../con/Con_Automatic.hh
../con/Subset_Contracted_System.hh
../con/con.cc
../con/con_apair.cc
../con/con_bpair.cc
../con/con_e1.cc
../con/con_f.cc
../con/con_f2.cc
../con/con_q2.cc
../con/con_write.cc
../dat/DAT_ARRAY_CONSTS.cc
../dat/DAT_ARRAY_CONSTS.hh
../dat/DAT_DEFORM_PARAMS.cc
../dat/DAT_DEFORM_PARAMS.hh
../dat/DAT_DISULFIDE_LINKS.cc
../dat/DAT_DISULFIDE_LINKS.hh
../dat/DAT_ENERGY_PARAMS.cc
../dat/DAT_ENERGY_PARAMS.hh
../dat/DAT_IGOR_DATA.cc
../dat/DAT_IGOR_DATA.hh
../dat/DAT_PHYSICS_CONSTS.cc
../dat/DAT_PHYSICS_CONSTS.hh
../dat/DAT_REGION_MAPS.cc
../dat/DAT_REGION_MAPS.hh
../dat/DAT_RESIDUE_MAPPINGS.cc
../dat/DAT_RESIDUE_MAPPINGS.hh
../def/Def_Automatic.hh
../def/def.cc
../def/def_clust.cc
../def/def_dev18.cc
../def/def_disce.cc
../def/def_discp.cc
../def/def_disct.cc
../def/def_segpt.cc
../def/def_setps.cc
../def/def_setsg.cc
../def/def_sett4.cc
../def/def_setth.cc
../def/def_setx1.cc
../def/def_setx2.cc
../def/def_setx3.cc
../def/def_setx4.cc
../def/def_setx5.cc
../def/def_sort.cc
../def/def_zero.cc
../def/def_zero_c3.cc
../deg/deg.cc
../dom/Domain_Definitions.cc
../dom/Domain_Definitions.hh
../dom/dom_reform.cc
../dst/Distance_Constraints.hh
../dst/dst.cc
../fil/Family.cc
../fil/Family.hh
../fil/Search_Subspace.cc
../fil/Search_Subspace.hh
../fil/Structure.cc
../fil/Structure.hh
../fil/Trajectory.cc
../fil/Trajectory.hh
../fil/car2fil.cc
../fil/cycstp.cc
../fil/docstp.cc
../fil/fam2str.cc
../fil/fil2car.cc
../fil/fil2cha.cc
../fil/fil2seq.cc
../fil/fil2stp.cc
../fil/fil2tor.cc
../fil/mechsys.cc
../fil/pckstp.cc
../fil/polarh.cc
../fil/reform.cc
../fil/seq2fil.cc
../fil/sta.cc
../fil/str2fam.cc
../fil/str2tra.cc
../fil/tor.cc
../fil/tor2fil.cc
../fil/tra2str.cc
../fil/unionsc.cc
../glo/Backbone_Defs.cc
../glo/Backbone_Defs.hh
../glo/Glo.hh
../glo/Glo_Automatic.cc
../glo/Glo_Automatic.hh
../glo/Ising_Model.cc
../glo/Ising_Model.hh
../glo/glo.cc
../glo/glo_a5.cc
../glo/glo_bbpck.cc
../glo/glo_chi.cc
../glo/glo_def.cc
../glo/glo_def2str.cc
../glo/glo_f2.cc
../glo/glo_q2.cc
../glo/glo_scpck.cc
../glo/glo_step.cc
../glo/glo_u2.cc
../glo/glo_wrt.cc
../hom/Homolog_Model.cc
../hom/Homolog_Model.hh
../hom/Sub_Automatic.hh
../hom/ali.cc
../hom/ali_def.cc
../hom/ali_sub.cc
../hom/ali_tem.cc
../hom/scr.cc
../hom/sub.cc
../hom/sub_bbpck.cc
../hom/sub_bse.cc
../hom/sub_gen.cc
../hom/sub_grp.cc
../hom/sub_scpck.cc
../hom/sub_usc.cc
../igo/Config_Merge.hh
../igo/Igor_Model.cc
../igo/Igor_Model.hh
../igo/Target_Surf.hh
../igo/igo.cc
../igo/igo_2traj.cc
../igo/igo_3traj.cc
../igo/igo_3traj_b.cc
../igo/igo_3traj_x.cc
../igo/igo_bhash.cc
../igo/igo_ehash.cc
../igo/igo_enq.cc
../igo/igo_gfilt.cc
../igo/igo_gloadb.cc
../igo/igo_gloadb_1.cc
../igo/igo_gloade.cc
../igo/igo_gseq.cc
../igo/igo_loq.cc
../igo/igo_loq_backup.cc
../igo/igo_loq_initlamda.cc
../igo/igo_loq_targetbeta.cc
../igo/igo_loq_update.cc
../igo/igo_loq_wrt.cc
../igo/igo_rload.cc
../igo/igo_rload_1.cc
../igo/igo_rprob.cc
../igo/igo_sco0.cc
../igo/igo_sco1.cc
../igo/igo_sco2.cc
../igo/igo_sco3.cc
../igo/igo_sco3_e.cc
../igo/igo_sco3_e1.cc
../igo/igo_sco3_e2.cc
../igo/igo_sco3_edoc.cc
../igo/igo_sco3_epck.cc
../igo/igo_sco3_epen.cc
../igo/igo_sco3_evis.cc
../igo/igo_sco3_optv.cc
../igo/igo_sco3_optw.cc
../igo/igo_sco3_w.cc
../igo/igo_sco3_w1.cc
../igo/igo_sco3_w1doc.cc
../igo/igo_sco3_w2.cc
../igo/igo_sco3_w2doc.cc
../igo/igo_sco3_wolp.cc
../igo/igo_sco3_wpol.cc
../igo/igo_step.cc
../igo/igo_uload.cc
../loc/Loc.hh
../loc/Loc_Automatic.hh
../loc/loc.cc
../loc/loc_f2.cc
../loc/loc_numeric.cc
../loc/loc_q2.cc
../loc/loc_u2.cc
../med/Defect_Automatic.hh
../med/Dielec_Continu.cc
../med/Dielec_Continu.hh
../med/defect.cc
../med/defect_bchg.cc
../med/defect_cav.cc
../med/defect_chg.cc
../med/defect_cnf.cc
../med/defect_con.cc
../med/defect_ehp.cc
../med/defect_flag.cc
../med/defect_hbnd.cc
../med/defect_mol.cc
../med/defect_olp.cc
../med/defect_ssp.cc
../med/defect_stp.cc
../med/defect_surf.cc
../med/med.cc
../med/med_adotsec.cc
../med/med_bdotsec.cc
../med/med_bse.cc
../med/med_buried.cc
../med/med_cdotsec.cc
../med/med_dot.cc
../med/med_dotrot.cc
../med/med_dottrans.cc
../med/med_func.cc
../med/med_mol.cc
../med/med_mol_chg.cc
../med/med_sig.cc
../med/med_sphere.cc
../med/med_surf.cc
../med/med_switch.cc
../med/med_torus.cc
../mov/Lagrange_Multiplier.hh
../mov/Local_Minimization.hh
../mov/lag_deltaf.cc
../mov/lag_diagonal.cc
../mov/lag_gradient.cc
../mov/lag_lamdastep.cc
../mov/lag_length.cc
../mov/lag_lower.cc
../mov/lag_normalize.cc
../mov/lag_step.cc
../mov/mov0.cc
../mov/mov0_mov.cc
../mov/mov0_oaccept.cc
../mov/mov0_obackup.cc
../mov/mov0_oreject.cc
../mov/mov1.cc
../mov/mov1_mov.cc
../mov/mov1_oaccept.cc
../mov/mov1_obackup.cc
../mov/mov1_obeta.cc
../mov/mov1_odelf.cc
../mov/mov1_oreject.cc
../mov/mov1_ostep.cc
../mov/mov2.cc
../mov/mov2_backup.cc
../mov/mov2_target_beta.cc
../mov/mov2_update.cc
../mov/mov4_backup.cc
../mov/mov4_initial_lamda.cc
../mov/mov4_target_beta.cc
../mov/mov4_update.cc
../mov/mov5.cc
../mov/mov5_backup.cc
../mov/mov5_target_beta.cc
../mov/mov5_update.cc
../mov/mov_initial_lamda.cc
../mov/wrt0.cc
../mov/wrt1.cc
../mov/wrt2.cc
../mov/wrt5.cc
../pck/Packing_Search.cc
../pck/Packing_Search.hh
../pck/pck.cc
../pck/pck_2bod.cc
../pck/pck_ehp.cc
../pck/pck_f.cc
../pck/pck_ico.cc
../pck/pck_mol.cc
../pck/pck_nbod.cc
../pck/pck_ndoc.cc
../pck/pck_sphere.cc
../pck/pck_surf.cc
../pck/pck_vis.cc
../phi/Block_Pair.cc
../phi/Block_Pair.hh
../phi/Conf_Dependent_System.hh
../phi/Coordinates.cc
../phi/Coordinates.hh
../phi/Energy_Surface.hh
../phi/Fourier1D_Coeffs.cc
../phi/Fourier1D_Coeffs.hh
../phi/Fourier2D_Coeffs.cc
../phi/Fourier2D_Coeffs.hh
../phi/Fourier3D_Coeffs.cc
../phi/Fourier3D_Coeffs.hh
../phi/Gaussian_Volume.cc
../phi/Gaussian_Volume.hh
../phi/Multipoles.cc
../phi/Multipoles.hh
../phi/Phi1_Automatic.hh
../phi/Phi_Automatic.hh
../phi/Rotation_Matrix.cc
../phi/Rotation_Matrix.hh
../phi/Rotation_Tensor.cc
../phi/Rotation_Tensor.hh
../phi/Scratch_Multipoles.cc
../phi/Scratch_Multipoles.hh
../phi/Spherical_Harmonics.cc
../phi/Spherical_Harmonics.hh
../phi/phi0.cc
../phi/phi0_hbnd.cc
../phi/phi0_r.cc
../phi/phi0_rexp.cc
../phi/phi1.cc
../phi/phi1_dchi.cc
../phi/phi1_e2.cc
../phi/phi1_hbnd.cc
../phi/phi1_o2.cc
../phi/phi1_r.cc
../phi/phi1_rexp.cc
../phi/phi2.cc
../phi/phi3.cc
../phi/phi3_a.cc
../phi/phi3_d.cc
../phi/phi3_g.cc
../phi/phi3_restch.cc
../phi/phi3_xq.cc
../phi/phi_a.cc
../phi/phi_c.cc
../phi/phi_cont.cc
../phi/phi_e.cc
../phi/phi_e1.cc
../phi/phi_e1_p.cc
../phi/phi_e1_wm.cc
../phi/phi_e8.cc
../phi/phi_e9.cc
../phi/phi_g.cc
../phi/phi_l.cc
../phi/phi_me.cc
../phi/phi_o8.cc
../phi/phi_o9.cc
../phi/phi_p.cc
../phi/phi_part.cc
../phi/phi_part1.cc
../phi/phi_ppar.cc
../phi/phi_pwm.cc
../phi/phi_resh.cc
../phi/phi_restch.cc
../phi/phi_t1d.cc
../phi/phi_t2d.cc
../phi/phi_wm.cc
../phi/phi_wpar.cc
../phi/phi_xq.cc
../phi/phid.cc
../phi/phid_tc.cc
../phi/phid_x.cc
../phi/phie.cc
../phi/phie_c.cc
../phi/phie_e.cc
../phi/phie_e1.cc
../phi/phie_gp.cc
../phi/phie_me.cc
../phi/phie_pwm.cc
../phi/phie_resh.cc
../phi/phie_restch.cc
../phi/phie_t1d.cc
../phi/phie_t2d.cc
../phi/phis.cc
../phi/qfac.cc
../reg/Regularization_Target.hh
../reg/reg.cc
../reg/reg_phi.cc
../set/Mechanical_System.hh
../set/Set_Automatic.hh
../set/car.cc
../set/set.cc
../set/set_c1.cc
../set/set_dist.cc
../set/set_e0.cc
../set/set_pass.cc
../set/set_q1.cc
../set/set_q2.cc
../set/set_q3.cc
../set/set_write.cc
../shf/shf.cc
../shf/shf_sco.cc
../str/Ionstate_Automatic.cc
../str/Ionstate_Automatic.hh
../str/Output_Streams.cc
../str/Output_Streams.hh
../str/Ptra_Automatic.cc
../str/Ptra_Automatic.hh
../str/Thread_Options.cc
../str/Thread_Options.hh
../str/edoc.cc
../str/ereg.cc
../str/estp.cc
../str/greg.cc
../str/hlog.cc
../str/igor.cc
../str/initcar.cc
../str/ionstate.cc
../str/prof.cc
../str/ptra.cc
../str/rcyc.cc
../str/seqformat.cc
../sup/Kabsch_Rotation.cc
../sup/Kabsch_Rotation.hh
../sup/paircnf.cc
../sup/sup.cc
../sup/sup_project.cc
../tra/Energy_Surf.cc
../tra/Energy_Surf.hh
../tra/Local_Minimiz.hh
../tra/Stp_Automatic.hh
../tra/Tra_Automatic.hh
../tra/tra_ene_a.cc
../tra/tra_ene_chain.cc
../tra/tra_ene_g.cc
../tra/tra_ene_part.cc
../tra/tra_enp.cc
../tra/tra_enq.cc
../tra/tra_enq_a.cc
../tra/tra_enq_c.cc
../tra/tra_enq_cont.cc
../tra/tra_enq_e.cc
../tra/tra_enq_e1p.cc
../tra/tra_enq_e1resh.cc
../tra/tra_enq_e1wm.cc
../tra/tra_enq_e2.cc
../tra/tra_enq_e9.cc
../tra/tra_enq_g.cc
../tra/tra_enq_l.cc
../tra/tra_enq_me.cc
../tra/tra_enq_o2.cc
../tra/tra_enq_o9.cc
../tra/tra_enq_p.cc
../tra/tra_enq_part.cc
../tra/tra_enq_part1.cc
../tra/tra_enq_ppar.cc
../tra/tra_enq_pwm.cc
../tra/tra_enq_resh.cc
../tra/tra_enq_restchm.cc
../tra/tra_enq_t1d.cc
../tra/tra_enq_t2d.cc
../tra/tra_enq_wm.cc
../tra/tra_enq_wpar.cc
../tra/tra_enq_xq.cc
../tra/tra_lop.cc
../tra/tra_lop_backup.cc
../tra/tra_lop_targetbeta.cc
../tra/tra_lop_update.cc
../tra/tra_lop_wrt.cc
../tra/tra_loq.cc
../tra/tra_loq_backup.cc
../tra/tra_loq_initlamda.cc
../tra/tra_loq_targetbeta.cc
../tra/tra_loq_update.cc
../tra/tra_loq_wrt.cc
../tra/tra_stp.cc
../tra/tra_stp_bchg.cc
../tra/tra_stp_cav.cc
../tra/tra_stp_chg.cc
../tra/tra_stp_cnf.cc
../tra/tra_stp_ehp.cc
../tra/tra_stp_hbnd.cc
../tra/tra_stp_mol.cc
../tra/tra_stp_olp.cc
../tra/tra_stp_ssp.cc
../tra/tra_stp_stp.cc
../tra/tra_stp_surf.cc
