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Molecule doesn't contain matching atoms for acidic_proton_loc:{}-> deprotonate returning original mol...
Molecule doesn't contain allowed_smarts: [NX3]([H])([H])[CX4][CX3](=O)[O] -> no pattern-based action will be made.
No matched atoms to delete -> embed returning original mol...
Molecule doesn't contain wanted_smarts: [NX3h1] -> continue with next pattern...
Molecule doesn't contain pattern: [NX3h1] -> linker label for N-term will not be made.
Molecule doesn't contain wanted_smarts: [CX3h1] -> continue with next pattern...
Molecule doesn't contain pattern: [CX3h1] -> linker label for C-term will not be made.
Molecule doesn't contain matching atoms for acidic_proton_loc:{}-> deprotonate returning original mol...
Molecule doesn't contain allowed_smarts: [NX3]([H])([H])[CX4][CX3](=O)[O] -> no pattern-based action will be made.
No matched atoms to delete -> embed returning original mol...
Atom # 0 (N) in mol doesn't have implicit Hs -> continue with next atom...
Molecule doesn't contain wanted_smarts: [NX3h1] -> continue with next pattern...
Molecule doesn't contain pattern: [NX3h1] -> linker label for N-term will not be made.
Molecule doesn't contain wanted_smarts: [CX3h1] -> continue with next pattern...
Molecule doesn't contain pattern: [CX3h1] -> linker label for C-term will not be made.
Template Failed to pass redundancy check -> skipping the template...
Molecule doesn't contain matching atoms for acidic_proton_loc:{}-> deprotonate returning original mol...
Molecule doesn't contain allowed_smarts: [NX3]([H])([H])[CX4][CX3](=O)[O] -> no pattern-based action will be made.
No matched atoms to delete -> embed returning original mol...
Molecule doesn't contain wanted_smarts: [NX3h1] -> continue with next pattern...
Molecule doesn't contain pattern: [NX3h1] -> linker label for N-term will not be made.
Molecule doesn't contain wanted_smarts: [CX3h1] -> continue with next pattern...
Molecule doesn't contain pattern: [CX3h1] -> linker label for C-term will not be made.
Template Failed to pass redundancy check -> skipping the template...
Lib Name: /Users/amyhe/Downloads/amber24_src/dat/leap/lib/amino19.lib
Skipping existing residue: ALA
Skipping existing residue: ARG
Skipping existing residue: ASH
Skipping existing residue: ASN
Skipping existing residue: ASP
Skipping existing residue: CYM
Skipping existing residue: CYS
Skipping existing residue: CYX
Skipping existing residue: GLH
Skipping existing residue: GLN
Skipping existing residue: GLU
Skipping existing residue: GLY
Skipping existing residue: HID
Skipping existing residue: HIE
Skipping existing residue: HIP
Success: HYP
Molecule doesn't contain the standard backbone of nucleotides or amino acids. -> no templates will be made.
Molecule doesn't contain matching atoms for acidic_proton_loc:{}-> deprotonate returning original mol...
Molecule doesn't contain allowed_smarts: [NX3]([H])([H])[CX4][CX3](=O)[O] -> no pattern-based action will be made.
No matched atoms to delete -> embed returning original mol...
[19:55:15]
****
Post-condition Violation
Element 'S-' not found
Violation occurred on line 93 in file /Users/runner/miniforge3/conda-bld/rdkit-meta_1727191760454/work/Code/GraphMol/PeriodicTable.h
Failed Expression: anum > -1
****
[19:55:15]
****
Post-condition Violation
Element 'S-' not found
Violation occurred on line 93 in file /Users/runner/miniforge3/conda-bld/rdkit-meta_1727191760454/work/Code/GraphMol/PeriodicTable.h
Failed Expression: anum > -1
****
Molecule doesn't contain wanted_smarts: [NX3h1] -> continue with next pattern...
Molecule doesn't contain pattern: [NX3h1] -> linker label for N-term will not be made.
Molecule doesn't contain wanted_smarts: [CX3h1] -> continue with next pattern...
Molecule doesn't contain pattern: [CX3h1] -> linker label for C-term will not be made.
Molecule doesn't contain matching atoms for acidic_proton_loc:{}-> deprotonate returning original mol...
Molecule doesn't contain allowed_smarts: [NX3]([H])([H])[CX4][CX3](=O)[O] -> no pattern-based action will be made.
No matched atoms to delete -> embed returning original mol...
Molecule doesn't contain allowed_smarts: [NX3][CX4][CX3](=O) -> no pattern-based action will be made.
No matched atoms to cap -> cap returning original mol...
[19:55:15]
****
Post-condition Violation
Element 'S-' not found
Violation occurred on line 93 in file /Users/runner/miniforge3/conda-bld/rdkit-meta_1727191760454/work/Code/GraphMol/PeriodicTable.h
Failed Expression: anum > -1
****
[19:55:15]
****
Post-condition Violation
Element 'S-' not found
Violation occurred on line 93 in file /Users/runner/miniforge3/conda-bld/rdkit-meta_1727191760454/work/Code/GraphMol/PeriodicTable.h
Failed Expression: anum > -1
****
Molecule doesn't contain wanted_smarts: [NX3h1] -> continue with next pattern...
Molecule doesn't contain pattern: [NX3h1] -> linker label for N-term will not be made.
Molecule doesn't contain wanted_smarts: [CX3h1] -> continue with next pattern...
Molecule doesn't contain pattern: [CX3h1] -> linker label for C-term will not be made.
Template Failed to pass redundancy check -> skipping the template...
Molecule doesn't contain matching atoms for acidic_proton_loc:{}-> deprotonate returning original mol...
Molecule doesn't contain allowed_smarts: [NX3]([H])([H])[CX4][CX3](=O)[O] -> no pattern-based action will be made.
No matched atoms to delete -> embed returning original mol...
[19:55:15]
****
Post-condition Violation
Element 'S-' not found
Violation occurred on line 93 in file /Users/runner/miniforge3/conda-bld/rdkit-meta_1727191760454/work/Code/GraphMol/PeriodicTable.h
Failed Expression: anum > -1
****
[19:55:15]
****
Post-condition Violation
Element 'S-' not found
Violation occurred on line 93 in file /Users/runner/miniforge3/conda-bld/rdkit-meta_1727191760454/work/Code/GraphMol/PeriodicTable.h
Failed Expression: anum > -1
****
Molecule doesn't contain wanted_smarts: [NX3h1] -> continue with next pattern...
Molecule doesn't contain pattern: [NX3h1] -> linker label for N-term will not be made.
Molecule doesn't contain wanted_smarts: [CX3h1] -> continue with next pattern...
Molecule doesn't contain pattern: [CX3h1] -> linker label for C-term will not be made.
Template Failed to pass redundancy check -> skipping the template...
No CCD template generated for: HYP
Skipping existing residue: ILE
Skipping existing residue: LEU
Skipping existing residue: LYN
Skipping existing residue: LYS
Skipping existing residue: MET
Skipping existing residue: PHE
Skipping existing residue: PRO
Skipping existing residue: SER
Skipping existing residue: THR
Skipping existing residue: TRP
Skipping existing residue: TYR
Skipping existing residue: VAL
Lib Name: /Users/amyhe/Downloads/amber24_src/dat/leap/lib/amino19ipq_0.9.lib
Skipping existing residue: ALA
Skipping existing residue: ARG
Skipping existing residue: ASH
Skipping existing residue: ASN
Skipping existing residue: ASP
Skipping existing residue: CYM
Skipping existing residue: CYS
Skipping existing residue: CYX
Skipping existing residue: GLH
Skipping existing residue: GLN
Skipping existing residue: GLU
Skipping existing residue: GLY
Skipping existing residue: HID
Skipping existing residue: HIE
Skipping existing residue: HIP
Skipping existing residue: ILE
Skipping existing residue: LEU
Skipping existing residue: LYN
Skipping existing residue: LYS
Skipping existing residue: MET
Success: MTB
Molecule doesn't contain the standard backbone of nucleotides or amino acids. -> no templates will be made.
Molecule doesn't contain matching atoms for acidic_proton_loc:{}-> deprotonate returning original mol...
Molecule doesn't contain allowed_smarts: [NX3]([H])([H])[CX4][CX3](=O)[O] -> no pattern-based action will be made.
No matched atoms to delete -> embed returning original mol...
Molecule doesn't contain wanted_smarts: [NX3h1] -> continue with next pattern...
Molecule doesn't contain pattern: [NX3h1] -> linker label for N-term will not be made.
Molecule doesn't contain wanted_smarts: [CX3h1] -> continue with next pattern...
Molecule doesn't contain pattern: [CX3h1] -> linker label for C-term will not be made.
Molecule doesn't contain matching atoms for acidic_proton_loc:{}-> deprotonate returning original mol...
Molecule doesn't contain allowed_smarts: [NX3]([H])([H])[CX4][CX3](=O)[O] -> no pattern-based action will be made.
No matched atoms to delete -> embed returning original mol...
Atom # 0 (N) in mol doesn't have implicit Hs -> continue with next atom...
Molecule doesn't contain wanted_smarts: [NX3h1] -> continue with next pattern...
Molecule doesn't contain pattern: [NX3h1] -> linker label for N-term will not be made.
Molecule doesn't contain wanted_smarts: [CX3h1] -> continue with next pattern...
Molecule doesn't contain pattern: [CX3h1] -> linker label for C-term will not be made.
Template Failed to pass redundancy check -> skipping the template...
Molecule doesn't contain matching atoms for acidic_proton_loc:{}-> deprotonate returning original mol...
Molecule doesn't contain allowed_smarts: [NX3]([H])([H])[CX4][CX3](=O)[O] -> no pattern-based action will be made.
No matched atoms to delete -> embed returning original mol...
Molecule doesn't contain wanted_smarts: [NX3h1] -> continue with next pattern...
Molecule doesn't contain pattern: [NX3h1] -> linker label for N-term will not be made.
Molecule doesn't contain wanted_smarts: [CX3h1] -> continue with next pattern...
Molecule doesn't contain pattern: [CX3h1] -> linker label for C-term will not be made.
Template Failed to pass redundancy check -> skipping the template...
No CCD template generated for: MTB
Success: NLE
Atom # 0 (N) in mol doesn't have implicit Hs -> continue with next atom...
Molecule doesn't contain wanted_smarts: [NX3h1] -> continue with next pattern...
Molecule doesn't contain pattern: [NX3h1] -> linker label for N-term will not be made.
Molecule doesn't contain wanted_smarts: [CX3h1] -> continue with next pattern...
Molecule doesn't contain pattern: [CX3h1] -> linker label for C-term will not be made.
Molecule doesn't contain matching atoms for acidic_proton_loc:{}-> deprotonate returning original mol...
[19:55:16]
****
Post-condition Violation
Element 'CH' not found
Violation occurred on line 93 in file /Users/runner/miniforge3/conda-bld/rdkit-meta_1727191760454/work/Code/GraphMol/PeriodicTable.h
Failed Expression: anum > -1
****
[19:55:16]
****
Post-condition Violation
Element 'NH' not found
Violation occurred on line 93 in file /Users/runner/miniforge3/conda-bld/rdkit-meta_1727191760454/work/Code/GraphMol/PeriodicTable.h
Failed Expression: anum > -1
****
[19:55:16]
****
Post-condition Violation
Element 'S-' not found
Violation occurred on line 93 in file /Users/runner/miniforge3/conda-bld/rdkit-meta_1727191760454/work/Code/GraphMol/PeriodicTable.h
Failed Expression: anum > -1
****
[19:55:16]
****
Post-condition Violation
Element 'S-' not found
Violation occurred on line 93 in file /Users/runner/miniforge3/conda-bld/rdkit-meta_1727191760454/work/Code/GraphMol/PeriodicTable.h
Failed Expression: anum > -1
****
Molecule doesn't contain matching atoms for acidic_proton_loc:{}-> deprotonate returning original mol...
Atom # 0 (N) in mol doesn't have implicit Hs -> continue with next atom...
[19:55:16]
****
Post-condition Violation
Element 'CH' not found
Violation occurred on line 93 in file /Users/runner/miniforge3/conda-bld/rdkit-meta_1727191760454/work/Code/GraphMol/PeriodicTable.h
Failed Expression: anum > -1
****
[19:55:16]
****
Post-condition Violation
Element 'S-' not found
Violation occurred on line 93 in file /Users/runner/miniforge3/conda-bld/rdkit-meta_1727191760454/work/Code/GraphMol/PeriodicTable.h
Failed Expression: anum > -1
****
[19:55:16]
****
Post-condition Violation
Element 'S-' not found
Violation occurred on line 93 in file /Users/runner/miniforge3/conda-bld/rdkit-meta_1727191760454/work/Code/GraphMol/PeriodicTable.h
Failed Expression: anum > -1
****
Molecule doesn't contain wanted_smarts: [NX3h1] -> continue with next pattern...
Molecule doesn't contain pattern: [NX3h1] -> linker label for N-term will not be made.
Molecule doesn't contain matching atoms for acidic_proton_loc:{}-> deprotonate returning original mol...
[19:55:16]
****
Post-condition Violation
Element 'NH' not found
Violation occurred on line 93 in file /Users/runner/miniforge3/conda-bld/rdkit-meta_1727191760454/work/Code/GraphMol/PeriodicTable.h
Failed Expression: anum > -1
****
[19:55:16]
****
Post-condition Violation
Element 'S-' not found
Violation occurred on line 93 in file /Users/runner/miniforge3/conda-bld/rdkit-meta_1727191760454/work/Code/GraphMol/PeriodicTable.h
Failed Expression: anum > -1
****
[19:55:16]
****
Post-condition Violation
Element 'S-' not found
Violation occurred on line 93 in file /Users/runner/miniforge3/conda-bld/rdkit-meta_1727191760454/work/Code/GraphMol/PeriodicTable.h
Failed Expression: anum > -1
****
[19:55:16]
****
Post-condition Violation
Element 'O-' not found
Violation occurred on line 93 in file /Users/runner/miniforge3/conda-bld/rdkit-meta_1727191760454/work/Code/GraphMol/PeriodicTable.h
Failed Expression: anum > -1
****
[19:55:16]
****
Post-condition Violation
Element 'O-' not found
Violation occurred on line 93 in file /Users/runner/miniforge3/conda-bld/rdkit-meta_1727191760454/work/Code/GraphMol/PeriodicTable.h
Failed Expression: anum > -1
****
Molecule doesn't contain wanted_smarts: [CX3h1] -> continue with next pattern...
Molecule doesn't contain pattern: [CX3h1] -> linker label for C-term will not be made.
Traceback (most recent call last):
File "/Users/amyhe/Desktop/0_forks/gemile/chemtempgen_for_amber.py", line 912, in fetch_from_pdb
with urllib.request.urlopen(url) as response:
File "/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/urllib/request.py", line 216, in urlopen
return opener.open(url, data, timeout)
File "/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/urllib/request.py", line 525, in open
response = meth(req, response)
File "/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/urllib/request.py", line 634, in http_response
response = self.parent.error(
File "/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/urllib/request.py", line 563, in error
return self._call_chain(*args)
File "/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/urllib/request.py", line 496, in _call_chain
result = func(*args)
File "/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/urllib/request.py", line 643, in http_error_default
raise HTTPError(req.full_url, code, msg, hdrs, fp)
urllib.error.HTTPError: HTTP Error 404: Not Found
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/Users/amyhe/Desktop/0_forks/gemile/write_additional.py", line 84, in <module>
cc_from_ccd = build_noncovalent_CC(resname)
File "/Users/amyhe/Desktop/0_forks/gemile/chemtempgen_for_amber.py", line 950, in build_noncovalent_CC
cc_from_cif = ChemicalComponent.from_cif(fetch_from_pdb(basename), basename)
File "/Users/amyhe/Desktop/0_forks/gemile/chemtempgen_for_amber.py", line 926, in fetch_from_pdb
raise RuntimeError(f"Ligand {resname} not available from rcsb.org") from e
RuntimeError: Ligand CCYM not available from rcsb.org
Molecule doesn't contain matching atoms for acidic_proton_loc:{}-> deprotonate returning original mol...
[19:55:16]
****
Post-condition Violation
Element 'CH' not found
Violation occurred on line 93 in file /Users/runner/miniforge3/conda-bld/rdkit-meta_1727191760454/work/Code/GraphMol/PeriodicTable.h
Failed Expression: anum > -1
****
[19:55:16]
****
Post-condition Violation
Element 'NH' not found
Violation occurred on line 93 in file /Users/runner/miniforge3/conda-bld/rdkit-meta_1727191760454/work/Code/GraphMol/PeriodicTable.h
Failed Expression: anum > -1
****
Molecule doesn't contain matching atoms for acidic_proton_loc:{}-> deprotonate returning original mol...
Atom # 0 (N) in mol doesn't have implicit Hs -> continue with next atom...
[19:55:16]
****
Post-condition Violation
Element 'CH' not found
Violation occurred on line 93 in file /Users/runner/miniforge3/conda-bld/rdkit-meta_1727191760454/work/Code/GraphMol/PeriodicTable.h
Failed Expression: anum > -1
****
Molecule doesn't contain wanted_smarts: [NX3h1] -> continue with next pattern...
Molecule doesn't contain pattern: [NX3h1] -> linker label for N-term will not be made.
Molecule doesn't contain matching atoms for acidic_proton_loc:{}-> deprotonate returning original mol...
[19:55:16]
****
Post-condition Violation
Element 'NH' not found
Violation occurred on line 93 in file /Users/runner/miniforge3/conda-bld/rdkit-meta_1727191760454/work/Code/GraphMol/PeriodicTable.h
Failed Expression: anum > -1
****
[19:55:16]
****
Post-condition Violation
Element 'O-' not found
Violation occurred on line 93 in file /Users/runner/miniforge3/conda-bld/rdkit-meta_1727191760454/work/Code/GraphMol/PeriodicTable.h
Failed Expression: anum > -1
****
[19:55:16]
****
Post-condition Violation
Element 'O-' not found
Violation occurred on line 93 in file /Users/runner/miniforge3/conda-bld/rdkit-meta_1727191760454/work/Code/GraphMol/PeriodicTable.h
Failed Expression: anum > -1
****
Molecule doesn't contain wanted_smarts: [CX3h1] -> continue with next pattern...
Molecule doesn't contain pattern: [CX3h1] -> linker label for C-term will not be made.
Traceback (most recent call last):
File "/Users/amyhe/Desktop/0_forks/gemile/chemtempgen_for_amber.py", line 912, in fetch_from_pdb
with urllib.request.urlopen(url) as response:
File "/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/urllib/request.py", line 216, in urlopen
return opener.open(url, data, timeout)
File "/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/urllib/request.py", line 525, in open
response = meth(req, response)
File "/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/urllib/request.py", line 634, in http_response
response = self.parent.error(
File "/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/urllib/request.py", line 563, in error
return self._call_chain(*args)
File "/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/urllib/request.py", line 496, in _call_chain
result = func(*args)
File "/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/urllib/request.py", line 643, in http_error_default
raise HTTPError(req.full_url, code, msg, hdrs, fp)
urllib.error.HTTPError: HTTP Error 404: Not Found
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/Users/amyhe/Desktop/0_forks/gemile/write_additional.py", line 84, in <module>
cc_from_ccd = build_noncovalent_CC(resname)
File "/Users/amyhe/Desktop/0_forks/gemile/chemtempgen_for_amber.py", line 950, in build_noncovalent_CC
cc_from_cif = ChemicalComponent.from_cif(fetch_from_pdb(basename), basename)
File "/Users/amyhe/Desktop/0_forks/gemile/chemtempgen_for_amber.py", line 926, in fetch_from_pdb
raise RuntimeError(f"Ligand {resname} not available from rcsb.org") from e
RuntimeError: Ligand CNLE not available from rcsb.org
Molecule doesn't contain matching atoms for acidic_proton_loc:{}-> deprotonate returning original mol...
Molecule doesn't contain allowed_smarts: [NX3]([H])([H])[CX4][CX3](=O)[O] -> no pattern-based action will be made.
No matched atoms to delete -> embed returning original mol...
Molecule doesn't contain wanted_smarts: [NX3h1] -> continue with next pattern...
Molecule doesn't contain pattern: [NX3h1] -> linker label for N-term will not be made.
Molecule doesn't contain wanted_smarts: [CX3h1] -> continue with next pattern...
Molecule doesn't contain pattern: [CX3h1] -> linker label for C-term will not be made.
Molecule doesn't contain matching atoms for acidic_proton_loc:{}-> deprotonate returning original mol...
Molecule doesn't contain allowed_smarts: [NX3]([H])([H])[CX4][CX3](=O)[O] -> no pattern-based action will be made.
No matched atoms to delete -> embed returning original mol...
Molecule doesn't contain allowed_smarts: [NX3][CX4][CX3](=O) -> no pattern-based action will be made.
No matched atoms to cap -> cap returning original mol...
Molecule doesn't contain wanted_smarts: [NX3h1] -> continue with next pattern...
Molecule doesn't contain pattern: [NX3h1] -> linker label for N-term will not be made.
Molecule doesn't contain wanted_smarts: [CX3h1] -> continue with next pattern...
Molecule doesn't contain pattern: [CX3h1] -> linker label for C-term will not be made.
Template Failed to pass redundancy check -> skipping the template...
Molecule doesn't contain matching atoms for acidic_proton_loc:{}-> deprotonate returning original mol...
Molecule doesn't contain allowed_smarts: [NX3]([H])([H])[CX4][CX3](=O)[O] -> no pattern-based action will be made.
No matched atoms to delete -> embed returning original mol...
Molecule doesn't contain wanted_smarts: [NX3h1] -> continue with next pattern...
Molecule doesn't contain pattern: [NX3h1] -> linker label for N-term will not be made.
Molecule doesn't contain wanted_smarts: [CX3h1] -> continue with next pattern...
Molecule doesn't contain pattern: [CX3h1] -> linker label for C-term will not be made.
Template Failed to pass redundancy check -> skipping the template...
Skipping existing residue: PHE
Skipping existing residue: PRO
Skipping existing residue: SER
Skipping existing residue: THR
Skipping existing residue: TRP
Skipping existing residue: TYR
Skipping existing residue: VAL
Lib Name: /Users/amyhe/Downloads/amber24_src/dat/leap/lib/aminoct19ipq_0.9.lib
Skipping existing residue: CALA
Skipping existing residue: CARG
Skipping existing residue: CASH
Skipping existing residue: CASN
Skipping existing residue: CASP
Success: CCYM
Error during template generation for: CCYM
Ligand CCYM not available from rcsb.org
Skipping existing residue: CCYS
Skipping existing residue: CCYX
Skipping existing residue: CGLH
Skipping existing residue: CGLN
Skipping existing residue: CGLU
Skipping existing residue: CGLY
Skipping existing residue: CHID
Skipping existing residue: CHIE
Skipping existing residue: CHIP
Skipping existing residue: CILE
Skipping existing residue: CLEU
Skipping existing residue: CLYN
Skipping existing residue: CLYS
Skipping existing residue: CMET
Success: CNLE
Error during template generation for: CNLE
Ligand CNLE not available from rcsb.org
Skipping existing residue: CPHE
Skipping existing residue: CPRO
Skipping existing residue: CSER
Skipping existing residue: CTHR
Skipping existing residue: CTRP
Skipping existing residue: CTYR
Skipping existing residue: CVAL
Success: NHE
Molecule doesn't contain the standard backbone of nucleotides or amino acids. -> no templates will be made.
Molecule doesn't contain matching atoms for acidic_proton_loc:{}-> deprotonate returning original mol...
Molecule doesn't contain allowed_smarts: [NX3]([H])([H])[CX4][CX3](=O)[O] -> no pattern-based action will be made.
No matched atoms to delete -> embed returning original mol...
[19:55:18]
****
Post-condition Violation
Element 'S-' not found
Violation occurred on line 93 in file /Users/runner/miniforge3/conda-bld/rdkit-meta_1727191760454/work/Code/GraphMol/PeriodicTable.h
Failed Expression: anum > -1
****
[19:55:18]
****
Post-condition Violation
Element 'S-' not found
Violation occurred on line 93 in file /Users/runner/miniforge3/conda-bld/rdkit-meta_1727191760454/work/Code/GraphMol/PeriodicTable.h
Failed Expression: anum > -1
****
[19:55:18]
****
Post-condition Violation
Element 'N+' not found
Violation occurred on line 93 in file /Users/runner/miniforge3/conda-bld/rdkit-meta_1727191760454/work/Code/GraphMol/PeriodicTable.h
Failed Expression: anum > -1
****
[19:55:18]
****
Post-condition Violation
Element 'N+' not found
Violation occurred on line 93 in file /Users/runner/miniforge3/conda-bld/rdkit-meta_1727191760454/work/Code/GraphMol/PeriodicTable.h
Failed Expression: anum > -1
****
Molecule doesn't contain wanted_smarts: [NX3h1] -> continue with next pattern...
Molecule doesn't contain pattern: [NX3h1] -> linker label for N-term will not be made.
Molecule doesn't contain wanted_smarts: [CX3h1] -> continue with next pattern...
Molecule doesn't contain pattern: [CX3h1] -> linker label for C-term will not be made.
Molecule doesn't contain matching atoms for acidic_proton_loc:{}-> deprotonate returning original mol...
Molecule doesn't contain allowed_smarts: [NX3]([H])([H])[CX4][CX3](=O)[O] -> no pattern-based action will be made.
No matched atoms to delete -> embed returning original mol...
Molecule doesn't contain allowed_smarts: [NX3][CX4][CX3](=O) -> no pattern-based action will be made.
No matched atoms to cap -> cap returning original mol...
[19:55:18]
****
Post-condition Violation
Element 'S-' not found
Violation occurred on line 93 in file /Users/runner/miniforge3/conda-bld/rdkit-meta_1727191760454/work/Code/GraphMol/PeriodicTable.h
Failed Expression: anum > -1
****
[19:55:18]
****
Post-condition Violation
Element 'S-' not found
Violation occurred on line 93 in file /Users/runner/miniforge3/conda-bld/rdkit-meta_1727191760454/work/Code/GraphMol/PeriodicTable.h
Failed Expression: anum > -1
****
[19:55:18]
****
Post-condition Violation
Element 'N+' not found
Violation occurred on line 93 in file /Users/runner/miniforge3/conda-bld/rdkit-meta_1727191760454/work/Code/GraphMol/PeriodicTable.h
Failed Expression: anum > -1
****
[19:55:18]
****
Post-condition Violation
Element 'N+' not found
Violation occurred on line 93 in file /Users/runner/miniforge3/conda-bld/rdkit-meta_1727191760454/work/Code/GraphMol/PeriodicTable.h
Failed Expression: anum > -1
****
Molecule doesn't contain wanted_smarts: [NX3h1] -> continue with next pattern...
Molecule doesn't contain pattern: [NX3h1] -> linker label for N-term will not be made.
Molecule doesn't contain wanted_smarts: [CX3h1] -> continue with next pattern...
Molecule doesn't contain pattern: [CX3h1] -> linker label for C-term will not be made.
Template Failed to pass redundancy check -> skipping the template...
Molecule doesn't contain matching atoms for acidic_proton_loc:{}-> deprotonate returning original mol...
Molecule doesn't contain allowed_smarts: [NX3]([H])([H])[CX4][CX3](=O)[O] -> no pattern-based action will be made.
No matched atoms to delete -> embed returning original mol...
[19:55:18]
****
Post-condition Violation
Element 'S-' not found
Violation occurred on line 93 in file /Users/runner/miniforge3/conda-bld/rdkit-meta_1727191760454/work/Code/GraphMol/PeriodicTable.h
Failed Expression: anum > -1
****
[19:55:18]
****
Post-condition Violation
Element 'S-' not found
Violation occurred on line 93 in file /Users/runner/miniforge3/conda-bld/rdkit-meta_1727191760454/work/Code/GraphMol/PeriodicTable.h
Failed Expression: anum > -1
****
[19:55:18]
****
Post-condition Violation
Element 'N+' not found
Violation occurred on line 93 in file /Users/runner/miniforge3/conda-bld/rdkit-meta_1727191760454/work/Code/GraphMol/PeriodicTable.h
Failed Expression: anum > -1
****
[19:55:18]
****
Post-condition Violation
Element 'N+' not found
Violation occurred on line 93 in file /Users/runner/miniforge3/conda-bld/rdkit-meta_1727191760454/work/Code/GraphMol/PeriodicTable.h
Failed Expression: anum > -1
****
Molecule doesn't contain wanted_smarts: [NX3h1] -> continue with next pattern...
Molecule doesn't contain pattern: [NX3h1] -> linker label for N-term will not be made.
Molecule doesn't contain wanted_smarts: [CX3h1] -> continue with next pattern...
Molecule doesn't contain pattern: [CX3h1] -> linker label for C-term will not be made.
Template Failed to pass redundancy check -> skipping the template...
Traceback (most recent call last):
File "/Users/amyhe/Desktop/0_forks/gemile/chemtempgen_for_amber.py", line 912, in fetch_from_pdb
with urllib.request.urlopen(url) as response:
File "/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/urllib/request.py", line 216, in urlopen
return opener.open(url, data, timeout)
File "/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/urllib/request.py", line 525, in open
response = meth(req, response)
File "/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/urllib/request.py", line 634, in http_response
response = self.parent.error(
File "/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/urllib/request.py", line 563, in error
return self._call_chain(*args)
File "/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/urllib/request.py", line 496, in _call_chain
result = func(*args)
File "/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/urllib/request.py", line 643, in http_error_default
raise HTTPError(req.full_url, code, msg, hdrs, fp)
urllib.error.HTTPError: HTTP Error 404: Not Found
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/Users/amyhe/Desktop/0_forks/gemile/write_additional.py", line 84, in <module>
cc_from_ccd = build_noncovalent_CC(resname)
File "/Users/amyhe/Desktop/0_forks/gemile/chemtempgen_for_amber.py", line 950, in build_noncovalent_CC
cc_from_cif = ChemicalComponent.from_cif(fetch_from_pdb(basename), basename)
File "/Users/amyhe/Desktop/0_forks/gemile/chemtempgen_for_amber.py", line 926, in fetch_from_pdb
raise RuntimeError(f"Ligand {resname} not available from rcsb.org") from e
RuntimeError: Ligand NCYM not available from rcsb.org
Molecule doesn't contain matching atoms for acidic_proton_loc:{}-> deprotonate returning original mol...
Molecule doesn't contain allowed_smarts: [NX3]([H])([H])[CX4][CX3](=O)[O] -> no pattern-based action will be made.
No matched atoms to delete -> embed returning original mol...
[19:55:18]
****
Post-condition Violation
Element 'N+' not found
Violation occurred on line 93 in file /Users/runner/miniforge3/conda-bld/rdkit-meta_1727191760454/work/Code/GraphMol/PeriodicTable.h
Failed Expression: anum > -1
****
[19:55:18]
****
Post-condition Violation
Element 'N+' not found
Violation occurred on line 93 in file /Users/runner/miniforge3/conda-bld/rdkit-meta_1727191760454/work/Code/GraphMol/PeriodicTable.h
Failed Expression: anum > -1
****
Molecule doesn't contain wanted_smarts: [NX3h1] -> continue with next pattern...
Molecule doesn't contain pattern: [NX3h1] -> linker label for N-term will not be made.
Molecule doesn't contain wanted_smarts: [CX3h1] -> continue with next pattern...
Molecule doesn't contain pattern: [CX3h1] -> linker label for C-term will not be made.
Molecule doesn't contain matching atoms for acidic_proton_loc:{}-> deprotonate returning original mol...
Molecule doesn't contain allowed_smarts: [NX3]([H])([H])[CX4][CX3](=O)[O] -> no pattern-based action will be made.
No matched atoms to delete -> embed returning original mol...
Molecule doesn't contain allowed_smarts: [NX3][CX4][CX3](=O) -> no pattern-based action will be made.
No matched atoms to cap -> cap returning original mol...
[19:55:18]
****
Post-condition Violation
Element 'N+' not found
Violation occurred on line 93 in file /Users/runner/miniforge3/conda-bld/rdkit-meta_1727191760454/work/Code/GraphMol/PeriodicTable.h
Failed Expression: anum > -1
****
[19:55:18]
****
Post-condition Violation
Element 'N+' not found
Violation occurred on line 93 in file /Users/runner/miniforge3/conda-bld/rdkit-meta_1727191760454/work/Code/GraphMol/PeriodicTable.h
Failed Expression: anum > -1
****
Molecule doesn't contain wanted_smarts: [NX3h1] -> continue with next pattern...
Molecule doesn't contain pattern: [NX3h1] -> linker label for N-term will not be made.
Molecule doesn't contain wanted_smarts: [CX3h1] -> continue with next pattern...
Molecule doesn't contain pattern: [CX3h1] -> linker label for C-term will not be made.
Template Failed to pass redundancy check -> skipping the template...
Molecule doesn't contain matching atoms for acidic_proton_loc:{}-> deprotonate returning original mol...
Molecule doesn't contain allowed_smarts: [NX3]([H])([H])[CX4][CX3](=O)[O] -> no pattern-based action will be made.
No matched atoms to delete -> embed returning original mol...
[19:55:18]
****
Post-condition Violation
Element 'N+' not found
Violation occurred on line 93 in file /Users/runner/miniforge3/conda-bld/rdkit-meta_1727191760454/work/Code/GraphMol/PeriodicTable.h
Failed Expression: anum > -1
****
[19:55:18]
****
Post-condition Violation
Element 'N+' not found
Violation occurred on line 93 in file /Users/runner/miniforge3/conda-bld/rdkit-meta_1727191760454/work/Code/GraphMol/PeriodicTable.h
Failed Expression: anum > -1
****
Molecule doesn't contain wanted_smarts: [NX3h1] -> continue with next pattern...
Molecule doesn't contain pattern: [NX3h1] -> linker label for N-term will not be made.
Molecule doesn't contain wanted_smarts: [CX3h1] -> continue with next pattern...
Molecule doesn't contain pattern: [CX3h1] -> linker label for C-term will not be made.
Template Failed to pass redundancy check -> skipping the template...
Traceback (most recent call last):
File "/Users/amyhe/Desktop/0_forks/gemile/chemtempgen_for_amber.py", line 912, in fetch_from_pdb
with urllib.request.urlopen(url) as response:
File "/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/urllib/request.py", line 216, in urlopen
return opener.open(url, data, timeout)
File "/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/urllib/request.py", line 525, in open
response = meth(req, response)
File "/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/urllib/request.py", line 634, in http_response
response = self.parent.error(
File "/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/urllib/request.py", line 563, in error
return self._call_chain(*args)
File "/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/urllib/request.py", line 496, in _call_chain
result = func(*args)
File "/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/urllib/request.py", line 643, in http_error_default
raise HTTPError(req.full_url, code, msg, hdrs, fp)
urllib.error.HTTPError: HTTP Error 404: Not Found
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/Users/amyhe/Desktop/0_forks/gemile/write_additional.py", line 84, in <module>
cc_from_ccd = build_noncovalent_CC(resname)
File "/Users/amyhe/Desktop/0_forks/gemile/chemtempgen_for_amber.py", line 950, in build_noncovalent_CC
cc_from_cif = ChemicalComponent.from_cif(fetch_from_pdb(basename), basename)
File "/Users/amyhe/Desktop/0_forks/gemile/chemtempgen_for_amber.py", line 926, in fetch_from_pdb
raise RuntimeError(f"Ligand {resname} not available from rcsb.org") from e
RuntimeError: Ligand NNLE not available from rcsb.org
/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/site-packages/parmed/amber/offlib.py:241: AmberWarning: Unexpected childsequence (3); expected 2 for residue S1P
warnings.warn(
/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/site-packages/parmed/amber/offlib.py:241: AmberWarning: Unexpected childsequence (3); expected 2 for residue SEP
warnings.warn(
/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/site-packages/parmed/amber/offlib.py:241: AmberWarning: Unexpected childsequence (3); expected 2 for residue H2D
warnings.warn(
/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/site-packages/parmed/amber/offlib.py:241: AmberWarning: Unexpected childsequence (3); expected 2 for residue S1P
warnings.warn(
/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/site-packages/parmed/amber/offlib.py:241: AmberWarning: Unexpected childsequence (3); expected 2 for residue SEP
warnings.warn(
/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/site-packages/parmed/amber/offlib.py:241: AmberWarning: Unexpected childsequence (3); expected 2 for residue H2D
warnings.warn(
Molecule doesn't contain matching atoms for acidic_proton_loc:{}-> deprotonate returning original mol...
Molecule doesn't contain allowed_smarts: [NX3]([H])([H])[CX4][CX3](=O)[O] -> no pattern-based action will be made.
No matched atoms to delete -> embed returning original mol...
[19:55:19]
****
Post-condition Violation
Element 'O-' not found
Violation occurred on line 93 in file /Users/runner/miniforge3/conda-bld/rdkit-meta_1727191760454/work/Code/GraphMol/PeriodicTable.h
Failed Expression: anum > -1
****
[19:55:19]
****
Post-condition Violation
Element 'O-' not found
Violation occurred on line 93 in file /Users/runner/miniforge3/conda-bld/rdkit-meta_1727191760454/work/Code/GraphMol/PeriodicTable.h
Failed Expression: anum > -1
****
Molecule doesn't contain wanted_smarts: [NX3h1] -> continue with next pattern...
Molecule doesn't contain pattern: [NX3h1] -> linker label for N-term will not be made.
Molecule doesn't contain wanted_smarts: [CX3h1] -> continue with next pattern...
Molecule doesn't contain pattern: [CX3h1] -> linker label for C-term will not be made.
Molecule doesn't contain matching atoms for acidic_proton_loc:{}-> deprotonate returning original mol...
Molecule doesn't contain allowed_smarts: [NX3]([H])([H])[CX4][CX3](=O)[O] -> no pattern-based action will be made.
No matched atoms to delete -> embed returning original mol...
Atom # 0 (N) in mol doesn't have implicit Hs -> continue with next atom...
[19:55:19]
****
Post-condition Violation
Element 'O-' not found
Violation occurred on line 93 in file /Users/runner/miniforge3/conda-bld/rdkit-meta_1727191760454/work/Code/GraphMol/PeriodicTable.h
Failed Expression: anum > -1
****
[19:55:19]
****
Post-condition Violation
Element 'O-' not found
Violation occurred on line 93 in file /Users/runner/miniforge3/conda-bld/rdkit-meta_1727191760454/work/Code/GraphMol/PeriodicTable.h
Failed Expression: anum > -1
****
Molecule doesn't contain wanted_smarts: [NX3h1] -> continue with next pattern...
Molecule doesn't contain pattern: [NX3h1] -> linker label for N-term will not be made.
Molecule doesn't contain wanted_smarts: [CX3h1] -> continue with next pattern...
Molecule doesn't contain pattern: [CX3h1] -> linker label for C-term will not be made.
Template Failed to pass redundancy check -> skipping the template...
Molecule doesn't contain matching atoms for acidic_proton_loc:{}-> deprotonate returning original mol...
Molecule doesn't contain allowed_smarts: [NX3]([H])([H])[CX4][CX3](=O)[O] -> no pattern-based action will be made.
No matched atoms to delete -> embed returning original mol...
[19:55:19]
****
Post-condition Violation
Element 'O-' not found
Violation occurred on line 93 in file /Users/runner/miniforge3/conda-bld/rdkit-meta_1727191760454/work/Code/GraphMol/PeriodicTable.h
Failed Expression: anum > -1
****
[19:55:19]
****
Post-condition Violation
Element 'O-' not found
Violation occurred on line 93 in file /Users/runner/miniforge3/conda-bld/rdkit-meta_1727191760454/work/Code/GraphMol/PeriodicTable.h
Failed Expression: anum > -1
****
Molecule doesn't contain wanted_smarts: [NX3h1] -> continue with next pattern...
Molecule doesn't contain pattern: [NX3h1] -> linker label for N-term will not be made.
Molecule doesn't contain wanted_smarts: [CX3h1] -> continue with next pattern...
Molecule doesn't contain pattern: [CX3h1] -> linker label for C-term will not be made.
Template Failed to pass redundancy check -> skipping the template...
No CCD template generated for: NHE
Skipping existing residue: NME
Num Failures: 2 Lib Name: /Users/amyhe/Downloads/amber24_src/dat/leap/lib/aminoct19ipq_0.9.lib
Lib Name: /Users/amyhe/Downloads/amber24_src/dat/leap/lib/aminont19ipq_0.9.lib
Skipping existing residue: ACE
Skipping existing residue: NALA
Skipping existing residue: NARG
Skipping existing residue: NASH
Skipping existing residue: NASN
Skipping existing residue: NASP
Success: NCYM
Error during template generation for: NCYM
Ligand NCYM not available from rcsb.org
Skipping existing residue: NCYS
Skipping existing residue: NCYX
Skipping existing residue: NGLH
Skipping existing residue: NGLN
Skipping existing residue: NGLU
Skipping existing residue: NGLY
Skipping existing residue: NHID
Skipping existing residue: NHIE
Skipping existing residue: NHIP
Skipping existing residue: NILE
Skipping existing residue: NLEU
Skipping existing residue: NLYS
Skipping existing residue: NMET
Success: NNLE
Error during template generation for: NNLE
Ligand NNLE not available from rcsb.org
Skipping existing residue: NPHE
Skipping existing residue: NPRO
Skipping existing residue: NSER
Skipping existing residue: NTHR
Skipping existing residue: NTRP
Skipping existing residue: NTYR
Skipping existing residue: NVAL
Num Failures: 2 Lib Name: /Users/amyhe/Downloads/amber24_src/dat/leap/lib/aminont19ipq_0.9.lib
Lib Name: /Users/amyhe/Downloads/amber24_src/dat/leap/lib/phosaa19SB.lib
Success: S1P
Molecule doesn't contain the standard backbone of nucleotides or amino acids. -> no templates will be made.
/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/site-packages/parmed/amber/offlib.py:241: AmberWarning: Unexpected childsequence (3); expected 2 for residue S1P
warnings.warn(
/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/site-packages/parmed/amber/offlib.py:241: AmberWarning: Unexpected childsequence (3); expected 2 for residue SEP
warnings.warn(
/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/site-packages/parmed/amber/offlib.py:241: AmberWarning: Unexpected childsequence (3); expected 2 for residue H2D
warnings.warn(
Molecule doesn't contain matching atoms for acidic_proton_loc:{}-> deprotonate returning original mol...
Molecule doesn't contain allowed_smarts: [NX3]([H])([H])[CX4][CX3](=O)[O] -> no pattern-based action will be made.
No matched atoms to delete -> embed returning original mol...
[19:55:20]
****
Post-condition Violation
Element 'O-' not found
Violation occurred on line 93 in file /Users/runner/miniforge3/conda-bld/rdkit-meta_1727191760454/work/Code/GraphMol/PeriodicTable.h
Failed Expression: anum > -1
****
[19:55:20]
****
Post-condition Violation
Element 'O-' not found
Violation occurred on line 93 in file /Users/runner/miniforge3/conda-bld/rdkit-meta_1727191760454/work/Code/GraphMol/PeriodicTable.h
Failed Expression: anum > -1
****
Molecule doesn't contain wanted_smarts: [NX3h1] -> continue with next pattern...
Molecule doesn't contain pattern: [NX3h1] -> linker label for N-term will not be made.
Molecule doesn't contain wanted_smarts: [CX3h1] -> continue with next pattern...
Molecule doesn't contain pattern: [CX3h1] -> linker label for C-term will not be made.
Molecule doesn't contain matching atoms for acidic_proton_loc:{}-> deprotonate returning original mol...
Molecule doesn't contain allowed_smarts: [NX3]([H])([H])[CX4][CX3](=O)[O] -> no pattern-based action will be made.
No matched atoms to delete -> embed returning original mol...
Atom # 0 (N) in mol doesn't have implicit Hs -> continue with next atom...
[19:55:20]
****
Post-condition Violation
Element 'O-' not found
Violation occurred on line 93 in file /Users/runner/miniforge3/conda-bld/rdkit-meta_1727191760454/work/Code/GraphMol/PeriodicTable.h
Failed Expression: anum > -1
****
[19:55:20]
****
Post-condition Violation
Element 'O-' not found
Violation occurred on line 93 in file /Users/runner/miniforge3/conda-bld/rdkit-meta_1727191760454/work/Code/GraphMol/PeriodicTable.h
Failed Expression: anum > -1
****
Molecule doesn't contain wanted_smarts: [NX3h1] -> continue with next pattern...
Molecule doesn't contain pattern: [NX3h1] -> linker label for N-term will not be made.
Molecule doesn't contain wanted_smarts: [CX3h1] -> continue with next pattern...
Molecule doesn't contain pattern: [CX3h1] -> linker label for C-term will not be made.
Template Failed to pass redundancy check -> skipping the template...
Molecule doesn't contain matching atoms for acidic_proton_loc:{}-> deprotonate returning original mol...
Molecule doesn't contain allowed_smarts: [NX3]([H])([H])[CX4][CX3](=O)[O] -> no pattern-based action will be made.
No matched atoms to delete -> embed returning original mol...
[19:55:20]
****
Post-condition Violation
Element 'O-' not found
Violation occurred on line 93 in file /Users/runner/miniforge3/conda-bld/rdkit-meta_1727191760454/work/Code/GraphMol/PeriodicTable.h
Failed Expression: anum > -1
****
[19:55:20]
****
Post-condition Violation
Element 'O-' not found
Violation occurred on line 93 in file /Users/runner/miniforge3/conda-bld/rdkit-meta_1727191760454/work/Code/GraphMol/PeriodicTable.h
Failed Expression: anum > -1
****
Molecule doesn't contain wanted_smarts: [NX3h1] -> continue with next pattern...
Molecule doesn't contain pattern: [NX3h1] -> linker label for N-term will not be made.
Molecule doesn't contain wanted_smarts: [CX3h1] -> continue with next pattern...
Molecule doesn't contain pattern: [CX3h1] -> linker label for C-term will not be made.
Template Failed to pass redundancy check -> skipping the template...
No CCD template generated for: S1P
Success: SEP
Atom # 0 (N) in mol doesn't have implicit Hs -> continue with next atom...
Molecule doesn't contain wanted_smarts: [NX3h1] -> continue with next pattern...
Molecule doesn't contain pattern: [NX3h1] -> linker label for N-term will not be made.
Molecule doesn't contain wanted_smarts: [CX3h1] -> continue with next pattern...
Molecule doesn't contain pattern: [CX3h1] -> linker label for C-term will not be made.
/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/site-packages/parmed/amber/offlib.py:241: AmberWarning: Unexpected childsequence (3); expected 2 for residue S1P
warnings.warn(
/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/site-packages/parmed/amber/offlib.py:241: AmberWarning: Unexpected childsequence (3); expected 2 for residue SEP
warnings.warn(
/Users/amyhe/micromamba/envs/has_espaloma/lib/python3.10/site-packages/parmed/amber/offlib.py:241: AmberWarning: Unexpected childsequence (3); expected 2 for residue H2D
warnings.warn(
Molecule doesn't contain matching atoms for acidic_proton_loc:{}-> deprotonate returning original mol...
Molecule doesn't contain allowed_smarts: [NX3]([H])([H])[CX4][CX3](=O)[O] -> no pattern-based action will be made.
No matched atoms to delete -> embed returning original mol...
[19:55:20]
****
Post-condition Violation
Element 'O-' not found
Violation occurred on line 93 in file /Users/runner/miniforge3/conda-bld/rdkit-meta_1727191760454/work/Code/GraphMol/PeriodicTable.h
Failed Expression: anum > -1
****
[19:55:20]
****
Post-condition Violation
Element 'O-' not found
Violation occurred on line 93 in file /Users/runner/miniforge3/conda-bld/rdkit-meta_1727191760454/work/Code/GraphMol/PeriodicTable.h
Failed Expression: anum > -1
****