Chempy: Difference between revisions
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transpose(m) | transpose(m) | ||
#------------------------------------------------------------------------------ | #------------------------------------------------------------------------------ | ||
</source> | |||
Example | |||
<source lang="python"> | |||
PyMOL>a = [1.2 , 3.4, 4.5] | |||
PyMOL>b = [2.2 , 4.4, 5.5] | |||
PyMOL>c = cpv.add(a,b) | |||
PyMOL>print c | |||
[3.4000000000000004, 7.800000000000001, 10.0] | |||
</source> | </source> |
Revision as of 06:00, 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)
#------------------------------------------------------------------------------
Example
PyMOL>a = [1.2 , 3.4, 4.5]
PyMOL>b = [2.2 , 4.4, 5.5]
PyMOL>c = cpv.add(a,b)
PyMOL>print c
[3.4000000000000004, 7.800000000000001, 10.0]