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Code to evaluate reaction coordinates and to optimize contact-based coordinates. References: https://doi.org/10.1063/1.1630572 https://doi.org/10.1073/pnas.0408098102 https://doi.org/10.1021/acs.jpcb.5b09741 Documentation and tests to be added. - assign_tp.cc : Assign transition paths based on some progress variable (which need not be a very good rc assign_tp2.cc ave_cmap.cc : average contact map ave_contacts.cc ave_pvec.cc common.cc : common stuff common.h config.h constN_proj.cc crossval.cc dcd2dcd.cc dcdinfo.cc dij.cc distance.cc drms.cc drms_pbc.cc dump_cmaps.cc dump_dists.cc extract_tp.cc ferguson.cc fixaaqaa.cc fret.cc go_correct.cc kmt.cc lqcalc.cc Makefile ncdiff_contacts.cc pTP_crd.cc pvec2mat.py pvec2qlist.py qcalc.cc qcalc_cmap.cc qcalc_discrete.cc qcalc_gen.cc qcalc_pbc.cc qcontig.cc qlist2pvec.py qphi.cc quick_epert.cc random_gen.cc random_gen.h rc_opt.cc : main rc opt code sum_ptp.py swapbytes.cc swapbytes.h traj.cc TrajFile.cc TrajFile.h traj.h trunctraj.cc tTP_crd.cc vector.cc xtr_pvec.cc
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Utitilies for calculating and optimizing reaction coordinates plus a bunch of random stuff
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