molecule.py File Reference

Go to the source code of this file.

Classes
class	src.molecule.ActuallyArcError
class	src.molecule.RawStreamHandler
	Exactly like output.StreamHandler except it does no extra formatting before sending logging messages to the stream. More...
class	src.molecule.MolfileTimestep
	Wrapper for the timestep C structure used in molfile plugins. More...
class	src.molecule.Molecule
	Lee-Ping's general file format conversion class. More...

Namespaces
	src.molecule

Functions
def	src.molecule.getElement (mass)
def	src.molecule.elem_from_atomname (atomname)
	Given an atom name, attempt to get the element in most cases. More...
def	src.molecule.unmangle (M1, M2)
	Create a mapping that takes M1's atom indices to M2's atom indices based on position. More...
def	src.molecule.nodematch (node1, node2)
def	src.molecule.isint (word)
	ONLY matches integers! If you have a decimal point? None shall pass! More...
def	src.molecule.isfloat (word)
	Matches ANY number; it can be a decimal, scientific notation, integer, or what have you. More...
def	src.molecule.CubicLattice (a)
	This function takes in three lattice lengths and three lattice angles, and tries to return a complete box specification. More...
def	src.molecule.BuildLatticeFromLengthsAngles (a, b, c, alpha, beta, gamma)
	This function takes in three lattice lengths and three lattice angles, and tries to return a complete box specification. More...
def	src.molecule.BuildLatticeFromVectors (v1, v2, v3)
	This function takes in three lattice vectors and tries to return a complete box specification. More...
def	src.molecule.TopEqual (mol1, mol2)
	For the nanoreactor project: Determine whether two Molecule objects have the same topologies. More...
def	src.molecule.MolEqual (mol1, mol2)
	Determine whether two Molecule objects have the same fragments by looking at elements and connectivity graphs. More...
def	src.molecule.format_xyz_coord (element, xyz, tinker=False)
	Print a line consisting of (element, x, y, z) in accordance with .xyz file format. More...
def	src.molecule.format_gro_coord (resid, resname, aname, seqno, xyz)
	Print a line in accordance with .gro file format, with six decimal points of precision. More...
def	src.molecule.format_xyzgen_coord (element, xyzgen)
	Print a line consisting of (element, p, q, r, s, t, ...) where (p, q, r) are arbitrary atom-wise data (this might happen, for instance, with atomic charges) More...
def	src.molecule.format_gro_box (box)
	Print a line corresponding to the box vector in accordance with .gro file format. More...
def	src.molecule.is_gro_coord (line)
	Determines whether a line contains GROMACS data or not. More...
def	src.molecule.is_charmm_coord (line)
	Determines whether a line contains CHARMM data or not. More...
def	src.molecule.is_gro_box (line)
	Determines whether a line contains a GROMACS box vector or not. More...
def	src.molecule.add_strip_to_mat (mat, strip)
def	src.molecule.pvec (vec)
def	src.molecule.grouper (n, iterable)
	Groups a big long iterable into groups of ten or what have you. More...
def	src.molecule.even_list (totlen, splitsize)
	Creates a list of number sequences divided as evenly as possible. More...
def	src.molecule.both (A, B, key)
def	src.molecule.diff (A, B, key)
def	src.molecule.either (A, B, key)
def	src.molecule.EulerMatrix (T1, T2, T3)
	Constructs an Euler matrix from three Euler angles. More...
def	src.molecule.ComputeOverlap (theta, elem, xyz1, xyz2)
	Computes an 'overlap' between two molecules based on some fictitious density. More...
def	src.molecule.AlignToDensity (elem, xyz1, xyz2, binary=False)
	Computes a "overlap density" from two frames. More...
def	src.molecule.AlignToMoments (elem, xyz1, xyz2=None)
	Pre-aligns molecules to 'moment of inertia'. More...
def	src.molecule.get_rotate_translate (matrix1, matrix2)
def	src.molecule.cartesian_product2 (arrays)
	Form a Cartesian product of two NumPy arrays. More...
def	src.molecule.extract_int (arr, avgthre, limthre, label="value", verbose=True)
	Get the representative integer value from an array. More...
def	src.molecule.extract_pop (M, verbose=True)
	Extract our best estimate of charge and spin-z from the comments section of a Molecule object created with Nanoreactor. More...
def	src.molecule.arc (Mol, begin=None, end=None, RMSD=True, align=True)
	Get the arc-length for a trajectory segment. More...
def	src.molecule.EqualSpacing (Mol, frames=0, dx=0, RMSD=True, align=True)
	Equalize the spacing of frames in a trajectory with linear interpolation. More...
def	src.molecule.AtomContact (xyz, pairs, box=None, displace=False)
	Compute distances between pairs of atoms. More...
def	src.molecule.form_rot (q)
	Given a quaternion p, form a rotation matrix from it. More...
def	src.molecule.axis_angle (axis, angle)
	Given a rotation axis and angle, return the corresponding 3x3 rotation matrix, which will rotate a (Nx3) array of xyz coordinates as x0_rot = np.dot(R, x0.T).T. More...
def	src.molecule.main ()

Variables
	src.molecule.input = raw_input
dictionary	src.molecule.FrameVariableNames
dictionary	src.molecule.AtomVariableNames
dictionary	src.molecule.MetaVariableNames
dictionary	src.molecule.QuantumVariableNames = {'qcrems', 'qctemplate', 'charge', 'mult', 'qcsuf', 'qm_ghost', 'qm_bondorder'}
dictionary	src.molecule.AllVariableNames = QuantumVariableNames | AtomVariableNames | MetaVariableNames | FrameVariableNames
string	src.molecule.package = "ForceBalance"
	src.molecule.logger = getLogger("MoleculeLogger")
	src.molecule.handler = RawStreamHandler()
	src.molecule.module_name = __name__.replace('.molecule','')
list	src.molecule.Radii
list	src.molecule.Elements
	src.molecule.PeriodicTable
bool	src.molecule.have_dcdlib = False
float	src.molecule.bohr2ang = 0.529177210
	One bohr equals this many angstroms. More...
	src.molecule.splitter = re.compile(r'(\s+|\S+)')
	src.molecule.Box = namedtuple('Box',['a','b','c','alpha','beta','gamma','A','B','C','V'])
int	src.molecule.radian = 180. / np.pi
	src.molecule.Alive