StructureBasic

ccpnmr.analysis.core.StructureBasic.alignCoordinates(coords1, coords0, allCoords, W)
Align on two sets of coordinates (may be sub sets of whole)
and then update all coordinates given this new position. Coordinates are weighted for alignment.
Input
List of List of Floats (x,y,z), List of List of Floats (reference x,y,z),
List of List of Floats (x,y,z), List of Floats (weights)
Output
List of List of Floats (aligned x,y,z),
List of List of Floats (all updated x,y,z), Float (fitting score)
ccpnmr.analysis.core.StructureBasic.alignStructures(structures)
Align structures by minimising weighted atomic RMSD.
All members of any entered ensembles are aligned.
Input

List of MolStructure.StructureEnsembles

Output
List of MolStructure.StructureEnsembles, Float (Fit error),
Float (overall RMSD), List of Floats (Atom RMSDs)
ccpnmr.analysis.core.StructureBasic.centerCoordinates(coords)

More the centre of mass of input coordinates to the origin. .. describe:: Input

List of List of Floats (x,z,y coords)

Output

List of List of Floats (x,z,y coords)

ccpnmr.analysis.core.StructureBasic.centerStructures(structures)

Move the input structures’ centre of mass to the origin. .. describe:: Input

List of MolStructure.StructureEnsembles

Output

None

ccpnmr.analysis.core.StructureBasic.compareEnsembles(structure1, structure2, compareBackboneOnly=False)
Compare models in two ensembles by minimising weighted atomic RMSD.
The alignment is only done in the C world, not in the Python world. If compareBackboneOnly then only backbone atoms are used.
Input

MolStructure.StructureEnsemble, MolStructure.StructureEnsemble, Boolean

Output

Float (overall RMSD), Dict: MolSystem.Residue –> RMSD

ccpnmr.analysis.core.StructureBasic.findMatchingMolSystemAtom(atomName, residue, namingSystem, excludeAtoms)

Find the best matching CCPN atom name in a residue for the input atom name in the input naming system Will try other naming systems if the input one doesn’t work

Input

Word (imported atom name), MolSystem.Residue, Word (ChemComp.NamingSystem.name), List of MolSystem.Atoms

Output

Word (MolSystem.Atom.name)

ccpnmr.analysis.core.StructureBasic.getAtomSetCoords(atomSet, structure, model=None)

Find the coordinates corresponsing to an NMR atom set in a given model of a given structure structure. The model defaults to an arbitrary one if none is specified.

Input

Nmr.AtomSet, MolStructure.StructureEnsemble, MolStructure.Model

Output

List of List of Floats (x,y,z for each atom)

ccpnmr.analysis.core.StructureBasic.getAtomSetsDihedral(atomSets, structure, model=None, inDegrees=True)
Measure the dihedral angle in a structure between four groups
of atoms (lists of atom sets). Input atom sets are a list of lists to allow for ambigous assignments (e.g. Ser Hb*) here the mean position is used. If mo nodel is specified the values are averates over the whole ensemble. Option to specify degrees or radians.
Input
4 List of List of Nmr.AtomSets or 4 List of Nmr.AtomSets,
MolStructure.StructureEnsemble, Int, Boolean
Output

Float

ccpnmr.analysis.core.StructureBasic.getAtomSetsDistance(atomSets1, atomSets2, structure, model=None, method='noe')

Find the distance between two atom sets in a specified structure or ensemble of structures. Distances for multi atom atom sets are calculated using the NOE sum method by default. A model may be specified if the structure ensemble has many models, otherwise all models in the ensemble will be considered and an avergate distance is returned. The method can be either “noe” for NOE sum, “min” for minimum distance or “max” for maximum distance.

Input

Nmr.AtomSet, Nmr.AtomSet, MolStructure.StructureEnsemble, MolStructure.Model or None, Word

Output

Float (distance)

ccpnmr.analysis.core.StructureBasic.getBestChemComp(project, resName, atomNames, molType=None)
Find the best matching ccpCode (often 3 letters) for the input
residue name that has the input atomNames
Input
Implementation.Project, Word (imported residue name),
List of Words (imported atom names)
Output

Word (Molecule.MolResidue.ccpCodes)

ccpnmr.analysis.core.StructureBasic.getBestMolType(atomNames, ccpCodes=None)
Determine the best molecule type (protein, DNA, RNA, carbohydrate or
nonpolymer) given the input atom names and residue ccpCodes
Input
List of Words (imported atom names),
List of Words (Molecule.MolResidue.ccpCodes)
Output

Word (Molecule.Molecule.molType)

ccpnmr.analysis.core.StructureBasic.getBestNamingSystem(residues, atomNamesList)
Determine the best naming system for a list of list of atom names
which correspond to the input residues.
Input

List of MolSystem.Residues, List of List of Words (imported atom names)

Output

Word (ChemAtomSysName.namingSystem)

ccpnmr.analysis.core.StructureBasic.getCentreOfMass(coords)

Find the center of mass of data model coordinates. (Uss atomic weights) .. describe:: Input

List of MolStructure.Coords

Output

List of Floats (x,y,z centre of mass)

ccpnmr.analysis.core.StructureBasic.getMeanCoords(coordList)

Find the mean position of data model coordinates. .. describe:: Input

List of MolStructure.Coords

Output

List of Floats (x,y,z coords of mean)

ccpnmr.analysis.core.StructureBasic.getMeanStrucCoords(structureCoords)

Find the mean position of input coordinates of multiple structures. .. describe:: Input

List of List of List of Floats (x,y,z per atom per structure)

Output

List of List of Floats (mean x,y,z per atom)

ccpnmr.analysis.core.StructureBasic.getResiduePhiPsi(residue, inDegrees=True, model=None)
Find the Phi and Psi backbone dihedral angles for a residue in a structure.
Option inDegrees can be set to False to get an angle in radians. Option to specify which model of an ensemble to use, otherwise all models are considered and the angles are an average.
Input

MolStructure.Residue, Boolean, MolStructure.Model

Output

2-List of Floats (Phi, Psi)

ccpnmr.analysis.core.StructureBasic.getRmsd(structureCoords)
Find the root mean square devatation for a list of structures
(their coordinates in lists)
Input

List of List of List of Floats (x,y,z per atom per structure)

Output

Float

ccpnmr.analysis.core.StructureBasic.getStructureCoordinates(structure, model=None, atomNameDict=None)
Get a list of coordinate objects from a structure in a consistent order.
Option to select coords from a given model if required. Option to extract only atoms of certain names
Input

MolStructure.StructureEnsemble, MolStructure.Model, List of Strings

Output

List of List of MolStructure.Coords (1st list per atom 2nd per model)

ccpnmr.analysis.core.StructureBasic.getStructureFromFile(molSystem, filePath, fileType='rough', doWarnings=True)
Creates a structure ensemble belonging to a molecular system
by loading a PDB style file. Option to specify the type of file loaded (proper PDB, rough PDB or CNS style)
Input

MolSystem.MolSystem, String (File Name), String (file type)

Output

MolStructure.StructureEmsemble

ccpnmr.analysis.core.StructureBasic.makeEnsemble(structures, replaceStructures=True, modelSerials=None)
Combine the input structure ensembles (or selected models from them)
into a single structure ensemble. Option to replace the input structures entirely (i.e. delete them), Option to use only certain models: If set uses only model numbers in input list.
Input
List of MolStructure.StructureEmsembles, Boolean,
List of Ints (MolStructure.Model.serial) or None
Output

MolStructure.StructureEmsemble

ccpnmr.analysis.core.StructureBasic.makePdbFromStructure(fileName, structure, model=None, useOxt=False)
Make a PDB file from a structure or ensemble of structures.
If a model is passed in the PDB style file will contain only that model’s coordinates, otherwise all models will be used.
Input
String (file name), MolStructure.StructureEnsemble,
MolStructure.Model
Output

None

ccpnmr.analysis.core.StructureBasic.makeStructureDictFromPdb(fileName, fileType)
Make a structure dictionary [model][chainCode][resNum][atomName] =
(x,y,z coords) from a CNS or true PDB format PDB file.
Input

String (file name), fileType (‘cns’ or ‘pdb’)

Output

Dictionary

ccpnmr.analysis.core.StructureBasic.makeStructureDictFromRoughPdb(fileName)
Make a structure dictionary [model][chainCode][resNum][atomName] =
(x,y,z coords) from a non-standard PDB file.
Input

String (file name)

Output

Dictionary

ccpnmr.analysis.core.StructureBasic.makeStructures(strucDict, molSystem, doWarnings=False)
Makes structure ensemble from a structure dictionary
[model][chainCode][resNum][atomName] = (x,y,z coords) in a mol system. Options to supress warnings and thus automatically link non-identical, but similar chains or make a new chain if none is found,
Input

Dictionary, MolSystem.MolSystem, Boolean

Output

MolStructures.StructureEnsemble

ccpnmr.analysis.core.StructureBasic.moveCoords(coords, vector)

Move data model coordinates according to a vactor. .. describe:: Input

List of MolStructure.Coords, List of Floats (translation vector)

Output

List of MolStructure.Coords

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