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Extend getDihedral to work on many coordinate sets #2009

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merged 4 commits into from
Dec 3, 2024
Merged

Extend getDihedral to work on many coordinate sets #2009

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66906b2
getDihedral from multi coordsets
jamesmkrieger Oct 23, 2024
d401316
extract single
jamesmkrieger Oct 23, 2024
2154509
Merge branch 'main' of github.com:prody/ProDy into getDihedral_many
jamesmkrieger Dec 1, 2024
ec0eafa
add get measure funcs
jamesmkrieger Dec 3, 2024
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22 changes: 13 additions & 9 deletions prody/measure/measure.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@

from numpy import ndarray, power, sqrt, array, zeros, arccos, dot
from numpy import sign, tile, concatenate, pi, cross, subtract, var
from numpy import unique, where
from numpy import unique, where, divide, power

from prody.atomic import Atomic, Residue, Atom, extendAtomicData
from prody.kdtree import KDTree
Expand All @@ -16,11 +16,11 @@
if PY2K:
range = xrange

__all__ = ['buildDistMatrix', 'calcDistance',
'calcCenter', 'calcGyradius', 'calcAngle',
'calcDihedral', 'calcOmega', 'calcPhi', 'calcPsi',
'calcMSF', 'calcRMSF',
'calcDeformVector',
__all__ = ['buildDistMatrix', 'calcDistance', 'calcGyradius',
'calcCenter', 'calcAngle', 'calcDihedral',
'getCenter', 'getAngle', 'getDihedral',
'calcOmega', 'calcPhi', 'calcPsi',
'calcMSF', 'calcRMSF', 'calcDeformVector',
'buildADPMatrix', 'calcADPAxes', 'calcADPs',
'pickCentral', 'pickCentralAtom', 'pickCentralConf', 'getWeights',
'calcInertiaTensor', 'calcPrincAxes', 'calcDistanceMatrix',
Expand Down Expand Up @@ -207,13 +207,17 @@ def getDihedral(coords1, coords2, coords3, coords4, radian=False):
a3 = coords4 - coords3

v1 = cross(a1, a2)
v1 = v1 / (v1 * v1).sum(-1)**0.5
v1 = divide(v1, power((v1 * v1).sum(-1), 0.5).reshape(-1,1))
v2 = cross(a2, a3)
v2 = v2 / (v2 * v2).sum(-1)**0.5
v2 = divide(v2, power((v2 * v2).sum(-1), 0.5).reshape(-1,1))
porm = sign((v1 * a3).sum(-1))
rad = arccos((v1*v2).sum(-1) / ((v1**2).sum(-1) * (v2**2).sum(-1))**0.5)
if not porm == 0:
if not all(porm == 0):
rad = rad * porm

if rad.shape[0] == 1:
rad = rad[0]

if radian:
return rad
else:
Expand Down
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