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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 09:52, 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)
        #------------------------------------------------------------------------------