Fix
incomparison of two residues, which now returns true if theresidueidentifier differs.
Generalize the type parameters of
MTRecordDenaturedModelso that its native and extended chains (and their SASAs) need not share the same concrete type, allowingMTRecordDenaturedModelto be built directly from aModel,Chain, or otherAbstractVector{<:Atom}subtype.
set_phi!andset_psi!to set backbone dihedral angles of a protein structure.extended_chainandextended_chain!to build the fully-extended (all-trans) conformation of a protein.*,+, and-to scale and combineTransferFreeEnergyobjects, used to simplify themvalue(::MTRecordDenaturedModel, ...)implementation.Implement
MTRecordtransfer model to compute m-values and transfer free energies, in urea or betaine.MTRecordmodel.
Import
saveandloadfrom MolSimToolkitShared.jl (v1.6) to share the name with ComplexMixtures.jl.
mvalue(::CreamerDenaturedModel)now returns a properMValueobject instead of a tuple of dicts.
saveandloadfunctions forMValue,TransferFreeEnergy, andSASAobjects.MValue,TransferFreeEnergy, andSASAtypes are now exported.
Accessibilitymodel.
mvalueortransfer_free_energy, do not run over all the residues of the object (structure of SASA), but only on the residues of the selection.
mvalues andtransfer_free_energys from precomputed SASA values. For that, dispatch on theCreamerUnitedAtomRadiitype the SASA calculation, for consistency. Otherwise, an error is thrown.unitcellkeyword argument intransfer_free_energyandmvaluefunctions, which will compute SASAs with periodic boundary conditions.
Faster
transfer_free_energyandmvaluecalculations with faster Creamer data fetching.
mvalueandtransfer_free_energyfunctions with sasa data, because the SASA method cannot be changed while preserving consistency among models.Accessibilitymodel.Accessibilityimplementation.
Accessibilitymodel to transfer free energy calculations.The
MoeserHorinekAppmodel was discontinued.urea-mhtoAutonBolenmodel solvent list.
MoeserHorinekAppmodel to use the Gly-activity freeMoeserHorinekmodel, with all cosolvents.MoeserHorinekFitmodel was discontinued, because it was not physically meaningful.
:cath_s20and:original(default - unchanged) options tocreamer_sasasandCreamerDenaturedModel, to use the parameterization of the denatured SASAs from the original or CATH S20 model sets.delta_sasaofCreamerDenaturedModelis computed upon construction, avoiding repeated evaluations if mvalues are computed for the same model in different cosolvents.
trehaloseandglycerolfor the computation of transfer free energies withAutonBolen.MoeserHorinekFitmodels.
MoeserHorinekFitmodel, after exhaustive fitting.
MoeserHorinekFitparameterizations, which introduce the Gly-activity correction to all models, by fitting the apparent TFEs to obtain the total predicted TFEs of Auton&Bolen.
read_pdbauto-detects if a file is ofmmCIF/PDBxformat and switches the parser. Therefore,read_pdbcan be used instead ofread_mmcifon all structures.
PDBTools.MacroKeyword,PDBTools.Keyword,PDBTools.macro_keywords, andPDBTools.keywordpublic, to allow the user to define custom macros for the selection syntax.
pdb_elementfield by theelementfunction.
AbstractStringinstead ofStringin several input signatures, notably for selections and file names.
CreamerDenaturedModelshow method.
CreamerDenaturedModeltype, andmvalue(::CreamerDenaturedModel)to compute m-values associated with denaturation directly.
isnucleoside,ispurine, andispyrimidinefunctions for atoms and residues, mirroring the existing protein-property predicates.add_nucleoside_residue!,remove_custom_nucleoside_residues!, andcustom_nucleoside_residues!(SIRAH)to support custom and force-field-specific nucleoside residues (SIRAH DNA: DAX, DGX, DTX, DCX).nucleoside,purine, andpyrimidineas selection string keywords.parse_queryreturns a function, no need forapply_queryanymore.
coortopositionsandposition(keepcooras a legacy alias for backwards compatibility).get_atomsis now imported fromMolSimToolkitShared.
stride_runsupports computing secondary structure of models with up to 94 chains, so many more CIF files will be properly handled. An error message is printed otherwise.
filter(f, ::HBonds)and slicingHBondsobjects withhbonds[1:5], or with index vectors.iterate,keys,eachindex) forHBondsdata structure, enablingforloops,collect,findfirst, etc.
scatterinsteadheatmapunder the hood to plot contact maps, to avoid memory issues. The API function continues to beheatmap.
paralleloption to contact and distance map calculations, set to false by default.
residue 1 to 5.
transfer_free_energyfunction to compute the TFE of a single structure to different solutions.cosolventfield, and shows the cosolvent.
ATOMstrings are found outside atom descriptors.
Structureobject, to contain atom arrays and meta-data.Atomobject equality is supported (all fields must be identical).
String15to store names, chains, etc, to support very large CIF files.
sasa_particles(SIRAH, args...; kargs...)computes SASAs with SIRAH parameters.
ContactMapobjects can be summed or subtracted, to obtain the effect of transformations on contact maps.
parallelkeyword argument tomvaluefunction to enable parallel computation of residue contributions.
mvalueis now case-insensitive.
MValuedata structure now contains a type parameter that indicates the model used, and aIntfield with the number of residues in the selection.
InlineStrings.String7forchaininAtomstruct to support longer chain IDs from mmCIF files.inimplementation for containment of atoms in residues, chains, models, segments.
stride_runanddssp_runfunctions to compute secondary structure from vectors of atoms.
mvaluefunction for computing m-values from protein structures.inis part of supported interface for iterators (e. g.atoms[1] in residues[1])
get_atomsgetter for fetching the vector of atoms of residues, models, chains, segments.hydrogen_bondsaccepts multiple pairs of selections, and is made stable.
hydrogen_bondsfunction to compute h-bonds in structures (with Hydrogen atoms added).
set_position!(::Atom, ::Union{Tuple,AbstractVector})to conveniently set coordinates from a vector or tuple of coordinates.sasa_particleswithunitcellkeyword argument.read_unitcell,lattice_to_matrix, andlattice_to_matrixfunctions to read and convert unitcells written in PDB or mmCIF files.
output_dotsoption tosasa_particlesto return the dots of the surface.atomic_sasatosasa_particles(keep alias for compatibility).AtomDotsof sasa calculation a contiguous memory block, to reduce GC pressure.n_dotsofatomic_sasacomputations to 512 instead of 500 such that it is a multiple of 16, the defaultN_SIMD.
n_dotsthe dots in the sphere. Use defaultn_dots=500.
sasa.
atomic_sasaandsasafunctions to compute solvent accessible surface area.vdw_radiusas element property, andelement_vdw_radiusfunction to fetch them.InlineStrings.String3.Float32values instead ofFloat64.
Plots.scatter(::Ramachandran)to plot Ramachandran objects.Ramachandranmethod and struct, to compute Ramachandran plots.dihedralmethod to compute directly dihedral given four Atom objects.
zetaandzeta_checkfunctions to check for Calpha chirality of protein residues.
select(atoms,"x > 0"))
or, as inresname ARG CYS ALA.
write_mmcifandwrite_pdbsupport a third positional argument,StringorFunction, to write a selection of the atoms.select_with_vmdreturns a vector ofAtoms if the input was a vector ofAtoms.select_with_vmdreturns a vector ofAtoms if the input was a vector ofAtoms.In all functions that accepted the
onlykeyword parameter to define selections with a Julia function, the keyword parameter was dropped and now the function can be provided as a positional second argument, or third argument forwrite_pdbandwrite_mmciffunctions.get_seqfunctions do not support anymore the input of the file name. An array ofAtoms must be provided. This is because internally it would be required to recognize PDB of mmCIF functions.
