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Chempy is a python-importable module that can be used to write PyMOL-executable [[scripts]]. | Chempy is a python-importable module that can be used to write PyMOL-executable [[scripts]]. | ||
<source lang="python"> | |||
from chempy import cpv | |||
help(cpv) | |||
# Generic vector and matrix routines for 3-Space | |||
# Assembled for usage in PyMOL and Chemical Python | |||
# | |||
# Assumes row-major matrices and arrays | |||
# [ [vector 1], [vector 2], [vector 3] ] | |||
# | |||
# Raises ValueError when given bad input | |||
FUNCTIONS | |||
add(v1, v2) | |||
#------------------------------------------------------------------------------ | |||
average(v1, v2) | |||
#------------------------------------------------------------------------------ | |||
cross_product(v1, v2) | |||
#------------------------------------------------------------------------------ | |||
distance(v1, v2) | |||
#------------------------------------------------------------------------------ | |||
distance_sq(v1, v2) | |||
#------------------------------------------------------------------------------ | |||
dot_product(v1, v2) | |||
#------------------------------------------------------------------------------ | |||
fit(target_array, source_array) | |||
fit(target_array, source_array) -> (t1, t2, rot_mtx, rmsd) [fit_result] | |||
Calculates the translation vectors and rotation matrix required | |||
to superimpose source_array onto target_array. Original arrays are | |||
not modified. NOTE: Currently assumes 3-dimensional coordinates | |||
t1,t2 are vectors from origin to centers of mass... | |||
fit_apply(fit_result, vec_array) | |||
fit_apply(fir_result,vec_array) -> vec_array | |||
Applies a fit result to an array of vectors | |||
get_angle(v1, v2) | |||
#------------------------------------------------------------------------------ | |||
get_angle_formed_by(p1, p2, p3) | |||
#------------------------------------------------------------------------------ | |||
get_identity() | |||
#------------------------------------------------------------------------------ | |||
get_null() | |||
#------------------------------------------------------------------------------ | |||
get_system2(x, y) | |||
#------------------------------------------------------------------------------ | |||
inverse_transform(m, v) | |||
#------------------------------------------------------------------------------ | |||
length(v) | |||
#------------------------------------------------------------------------------ | |||
multiply(m1, m2) | |||
#------------------------------------------------------------------------------ | |||
negate(v) | |||
#------------------------------------------------------------------------------ | |||
normalize(v) | |||
#------------------------------------------------------------------------------ | |||
normalize_failsafe(v) | |||
#------------------------------------------------------------------------------ | |||
project(v, n) | |||
#------------------------------------------------------------------------------ | |||
random_displacement(v, radius) | |||
#------------------------------------------------------------------------------ | |||
random_sphere(v, radius) | |||
#------------------------------------------------------------------------------ | |||
random_vector() | |||
#------------------------------------------------------------------------------ | |||
remove_component(v, n) | |||
#------------------------------------------------------------------------------ | |||
reverse(v) | |||
#------------------------------------------------------------------------------ | |||
rotation_matrix(angle, axis) | |||
#------------------------------------------------------------------------------ | |||
scale(v, factor) | |||
#------------------------------------------------------------------------------ | |||
scale_system(s, factor) | |||
#------------------------------------------------------------------------------ | |||
sub(v1, v2) | |||
#------------------------------------------------------------------------------ | |||
transform(m, v) | |||
#------------------------------------------------------------------------------ | |||
transform_about_point(m, v, p) | |||
#------------------------------------------------------------------------------ | |||
transform_array(rot_mtx, vec_array) | |||
transform_array( matrix, vector_array ) -> vector_array | |||
translate_array(trans_vec, vec_array) | |||
translate_array(trans_vec,vec_array) -> vec_array | |||
Adds 'mult'*'trans_vec' to each element in vec_array, and returns | |||
the translated vector. | |||
transpose(m) | |||
#------------------------------------------------------------------------------ | |||
</source> |
Revision as of 05:52, 31 August 2011
Chempy is a python-importable module that can be used to write PyMOL-executable scripts.
from chempy import cpv
help(cpv)
# Generic vector and matrix routines for 3-Space
# Assembled for usage in PyMOL and Chemical Python
#
# Assumes row-major matrices and arrays
# [ [vector 1], [vector 2], [vector 3] ]
#
# Raises ValueError when given bad input
FUNCTIONS
add(v1, v2)
#------------------------------------------------------------------------------
average(v1, v2)
#------------------------------------------------------------------------------
cross_product(v1, v2)
#------------------------------------------------------------------------------
distance(v1, v2)
#------------------------------------------------------------------------------
distance_sq(v1, v2)
#------------------------------------------------------------------------------
dot_product(v1, v2)
#------------------------------------------------------------------------------
fit(target_array, source_array)
fit(target_array, source_array) -> (t1, t2, rot_mtx, rmsd) [fit_result]
Calculates the translation vectors and rotation matrix required
to superimpose source_array onto target_array. Original arrays are
not modified. NOTE: Currently assumes 3-dimensional coordinates
t1,t2 are vectors from origin to centers of mass...
fit_apply(fit_result, vec_array)
fit_apply(fir_result,vec_array) -> vec_array
Applies a fit result to an array of vectors
get_angle(v1, v2)
#------------------------------------------------------------------------------
get_angle_formed_by(p1, p2, p3)
#------------------------------------------------------------------------------
get_identity()
#------------------------------------------------------------------------------
get_null()
#------------------------------------------------------------------------------
get_system2(x, y)
#------------------------------------------------------------------------------
inverse_transform(m, v)
#------------------------------------------------------------------------------
length(v)
#------------------------------------------------------------------------------
multiply(m1, m2)
#------------------------------------------------------------------------------
negate(v)
#------------------------------------------------------------------------------
normalize(v)
#------------------------------------------------------------------------------
normalize_failsafe(v)
#------------------------------------------------------------------------------
project(v, n)
#------------------------------------------------------------------------------
random_displacement(v, radius)
#------------------------------------------------------------------------------
random_sphere(v, radius)
#------------------------------------------------------------------------------
random_vector()
#------------------------------------------------------------------------------
remove_component(v, n)
#------------------------------------------------------------------------------
reverse(v)
#------------------------------------------------------------------------------
rotation_matrix(angle, axis)
#------------------------------------------------------------------------------
scale(v, factor)
#------------------------------------------------------------------------------
scale_system(s, factor)
#------------------------------------------------------------------------------
sub(v1, v2)
#------------------------------------------------------------------------------
transform(m, v)
#------------------------------------------------------------------------------
transform_about_point(m, v, p)
#------------------------------------------------------------------------------
transform_array(rot_mtx, vec_array)
transform_array( matrix, vector_array ) -> vector_array
translate_array(trans_vec, vec_array)
translate_array(trans_vec,vec_array) -> vec_array
Adds 'mult'*'trans_vec' to each element in vec_array, and returns
the translated vector.
transpose(m)
#------------------------------------------------------------------------------