moleculekit.readers module

moleculekit.readers.BINCOORread(filename, frame=None, topoloc=None)
moleculekit.readers.CRDCARDread(filename, frame=None, topoloc=None)

https://www.charmmtutorial.org/index.php/CHARMM:The_Basics title = * WATER title = * DATE: 4/10/07 4:25:51 CREATED BY USER: USER title = * Number of atoms (NATOM) = 6 Atom number (ATOMNO) = 1 (just an exmaple) Residue number (RESNO) = 1 Residue name (RESName) = TIP3 Atom type (TYPE) = OH2 Coordinate (X) = -1.30910 Coordinate (Y) = -0.25601 Coordinate (Z) = -0.24045 Segment ID (SEGID) = W Residue ID (RESID) = 1 Atom weight (Weighting) = 0.00000

now what that looks like…

  • WATER

  • DATE: 4/10/07 4:25:51 CREATED BY USER: USER

  • 6 1 1 TIP3 OH2 -1.30910 -0.25601 -0.24045 W 1 0.00000 2 1 TIP3 H1 -1.85344 0.07163 0.52275 W 1 0.00000 3 1 TIP3 H2 -1.70410 0.16529 -1.04499 W 1 0.00000 4 2 TIP3 OH2 1.37293 0.05498 0.10603 W 2 0.00000 5 2 TIP3 H1 1.65858 -0.85643 0.10318 W 2 0.00000 6 2 TIP3 H2 0.40780 -0.02508 -0.02820 W 2 0.00000

moleculekit.readers.CRDread(filename, frame=None, topoloc=None)
exception moleculekit.readers.FormatError(value)

Bases: Exception

moleculekit.readers.GJFread(filename, frame=None, topoloc=None)
moleculekit.readers.GROTOPread(filename, frame=None, topoloc=None)
moleculekit.readers.MAEread(fname, frame=None, topoloc=None)

Reads maestro files.

Parameters

fname (str) – .mae file

Returns

  • topo (Topology)

  • coords (list of lists)

moleculekit.readers.MDTRAJTOPOread(filename, frame=None, topoloc=None)
moleculekit.readers.MDTRAJread(filename, frame=None, topoloc=None)
moleculekit.readers.MOL2read(filename, frame=None, topoloc=None, singlemol=True)
class moleculekit.readers.MolFactory

Bases: object

This class converts Topology and Trajectory data into Molecule objects

static construct(topos, trajs, filename, frame, validateElements=True, uniqueBonds=False)
moleculekit.readers.PDBQTread(filename, frame=None, topoloc=None)
moleculekit.readers.PDBXMMCIFread(filename, frame=None, topoloc=None)
moleculekit.readers.PDBread(filename, mode='pdb', frame=None, topoloc=None, validateElements=True, uniqueBonds=True)
moleculekit.readers.PREPIread(filename, frame=None, topoloc=None)
moleculekit.readers.PRMTOPread(filename, frame=None, topoloc=None)
moleculekit.readers.PSFread(filename, frame=None, topoloc=None, validateElements=True)
moleculekit.readers.RTFread(filename, frame=None, topoloc=None)
class moleculekit.readers.Topology(pandasdata=None)

Bases: object

property atominfo
fromMolecule(mol)
exception moleculekit.readers.TopologyInconsistencyError(value)

Bases: Exception

class moleculekit.readers.Trajectory(coords=None, box=None, boxangles=None, fileloc=None, step=None, time=None)

Bases: object

property numFrames
moleculekit.readers.XSCread(filename, frame=None, topoloc=None)
moleculekit.readers.XTCread(filename, frame=None, topoloc=None)

Reads XTC file

Parameters
  • filename (str) – Path of xtc file.

  • frame (list) – A list of integer frames which we want to read from the file. If None will read all.

Returns

  • coords (nd.array)

  • box (nd.array)

  • boxangles (nd.array)

  • step (nd.array)

  • time (nd.array)

moleculekit.readers.XYZread(filename, frame=None, topoloc=None)
moleculekit.readers.pdbGuessElementByName(elements, names, onlymissing=True)

https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#misalignment which states that elements should be right-aligned in columns 13-14 unless it’s a 4 letter name when it would end up being left-aligned.