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centralSpinSystem.m
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centralSpinSystem.m
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% Load pdb file into structure
%
% Nuclei = parseNuclei(System,Method,datafile)
%
% Input:
% System structure with fields for the spin system
% Method structure with fields for the method
% pdbFileName name of PDB file
function [Nuclei, System]= centralSpinSystem(System,Method,Data,pdb_)
System = setCentralSpinSystemDefaults(System,Method);
ienum = 1;
PARTICLE_CENTRALSPIN = ienum; ienum = ienum + 1;
PARTICLE_ELECTRON = ienum; ienum = ienum + 1;
PARTICLE_HYDROGEN = ienum; ienum = ienum + 1;
PARTICLE_PROTIUM = ienum; ienum = ienum + 1;
PARTICLE_1H_EXCHANGEABLE = ienum; ienum = ienum + 1;
PARTICLE_1H_NONEXCHANGEABLE = ienum; ienum = ienum + 1;
PARTICLE_1H_METHYL = ienum; ienum = ienum + 1;
PARTICLE_DEUTERIUM = ienum; ienum = ienum + 1;
PARTICLE_2H_EXCHANGEABLE = ienum; ienum = ienum + 1;
PARTICLE_2H_NONEXCHANGEABLE = ienum; ienum = ienum + 1;
PARTICLE_2H_METHYL = ienum; ienum = ienum + 1;
PARTICLE_CARBON = ienum; ienum = ienum + 1;
PARTICLE_12C = ienum; ienum = ienum + 1;
PARTICLE_13C = ienum; ienum = ienum + 1;
PARTICLE_C_METHYL = ienum; ienum = ienum + 1;
PARTICLE_13C_METHYL = ienum; ienum = ienum + 1;
PARTICLE_NITROGEN = ienum; ienum = ienum + 1;
PARTICLE_14N = ienum; ienum = ienum + 1;
PARTICLE_15N = ienum; ienum = ienum + 1;
PARTICLE_OXYGEN = ienum; ienum = ienum + 1;
PARTICLE_16O = ienum; ienum = ienum + 1;
PARTICLE_17O = ienum; ienum = ienum + 1;
PARTICLE_SILICON = ienum; ienum = ienum + 1;
PARTICLE_28SI = ienum; ienum = ienum + 1;
PARTICLE_29SI = ienum; ienum = ienum + 1;
PARTICLE_UNSET = ienum; ienum = ienum + 1;
PARTICLE_NONE = ienum; ienum = ienum + 1;
PARTICLE_VOID = ienum; ienum = ienum + 1;
PARTICLE_ALL = ienum; ienum = ienum + 1;
PARTICLE_ENUM = ienum; ienum = ienum + 1;
if(PARTICLE_ENUM+1-ienum ~= 0)
error(['Error in centralSpinSystem(): ', 'enums are incorrect.']);
end
associatedParticleMatrix_ = sparse(0,0); % indexed by CluE indices.
associatedPDBMatrix_ = sparse(pdb_.number,pdb_.number); % indexed by pdb ID.
cellShifts_ = [];
% methylIDs_ = [];
moleculeID_ = [];
number_ = 0;
% numberMethyls_ = 0;
numberParticleClasses_ = 0;
particleClassID_ = [];
particles_ = cell(0,0);
%pdb_ = parsePDBfile(Data.InputData, System.angstrom);
originVec_ = getElectronCoordinates(...
System,[pdb_.x,pdb_.y,pdb_.z],pdb_.serial);
pdbID_ = [];
residueList_ = cell(0,0);
uniqueResidueList_ = {};
zeroIndex_ = {};
r0_ = System.load_radius;
r0_nonHalf_ = Method.vertexCutoff.radius_nonSpinHalf(1);
verbose_ = Method.verbose;
buildSystem();
% Finish setup.
coordinates_ = [];
refreshSystem();
% Print total number of particles.
fprintf('\nFound %d particles.\n', number_);
% Loop through all initialized ParticleClasses and print details.
for iitype = 1:numberParticleClasses_
printParticleInfo( particles_{iitype} );
end
Nuclei = struct();
assembleNuclei();
return;
% Start of nested functions
%<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
function uniqueID = addParticle(particleEnum, resName, ...
associatedParticles, iparticle, ucpdb)
% Initialize return value.
uniqueID = -1;
% Get PDB number.
ipdb = mod(ucpdb, pdb_.number);
if ipdb==0, ipdb = pdb_.number; end
uc = ceil(ucpdb/pdb_.number);
% Check if particle type with resName has been initialized.
isUnique = true;
for itype=1:numberParticleClasses_
if (particleEnum==particles_{itype}.particleEnum) && ...
strcmp( resName, particles_{itype}.resName)
isUnique = false;
end
if ~isUnique
uniqueID = particles_{itype}.ID;
% Record which particle class this particle is in;
particleClassID_(iparticle) = itype;
break;
end
end
% Initialize if it does not already exist.
if isUnique && isParticleValid(particleEnum, pdb_.resName{ipdb})
addParticle_new(particleEnum, resName);
% Create new particle type.
uniqueID = particles_{numberParticleClasses_}.ID;
% Record which particle class this particle is in;
particleClassID_(iparticle) = particles_{numberParticleClasses_}.ID;
end
% Check if the particle is already a member of this particle class.
if any(pdbID_(particles_{uniqueID}.members)==ucpdb)
return;
end
% Add parttcle to member set.
particles_{uniqueID}.members = unique(...
[particles_{uniqueID}.members,iparticle]);
particles_{uniqueID}.number = length(particles_{uniqueID}.members);
% TO DO: REPLACE associatedParticlesCollection WITH associatedPDBMatrix.
particles_{uniqueID}.associatedParticlesCollection{...
particles_{uniqueID}.number} = associatedParticles;
if uc==1
for iAsso = 1:numel(associatedParticles)
iaParticle = associatedParticles(iAsso);
associatedPDBMatrix_(iaParticle,ipdb) = iaParticle;
end
end
% Record molecule ID number.
moleculeID_(iparticle) = pdb_.resSeq(ipdb) + (uc-1)*pdb_.number;
% Record PDB number.
if numel(pdbID_) >= iparticle && pdbID_(iparticle) ~= ucpdb
error(['Error in addParticle(): ',...
'particle ', num2str(iparticle), 'is already asigned pdb ID ',...
num2str(pdbID_(iparticle)), ' and cannot be re-asigned pdb ID ', ...
num2str(ucpdb), '.']);
end
pdbID_(iparticle) = ucpdb;
if iparticle == number_+1
% Count this particle.
number_ = number_ + 1;
elseif iparticle > number_ + 1
error('Error in addParticle(): particle count is incorrect.');
end
% Update residue list.
residueList_{iparticle} = resName;
if ~particles_{uniqueID}.exchangeable && ~any(moleculeID_(iparticle)...
==moleculeID_(particles_{uniqueID}.membersOnePerMolecule))
particles_{uniqueID}.membersOnePerMolecule = ...
[particles_{uniqueID}.membersOnePerMolecule,iparticle];
particles_{uniqueID}.numberMolecules = particles_{uniqueID}.numberMolecules+1;
end
end
%>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
%<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
function addParticle_new(particleEnum, resName)
% Update particle type number.
numberParticleClasses_ = numberParticleClasses_ + 1;
% Set identification values.
particles_{numberParticleClasses_}.particleName = ...
getParticleString(particleEnum);
particles_{numberParticleClasses_}.resName = resName;
particles_{numberParticleClasses_}.particleEnum = particleEnum;
particles_{numberParticleClasses_}.ID = numberParticleClasses_;
% Initialize other values.
particles_{numberParticleClasses_}.members = [];
particles_{numberParticleClasses_}.membersOnePerMolecule = [];
particles_{numberParticleClasses_}.number = 0;
particles_{numberParticleClasses_}.numberMolecules = 0;
% Initialize option values.
particles_{numberParticleClasses_}.abundance = 1;
particles_{numberParticleClasses_}.active = true;
particles_{numberParticleClasses_}.atomType = PARTICLE_UNSET;
particles_{numberParticleClasses_}.associatedParticlesCollection = {};
particles_{numberParticleClasses_}.barrierPotential = 0;
particles_{numberParticleClasses_}.doRandomIsotopes = [];
particles_{numberParticleClasses_}.exchangeable = true;
particles_{numberParticleClasses_}.gFactor = 0;
particles_{numberParticleClasses_}.hf_Tzz = 0;
particles_{numberParticleClasses_}.hf_FermiContact = 0;
particles_{numberParticleClasses_}.hf_x = {};
particles_{numberParticleClasses_}.hf_y = {};
particles_{numberParticleClasses_}.hf_z = {};
particles_{numberParticleClasses_}.isNucleus = false;
particles_{numberParticleClasses_}.NQ_e2qQh = 0;
particles_{numberParticleClasses_}.NQ_eta = 0;
particles_{numberParticleClasses_}.NQ_x = {};
particles_{numberParticleClasses_}.NQ_y = {};
particles_{numberParticleClasses_}.NQ_z = {};
particles_{numberParticleClasses_}.spinMultiplicity = 1;
particles_{numberParticleClasses_}.switchParticle = PARTICLE_UNSET;
particles_{numberParticleClasses_}.extraCellSwitchParticle = PARTICLE_UNSET;
particles_{numberParticleClasses_}.tunnelSplitting = 0;
% Set default options.
setParticle(numberParticleClasses_, particleEnum,resName);
% Set user specified options.
setParticleOptions(numberParticleClasses_, System.particleOptions);
particleClassIndex = findParticleClasses(...
particles_{numberParticleClasses_}.switchParticle, resName);
if numel(particleClassIndex)==1 ...
&& particles_{particleClassIndex}.doRandomIsotopes
particles_{numberParticleClasses_}.abundance = ...
1 - particles_{particleClassIndex}.abundance;
elseif numel(particleClassIndex) > 1
error(['Error in addParticle_new():',...
' multiple switch particles found.']);
end
if isempty(particles_{numberParticleClasses_}.doRandomIsotopes)
particles_{numberParticleClasses_}.doRandomIsotopes = ...
(particles_{numberParticleClasses_}.abundance<1) && ...
particles_{numberParticleClasses_}.switchParticle ~= PARTICLE_UNSET;
end
return;
end
%>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
%<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
function preliminaryParticle = analyzeParticle(index_pdb)
pdbParticle = getParticleClass(pdb_.element{index_pdb});
preliminaryParticle.particleEnum = PARTICLE_NONE;
preliminaryParticle.associatedParticles = [];
switch pdbParticle
% Hydrogen
case {PARTICLE_HYDROGEN, PARTICLE_PROTIUM, PARTICLE_DEUTERIUM}
if ~System.include_hydrogen
return;
end
% Assume protium unless specified otherwise.
isH1 = pdbParticle ~= PARTICLE_DEUTERIUM;
if (isH1 && ~System.include_1H) || (~isH1 && ~System.include_2H)
return;
end
isExchangeable = isHydronExchangeable(index_pdb);
% Set hydron type.
if isH1 && isExchangeable
preliminaryParticle.particleEnum = PARTICLE_1H_EXCHANGEABLE;
elseif ~isH1 && isExchangeable
preliminaryParticle.particleEnum = PARTICLE_2H_EXCHANGEABLE;
elseif isH1 && ~isExchangeable
preliminaryParticle.particleEnum = PARTICLE_1H_NONEXCHANGEABLE;
else
preliminaryParticle.particleEnum = PARTICLE_2H_NONEXCHANGEABLE;
end
% Carbon
case PARTICLE_CARBON
if System.Methyl.include
% Check if carbon is a methyl carbon.
methylHydrons = isMethyl(index_pdb);
% All indices will be unique if it is a methyl.
if ~(methylHydrons(1)==methylHydrons(2) ...
|| methylHydrons(1) == methylHydrons(3) ...
|| methylHydrons(2) == methylHydrons(3))
preliminaryParticle.particleEnum = PARTICLE_C_METHYL;
preliminaryParticle.associatedParticles = methylHydrons;
% numberMethyls_ = numberMethyls_ + 1;
% methylIDs_(numberMethyls_) = index_pdb;
end
elseif System.include_13C
preliminaryParticle.particleEnum = PARTICLE_12C;
end
% Nitrogen
case PARTICLE_NITROGEN
if System.include_14N
preliminaryParticle.particleEnum = PARTICLE_14N;
elseif System.include_15N
preliminaryParticle.particleEnum = PARTICLE_15N;
end
% Silicon
case PARTICLE_SILICON
if System.include_29Si
preliminaryParticle.particleEnum = PARTICLE_29SI;
end
% Electron
case PARTICLE_ELECTRON
if System.include_electron
preliminaryParticle.particleEnum = PARTICLE_ELECTRON;
end
otherwise
preliminaryParticle.particleEnum = PARTICLE_NONE;
end
return;
end
%>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
%<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
% TO DO: THIS FUNCTION IS TEMPORARY. CluE SHOULD BE RECONFIGURED TO WORK WITH
% THE DATA STRUCTURE OF centralSpinSystem(), WITHOUT A CONVERSION STEP.
function assembleNuclei()
% Initialize
Nuclei.Index = 1:(number_-1); % set here.
Nuclei.Type = cell(1,number_-1);
Nuclei.Element = cell(number_-1,1);
% Nuclei.Connected = cell(number_,1); % not needed.
Nuclei.Spin = zeros(1,number_-1);
Nuclei.StateMultiplicity = zeros(1,number_-1);
Nuclei.Nuclear_g = zeros(1,number_-1);
Nuclei.Coordinates = coordinates_(:,2:number_)'; % set here.
Nuclei.PDBCoordinates = zeros(number_ - 1,3);
Nuclei.pdbID = zeros(1,number_-1);
Nuclei.ucpdbID = zeros(1,number_-1);
Nuclei.MoleculeID = moleculeID_; % set here.
Nuclei.methylTunnelingSplitting = sparse(number_-1,number_-1);
Nuclei.Exchangeable = zeros(1,number_-1);
Nuclei.NumberStates = int8(zeros(1,number_-1));
Nuclei.MethylID = zeros(1,number_-1);
methylCounter = 0;
% Nuclei.valid = true(1,number_-1); % not needed.
% Nuclei.isWater = true(1,number_-1); % not needed.
Nuclei.isSolvent = true(1,number_-1);
Nuclei.valid = true(1,number_-1);
% Nuclei.hyperfine2lab = sparse(3*3,num_);
Nuclei.Atensor = sparse(number_-1,9);
Nuclei.FermiContact = sparse(number_-1,1);
Nuclei.hf_Tzz = sparse(number_-1,1);
Nuclei.associatedParticleMatrix = associatedParticleMatrix_;
Nuclei.associatedParticleMatrix(...
find(nonzeros(Nuclei.associatedParticleMatrix)));
Nuclei.number_1H_exchangeable = ...
findParticles(PARTICLE_1H_EXCHANGEABLE, 'ALL', true);
Nuclei.number_1H_nonExchangeable = ...
findParticles(PARTICLE_1H_NONEXCHANGEABLE, 'ALL', true)...
+ findParticles(PARTICLE_1H_METHYL, 'ALL', true);
Nuclei.number_2H_exchangeable = ...
findParticles(PARTICLE_2H_EXCHANGEABLE, 'ALL', true);
Nuclei.number_2H_nonExchangeable = ...
findParticles(PARTICLE_2H_NONEXCHANGEABLE, 'ALL', true)...
+ findParticles(PARTICLE_2H_METHYL, 'ALL', true);
if ~System.limitToSpinHalf
Nuclei.Qtensor = zeros(3,3,number_-1);
end
for iparticle = 2:number_
iNuc = iparticle - 1;
itype = particleClassID_(iparticle);
particleEnum = particles_{itype}.particleEnum;
ipdb = mod(pdbID_(iparticle),pdb_.number);
if ipdb==0, ipdb = pdb_.number; end
uc = ceil(pdbID_(iparticle)/pdb_.number);
Nuclei.Type{iNuc} = getParticleTypeString(particleEnum);
Nuclei.Element{iNuc} = pdb_.element{ipdb};
Nuclei.PDBCoordinates(iNuc,:) = [pdb_.x(ipdb),pdb_.y(ipdb),pdb_.z(ipdb)]...
+ cellShifts_(:,uc)';
Nuclei.pdbID(iNuc) = pdbID_(iparticle);
Nuclei.Spin(iNuc) = (particles_{itype}.spinMultiplicity - 1)/2;
Nuclei.StateMultiplicity(iNuc) = particles_{itype}.spinMultiplicity;
Nuclei.Nuclear_g(iNuc) = particles_{itype}.gFactor;
Nuclei.Exchangeable(iNuc) = particles_{itype}.exchangeable;
Nuclei.NumberStates(iNuc) = int8(particles_{itype}.spinMultiplicity);
Nuclei.isSolvent(iNuc) = isMoleculeSolvent(particles_{itype}.resName);
if Nuclei.valid(iNuc)
Nuclei.valid(iNuc) = particles_{itype}.active;
end
if particles_{itype}.NQ_e2qQh ~= 0
idx = particles_{itype}.members==iparticle;
Nuclei.Qtensor(:,:,iNuc) = particles_{itype}.Qtensor{idx};
end
if particles_{itype}.hf_Tzz ~= 0 || particles_{itype}.hf_FermiContact ~= 0
idx = particles_{itype}.members==iparticle;
Nuclei.Atensor(iNuc,:) = particles_{itype}.Atensor{idx}(:);
end
if particleEnum == PARTICLE_C_METHYL
methylCounter = methylCounter + 1;
% hydrons = getAssociatedParticles(itype,iparticle);
associatedWithMethyl = nonzeros(associatedParticleMatrix_(:,iparticle));
if System.Methyl.method==1
Nuclei.valid(associatedWithMethyl-1) = false;
end
hydrons = zeros(3,1);
hydronCounter = 0;
for iasso =associatedWithMethyl'
if particles_{particleClassID_(iasso)}.particleEnum ~=PARTICLE_1H_METHYL...
&& particles_{particleClassID_(iasso)}.particleEnum ~=PARTICLE_2H_METHYL
continue;
end
hydronCounter = hydronCounter + 1;
hydrons(hydronCounter) = iasso - 1;
end
if hydronCounter ~= 3
error(['Error in assembleNuclei(): ', ...
'methyl group has', num2str(hydronCounter), ' protons.']);
end
% hydrons = nonzeros(associatedParticleMatrix_(:,iparticle)) - 1;
nuT = particles_{itype}.tunnelSplitting;
for ih = 1:2
iH = hydrons(ih);
for jh = ih+1:3
jH = hydrons(jh);
Nuclei.methylTunnelingSplitting(iH,jH) = nuT;
Nuclei.methylTunnelingSplitting(jH,iH) = nuT;
end
end
Nuclei.MethylID(iNuc) = -methylCounter;
for ih = 1:3
iH = hydrons(ih);
Nuclei.MethylID(iH) = methylCounter;
end
% error(['Error in assembleNuclei(): ', ...
% 'Nuclei.MethylID not set. Please update source code.'])
end
end
defineSpinOperators();
Nuclei.nStates = System.nStates;
Nuclei.number = 0;
% Define spin operators.
%Nuclei =
%Nuclei,System, Method);
% Copy graphCriterion to Nuclei.
Nuclei.graphCriterion = Method.graphCriterion;
% Set electron coordinates in the pdb frame.
Nuclei.Electron_pdbCoordinates = originVec_';
if System.Methyl.include %&& System.Methyl.method ~= 2
Nuclei.Methyl_Data.number_methyls = methylCounter;
% error('Error in centralSpinSystem(): methyl code not yet implemented.');
else
Nuclei.Methyl_Data = [];
end
% Decide whether or not to add randomly distributed hard spheres.
if System.RandomEnsemble.include
error('Error in centralSpinSystem(): addRandomSpins() not yet implemented.');
end
% get number of nuclei
Nuclei.number = number_-1;
% Rotate coordinates if requested by user via System.X/Y/Z
% [Nuclei,System] =
setOrientation(); %Nuclei,System, pdbCoordinates);
% Clear excess entries.
% Nuclei =
% cleanUpNuclei(); %Nuclei,System,Method,Npdb);
% Get coupling statistics.
% Nuclei =
computeNuclearInteractions(); %Nuclei,System, Method,scaleFactor);
if Data.writeSpinPDB
% try
outPDBfile = Data.OutputData;
if numel(outPDBfile)>3 && strcmp(outPDBfile(end-3:end),'.mat')
outPDBfile = outPDBfile(1:end-4);
end
outPDBfile = [outPDBfile,'_spinSystem.pdb'];
writeSpinPDB(Nuclei,ones(1,Nuclei.number),...
outPDBfile,Data.outPDBoptions);
% catch
% warning('Warning: could not write spin pdb.')
% end
end
% Clean
% Nuclei.State = [];
if ~Method.getNuclearStatistics
Statistics = struct();
Statistics.Nuclear_Dipole = Nuclei.Statistics.Nuclear_Dipole;
Statistics.Nuclear_Dipole_x_iy_Z = Nuclei.Statistics.Nuclear_Dipole_x_iy_Z;
if strcmp(Method.method,'rCCE') ||strcmp(Method.method,'rCE')
Statistics.Modulation_Depth_methyl = Nuclei.Statistics.Modulation_Depth_methyl;
Statistics.Frequency_Pair_methyl = Nuclei.Statistics.Frequency_Pair_methyl;
end
Nuclei.Statistics = Statistics;
Nuclei.DistanceMatrix = [];
end
if ~Method.getNuclearContributions
Nuclei.PDBCoordinates = [];
Nuclei.Element = [];
end
% if System.newIsotopologuePerOrientation
Nuclei.MoleculeIDunique = unique(Nuclei.MoleculeID);
% else
% Nuclei.MoleculeID = [];
% Nuclei.Connected = [];
% Nuclei.isWater = [];
% end
checkNuclei();
return;
end
%>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
%<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
function buildAssociatedParticleMatrix()
% Resize matrix.
associatedParticleMatrix_(number_,number_) = 0;
% Loop through all particles in system.
for iParticle = 1:number_
% Get pdb information.
ucpdb = pdbID_(iParticle);
uc = ceil(ucpdb/pdb_.number);
ipdb = mod(ucpdb,pdb_.number);
if ipdb==0, ipdb = pdb_.number; end
% Get non-zero column elements, the particles associated with ipdb.
associatedPDBcol = nonzeros(associatedPDBMatrix_(:,ipdb));
for iAsso = 1:numel(associatedPDBcol)
% Find associated particles if they exist.
assoiParticle = find(pdbID_ == ...
(associatedPDBcol(iAsso) + (uc-1)*pdb_.number));
% Add missing associated particles.
if isempty(assoiParticle)
itype = particleClassID_(iParticle);
assoiParticle = number_;
associatedPart = analyzeParticle(associatedPDBcol(iAsso));
addParticle(associatedPart.particleEnum, particles_{itype}.resName, ...
[], number_+1, (uc-1)*pdb_.number + associatedPDBcol(iAsso));
if assoiParticle==number_
error(['Error in buildAssociatedParticlematrix(): ', ...
'particle could not be added.']);
else
assoiParticle = number_;
end
elseif numel(assoiParticle)>1
error(['Error in buildAssociatedParticlematrix(): ', ...
'particle has been added multiple times.']);
end
associatedParticleMatrix_(assoiParticle,iParticle) = assoiParticle;
end
end
end
%>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
%<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
function buildExtraCells()
cellShifts_ = getCellShifts()';
generateUniqueResidueList();
% Print matrix.
if verbose_
disp("cells shifts (meter) = ");
disp(cellShifts_);
end
% Copy pdbID before erasing.
pdbID = pdbID_;
% Remove all particles but leave settings.
clearBath();
numUnitCells = size( cellShifts_,2);
if numUnitCells == 0
return;
end
for itype = 1:numberParticleClasses_
% Get particle label.
particleEnum = particles_{itype}.particleEnum;
if particleEnum==PARTICLE_CENTRALSPIN
continue;
end
% Get number of particles in one cell.
if particles_{itype}.exchangeable
% Copy particle indices.
indices = particles_{itype}.members;
N = particles_{itype}.number;
else
% Copy particle indices.
indices = particles_{itype}.membersOnePerMolecule;
N = particles_{itype}.numberMolecules;
end
ucN = numUnitCells*N ;
clearMembers(itype);
useRandomParticles = false;
if particles_{itype}.switchParticle == PARTICLE_VOID ...
&& particles_{itype}.abundance < 1
useRandomParticles = true;
% Get total number of particles in all unit cells.
ucNtotal = numUnitCells*N;
% Get number to use.
pd = makedist('Binomial','N',ucNtotal,'p',particles_{itype}.abundance);
ucN = random(pd);
% Draw a random set of indices.
selectedIndices = randperm(ucNtotal,ucN);
elseif particles_{itype}.extraCellSwitchParticle == PARTICLE_VOID ...
&& particles_{itype}.abundance < 1
useRandomParticles = true;
% Get total number of particles in all unit cells outside the primary cell.
ucNtotal = (numUnitCells-1)*N;
% Get number to use.
pd = makedist('Binomial','N',ucNtotal,'p',particles_{itype}.abundance);
ucN = random(pd);
% Use all indices from the primary cell
% and draw a random set of indices for the extra cells.
selectedIndices =[1:N, N + randperm(ucNtotal,ucN)];
ucN = ucN + N;
end
% Loop through particles.
for ii=1:ucN
particleIndex = ii;
if useRandomParticles
particleIndex = selectedIndices(ii);
end
% Get unit cell. Note that N = particles_{itype}.number. The devision by
% N rather than pdb_.number is because particleIndex runs over particles
% of particles_{itype}.
uc = ceil( particleIndex/ N );
% Define index to store unit cell and ipdb info together.
ucIndexOffset = (uc - 1)*pdb_.number;
% Get index of particle copy in the primary cell.
particleIndex = mod( particleIndex, N);
if particleIndex==0, particleIndex = N; end
baseIndex = indices( particleIndex );
% Get PDB number.
ipdb = pdbID( baseIndex );
if particles_{itype}.exchangeable
sameMoleculeList = pdbID(baseIndex);
else
sameMoleculeList = pdb_.serial( pdb_.resSeq==pdb_.resSeq(ipdb) );
end
% Add particle copy of particle in this unit cell.
resName = particles_{itype}.resName;
for jpdb=sameMoleculeList'
if ~strcmp(pdb_.resName(jpdb),resName)
continue;
end
if ~isParticleWithinSystem(r0_, jpdb, cellShifts_(:,uc),true), continue; end
% Get particleEnum and associatedParticles.
preliminaryParticle = analyzeParticle(jpdb);
if preliminaryParticle.particleEnum ~= particleEnum, continue; end
% Define index to store unit cell and ipdb info together.
ucpdb = jpdb + ucIndexOffset;
% Add unit cell offset to associatedParticles.
associatedParticles = preliminaryParticle.associatedParticles ...
+ ucIndexOffset;
% Since methyl carbons add their hydrons, some particle may already be
% added.
alreadyAdded = find(pdbID_==ucpdb);
if ~isempty(alreadyAdded)
if numel(alreadyAdded) > 1
error(['Error in buidExtraCellss(): ', ...
'pdb ID ',num2str(ucpbd),' added multiple times.']);
end
alreadyAddedID = particleClassID_(alreadyAdded);
if particles_{alreadyAddedID}.particleEnum ...
~= preliminaryParticle.particleEnum
error(['Error in buildExtraCells: ',...
'cannot overwrite particle index ', num2str(alreadyAdded), ...
', ', getParticleString(particles_{alreadyAddedID}.particleEnum),...
' with ',getParticleString(preliminaryParticle.particleEnum), '.']);
end
continue;
end
addParticle(particleEnum,resName, associatedParticles, number_+1, ucpdb);
end
end
end
end
%>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
%<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
function buildPrimaryCell()
% numberMethyls_ = 0;
% Loop through all nuclei.
for ipdb = 1:pdb_.number
% Ignore particles outside the system radius.
if ~isParticleWithinSystem(r0_, ipdb, 0, false), continue; end
preliminaryParticle = analyzeParticle(ipdb);
if preliminaryParticle.particleEnum ~= PARTICLE_NONE
% Add particle.
resName = pdb_.resName{ipdb};
addParticle(preliminaryParticle.particleEnum,resName,...
preliminaryParticle.associatedParticles, number_+1, ipdb);
end
end
return;
end
%>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
%<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
function buildSystem()
% Initialize the observed spin.
addParticle_new(PARTICLE_CENTRALSPIN, 'detect');
particles_{numberParticleClasses_}.members = 0;
particles_{numberParticleClasses_}.number = 1;
residueList_{numberParticleClasses_} = 'detect';
particleClassID_(numberParticleClasses_) = numberParticleClasses_;
moleculeID_(numberParticleClasses_) = 0;
number_ = number_ + 1;
zeroIndex_ = number_;
generateUniqueResidueList();
buildPrimaryCell();
buildExtraCells();
buildAssociatedParticleMatrix()
% Adjust indices for dropped particles.
%adjustAssociatedParticles();
% Set methyls.
setMethyls();
return;
end
%>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
%<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
function changeIsotope(iParticle)
% Get ParticleClass index number.
type_idx = particleClassID_(iParticle);
% Get the new particle type.
newParticle = particles_{type_idx}.switchParticle;
% Get the unit cell pdb number.
ucpdb = pdbID_(iParticle);
% Get unit cell index.
uc = ceil(ucpdb/pdb_.number);
% Check if the particle is outside the primary cell and has a different
% switch particle defined for the extra cell.
% Note, void particle should have accounted for already.
if uc > 1 ...
&& isParticleValid(particles_{type_idx}.extraCellSwitchParticle, ...
particles_{type_idx}.resName) ...
&& particles_{type_idx}.extraCellSwitchParticle ~= PARTICLE_VOID
newParticle = particles_{type_idx}.extraCellSwitchParticle;
end
% Get the indices for any associated particles.
associatedParticles = ...
particles_{type_idx}.associatedParticlesCollection{...
particles_{type_idx}.members==iParticle};
% Remove particle from current ParticleClass.
if ~removeMember(type_idx, iParticle)
error(['Error in changeIsotope(): could not remove particle ', ...
num2str(ucpdb), ' from particle class ', ...
getParticleString(particles_{type_idx}.particleEnum), ' ', ...
particles_{type_idx}.resName, '.']);
end
resName = particles_{type_idx}.resName;
addParticle(newParticle, resName, associatedParticles , iParticle, ucpdb);
return;
end
%>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
%<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
function allPass = checkNuclei()
METHYLID = 1;
pass(METHYLID) = true;
if System.Methyl.include
for ii=1:Nuclei.number
if Nuclei.MethylID(ii) > 0
pass(METHYLID) = pass(METHYLID)*( ...
sum(Nuclei.MethylID==Nuclei.MethylID(ii)) ==3);
elseif Nuclei.MethylID(ii) < 0
pass(METHYLID) = pass(METHYLID)*( ...
sum(Nuclei.MethylID==Nuclei.MethylID(ii)) ==1);
end
if ~pass(METHYLID)
error(['Error in checkNuclei(): ', 'methylID is not correctly set up.']);
end
end
end
allPass = all(pass(METHYLID));
end
%>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
%<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
% This function checks the system for errors. More checks should be added as
% as bugs are are found and/or the code grows.
function checkSystem()
n = 0;
nCmethyl = 0;
nHmethyl = 0;
nDmethyl = 0;
allMembers = zeros(number_,1) - 1;
% Check that the number of particles matches the count from all particle
% classes.
for itype=1:numberParticleClasses_
n0 = particles_{itype}.number;
n1 = length(particles_{itype}.members);
if n0 ~= n1
error([ ...
'Error in checkSystem(): ', 'particle class ', ...