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]: