To align to any frame other than the current active one Or the current frame of a different reference molecule. addBond ( 13, 18, "2" ) # Adds a double bond align ( sel, refmol = None, refsel = None, frames = None, matchingframes = False, mode = 'index', _logger = True ) #Īlign a given set of frames of this molecule to either the current active frame of this molecule (mol.frame) Idx2 ( int) – The index of the other atomītype ( str) – The type of the bond as a string ![]() If the bond already exists it will only update it’s type Parameters : The name used for the molecule in the viewer Type : The step for each frame of the simulation Type :Ī list of representations that is used when visualizing the molecule Type : The time for each frame of the simulation Type : The location of the files used to read this Molecule Type : atomselection and get commands will be calculated on this frame. Type :Ī dictionary containing crystallographic information. Type :Ītom quadruplets corresponding to improper dihedral terms. Type :Ītom quadruplets corresponding to dihedral terms. Type :Ītom triplets corresponding to angle terms. The type of each bond in Molecule.bonds if available. Type :Ītom pairs corresponding to bond terms. If none are set they are assumed to be 90 degrees. Type :Ī float32 array with shape (3, nframes) containing the periodic box dimensions of an MD trajectory. Type :Ī float32 array with shape (natoms, 3, nframes) containing the coordinates of the Molecule. The beta factor value of each atom if read from a PDB. The occupancy value of each atom if read from a PDB. The insertion flag of the atoms if read from a PDB. ![]() The alternative location flag of the atoms if read from a PDB. The record field of a PDB file if the topology was read from a PDB. Number of residues in the Molecule Type : Number of conformers / simulation frames in the Molecule Type : > mol = Molecule ( './test/data/dhfr/dhfr.pdb' ) > mol = Molecule ( '3PTB', name = 'Trypsin' ) > print ( mol ) Molecule with 1701 atoms and 1 frames Atom field - altloc shape: (1701,) Atom field - atomtype shape: (1701,). Kwargs – Accepts any further arguments that should be passed to the Molecule.read method. Name ( str) – Give a name to the Molecule that will be used for visualization ![]() If there’s no file and the value is four characters longĪssume it is a PDB accession code and try to download from the RCSB web server. Parameters :įilename ( str or list of str) – Optionally load a PDB file from the specified file. The coordinates are accessible via the coords attribute Occupancy, beta, segid, element, charge). The following PDB fieldsĪre accessible as attributes (record, serial, name, altloc, resname, chain, resid, insertion, coords, It can contain multipleĬonformations and trajectories, however all operations are done on the current frame. Molecule contains all the fields of a PDB and it is independent of any force field. Molecule ( filename = None, name = None, ** kwargs ) #Ĭlass to manipulate molecular structures. Moleculekit.molecule module # class moleculekit.molecule.
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