diff --git a/dnarbd/MANIFEST.in b/dnarbd/MANIFEST.in
new file mode 100644
index 0000000000000000000000000000000000000000..b5d192857288eb5cc0fe9ea4ba76874a14b01ac3
--- /dev/null
+++ b/dnarbd/MANIFEST.in
@@ -0,0 +1 @@
+include resources
\ No newline at end of file
diff --git a/dnarbd/__init__.py b/dnarbd/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..493251d9e522b04a7c7e7eb21b704ed596db3fef
--- /dev/null
+++ b/dnarbd/__init__.py
@@ -0,0 +1,8 @@
+import os
+
+_RESOURCE_DIR = os.path.join(os.path.dirname(__file__), 'resources')
+def get_resource_path(relative_path):
+ return os.path.join(_RESOURCE_DIR, relative_path)
+
+from .segmentmodel import SegmentModel, SingleStrandedSegment, DoubleStrandedSegment
+from .simulate import multiresolution_simulation
diff --git a/dnarbd/coords.py b/dnarbd/coords.py
index 11833fac09e7faf771e6cd965522f908c0017928..70b6216d5e4a478da96a0bbb594d16d17278c0a8 100644
--- a/dnarbd/coords.py
+++ b/dnarbd/coords.py
@@ -1,7 +1,6 @@
import numpy as np
from scipy.optimize import newton
-
def minimizeRmsd(coordsB, coordsA, weights=None, maxIter=100):
## Going through many iterations wasn't really needed
tol = 1
diff --git a/dnarbd/examples/run.py b/dnarbd/examples/run.py
index fd24ebc674b58885ca43087ae4d23536765312c0..6d5f77d6977c24be6e9b61bf5e5e97e4b8adb546 100644
--- a/dnarbd/examples/run.py
+++ b/dnarbd/examples/run.py
@@ -2,8 +2,9 @@
import sys
from glob import glob
import re
-from cadnano_segments import read_json_file, read_model
-from simulate import run_simulation_protocol
+
+from dnarbd.readers import cadnano_reader()
+from dnarbd.simulate import run_simulation_protocol
if __name__ == '__main__':
if len(sys.argv) > 1:
diff --git a/dnarbd/model/CanonicalNucleotideAtoms.py b/dnarbd/model/CanonicalNucleotideAtoms.py
index f2eb3aebf9174757a54b22733d27503291d2dc23..39613912c421b93406767ae57f063bc18ce33190 100644
--- a/dnarbd/model/CanonicalNucleotideAtoms.py
+++ b/dnarbd/model/CanonicalNucleotideAtoms.py
@@ -1,8 +1,9 @@
import json
import numpy as np
import copy
-from coords import rotationAboutAxis
-from arbdmodel import Group, PointParticle, ParticleType
+from ..coords import rotationAboutAxis
+from .arbdmodel import Group, PointParticle, ParticleType
+from .. import get_resource_path
seqComplement = dict(A='T',G='C')
resnames = dict(A="ADE", G="GUA", C="CYT", T="THY")
@@ -130,7 +131,7 @@ canonicalNtFwd = dict()
direction = 'fwd'
for seq in seqComplement.keys():
for keystring,suff in zip(("5%s","%s","%s3","5%s3"),("-5prime","","-3prime","-singlet")):
- prefix = 'resources/%s-%s%s' % (seq,direction,suff)
+ prefix = get_resource_path('%s-%s%s' % (seq,direction,suff))
key = keystring % seq
canonicalNtFwd[key] = CanonicalNucleotideFactory( prefix, seq )
@@ -138,13 +139,13 @@ canonicalNtRev = dict()
direction = 'rev'
for seq in seqComplement.keys():
for keystring,suff in zip(("5%s","%s","%s3","5%s3"),("-5prime","","-3prime","-singlet")):
- prefix = 'resources/%s-%s%s' % (seq,direction,suff)
+ prefix = get_resource_path('%s-%s%s' % (seq,direction,suff))
key = keystring % seq
canonicalNtRev[key] = CanonicalNucleotideFactory( prefix, seq )
-with open("resources/enm-template-honeycomb.json") as ch:
+with open(get_resource_path("enm-template-honeycomb.json")) as ch:
enmTemplateHC = json.load(ch)
-with open("resources/enm-template-square.json") as ch:
+with open(get_resource_path("enm-template-square.json")) as ch:
enmTemplateSQ = json.load(ch)
-with open("resources/enm-corrections-honecomb.json") as ch:
+with open(get_resource_path("enm-corrections-honecomb.json")) as ch:
enmCorrectionsHC = json.load(ch)
diff --git a/dnarbd/model/dna_sequence.py b/dnarbd/model/dna_sequence.py
new file mode 100644
index 0000000000000000000000000000000000000000..a189f114ed1421f13dd83fa1a9c2632f36c9f18b
--- /dev/null
+++ b/dnarbd/model/dna_sequence.py
@@ -0,0 +1,13 @@
+from .. import get_resource_path
+
+_m13_path = get_resource_path("cadnano2pdb.seq.m13mp18.dat")
+def read_sequence_file(sequenceFile=_m13_path):
+ seq = []
+ with open(sequenceFile) as ch:
+ for l in ch:
+ l = l.strip().replace(" ", "")
+ if l[0] in (";","#"): continue
+ seq.extend([c.upper() for c in l])
+ return seq
+
+m13 = read_sequence_file()
diff --git a/dnarbd/model/nbPot.py b/dnarbd/model/nbPot.py
index 20757abbcdeed481c23632e2001a0e7ed75fd17b..1b9c145b4c229a76d32eae8b9e9383b9e0db08cd 100644
--- a/dnarbd/model/nbPot.py
+++ b/dnarbd/model/nbPot.py
@@ -3,7 +3,8 @@ import scipy.optimize as opt
from scipy.interpolate import interp1d
from scipy.signal import savgol_filter as savgol
-from nonbonded import NonbondedScheme
+from .nonbonded import NonbondedScheme
+from .. import get_resource_path
dxParam = -1
@@ -25,7 +26,7 @@ def maxForce(x,u,maxForce=40):
return u
# d = np.loadtxt("resources/jj-nar-dna-pmf-20Mg-200Na.dat")
-d = np.loadtxt("resources/jj-nar-dna-pmf-100Mg.dat")
+d = np.loadtxt(get_resource_path("jj-nar-dna-pmf-100Mg.dat"))
x0 = d[:,1] + dxParam
y0 = d[:,0] # kcal/mol for 10bp with 10bp, according to JY
diff --git a/dnarbd/readers/__init__.py b/dnarbd/readers/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..b846d7228dc75cef0c6c38e2904686d12079d97c
--- /dev/null
+++ b/dnarbd/readers/__init__.py
@@ -0,0 +1,25 @@
+from ..segmentmodel import SegmentModel
+
+""" cadnano """
+from .cadnano_segments import read_json_file
+from .cadnano_segments import read_model as model_from_cadnano_json
+
+""" vHelix """
+from .polygon_mesh import parse_maya_file, convert_maya_to_segments
+
+""" Atomic PDB """
+from .segmentmodel_from_pdb import SegmentModelFromPdb
+
+## TODO: make module this package conform to a single style for input/output
+
+def read_cadnano(json_file, **model_parameters):
+ data = read_json_file
+ return model_from_cadnano_json(data)
+
+def read_vhelix(maya_file, **model_parameters):
+ data = parse_maya_file(maya_file)
+ segments, dsSegmentDict = convert_maya_to_segments( data )
+ return SegmentModel( segments,**model_parameters )
+
+def read_atomic_pdb(pdb_file, **model_parameters):
+ return SegmentModelFromPdb(pdb_file)
diff --git a/dnarbd/readers/cadnano_segments.py b/dnarbd/readers/cadnano_segments.py
index 4bb7b062892b89146e7ad1054a0008b7ca0ef5a2..f2a4836bb1df13405a9e26bcdcc855c3061b4ec2 100644
--- a/dnarbd/readers/cadnano_segments.py
+++ b/dnarbd/readers/cadnano_segments.py
@@ -5,22 +5,9 @@ import os,sys
from glob import glob
import re
-from coords import readArbdCoords, readAvgArbdCoords
-from segmentmodel import SegmentModel, SingleStrandedSegment, DoubleStrandedSegment
-
-arbd="/home/cmaffeo2/development/cuda/arbd.dbg/src/arbd" # reduced the mem footprint cause vmd
-namd="/home/cmaffeo2/development/namd-bin/NAMD_Git-2017-07-06_Linux-x86_64-multicore-CUDA/namd2"
-
-def readSequenceFile(sequenceFile='resources/cadnano2pdb.seq.m13mp18.dat'):
- seq = []
- with open(sequenceFile) as ch:
- for l in ch:
- l = l.strip().replace(" ", "")
- if l[0] in (";","#"): continue
- seq.extend([c.upper() for c in l])
- return seq
-
-m13seq = readSequenceFile(sequenceFile='resources/cadnano2pdb.seq.m13mp18.dat')
+from ..coords import readArbdCoords, readAvgArbdCoords
+from ..segmentmodel import SegmentModel, SingleStrandedSegment, DoubleStrandedSegment
+from ..model.dna_sequence import m13 as m13seq
## TODO: separate SegmentModel from ArbdModel so multiple parts can be combined
## TODO: catch circular strands in "get_5prime" cadnano calls
diff --git a/dnarbd/readers/polygon_mesh.py b/dnarbd/readers/polygon_mesh.py
index c7e5f23b4452d4bff56f39a077148eecb73e6796..15c4c88a097951e264b75dd47f1bb2608f57d878 100644
--- a/dnarbd/readers/polygon_mesh.py
+++ b/dnarbd/readers/polygon_mesh.py
@@ -1,9 +1,9 @@
import numpy as np
import sys
import re
-from coords import rotationAboutAxis
+from ..coords import rotationAboutAxis
-from segmentmodel import SegmentModel, SingleStrandedSegment, DoubleStrandedSegment
+from ..segmentmodel import SegmentModel, SingleStrandedSegment, DoubleStrandedSegment
class MayaObj():
def __init__(self, maya_lines):
diff --git a/dnarbd/readers/segmentmodel_from_pdb.py b/dnarbd/readers/segmentmodel_from_pdb.py
index cb3c9e4ff489a3e26c8b912316007dc0ad664e01..cc9708d85926126c0cc75159d518425bce803d7d 100644
--- a/dnarbd/readers/segmentmodel_from_pdb.py
+++ b/dnarbd/readers/segmentmodel_from_pdb.py
@@ -10,21 +10,8 @@ import MDAnalysis as mda
import MDAnalysis.analysis.align as align
from MDAnalysis.analysis.distances import distance_array
-from segmentmodel import SegmentModel, SingleStrandedSegment, DoubleStrandedSegment
-
-arbd="/home/cmaffeo2/development/cuda/arbd.dbg/src/arbd" # reduced the mem footprint cause vmd
-namd="/home/cmaffeo2/development/namd-bin/NAMD_Git-2017-07-06_Linux-x86_64-multicore-CUDA/namd2"
-
-def readSequenceFile(sequenceFile='resources/cadnano2pdb.seq.m13mp18.dat'):
- seq = []
- with open(sequenceFile) as ch:
- for l in ch:
- l = l.strip().replace(" ", "")
- if l[0] in (";","#"): continue
- seq.extend([c.upper() for c in l])
- return seq
-
-m13seq = readSequenceFile(sequenceFile='resources/cadnano2pdb.seq.m13mp18.dat')
+from ..segmentmodel import SegmentModel, SingleStrandedSegment, DoubleStrandedSegment
+from .. import get_resource_path
resnames = dict(A='ADE DA DA5 DA3', T='THY DT DT5 DT3',
C='CYT DC DC5 DC3', G='GUA DG DG5 DG3')
@@ -34,7 +21,7 @@ bases = resnames.keys()
resname_to_key = {n:k for k,v in resnames.items() for n in v.split()}
complement = dict(A='T', C='G', T='A', G='C')
-refUnis = {b:mda.Universe("resources/generate-nts/1-w3dna/{}{}.pdb".format(b,complement[b]))
+refUnis = {b:mda.Universe(get_resource_path("generate-nts/1-w3dna/{}{}.pdb".format(b,complement[b])))
for b in bases}
stack_text = "not name O5' P O1P O2P OP1 OP2 O3' H*"
diff --git a/dnarbd/segmentmodel.py b/dnarbd/segmentmodel.py
index 88f152cc660f1bd95332ed310eacf04d71f2ebb2..657ab574da405a60aa895f191af151545b83b8b2 100644
--- a/dnarbd/segmentmodel.py
+++ b/dnarbd/segmentmodel.py
@@ -1,18 +1,18 @@
import pdb
import numpy as np
import random
-from arbdmodel import PointParticle, ParticleType, Group, ArbdModel
-from coords import rotationAboutAxis, quaternion_from_matrix, quaternion_to_matrix
-from nonbonded import *
+from .model.arbdmodel import PointParticle, ParticleType, Group, ArbdModel
+from .coords import rotationAboutAxis, quaternion_from_matrix, quaternion_to_matrix
+from .model.nonbonded import *
from copy import copy, deepcopy
-from nbPot import nbDnaScheme
+from .model.nbPot import nbDnaScheme
from scipy.special import erf
import scipy.optimize as opt
from scipy import interpolate
-from CanonicalNucleotideAtoms import canonicalNtFwd, canonicalNtRev, seqComplement
-from CanonicalNucleotideAtoms import enmTemplateHC, enmTemplateSQ, enmCorrectionsHC
+from .model.CanonicalNucleotideAtoms import canonicalNtFwd, canonicalNtRev, seqComplement
+from .model.CanonicalNucleotideAtoms import enmTemplateHC, enmTemplateSQ, enmCorrectionsHC
# import pdb
"""
diff --git a/dnarbd/simulate.py b/dnarbd/simulate.py
index 933db19e0cd13cdc92e25c5841df6862a9e01a3a..fe8e0b0d42ced786b76dcd48b11cd45678eb3781 100644
--- a/dnarbd/simulate.py
+++ b/dnarbd/simulate.py
@@ -1,22 +1,22 @@
import os
-from coords import readArbdCoords, readAvgArbdCoords
+import tempfile
+from .coords import readArbdCoords, readAvgArbdCoords
arbd="/home/cmaffeo2/development/cuda/arbd.dbg/src/arbd" # reduced the mem footprint cause vmd
namd="/home/cmaffeo2/development/namd-bin/NAMD_Git-2017-07-06_Linux-x86_64-multicore-CUDA/namd2"
-def run_simulation_protocol( output_name, job_id, model,
- remove_long_bonds=False,
- gpu = 0,
- directory=None,
- coarse_steps = 5e7+1,
- fine_steps = 5e7+1
- ):
+def multiresolution_simulation( output_name, job_id, model,
+ remove_long_bonds=False,
+ gpu = 0,
+ directory=None,
+ coarse_steps = 5e7+1,
+ fine_steps = 5e7+1
+ ):
ret = None
d_orig = os.getcwd()
try:
if directory is None:
- import tempfile
directory = tempfile.mkdtemp(prefix='origami-%s-' % job_id, dir='/dev/shm/')
elif not os.path.exists(directory):
os.makedirs(directory)