Merge pull request #832 from padix-key/solvent-filter

padix-key · web-flow · commit 18b3fe3fe64c · 2025-10-10T12:34:19.000+02:00
Expand list of solvent compounds
diff --git a/src/biotite/structure/filter.py b/src/biotite/structure/filter.py
@@ -63,7 +63,8 @@
 ]
 _canonical_nucleotide_list = ["A", "DA", "G", "DG", "C", "DC", "U", "DT"]
 
-_solvent_list = ["HOH", "SOL"]
+# Residue names of solvent molecules non only in CCD, but also from modeling software
+_solvent_list = ["HOH", "DOD", "SOL", "WAT", "H2O", "TIP3", "TIP4", "TIP5"]
 
 _peptide_backbone_atoms = ["N", "CA", "C"]
 _phosphate_backbone_atoms = ["P", "O5'", "C5'", "C4'", "C3'", "O3'"]

Original file line number	Diff line number	Diff line change
`@@ -63,7 +63,8 @@`
`63`	`63`	`]`
`64`	`64`	`_canonical_nucleotide_list = ["A", "DA", "G", "DG", "C", "DC", "U", "DT"]`
`65`	`65`
`66`		`-_solvent_list = ["HOH", "SOL"]`
	`66`	`+# Residue names of solvent molecules non only in CCD, but also from modeling software`
	`67`	`+_solvent_list = ["HOH", "DOD", "SOL", "WAT", "H2O", "TIP3", "TIP4", "TIP5"]`
`67`	`68`
`68`	`69`	`_peptide_backbone_atoms = ["N", "CA", "C"]`
`69`	`70`	`_phosphate_backbone_atoms = ["P", "O5'", "C5'", "C4'", "C3'", "O3'"]`