families[1] = [10, mainPocket, sidePocket1]
families[2] = [31, mainPocket, sidePocket2]
#families[3] = [7,mainPocket,sidePocket3]
#families[4] = [46,mainPocket,sidePocket4]
#families[5] = [17,mainPocket]
#families[6] = [25,mainPocket,sidePocket1,sidePocket2]
#families[7] = [2,mainPocket,sidePocket1,sidePocket4]
#families[8] = [18,mainPocket,sidePocket1,sidePocket2,sidePocket4]
#families[9] = [27,mainPocket,sidePocket1,sidePocket2,sidePocket3,sidePocket4]
familyMembership = []
#for index, family in enumerate(families.keys()):
for family in list(families.keys()):
for replicate in range(families[family][0]):
outPrefix = 'family%i_rep%02i' % (family, replicate)
this_fm = peel.featureMap([-20, 20, -20, 20, -20, 20], 1)
for pocket in families[family][1:]:
randomShift = peel.point(np.random.normal(0, randomFactor, (3)))
this_fm.add_sphere(pocket[0].point_sum_new(randomShift), pocket[1])
familyMembership.append((family, outPrefix, this_fm))
if createPdbs == True:
this_fm.write_pdb(outPrefix + '.pdb')
if createNpys == True:
np.save(outPrefix + '.npy', this_fm.toPovmeList()[:, :3])
familyMap = np.zeros((len(familyMembership), len(familyMembership)))
for iInd, i in enumerate(familyMembership):
for jInd, j in enumerate(familyMembership):
if i[0] == j[0]:
familyMap[iInd, jInd] = 1
families[1] = [10,mainPocket,sidePocket1]
families[2] = [31,mainPocket,sidePocket2]
families[3] = [7,mainPocket,sidePocket3]
families[4] = [46,mainPocket,sidePocket4]
families[5] = [17,mainPocket]
#families[6] = [25,mainPocket,sidePocket1,sidePocket2]
#families[7] = [2,mainPocket,sidePocket1,sidePocket4]
#families[8] = [18,mainPocket,sidePocket1,sidePocket2,sidePocket4]
#families[9] = [27,mainPocket,sidePocket1,sidePocket2,sidePocket3,sidePocket4]
familyMembership = []
#for index, family in enumerate(families.keys()):
for family in families.keys():
for replicate in range(families[family][0]):
outPrefix = 'family%i_rep%02i' %(family, replicate)
this_fm = peel.featureMap([-20,20,-20,20,-20,20],1)
for pocket in families[family][1:]:
randomShift = peel.point(np.random.normal(0,randomFactor,(3)))
this_fm.add_sphere(pocket[0].point_sum_new(randomShift),
pocket[1])
familyMembership.append((family, outPrefix, this_fm))
if createPdbs == True:
this_fm.write_pdb(outPrefix+'.pdb')
if createNpys == True:
np.save(outPrefix+'.npy', this_fm.toPovmeList()[:,:3])
familyMap = np.zeros((len(familyMembership),len(familyMembership)))
for iInd, i in enumerate(familyMembership):
for jInd, j in enumerate(familyMembership):
if i[0] == j[0]: