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pierrepo / grodecoder

GroDecoder extracts and identifies the molecular components of a structure file (PDB or GRO) issued from a molecular dynamics simulation.
https://grodecoder.streamlit.app/
BSD 3-Clause "New" or "Revised" License
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Add water model tip5pe, tip4pew and spce #28

Closed pierrepo closed 3 months ago

pierrepo commented 3 months ago
KarinDuong commented 3 months ago

@pierrepo but it's already added to SOLVANTS_LIST (file : mol_def.py, line 76 to 81)

SOLVANTS_LIST = [{"name": "solvant water TIP3P", "res_name": "TIP3", "atom_names": ["OH2"]}, {"name": "solvant water TIP3P", "res_name": "SOL", "atom_names": ["OW", "HW1", "HW2"]}, # TIP3 {"name": "solvant water TIP4P", "res_name": "SOL", "atom_names": ["OW", "HW1", "HW2", "MW"]}, # TIP4 {"name": "solvant water TIP5P", "res_name": "SOL", "atom_names": ["OW", "HW1", "HW2", "LP1", "LP2"]}, # TIP5 {"name": "solvant urea", "res_name": "URE", "atom_names": ["C", "O", "N1", "H11", "H12", "N2", "H21", "H22"]}, ]

pierrepo commented 3 months ago

@KarinDuong please be explicit if models are identical based on their residue and atom names by expanding the name field.

For instance : solvant water TIP3P -> solvant water TIP3P/spc/spce