Mercurial > repos > chemteam > biomd_extract_clusters
comparison NEQGamma.py @ 2:e0ecaf2d05fb draft default tip
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f1c3c88c7395f2e84cbc533199406aadb79c5c07"
author | chemteam |
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date | Fri, 13 Nov 2020 19:39:27 +0000 |
parents | 078dfd7fb26d |
children |
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1:078dfd7fb26d | 2:e0ecaf2d05fb |
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127 | 127 |
128 sys.stdout.write("writing output...\n") | 128 sys.stdout.write("writing output...\n") |
129 dist = open(output, "w") | 129 dist = open(output, "w") |
130 frict = open(output_frict, "w") | 130 frict = open(output_frict, "w") |
131 | 131 |
132 dist.write( | 132 dist.write('\t'.join(('#x', 'force_integral', 'frict_coeff', |
133 "#x force_integral frict_coeff wdiss corrected_force_integral\n") | 133 'wdiss', 'corrected_force_integral\n'))) |
134 for i in range(length_data): | 134 for i in range(length_data): |
135 dist.write("{:15.8f} {:20.8f} {:20.8f} {:20.8f} {:20.8f}\n".format( | 135 dist.write("{:.8f}\t{:.8f}\t{:.8f}\t{:.8f}\t{:.8f}\n".format( |
136 x[i], av_forceintegral[i], av_intcorr[i], wdiss[i], | 136 x[i], av_forceintegral[i], av_intcorr[i], wdiss[i], |
137 av_forceintegral[i] - wdiss[i])) | 137 av_forceintegral[i] - wdiss[i])) |
138 | 138 |
139 frict.write("""#x ACF frict_coeff """ | 139 frict.write('\t'.join(('#x', 'ACF', 'frict_coeff', |
140 """gauss_filtered_frict_coeff av_window_frict_coeff\n""") | 140 'gauss_filtered_frict_coeff', |
141 for i in range(length_data): | 141 'av_window_frict_coeff\n'))) |
142 frict.write("{:15.8f} {:20.8f} {:20.8f} {:20.8f} {:20.8f}\n".format( | 142 for i in range(length_data): |
143 frict.write("{:.8f}\t{:.8f}\t{:.8f}\t{:.8f}\t{:.8f}\n".format( | |
143 x[i], autocorr_set[i], av_intcorr[i], blurred[i], runn_av[i])) | 144 x[i], autocorr_set[i], av_intcorr[i], blurred[i], runn_av[i])) |
144 | 145 |
145 dist.close() | 146 dist.close() |
146 frict.close() | 147 frict.close() |
147 | 148 |
148 sys.stdout.write("Done!\n") | 149 sys.stdout.write("Done!\n") |
149 | 150 |
150 | 151 |
151 def main(): | 152 def main(): |
152 parser = argparse.ArgumentParser(description="""dcTMD friciton correction | 153 parser = argparse.ArgumentParser(description="""dcTMD friction correction |
153 (please cite: Wolf, S., Stock, G. Targeted Molecular Dynamics | 154 (please cite: Wolf, S., Stock, G. Targeted Molecular Dynamics |
154 Calculations of Free Energy Profiles Using a Nonequilibrium | 155 Calculations of Free Energy Profiles Using a Nonequilibrium |
155 Friction Correction. J. Chem. Theory Comput. 2018, 14(12), 6175-6182, | 156 Friction Correction. J. Chem. Theory Comput. 2018, 14(12), 6175-6182, |
156 DOI: 10.1021/acs.jctc.8b00835). Integrates a constraint force file via | 157 DOI: 10.1021/acs.jctc.8b00835). Integrates a constraint force file via |
157 trapezoid rule, calculates the NEQ memory friction kernel and friction | 158 trapezoid rule, calculates the NEQ memory friction kernel and friction |