diff --git a/modules/mol/alg/pymod/structure_analysis.py b/modules/mol/alg/pymod/structure_analysis.py index 2103b14a71aa4ebd0be528df66d3fe21d6782313..387102c06a1f34632272e4f461b419f9b6129ab6 100644 --- a/modules/mol/alg/pymod/structure_analysis.py +++ b/modules/mol/alg/pymod/structure_analysis.py @@ -71,7 +71,7 @@ def GetMinDistBetwCenterOfMassAndView(sele1,sele2): :type sele1: :class:`~ost.mol.EntityView` :type sele2: :class:`~ost.mol.EntityView` - :return: distance (\ :class:`float`\ ) + :return: distance (\\ :class:`float`\\ ) """ if not sele1.IsValid() and sele2.IsValid(): print('invalid view') @@ -155,7 +155,7 @@ def CalculateHelixAxis(sele1): def CalculateDistanceDifferenceMatrix(sele1,sele2): """ - This function calculates the pairwise distance differences between two selections (\ :class:`~ost.mol.EntityView`\ ). + This function calculates the pairwise distance differences between two selections (\\ :class:`~ost.mol.EntityView`\\ ). The two selections should have the same number of atoms It returns an NxN DistanceDifferenceMatrix M (where N is the number of atoms in sele1) where M[i,j]=||(sele2.atoms[i].pos-sele2.atoms[j].pos)||-||(sele1.atoms[i].pos-sele1.atoms[j].pos)|| diff --git a/modules/mol/alg/pymod/trajectory_analysis.py b/modules/mol/alg/pymod/trajectory_analysis.py index 9ff4b341ef55ebde0d3a8c966df2292793a3fa95..bbb354d35fd2e6a8b266c83bcc999689418092d4 100644 --- a/modules/mol/alg/pymod/trajectory_analysis.py +++ b/modules/mol/alg/pymod/trajectory_analysis.py @@ -70,8 +70,8 @@ def RMSD_Matrix_From_Traj(t,sele,first=0,last=-1,align=True,align_sele=None): :type first: :class:`int` :type last: :class:`int` - :return: Returns a numpy N\ :subscript:`frames`\ xN\ :subscript:`frames` matrix, - where N\ :subscript:`frames` is the number of frames. + :return: Returns a numpy N\\ :subscript:`frames`\\ xN\\ :subscript:`frames` matrix, + where N\\ :subscript:`frames` is the number of frames. """ if not align_sele:align_sele=sele try: @@ -98,8 +98,8 @@ def PairwiseDistancesFromTraj(t,sele,first=0,last=-1,seq_sep=1): """ This function calculates the distances between any pair of atoms in **sele** with sequence separation larger than **seq_sep** from a trajectory **t**. - It return a matrix containing one line for each atom pair and N\ :subscript:`frames` columns, where - N\ :subscript:`frames` is the number of frames in the trajectory. + It return a matrix containing one line for each atom pair and N\\ :subscript:`frames` columns, where + N\\ :subscript:`frames` is the number of frames in the trajectory. :param t: the trajectory :param sele: the selection used to determine the atom pairs @@ -112,7 +112,7 @@ def PairwiseDistancesFromTraj(t,sele,first=0,last=-1,seq_sep=1): :type last: :class:`int` :type seq_sep: :class:`int` - :return: a numpy N\ :subscript:`pairs`\ xN\ :subscript:`frames` matrix. + :return: a numpy N\\ :subscript:`pairs`\\ xN\\ :subscript:`frames` matrix. """ try: import numpy as npy @@ -139,10 +139,10 @@ def PairwiseDistancesFromTraj(t,sele,first=0,last=-1,seq_sep=1): def DistanceMatrixFromPairwiseDistances(distances,p=2): """ - This function calculates an distance matrix M(N\ :subscript:`frames`\ xN\ :subscript:`frames`\ ) from - the pairwise distances matrix D(N\ :subscript:`pairs`\ xN\ :subscript:`frames`\ ), where - N\ :subscript:`frames` is the number of frames in the trajectory - and N\ :subscript:`pairs` the number of atom pairs. + This function calculates an distance matrix M(N\\ :subscript:`frames`\\ xN\\ :subscript:`frames`\\ ) from + the pairwise distances matrix D(N\\ :subscript:`pairs`\\ xN\\ :subscript:`frames`\\ ), where + N\\ :subscript:`frames` is the number of frames in the trajectory + and N\\ :subscript:`pairs` the number of atom pairs. M[i,j] is the distance between frame i and frame j calculated as a p-norm of the differences in distances from the two frames (distance-RMSD for p=2). @@ -151,7 +151,7 @@ def DistanceMatrixFromPairwiseDistances(distances,p=2): :py:func:`~mol.alg.trajectory_analysis.PairwiseDistancesFromTraj` :param p: exponent used for the p-norm. - :return: a numpy N\ :subscript:`frames`\ xN\ :subscript:`frames` matrix, where N\ :subscript:`frames` + :return: a numpy N\\ :subscript:`frames`\\ xN\\ :subscript:`frames` matrix, where N\\ :subscript:`frames` is the number of frames. """ try: @@ -196,7 +196,7 @@ def DistRMSDFromTraj(t,sele,ref_sele,radius=7.0,average=False,seq_sep=4,first=0, :type last: :class:`int` :type seq_sep: :class:`int` - :return: a numpy vecor dist_rmsd(N\ :subscript:`frames`). + :return: a numpy vecor dist_rmsd(N\\ :subscript:`frames`). """ if not sele.GetAtomCount()==ref_sele.GetAtomCount(): print('Not same number of atoms in the two views') @@ -243,7 +243,7 @@ def AverageDistanceMatrixFromTraj(t,sele,first=0,last=-1): :type first: :class:`int` :type last: :class:`int` - :return: a numpy N\ :subscript:`pairs`\ xN\ :subscript:`pairs` matrix, where N\ :subscript:`pairs` + :return: a numpy N\\ :subscript:`pairs`\\ xN\\ :subscript:`pairs` matrix, where N\\ :subscript:`pairs` is the number of atom pairs in **sele**. """ try: