htmd.util module

htmd.util.assertSameAsReferenceDir(compareDir, outdir='.')

Check if files in refdir are present in the directory given as second argument AND their content matches.

Raise an exception if not.

htmd.util.diffMolecules(mol1, mol2, sel=None)

Check that name, resname, resid, insertion codes match between two molecules.

Coordinates are not checked.

Parameters

  • mol1 (Molecule) – first structure to compare

  • mol2 (Molecule) – second structure to compare

  • sel (str) – compare only after filtering to this Atom selection string. See more here

Returns

diff – a list of differences, as human-readable strings (empty if structures are equal).

Return type

list

Examples

>>> m=Molecule("3PTB")
>>> m2=m.copy()
>>> m2.set("resname","HIE","resid 91")
>>> diffMolecules(m,m2,sel="name CA")
['CA   HIS    91     vs   CA   HIE    91  ']
htmd.util.ensurelist(tocheck, tomod=None)

Convert np.ndarray and scalars to lists.

Lists and tuples are left as is. If a second argument is given, the type check is performed on the first argument, and the second argument is converted.

htmd.util.getPdbStrings(mol, sel=None, onlyAtom=True)

Return the PDB corresponding to molecule and selection, as a list of strings.

Parameters

  • mol (Molecule object) – The Molecule object

  • sel (str) – Atom selection string for what to be outputted. See more here

  • onlyAtom (bool) – Only return ATOM/HETATM records (default True)

Examples

>>> m = Molecule("3PTB")
>>> getPdbStrings(m, "resname BEN")         
['HETATM    1  C1  BEN A   1      -1.853  14.311  16.658  1.00 19.86      1    C  ',
 'HETATM    2  C2  BEN A   1      -2.107  15.653  16.758  1.00 19.86      1    C  ',
 'HETATM    3  C3  BEN A   1      -1.774  16.341  17.932  1.00 19.86      1    C  ',
 'HETATM    4  C4  BEN A   1      -1.175  15.662  19.005  1.00 19.86      1    C  ',
 'HETATM    5  C5  BEN A   1      -0.914  14.295  18.885  1.00 19.86      1    C  ',
 'HETATM    6  C6  BEN A   1      -1.257  13.634  17.708  1.00 19.86      1    C  ',
 'HETATM    7  C   BEN A   1      -2.193  13.627  15.496  1.00 19.86      1    C  ',
 'HETATM    8  N1  BEN A   1      -2.797  14.235  14.491  1.00 19.86      1    N  ',
 'HETATM    9  N2  BEN A   1      -1.762  12.391  15.309  1.00 19.86      1    N  ']
htmd.util.tempname(suffix='', create=False)
htmd.util.testDHFR()