Larkinsd/feature energy injection#247
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…f only judging the first atom.
This is typical in qFit refined structures, where only one alt_loc is kept after removing marginal conformations.
Shaoqz/feature exp esm support
…nd. Change the position of conda activate command to make sure python environment is not subsituted by the one in the software stack.
when moldesc file is found in ncaa and is mol2. Also fix a potential problem that when a parameterizer.run() is used multiple times, the self.additional_tleap_lines will accumulate the bond lines and cause problems. Now run() use a local variable to store the additional tleap lines and will not change the self.additional_tleap_lines.
Bugfix: fix the problem that not adding bond lines when moldesc file is found in ncaa_lib and is mol2.
multiwfn_interface.get_bond_dipole returns 0.0 and (0.0, 0.0, 0.0) sliently. Now, it will check both target_bond and reverse_bond in the dip file, and return the correct value if reverse_bond exist. If neither target_bond nor reverse_bond exist, it will raise ValueError.
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