Reading PDB files from string

Launching MSpaceEasy with a PDB String


And still being able to switch off and one the chains, waters, ligand etc








We're trying to create an instance of MSpaceEasy and pass into it a PDB file as a string.


If we use the MolImporter class to instantiate a Molecule from the string and pass it to MarvinSpace using:





MspaceEasy.AddMolecule(Molecule m ), we can view the molecule fine but the information inside the PDB is lost it considers it to be one large molecule with fragment loosing the identification of the ligand, chains etc.





This has forced us to use the AddMolecule method with the string overload. However this only works correctly if we write the PDB file to disc and read from file using the full file path to the PDB.





MspaceEasy.AddMolecule(string s) where s= File path to PDF file





Then we get everthing in MSpace and the ligands etc work.





What we'd like to be able todo is pass the PDB file as a single string in memory and have Mspace still know about its ligand, chains, waters etc.








Can you tell us the best way to achieve this or put in an enhancement to allow the PDB text to passed in programmatically.





Thanks Andrew


PS: This is used to visualise proteins in nodes4knime.


http://sourceforge.net/projects/nodes4knime/ .

Hi Andrew,





thank you, this function will be available in the next patch release.


(Probably it will come with 5.0.1 in the days, we will put a notification here.)





Kind regards,


Judit

Hi Andrew,





The development of Marvinspace has very low priority at the moment. This, however, does not mean that the feature you proposed is not considered to be an important one. At present we do not have enough capacity to do this work.





Thank you for your understanding,





Miklos Vargyas