wechrom Classes and Modules

Class: wechrom.WechromSystem

class wechrom.WechromSystem(pdbxFile, xmlFile='DEFAULT', memoryRange=4, verbose=False)[source]

Build a WEChroM system with topology and system information for openmm simulations The vanilla version should only have DNA beads

positions

positions of all atoms in the initial pdbx file

Type

np.array, N x 3

atoms

index of all atoms (DNA)

Type

list of openmm Atoms

residues

index of all residues (base pairs)

Type

list of openmm Residues

dnaStrands

index of all atoms in the two strands I and J

Type

dict of list of int

dnaRes

index of all DNA residues

Type

list of int

nBp

number of DNA residues

Type

int

dna_Atom2Res, dna_Res2Atom

atom2res and res2atom relation for the two dna strands

Type

dict of dict

dnaTypes

name of the two strands I and J

Type

list

pdbx
Type

openmm PDBxFile

forcefield

built on the xml file

Type

openmm forcefield

system

built on topology from pdbx and forcefield

Type

openmm system

constructDNAIndex()[source]

Construct DNA atom and residue index, as well as their relations

addForce(force, forceName)[source]

Add a force to the system, set the force group and store the corresponding str name

Parameters

  • forces (openmm force) –

  • forceName (str) –

addConnetivityForce(kCon=3000.0, bondLength=2.0, forceName='Con')[source]

Add a connectivity force to the system

Parameters

  • kCon (float, optional) – k in harmonic spring 0.5k(r-r0)^2. Defaults to 3000.0.

  • bondLength (float, optional) – r0 in harmonic spring 0.5k(r-r0)^2. Defaults to 2.0.

  • forceName (str, optional) – Defaults to ‘Connectivity’.

addExcludVolumeForce(kExcl=5856.0, rExcl=2.07, forceName='Ex-vol')[source]

Add the connectivity term to the system

addIntraStrandMemoryForce(temPos, depth=0.3, width=0.2, forceName='Intra_m')[source]

Add the intra-strand associative memory force to the system

Parameters

  • temPos (dict) – dict, 10 x 2 x memory_range x 3: positions of templates

  • depth (float, optional) – depth of the Gaussian Well. Defaults to 0.3. unit = kT

  • width (float, optional) – width of the Gaussian Well. Defaults to 0.2. unit = reduced length

  • Available (depth, width) – (0.15, 0.1),(0.2, 0.15), (0.25, 0.17), (0.3, 0.2)

addInterStrandMemoryForce(temPos, depth=0.3, width=0.2, forceName='Inter_m')[source]

Add the inter-strand associative memory force to the system

Parameters

  • temPos (dict) – dict, 10 x 2 x memory_range x 3: positions of templates

  • depth (float, optional) – depth of the Gaussian Well. Defaults to 0.3. unit = kT

  • width (float, optional) – width of the Gaussian Well, has a factor of 2 compared with the intra-strand width. Defaults to 0.2. unit = reduced length

  • Available (depth, width) – (0.15, 0.1),(0.2, 0.15), (0.25, 0.17), (0.3, 0.2) should keep the same as intra-strand

addDefaultForces()[source]

Add default forces designed for the wechrom system, including the connectivity term, the excluded-volume term, generating associative memory templates and adding inter- and intra- strand associative memory terms

initializeSimulation(platform='CPU', temperature=300, collisionRate=1.0, timeStep=20.0)[source]

Initialize an openmm simulation.

Parameters

  • platform (str, optional) – platform. Defaults to ‘CPU’. Can be ‘CPU’, ‘CUDA’ or ‘OpenCL’

  • temperature (int, optional) – temperature in kelvin. Defaults to 300.

  • collisionRate (float, optional) – collision rate for the langevin integrator in 1/picosecond. Defaults to 1.0.

  • timeStep (float, optional) – simulation time step in femtosecond. Defaults to 20.0.

platform

CPU, CUDA or OpenCL. Defaults to CPU

Type

openmm platform

integrator

a LangevinIntegrator with given temperature, collision rate and timestep

Type

openmm integrator

simulation

a simulation with wechrom topology, system, instance’s integrator and given platform. The initial positions are set by wechrom pdbx file and the initial velocities are set to temperature. Local energy is minimized.

Type

openmm simulation

runSteps(steps=1000, reportFreq=100, append=False, outputDir='DEFAULT', energyFilename='energy.txt', dcdFilename='movie.dcd', chkFilename='checkpt.chk')[source]

Run simulation on openmm. Should be called after initializeSimulation(). Report energy for each force and trajectories in dcd format at the given report frequency. Save the last checkpoint

Parameters

  • outputDir (str, optional) – output directory. Defaults to ‘DEFAULT’.

  • steps (int, optional) – total steps for the simulation. Defaults to 1000.

  • reportFreq (int, optional) – report frequency. Defaults to 100.

  • append (bool, optional) – append to an old trajectory and energy or not. Defaults to False.

  • energyFilename (str, optional) – file name to report energy. Defaults to ‘energy.txt’.

  • dcdFilename (str, optional) – file name to report trajectory. Defaults to ‘movie.dcd’.

  • chkFilename (str, optional) – file name for the last checkpoint. Defaults to ‘checkpt.chk’.

Class: wechrom.SingleNucleoSystem

class wechrom.SingleNucleoSystem(pdbxFile, xmlFile='DEFAULT', memoryRange=4, nucZero=- 1, verbose=False)[source]

Build a single-nucleosome WEChroM system with topology and system information for openmm simulations

Parameters

WechromSystem (object) – DNA only system

proTypes

names of protein atoms

Type

list of str

protein

index of protein atoms

Type

list of int

proRes

index of protein residues

Type

list of int

pro_Atom2Res

atom id to res id relation for proteins

Type

dict

pro_Res2Atom

res id to atom id relation for proteins

Type

dict

nucZero

res id of the zero point DNA bp of the nucleosome

Type

int

addExcludVolumeForce(kExcl=5856.0, rExclDna=2.07, rExclPro=26.0, forceName='Ex-vol')[source]

Add the connectivity term to the system. Overide the original method in WechromSystem

addNucleoCenterMemoryForce(centerBonds, centerDepth=0.4, centerWidth=3.0, forceName='cen_nuc')[source]

Add the nucleosome center associative memory term to the system.

addNucleoNeighborMemoryForce(neighborBonds, neighborDepth=0.2, neighborWidth=1.0, forceName='ngb_nuc')[source]

Add the nucleosome neighbor associative memory term to the system.

addDefaultForces()[source]

Add default forces designed for the wechrom system, including all DNA forces, updated excluded-volume forces and nucleosome associative memory forces

Module: wechrom.prepare_memory

wechrom.prepare_memory.generate_naked_memory_files(memory_dir='DEFAULT', memory_filename='naked.mem', memory_range=4)[source]

generate the file to store associative memory fragments

Parameters

  • memory_dir (str, optional) – Defaults to current workin directory.

  • memory_filename (str, optional) – Defaults to ‘naked.mem’.

  • memory_range (int, optional) – Defaults to 4.

wechrom.prepare_memory.generate_nucleo_memory_files(memory_dir='DEFAULT', memory_filename='nucleo.mem', database_location='data/memory_template/', neighbor_radius=100.0)[source]

generate the file to store associative memory fragments for nucleosomes

Parameters

  • memory_dir (str, optional) – Defaults to current workin directory.

  • memory_filename (str, optional) – Defaults to ‘nucleo.mem’.

  • database_location (str, optional) – Defaults to ‘data/memory_template/’.

  • neighbor_radius (float, optional) – the radius to select neighbor contacts. in Angstrom for MDAnalysis. Defaults to 100.0

wechrom.prepare_memory.get_naked_memory_template_bonds(memory_list_dir='DEFAULT', memory_list_filename='naked.mem', database_location='data/memory_template/')[source]

Extract the positions of template associative memory fragments

Parameters

  • memory_list_dir (str, optional) – directory of the memory list. Defaults to current workin directory.

  • memory_list_filename (str, optional) – filename of the memory list. Defaults to ‘naked.mem’.

  • database_location (str, optional) – location of the database. Defaults to ‘data/memory_template/’.

Returns

positions of templates

layer 1(10): template, keys 0-9 layer 2(2): dna type (strand), keys ‘I’, ‘J’ layer 3(np.array, memory_range x 3): positions of template residues in the range of memory_range

Return type

dict, 10 x 2 x memory_range x 3

wechrom.prepare_memory.get_nucleo_memory_template_bonds(memory_list_dir='DEFAULT', memory_list_filename='nucleo.mem', database_location='data/memory_template/')[source]

Extract the positions of template associative memory fragments

Parameters

  • memory_list_dir (str, optional) – directory of the memory list. Defaults to current workin directory.

  • memory_list_filename (str, optional) – filename of the memory list. Defaults to ‘nucleo.mem’.

  • database_location (str, optional) – location of the database. Defaults to ‘data/memory_template/’.

Returns

lengths of center templates bonds, 1st layer is type, 2nd layer is relative res_id dict, 2 x 2 x N1 x N2: lengths of neighbor templates bonds between the pair of (type, res_id) atoms

Return type

dict, 2 x N

wechrom.prepare_memory.read_memory_template(template_list_dir='DEFAULT', template_list_filename='data/naked_database_list')[source]

Read the list of associative memory template filenames

Parameters

  • template_list_dir (str, optional) – directory of the template list file. Defaults to ‘DEFAULT’.

  • template_list (str, optional) – name of the template list file. Defaults to ‘data/naked_database_list’.

Raises

Exception – custom template list is not supported right now

Returns

fist column ‘filename’ and second column ‘n_bp’

Return type

pandas.DataFrame

Module: wechrom.utils

wechrom.utils.coarse_grain_atompdb_2_wechromcif(pdb_filename, out_dir='/home/docs/checkouts/readthedocs.org/user_builds/wechrom/checkouts/latest/docs/source', out_file_prefix='coarse_grain', out_pdb=False)[source]

Coarse grain an atomistic DNA pdb file into a wechrom cif file. *YOU MAY NEED TO MODIFY THIS FUNCTION DEPENDING ON YOUR PDB FILE*

Parameters

  • pdb_filename (str or file) – pdb file

  • out_dir (str, optional) – output directory. Defaults to os.getcwd().

  • out_file_prefix (str, optional) – output file prefix. Defaults to ‘coarse_grain’.

  • out_pdb (bool, optional) – whether to generate a corase grained pdb file. Defaults to False.

wechrom.utils.num_inter_memory_bonds(n_bp, memory_range, n_template)[source]

Calculate the expected number of bonds for inter-strand associative memory force

Parameters

  • n_bp (int) – number of basepairs in the system

  • memory_range (int) – size of the memory

  • n_template (int) – number of templates used as memories

Returns

number of expected inter-strand bonds

Return type

int

wechrom.utils.num_intra_memory_bonds(n_bp, memory_range, n_template)[source]

Calculate the expected number of bonds for intra-strand associative memory force

Parameters

  • n_bp (int) – number of basepairs in the system

  • memory_range (int) – size of the memory

  • n_template (int) – number of templates used as memories

Returns

number of expected intra-strand bonds

Return type

int