Python zmat2atom Examples

Example #1

def check_oniom7(line, rw):
    x = iolines.zmat2atom(line)
    failed = []
    if not (x.element == element):
        failed.append('element')
    if not (x.oniom.mask == 0):
        failed.append('mask')
    if not (x.get_coordinates() == expected_xyz).all():
        failed.append('coordinates')
    if not (x.oniom.layer == 'L'):
        failed.append('layer')
    if not (x.oniom.link_bound_to == 123):
        failed.append('link bound to')
    if not (x.oniom.link_atom.element == 'H'):
        failed.append('link element')
    if not (x.oniom.link_atom.mm.atype == 'HC'):
        failed.append('link atype')
    if not (x.oniom.link_atom.mm.charge == 0.4):
        failed.append('link charge')
    if not (x.mm.charge == -0.10):
        failed.append('charge')
    if not (x.mm.atype == 'C3'):
        failed.append('atype')
    if not (x.oniom.link_scale1 == 0.9):
        failed.append('link scale1')
    if len(failed):
        sys.stderr.write('FAIL: oniom_line7 (%s: %s)\n' %
                         (rw, ','.join(failed)))
    else:
        print('OK: oniom_line7 (%s)' % rw)

Example #2

File: test_line_IO.py Project: eduardoftoliveira/oniomMacGyver

def check_oniom7(line, rw):
    x = iolines.zmat2atom(line)
    failed = []
    if not (x.element == element):
        failed.append('element')
    if not (x.oniom.mask == 0):
        failed.append('mask')
    if not (x.get_coordinates() == expected_xyz).all():
        failed.append('coordinates')
    if not (x.oniom.layer == 'L'):
        failed.append('layer')
    if not (x.oniom.link_bound_to == 123):
        failed.append('link bound to')
    if not (x.oniom.link_atom.element == 'H'):
        failed.append('link element')
    if not (x.oniom.link_atom.mm.atype == 'HC'):
        failed.append('link atype')
    if not (x.oniom.link_atom.mm.charge == 0.4):
        failed.append('link charge')
    if not (x.mm.charge == -0.10):
        failed.append('charge')
    if not (x.mm.atype == 'C3'):
        failed.append('atype')
    if not (x.oniom.link_scale1 == 0.9):
        failed.append('link scale1')
    if len(failed):
        sys.stderr.write('FAIL: oniom_line7 (%s: %s)\n' % (rw, ','.join(failed)))
    else:
        print('OK: oniom_line7 (%s)' % rw)

Example #3

File: test_line_IO.py Project: eduardoftoliveira/oniomMacGyver

def check_oniom7(line, rw):
    x = iolines.zmat2atom(line)
    failed = []
    if not (x.element == element):
        failed.append("element")
    if not (x.oniom.mask == 0):
        failed.append("mask")
    if not (x.get_coordinates() == expected_xyz).all():
        failed.append("coordinates")
    if not (x.oniom.layer == "L"):
        failed.append("layer")
    if not (x.oniom.link_bound_to == 123):
        failed.append("link bound to")
    if not (x.oniom.link_atom.element == "H"):
        failed.append("link element")
    if not (x.oniom.link_atom.mm.atype == "HC"):
        failed.append("link atype")
    if not (x.oniom.link_atom.mm.charge == 0.4):
        failed.append("link charge")
    if not (x.mm.charge == -0.10):
        failed.append("charge")
    if not (x.mm.atype == "C3"):
        failed.append("atype")
    if not (x.oniom.link_scale1 == 0.9):
        failed.append("link scale1")
    if len(failed):
        sys.stderr.write("FAIL: oniom_line7 (%s: %s)\n" % (rw, ",".join(failed)))
    else:
        print("OK: oniom_line7 (%s)" % rw)

Example #4

File: test_line_IO.py Project: eduardoftoliveira/oniomMacGyver

def check_mm(line, rw):
    x = iolines.zmat2atom(line)
    failed = []
    if not (x.element == mm_element):
        failed.append("element")
    if not (x.get_coordinates() == mm_xyz).all():
        failed.append("coordinates")
    if not (x.mm.charge == 0.0):
        failed.append("charge")
    if not (x.mm.atype == "O2"):
        failed.append("atype")
    if len(failed):
        sys.stderr.write("FAIL: mm_line (%s: %s)\n" % (rw, ",".join(failed)))
    else:
        print("OK: mm_line (%s)" % rw)

Example #5

File: test_line_IO.py Project: eduardoftoliveira/oniomMacGyver

def check_mm(line, rw):
    x = iolines.zmat2atom(line)
    failed = []
    if not (x.element == mm_element):
        failed.append('element')
    if not (x.get_coordinates() == mm_xyz).all():
        failed.append('coordinates')
    if not (x.mm.charge == 0.0):
        failed.append('charge')
    if not (x.mm.atype == 'O2'):
        failed.append('atype')
    if len(failed):
        sys.stderr.write('FAIL: mm_line (%s: %s)\n' % (rw, ','.join(failed)))
    else:
        print('OK: mm_line (%s)' % rw)

Example #6

def check_mm(line, rw):
    x = iolines.zmat2atom(line)
    failed = []
    if not (x.element == mm_element):
        failed.append('element')
    if not (x.get_coordinates() == mm_xyz).all():
        failed.append('coordinates')
    if not (x.mm.charge == 0.0):
        failed.append('charge')
    if not (x.mm.atype == 'O2'):
        failed.append('atype')
    if len(failed):
        sys.stderr.write('FAIL: mm_line (%s: %s)\n' % (rw, ','.join(failed)))
    else:
        print('OK: mm_line (%s)' % rw)

Example #7

def zmat2atom_xyz_read(line):
    atom = iolines.zmat2atom(line)
    T1 = atom.element == xyz_el
    T2 = atom.atomic_nr == xyz_atomic_nr
    T3 = atom.get_coordinates() == xyz_xyz
    if not T1:
        sys.stderr.write('zmat2atom xyz - failed element\n')
    if not T2:
        sys.stderr.write('zmat2atom xyz - failed atomic_nr\n')
    if not T3.all():
        sys.stderr.write('zmat2atom xyz - failed coordinates\n')
    if T1 and T2 and T3.all():
        return (True, atom)
    else:
        return (False, None)

Example #8

File: test_line_IO.py Project: eduardoftoliveira/oniomMacGyver

def zmat2atom_xyz_read(line):
    atom = iolines.zmat2atom(line)
    T1 = atom.element == xyz_el
    T2 = atom.atomic_nr == xyz_atomic_nr
    T3 = atom.get_coordinates() == xyz_xyz
    if not T1:
        sys.stderr.write('zmat2atom xyz - failed element\n')
    if not T2:
        sys.stderr.write('zmat2atom xyz - failed atomic_nr\n')
    if not T3.all():
        sys.stderr.write('zmat2atom xyz - failed coordinates\n')
    if T1 and T2 and T3.all():
        return (True, atom)
    else:
        return (False, None)

Example #9

File: test_line_IO.py Project: eduardoftoliveira/oniomMacGyver

def check_oniom1(line, rw):
    x = iolines.zmat2atom(line)
    failed = []
    if not (x.element == element):
        failed.append("element")
    if not (x.oniom.mask == 0):
        failed.append("mask")
    if not (x.get_coordinates() == expected_xyz).all():
        failed.append("coordinates")
        print(x.get_coordinates())
    if not (x.oniom.layer == "L"):
        failed.append("layer")
    if len(failed):
        sys.stderr.write("FAIL: oniom_line1 (%s: %s)\n" % (rw, ",".join(failed)))
    else:
        print("OK: oniom_line1 (%s)" % rw)

Example #10

File: test_line_IO.py Project: sperezl/oniomMacGyver

def check_oniom1(line, rw):
    x = iolines.zmat2atom(line)
    failed = []
    if not (x.element == element):
        failed.append('element')
    if not (x.oniom.mask == 0):
        failed.append('mask')
    if not (x.get_coordinates() == expected_xyz).all():
        failed.append('coordinates')
        print (x.get_coordinates())
    if not (x.oniom.layer == 'L'):
        failed.append('layer')
    if len(failed):
        sys.stderr.write('FAIL: oniom_line1 (%s: %s)\n' % (rw, ','.join(failed)))
    else:
        print('OK: oniom_line1 (%s)' % rw)

Example #11

File: test_line_IO.py Project: eduardoftoliveira/oniomMacGyver

def check_oniom2(line, rw):
    x = iolines.zmat2atom(line)
    failed = []
    if not (x.element == element):
        failed.append("element")
    if not (x.oniom.mask == 0):
        failed.append("mask")
    if not (x.get_coordinates() == expected_xyz).all():
        failed.append("coordinates")
    if not (x.oniom.layer == "L"):
        failed.append("layer")
    if not (x.oniom.link_bound_to == 123):
        failed.append("link bound to")
    if not (x.oniom.link_atom.element == "H"):
        failed.append("link element")
    if hasattr(x.oniom.link_atom, "mm"):
        failed.append("link MM")
    if len(failed):
        sys.stderr.write("FAIL: oniom_line2 (%s: %s)\n" % (rw, ",".join(failed)))
    else:
        print("OK: oniom_line2 (%s)" % rw)

Example #12

def check_oniom2(line, rw):
    x = iolines.zmat2atom(line)
    failed = []
    if not (x.element == element):
        failed.append('element')
    if not (x.oniom.mask == 0):
        failed.append('mask')
    if not (x.get_coordinates() == expected_xyz).all():
        failed.append('coordinates')
    if not (x.oniom.layer == 'L'):
        failed.append('layer')
    if not (x.oniom.link_bound_to == 123):
        failed.append('link bound to')
    if not (x.oniom.link_atom.element == 'H'):
        failed.append('link element')
    if hasattr(x.oniom.link_atom, 'mm'):
        failed.append('link MM')
    if len(failed):
        sys.stderr.write('FAIL: oniom_line2 (%s: %s)\n' %
                         (rw, ','.join(failed)))
    else:
        print('OK: oniom_line2 (%s)' % rw)

Example #13

def check_oniom8(line, rw):
    x = iolines.zmat2atom(oniom_line8)
    failed = []
    if not (x.element == 'C'):
        failed.append('element')
    if not (x.oniom.mask == -1):
        failed.append('mask')
    if not (x.get_coordinates() == (-2.489649, 1.976316, -0.712795)).all():
        failed.append('coordinates')
    if not (x.oniom.layer == 'L'):
        failed.append('layer')
    if not (x.oniom.link_bound_to == 5455):
        failed.append('link bound to')
    if not (x.oniom.link_atom.element == 'H'):
        failed.append('link element')
    if not (x.oniom.link_atom.mm.atype == 'HX'):
        failed.append('link atype')
    if not (x.oniom.link_atom.mm.charge == 0):
        failed.append('link charge')
    if not (x.mm.charge == 0.0569770):
        failed.append('charge')
    if not (x.mm.atype == 'C2'):
        failed.append('atype')
    if not (x.oniom.link_scale1 == 0.):
        failed.append('link scale1')
    if not (x.resinfo.name == 'C7'):
        failed.append('resinfo_name')
    if not (x.resinfo.resname == 'FPP'):
        failed.append('resinfo_resname')
    if not (x.resinfo.resnum == 336):
        failed.append('resinfo_resnum')
    if not (x.resinfo.chain == ''):
        failed.append('resinfo_chain')
    if len(failed):
        sys.stderr.write('FAIL: oniom_line8 (%s: %s)\n' %
                         (rw, ','.join(failed)))
    else:
        print('OK: oniom_line8 (%s)' % rw)

Example #14

File: test_line_IO.py Project: eduardoftoliveira/oniomMacGyver

def check_oniom8(line, rw):
    x = iolines.zmat2atom(oniom_line8)
    failed = []
    if not (x.element == "C"):
        failed.append("element")
    if not (x.oniom.mask == -1):
        failed.append("mask")
    if not (x.get_coordinates() == (-2.489649, 1.976316, -0.712795)).all():
        failed.append("coordinates")
    if not (x.oniom.layer == "L"):
        failed.append("layer")
    if not (x.oniom.link_bound_to == 5455):
        failed.append("link bound to")
    if not (x.oniom.link_atom.element == "H"):
        failed.append("link element")
    if not (x.oniom.link_atom.mm.atype == "HX"):
        failed.append("link atype")
    if not (x.oniom.link_atom.mm.charge == 0):
        failed.append("link charge")
    if not (x.mm.charge == 0.0569770):
        failed.append("charge")
    if not (x.mm.atype == "C2"):
        failed.append("atype")
    if not (x.oniom.link_scale1 == 0.0):
        failed.append("link scale1")
    if not (x.resinfo.name == "C7"):
        failed.append("resinfo_name")
    if not (x.resinfo.resname == "FPP"):
        failed.append("resinfo_resname")
    if not (x.resinfo.resnum == 336):
        failed.append("resinfo_resnum")
    if not (x.resinfo.chain == ""):
        failed.append("resinfo_chain")
    if len(failed):
        sys.stderr.write("FAIL: oniom_line8 (%s: %s)\n" % (rw, ",".join(failed)))
    else:
        print("OK: oniom_line8 (%s)" % rw)

Example #15

File: test_line_IO.py Project: eduardoftoliveira/oniomMacGyver

def check_oniom8(line, rw):
    x = iolines.zmat2atom(oniom_line8)
    failed = []
    if not (x.element == 'C'):
        failed.append('element')
    if not (x.oniom.mask == -1):
        failed.append('mask')
    if not (x.get_coordinates() == (-2.489649, 1.976316, -0.712795)).all():
        failed.append('coordinates')
    if not (x.oniom.layer == 'L'):
        failed.append('layer')
    if not (x.oniom.link_bound_to == 5455):
        failed.append('link bound to')
    if not (x.oniom.link_atom.element == 'H'):
        failed.append('link element')
    if not (x.oniom.link_atom.mm.atype == 'HX'):
        failed.append('link atype')
    if not (x.oniom.link_atom.mm.charge == 0):
        failed.append('link charge')
    if not (x.mm.charge == 0.0569770):
        failed.append('charge')
    if not (x.mm.atype == 'C2'):
        failed.append('atype')
    if not (x.oniom.link_scale1 == 0.):
        failed.append('link scale1')
    if not (x.resinfo.name == 'C7'):
        failed.append('resinfo_name')
    if not (x.resinfo.resname == 'FPP'):
        failed.append('resinfo_resname')
    if not (x.resinfo.resnum == 336):
        failed.append('resinfo_resnum')
    if not (x.resinfo.chain == ''):
        failed.append('resinfo_chain')
    if len(failed):
        sys.stderr.write('FAIL: oniom_line8 (%s: %s)\n' % (rw, ','.join(failed)))
    else:
        print('OK: oniom_line8 (%s)' % rw)

Example #16

        failed.append('element')
    if not (x.get_coordinates() == mm_xyz).all():
        failed.append('coordinates')
    if not (x.mm.charge == 0.0):
        failed.append('charge')
    if not (x.mm.atype == 'O2'):
        failed.append('atype')
    if len(failed):
        sys.stderr.write('FAIL: mm_line (%s: %s)\n' % (rw, ','.join(failed)))
    else:
        print('OK: mm_line (%s)' % rw)


#1
check_oniom1(oniom_line1, 'read')
atom1 = iolines.zmat2atom(oniom_line1)
new_line1 = iolines.atom2zmat(atom1)
check_oniom1(new_line1, 'write')

# 2
check_oniom2(oniom_line2, 'read')
atom2 = iolines.zmat2atom(oniom_line2)
new_line2 = iolines.atom2zmat(atom2)
check_oniom2(new_line2, 'write')

# 3
check_oniom3(oniom_line3, 'read')
atom3 = iolines.zmat2atom(oniom_line3)
new_line3 = iolines.atom2zmat(atom3)
check_oniom3(new_line3, 'write')

Example #17

File: test_line_IO.py Project: eduardoftoliveira/oniomMacGyver

        failed.append('element')
    if not (x.get_coordinates() == mm_xyz).all():
        failed.append('coordinates')
    if not (x.mm.charge == 0.0):
        failed.append('charge')
    if not (x.mm.atype == 'O2'):
        failed.append('atype')
    if len(failed):
        sys.stderr.write('FAIL: mm_line (%s: %s)\n' % (rw, ','.join(failed)))
    else:
        print('OK: mm_line (%s)' % rw)


#1
check_oniom1(oniom_line1, 'read')
atom1 = iolines.zmat2atom(oniom_line1)
new_line1 = iolines.atom2zmat(atom1)
check_oniom1(new_line1, 'write')

# 2
check_oniom2(oniom_line2, 'read')
atom2 = iolines.zmat2atom(oniom_line2)
new_line2 = iolines.atom2zmat(atom2)
check_oniom2(new_line2, 'write')

# 3
check_oniom3(oniom_line3, 'read')
atom3 = iolines.zmat2atom(oniom_line3)
new_line3 = iolines.atom2zmat(atom3)
check_oniom3(new_line3, 'write')