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Pymol-Scripts / Pymol-script-repo

Collected scripts for Pymol
http://www.pymolwiki.org/index.php/Git_intro
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Optimize: Read MOL strings instead of PDB strings #117

Closed Polo-Zecc closed 3 years ago

Polo-Zecc commented 3 years ago

Reading and writing to PDB strings can alter the structure of output molecules due to poor information on bonding in PDB strings. Reading and writing to MOL strings maintains structural information of output molecules.

Changes: Line 250 -> mol_string = cmd.get_str('mol',selection) 253 -> obconversion.SetInAndOutFormats('mol', 'mol') 255 -> obconversion.ReadString(mol, mol_string) 256 -> removed 269 -> mol_string = obconversion.WriteString(mol) 273 -> cmd.read_molstr(mol_string, name,state=0,finish=1,discrete=1) 280 -> mol_string = cmd.get_str('mol',selection) 283 -> obconversion.SetInAndOutFormats('mol', 'mol') 285 -> obconversion.ReadString(mol, mol_string) 286 -> removed 320 -> mol_string = obconversion.WriteString(mol) 321 -> cmd.read_molstr(mol_string, name_n,state=0,finish=1,discrete=1) 329 -> mol_string = obconversion.WriteString(mol) 331 -> cmd.read_molstr(mol_string, name,state=0,finish=1,discrete=1)

pslacerda commented 3 years ago

Thank you, @Polo-Zecc! Sorry for the delay.