	|--(group) ['I'] atom_site_labels=['I1'] denticity=1
+	C-O (ligand) smiles=[C-]#[O+] denticity=1 totcharge=0
+	|--(group) ['C'] atom_site_labels=['C23'] denticity=1 connected_metals=['Re1']
+	H24-C22-P (ligand) smiles=[H]c1c([H])c([H])c(P(c2c([H])c([H])c([H])c([H])c2[H])C([H])([H])[c-]2c(C([H])([H])[H])c(C([H])([H])[H])c(C([H])([H])[H])c2C([H])([H])[H])c([H])c1[H] denticity=6 totcharge=-1
+	|--(group) ['C', 'C', 'C', 'C', 'C'] atom_site_labels=['C1', 'C2', 'C3', 'C4', 'C5'] denticity=5 haptic_type=eta5(Cp) connected_metals=['Re1']
+	|--(group) ['P'] atom_site_labels=['P1'] denticity=1 connected_metals=['Re1']
+	I (ligand) smiles=[I-] denticity=1 totcharge=-1
+	|--(group) ['I'] atom_site_labels=['I2'] denticity=1 connected_metals=['Re1']
+	I (ligand) smiles=[I-] denticity=1 totcharge=-1
+	|--(group) ['I'] atom_site_labels=['I1'] denticity=1 connected_metals=['Re1']
+Molecule 2: H24-C23-O-P-I2-Re (TM Complex) totcharge=0 spin_multiplicity=1 smiles=C[c]12->[Re+3]3456(<-[I-])(<-[I-])(<-[C-]#[O+])<-[c]1(C)[c]->3(C)[c-]->4(C[P]->5(c1ccccc1)c1ccccc1)[c]->62C
+	Re (metal) atom_site_label=Re1 metal_OS=3 metal_spin=1
+	|--coord_sphere_formula=C6-P-I2
+	|--coord_nr=5 coord_geometry=Trigonal bipyramidal geom_deviation=3.348
+	|--(group) ['C'] atom_site_labels=['C23'] denticity=1
+	|--(group) ['C', 'C', 'C', 'C', 'C'] atom_site_labels=['C1', 'C5', 'C2', 'C3', 'C4'] denticity=5 haptic_type=eta5(Cp)
+	|--(group) ['P'] atom_site_labels=['P1'] denticity=1
+	|--(group) ['I'] atom_site_labels=['I2'] denticity=1
+	|--(group) ['I'] atom_site_labels=['I1'] denticity=1
+	C-O (ligand) smiles=[C-]#[O+] denticity=1 totcharge=0
+	|--(group) ['C'] atom_site_labels=['C23'] denticity=1 connected_metals=['Re1']
+	H24-C22-P (ligand) smiles=[H]c1c([H])c([H])c(P(c2c([H])c([H])c([H])c([H])c2[H])C([H])([H])[c-]2c(C([H])([H])[H])c(C([H])([H])[H])c(C([H])([H])[H])c2C([H])([H])[H])c([H])c1[H] denticity=6 totcharge=-1
+	|--(group) ['C', 'C', 'C', 'C', 'C'] atom_site_labels=['C1', 'C5', 'C2', 'C3', 'C4'] denticity=5 haptic_type=eta5(Cp) connected_metals=['Re1']
+	|--(group) ['P'] atom_site_labels=['P1'] denticity=1 connected_metals=['Re1']
+	I (ligand) smiles=[I-] denticity=1 totcharge=-1
+	|--(group) ['I'] atom_site_labels=['I2'] denticity=1 connected_metals=['Re1']
+	I (ligand) smiles=[I-] denticity=1 totcharge=-1
+	|--(group) ['I'] atom_site_labels=['I1'] denticity=1 connected_metals=['Re1']
+Molecule 3: H24-C23-O-P-I2-Re (TM Complex) totcharge=0 spin_multiplicity=1 smiles=C[c]12->[Re+3]3456(<-[I-])(<-[I-])(<-[C-]#[O+])<-[c]1(C)[c]->3(C)[c-]->4(C[P]->5(c1ccccc1)c1ccccc1)[c]->62C
+	Re (metal) atom_site_label=Re1 metal_OS=3 metal_spin=1
+	|--coord_sphere_formula=C6-P-I2
+	|--coord_nr=5 coord_geometry=Trigonal bipyramidal geom_deviation=3.348
+	|--(group) ['C'] atom_site_labels=['C23'] denticity=1
+	|--(group) ['C', 'C', 'C', 'C', 'C'] atom_site_labels=['C1', 'C2', 'C3', 'C4', 'C5'] denticity=5 haptic_type=eta5(Cp)
+	|--(group) ['P'] atom_site_labels=['P1'] denticity=1
+	|--(group) ['I'] atom_site_labels=['I2'] denticity=1
+	|--(group) ['I'] atom_site_labels=['I1'] denticity=1
+	C-O (ligand) smiles=[C-]#[O+] denticity=1 totcharge=0
+	|--(group) ['C'] atom_site_labels=['C23'] denticity=1 connected_metals=['Re1']
+	H24-C22-P (ligand) smiles=[H]c1c([H])c([H])c(P(c2c([H])c([H])c([H])c([H])c2[H])C([H])([H])[c-]2c(C([H])([H])[H])c(C([H])([H])[H])c(C([H])([H])[H])c2C([H])([H])[H])c([H])c1[H] denticity=6 totcharge=-1
+	|--(group) ['C', 'C', 'C', 'C', 'C'] atom_site_labels=['C1', 'C2', 'C3', 'C4', 'C5'] denticity=5 haptic_type=eta5(Cp) connected_metals=['Re1']
+	|--(group) ['P'] atom_site_labels=['P1'] denticity=1 connected_metals=['Re1']
+	I (ligand) smiles=[I-] denticity=1 totcharge=-1
+	|--(group) ['I'] atom_site_labels=['I2'] denticity=1 connected_metals=['Re1']
+	I (ligand) smiles=[I-] denticity=1 totcharge=-1
+	|--(group) ['I'] atom_site_labels=['I1'] denticity=1 connected_metals=['Re1']
+UnitCell Error (mode=reconstruction): No errors found
+UnitCell Error (mode=balance_charges): No errors found
+UnitCell Error (mode=charge_assignment): No errors found
+UnitCell Error (mode=spin_assignment): No errors found