Items and forms

Forms

Molecular systems can take different forms. The same system can be encoded for instance as a pdb file, as a python object of mdtraj.Trajectory class, as a UniProt id code or as an aminoacid sequence. Not all forms have the same level of detail, probably some forms have more information, some other less information, but all are forms of the same molecular system. MolSysMT takes the concept ‘form’ as a central concept at the center of the multitool. Sometimes we have the system in form A, an mmtf file for example, and to be able to make a specific analysis with a given tool form A needs to be converted to form B -an mdtraj.Topology-, and then we probably need a third library to modify the system but this time the system must be encoded in form C -a parmed.Structure-. And so on. Usually, you can find the way to convert these forms in the documentation of those libraries as well as the way those analysis are invoked. To avoid the time of connecting those pieces, MolSysMT provides with a framework where different tools, nativo and coming from other libraries, can be easily plugged to build up the structure of pipes configuring the workflow you need.

At this moment these are the forms MolSysMT can handle.

Files

The updated list of forms type file can be printed out with the method MolSysMT.info_forms().

msm.info_forms(form_type='file')

Form	Type	Info
file:crd	file	CHARMM card (CRD) file format with coordinates.
file:dcd	file
file:fasta	file
file:gro	file	Gromacs gro file format
file:h5	file
file:inpcrd	file	AMBER ASCII restart/inpcrd file format
file:mdcrd	file	AMBER mdcrd file format
file:mmtf	file
file:mol2	file
file:pdb	file	Protein Data Bank file format
file:pir	file
file:prmtop	file	AMBER parameter/topology file format
file:smi	file
file:top	file
file:xtc	file
file:xyz	file	XYZ file format
file:xyznpy	file	XYZ file format like saved with Numpy

Classes

MolSysMT works with python classes coming from many other libraries such as MDTraj, PyTraj, MDAnalysis, OpenMM, ParmEd among others; as well as some native classes.

msm.info_forms(form_type='class')

Form	Type	Info
MolecularMechanicsDict	class
SimulationDict	class
XYZ	class
mdanalysis.Topology	class
mdanalysis.Universe	class
mdtraj.AmberRestartFile	class
mdtraj.GroTrajectoryFile	class
mdtraj.HDF5TrajectoryFile	class
mdtraj.PDBTrajectoryFile	class
mdtraj.Topology	class
mdtraj.Trajectory	class
mdtraj.XTCTrajectoryFile	class
mmtf.MMTFDecoder	class
molsysmt.MolSys	class
molsysmt.MolecularMechanics	class
molsysmt.Simulation	class
molsysmt.Topology	class
molsysmt.Trajectory	class
molsysmt.TrajectoryFile	class
networkx.Graph	class
openmm.AmberInpcrdFile	class
openmm.AmberPrmtopFile	class
openmm.Context	class
openmm.GromacsGroFile	class
openmm.GromacsTopFile	class
openmm.Modeller	class
openmm.PDBFile	class
openmm.Simulation	class
openmm.System	class
openmm.Topology	class
parmed.GromacsTopologyFile	class
parmed.Structure	class
pdbfixer.PDBFixer	class
pytraj.Topology	class
pytraj.Trajectory	class

Ids

There are several databases or encoding systems where molecular systems take the form of a string of characters. This is the case of the Protein Data Bank, the ChEMBL database or the UniProt codes. The following table summarizes the list of Ids recognized by MolSysMT.

msm.info_forms(form_type='id')

Form	Type	Info
id:PDB	id

Notice that form names here ends with ‘:id’. This suffix is used to distinguish them from other form types. ‘pdb’ is a form name corresponding to a file and ‘pdb:id’ is the id form.

Sequences

Molecular systems can be determined by a sequence of elements. For instance, a peptide as Metenkephaline can be defined by means of its aminoacids sequence. These are the forms of type sequence MolSysMT can handle:

msm.info_forms(form_type='string')

Form	Type	Info
string:aminoacids1	string
string:aminoacids3	string
string:pdb	string	Protein Data Bank file format

Viewers

The last molecular systems form we usually need its the graphical representation: the viewer. MolSysMT works with viewers as if they were a different form type. These are the viewers MolSysMT can work with:

msm.info_forms(form_type='viewer')

Form	Type	Info
nglview.NGLWidget	viewer	NGLView visualization native object