# HG changeset patch # User chemteam # Date 1605296275 0 # Node ID 9ca30ad954445dcc41413b45c99706c9ff49eca5 # Parent 6f2029791c946a16246c6d2438174b3ef608d21b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f1c3c88c7395f2e84cbc533199406aadb79c5c07" diff -r 6f2029791c94 -r 9ca30ad95444 NEQGamma.py --- a/NEQGamma.py Fri Sep 11 21:55:57 2020 +0000 +++ b/NEQGamma.py Fri Nov 13 19:37:55 2020 +0000 @@ -129,17 +129,18 @@ dist = open(output, "w") frict = open(output_frict, "w") - dist.write( - "#x force_integral frict_coeff wdiss corrected_force_integral\n") + dist.write('\t'.join(('#x', 'force_integral', 'frict_coeff', + 'wdiss', 'corrected_force_integral\n'))) for i in range(length_data): - dist.write("{:15.8f} {:20.8f} {:20.8f} {:20.8f} {:20.8f}\n".format( + dist.write("{:.8f}\t{:.8f}\t{:.8f}\t{:.8f}\t{:.8f}\n".format( x[i], av_forceintegral[i], av_intcorr[i], wdiss[i], av_forceintegral[i] - wdiss[i])) - frict.write("""#x ACF frict_coeff """ - """gauss_filtered_frict_coeff av_window_frict_coeff\n""") + frict.write('\t'.join(('#x', 'ACF', 'frict_coeff', + 'gauss_filtered_frict_coeff', + 'av_window_frict_coeff\n'))) for i in range(length_data): - frict.write("{:15.8f} {:20.8f} {:20.8f} {:20.8f} {:20.8f}\n".format( + frict.write("{:.8f}\t{:.8f}\t{:.8f}\t{:.8f}\t{:.8f}\n".format( x[i], autocorr_set[i], av_intcorr[i], blurred[i], runn_av[i])) dist.close() @@ -149,7 +150,7 @@ def main(): - parser = argparse.ArgumentParser(description="""dcTMD friciton correction + parser = argparse.ArgumentParser(description="""dcTMD friction correction (please cite: Wolf, S., Stock, G. Targeted Molecular Dynamics Calculations of Free Energy Profiles Using a Nonequilibrium Friction Correction. J. Chem. Theory Comput. 2018, 14(12), 6175-6182, diff -r 6f2029791c94 -r 9ca30ad95444 get_clusters.py --- a/get_clusters.py Fri Sep 11 21:55:57 2020 +0000 +++ b/get_clusters.py Fri Nov 13 19:37:55 2020 +0000 @@ -23,7 +23,7 @@ parser = argparse.ArgumentParser() parser.add_argument('--Z', required=True, help='File for cluster linkage array.') - parser.add_argument('--threshold', type=int, required=True, + parser.add_argument('--threshold', type=float, required=True, help='Distance cutoff.') parser.add_argument('--min-members', type=int, required=True, help='Minimum number of members of the cluster.') diff -r 6f2029791c94 -r 9ca30ad95444 rmsd_clustering.py --- a/rmsd_clustering.py Fri Sep 11 21:55:57 2020 +0000 +++ b/rmsd_clustering.py Fri Nov 13 19:37:55 2020 +0000 @@ -48,7 +48,8 @@ def plot_dendrogram(Z, output): - plt.figure(figsize=(25, 10)) + # figure width scales with number of leaves + plt.figure(figsize=(0.25 * Z.shape[0], 10)) plt.title('Hierarchical Clustering Dendrogram') plt.xlabel('Trajectory index') plt.ylabel('distance') diff -r 6f2029791c94 -r 9ca30ad95444 test-data/NEQGamma_ofrict.txt --- a/test-data/NEQGamma_ofrict.txt Fri Sep 11 21:55:57 2020 +0000 +++ b/test-data/NEQGamma_ofrict.txt Fri Nov 13 19:37:55 2020 +0000 @@ -1,102 +1,102 @@ -#x ACF frict_coeff gauss_filtered_frict_coeff av_window_frict_coeff - 0.00000000 439653.22756622 0.00000000 39.85704130 -164.30975524 - 0.00000200 41861.51118060 -309.80490686 39.90128147 -42.50284457 - 0.00000400 -4760.58383990 -1433.31122481 39.98937507 132.75776205 - 0.00000600 -52063.97568219 -1302.42266399 40.10796653 273.24484877 - 0.00000800 -94137.43307581 -696.00283593 40.26787861 322.90057440 - 0.00001000 -109240.44374298 59.67135417 40.47438205 310.49706801 - 0.00001200 -91296.29474097 200.26534006 40.74119359 300.71687201 - 0.00001400 -42279.73264591 -211.00314767 41.08344474 307.77939795 - 0.00001600 29083.13222726 -299.86397145 41.51045417 289.59363364 - 0.00001800 100957.95082594 706.27695160 42.02391473 213.62523715 - 0.00002000 150492.32652407 2436.13821354 42.62185633 115.80351000 - 0.00002200 163610.52308989 3505.21213240 43.30185229 72.52474633 - 0.00002400 137798.21546909 2809.74173435 44.06395945 119.32042200 - 0.00002600 86552.97296922 993.11451262 44.91354630 219.23877027 - 0.00002800 30065.89230936 -248.07012791 45.85833909 214.16642537 - 0.00003000 -15271.83960767 -195.60392001 46.90428227 107.42336841 - 0.00003200 -41143.37576909 141.25051892 48.05595140 -10.23715919 - 0.00003400 -45603.75654834 -363.71528632 49.31891708 -41.13071129 - 0.00003600 -31933.14574422 -1519.36792976 50.67717643 11.13789839 - 0.00003800 -11580.24564270 -1956.43454302 52.14035913 47.86749694 - 0.00004000 1795.96943076 -865.57527338 53.69638462 -13.42971260 - 0.00004200 -6069.40567724 626.10860652 55.34660090 -151.70147237 - 0.00004400 -36605.44103603 565.05574074 57.08967355 -284.06117371 - 0.00004600 -88409.03954732 -1403.86956218 58.91185508 -352.46208669 - 0.00004800 -119187.64656330 -2830.86397506 60.79652934 -358.13736161 - 0.00005000 -126958.63383213 -2293.53919791 62.72537859 -329.02117947 - 0.00005200 -105144.23378691 -417.60570188 64.67974189 -286.64057459 - 0.00005400 -57578.18477311 834.36904591 66.64059843 -231.16675138 - 0.00005600 7642.76668942 434.72799961 68.58976595 -160.41908396 - 0.00005800 73314.58537446 -519.66723923 70.51136345 -97.11322986 - 0.00006000 117239.42596973 -329.29698187 72.38916035 -71.95507125 - 0.00006200 122335.84589389 858.01810556 74.20116994 -72.69735215 - 0.00006400 90700.59252948 1441.72347492 75.92201577 -50.06936146 - 0.00006600 40928.26316446 879.60901414 77.52654008 55.63484244 - 0.00006800 -3181.66487546 334.25351485 78.99192675 197.17614864 - 0.00007000 -31227.72623817 652.00817770 80.29696328 378.84255238 - 0.00007200 -43642.08135556 1250.72698300 81.42019653 507.21229626 - 0.00007400 -37578.91493866 1051.23806218 82.34208812 533.01944777 - 0.00007600 -9313.59450148 -253.25084775 83.04041098 497.57963010 - 0.00007800 35606.42432047 -1453.27137086 83.53076487 484.49556872 - 0.00008000 74825.06321773 -880.42089139 83.79365831 512.38603041 - 0.00008200 87450.95751560 1078.66842032 83.81028733 508.57269634 - 0.00008400 84964.54130532 2679.13981866 83.55962529 417.18682766 - 0.00008600 33723.38650302 1426.95656188 83.03964822 275.01069883 - 0.00008800 26888.00526112 802.46409967 82.26457780 159.07974622 - 0.00009000 15764.22367820 273.85567979 81.25039304 86.68872404 - 0.00009200 -1018.04050367 98.53732822 80.00383608 19.95207715 - 0.00009400 -18778.21955924 125.57269254 78.52437737 -55.26075096 - 0.00009600 -25696.85381088 173.04677203 76.81790266 -95.82294253 - 0.00009800 -19020.27963144 38.14199457 74.90534804 -40.08283716 - 0.00010000 -13853.36236626 -405.56366316 72.81359766 112.25327202 - 0.00010200 -22360.23253615 -969.69926808 70.56500733 263.50051564 - 0.00010400 -39525.81005506 -1401.79910164 68.18385377 320.37515633 - 0.00010600 -47887.23125912 -1439.01003806 65.70767268 323.43291333 - 0.00010800 -38703.50620624 -1113.56692890 63.18337712 284.23466280 - 0.00011000 -15756.47051989 -682.72476001 60.65377002 277.77044438 - 0.00011200 10148.75573217 -253.52957929 58.15278984 250.27515323 - 0.00011400 32489.76783313 239.99423089 55.71193773 178.79248872 - 0.00011600 48846.14416151 861.55125965 53.36798832 70.38368037 - 0.00011800 60211.15804332 1593.45081266 51.19169051 -55.24610237 - 0.00012000 64597.66151097 2144.52398093 49.22113114 -170.30467384 - 0.00012200 58795.32774769 2216.16123424 47.49918918 -248.93156307 - 0.00012400 63226.50291119 2740.29495857 46.05677747 -270.24081648 - 0.00012600 7112.67333129 642.99155129 44.93086250 -206.96775261 - 0.00012800 4737.67676382 673.17973142 44.16608448 -50.37244372 - 0.00013000 -10629.83066809 -276.05014319 43.80477020 154.04681427 - 0.00013200 -24445.08596782 -1331.11596207 43.87860095 320.32723893 - 0.00013400 -38089.44576760 -2042.60347448 44.40990189 378.66585808 - 0.00013600 -53888.48385453 -2339.54888278 45.42258092 320.31441637 - 0.00013800 -65525.93331796 -2263.02943488 46.94717499 192.76961767 - 0.00014000 -66605.80950981 -1978.10144773 49.01173919 46.49351043 - 0.00014200 -59461.87405093 -1395.88433631 51.62964197 -100.43225450 - 0.00014400 -50082.83777468 -136.33782409 54.79891493 -258.31822307 - 0.00014600 -36265.73051644 1692.89613965 58.50910094 -447.27992440 - 0.00014800 -11065.11218743 2974.81823090 62.74931610 -601.98154580 - 0.00015000 24574.77396976 2642.88373319 67.50830566 -716.60080679 - 0.00015200 53704.30727291 913.24280375 72.76914377 -754.65637852 - 0.00015400 62641.21173742 -927.03460327 78.50486320 -713.36174226 - 0.00015600 50475.22167026 -1689.34471443 84.67941051 -602.77004154 - 0.00015800 27415.48879178 -1332.07133205 91.25069147 -429.82867913 - 0.00016000 659.52027909 -793.99131765 98.16114225 -214.90982911 - 0.00016200 -27358.17056213 -941.55813718 105.35683648 -1.93703392 - 0.00016400 -36359.81639946 -1038.93906805 112.78930315 141.63166343 - 0.00016600 -103478.83628142 -2451.04087672 120.41222030 155.07119820 - 0.00016800 -98122.08801466 -1619.20548854 128.15466148 39.58301004 - 0.00017000 -91470.31369949 -1037.16157762 135.94071127 -128.72347744 - 0.00017200 -70167.76251890 -505.22323695 143.69516807 -240.17685720 - 0.00017400 -43298.45234300 169.23053990 151.35171103 -223.11938998 - 0.00017600 -13147.13005351 1119.27836540 158.84649112 -87.45006406 - 0.00017800 13812.88135432 2035.34756564 166.10612536 85.27603300 - 0.00018000 29405.90836664 2281.35445610 173.04701036 209.91332866 - 0.00018200 27785.78282904 1475.48961051 179.59291666 253.65425754 - 0.00018400 16400.24253711 132.45287134 185.68841711 300.73216440 - 0.00018600 5032.51740518 -616.86762340 191.28914198 352.67911780 - 0.00018800 -684.42414340 -391.31151887 196.34017758 475.23116164 - 0.00019000 -2606.74806622 413.81613798 200.77390679 556.19143606 - 0.00019200 -4228.75142469 1254.39214820 204.53041970 608.04951495 - 0.00019400 -2944.53596867 1786.35191510 207.57544804 633.31067679 - 0.00019600 4064.05842526 1765.17722675 209.89395091 624.84914980 - 0.00019800 11878.81314410 1160.67458116 211.46967661 568.88523153 - 0.00020000 12188.47862387 80.82726004 212.27097983 467.11785325 +#x ACF frict_coeff gauss_filtered_frict_coeff av_window_frict_coeff +0.00000000 439653.22756622 0.00000000 39.85704130 -164.30975524 +0.00000200 41861.51118060 -309.80490686 39.90128147 -42.50284457 +0.00000400 -4760.58383990 -1433.31122481 39.98937507 132.75776205 +0.00000600 -52063.97568219 -1302.42266399 40.10796653 273.24484877 +0.00000800 -94137.43307581 -696.00283593 40.26787861 322.90057440 +0.00001000 -109240.44374298 59.67135417 40.47438205 310.49706801 +0.00001200 -91296.29474097 200.26534006 40.74119359 300.71687201 +0.00001400 -42279.73264591 -211.00314767 41.08344474 307.77939795 +0.00001600 29083.13222726 -299.86397145 41.51045417 289.59363364 +0.00001800 100957.95082594 706.27695160 42.02391473 213.62523715 +0.00002000 150492.32652407 2436.13821354 42.62185633 115.80351000 +0.00002200 163610.52308989 3505.21213240 43.30185229 72.52474633 +0.00002400 137798.21546909 2809.74173435 44.06395945 119.32042200 +0.00002600 86552.97296922 993.11451262 44.91354630 219.23877027 +0.00002800 30065.89230936 -248.07012791 45.85833909 214.16642537 +0.00003000 -15271.83960767 -195.60392001 46.90428227 107.42336841 +0.00003200 -41143.37576909 141.25051892 48.05595140 -10.23715919 +0.00003400 -45603.75654834 -363.71528632 49.31891708 -41.13071129 +0.00003600 -31933.14574422 -1519.36792976 50.67717643 11.13789839 +0.00003800 -11580.24564270 -1956.43454302 52.14035913 47.86749694 +0.00004000 1795.96943076 -865.57527338 53.69638462 -13.42971260 +0.00004200 -6069.40567724 626.10860652 55.34660090 -151.70147237 +0.00004400 -36605.44103603 565.05574074 57.08967355 -284.06117371 +0.00004600 -88409.03954732 -1403.86956218 58.91185508 -352.46208669 +0.00004800 -119187.64656330 -2830.86397506 60.79652934 -358.13736161 +0.00005000 -126958.63383213 -2293.53919791 62.72537859 -329.02117947 +0.00005200 -105144.23378691 -417.60570188 64.67974189 -286.64057459 +0.00005400 -57578.18477311 834.36904591 66.64059843 -231.16675138 +0.00005600 7642.76668942 434.72799961 68.58976595 -160.41908396 +0.00005800 73314.58537446 -519.66723923 70.51136345 -97.11322986 +0.00006000 117239.42596973 -329.29698187 72.38916035 -71.95507125 +0.00006200 122335.84589389 858.01810556 74.20116994 -72.69735215 +0.00006400 90700.59252948 1441.72347492 75.92201577 -50.06936146 +0.00006600 40928.26316446 879.60901414 77.52654008 55.63484244 +0.00006800 -3181.66487546 334.25351485 78.99192675 197.17614864 +0.00007000 -31227.72623817 652.00817770 80.29696328 378.84255238 +0.00007200 -43642.08135556 1250.72698300 81.42019653 507.21229626 +0.00007400 -37578.91493866 1051.23806218 82.34208812 533.01944777 +0.00007600 -9313.59450148 -253.25084775 83.04041098 497.57963010 +0.00007800 35606.42432047 -1453.27137086 83.53076487 484.49556872 +0.00008000 74825.06321773 -880.42089139 83.79365831 512.38603041 +0.00008200 87450.95751560 1078.66842032 83.81028733 508.57269634 +0.00008400 84964.54130532 2679.13981866 83.55962529 417.18682766 +0.00008600 33723.38650302 1426.95656188 83.03964822 275.01069883 +0.00008800 26888.00526112 802.46409967 82.26457780 159.07974622 +0.00009000 15764.22367820 273.85567979 81.25039304 86.68872404 +0.00009200 -1018.04050367 98.53732822 80.00383608 19.95207715 +0.00009400 -18778.21955924 125.57269254 78.52437737 -55.26075096 +0.00009600 -25696.85381088 173.04677203 76.81790266 -95.82294253 +0.00009800 -19020.27963144 38.14199457 74.90534804 -40.08283716 +0.00010000 -13853.36236626 -405.56366316 72.81359766 112.25327202 +0.00010200 -22360.23253615 -969.69926808 70.56500733 263.50051564 +0.00010400 -39525.81005506 -1401.79910164 68.18385377 320.37515633 +0.00010600 -47887.23125912 -1439.01003806 65.70767268 323.43291333 +0.00010800 -38703.50620624 -1113.56692890 63.18337712 284.23466280 +0.00011000 -15756.47051989 -682.72476001 60.65377002 277.77044438 +0.00011200 10148.75573217 -253.52957929 58.15278984 250.27515323 +0.00011400 32489.76783313 239.99423089 55.71193773 178.79248872 +0.00011600 48846.14416151 861.55125965 53.36798832 70.38368037 +0.00011800 60211.15804332 1593.45081266 51.19169051 -55.24610237 +0.00012000 64597.66151097 2144.52398093 49.22113114 -170.30467384 +0.00012200 58795.32774769 2216.16123424 47.49918918 -248.93156307 +0.00012400 63226.50291119 2740.29495857 46.05677747 -270.24081648 +0.00012600 7112.67333129 642.99155129 44.93086250 -206.96775261 +0.00012800 4737.67676382 673.17973142 44.16608448 -50.37244372 +0.00013000 -10629.83066809 -276.05014319 43.80477020 154.04681427 +0.00013200 -24445.08596782 -1331.11596207 43.87860095 320.32723893 +0.00013400 -38089.44576760 -2042.60347448 44.40990189 378.66585808 +0.00013600 -53888.48385453 -2339.54888278 45.42258092 320.31441637 +0.00013800 -65525.93331796 -2263.02943488 46.94717499 192.76961767 +0.00014000 -66605.80950981 -1978.10144773 49.01173919 46.49351043 +0.00014200 -59461.87405093 -1395.88433631 51.62964197 -100.43225450 +0.00014400 -50082.83777468 -136.33782409 54.79891493 -258.31822307 +0.00014600 -36265.73051644 1692.89613965 58.50910094 -447.27992440 +0.00014800 -11065.11218743 2974.81823090 62.74931610 -601.98154580 +0.00015000 24574.77396976 2642.88373319 67.50830566 -716.60080679 +0.00015200 53704.30727291 913.24280375 72.76914377 -754.65637852 +0.00015400 62641.21173742 -927.03460327 78.50486320 -713.36174226 +0.00015600 50475.22167026 -1689.34471443 84.67941051 -602.77004154 +0.00015800 27415.48879178 -1332.07133205 91.25069147 -429.82867913 +0.00016000 659.52027909 -793.99131765 98.16114225 -214.90982911 +0.00016200 -27358.17056213 -941.55813718 105.35683648 -1.93703392 +0.00016400 -36359.81639946 -1038.93906805 112.78930315 141.63166343 +0.00016600 -103478.83628142 -2451.04087672 120.41222030 155.07119820 +0.00016800 -98122.08801466 -1619.20548854 128.15466148 39.58301004 +0.00017000 -91470.31369949 -1037.16157762 135.94071127 -128.72347744 +0.00017200 -70167.76251890 -505.22323695 143.69516807 -240.17685720 +0.00017400 -43298.45234300 169.23053990 151.35171103 -223.11938998 +0.00017600 -13147.13005351 1119.27836540 158.84649112 -87.45006406 +0.00017800 13812.88135432 2035.34756564 166.10612536 85.27603300 +0.00018000 29405.90836664 2281.35445610 173.04701036 209.91332866 +0.00018200 27785.78282904 1475.48961051 179.59291666 253.65425754 +0.00018400 16400.24253711 132.45287134 185.68841711 300.73216440 +0.00018600 5032.51740518 -616.86762340 191.28914198 352.67911780 +0.00018800 -684.42414340 -391.31151887 196.34017758 475.23116164 +0.00019000 -2606.74806622 413.81613798 200.77390679 556.19143606 +0.00019200 -4228.75142469 1254.39214820 204.53041970 608.04951495 +0.00019400 -2944.53596867 1786.35191510 207.57544804 633.31067679 +0.00019600 4064.05842526 1765.17722675 209.89395091 624.84914980 +0.00019800 11878.81314410 1160.67458116 211.46967661 568.88523153 +0.00020000 12188.47862387 80.82726004 212.27097983 467.11785325 diff -r 6f2029791c94 -r 9ca30ad95444 test-data/NEQGamma_ofrict1.txt --- a/test-data/NEQGamma_ofrict1.txt Fri Sep 11 21:55:57 2020 +0000 +++ b/test-data/NEQGamma_ofrict1.txt Fri Nov 13 19:37:55 2020 +0000 @@ -1,102 +1,102 @@ -#x ACF frict_coeff gauss_filtered_frict_coeff av_window_frict_coeff - 0.00000000 -131993.41016925 0.00000000 -31.41159270 -71.62375840 - 0.00000200 16345.04469682 -1345.26646099 -31.23092179 16.85099383 - 0.00000400 29113.39120702 -1454.28761686 -30.88206666 43.12225366 - 0.00000600 27656.43517472 -264.14035591 -30.38447804 -24.61744170 - 0.00000800 22081.05883970 570.71230720 -29.75116213 -124.82229209 - 0.00001000 9926.50084650 482.67878751 -28.98362546 -148.88674802 - 0.00001200 -5957.22964270 -306.50010800 -28.07154561 -44.25804572 - 0.00001400 -21071.08253355 -678.79838871 -27.00311927 120.09671342 - 0.00001600 -30206.93805045 129.24578885 -25.77749754 210.63856614 - 0.00001800 -30292.41328536 1433.88087902 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0.00019800 -6620.62218248 1426.36740716 494.94559802 744.12013707 + 0.00020000 563.32886370 -123.79373740 496.04678396 599.88305724 diff -r 6f2029791c94 -r 9ca30ad95444 test-data/NEQGamma_ofrict2.txt --- a/test-data/NEQGamma_ofrict2.txt Fri Sep 11 21:55:57 2020 +0000 +++ b/test-data/NEQGamma_ofrict2.txt Fri Nov 13 19:37:55 2020 +0000 @@ -1,102 +1,102 @@ -#x ACF frict_coeff gauss_filtered_frict_coeff av_window_frict_coeff - 0.00000000 820049.57805000 0.00000000 -88.35169831 -280.48699846 - 0.00000200 -4358.85795000 -133.28849699 -88.22972067 -88.19151898 - 0.00000400 -87816.09622050 -2381.86180009 -87.98019601 206.78227553 - 0.00000600 -131399.91872250 -2484.15267240 -87.60563052 420.75577467 - 0.00000800 -157962.78872850 -1272.80096612 -87.09850727 415.54857404 - 0.00001000 -138547.98040200 423.68679663 -86.46203739 220.05544591 - 0.00001200 -75149.24467650 831.83995256 -85.69381797 -19.39421284 - 0.00001400 17412.26728800 -230.42745195 -84.78750605 -184.44489621 - 0.00001600 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