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"""
Program to analyse the trace of atoms in a plane
Examples:
md_planetrace.py -f md.xtc -s md.tpr --sel "resname AAC and name C1"
"""
import numpy as np
import matplotlib.pylab as plt
from sgenlib import moldyn
from sgenlib import mdactions
from sgenlib import colors
class PlaneTraceAnalysis(mdactions.Trajecto... | {
"repo_name": "SGenheden/Scripts",
"path": "Md/md_planetrace.py",
"copies": "1",
"size": "2625",
"license": "mit",
"hash": 6310725680459119000,
"line_mean": 33.5394736842,
"line_max": 81,
"alpha_frac": 0.5935238095,
"autogenerated": false,
"ratio": 3.4448818897637796,
"config_test": false,
"h... |
"""
Program to analyse the weights of all solutes in a list
The solutes are taken from the Minnesota solvation database
"""
import argparse
import re
import numpy as np
import matplotlib.pylab as plt
import dblib
mass = { 'H' : 1.0079 , 'He' : 4.0026 , 'Li' : 6.941 ,
'Be' : 9.0122 , 'B' : 10.8... | {
"repo_name": "SGenheden/Scripts",
"path": "Projects/Solvation/analyse_weight.py",
"copies": "1",
"size": "4657",
"license": "mit",
"hash": 1726759675746831600,
"line_mean": 41.7247706422,
"line_max": 111,
"alpha_frac": 0.4524371913,
"autogenerated": false,
"ratio": 2.4863854778430325,
"config_... |
"""
Program to analyze the extent of alcohols
"""
import numpy as np
import MDAnalysis.core.distances as mddist
from sgenlib import moldyn
from sgenlib import mdactions
from sgenlib import pbc
class AlcoholLenAnalysis(mdactions.TrajectoryAction) :
def add_arguments(self, parser):
parser.add_argument('-... | {
"repo_name": "SGenheden/Scripts",
"path": "Projects/Yeast/md_alcohol_len.py",
"copies": "1",
"size": "1477",
"license": "mit",
"hash": 6744343981349602000,
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"line_max": 89,
"alpha_frac": 0.6668923494,
"autogenerated": false,
"ratio": 3.3265765765765765,
"config_test"... |
"""
Program to build a CG or AA/CG dual-resolution
system from an AA system. Converts AA residues
automatically to CG using dictionary of conversions.
Writes out LAMMPS datafiles and include file
for the force field, as well as a PDB-file.
"""
import sys
import math
import random
import argparse
import os
import cop... | {
"repo_name": "SGenheden/Scripts",
"path": "Lammps/aa2cg.py",
"copies": "1",
"size": "11978",
"license": "mit",
"hash": -4079916321603657700,
"line_mean": 38.5313531353,
"line_max": 171,
"alpha_frac": 0.6001001837,
"autogenerated": false,
"ratio": 3.2372972972972973,
"config_test": false,
"ha... |
"""
Program to build lipids from a template, similarly to MARTINI INSANE
Is VERY experimental!
"""
import argparse
import os
import xml.etree.ElementTree as ET
import numpy as np
from sgenlib import pdb
class BeadDefinition(object):
def __init__(self):
self.name = None
self.xyz = None
de... | {
"repo_name": "SGenheden/Scripts",
"path": "Membrane/build_lipid.py",
"copies": "1",
"size": "3765",
"license": "mit",
"hash": -8760421902141514000,
"line_mean": 26.6838235294,
"line_max": 87,
"alpha_frac": 0.5561752988,
"autogenerated": false,
"ratio": 3.613243761996161,
"config_test": false,
... |
"""
Program to build molecules by looking up there SMILES string in
ChemSpider and then converting the SMILES to an xyz file.
The SPIDERKEY environmental variable needs to be set ChemSpider access key.
If the molecule could not be found in ChemSpider the molecule name is
printed with a double exclamation mark (!!) a... | {
"repo_name": "SGenheden/Scripts",
"path": "Mol/build_mols.py",
"copies": "1",
"size": "1713",
"license": "mit",
"hash": 8129505886533388000,
"line_mean": 29.0526315789,
"line_max": 91,
"alpha_frac": 0.6567425569,
"autogenerated": false,
"ratio": 3.6369426751592355,
"config_test": false,
"has... |
"""
Program to calculate bond force constant with the Seminario method
for specific bonds
Ref:
JM Seminario, Int. J. Quant. Chem. 1996, 60(7), 1271-1277
Examples:
seminario.py -f model.fchk -s model.gro -b 1:N-4:CU 1:ND1-4:CU 2:NE2-4:CU
"""
import argparse
import os
import numpy as np
from sgenlib import pdb
def... | {
"repo_name": "SGenheden/Scripts",
"path": "Mol/seminario.py",
"copies": "1",
"size": "3971",
"license": "mit",
"hash": -6715517803161007000,
"line_mean": 31.5491803279,
"line_max": 107,
"alpha_frac": 0.6154621002,
"autogenerated": false,
"ratio": 2.8344039971448964,
"config_test": false,
"ha... |
"""
Program to calculate how many water molecules are leaking into the membrane
"""
import argparse
import math
import numpy as np
from sgenlib import parsing
from sgenlib import mol
def _count_water_inside(dens1, dens2, fi, li, fx, lx) :
return sum(dens1[fi:li])
def _count_water_inside2(dens1, dens2, fi, l... | {
"repo_name": "SGenheden/Scripts",
"path": "Membrane/water_leakage.py",
"copies": "1",
"size": "3011",
"license": "mit",
"hash": 1650182540499696600,
"line_mean": 39.1466666667,
"line_max": 92,
"alpha_frac": 0.6496180671,
"autogenerated": false,
"ratio": 2.8868648130393098,
"config_test": false... |
"""
Program to calculate RDF in a two-component system
"""
import argparse
import MDAnalysis
from MDAnalysis.analysis import rdf
def _anal_rdf(u, sel1, sel2, exl, filename):
g1 = u.select_atoms(sel1)
g2 = u.select_atoms(sel2)
rdfo = rdf.InterRDF(g1, g2, exclusion_block=exl, step=50)
rdfo.run()
... | {
"repo_name": "SGenheden/Scripts",
"path": "Projects/Trehalose/anal_rdf_twocomp.py",
"copies": "1",
"size": "3270",
"license": "mit",
"hash": 3698655820952567300,
"line_mean": 55.3793103448,
"line_max": 145,
"alpha_frac": 0.6259938838,
"autogenerated": false,
"ratio": 2.6076555023923444,
"confi... |
"""
Program to calculate the RDF of a group of atoms
Experimental code!
"""
import numpy as np
import MDAnalysis.core.distances as mddist
from sgenlib import moldyn
from sgenlib import mdactions
from sgenlib import pbc
class RdfAnalysis(mdactions.TrajectoryAction) :
def add_arguments(self, parser):
p... | {
"repo_name": "SGenheden/Scripts",
"path": "Md/md_rdf.py",
"copies": "1",
"size": "3382",
"license": "mit",
"hash": -5761366409229040000,
"line_mean": 39.7469879518,
"line_max": 106,
"alpha_frac": 0.6105854524,
"autogenerated": false,
"ratio": 3.3551587301587302,
"config_test": false,
"has_no... |
"""
Program to calculate the RDF of a solute in a membrane
Experimental code!
"""
import numpy as np
import MDAnalysis.lib.distances as mddist
import scipy.spatial.distance as scidist
from sgenlib import moldyn
from sgenlib import mdactions
from sgenlib import pbc
class SolMemRdf(mdactions.TrajectoryAction) :
... | {
"repo_name": "SGenheden/Scripts",
"path": "Md/md_solmem_rdf.py",
"copies": "1",
"size": "3860",
"license": "mit",
"hash": 150321294595210460,
"line_mean": 40.9565217391,
"line_max": 120,
"alpha_frac": 0.5829015544,
"autogenerated": false,
"ratio": 3.468104222821204,
"config_test": false,
"ha... |
"""
Program to calculate the vdW energy between a ROH bead and protein beads
on a rectangular grid
Writes out the 3D grid in dx-format and an averaged 2D plot in png-format
Example:
gpcr_plot_gridenergy.py -p system.top -m b2
"""
import argparse
import os
import sys
import numpy as np
import matplotlib
if not "D... | {
"repo_name": "SGenheden/Scripts",
"path": "Projects/Gpcr/gpcr_plot_gridenergy.py",
"copies": "1",
"size": "5586",
"license": "mit",
"hash": 1086574698830983600,
"line_mean": 33.4814814815,
"line_max": 138,
"alpha_frac": 0.6407089151,
"autogenerated": false,
"ratio": 2.787425149700599,
"config_... |
"""
Program to collect APR results for a list of output
Examples:
collect_apr.py list
"""
import argparse
import glob
import logging
import os
import numpy as np
from sgenlib import parsing
from sgenlib import series
from sgenlib import umbrella
def _pull_win(str) :
a, b = str.split("_p")
return int(b.sp... | {
"repo_name": "SGenheden/Scripts",
"path": "Lammps/collect_apr.py",
"copies": "1",
"size": "8729",
"license": "mit",
"hash": 4343058596077332500,
"line_mean": 36.952173913,
"line_max": 100,
"alpha_frac": 0.6039637988,
"autogenerated": false,
"ratio": 2.9720803541028262,
"config_test": false,
... |
"""
Program to collect TI results and put them in an Excel sheet
Examples:
collect_results.py -db MNSol_alldata.txt -solvent hexanol -solutes hexanolwater.txt
-xls out.xlsx -sheet hexanolwater
"""
import argparse
import os
import openpyxl as xl
import numpy as np
import scipy.stats as stats
fro... | {
"repo_name": "SGenheden/Scripts",
"path": "Projects/Solvation/collect_results.py",
"copies": "1",
"size": "9215",
"license": "mit",
"hash": -1476078661439771100,
"line_mean": 39.5947136564,
"line_max": 116,
"alpha_frac": 0.6086814976,
"autogenerated": false,
"ratio": 2.9096937164509,
"config_t... |
"""
Program to collect TI results for a list of output
Examples:
collect_ti.py list
"""
import argparse
import os
import numpy as np
def _integrate(filename):
"""
Read a PMF from an Lammps output file and integrate it
"""
lines = []
with open(filename,"r") as f :
lines = f.readlines()
... | {
"repo_name": "SGenheden/Scripts",
"path": "Lammps/collect_ti.py",
"copies": "1",
"size": "2550",
"license": "mit",
"hash": -520111865741755900,
"line_mean": 32.5526315789,
"line_max": 120,
"alpha_frac": 0.5854901961,
"autogenerated": false,
"ratio": 3.474114441416894,
"config_test": false,
"... |
"""
Program to collect TI results for Zhang solutes
Examples:
collect_zhange.py -solvent octanol -solutes list
"""
import argparse
import os
import numpy as np
def _integrate(filename):
"""
Read a PMF from an Lammps output file and integrate it
"""
lines = []
with open(filename,"r") as f :
... | {
"repo_name": "SGenheden/Scripts",
"path": "Projects/Solvation/collect_zhang.py",
"copies": "1",
"size": "2031",
"license": "mit",
"hash": -4678289076901469000,
"line_mean": 32.2950819672,
"line_max": 99,
"alpha_frac": 0.5814869522,
"autogenerated": false,
"ratio": 3.37375415282392,
"config_tes... |
"""
Program to compute BEDROC metrics for a set of solutes
The -f file should contain the true value in the first
column and the test value in the second column
For each super group, it will compute:
- BEDROC metric assuming a uniform distribution
- BEDROC metric on the observed data
- A p-value on the d... | {
"repo_name": "SGenheden/Scripts",
"path": "Mol/solute_bedroc.py",
"copies": "1",
"size": "5650",
"license": "mit",
"hash": -1098442233394960900,
"line_mean": 36.9194630872,
"line_max": 112,
"alpha_frac": 0.5725663717,
"autogenerated": false,
"ratio": 3.309900410076157,
"config_test": false,
... |
"""
Program to compute bulk density of solutes from densities
"""
import argparse
import math
import re
import numpy as np
from sgenlib import parsing
from sgenlib import mol
def _count_solute_inside(dens1, dens2, fi, li, fx, lx, **kwargs) :
return sum(kwargs["soldens"][fi:li])
def _membrane_vol(dens1, dens2... | {
"repo_name": "SGenheden/Scripts",
"path": "Projects/Yeast/calc_bulk_dens.py",
"copies": "1",
"size": "4974",
"license": "mit",
"hash": -4445635610758369300,
"line_mean": 40.45,
"line_max": 98,
"alpha_frac": 0.6399276236,
"autogenerated": false,
"ratio": 2.7420066152149944,
"config_test": false... |
"""
Program to compute the contact matrix
Examples:
"""
import numpy as np
import MDAnalysis as md
import MDAnalysis.analysis.distances as mddist
from MDAnalysis.core.groups import AtomGroup
from sgenlib import moldyn
from sgenlib import mdactions
class ContactMatrixAnalysis(mdactions.TrajectoryAction) :
def... | {
"repo_name": "SGenheden/Scripts",
"path": "Md/md_contactmat.py",
"copies": "1",
"size": "2136",
"license": "mit",
"hash": 26247113585507070,
"line_mean": 30.4117647059,
"line_max": 84,
"alpha_frac": 0.5936329588,
"autogenerated": false,
"ratio": 3.513157894736842,
"config_test": false,
"has_... |
"""
Program to compute the potential of mean force (PMF) from
a set of umbrella simulations of small solutes in a membrane
"""
import argparse
import matplotlib
matplotlib.use('Agg')
import matplotlib.pylab as plt
import numpy as np
import numpy.random as random
import scipy.stats as stats
import wham
if __name__ ... | {
"repo_name": "SGenheden/Scripts",
"path": "Membrane/calc_pmf.py",
"copies": "1",
"size": "10660",
"license": "mit",
"hash": -6764018850449185000,
"line_mean": 49.0469483568,
"line_max": 160,
"alpha_frac": 0.6397748593,
"autogenerated": false,
"ratio": 3.4101087651951376,
"config_test": false,
... |
"""
Program to compute where two densities cross
"""
import argparse
import math
import numpy as np
from sgenlib import parsing
if __name__ == '__main__' :
parser = argparse.ArgumentParser(description="Calculate density intercept")
parser.add_argument('-f', '--file', help="the density file from g_density"... | {
"repo_name": "SGenheden/Scripts",
"path": "Membrane/density_intercept.py",
"copies": "1",
"size": "1151",
"license": "mit",
"hash": -3282447309238946300,
"line_mean": 30.9722222222,
"line_max": 127,
"alpha_frac": 0.6298870547,
"autogenerated": false,
"ratio": 2.849009900990099,
"config_test": ... |
"""
Program to convert a GRO file to PDB and in the process add CONECT records
"""
import sys,os
from sgenlib import pdb
import argparse
def make_con(filename) :
lines = open(filename,"r").readlines()
con_raw = []
all_ind = []
for line in lines :
cols = line.strip().split()
con_raw.append((int(cols[... | {
"repo_name": "SGenheden/Scripts",
"path": "Pdb/gro2pdb_con.py",
"copies": "1",
"size": "2384",
"license": "mit",
"hash": 390743751437694140,
"line_mean": 29.1772151899,
"line_max": 120,
"alpha_frac": 0.6371644295,
"autogenerated": false,
"ratio": 3.0292249047013975,
"config_test": false,
"ha... |
"""
Program to convert a Gromacs top file to an itp-file.
This is not a bullet-proof procedure that works in all situations!
Works for small solutes created with param_solutes.py and this was the usage
it was created for
Examples:
top2itp.py file1.itp file2.itp
"""
import argparse
import os
def _convert(filename, ... | {
"repo_name": "SGenheden/Scripts",
"path": "Gromacs/top2itp.py",
"copies": "1",
"size": "1574",
"license": "mit",
"hash": -7753719622631931000,
"line_mean": 29.2692307692,
"line_max": 103,
"alpha_frac": 0.5978398983,
"autogenerated": false,
"ratio": 3.4669603524229076,
"config_test": false,
"... |
"""
Program to convert a LAMMPS datafile into a PDB file
using a conversion dictionary or a template PDB file
Example:
lmp_data2pdb.py data.128dopc_kalp23 -o 128dopc_kalp23_initial.pdb -d 0:wat 1-128:dop 129:kalp23_leap.pdb
"""
import argparse
import os
import sys
import numpy as np
from sgenlib import lammps
fr... | {
"repo_name": "SGenheden/Scripts",
"path": "Lammps/lmp_data2pdb.py",
"copies": "1",
"size": "6725",
"license": "mit",
"hash": 4567521565773612000,
"line_mean": 33.3112244898,
"line_max": 144,
"alpha_frac": 0.6617100372,
"autogenerated": false,
"ratio": 3.2535074987905177,
"config_test": false,
... |
"""
Program to convert a SMILES string to 3D coordinates using
one of two web services.
The format of the list when using the --inlist option should be
name1 SMILES1
name2 SMILES2
...
Examples
--------
smiles2xyz.py COH
smiles2xyz.py -o ethanol.xyz CCOH
smiles2xyz.py --inlist smiles.txt
"""
import argparse
f... | {
"repo_name": "SGenheden/Scripts",
"path": "Mol/smiles2xyz.py",
"copies": "1",
"size": "1332",
"license": "mit",
"hash": -6230522817697499000,
"line_mean": 35,
"line_max": 198,
"alpha_frac": 0.6869369369,
"autogenerated": false,
"ratio": 3.2487804878048783,
"config_test": false,
"has_no_keywo... |
"""
Program to convert a unsaturated acyl chain to a saturated chain in a
topology (itp-file). Works for Slipid force field.
Uses in membrane engineering project
Examples
--------
saturate_topol.py -f dopc.top -a C29 -o dopc_saturated.itp
"""
import argparse
import os
import parmed
def _get_atom(parm, name) :
... | {
"repo_name": "SGenheden/Scripts",
"path": "Membrane/saturate_topol.py",
"copies": "1",
"size": "4880",
"license": "mit",
"hash": -2426592454349267500,
"line_mean": 33.3661971831,
"line_max": 103,
"alpha_frac": 0.6227459016,
"autogenerated": false,
"ratio": 2.840512223515716,
"config_test": fal... |
"""
Program to count hydrogen bonds in a protein
The analysis is done on all atoms but also on only backbone
and only side chain atoms
Examples
--------
md_hbonds.py -f md2.xtc -s md1.gro
"""
import argparse
import MDAnalysis
from MDAnalysis.analysis import hbonds
class HydrogenBondAnalysis_mainchain(hbonds.Hydro... | {
"repo_name": "SGenheden/Scripts",
"path": "Md/md_hbonds.py",
"copies": "1",
"size": "2019",
"license": "mit",
"hash": 7958351633811658000,
"line_mean": 33.2203389831,
"line_max": 94,
"alpha_frac": 0.6225854383,
"autogenerated": false,
"ratio": 3,
"config_test": false,
"has_no_keywords": fals... |
"""
Program to count hydrogen bonds in a two-component system
Examples:
python calc_hbonds_twocomp.py -f r1_md2_whole.xtc -s r1_md2.tpr --sel "all" -out r1_hbonds.pickle
python calc_hbonds_twocomp.py -f template.xyz wt1kalpotAllAtoms.xyz -s template.pdb --angle 150
"""
import argparse
import MDAnalysis
from... | {
"repo_name": "SGenheden/Scripts",
"path": "Projects/Trehalose/calc_hbonds_twocomp.py",
"copies": "1",
"size": "1674",
"license": "mit",
"hash": -7091120357145300000,
"line_mean": 37.9302325581,
"line_max": 101,
"alpha_frac": 0.6720430108,
"autogenerated": false,
"ratio": 3.1885714285714286,
"c... |
"""
Program to create a hybrid MARTINI topology
The AA structure should have the same order as the structure
created by automartini. This is important since antechamber reshuffles
the atoms.
This script requires the branch write_virtualn of my version of parmed
available at https://github.com/SGenheden/ParmEd/
Exam... | {
"repo_name": "SGenheden/Scripts",
"path": "Mol/make_hybridtop.py",
"copies": "1",
"size": "2749",
"license": "mit",
"hash": 1402394134033674200,
"line_mean": 34.7012987013,
"line_max": 92,
"alpha_frac": 0.6413241179,
"autogenerated": false,
"ratio": 3.414906832298137,
"config_test": false,
"... |
"""
Program to create RESP input
Used in membrane engineering project
Examples
--------
make_respin.py -f model0_1.pdb -e model0_1.esp --zero C8 H81 H82 H83 C2 H22 H23 C1 H11 H12 H13 -q "C3 C7" "H71 H72 H31 H32" "H51 H10" "C4 C6" "H41 H61" -n 38
make input based on model0_1, zerp charges on C8 H81, etc and equiv... | {
"repo_name": "SGenheden/Scripts",
"path": "Mol/make_respin.py",
"copies": "1",
"size": "2865",
"license": "mit",
"hash": -3965491508126810000,
"line_mean": 35.2658227848,
"line_max": 157,
"alpha_frac": 0.5469458988,
"autogenerated": false,
"ratio": 3.114130434782609,
"config_test": false,
"h... |
"""
Program to do hydrogen mass repartition on a lammps datafile
Will increase the mass of the hydrogen and decrease mass of the heavy atoms bonded to
them.
The default output is the input data file with a "_heavyh" string appended
Examples
lmp_massrepart.py data.kalp23 -f 3
"""
import argparse
import copy
fro... | {
"repo_name": "SGenheden/Scripts",
"path": "Lammps/lmp_massrepart.py",
"copies": "1",
"size": "4723",
"license": "mit",
"hash": 3148137033583823000,
"line_mean": 37.7131147541,
"line_max": 124,
"alpha_frac": 0.6540334533,
"autogenerated": false,
"ratio": 3.169798657718121,
"config_test": false,... |
"""
Program to draw CRAC and CCM motifs on x-ray structures
No arguments are necessary, all structures are taken from standard locations
"""
import os
import sys
import numpy as np
import matplotlib
if not "DISPLAY" in os.environ or os.environ["DISPLAY"] == "" :
matplotlib.use('Agg')
import matplotlib.pyplot as ... | {
"repo_name": "SGenheden/Scripts",
"path": "Projects/Gpcr/gpcr_plot_motif.py",
"copies": "1",
"size": "3807",
"license": "mit",
"hash": -9186679386970050000,
"line_mean": 32.3947368421,
"line_max": 124,
"alpha_frac": 0.5873391122,
"autogenerated": false,
"ratio": 2.6659663865546217,
"config_tes... |
"""
Program to draw roughness (fractal) pies on structures
No arguments are necessary, all structures are taken from standard locations
"""
import argparse
import os
import sys
import numpy as np
import scipy.stats as stats
import matplotlib
if not "DISPLAY" in os.environ or os.environ["DISPLAY"] == "" :
matplot... | {
"repo_name": "SGenheden/Scripts",
"path": "Projects/Gpcr/gpcr_anal_exposure.py",
"copies": "1",
"size": "2615",
"license": "mit",
"hash": -8144343289943158000,
"line_mean": 34.8219178082,
"line_max": 116,
"alpha_frac": 0.6084130019,
"autogenerated": false,
"ratio": 3.0584795321637426,
"config_... |
"""
Program to extend the topology (itp-file) of a lipid such that
the acyl chains are longer. Assumes Slipid force field.
Used in membrane engineering project
Examples
--------
extend_topol.py -f dopc.top -a 20 -o dopx.itp
extends DOPC to C20 chains
"""
import argparse
import os
import parmed
def _get_atom(pa... | {
"repo_name": "SGenheden/Scripts",
"path": "Membrane/extend_topol.py",
"copies": "1",
"size": "5263",
"license": "mit",
"hash": -8004263362137716000,
"line_mean": 33.3986928105,
"line_max": 101,
"alpha_frac": 0.6241687251,
"autogenerated": false,
"ratio": 3.160960960960961,
"config_test": false... |
"""
Program to extract information from a Gaussian dihedral scan
It will write out energies and plot them to a .png file
I can create input for single-point calculations and PDB files for future use
Used in membrane engineering project
Examples
--------
extract_scan.py theta1_opt.log -c 6 5 1 2 -p "theta1_mp2=#MP2... | {
"repo_name": "SGenheden/Scripts",
"path": "Mol/extract_scan.py",
"copies": "1",
"size": "5734",
"license": "mit",
"hash": 126500502319601040,
"line_mean": 34.3950617284,
"line_max": 115,
"alpha_frac": 0.5816184165,
"autogenerated": false,
"ratio": 3.4253285543608123,
"config_test": false,
"h... |
"""
Program to find missing force field parameters and look them up in CHARMM36
Parses a log file from grompp and files in the toppar archive
Used in membrane engineering project
Examples
--------
find_missing_lipidff.py -l grompp.log -p model0.top -f toppar/par_all36_cgenff.prm toppar/stream/lipid/toppar_all36_li... | {
"repo_name": "SGenheden/Scripts",
"path": "Mol/find_missing_lipidff.py",
"copies": "1",
"size": "5772",
"license": "mit",
"hash": -3036020967456874000,
"line_mean": 32.5581395349,
"line_max": 136,
"alpha_frac": 0.5438322938,
"autogenerated": false,
"ratio": 3.445970149253731,
"config_test": fa... |
"""
Program to fit an AA structure onto a CG structure by overlaying
the backbone atoms at the BB bead
"""
import argparse
import os
import sys
import numpy as np
from sgenlib import fitting
from sgenlib import pdb
if __name__ == '__main__' :
# Setup a parser of the command-line arguments
parser = argparse.Ar... | {
"repo_name": "SGenheden/Scripts",
"path": "Pdb/fit_aa2cg.py",
"copies": "1",
"size": "1716",
"license": "mit",
"hash": -4394051575587396000,
"line_mean": 25.8125,
"line_max": 98,
"alpha_frac": 0.6445221445,
"autogenerated": false,
"ratio": 3.0052539404553413,
"config_test": false,
"has_no_ke... |
"""
Program to insert a solute at different depths in a liposome
Two solutes will be inserted by moving them in the opposite direction
from the center of the liposome
The solute will all likely overlap with the liposome and therefore
it is essential to grow it before attemping e.g. umbrella sampling
Example:
inse... | {
"repo_name": "SGenheden/Scripts",
"path": "Membrane/insert_in_liposome.py",
"copies": "1",
"size": "3691",
"license": "mit",
"hash": 4790540717745369000,
"line_mean": 33.820754717,
"line_max": 115,
"alpha_frac": 0.6393931184,
"autogenerated": false,
"ratio": 3.165523156089194,
"config_test": f... |
"""
Program to insert a solute at different depths in a membrane
Two solutes will be inserted separated by half a box length in
the membrane plane and the total separation in z.
The solute will all likely overlap with the membrane and therefore
it is essential to grow it before attemping e.g. umbrella sampling
Exam... | {
"repo_name": "SGenheden/Scripts",
"path": "Membrane/insert_in_membrane.py",
"copies": "1",
"size": "4405",
"license": "mit",
"hash": -5138116765120569000,
"line_mean": 33.4140625,
"line_max": 101,
"alpha_frac": 0.5952326901,
"autogenerated": false,
"ratio": 2.9683288409703503,
"config_test": f... |
"""
Program to insert cholesterol in a CG membrane by replacing phospholipids
The current mapping is:
C2 --> C3B
C1 --> C2B
R5 --> C1B
R2 --> C1A
R1 --> GL2
ROH --> GL1
Example:
python insert_chol.py -f popc_mem.gro -c chol_single.gro -n 60
"""
import argparse
import copy
import numpy a... | {
"repo_name": "SGenheden/Scripts",
"path": "Membrane/insert_chol.py",
"copies": "1",
"size": "4040",
"license": "mit",
"hash": 5739050832921598000,
"line_mean": 32.6666666667,
"line_max": 101,
"alpha_frac": 0.6205445545,
"autogenerated": false,
"ratio": 3.263327948303716,
"config_test": false,
... |
"""
Program to list the SMILES string for each solute in a list
"""
import argparse
import os
from chemspipy import ChemSpider
import dblib
if __name__ == '__main__':
argparser = argparse.ArgumentParser(description="Script to list SMILES for a solutes in a list")
argparser.add_argument('-db', '--db', help... | {
"repo_name": "SGenheden/Scripts",
"path": "Projects/Solvation/create_smiles_list.py",
"copies": "1",
"size": "1273",
"license": "mit",
"hash": -1453221160674888000,
"line_mean": 37.5757575758,
"line_max": 100,
"alpha_frac": 0.6535742341,
"autogenerated": false,
"ratio": 3.2724935732647813,
"co... |
"""
Program to make 2D scatter plots of data
"""
import argparse
import numpy as np
import matplotlib.pylab as plt
import matplotlib.lines as mlines
import matplotlib.transforms as transforms
from sgenlib import colors
from sgenlib import parsing
from sgenlib import series
if __name__ == '__main__' :
parser =... | {
"repo_name": "SGenheden/Scripts",
"path": "Plot/plot_xy.py",
"copies": "1",
"size": "8120",
"license": "mit",
"hash": -8955793941713085000,
"line_mean": 46.485380117,
"line_max": 131,
"alpha_frac": 0.609729064,
"autogenerated": false,
"ratio": 3.2610441767068274,
"config_test": false,
"has_n... |
"""
Program to make 2D scatter plots of densities computed with g_density
"""
import argparse
import re
import numpy as np
import matplotlib.pylab as plt
from sgenlib import colors
def _parse_xvgfile(filename) :
lines = []
with open(filename, 'r') as f:
lines = f.readlines()
i = 0
while l... | {
"repo_name": "SGenheden/Scripts",
"path": "Plot/plot_densities.py",
"copies": "1",
"size": "3526",
"license": "mit",
"hash": 4043494891439537700,
"line_mean": 34.6161616162,
"line_max": 104,
"alpha_frac": 0.5899035735,
"autogenerated": false,
"ratio": 3.3076923076923075,
"config_test": false,
... |
"""
Program to make a datafile prettier
If the datafile was created from a restart, the atoms are for instance not in order,
this fixes that
The default output is the input data file with a "_pretty" string appended
Examples:
lmp_prettify.py data.128dmpc_kalp23_pushed
lmp_prettify.py data.128dmpc_kalp23_pushed... | {
"repo_name": "SGenheden/Scripts",
"path": "Lammps/lmp_prettify.py",
"copies": "1",
"size": "1343",
"license": "mit",
"hash": 9141222514167578000,
"line_mean": 29.5227272727,
"line_max": 113,
"alpha_frac": 0.7163067759,
"autogenerated": false,
"ratio": 3.2916666666666665,
"config_test": false,
... |
"""
Program to make a Gromacs ndx-file
for deuterium order parameter calculations
"""
import sys
import os
import argparse
from sgenlib import pdb
from sgenlib import groups
if __name__ == "__main__":
# Setup a parser of the command-line arguments
parser = argparse.ArgumentParser(description="Program make S2... | {
"repo_name": "SGenheden/Scripts",
"path": "Gromacs/gmx_s2_groups.py",
"copies": "1",
"size": "1584",
"license": "mit",
"hash": 5416973631844728000,
"line_mean": 31.3265306122,
"line_max": 77,
"alpha_frac": 0.6887626263,
"autogenerated": false,
"ratio": 3.3488372093023258,
"config_test": false,... |
"""
Program to make a Gromacs residue template file
"""
import argparse
import parmed
if __name__ == "__main__":
parser = argparse.ArgumentParser(description="Program to make RTP entries")
parser.add_argument('-f','--file',help="the input structure file")
parser.add_argument('-t','--template',help="a t... | {
"repo_name": "SGenheden/Scripts",
"path": "Gromacs/gmx_make_dbentry.py",
"copies": "1",
"size": "1397",
"license": "mit",
"hash": 4807580321592115000,
"line_mean": 28.7234042553,
"line_max": 79,
"alpha_frac": 0.5619183966,
"autogenerated": false,
"ratio": 3.4324324324324325,
"config_test": fal... |
"""
Program to make a Lammps datafile from a PDB file
"""
import sys
import math
import random
import argparse
import os
import copy
import numpy as np
from sgenlib import lammps
from sgenlib import pdb
if __name__ == '__main__' :
# Command-line input
parser = argparse.ArgumentParser(description="Make a Lammp... | {
"repo_name": "SGenheden/Scripts",
"path": "Lammps/lmp_makedata.py",
"copies": "1",
"size": "3323",
"license": "mit",
"hash": -700147181451821600,
"line_mean": 33.9789473684,
"line_max": 115,
"alpha_frac": 0.6746915438,
"autogenerated": false,
"ratio": 3.164761904761905,
"config_test": false,
... |
"""
Program to make a PDB structure whole after wrapping in central periodic box
Default name is input with "_whole" appended to the end
Examples
--------
pdb_makewhole.py prot.pdb
"""
import argparse
import os
import sys
from sgenlib import pbc
from sgenlib import pdb
if __name__ == '__main__' :
# Command-l... | {
"repo_name": "SGenheden/Scripts",
"path": "Pdb/pdb_makewhole.py",
"copies": "1",
"size": "1530",
"license": "mit",
"hash": -1329578805172829700,
"line_mean": 27.3333333333,
"line_max": 86,
"alpha_frac": 0.668627451,
"autogenerated": false,
"ratio": 3.1875,
"config_test": false,
"has_no_keywo... |
"""
Program to make a plummed-common input file for umbrella
sampling of the distance between a membrane and one or more solutes
The atom indices are taken from a Gromacs index file
Examples:
make_plumed.py --solutes AAC1 AAC2
"""
import argparse
from sgenlib import groups
if __name__ == '__main__' :
parse... | {
"repo_name": "SGenheden/Scripts",
"path": "Membrane/make_plumed.py",
"copies": "1",
"size": "1220",
"license": "mit",
"hash": -4964994281114684000,
"line_mean": 35.9696969697,
"line_max": 99,
"alpha_frac": 0.6598360656,
"autogenerated": false,
"ratio": 3.0964467005076144,
"config_test": false,... |
"""
Program to make a polyunsaturated lipid, e.g. add an additional double bond in a
DOPC topology (itp-file). Works for Slipid force field.
Uses in membrane engineering project
Examples
--------
unsaturate_topol.py -f dopc.top -sn1 9 12 -sn2 9 12 -o dupc.itp
unsaturate_topol.py -f dopc.top -sn1 9 122 -sn2 9 12 15 -... | {
"repo_name": "SGenheden/Scripts",
"path": "Membrane/unsaturate_topol.py",
"copies": "1",
"size": "6138",
"license": "mit",
"hash": 3005349041947979000,
"line_mean": 32.7252747253,
"line_max": 105,
"alpha_frac": 0.5925382861,
"autogenerated": false,
"ratio": 3.2119309262166404,
"config_test": f... |
"""
Program to make bar plots of data
DOES NOT work great
"""
import argparse
import numpy as np
import matplotlib.pylab as plt
from sgenlib import colors
from sgenlib import parsing
def _plot_single(data, errors, headers, barlabels, ylabel, fig):
a = fig.add_axes((0.2,0.15,0.75,0.75))
ngroups = data.s... | {
"repo_name": "SGenheden/Scripts",
"path": "Plot/plot_multibars.py",
"copies": "1",
"size": "3660",
"license": "mit",
"hash": 2308265470903816000,
"line_mean": 32.5779816514,
"line_max": 104,
"alpha_frac": 0.606010929,
"autogenerated": false,
"ratio": 3.0098684210526314,
"config_test": false,
... |
"""
Program to make bar plots of data
"""
import argparse
import numpy as np
import matplotlib.pylab as plt
from sgenlib import colors
from sgenlib import parsing
if __name__ == '__main__' :
parser = argparse.ArgumentParser(description="Plot bar plots")
parser.add_argument('-f','--file',nargs="+",help="the ba... | {
"repo_name": "SGenheden/Scripts",
"path": "Plot/plot_bars.py",
"copies": "1",
"size": "1497",
"license": "mit",
"hash": 3266267380024218600,
"line_mean": 36.425,
"line_max": 141,
"alpha_frac": 0.6786907148,
"autogenerated": false,
"ratio": 2.9468503937007875,
"config_test": false,
"has_no_ke... |
"""
Program to make input to Gaussian for (R)ESPA calculations
Examples
--------
pdb2respa_inp.py mol1.pdb mol2.pdb
pdb2respa_inp.py mol1.pdb -v ff03 -c -1
"""
import sys
import os
import argparse
import time
import numpy as np
from sgenlib import pdb
if __name__ == '__main__' :
# Command-line input
... | {
"repo_name": "SGenheden/Scripts",
"path": "Pdb/pdb2respa_inp.py",
"copies": "1",
"size": "1634",
"license": "mit",
"hash": -6548830868626519000,
"line_mean": 33.0416666667,
"line_max": 137,
"alpha_frac": 0.6444308446,
"autogenerated": false,
"ratio": 2.92831541218638,
"config_test": false,
"... |
"""
Program to make input to the colvars library to perform umbrella sampling simulations
with Lammps
It will produce an output file for each value of the --zdepth argument
Example:
make_colvars.py data.elba_toluene_z0 -m 1 128 -s 129 -z {0..30}
"""
import argparse
from sgenlib import lammps
if __name__ == '__m... | {
"repo_name": "SGenheden/Scripts",
"path": "Lammps/make_colvars.py",
"copies": "1",
"size": "2112",
"license": "mit",
"hash": 2368670337701534700,
"line_mean": 25.7341772152,
"line_max": 108,
"alpha_frac": 0.6647727273,
"autogenerated": false,
"ratio": 3.119645494830133,
"config_test": false,
... |
"""
Program to make PQR file from a Gromacs topology and a structure file
"""
import argparse
import os
import sys
from sgenlib import pdb
from sgenlib import gmx
def _parse_radii(atom, topol) :
def _neigh(iatom, topol, hydrogen=False):
neigh = []
for bond in topol.bonds :
if len(bo... | {
"repo_name": "SGenheden/Scripts",
"path": "Gromacs/gmx2pqr.py",
"copies": "1",
"size": "2658",
"license": "mit",
"hash": 9031726548694923000,
"line_mean": 29.9069767442,
"line_max": 100,
"alpha_frac": 0.5583145222,
"autogenerated": false,
"ratio": 3.3266583229036297,
"config_test": false,
"h... |
"""
Program to make proper Glycam pair parameters for 1-4 neighbours that
acpype.py cannot hanndle
"""
import argparse
import math
from sgenlib import gmx
if __name__ == "__main__":
parser = argparse.ArgumentParser(description="Program make Glycam pair params")
parser.add_argument('-f','--file',help="the i... | {
"repo_name": "SGenheden/Scripts",
"path": "Gromacs/gmx_glycampairs.py",
"copies": "1",
"size": "1441",
"license": "mit",
"hash": 3772861129860108300,
"line_mean": 27.82,
"line_max": 83,
"alpha_frac": 0.6030534351,
"autogenerated": false,
"ratio": 3.216517857142857,
"config_test": false,
"has... |
"""
Program to make the molecules in a datafile whole
The default output is the input data file with a "_whole" string appended
Example:
lmp_makewhole.py data.128dopc_4232wat
"""
import argparse
import os
import sys
import numpy as np
from sgenlib import lammps
from sgenlib import pdb
from sgenlib import pbc
i... | {
"repo_name": "SGenheden/Scripts",
"path": "Lammps/lmp_makewhole.py",
"copies": "1",
"size": "1436",
"license": "mit",
"hash": 2582619617298987500,
"line_mean": 24.1929824561,
"line_max": 93,
"alpha_frac": 0.6733983287,
"autogenerated": false,
"ratio": 2.9916666666666667,
"config_test": false,
... |
"""
Program to match the residue numbers of one structure
with another.
"""
import sys
import argparse
from sgenlib import pdb
if __name__ == "__main__":
# Setup a parser of the command-line arguments
parser = argparse.ArgumentParser(description="Program to match residue number of 2 PDB files")
parser.add_a... | {
"repo_name": "SGenheden/Scripts",
"path": "Pdb/pdb_matchres.py",
"copies": "1",
"size": "2306",
"license": "mit",
"hash": -5738300670936033000,
"line_mean": 36.8032786885,
"line_max": 114,
"alpha_frac": 0.6452732003,
"autogenerated": false,
"ratio": 2.9716494845360826,
"config_test": false,
... |
"""
Program to modify LJ parameters in LAMMPS inclusion file
"""
import argparse
from collections import namedtuple
import numpy as np
from sgenlib import lammps
if __name__ == '__main__':
# Command-line input
parser = argparse.ArgumentParser(description="Modifying LJ parameters in LAMMPS inclusion file")... | {
"repo_name": "SGenheden/Scripts",
"path": "Lammps/lmp_mod_lj.py",
"copies": "1",
"size": "2061",
"license": "mit",
"hash": -1581642278163860700,
"line_mean": 35.1578947368,
"line_max": 116,
"alpha_frac": 0.6263949539,
"autogenerated": false,
"ratio": 3.5110732538330494,
"config_test": false,
... |
"""
Program to modify the atom type of some atoms in a datafile
The --atoms argument is a list of atom specification, which is in format
MOLRANGE:ATOMID
The default output is the input data file with a "_mod" string appended
Examples
lmp_mod_atype.py data.128dopc_4232wat -a 1-128:9 1-128:15 -t 7 --increase
"""
i... | {
"repo_name": "SGenheden/Scripts",
"path": "Lammps/lmp_mod_atype.py",
"copies": "1",
"size": "1809",
"license": "mit",
"hash": -297910521752958140,
"line_mean": 33.1320754717,
"line_max": 106,
"alpha_frac": 0.7009397457,
"autogenerated": false,
"ratio": 3.3314917127071824,
"config_test": false,... |
"""
Program to
"""
import argparse
import os
import subprocess
import numpy as np
import dblib
if __name__ == '__main__':
argparser = argparse.ArgumentParser(description="Script to check output")
argparser.add_argument('-db', '--db', help="the molecule database")
argparser.add_argument('-solvent', '--... | {
"repo_name": "SGenheden/Scripts",
"path": "Projects/Solvation/check_results.py",
"copies": "1",
"size": "1941",
"license": "mit",
"hash": 3432788773369506300,
"line_mean": 40.2978723404,
"line_max": 121,
"alpha_frac": 0.6331787738,
"autogenerated": false,
"ratio": 3.491007194244604,
"config_te... |
"""
Program to obtain SMILES for the solutes in the Minnesota solvation database
Examples:
param_solutes.py -db MNSol_alldata.txt -solvent hexanol -solutes hexanolwater.txt
-xyzdir MNSolDatabase-v2012/all_solutes/
"""
import argparse
import os
from chemspipy import ChemSpider
import dblib
if __nam... | {
"repo_name": "SGenheden/Scripts",
"path": "Projects/Solvation/collect_smiles.py",
"copies": "1",
"size": "1581",
"license": "mit",
"hash": -180486705063321200,
"line_mean": 32.6382978723,
"line_max": 102,
"alpha_frac": 0.6521189121,
"autogenerated": false,
"ratio": 3.3354430379746836,
"config_... |
"""
Program to optimize LJ parameters
Used in a project to paramettrize ELBA ions
"""
import argparse
import numpy as np
import matplotlib.pylab as plt
import scipy.optimize as opt
from sgenlib import parsing
def objfunc(x,hfecoeff,iodcoeff,hfefit,iodfit):
x2 = x*x
x3 = x2*x
hfex = hfecoeff[0]*x3+hfe... | {
"repo_name": "SGenheden/Scripts",
"path": "Mol/optimize_rmin2.py",
"copies": "1",
"size": "1905",
"license": "mit",
"hash": 4514896152470490600,
"line_mean": 31.8448275862,
"line_max": 141,
"alpha_frac": 0.6304461942,
"autogenerated": false,
"ratio": 2.42984693877551,
"config_test": false,
"... |
"""
Program to parametrise solutes from a list
Examples:
param_solutes.py list
"""
import argparse
import os
import string
import numpy as np
import MDAnalysis as md
import parmed
from sgenlib import ambertools
leapcmd="""
source leaprc.gaff
loadamberprep %s.prepi
loadamberparams %s.frcmod
x=loadpdb %s.pdb
saveam... | {
"repo_name": "SGenheden/Scripts",
"path": "Mol/param_solutes.py",
"copies": "1",
"size": "3553",
"license": "mit",
"hash": 3720365775096932000,
"line_mean": 29.8956521739,
"line_max": 105,
"alpha_frac": 0.5966788629,
"autogenerated": false,
"ratio": 3.2776752767527677,
"config_test": false,
... |
"""
Program to parametrise solutes from the Minnesota solvation database
Examples:
param_solutes.py -db MNSol_alldata.txt -solvent hexanol -solutes hexanolwater.txt
-xyzdir MNSolDatabase-v2012/all_solutes/
"""
import argparse
import os
import numpy as np
import MDAnalysis as md
import dblib
from sg... | {
"repo_name": "SGenheden/Scripts",
"path": "Projects/Solvation/param_solutes.py",
"copies": "1",
"size": "3961",
"license": "mit",
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"line_max": 98,
"alpha_frac": 0.5854582176,
"autogenerated": false,
"ratio": 3.0075930144267273,
"config_te... |
"""
Program to perform hydrogen mass repartitioning of a Gromacs topology file
Used in membrane engineering project
Examples
--------
gmx_hmassrepart.py -f dopc.top -o dopc_heavyh.itp
"""
import argparse
import os
import sys
import parmed
if __name__ == "__main__":
parser = argparse.ArgumentParser(description... | {
"repo_name": "SGenheden/Scripts",
"path": "Gromacs/gmx_hmassrepart.py",
"copies": "1",
"size": "1365",
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"line_mean": 30.0227272727,
"line_max": 95,
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"autogenerated": false,
"ratio": 3.3455882352941178,
"config_test": fals... |
"""
Program to perform MSD analysis of a trajectory
Experimental code!
"""
import numpy as np
from sgenlib import moldyn
from sgenlib import mdactions
from sgenlib import pbc
class MsdWalker(object):
def __init__(self, time, owner):
self.time = time
self.origin = owner.atoms.get_positions()
... | {
"repo_name": "SGenheden/Scripts",
"path": "Md/md_msd.py",
"copies": "1",
"size": "5180",
"license": "mit",
"hash": 322608838950741700,
"line_mean": 39.7874015748,
"line_max": 116,
"alpha_frac": 0.5922779923,
"autogenerated": false,
"ratio": 3.5997220291869354,
"config_test": false,
"has_no_k... |
"""
Program to place a protein next to a membrane for "push"-simulation
Example:
place_protein.py -prot prot.gro -mem membrane.gro
"""
import argparse
import os
import sys
import numpy as np
from sgenlib import pdb
def _clashes(xyz1, xyz2):
for i in range(xyz1.shape[0]) :
d = np.sum(np.power(xyz2-x... | {
"repo_name": "SGenheden/Scripts",
"path": "Membrane/place_protein.py",
"copies": "1",
"size": "2642",
"license": "mit",
"hash": -7500325625220525000,
"line_mean": 33.7631578947,
"line_max": 102,
"alpha_frac": 0.6551854656,
"autogenerated": false,
"ratio": 2.9685393258426966,
"config_test": fal... |
"""
Program to plot 2D maps. The maps are named after the input files but
with a "png"-extension.
Example:
plot_2dmap.py -f grid_dhh_low.dat grid_dhh_upp.dat
plot_2dmap.py -f grid_dhh_low.dat grid_dhh_upp.dat --ylabel "Y [nm]" --xlabel "X [nm]" --extent 0 10 0 10 --cblabel "Dhh [nm]" --max 5.0
plot_2dmap.... | {
"repo_name": "SGenheden/Scripts",
"path": "Plot/plot_2dmap.py",
"copies": "1",
"size": "4835",
"license": "mit",
"hash": 1347730343664172500,
"line_mean": 38.3089430894,
"line_max": 159,
"alpha_frac": 0.6374353671,
"autogenerated": false,
"ratio": 2.977216748768473,
"config_test": false,
"ha... |
"""
Program to plot boxplots
"""
import argparse
import numpy as np
import matplotlib.pylab as plt
from sgenlib import parsing
if __name__ == '__main__':
argparser = argparse.ArgumentParser(description="Script to plot boxplots")
argparser.add_argument('-f', '--files', nargs="+", help="the results")
ar... | {
"repo_name": "SGenheden/Scripts",
"path": "Plot/plot_boxplot.py",
"copies": "1",
"size": "2637",
"license": "mit",
"hash": -5741195476757583000,
"line_mean": 40.203125,
"line_max": 105,
"alpha_frac": 0.622298066,
"autogenerated": false,
"ratio": 3.2880299251870326,
"config_test": false,
"has... |
"""
Program to plot molecular densities
The program takes as input two sets of files and average
the densities in the two sets, creating two averaged densities.
The densities are created by gpcr_mdanal.py
These densities are then plotted next to each other, for easy comparison, along
with a representation of the ba... | {
"repo_name": "SGenheden/Scripts",
"path": "Projects/Gpcr/gpcr_plot_density.py",
"copies": "1",
"size": "7979",
"license": "mit",
"hash": 4116028268894349000,
"line_mean": 44.5942857143,
"line_max": 153,
"alpha_frac": 0.6863015415,
"autogenerated": false,
"ratio": 2.814462081128748,
"config_tes... |
"""
Program to plot PMFs of small molecules pulled through membranes
Very shaky code!
"""
import sys
import matplotlib
#matplotlib.use('Agg')
import matplotlib.pylab as plt
import numpy as np
import os
import argparse
import wham
from sgenlib import colors
from sgenlib import parsing
# The column index into the de... | {
"repo_name": "SGenheden/Scripts",
"path": "Membrane/plot_pmf.py",
"copies": "1",
"size": "5524",
"license": "mit",
"hash": -6284498285847141000,
"line_mean": 37.3611111111,
"line_max": 271,
"alpha_frac": 0.6030050688,
"autogenerated": false,
"ratio": 2.6596051998074146,
"config_test": false,
... |
"""
Program to plot residue joint contact probability
Examples
--------
gpcr_plot_rescontacts.py -f r1_md3_en_fit_joint.npz -m ohburr -l oh --mol b2
"""
import os
import argparse
import sys
import numpy as np
import matplotlib
if not "DISPLAY" in os.environ or os.environ["DISPLAY"] == "" :
matplotlib.use('Agg')
i... | {
"repo_name": "SGenheden/Scripts",
"path": "Projects/Gpcr/gpcr_plot_resjointcontacts.py",
"copies": "1",
"size": "3408",
"license": "mit",
"hash": 3910432250774230000,
"line_mean": 33.7755102041,
"line_max": 140,
"alpha_frac": 0.6775234742,
"autogenerated": false,
"ratio": 3.0079435127978815,
"... |
"""
Program to plot the correlation between calculated and experimental free energies
Examples:
plot_correlations.py -xls raw.xlsx -solvents hexane octane nonane hexanol octanol nonanol water
"""
import argparse
import os
import openpyxl as xl
import numpy as np
import matplotlib
import matplotlib.pylab as plt
im... | {
"repo_name": "SGenheden/Scripts",
"path": "Projects/Solvation/plot_correlations_hybrid.py",
"copies": "1",
"size": "6027",
"license": "mit",
"hash": 8209911429270430000,
"line_mean": 39.4496644295,
"line_max": 109,
"alpha_frac": 0.6006304961,
"autogenerated": false,
"ratio": 3.0797138477261115,
... |
"""
Program to prep a PDB structure for APR simulations
1.) Align the long axis of the host with the z-axis
2.) Align the short axis of the host with the y-axis
3.) Set origin of the G1 atom
4.) Add dummy atoms to the structure
The -a flag specifies the axes of the host
It takes to arguments and each argument is a li... | {
"repo_name": "SGenheden/Scripts",
"path": "Pdb/apr_prep.py",
"copies": "1",
"size": "4084",
"license": "mit",
"hash": -558158919627459300,
"line_mean": 30.6589147287,
"line_max": 103,
"alpha_frac": 0.6224289912,
"autogenerated": false,
"ratio": 3.377998345740281,
"config_test": false,
"has_n... |
"""
Program to prepare a PDB-file semi-automatically
The program will download the PDB file and metadata automatically
from the PDB database. It will describe the most important
features about the structure. It will then prompt the user
for removal of chains, alternative conformations, hetero residues
and the protona... | {
"repo_name": "SGenheden/Scripts",
"path": "Pdb/pdb_prep.py",
"copies": "1",
"size": "26188",
"license": "mit",
"hash": 4149859943267626000,
"line_mean": 34.6784741144,
"line_max": 179,
"alpha_frac": 0.593401558,
"autogenerated": false,
"ratio": 3.0146195464487167,
"config_test": false,
"has_... |
"""
Program to put one PDB-file next to another
If no output file is given the mobile PDB file will be overwritten
Examples
--------
next_to.py -r pdb1.pdb -m pdb2.pdb
next_to.py -r pdb1.pdb -m pdb2.pdb -s 0.0 10.0 0.0
next_to.py -r pdb1.pdb -m pdb2.pdb -s 0.0 10.0 0.0 --fromedge
"""
import argparse
import os... | {
"repo_name": "SGenheden/Scripts",
"path": "Pdb/next_to.py",
"copies": "1",
"size": "1887",
"license": "mit",
"hash": 7183685584645675000,
"line_mean": 30.9830508475,
"line_max": 137,
"alpha_frac": 0.6984631691,
"autogenerated": false,
"ratio": 3.1928934010152283,
"config_test": false,
"has_n... |
"""
Program to reduce the number of water in a membrane, from
e.g. 50 to 40 waters per lipid
"""
import argparse
import numpy as np
from sgenlib import pdb
if __name__ == '__main__' :
parser = argparse.ArgumentParser(description="Remove water from mebrane")
parser.add_argument('-f','--file',help="the inpu... | {
"repo_name": "SGenheden/Scripts",
"path": "Membrane/remove_water.py",
"copies": "1",
"size": "2230",
"license": "mit",
"hash": 4605971290778515500,
"line_mean": 32.2835820896,
"line_max": 107,
"alpha_frac": 0.6224215247,
"autogenerated": false,
"ratio": 3.2272069464544137,
"config_test": false... |
"""
Program to rename atoms and residue
Examples
--------
pdb_rename.py mystruct.pdb -atoms POPC=names_popc.txt TIP3P=names_wat.txt -from Charmm -to Berger -residues TIP3P=SOL
"""
import argparse
import os
import sys
import numpy as np
from sgenlib import pdb
def _readconv(filename,fro,to) :
lines = open(fil... | {
"repo_name": "SGenheden/Scripts",
"path": "Pdb/pdb_rename.py",
"copies": "1",
"size": "1978",
"license": "mit",
"hash": -921862758901061600,
"line_mean": 28.0882352941,
"line_max": 119,
"alpha_frac": 0.6577350859,
"autogenerated": false,
"ratio": 3.1648,
"config_test": false,
"has_no_keyword... |
"""
Program to replace a double bond in a lipid acyl chain with a cyclopropane group.
Assumes Slipid force field.
Used in membrane engineering project
Examples
--------
grow_cyclic.py -f single_popi.gro -r POPI -o single_popi_cyc.gro -t slipids.ff/popi.top -d popi_cyc.rtp
Make a Gromacs residue template (rtp) fi... | {
"repo_name": "SGenheden/Scripts",
"path": "Membrane/grow_cyclic.py",
"copies": "1",
"size": "11096",
"license": "mit",
"hash": -5196430017614651000,
"line_mean": 37,
"line_max": 130,
"alpha_frac": 0.5649783706,
"autogenerated": false,
"ratio": 3.1666666666666665,
"config_test": false,
"has_n... |
"""
Program to replace some POPI residues in a membrane patch with IPC lipids.
Assumes Slipid force field.
Used in membrane engineering project
Examples
--------
popimem2ipcmem.py -f ../32popi_22dopc_10erg/em_whole.gro -t ipc.pdb -z ipc.zmat -i ../slipids.ff/ipc.itp -n 10 > replaced.gro
"""
import sys
import argpar... | {
"repo_name": "SGenheden/Scripts",
"path": "Membrane/popimem2ipcmem.py",
"copies": "1",
"size": "8346",
"license": "mit",
"hash": -5879097914403328000,
"line_mean": 42.2435233161,
"line_max": 208,
"alpha_frac": 0.6379103762,
"autogenerated": false,
"ratio": 2.7699966810487884,
"config_test": fa... |
"""
Program to replace the coordinates in a datafile with those of a PDB
The default output is the input data file with a "_repxyz" string appended
Example:
lmp_replace_dataxyz.py -f data.200popc_b2 -p 200popc_b2_pushed.pdb
"""
import os
import sys
import argparse
import numpy as np
from sgenlib import pdb
from... | {
"repo_name": "SGenheden/Scripts",
"path": "Lammps/lmp_replace_dataxyz.py",
"copies": "1",
"size": "1259",
"license": "mit",
"hash": -2207313695355755000,
"line_mean": 27.6136363636,
"line_max": 115,
"alpha_frac": 0.7084988086,
"autogenerated": false,
"ratio": 3.1712846347607053,
"config_test":... |
"""
Program to run external commands on a solutes from the Minnesota solvation database
Examples:
run_commands.py -db MNSol_alldata.txt -solvent hexanol -solutes hexanolwater.txt
-commands insert_command
"""
import argparse
import dblib
from sgenlib import ambertools
if __name__ == '__main__':
... | {
"repo_name": "SGenheden/Scripts",
"path": "Projects/Solvation/run_commands.py",
"copies": "1",
"size": "1565",
"license": "mit",
"hash": 1039110399167573900,
"line_mean": 37.1707317073,
"line_max": 104,
"alpha_frac": 0.6479233227,
"autogenerated": false,
"ratio": 3.699763593380615,
"config_tes... |
"""
Program to scale CG-AA pair interactions in LAMMPS inclusion file
The CG-AA pairs need to have a comment including "AA-CG mixed" to be regonized
as such.
The --beads argument is a list of bead specification, each one contains a comma-separated
list of atom types. The pairs between these atom types and AA types w... | {
"repo_name": "SGenheden/Scripts",
"path": "Lammps/scale_elba_pairs.py",
"copies": "1",
"size": "2694",
"license": "mit",
"hash": -5616976688091390000,
"line_mean": 36.9436619718,
"line_max": 151,
"alpha_frac": 0.6796585004,
"autogenerated": false,
"ratio": 3.301470588235294,
"config_test": fal... |
"""
Program to setup a ComQum-ELBA run
Part of ComQum-ELBA
"""
import argparse
import numpy as np
from sgenlib import lammps
control_str = \
"""$point_charges file=pointcharges
$operating system unix
$path
$symmetry c1
$coord file=coord
$scfintunit
unit=30 size=0 file=twoint
$scfconv 6
$scfiterl... | {
"repo_name": "SGenheden/Scripts",
"path": "Lammps/lmp_comqum.py",
"copies": "1",
"size": "2693",
"license": "mit",
"hash": -8545883923262683000,
"line_mean": 25.6633663366,
"line_max": 119,
"alpha_frac": 0.6037875975,
"autogenerated": false,
"ratio": 2.8317560462670874,
"config_test": false,
... |
"""
Program to setup LAMMPS restraints for APR calculations
"""
import argparse
import numpy as np
from sgenlib import geo
from sgenlib import pdb
colvarstr="""
colvarsTrajFrequency 2500
colvarsRestartFrequency 0
colvar {
name d1
width 1.0
distance {
group1 { atomNumbers 1 }
group2 { a... | {
"repo_name": "SGenheden/Scripts",
"path": "Lammps/make_apr_rest.py",
"copies": "1",
"size": "5458",
"license": "mit",
"hash": 1200641399341220600,
"line_mean": 33.3270440252,
"line_max": 123,
"alpha_frac": 0.5538658849,
"autogenerated": false,
"ratio": 2.7961065573770494,
"config_test": false,... |
"""
Program to shorten the topology (itp-file) of a lipid such that
the acyl chains are shorter. Assumes Slipid force field.
Uses in membrane engineering project
Examples
--------
shorten_topol.py -f dopc.top -a 16 -o dopx.itp
shorten DOPC to C16 chains
"""
import argparse
import os
import parmed
def _get_atom... | {
"repo_name": "SGenheden/Scripts",
"path": "Membrane/shorten_topol.py",
"copies": "1",
"size": "4409",
"license": "mit",
"hash": -4423929794572489000,
"line_mean": 30.9492753623,
"line_max": 101,
"alpha_frac": 0.6103424813,
"autogenerated": false,
"ratio": 3.3200301204819276,
"config_test": fal... |
"""
Program to solvate a MARTINI CG or GAFF/CG system
Assumes last include is the solute itp file
Examples:
solvate_martini.py -b octanol_box.gro -s eth_cg_box.gro -os eth_solvated.gro -i martini_v2.2.itp martini_v2.0_solvents.itp eth_cg.itp -m OCO -ot eth_system.top
solvate_martini.py -b water_box.gro -s et... | {
"repo_name": "SGenheden/Scripts",
"path": "Projects/Solvation/solvate_martini.py",
"copies": "1",
"size": "3939",
"license": "mit",
"hash": 3761266142746668500,
"line_mean": 34.1696428571,
"line_max": 163,
"alpha_frac": 0.5346534653,
"autogenerated": false,
"ratio": 3.2580645161290325,
"config... |
"""
Program to sort the residues in a PDB file
Default name is input with "_sorted" appended to the end
Examples
--------
sort_residues.py prot.pdb -r SOL WAT CL
"""
import sys
import argparse
import os
import numpy as np
from sgenlib import pdb
if __name__ == '__main__' :
# Command-line input
parser = ar... | {
"repo_name": "SGenheden/Scripts",
"path": "Pdb/sort_residues.py",
"copies": "1",
"size": "1352",
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"line_max": 86,
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"""
Program to truncate a data file to a QM system
Part of ComQum-ELBA
"""
import argparse
from collections import namedtuple
import numpy as np
from sgenlib import lammps
def _trunc_connectivity(conlist, atom_ids) :
newlist = []
for con in conlist:
keep = False
for atom in con.atoms :
... | {
"repo_name": "SGenheden/Scripts",
"path": "Lammps/lmp_truncate.py",
"copies": "1",
"size": "1597",
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"line_max": 89,
"alpha_frac": 0.6418284283,
"autogenerated": false,
"ratio": 3.5176211453744495,
"config_test": false,
... |
"""
Routines and classes to read in output files from umbrella sampling,
execute weighted histogram analysis method (WHAM) and calculate
the PMF along a 1D reaction coordinate
"""
import os
import tempfile
import shutil
import subprocess
import numpy as np
import numpy.random as random
import matplotlib.pylab as plt... | {
"repo_name": "SGenheden/Scripts",
"path": "Membrane/wham.py",
"copies": "1",
"size": "34313",
"license": "mit",
"hash": 2597730237943106600,
"line_mean": 29.4193262411,
"line_max": 172,
"alpha_frac": 0.6281875674,
"autogenerated": false,
"ratio": 3.3178302069232255,
"config_test": false,
"ha... |
"""
Routines to fit structures
"""
import math
import sys
import numpy as np
def dofit(ref,mob,xyz) :
"""
Performing fitting of mobile coordinates on top of references
coordinates and then move a full set of coordinates
Parameters
----------
ref : numpy.ndarray
the reference coordinates
mob : ... | {
"repo_name": "SGenheden/Scripts",
"path": "sgenlib/fitting.py",
"copies": "1",
"size": "4276",
"license": "mit",
"hash": -3347773446667497500,
"line_mean": 24.9151515152,
"line_max": 113,
"alpha_frac": 0.6078110384,
"autogenerated": false,
"ratio": 2.593086719223772,
"config_test": false,
"h... |
"""
Routines to geometrical calculations
"""
import math
import numpy as np
def sphere_surf_rand():
u1 = 100
u2 = 1000
while u1*u1 + u2*u2 >= 1 :
u1 = np.random.uniform(low=-1,high=1)
u2 = np.random.uniform(low=-1,high=1)
x = 2*u1*np.sqrt(1-u1*u1-u2*u2)
y = 2*u2*np.sqrt(1-u1*u1-u2*u2)
z = 1 - 2... | {
"repo_name": "SGenheden/Scripts",
"path": "sgenlib/geo.py",
"copies": "1",
"size": "9926",
"license": "mit",
"hash": -9035210773981671000,
"line_mean": 24.8489583333,
"line_max": 117,
"alpha_frac": 0.5515817046,
"autogenerated": false,
"ratio": 2.4370243064080532,
"config_test": false,
"has_... |
"""
Routines to manipulate with SMILES
"""
import urllib
class RetrieveSmilesException(Exception):
pass
def _get_cactus(smiles):
"""
Convert SMILES using Cactus service
Parameters
----------
smiles : string
the SMILES string
Returns
-------
string
the path to the do... | {
"repo_name": "SGenheden/Scripts",
"path": "sgenlib/smiles.py",
"copies": "1",
"size": "4349",
"license": "mit",
"hash": 7298305725338298000,
"line_mean": 26.18125,
"line_max": 231,
"alpha_frac": 0.5730052886,
"autogenerated": false,
"ratio": 3.8384819064430715,
"config_test": false,
"has_no_... |
"""
Routines to modify coordinates in periodic boxes.
Only works with rectangular geometries.
"""
import numpy as np
def unwrap_vector(dr,box):
"""
Unwraps a vector
"""
dr = np.divide(dr,box)
dr = np.around(dr)
return np.multiply(box,dr)
def make_whole(atoms,box) :
"""
Make a set of ... | {
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"size": "3156",
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"autogenerated": false,
"ratio": 3.495016611295681,
"config_test": false,
"has_no... |
"""
Routines to parse files and streams
"""
import fileinput
import re
import numpy as np
from units import *
def stdin2ndarray() :
"""
Parse columns and rows of data from standard input into a numpy.ndarray
"""
data = []
for line in fileinput.input() :
if line[0] not in ["#","@"] :
... | {
"repo_name": "SGenheden/Scripts",
"path": "sgenlib/parsing.py",
"copies": "1",
"size": "9364",
"license": "mit",
"hash": -6567313935266222000,
"line_mean": 28.5394321767,
"line_max": 103,
"alpha_frac": 0.579880393,
"autogenerated": false,
"ratio": 3.7188244638602064,
"config_test": false,
"h... |
"""
Routines to perform analysis on series
"""
import numpy as np
from scipy.stats import spearmanr
def find_equilibration(x,y,atleast=50,threshold=0.05,nperm=0) :
"""
Find the equilibration time of a data series
Parameters
----------
x : Numpy array
the x data
y : Numpy array
the y data
atlea... | {
"repo_name": "SGenheden/Scripts",
"path": "sgenlib/series.py",
"copies": "1",
"size": "2106",
"license": "mit",
"hash": 9046315538647219000,
"line_mean": 25.325,
"line_max": 89,
"alpha_frac": 0.5740740741,
"autogenerated": false,
"ratio": 3.391304347826087,
"config_test": false,
"has_no_keyw... |
"""
Scripts used to convert the provided all-atom system input in Lammps format
to a hybrid description. The solute is retained as all-atom, whereas the
solvent molecules are made into CG.
The script creates the following files:
1) A PDB-file for the solute
2) A Lammps datafile for the solute, include force field par... | {
"repo_name": "SGenheden/Scripts",
"path": "Projects/Sampl5/convert_aa.py",
"copies": "1",
"size": "7344",
"license": "mit",
"hash": 2809168107841235000,
"line_mean": 33.4788732394,
"line_max": 98,
"alpha_frac": 0.6209150327,
"autogenerated": false,
"ratio": 3.287376902417189,
"config_test": fa... |
"""
Script to calculate PMF properties, i.e. penetration and water/lipid barriers
"""
import sys
import numpy as np
from scipy.interpolate import interp1d
from sgenlib import parsing
from sgenlib import snum
data = parsing.parse2ndarray(sys.argv[1])
x = data[:,0]
pmf = data[:,1]
err = data[:,2]
mini = np.argmin(p... | {
"repo_name": "SGenheden/Scripts",
"path": "Projects/Liposome/calc_pmf_prop_mem.py",
"copies": "1",
"size": "1536",
"license": "mit",
"hash": -534936717331833860,
"line_mean": 25.9473684211,
"line_max": 84,
"alpha_frac": 0.62109375,
"autogenerated": false,
"ratio": 2.3343465045592704,
"config_t... |
"""
Script to calculate PMF properties, i.e. penetration and water/lipid barriers
"""
import sys
import numpy as np
from sgenlib import parsing
data = parsing.parse2ndarray(sys.argv[1])
x = data[:,0]
pmf = data[:,1]
err = data[:,2]
l = data.shape[0]
imid = int(np.floor(0.5*l))
ifourth = int(np.floor(0.25*l))
dt =... | {
"repo_name": "SGenheden/Scripts",
"path": "Projects/Liposome/calc_pmf_prop.py",
"copies": "1",
"size": "1483",
"license": "mit",
"hash": 4738127159494352000,
"line_mean": 29.8958333333,
"line_max": 77,
"alpha_frac": 0.6345246123,
"autogenerated": false,
"ratio": 2.5926573426573425,
"config_tes... |
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