コード例 #1
0
ファイル: pdbfile.py プロジェクト: luponzo86/ProDy
def writePQRStream(stream, atoms, **kwargs):
    if isinstance(atoms, Atom):
        atoms = Selection(atoms.getAtomGroup(), [atoms.getIndex()],
                          atoms.getACSIndex(),
                          'index ' + str(atoms.getIndex()))
    n_atoms = atoms.numAtoms()
    atomnames = atoms.getNames()
    if atomnames is None:
        raise RuntimeError('atom names are not set')
    for i, an in enumerate(atomnames):
        lenan = len(an)
        if lenan < 4:
            atomnames[i] = ' ' + an
        elif lenan > 4:
            atomnames[i] = an[:4]

    s_or_u = np.array(['a']).dtype.char

    resnames = atoms._getResnames()
    if resnames is None:
        resnames = ['UNK'] * n_atoms
    resnums = atoms._getResnums()
    if resnums is None:
        resnums = np.ones(n_atoms, int)
    chainids = atoms._getChids()
    if chainids is None:
        chainids = np.zeros(n_atoms, s_or_u + '1')
    charges = atoms._getCharges()
    if charges is None:
        charges = np.zeros(n_atoms, float)
    radii = atoms._getRadii()
    if radii is None:
        radii = np.zeros(n_atoms, float)
    icodes = atoms._getIcodes()
    if icodes is None:
        icodes = np.zeros(n_atoms, s_or_u + '1')
    hetero = ['ATOM'] * n_atoms
    heteroflags = atoms._getFlags('hetatm')
    if heteroflags is None:
        heteroflags = atoms._getFlags('hetero')
    if heteroflags is not None:
        hetero = np.array(hetero, s_or_u + '6')
        hetero[heteroflags] = 'HETATM'
    altlocs = atoms._getAltlocs()
    if altlocs is None:
        altlocs = np.zeros(n_atoms, s_or_u + '1')

    format = ('{0:6s} {1:5d} {2:4s} {3:1s}' +
              '{4:4s} {5:1s} {6:4d} {7:1s}   ' +
              '{8:8.3f} {9:8.3f} {10:8.3f}' + '{11:8.4f} {12:7.4f}\n').format
    coords = atoms._getCoords()
    write = stream.write
    for i, xyz in enumerate(coords):
        write(
            format(hetero[i], i + 1,
                   atomnames[i], altlocs[i], resnames[i], chainids[i],
                   int(resnums[i]), icodes[i], xyz[0], xyz[1], xyz[2],
                   charges[i], radii[i]))
コード例 #2
0
ファイル: pdbfile.py プロジェクト: prody/ProDy
def writePQRStream(stream, atoms, **kwargs):
    if isinstance(atoms, Atom):
        atoms = Selection(atoms.getAtomGroup(), [atoms.getIndex()],
                          atoms.getACSIndex(),
                          'index ' + str(atoms.getIndex()))
    n_atoms = atoms.numAtoms()
    atomnames = atoms.getNames()
    if atomnames is None:
        raise RuntimeError('atom names are not set')
    for i, an in enumerate(atomnames):
        lenan = len(an)
        if lenan < 4:
            atomnames[i] = ' ' + an
        elif lenan > 4:
            atomnames[i] = an[:4]

    s_or_u = np.array(['a']).dtype.char

    resnames = atoms._getResnames()
    if resnames is None:
        resnames = ['UNK'] * n_atoms
    resnums = atoms._getResnums()
    if resnums is None:
        resnums = np.ones(n_atoms, int)
    chainids = atoms._getChids()
    if chainids is None:
        chainids = np.zeros(n_atoms, s_or_u + '1')
    charges = atoms._getCharges()
    if charges is None:
        charges = np.zeros(n_atoms, float)
    radii = atoms._getRadii()
    if radii is None:
        radii = np.zeros(n_atoms, float)
    icodes = atoms._getIcodes()
    if icodes is None:
        icodes = np.zeros(n_atoms, s_or_u + '1')
    hetero = ['ATOM'] * n_atoms
    heteroflags = atoms._getFlags('hetatm')
    if heteroflags is None:
        heteroflags = atoms._getFlags('hetero')
    if heteroflags is not None:
        hetero = np.array(hetero, s_or_u + '6')
        hetero[heteroflags] = 'HETATM'
    altlocs = atoms._getAltlocs()
    if altlocs is None:
        altlocs = np.zeros(n_atoms, s_or_u + '1')

    format = ('{0:6s} {1:5d} {2:4s} {3:1s}' +
              '{4:4s} {5:1s} {6:4d} {7:1s}   ' +
              '{8:8.3f} {9:8.3f} {10:8.3f}' +
              '{11:8.4f} {12:7.4f}\n').format
    coords = atoms._getCoords()
    write = stream.write
    for i, xyz in enumerate(coords):
        write(format(hetero[i], i+1, atomnames[i], altlocs[i],
                     resnames[i], chainids[i], int(resnums[i]),
                     icodes[i], xyz[0], xyz[1], xyz[2], charges[i], radii[i]))
コード例 #3
0
def writePQR(filename, atoms):
    """Write *atoms* in PQR format to a file with name *filename*.  Only
    current coordinate set is written.  Returns *filename* upon success.  If
    *filename* ends with :file:`.gz`, a compressed file will be written."""

    if not isinstance(atoms, Atomic):
        raise TypeError('atoms does not have a valid type')
    if isinstance(atoms, Atom):
        atoms = Selection(atoms.getAtomGroup(), [atoms.getIndex()],
                          atoms.getACSIndex(),
                          'index ' + str(atoms.getIndex()))
    stream = openFile(filename, 'w')
    n_atoms = atoms.numAtoms()
    atomnames = atoms.getNames()
    if atomnames is None:
        raise RuntimeError('atom names are not set')
    for i, an in enumerate(atomnames):
        lenan = len(an)
        if lenan < 4:
            atomnames[i] = ' ' + an
        elif lenan > 4:
            atomnames[i] = an[:4]

    s_or_u = np.array(['a']).dtype.char

    resnames = atoms._getResnames()
    if resnames is None:
        resnames = ['UNK'] * n_atoms
    resnums = atoms._getResnums()
    if resnums is None:
        resnums = np.ones(n_atoms, int)
    chainids = atoms._getChids()
    if chainids is None:
        chainids = np.zeros(n_atoms, s_or_u + '1')
    charges = atoms._getCharges()
    if charges is None:
        charges = np.zeros(n_atoms, float)
    radii = atoms._getRadii()
    if radii is None:
        radii = np.zeros(n_atoms, float)
    icodes = atoms._getIcodes()
    if icodes is None:
        icodes = np.zeros(n_atoms, s_or_u + '1')
    hetero = ['ATOM'] * n_atoms
    heteroflags = atoms._getFlags('hetatm')
    if heteroflags is None:
        heteroflags = atoms._getFlags('hetero')
    if heteroflags is not None:
        hetero = np.array(hetero, s_or_u + '6')
        hetero[heteroflags] = 'HETATM'
    altlocs = atoms._getAltlocs()
    if altlocs is None:
        altlocs = np.zeros(n_atoms, s_or_u + '1')

    format = ('{0:6s}{1:5d} {2:4s}{3:1s}' + '{4:4s}{5:1s}{6:4d}{7:1s}   ' +
              '{8:8.3f}{9:8.3f}{10:8.3f}' + '{11:8.4f}{12:7.4f}\n').format
    coords = atoms._getCoords()
    write = stream.write
    for i, xyz in enumerate(coords):
        write(
            format(hetero[i], i + 1,
                   atomnames[i], altlocs[i], resnames[i], chainids[i],
                   int(resnums[i]), icodes[i], xyz[0], xyz[1], xyz[2],
                   charges[i], radii[i]))
    write('TER\nEND')
    stream.close()
    return filename
コード例 #4
0
ファイル: functions.py プロジェクト: gokceneraslan/ProDy
def writePQR(filename, atoms):
    """Write *atoms* in PQR format to a file with name *filename*.  Only 
    current coordinate set is written.  Returns *filename* upon success.  If 
    *filename* ends with :file:`.gz`, a compressed file will be written."""

    if not isinstance(atoms, Atomic):
        raise TypeError("atoms does not have a valid type")
    if isinstance(atoms, Atom):
        atoms = Selection(
            atoms.getAtomGroup(), [atoms.getIndex()], atoms.getACSIndex(), "index " + str(atoms.getIndex())
        )
    stream = openFile(filename, "w")
    n_atoms = atoms.numAtoms()
    atomnames = atoms.getNames()
    if atomnames is None:
        raise RuntimeError("atom names are not set")
    for i, an in enumerate(atomnames):
        lenan = len(an)
        if lenan < 4:
            atomnames[i] = " " + an
        elif lenan > 4:
            atomnames[i] = an[:4]
    resnames = atoms._getResnames()
    if resnames is None:
        resnames = ["UNK"] * n_atoms
    resnums = atoms._getResnums()
    if resnums is None:
        resnums = np.ones(n_atoms, int)
    chainids = atoms._getChids()
    if chainids is None:
        chainids = np.zeros(n_atoms, "|S1")
    charges = atoms._getCharges()
    if charges is None:
        charges = np.zeros(n_atoms, float)
    radii = atoms._getRadii()
    if radii is None:
        radii = np.zeros(n_atoms, float)
    icodes = atoms._getIcodes()
    if icodes is None:
        icodes = np.zeros(n_atoms, "|S1")
    hetero = ["ATOM"] * n_atoms
    heteroflags = atoms._getHeteros()
    if heteroflags is not None:
        hetero = np.array(hetero, "|S6")
        hetero[heteroflags] = "HETATM"
    altlocs = atoms._getAltlocs()
    if altlocs is None:
        altlocs = np.zeros(n_atoms, "|S1")

    format = (
        "{0:6s}{1:5d} {2:4s}{3:1s}"
        + "{4:4s}{5:1s}{6:4d}{7:1s}   "
        + "{8:8.3f}{9:8.3f}{10:8.3f}"
        + "{11:8.4f}{12:7.4f}\n"
    ).format
    coords = atoms._getCoords()
    write = stream.write
    for i, xyz in enumerate(coords):
        write(
            format(
                hetero[i],
                i + 1,
                atomnames[i],
                altlocs[i],
                resnames[i],
                chainids[i],
                int(resnums[i]),
                icodes[i],
                xyz[0],
                xyz[1],
                xyz[2],
                charges[i],
                radii[i],
            )
        )
    write("TER\nEND")
    stream.close()
    return filename
コード例 #5
0
def writePQR(filename, atoms):
    """Write *atoms* in PQR format to a file with name *filename*.  Only
    current coordinate set is written.  Returns *filename* upon success.  If
    *filename* ends with :file:`.gz`, a compressed file will be written."""

    if not isinstance(atoms, Atomic):
        raise TypeError('atoms does not have a valid type')
    if isinstance(atoms, Atom):
        atoms = Selection(atoms.getAtomGroup(), [atoms.getIndex()],
                          atoms.getACSIndex(),
                          'index ' + str(atoms.getIndex()))
    stream = openFile(filename, 'w')
    n_atoms = atoms.numAtoms()
    atomnames = atoms.getNames()
    if atomnames is None:
        raise RuntimeError('atom names are not set')
    for i, an in enumerate(atomnames):
        lenan = len(an)
        if lenan < 4:
            atomnames[i] = ' ' + an
        elif lenan > 4:
            atomnames[i] = an[:4]

    s_or_u = np.array(['a']).dtype.char

    resnames = atoms._getResnames()
    if resnames is None:
        resnames = ['UNK'] * n_atoms
    resnums = atoms._getResnums()
    if resnums is None:
        resnums = np.ones(n_atoms, int)
    chainids = atoms._getChids()
    if chainids is None:
        chainids = np.zeros(n_atoms, s_or_u + '1')
    charges = atoms._getCharges()
    if charges is None:
        charges = np.zeros(n_atoms, float)
    radii = atoms._getRadii()
    if radii is None:
        radii = np.zeros(n_atoms, float)
    icodes = atoms._getIcodes()
    if icodes is None:
        icodes = np.zeros(n_atoms, s_or_u + '1')
    hetero = ['ATOM'] * n_atoms
    heteroflags = atoms._getFlags('hetatm')
    if heteroflags is None:
        heteroflags = atoms._getFlags('hetero')
    if heteroflags is not None:
        hetero = np.array(hetero, s_or_u + '6')
        hetero[heteroflags] = 'HETATM'
    altlocs = atoms._getAltlocs()
    if altlocs is None:
        altlocs = np.zeros(n_atoms, s_or_u + '1')

    format = ('{0:6s}{1:5d} {2:4s}{3:1s}' +
              '{4:4s}{5:1s}{6:4d}{7:1s}   ' +
              '{8:8.3f}{9:8.3f}{10:8.3f}' +
              '{11:8.4f}{12:7.4f}\n').format
    coords = atoms._getCoords()
    write = stream.write
    for i, xyz in enumerate(coords):
        write(format(hetero[i], i+1, atomnames[i], altlocs[i],
                     resnames[i], chainids[i], int(resnums[i]),
                     icodes[i], xyz[0], xyz[1], xyz[2], charges[i], radii[i]))
    write('TER\nEND')
    stream.close()
    return filename