Will's PyMOL Scripts
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Intro
1Tutorial
3D Geometry Library (not pymol specific)
General Pymol Utilities
Symmetric Modeling Utilities
Symmetric Component Generation Utilities
Will's PyMOL Scripts
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A
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B
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C
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D
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E
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F
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G
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H
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I
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K
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L
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M
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N
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O
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P
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R
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S
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T
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U
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V
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X
A
abs() (xyzMath.Vec method)
acosdeg() (in module xyzMath)
add_diagonal() (xyzMath.Mat method)
align_helix() (in module sym_util)
align_skew_line_pairs() (in module xyzMath)
alignall() (in module pymol_util)
alignallrms() (in module pymol_util)
alignaroundaxis() (in module xyzMath)
alignaxis() (in module pymol_util)
alignbb() (in module pymol_util)
aligncx() (in module sym_util)
aligndx() (in module sym_util)
alignsym() (in module sym_util)
alignvector() (in module xyzMath)
alignvectors() (in module xyzMath)
alignvectors_minangle() (in module xyzMath)
angle() (in module xyzMath)
(xyzMath.Vec method)
angle_degrees() (in module xyzMath)
(xyzMath.Vec method)
asindeg() (in module xyzMath)
B
bestalign() (in module pymol_util)
bond_zns() (in module pymol_util)
bondzn() (in module pymol_util)
C
cbow() (in module pymol_util)
centerall() (in module pymol_util)
cgo_cyl() (in module pymol_util)
cgo_lineabs() (in module pymol_util)
cgo_segment() (in module pymol_util)
cgo_sphere() (in module pymol_util)
chaincount() (in module pymol_util)
charge() (in module pymol_util)
chirality() (in module pymol_util)
col() (xyzMath.Mat method)
color_by_2component() (in module sym_util)
color_by_chain() (in module pymol_util)
color_obj() (in module pymol_util)
colorI53() (in module sym_util)
colx() (xyzMath.Mat method)
coly() (xyzMath.Mat method)
colz() (xyzMath.Mat method)
com() (in module pymol_util)
conelineinter() (in module pymol_util)
contractRadii() (in module pymol_util)
coplanar() (in module xyzMath)
corneraxes() (in module pymol_util)
corresponding_atom_names() (in module pymol_util)
cosdeg() (in module xyzMath)
createpoint() (in module pymol_util)
cross() (xyzMath.Vec method)
cube() (in module pymol_util)
cyclic_axis() (in module xyzMath)
D
det() (xyzMath.Mat method)
dihedral() (in module xyzMath)
dihedral_degrees() (in module xyzMath)
distance() (xyzMath.Vec method)
distance_squared() (xyzMath.Vec method)
disulf_rms() (pymol_util.DisulfLib method)
DisulfLib (class in pymol_util)
dot() (xyzMath.Vec method)
drawlines() (in module pymol_util)
drawring() (in module pymol_util)
drawringcar() (in module pymol_util)
drawsph() (in module pymol_util)
drawtestconeva() (in module pymol_util)
dsf() (in module pymol_util)
E
euler_angles() (xyzMath.Mat method)
expand_xforms() (in module xyzMath)
expandRadii() (in module pymol_util)
F
find_identities() (in module xyzMath)
find_symelems() (in module sym_util)
fitall() (in module pymol_util)
floats2vecs() (in module pymol_util)
from_euler_angles() (xyzMath.Mat method)
from_four_points() (xyzMath.Xform method)
from_two_vecs() (xyzMath.Xform method)
G
gen_helical_alignments() (in module sym_util)
get_cell_bounds_orthogonal_only() (in module xyzMath)
get_closest_atom_pair() (in module pymol_util)
get_contigs() (in module sym_util)
get_first_last_resi() (in module pymol_util)
get_fixed_size_contigs() (in module sym_util)
get_test_generators1() (in module xyzMath)
get_xforms_by_chain() (in module sym_util)
getaa() (in module pymol_util)
getchain() (in module pymol_util)
getframe() (in module pymol_util)
getname1() (in module pymol_util)
getnative() (in module pymol_util)
getrelframe() (in module pymol_util)
getrelframe_rmsalign() (in module pymol_util)
getres() (in module pymol_util)
getrestypes() (in module pymol_util)
guesscxaxis() (in module sym_util)
guessdxaxes() (in module sym_util)
H
homogenizechains() (in module sym_comp)
hsv_to_rgb() (in module pymol_util)
I
ifsphab() (in module pymol_util)
inpymol() (in module pymol_util)
inverse() (xyzMath.Xform method)
inversion() (in module pymol_util)
is_rotation() (xyzMath.Mat method)
iscontig() (in module sym_comp)
isfloat() (in module xyzMath)
isint() (in module xyzMath)
isiter() (in module xyzMath)
islist() (in module xyzMath)
ismat() (in module xyzMath)
isnum() (in module xyzMath)
istuple() (in module xyzMath)
isvec() (in module xyzMath)
isxform() (in module xyzMath)
K
key() (xyzMath.Vec method)
L
lcs() (in module pymol_util)
length() (xyzMath.Vec method)
length_squared() (xyzMath.Vec method)
line_line_angle() (in module xyzMath)
line_line_angle_degrees() (in module xyzMath)
line_line_closest_points() (in module xyzMath)
line_line_distance() (in module xyzMath)
line_plane_intersection() (in module xyzMath)
lineangle() (xyzMath.Vec method)
lineangle_degrees() (xyzMath.Vec method)
load() (pymol_util.PutCenterCallback method)
load_tests() (in module sym_comp)
(in module sym_util)
loadmov() (in module pymol_util)
M
make_ab_components() (in module sym_util)
make_cryst1_23() (in module sym_comp)
make_cryst1_I213() (in module sym_comp)
make_cryst1_P432() (in module sym_comp)
make_helix_old() (in module sym_util)
make_inputs_from_cb_only() (in module pymol_util)
make_zdock_set() (in module pymol_util)
makekinwire() (in module sym_util)
Mat (class in xyzMath)
meancoords() (in module pymol_util)
mirror() (in module pymol_util)
mkc2() (in module pymol_util)
mkc3() (in module pymol_util)
mkc4() (in module pymol_util)
mkd2() (in module pymol_util)
mkhelix() (in module pymol_util)
mkhelix4() (in module pymol_util)
mkifaceresfile() (in module pymol_util)
mkpntx() (in module pymol_util)
move_down() (in module pymol_util)
move_up() (in module pymol_util)
move_up_down_add_to_ignore_list() (in module pymol_util)
my_get_obj() (in module pymol_util)
mygetview() (in module pymol_util)
myint() (in module sym_util)
mysetview() (in module pymol_util)
N
natom() (in module pymol_util)
nca() (in module pymol_util)
nnb() (in module pymol_util)
normalize() (xyzMath.Vec method)
normalized() (xyzMath.Vec method)
normdot() (xyzMath.Vec method)
nulltest() (in module sym_comp)
(in module sym_util)
O
orb_cyl() (in module pymol_util)
outer() (xyzMath.Vec method)
P
point_line_distance() (in module xyzMath)
pointaxis() (in module pymol_util)
prepare_c2_nmr() (in module sym_comp)
pretty() (xyzMath.Xform method)
prev_v (pymol_util.PutCenterCallback attribute)
print_chains() (in module pymol_util)
procCdat() (in module sym_comp)
procD2dat() (in module sym_comp)
procD5dat() (in module pymol_util)
process_native() (in module pymol_util)
processhomomers() (in module sym_comp)
proj() (in module xyzMath)
projection_matrix() (in module xyzMath)
projperp() (in module xyzMath)
PutCenterCallback (class in pymol_util)
pymol_util (module)
R
RAD() (in module xyzMath)
rainbow_chains() (in module pymol_util)
randnorm() (in module xyzMath)
randrot() (in module xyzMath)
randvec() (in module xyzMath)
randvecball() (in module xyzMath)
randveccube() (in module xyzMath)
randxform() (in module xyzMath)
ray_sphere_intersection() (in module xyzMath)
read_tokens() (in module xyzMath)
read_xforms() (in module xyzMath)
rechain() (in module sym_util)
redoA() (in module pymol_util)
redopent() (in module pymol_util)
redotoi() (in module pymol_util)
renumber() (in module pymol_util)
ResBB (class in pymol_util)
rms() (pymol_util.ResBB method)
rmsd() (in module xyzMath)
rot() (in module pymol_util)
rot_by_matrix() (in module pymol_util)
rotation_around() (in module xyzMath)
rotation_around_degrees() (in module xyzMath)
rotation_around_dof_to_set_vec_vec_angle() (in module xyzMath)
rotation_axis() (xyzMath.Mat method)
(xyzMath.Xform method)
rotation_axis_center() (xyzMath.Xform method)
rotation_matrix() (in module xyzMath)
rotation_matrix_degrees() (in module xyzMath)
rotrad() (in module pymol_util)
rotview() (in module pymol_util)
rotx() (in module pymol_util)
roty() (in module pymol_util)
rotz() (in module pymol_util)
round0() (xyzMath.Vec method)
rounded() (xyzMath.Vec method)
row() (xyzMath.Mat method)
rowx() (xyzMath.Mat method)
rowy() (xyzMath.Mat method)
rowz() (xyzMath.Mat method)
S
selbycomp() (in module sym_util)
show_res_frames() (in module pymol_util)
showaxes() (in module pymol_util)
showaxes2() (in module pymol_util)
showcom() (in module pymol_util)
showcst() (in module pymol_util)
showcxaxis() (in module sym_util)
showcyl() (in module pymol_util)
showline() (in module pymol_util)
showlineabs() (in module pymol_util)
showsegment() (in module pymol_util)
showsphere() (in module pymol_util)
showvecfrompoint() (in module pymol_util)
sin_cos_range() (in module xyzMath)
sindeg() (in module xyzMath)
skew_lines_center() (in module xyzMath)
skew_lines_relation() (in module xyzMath)
skew_lines_relation_z() (in module xyzMath)
slide_to_make_lines_intersect() (in module xyzMath)
sort_dcoms() (in module pymol_util)
stub() (in module xyzMath)
(pymol_util.ResBB method)
stubalign() (in module pymol_util)
swell() (in module pymol_util)
sym_comp (module)
sym_util (module)
symmetrize() (in module sym_util)
symmetrize_xform() (in module xyzMath)
symmetrizec2() (in module pymol_util)
T
tcdock_set_chain_by_cluster() (in module pymol_util)
test() (in module pymol_util)
(in module xyzMath)
test_conelineinter() (in module pymol_util)
test_rotation_mat() (in module xyzMath)
testhsphere() (in module pymol_util)
testsphere() (in module pymol_util)
tmpdoit() (in module pymol_util)
tmpname() (in module sym_util)
tmpvis() (in module pymol_util)
to_rosetta() (xyzMath.Mat method)
(xyzMath.Vec method)
toglobal() (xyzMath.Xform method)
tolocal() (xyzMath.Xform method)
trace() (xyzMath.Mat method)
trans() (in module pymol_util)
transpose() (xyzMath.Mat method)
transposed() (xyzMath.Mat method)
transx() (in module pymol_util)
transy() (in module pymol_util)
transz() (in module pymol_util)
trim_sym() (in module sym_util)
tuple() (xyzMath.Vec method)
U
unit() (xyzMath.Vec method)
untangle_sidechains() (in module pymol_util)
useOccColors() (in module pymol_util)
useOccRadii() (in module pymol_util)
useRosettaRadii() (in module pymol_util)
useTempColors() (in module pymol_util)
useTempRadii() (in module pymol_util)
V
Vec (class in xyzMath)
X
Xform (class in xyzMath)
xform() (in module pymol_util)
xtal_frames() (in module sym_util)
xyzMath (module)
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