parmed.geometry module¶
This module contains the functionality for carrying out geometrical calculations for molecules and molecular systems
Author: Jason Swails Contributors:
Copyright (C) 2014  2015 Jason Swails
This program is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place  Suite 330 Boston, MA 021111307, USA.

parmed.geometry.
angle
(a1, a2, a3)[source]¶ Computes the cartesian angle between three atoms. Ignores periodic boundary conditions.
 Parameters
 a1, a2, a3Atom or collection of 3 coordinates
The three atoms between whom the angle should be calculated (with a2 being the central atoms)
 Returns
 angfloat
The angle between the vectors a1a2 and a2a3 in degrees
 Raises
 TypeError if a1, a2, or a3 are not Atom or iterable
 ValueError if a1, a2, or a3 are iterable, but do not have exactly 3 items
Notes
This is done in pure Python, so it should not be used for large numbers of distance calculations. For that, use numpyvectorized routines and the numpy coordinate arrays

parmed.geometry.
box_lengths_and_angles_to_vectors
(a, b, c, alpha, beta, gamma)[source]¶ This function takes the lengths of the unit cell vectors and the angles between them and returns 3 unit cell vectors satisfying those dimensions
 Parameters
 adouble (or length Quantity)
Length of the first unit cell vector
 bdouble (or length Quantity)
Length of the second unit cell vector
 cdouble (or length Quantity)
Length of the third unit cell vector
 alphadouble (or angle Quantity)
Angle between vectors b and c
 betadouble (or angle Quantity)
Angle between vectors a and c
 gammadouble (or angle Quantity)
Angle between vectors a and b
 Returns
 list Quantity, list Quantity, list Quantity
The 3, 3element vectors as quantities with dimension length
Notes
The unit cell lengths are assumed to be Angstroms if no explicit unit is given. The angles are assumed to be degrees

parmed.geometry.
box_vectors_to_lengths_and_angles
(a, b, c)[source]¶ This function takes the lengths of the unit cell vectors and the angles between them and returns 3 unit cell vectors satisfying those dimensions
 Parameters
 acollection of 3 floats (or length Quantity)
The first unit cell vector
 bcollection of 3 floats (or length Quantity)
The second unit cell vector
 ccollection of 3 floats (or length Quantity)
The third unit cell vector
 Returns
 (a, b, c), (alpha, beta, gamma)
Two tuples, the first is the 3 unit cell vector lengths as lengthdimension Quantity objects and the second is the set of angles between the unit cell vectors as angledimension Quantity objects
Notes
The unit cell lengths are assumed to be Angstroms if no explicit unit is given.

parmed.geometry.
center_of_mass
(coordinates, masses)[source]¶ Compute the center of mass of a group of coordinates.
 Parameters
 coordinatesnumpy.ndarray
Coordinate array
 massesnumpy.ndarray
Array of masses
 Returns
 COM
np.ndarray of shape (3,) identifying the cartesian center of mass
Notes
This method requires that the parameters be passed in as numpy arrays. AttributeError’s will ensue if this is not the case. Also, coordinates must be able to be reshaped to (len(masses), 3), or ValueError’s will ensue

parmed.geometry.
dihedral
(a1, a2, a3, a4)[source]¶ Computes the angle between three vectors made up of four points (all three vectors share one point with one other vector)
 Parameters
 a1, a2, a3, a4Atom or collection of 4 coordinates
The four atoms between whom the torsion angle should be calculated (with a1 and a4 being the two endpoint atoms not shared between two vectors)
 Returns
 dihedfloat
The measured dihedral between the 4 points in degrees

parmed.geometry.
distance2
(a1, a2)[source]¶ Computes the cartesian distance between two atoms. Ignores periodic boundary conditions.
 Parameters
 a1, a2Atom or collection of 3 coordinates
The two atoms between whom the distance should be calculated
 Returns
 d2float
The square of the distance between the two atoms
 Raises
 TypeError if a1 or a2 are not Atom or iterable
 ValueError if a1 or a2 are iterable, but do not have exactly 3 items
Notes
This is done in pure Python, so it should not be used for large numbers of distance calculations. For that, use numpyvectorized routines and the numpy coordinate arrays

parmed.geometry.
reduce_box_vectors
(a, b, c)[source]¶ This function puts three unit cell vectors in a reduced form where a is “mostly” in x, b is “mostly” in y, and c is “mostly” in z. This form is necessary for some programs (notably OpenMM and Gromacs)
 Parameters
 a3element collection of float
First unit cell vector
 b3element collection of float
Second unit cell vector
 c3element collection of float
Third unit cell vector
 Returns
 red_a, red_b, red_cVec3, Vec3, Vec3
The reduced unit cell vectors in units of angstroms
Notes
The implementation here is taken from the OpenMM Python application layer written by Peter Eastman