Path C - Module 53: Capability Matrix & Config

Identify which forms support drug binding attributes. In this module, you will learn about molsysmt.supported.

import molsysmt as msm
msm.supported.forms()

Form	Type	Dependency	Info
biopython.PDBStructure	class	Bio
biopython.Seq	class	Bio
biopython.SeqRecord	class	Bio
cupy_ndarray	class	cupy
MDAnalysis.AtomGroup	class	MDAnalysis
MDAnalysis.Topology	class	MDAnalysis
MDAnalysis.topology.PDBParser	class	MDAnalysis
MDAnalysis.Universe	class	MDAnalysis
mdtraj.AmberRestartFile	class	mdtraj
mdtraj.DCDTrajectoryFile	class	mdtraj
mdtraj.GroTrajectoryFile	class	mdtraj
mdtraj.HDF5TrajectoryFile	class	mdtraj
mdtraj.PDBTrajectoryFile	class	mdtraj
mdtraj.Topology	class	mdtraj
mdtraj.Trajectory	class	mdtraj
mdtraj.XTCTrajectoryFile	class	mdtraj
mmcif.PdbxContainers.DataContainer	class	Native
molsysmt.CIFFileHandler	class	Native
molsysmt.GROFileHandler	class	Native
molsysmt.H5MSMFileHandler	class	Native
molsysmt.MolecularMechanics	class	Native
molsysmt.MolecularMechanicsDict	class	Native
molsysmt.MolSys	class	Native
molsysmt.MolSysBuilder	class	Native	Editable native molecular system builder.
molsysmt.MolSysDict	class	Native	Declarative serializable molecular system dictionary.
molsysmt.PDBFileHandler	class	Native
molsysmt.Structures	class	Native
molsysmt.StructuresDict	class	Native
molsysmt.Topology	class	Native
molsysmt.TopologyDict	class	Native	Declared, serializable topology representation.
molsysmt.ViewerJSON	class	Native
molsysviewer.MolSysView	class	molsysviewer	MolSysViewer visualization native object.
networkx.Graph	class	Native
nglview.NGLWidget	class	nglview
openff.Molecule	class	openff.toolkit	OpenFF Toolkit Molecule
openff.Topology	class	openff.toolkit	OpenFF Toolkit Topology
openmm.AmberInpcrdFile	class	Native
openmm.AmberPrmtopFile	class	Native
openmm.CharmmCrdFile	class	Native
openmm.CharmmPsfFile	class	Native
openmm.Context	class	openmm
openmm.GromacsGroFile	class	openmm
openmm.GromacsTopFile	class	openmm
openmm.Modeller	class	openmm
openmm.PDBFile	class	openmm
openmm.Simulation	class	openmm
openmm.State	class	Native
openmm.System	class	openmm
openmm.Topology	class	openmm
parmed.GromacsTopologyFile	class	parmed
parmed.Structure	class	parmed
pdbfixer.PDBFixer	class	pdbfixer
pytraj.Topology	class	pytraj
pytraj.Trajectory	class	pytraj
rdkit.Mol	class	rdkit
XYZ	class	Native
file:bcif	file	Native
file:bcif.gz	file	Native
file:cif	file	Native
file:cif.gz	file	Native
file:crd	file	Native	CHARMM card (CRD) file format with coordinates.
file:dcd	file	mdtraj
file:fasta	file	Native	FASTA sequence file format
file:gro	file	openmm	Gromacs gro file format
file:h5	file	mdtraj
file:h5msm	file	Native
file:inpcrd	file	openmm	AMBER ASCII restart/inpcrd file format
file:mdcrd	file	Native	AMBER MDCRD coordinate/trajectory file format
file:mol2	file	parmed
file:molsys_yaml	file	yaml	Human-authored declarative YAML molecular system file.
file:pdb	file	Native	Protein Data Bank file format
file:pir	file	Native	PIR/NBRF sequence file format
file:prmtop	file	openmm	AMBER parameter/topology file format
file:psf	file	openmm	CHARMM Protein Structure File (PSF).
file:smi	file	rdkit	SMILES file format (.smi)
file:structures_yaml	file	yaml	Human-authored declarative YAML structures file.
file:top	file	parmed	GROMACS topology file format
file:topology_yaml	file	yaml	Human-authored declarative YAML topology file.
file:trjpk	file	Native
file:xtc	file	mdtraj
file:xyz	file	Native	MolSysMT ASCII XYZ coordinate file format
file:xyznpy	file	Native	XYZ file format like saved with Numpy
string:alphafold_id	string	Native
string:amino_acids_1	string	Native
string:amino_acids_3	string	Native
string:pdb_id	string	Native
string:pdb_text	string	Native	Protein Data Bank file format
string:smiles	string	rdkit	SMILES (Simplified Molecular Input Line Entry System) string
string:uniprot_id	string	Native	UniProt accession number string