Pyadmin: 5 revisions

2014-03-28T01:43:01Z

5 revisions

Tlinnet at 10:01, 31 August 2011

2011-08-31T10:01:05Z

Tlinnet at 10:00, 31 August 2011

2011-08-31T10:00:10Z

Tlinnet at 09:52, 31 August 2011

2011-08-31T09:52:15Z

Cank at 18:26, 11 March 2009

2009-03-11T18:26:45Z

Cank: New page: Chempy is a python-importable module that can be used to write PyMOL-executable scripts.

2009-03-11T18:26:32Z

New page: Chempy is a python-importable module that can be used to write PyMOL-executable scripts.

New page

Chempy is a python-importable module that can be used to write PyMOL-executable scripts.

@@ Line 129: / Line 129: @@
 Example
 <source lang="python">
 PyMOL>a = [1.2 , 3.4, 4.5]
 PyMOL>b = [2.2 , 4.4, 5.5]

@@ Line 125: / Line 125: @@
      transpose(m)
          #------------------------------------------------------------------------------
 </source>

← Older revision		Revision as of 09:52, 31 August 2011
Line 1:		Line 1:
	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>

← Older revision		Revision as of 18:26, 11 March 2009
Line 1:		Line 1:
−	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]].