From 9662761150fc6870a27ef86fd952ddbbd9ac64c7 Mon Sep 17 00:00:00 2001 From: Ryan Lee Hayes Date: Thu, 29 Jun 2023 14:22:30 -0700 Subject: [PATCH] ALF v3.2 directory restructure --- v3.2beta/OLDREADME.md => OLDREADME.md | 0 v3.2beta/README.md => README.md | 0 v3.2beta/Setup.sh => Setup.sh | 0 {blade/template/ALF => alf}/G_imp/Entropy1.py | 0 {blade/template/ALF => alf}/G_imp/Entropy11.py | 0 {blade/template/ALF => alf}/G_imp/Entropy12.py | 0 {blade/template/ALF => alf}/G_imp/Entropy2.py | 0 {blade/template/ALF => alf}/G_imp/G12_10.dat | 0 {blade/template/ALF => alf}/G_imp/G12_2.dat | 0 {blade/template/ALF => alf}/G_imp/G12_3.dat | 0 {blade/template/ALF => alf}/G_imp/G12_4.dat | 0 {blade/template/ALF => alf}/G_imp/G12_5.dat | 0 {blade/template/ALF => alf}/G_imp/G12_6.dat | 0 {blade/template/ALF => alf}/G_imp/G12_7.dat | 0 {blade/template/ALF => alf}/G_imp/G12_8.dat | 0 {blade/template/ALF => alf}/G_imp/G12_9.dat | 0 {blade/template/ALF => alf}/G_imp/G1_10.dat | 0 {blade/template/ALF => 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v3.1/charmm/template/systems/T4L149F}/prep/aa_stream/maybejunk/top_arg.str (100%) rename {charmm/template/systems/T4L149U => v3.1/charmm/template/systems/T4L149F}/prep/aa_stream/maybejunk/top_asn.str (100%) rename {charmm/template/systems/T4L149U => v3.1/charmm/template/systems/T4L149F}/prep/aa_stream/maybejunk/top_lys.str (100%) rename {charmm/template/systems/T4L149U => v3.1/charmm/template/systems/T4L149F}/prep/aa_stream/sele_ala.str (100%) rename {charmm/template/systems/T4L149U => v3.1/charmm/template/systems/T4L149F}/prep/aa_stream/sele_arg.str (100%) rename {charmm/template/systems/T4L149U => v3.1/charmm/template/systems/T4L149F}/prep/aa_stream/sele_asn.str (100%) rename {charmm/template/systems/T4L149U => v3.1/charmm/template/systems/T4L149F}/prep/aa_stream/sele_asp.str (100%) rename {charmm/template/systems/T4L149U => v3.1/charmm/template/systems/T4L149F}/prep/aa_stream/sele_cys.str (100%) rename {charmm/template/systems/T4L149U => v3.1/charmm/template/systems/T4L149F}/prep/aa_stream/sele_gln.str (100%) rename {charmm/template/systems/T4L149U => v3.1/charmm/template/systems/T4L149F}/prep/aa_stream/sele_glu.str (100%) rename {charmm/template/systems/T4L149U => v3.1/charmm/template/systems/T4L149F}/prep/aa_stream/sele_hsd.str (100%) rename {charmm/template/systems/T4L149U => v3.1/charmm/template/systems/T4L149F}/prep/aa_stream/sele_hse.str (100%) rename {charmm/template/systems/T4L149U => v3.1/charmm/template/systems/T4L149F}/prep/aa_stream/sele_hsp.str (100%) rename {charmm/template/systems/T4L149U => v3.1/charmm/template/systems/T4L149F}/prep/aa_stream/sele_ile.str (100%) rename {charmm/template/systems/T4L149U => v3.1/charmm/template/systems/T4L149F}/prep/aa_stream/sele_leu.str (100%) rename {charmm/template/systems/T4L149U => v3.1/charmm/template/systems/T4L149F}/prep/aa_stream/sele_lys.str (100%) rename {charmm/template/systems/T4L149U => v3.1/charmm/template/systems/T4L149F}/prep/aa_stream/sele_met.str (100%) 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v3.1/charmm}/template/systems/T4L149F/prep/protein.pdb (100%) rename {charmm => v3.1/charmm}/template/systems/T4L149F/prep/solvent00.pdb (100%) rename {charmm => v3.1/charmm}/template/systems/T4L149F/prep/solvent01.pdb (100%) rename {charmm/template/systems/T4L149U => v3.1/charmm/template/systems/T4L149F}/prep/toppar/par_all36_cgenff.prm (100%) rename {charmm/template/systems/T4L149U => v3.1/charmm/template/systems/T4L149F}/prep/toppar/par_all36_msld.prm (100%) rename {charmm/template/systems/T4L149U => v3.1/charmm/template/systems/T4L149F}/prep/toppar/top_all36_cgenff.rtf (100%) rename {charmm/template/systems/T4L149U => v3.1/charmm/template/systems/T4L149F}/prep/toppar/top_all36_msld.rtf (100%) rename {charmm => v3.1/charmm}/template/systems/T4L149F/variables1.inp (100%) rename {charmm => v3.1/charmm}/template/systems/T4L149U/Notes.txt (100%) rename {v3.2beta/test_beta/T4L149U_charmm/prep => v3.1/charmm/template/systems/T4L149U}/Target.txt (100%) rename {charmm => v3.1/charmm}/template/systems/T4L149U/analysis0/b.dat (100%) rename {charmm => v3.1/charmm}/template/systems/T4L149U/analysis0/b_prev.dat (100%) rename {charmm => v3.1/charmm}/template/systems/T4L149U/analysis0/b_sum.dat (100%) rename {charmm => v3.1/charmm}/template/systems/T4L149U/analysis0/c.dat (100%) rename {charmm => v3.1/charmm}/template/systems/T4L149U/analysis0/c_prev.dat (100%) rename {charmm => v3.1/charmm}/template/systems/T4L149U/analysis0/c_sum.dat (100%) rename {charmm => v3.1/charmm}/template/systems/T4L149U/analysis0/s.dat (100%) rename {charmm => v3.1/charmm}/template/systems/T4L149U/analysis0/s_prev.dat (100%) rename {charmm => v3.1/charmm}/template/systems/T4L149U/analysis0/s_sum.dat (100%) rename {charmm => v3.1/charmm}/template/systems/T4L149U/analysis0/x.dat (100%) rename {charmm => v3.1/charmm}/template/systems/T4L149U/analysis0/x_prev.dat (100%) rename {charmm => v3.1/charmm}/template/systems/T4L149U/analysis0/x_sum.dat (100%) rename {charmm => v3.1/charmm}/template/systems/T4L149U/name (100%) rename {charmm => v3.1/charmm}/template/systems/T4L149U/nblocks (100%) rename {v3.2beta/test_beta/T4L149U_charmm/prep => v3.1/charmm/template/systems/T4L149U}/nbond.str (100%) rename {charmm => v3.1/charmm}/template/systems/T4L149U/nbshift/b_shift.dat (100%) rename {charmm => v3.1/charmm}/template/systems/T4L149U/nbshift/c_shift.dat (100%) rename {charmm => v3.1/charmm}/template/systems/T4L149U/nbshift/s_shift.dat (100%) rename {charmm => v3.1/charmm}/template/systems/T4L149U/nbshift/x_shift.dat (100%) rename {charmm => v3.1/charmm}/template/systems/T4L149U/ncentral (100%) rename {charmm => v3.1/charmm}/template/systems/T4L149U/nnodes (100%) rename {charmm => v3.1/charmm}/template/systems/T4L149U/nreps (100%) rename {v3.2beta/test_beta/T4L149U_charmm/prep => v3.1/charmm/template/systems/T4L149U}/nsubs (100%) rename {v3.2beta/test_beta/T4L149U_charmm => v3.1/charmm/template/systems/T4L149U}/prep/T4L149U.inp (100%) rename {v3.2beta/test_beta/T4L149U_charmm => v3.1/charmm/template/systems/T4L149U}/prep/aa_stream/MakeSele.sh (100%) rename {v3.2beta/test_beta/T4L149U_charmm => v3.1/charmm/template/systems/T4L149U}/prep/aa_stream/ca_ala.str (100%) rename {v3.2beta/test_beta/T4L149U_charmm => v3.1/charmm/template/systems/T4L149U}/prep/aa_stream/ca_arg.str (100%) rename {v3.2beta/test_beta/T4L149U_charmm => v3.1/charmm/template/systems/T4L149U}/prep/aa_stream/ca_asn.str (100%) rename {v3.2beta/test_beta/T4L149U_charmm => v3.1/charmm/template/systems/T4L149U}/prep/aa_stream/ca_asp.str (100%) rename {v3.2beta/test_beta/T4L149U_charmm => v3.1/charmm/template/systems/T4L149U}/prep/aa_stream/ca_cys.str (100%) rename {v3.2beta/test_beta/T4L149U_charmm => v3.1/charmm/template/systems/T4L149U}/prep/aa_stream/ca_gln.str (100%) rename {v3.2beta/test_beta/T4L149U_charmm => v3.1/charmm/template/systems/T4L149U}/prep/aa_stream/ca_glu.str (100%) rename {v3.2beta/test_beta/T4L149U_charmm => v3.1/charmm/template/systems/T4L149U}/prep/aa_stream/ca_hsd.str (100%) rename {v3.2beta/test_beta/T4L149U_charmm => v3.1/charmm/template/systems/T4L149U}/prep/aa_stream/ca_hse.str (100%) rename {v3.2beta/test_beta/T4L149U_charmm => v3.1/charmm/template/systems/T4L149U}/prep/aa_stream/ca_hsp.str (100%) rename {v3.2beta/test_beta/T4L149U_charmm => v3.1/charmm/template/systems/T4L149U}/prep/aa_stream/ca_ile.str (100%) rename {v3.2beta/test_beta/T4L149U_charmm => v3.1/charmm/template/systems/T4L149U}/prep/aa_stream/ca_leu.str (100%) rename {v3.2beta/test_beta/T4L149U_charmm => v3.1/charmm/template/systems/T4L149U}/prep/aa_stream/ca_lys.str (100%) rename {v3.2beta/test_beta/T4L149U_charmm => v3.1/charmm/template/systems/T4L149U}/prep/aa_stream/ca_met.str (100%) rename {v3.2beta/test_beta/T4L149U_charmm => v3.1/charmm/template/systems/T4L149U}/prep/aa_stream/ca_phe.str (100%) rename {v3.2beta/test_beta/T4L149U_charmm => v3.1/charmm/template/systems/T4L149U}/prep/aa_stream/ca_ser.str (100%) 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{v3.2beta/test_beta/T4L149U_charmm => v3.1/charmm/template/systems/T4L149U}/prep/aa_stream/maybejunk/top_lys.str (100%) rename {v3.2beta/test_beta/T4L149U_charmm => v3.1/charmm/template/systems/T4L149U}/prep/aa_stream/sele_ala.str (100%) rename {v3.2beta/test_beta/T4L149U_charmm => v3.1/charmm/template/systems/T4L149U}/prep/aa_stream/sele_arg.str (100%) rename {v3.2beta/test_beta/T4L149U_charmm => v3.1/charmm/template/systems/T4L149U}/prep/aa_stream/sele_asn.str (100%) rename {v3.2beta/test_beta/T4L149U_charmm => v3.1/charmm/template/systems/T4L149U}/prep/aa_stream/sele_asp.str (100%) rename {v3.2beta/test_beta/T4L149U_charmm => v3.1/charmm/template/systems/T4L149U}/prep/aa_stream/sele_cys.str (100%) rename {v3.2beta/test_beta/T4L149U_charmm => v3.1/charmm/template/systems/T4L149U}/prep/aa_stream/sele_gln.str (100%) rename {v3.2beta/test_beta/T4L149U_charmm => v3.1/charmm/template/systems/T4L149U}/prep/aa_stream/sele_glu.str (100%) rename {v3.2beta/test_beta/T4L149U_charmm => v3.1/charmm/template/systems/T4L149U}/prep/aa_stream/sele_hsd.str (100%) rename {v3.2beta/test_beta/T4L149U_charmm => v3.1/charmm/template/systems/T4L149U}/prep/aa_stream/sele_hse.str (100%) rename {v3.2beta/test_beta/T4L149U_charmm => v3.1/charmm/template/systems/T4L149U}/prep/aa_stream/sele_hsp.str (100%) rename {v3.2beta/test_beta/T4L149U_charmm => v3.1/charmm/template/systems/T4L149U}/prep/aa_stream/sele_ile.str (100%) rename {v3.2beta/test_beta/T4L149U_charmm => v3.1/charmm/template/systems/T4L149U}/prep/aa_stream/sele_leu.str (100%) rename {v3.2beta/test_beta/T4L149U_charmm => v3.1/charmm/template/systems/T4L149U}/prep/aa_stream/sele_lys.str (100%) rename {v3.2beta/test_beta/T4L149U_charmm => v3.1/charmm/template/systems/T4L149U}/prep/aa_stream/sele_met.str (100%) rename {v3.2beta/test_beta/T4L149U_charmm => v3.1/charmm/template/systems/T4L149U}/prep/aa_stream/sele_phe.str (100%) rename {v3.2beta/test_beta/T4L149U_charmm => v3.1/charmm/template/systems/T4L149U}/prep/aa_stream/sele_ser.str (100%) rename {v3.2beta/test_beta/T4L149U_charmm => v3.1/charmm/template/systems/T4L149U}/prep/aa_stream/sele_thr.str (100%) rename {v3.2beta/test_beta/T4L149U_charmm => v3.1/charmm/template/systems/T4L149U}/prep/aa_stream/sele_trp.str (100%) rename {v3.2beta/test_beta/T4L149U_charmm => v3.1/charmm/template/systems/T4L149U}/prep/aa_stream/sele_tyr.str (100%) rename {v3.2beta/test_beta/T4L149U_charmm => v3.1/charmm/template/systems/T4L149U}/prep/aa_stream/sele_val.str (100%) rename {v3.2beta/test_beta/T4L149U_charmm => v3.1/charmm/template/systems/T4L149U}/prep/ions.pdb (100%) rename {v3.2beta/test_beta/T4L149U_charmm => v3.1/charmm/template/systems/T4L149U}/prep/minimized.pdb (100%) rename {v3.2beta/test_beta/T4L149U_charmm => v3.1/charmm/template/systems/T4L149U}/prep/minimized.psf (100%) rename {v3.2beta/test_beta/T4L149U_charmm => v3.1/charmm/template/systems/T4L149U}/prep/protein.pdb (100%) rename {v3.2beta/test_beta/T4L149U_charmm => v3.1/charmm/template/systems/T4L149U}/prep/solvent00.pdb (100%) rename {v3.2beta/test_beta/T4L149U_charmm => v3.1/charmm/template/systems/T4L149U}/prep/toppar/par_all36_cgenff.prm (100%) rename {v3.2beta/test_beta/T4L149U_charmm => v3.1/charmm/template/systems/T4L149U}/prep/toppar/par_all36_msld.prm (100%) rename {v3.2beta/test_beta/T4L149U_charmm => v3.1/charmm/template/systems/T4L149U}/prep/toppar/top_all36_cgenff.rtf (100%) rename {v3.2beta/test_beta/T4L149U_charmm => v3.1/charmm/template/systems/T4L149U}/prep/toppar/top_all36_msld.rtf (100%) rename {charmm => v3.1/charmm}/template/systems/T4L149U/variables1.inp (100%) rename {charmm => v3.1/charmm}/template/systems/u58-64/analysis0/InitVars.py (100%) rename {charmm => v3.1/charmm}/template/systems/u58-64/analysis0/b.dat (100%) rename {charmm => v3.1/charmm}/template/systems/u58-64/analysis0/b_prev.dat (100%) rename {charmm => v3.1/charmm}/template/systems/u58-64/analysis0/b_sum.dat (100%) 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diff --git a/charmm/template/ALF/G_imp/G2_8.dat b/v3.1/bladelib4jzv/template/ALF/G_imp/G2_8.dat similarity index 100% rename from charmm/template/ALF/G_imp/G2_8.dat rename to v3.1/bladelib4jzv/template/ALF/G_imp/G2_8.dat diff --git a/charmm/template/ALF/G_imp/G2_9.dat b/v3.1/bladelib4jzv/template/ALF/G_imp/G2_9.dat similarity index 100% rename from charmm/template/ALF/G_imp/G2_9.dat rename to v3.1/bladelib4jzv/template/ALF/G_imp/G2_9.dat diff --git a/charmm/template/ALF/G_imp/old/Entropy1.m b/v3.1/bladelib4jzv/template/ALF/G_imp/old/Entropy1.m similarity index 100% rename from charmm/template/ALF/G_imp/old/Entropy1.m rename to v3.1/bladelib4jzv/template/ALF/G_imp/old/Entropy1.m diff --git a/charmm/template/ALF/G_imp/old/Entropy12.m b/v3.1/bladelib4jzv/template/ALF/G_imp/old/Entropy12.m similarity index 100% rename from charmm/template/ALF/G_imp/old/Entropy12.m rename to v3.1/bladelib4jzv/template/ALF/G_imp/old/Entropy12.m diff --git a/charmm/template/ALF/G_imp/old/Entropy2.m 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