a

mrdna/readers/.ipynb_checkpoints/Untitled-checkpoint.ipynb

+{
+ "cells": [],
+ "metadata": {},
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

mrdna/readers/list.pdb

+CRYST1 5000.000 5000.000 5000.000  90.00  90.00  90.00 P 1           1
+ATOM      1 DNA  DNA A 1       0.50000 0.00000 5.10000  0.00  0.00   0     0
+ATOM      2 DNA  DNA A 2       0.50000 0.00000 11.9000  0.00  0.00   0     0
+ATOM      3 DNA  DNA A 3       0.50000 0.00000 18.7000  0.00  0.00   0     0
+ATOM      4 NAS  NAS A 4       0.00000 0.00000-1.70000  0.00  0.00   0     1
+ATOM      5 NAS  NAS A 5       0.00000 0.00000 1.70000  0.00  0.00   0     1
+ATOM      6 NAS  NAS A 6       0.00000 0.00000 5.10000  0.00  0.00   0     1
+ATOM      7 NAS  NAS A 7       0.00000 0.00000 20.4000  0.00  0.00   0     2

mrdna/readers/list.pdf

+PSF NAMD
+
+       0 !NTITLE
+
+       7 !NATOM
+         1 0        1        DNA      DNA      D000   0.000000      150.0000 0
+         2 0        2        DNA      DNA      D001   0.000000      300.0000 0
+         3 0        3        DNA      DNA      D001   0.000000      300.0000 0
+         4 1        4        NAS      NAS      S000   0.000000      150.0000 0
+         5 1        5        NAS      NAS      S000   0.000000      150.0000 0
+         6 1        6        NAS      NAS      S001   0.000000       75.0000 0
+         7 2        7        NAS      NAS      S000   0.000000      150.0000 0
+
+       7 !NBOND
+       1       6        3       7        2       3        5       6
+       4       5        1       2        4       7 
+
+       3 !NTHETA
+       1       2       3        5       4       7        4       5       6
+
+       0 !NPHI
+
+       0 !NIMPHI
+
+
+       0 !NDON: donors
+
+
+
+       0 !NACC: acceptors
+
+
+
+       0 !NNB
+
+      0      0      0      0      0      0      0
+
+       1       0 !NGRP
+

mrdna/readers/segmentmodel_from_lists.py

@@ -6,9 +6,9 @@ import os,sys
 import scipy
 
 from mrdna import logger, devlogger
-from ..segmentmodel import SegmentModel, SingleStrandedSegment, DoubleStrandedSegment
-from ..arbdmodel.coords import quaternion_from_matrix, rotationAboutAxis, quaternion_slerp
-from .. import get_resource_path
+from mrdna.segmentmodel import SegmentModel, SingleStrandedSegment, DoubleStrandedSegment
+from mrdna.arbdmodel.coords import quaternion_from_matrix, rotationAboutAxis, quaternion_slerp
+from mrdna import get_resource_path
 
 ref_stack_position = np.array((-2.41851735, -0.259761333, 3.39999978))
 

mrdna/readers/unittest/circular.bd

+
+timestep 5e-05
+steps 100000000
+numberFluct 0                   # deprecated
+
+interparticleForce 1            # other values deprecated
+fullLongRange 0                 # deprecated
+temperature 291
+ParticleDynamicType Brown
+
+outputPeriod 10000.0
+## Energy doesn't actually get printed!
+outputEnergyPeriod 10000.0
+outputFormat dcd
+
+## Infrequent domain decomposition because this kernel is still very slow
+decompPeriod 10000
+cutoff 50
+pairlistDistance 30
+
+origin -2500.0 -2500.0 -2500.0
+systemSize 5000 5000 5000
+
+
+
+
+particle D000
+num 1
+diffusion 111.80339887498948
+gridFile potentials/null.dx
+
+particle D001
+num 2
+diffusion 79.05694150420948
+gridFile potentials/null.dx
+
+particle O000
+num 2
+diffusion 120
+gridFile potentials/null.dx
+
+particle O001
+num 1
+diffusion 79.05694150420948
+gridFile potentials/null.dx
+
+particle S000
+num 3
+diffusion 111.80339887498948
+gridFile potentials/null.dx
+
+particle S001
+num 1
+diffusion 120
+gridFile potentials/null.dx
+
+## Input coordinates
+inputParticles circular.particles.txt
+
+
+## Interaction potentials
+tabulatedPotential  1
+## The i@j@file syntax means particle type i will have NB interactions with particle type j using the potential in file
+tabulatedFile 0@0@potentials/circular-nb.D000-D000.dat
+tabulatedFile 0@1@potentials/circular-nb.D000-D001.dat
+tabulatedFile 0@2@potentials/circular-nb.D000-O000.dat
+tabulatedFile 0@3@potentials/circular-nb.D000-O001.dat
+tabulatedFile 0@4@potentials/circular-nb.D000-S000.dat
+tabulatedFile 0@5@potentials/circular-nb.D000-S001.dat
+tabulatedFile 1@1@potentials/circular-nb.D001-D001.dat
+tabulatedFile 1@2@potentials/circular-nb.D001-O000.dat
+tabulatedFile 1@3@potentials/circular-nb.D001-O001.dat
+tabulatedFile 1@4@potentials/circular-nb.D001-S000.dat
+tabulatedFile 1@5@potentials/circular-nb.D001-S001.dat
+tabulatedFile 2@2@potentials/circular-nb.O000-O000.dat
+tabulatedFile 2@3@potentials/circular-nb.O000-O001.dat
+tabulatedFile 2@4@potentials/circular-nb.O000-S000.dat
+tabulatedFile 2@5@potentials/circular-nb.O000-S001.dat
+tabulatedFile 3@3@potentials/circular-nb.O001-O001.dat
+tabulatedFile 3@4@potentials/circular-nb.O001-S000.dat
+tabulatedFile 3@5@potentials/circular-nb.O001-S001.dat
+tabulatedFile 4@4@potentials/circular-nb.S000-S000.dat
+tabulatedFile 4@5@potentials/circular-nb.S000-S001.dat
+tabulatedFile 5@5@potentials/circular-nb.S001-S001.dat
+tabulatedBondFile potentials/bond-4.000-12.000.dat
+tabulatedBondFile potentials/bond-30.000-1.500.dat
+tabulatedBondFile potentials/wlcbond-9.400-12.000.dat
+tabulatedBondFile potentials/wlcbond-6.400-12.000.dat
+tabulatedBondFile potentials/gbond-4.233-3.400.dat
+tabulatedAngleFile potentials/wlcangle-12.800-12.000.dat
+tabulatedAngleFile potentials/angle-20.882-90.000.dat
+tabulatedAngleFile potentials/angle-31.289-180.000.dat
+tabulatedDihedralFile potentials/dihedral-76.537-34.483.dat
+tabulatedDihedralFile potentials/dihedral-10.430-180.000.dat
+tabulatedDihedralFile potentials/dihedral-21.531--120.000.dat
+tabulatedDihedralFile potentials/dihedral-21.531-120.000.dat
+inputBonds potentials/circular.bonds.txt
+inputAngles potentials/circular.angles.txt
+inputDihedrals potentials/circular.dihedrals.txt
+inputExcludes potentials/circular.exculsions.txt

mrdna/readers/unittest/circular.particles.txt

+ATOM 0 D000 0.500000 0.000000 5.100000
+ATOM 1 O000 1.932597 -0.444597 5.100000
+ATOM 2 D001 0.500000 0.000000 11.900000
+ATOM 3 O001 1.932597 0.444597 11.900000
+ATOM 4 D001 0.500000 0.000000 18.700000
+ATOM 5 O000 1.429173 1.177556 18.700000
+ATOM 6 S000 0.000000 0.000000 -1.700000
+ATOM 7 S000 0.000000 0.000000 1.700000
+ATOM 8 S001 0.000000 0.000000 5.100000
+ATOM 9 S000 0.000000 0.000000 20.400000

mrdna/readers/unittest/circular.pdb

+CRYST1 5000.000 5000.000 5000.000  90.00  90.00  90.00 P 1           1
+ATOM      1 DNA  DNA A 1       0.50000 0.00000 5.10000  0.00  0.00   0     0
+ATOM      2  O   O   A 2       1.93259-0.44459 5.10000  0.00  0.00   0     0
+ATOM      3 DNA  DNA A 3       0.50000 0.00000 11.9000  0.00  0.00   0     0
+ATOM      4  O   O   A 4       1.93259 0.44459 11.9000  0.00  0.00   0     0
+ATOM      5 DNA  DNA A 5       0.50000 0.00000 18.7000  0.00  0.00   0     0
+ATOM      6  O   O   A 6       1.42917 1.17755 18.7000  0.00  0.00   0     0
+ATOM      7 NAS  NAS A 7       0.00000 0.00000-1.70000  0.00  0.00   0     1
+ATOM      8 NAS  NAS A 8       0.00000 0.00000 1.70000  0.00  0.00   0     1
+ATOM      9 NAS  NAS A 9       0.00000 0.00000 5.10000  0.00  0.00   0     1
+ATOM     10 NAS  NAS A 10      0.00000 0.00000 20.4000  0.00  0.00   0     2

mrdna/readers/unittest/circular.psf

+PSF NAMD
+
+       0 !NTITLE
+
+      10 !NATOM
+         1 0        1        DNA      DNA      D000   0.000000      150.0000 0
+         2 0        2        O        O        O000   0.000000        0.0000 0
+         3 0        3        DNA      DNA      D001   0.000000      300.0000 0
+         4 0        4        O        O        O001   0.000000      300.0000 0
+         5 0        5        DNA      DNA      D001   0.000000      300.0000 0
+         6 0        6        O        O        O000   0.000000        0.0000 0
+         7 1        7        NAS      NAS      S000   0.000000      150.0000 0
+         8 1        8        NAS      NAS      S000   0.000000      150.0000 0
+         9 1        9        NAS      NAS      S001   0.000000       75.0000 0
+        10 2        10       NAS      NAS      S000   0.000000      150.0000 0
+
+      10 !NBOND
+       3       5        5      10        1       2        8       9
+       7      10        7       8        1       9        3       4
+       1       3        5       6 
+
+       7 !NTHETA
+       1       3       5        8       7      10        4       3       5
+       3       5       6        2       1       3        1       3       4
+       7       8       9 
+
+       5 !NPHI
+       1       3       4       5       10       5       3       6
+       2       1       3       4        4       3       5       6
+       9       1       3       2 
+
+       0 !NIMPHI
+
+
+       0 !NDON: donors
+
+
+
+       0 !NACC: acceptors
+
+
+
+       0 !NNB
+
+      0       0       0       0       0       0       0       0
+      0      0
+
+       1       0 !NGRP
+