# HG changeset patch
# User chemteam
# Date 1605296337 0
# Node ID b9c46dbe9605047290ae76bbb1bf2bc51ef1557b
# Parent b001ebc8bf585a0cb819fccc6ba1631bb2c9a9a4
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f1c3c88c7395f2e84cbc533199406aadb79c5c07"
diff -r b001ebc8bf58 -r b9c46dbe9605 NEQGamma.py
--- a/NEQGamma.py Fri Sep 11 21:55:34 2020 +0000
+++ b/NEQGamma.py Fri Nov 13 19:38:57 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 b001ebc8bf58 -r b9c46dbe9605 get_clusters.py
--- a/get_clusters.py Fri Sep 11 21:55:34 2020 +0000
+++ b/get_clusters.py Fri Nov 13 19:38:57 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 b001ebc8bf58 -r b9c46dbe9605 rmsd_clustering.py
--- a/rmsd_clustering.py Fri Sep 11 21:55:34 2020 +0000
+++ b/rmsd_clustering.py Fri Nov 13 19:38:57 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 b001ebc8bf58 -r b9c46dbe9605 rmsd_clustering.xml
--- a/rmsd_clustering.xml Fri Sep 11 21:55:34 2020 +0000
+++ b/rmsd_clustering.xml Fri Nov 13 19:38:57 2020 +0000
@@ -2,7 +2,7 @@
from MD RMSD matrix data
1.5.2
- 0
+ 1
scipy
@@ -28,7 +28,7 @@
#end if
--start '$start'
--end '$end'
- '$normalize'
+ $normalize
]]>
@@ -75,6 +75,18 @@
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