Mercurial > repos > chemteam > biomd_rmsd_clustering

annotate NEQGamma.py @ 1:b001ebc8bf58 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
author chemteam
date Fri, 11 Sep 2020 21:55:34 +0000
parents
children b9c46dbe9605
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
1 #!/usr/bin/env python
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
2
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
3 # coding: utf-8
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
4 # This script is a modified version of a script written
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
5 # by Steffen Wolf under the GPL v3.0.
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
6 # The original version can be accessed at
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
7 # https://github.com/moldyn/dcTMD/blob/master/NEQGamma.py
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
8
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
9 import argparse
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
10 import json
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
11 import sys
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
12
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
13 import numpy as np
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
14
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
15 import pandas as pd
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
16
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
17 import scipy
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
18 import scipy.integrate
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
19 from scipy.ndimage.filters import gaussian_filter
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
20
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
21
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
22 def get_file_names(list_file):
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
23 with open(list_file) as f:
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
24 return [line for line in f.read().split('\n') if line]
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
25
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
26
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
27 def NEQGamma(file_names, output, output_frict, vel, T, av, sigma):
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
28 N = len(file_names)
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
29 RT = 0.0083144598 * T
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
30
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
31 sys.stdout.write("reading data...\n")
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
32
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
33 # read in initial data to get length of necessary array
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
34 test_file = pd.read_csv(file_names[0], delim_whitespace=True,
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
35 header=None, skiprows=17, dtype=float)
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
36 length_data = len(test_file[0].values)
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
37 full_force_set = np.zeros((N, length_data))
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
38 x = np.zeros(length_data)
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
39 t = np.zeros(length_data)
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
40 t = test_file[0].values
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
41 x = test_file[0].values * vel
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
42
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
43 # read in data
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
44 for i in range(0, N):
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
45 current_file_name = file_names[i]
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
46 sys.stdout.write("reading file {}\n".format(current_file_name))
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
47 input_file_data = pd.read_csv(current_file_name, delim_whitespace=True,
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
48 header=None, skiprows=17, dtype=float)
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
49 full_force_set[i, :] = input_file_data[1].values
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
50
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
51 # preprocessing
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
52 # * force average: calculate $\left< f_c (t)\right>_N$.
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
53 # **Important:** this is an ensemble average over the trajectory ensemble
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
54 # $N$, not the time average over $t$
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
55 av_force = np.zeros(length_data)
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
56 av_forceintegral = np.zeros(length_data)
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
57 for i in range(length_data):
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
58 av_force[i] = np.mean(full_force_set[:, i])
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
59 av_forceintegral[1:] = scipy.integrate.cumtrapz(av_force, x)
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
60
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
61 # calculate $\delta f_c(t) = f_c(t) - \left< f_c (t) \right>_N$ for all $t$
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
62 sys.stdout.write("calculating fluctuations...\n")
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
63 delta_force_set = np.zeros((N, length_data))
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
64 for i in range(length_data):
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
65 delta_force_set[:, i] = full_force_set[:, i] - av_force[i]
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
66
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
67 # evaluation
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
68 # * optimized algorithm for numerical evaluation:
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
69 # * integrate: $\int_0^t dt' \delta f_c(t')$ for all $t'$
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
70 # * multiply by $\delta f_c(t)$ to yield
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
71 # $\int_0^t dt'\delta f_c(t) \delta f_c(t')$ for $t$
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
72 # with all $t' \leq t$ each
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
73 # * then calculate the ensemble average
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
74 # $\left< \int_0^t dt' \delta f_c(t) \delta f_c(t') \right>$
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
75 int_delta_force_set = np.zeros((N, length_data))
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
76 for n in range(N):
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
77 int_delta_force_set[n, 1:] = scipy.integrate.cumtrapz(
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
78 delta_force_set[n, :], t)
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
79
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
80 sys.stdout.write("averaging and integrating...\n")
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
81 intcorr = np.zeros((N, length_data))
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
82
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
83 for n in range(N):
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
84 for i in range(length_data):
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
85 intcorr[n, i] = delta_force_set[n, i] * int_delta_force_set[n, i]
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
86 if i % 1000 == 0:
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
87 sys.stdout.write("Trajectory {:2d} {:3.1f} % done\r".format(
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
88 n + 1, (i / length_data) * 100))
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
89
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
90 # shape of $\int_0^t dt' \delta f_c(t) \delta f_c(t')$:
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
91 sys.stdout.write("final average...\n")
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
92 av_intcorr = np.zeros(length_data)
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
93 for i in range(length_data):
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
94 av_intcorr[i] = np.mean(intcorr[:, i]) / RT
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
95
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
96 # autocorrelation function evaluation:
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
97 # * calculate $\left< \delta f_c(t) \delta f_c(t') \right>$
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
98 # for the last $t$
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
99
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
100 corr_set = np.zeros((N, length_data))
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
101 autocorr_set = np.zeros(length_data)
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
102
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
103 sys.stdout.write("calculating and processing ACF...\n")
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
104 for n in range(N):
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
105 for i in range(length_data):
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
106 corr_set[n, i] = delta_force_set[
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
107 n, i] * delta_force_set[n, length_data - 1]
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
108
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
109 for i in range(length_data):
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
110 autocorr_set[i] = np.mean(corr_set[:, i])
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
111
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
112 # * Gauss filter:
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
113 sys.stdout.write("applying Gauss filter...\n")
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
114 blurr = sigma
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
115 blurred = np.zeros(length_data)
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
116 blurred = gaussian_filter(av_intcorr, sigma=blurr)
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
117
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
118 # * sliding window average:
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
119 sys.stdout.write("applying sliding window average...\n")
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
120 window = av
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
121 runn_av = np.zeros(length_data)
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
122 runn_av = np.convolve(av_intcorr, np.ones((window,)) / window, mode='same')
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
123
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
124 # * $W_{diss}$ from integration:
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
125 wdiss = np.zeros(length_data)
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
126 wdiss[1:] = scipy.integrate.cumtrapz(av_intcorr, x) * vel
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
127
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
128 sys.stdout.write("writing output...\n")
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
129 dist = open(output, "w")
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
130 frict = open(output_frict, "w")
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
131
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
132 dist.write(
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
133 "#x force_integral frict_coeff wdiss corrected_force_integral\n")
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
134 for i in range(length_data):
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
135 dist.write("{:15.8f} {:20.8f} {:20.8f} {:20.8f} {:20.8f}\n".format(
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
136 x[i], av_forceintegral[i], av_intcorr[i], wdiss[i],
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
137 av_forceintegral[i] - wdiss[i]))
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
138
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
139 frict.write("""#x ACF frict_coeff """
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
140 """gauss_filtered_frict_coeff av_window_frict_coeff\n""")
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
141 for i in range(length_data):
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
142 frict.write("{:15.8f} {:20.8f} {:20.8f} {:20.8f} {:20.8f}\n".format(
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
143 x[i], autocorr_set[i], av_intcorr[i], blurred[i], runn_av[i]))
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
144
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
145 dist.close()
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
146 frict.close()
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
147
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
148 sys.stdout.write("Done!\n")
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
149
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
150
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
151 def main():
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
152 parser = argparse.ArgumentParser(description="""dcTMD friciton correction
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
153 (please cite: Wolf, S., Stock, G. Targeted Molecular Dynamics
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
154 Calculations of Free Energy Profiles Using a Nonequilibrium
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
155 Friction Correction. J. Chem. Theory Comput. 2018, 14(12), 6175-6182,
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
156 DOI: 10.1021/acs.jctc.8b00835). Integrates a constraint force file via
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
157 trapezoid rule, calculates the NEQ memory friction kernel and friction
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
158 factors, and performs a friction correction. First column: reaction
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
159 coordinate in nm calculated via t * vel. Second column: force integral,
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
160 i.e. the work profile. Third column: friction factors. Fourth column:
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
161 trapezoid integral (final value) of friction work along reaction
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
162 coordinate. Fourth column: friction corrected work profile. ATTENTION:
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
163 Use with python3 or higher!""")
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
164 parser.add_argument('-i', metavar='<xvg force file>', type=str,
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
165 help="""List of xvg constraint force files prefix
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
166 as given by Gromacs mdrun -pf option before running
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
167 number.""")
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
168 parser.add_argument('-o', metavar='<combined results>', type=str,
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
169 help="""file to write x, dG(x), friction coefficeint by
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
170 integration (time resolved), and the friction-corrected
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
171 dG(x).""")
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
172 parser.add_argument('-ofrict', metavar='<combined friction results>',
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
173 type=str,
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
174 help="""file to write x, ACF, friction coefficeint by
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
175 integration (time resolved), gauss filtered friction
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
176 coefficient, and slide window averaged friction.""")
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
177 parser.add_argument('-vel', metavar='<pull velocity>', type=float,
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
178 help="""pull velocity in nm/ps for converting simulation
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
179 time t into distance x""")
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
180 parser.add_argument('-T', metavar='<temperature>', type=float,
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
181 help='temperature in K')
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
182 parser.add_argument('-av', metavar='<average window>', type=int,
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
183 help="""size of averaging window for displaying
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
184 Gamma(x) (recommended: 4 to 20 per 100 data points)""")
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
185 parser.add_argument('-sigma', metavar='<gauss blurr>', type=int,
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
186 help="""sigma value for Gauss filter for displaying
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
187 Gamma(x) (recommended: 4 per 100 data points)""")
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
188 parser.add_argument('-json', metavar='<json>', type=str,
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
189 help='JSON file defining cluster membership')
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
190
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
191 args = parser.parse_args()
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
192
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
193 file_names = get_file_names(args.i)
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
194 if args.json:
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
195 with open(args.json) as f:
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
196 j = json.load(f)
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
197 file_names_dct = {n: [file_names[int(m)] for m in j[n]] for n in j}
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
198
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
199 for cluster in file_names_dct:
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
200 NEQGamma(file_names_dct[cluster],
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
201 'cluster{}_{}'.format(cluster, args.o),
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
202 'cluster{}_{}'.format(cluster, args.ofrict),
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
203 args.vel, args.T, args.av, args.sigma)
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
204 else:
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
205 NEQGamma(file_names, args.o, args.ofrict, args.vel,
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
206 args.T, args.av, args.sigma)
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
207
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
208
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
209 if __name__ == "__main__":
b001ebc8bf58 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
chemteam
parents:
diff changeset
210 main()