OBMol Class Reference

Constructor.

Copy constructor, copies atoms,bonds and OBGenericData.

Destructor.

Start kekulizing one or a fused set of aromatic ring(s).

The initial electronic state indicates if an atoms must make a double bond or not Kekulizing is attempted recursively for all the atoms bonded to the first atom of the cycle.

recursively assign single and double bonds according to the electronical state of the atoms of the current bond

Give the priority to give two electrons instead of 1.

Recursively find the aromatic atoms with an aromatic bond to the current atom.

Assignment, copies atoms,bonds and OBGenericData.

Copies atoms and bonds but not OBGenericData.

Reserve a minimum number of atoms for internal storage This improves performance since the internal atom vector does not grow.

Create a new OBAtom pointer. Does no bookkeeping

Deprecated:

Use NewAtom instead, which ensures internal connections

Create a new OBBond pointer. Does no bookkeeping

Deprecated:

Use NewBond instead, which ensures internal connections

Create a new OBResidue pointer. Does no bookkeeping

Deprecated:

Use NewResidue instead, which ensures internal connections

Free an OBAtom pointer if defined. Does no bookkeeping

See also:

DeleteAtom which ensures internal connections

Free an OBBond pointer if defined. Does no bookkeeping

See also:

DeleteBond which ensures internal connections

Free an OBResidue pointer if defined. Does no bookkeeping

See also:

DeleteResidue which ensures internal connections

Add an atom to a molecule.

Add the specified atom to this molecule

Returns:

Whether the method was successful

Add a new atom to this molecule (like AddAtom) Calls BeginModify() before insertion and EndModify() after insertion

Add a new bond to the molecule with the specified parameters

Parameters:

	beginIdx	the atom index of the "start" atom
	endIdx	the atom index of the "end" atom
	order	the bond order (see OBBond::GetBO())
	flags	any bond flags such as stereochemistry (default = none)
	insertpos	the position index to insert the bond (default = none)

Returns:

Whether the new bond creation was successful

Add the specified residue to this molecule and update connections

Returns:

Whether the method was successful

Add the specified residue to this molecule and update connections

Returns:

Whether the method was successful

Instantiate a New Atom and add it to the molecule.

Create a new OBAtom in this molecule and ensure connections. (e.g. OBAtom::GetParent()

Instantiate a New Bond and add it to the molecule.

Create a new OBBond in this molecule and ensure connections. (e.g. OBBond::GetParent()

Create a new OBResidue in this molecule and ensure connections.

Deletes an atom from this molecule and all appropriate bonds. Updates the molecule and atom and bond indexes accordingly.

Warning:

Does not update any residues which may contain this atom

Returns:

Whether deletion was successful

Deletes an bond from this molecule and updates accordingly

Returns:

Whether deletion was successful

Deletes a residue from this molecule and updates accordingly.

Returns:

Whether deletion was successful

Call when making many modifications -- clears conformer/rotomer data. The method "turns off" perception routines, improving performance. Changes in molecular structure will be re-considered after modifications.

Call when done with modificaions -- re-perceive data as needed. This method "turns on" perception routines and re-evaluates molecular structure.

Returns:

The number of nested BeginModify() calls. Used internally.

Increase the number of nested BeginModify calls. Dangerous! Instead, properly use BeginModify as needed.

Decrease the number of nested BeginModify calls. Dangerous! Instead, properly use EndModify as needed.

Returns:

the entire set of flags. (Internal use, mainly.)

Returns:

the title of this molecule (often the filename)

Returns:

the number of atoms (i.e. OBAtom children)

Returns:

the number of bonds (i.e. OBBond children)

Returns:

the number of non-hydrogen atoms

Returns:

the number of residues (i.e. OBResidue substituents)

Returns:

the number of rotatble bonds. See OBBond::IsRotor() for details

Returns:

the atom at index idx or NULL if it does not exist.

Warning:

Atom indexing will change. Use iterator methods instead.

Returns:

the first atom in this molecule, or NULL if none exist.

Deprecated:

Will be removed in favor of more standard iterator methods

Returns:

the bond at index idx or NULL if it does not exist.

Warning:

Bond indexing may change. Use iterator methods instead.

Returns:

the bond connecting the atom indexed by a and b or NULL if none exists.

Warning:

Atom indexing will change. Use atom objects and iterators instead.

Returns:

the bond between the atoms bgn and end or NULL if none exists

Returns:

the residue indexed by idx, or NULL if none exists

Warning:

Residue indexing may change. Use iterator methods instead.

Returns:

the dihedral angle between the four atoms supplied a1-a2-a3-a4)

Returns:

the dihedral angle between the four atoms a, b, c, and d)

Returns:

the angle between the three atoms a, b and c (where a-> b (vertex) -> c )

Returns:

the stochoimetric formula (e.g., C4H6O)

Stochoimetric formula (e.g., C4H6O). This is either set by OBMol::SetFormula() or generated on-the-fly using the "Hill order" -- i.e., C first if present, then H if present all other elements in alphabetical order.

Returns:

the stochoimetric formula in spaced format e.g. C 4 H 6 O 1

Stochoimetric formula in spaced format e.g. C 4 H 6 O 1 No pair data is stored. Normally use without parameters: GetSpacedFormula()

Since:

version 2.1

Returns:

the heat of formation for this molecule (in kcal/mol)

Returns:

the standard molar mass given by IUPAC atomic masses (amu)

Returns:

the mass given by isotopes (or most abundant isotope, if not specified)

Returns:

the total charge on this molecule (i.e., 0 = neutral, +1, -1...)

Returns the total molecular charge -- if it has not previously been set it is calculated from the atomic formal charge information. (This may or may not be correct!) If you set atomic charges with OBAtom::SetFormalCharge() you really should set the molecular charge with OBMol::SetTotalCharge()

Returns:

the total spin on this molecule (i.e., 1 = singlet, 2 = doublet...)

Returns the total spin multiplicity -- if it has not previously been set it is calculated from the atomic spin multiplicity information assuming the high-spin case (i.e. it simply sums the atomic spins, making no attempt to pair spins). However, if you set atomic spins with OBAtom::SetSpinMultiplicity() you really should set the molecular spin with OBMol::SetTotalSpinMultiplicity()

Returns:

the dimensionality of coordinates (i.e., 0 = unknown or no coord, 2=2D, 3=3D)

Returns:

the set of all atomic coordinates. See OBAtom::GetCoordPtr for more

Implements blue-obelisk:findSmallestSetOfSmallestRings.

Get the current flag for whether formal charges are set with pH correction.

Get the current flag for whether partial charges are auto-determined.

Set the title of this molecule to title.

Set the title of this molecule to title.

Set the stochiometric formula for this molecule.

Set the heat of formation for this molecule (in kcal/mol).

Set the dimension of this molecule (i.e., 0, 1 , 2, 3).

Set the total charge of this molecule to charge.

Set the total spin multiplicity of this molecule to spin (i.e., 0 = singlet (default), 1 = doublet, 2 = triplet, etc.)

Set the internal coordinates to int_coord (Does not call InternalToCartesian to update the 3D cartesian coordinates)

Set the flag for determining automatic formal charges with pH (default=true).

Set the flag for determining partial charges automatically (default=true).

Mark that aromaticity has been perceived for this molecule (see OBAromaticTyper).

Mark that Smallest Set of Smallest Rings has been run (see OBRing class).

Mark that rings have been perceived (see OBRing class for details).

Mark that atom types have been perceived (see OBAtomTyper for details).

Mark that chains and residues have been perceived (see OBChainsParser).

Mark that chirality has been perceived.

Mark that partial charges have been assigned.

Mark that hybridization of all atoms has been assigned.

Mark that the implicit hydrogen valence of all atoms has been assigned.

Mark that Kekule forms have been assigned by Kekulize().

Mark that ring closure bonds have been assigned by graph traversal.

Mark that explicit hydrogen atoms have been added.

Perform a set of transformations specified by the user

Typically these are program options to filter or modify an object For example, see OBMol::DoTransformations() and OBMol::ClassDescription()

Reimplemented from OBBase.

Returns:

A list of descriptions of command-line options for DoTransformations()

Reimplemented from OBBase.

Clear all information from a molecule.

Reimplemented from OBBase.

Renumber the atoms of this molecule according to the order in the supplied vector.

Renumber the atoms in this molecule according to the order in the supplied vector. This will return without action if the supplied vector is empty or does not have the same number of atoms as the molecule.

Translate one conformer and rotate by a rotation matrix (which is returned) to the inertial frame-of-reference.

Translate all conformers to the inertial frame-of-reference.

Translates all conformers in the molecule by the supplied vector.

this method adds the vector v to all atom positions in all conformers

Translates one conformer in the molecule by the supplied vector.

this method adds the vector v to all atom positions in the conformer nconf. If nconf == OB_CURRENT_CONFORMER, then the atom positions in the current conformer are translated.

Rotate all conformers using the supplied matrix u (a 3x3 array of double).

Rotate all conformers using the supplied matrix m (a linear 3x3 row-major array of double).

Rotate a specific conformer nconf using the supplied rotation matrix m.

Translate to the center of all coordinates (for this conformer).

Transform to standard Kekule bond structure (presumably from an aromatic form).

Kekulize aromatic rings without using implicit valence.

This new perceive kekule bonds function has been especifically designed to handle molecule files without explicit hydrogens such as pdb or xyz. The function does not rely on GetImplicitValence function The function looks for groups of aromatic cycle For each group it tries to guess the number of electrons given by each atom in order to satisfy the huckel (4n+2) rule If the huckel rule cannot be satisfied the algorithm try with its best alternative guess Then it recursively walk on the atoms of the cycle and assign single and double bonds

Delete all hydrogens from the molecule

Returns:

Success

Delete all hydrogens from the supplied atom

Returns:

Success

Delete all hydrogen atoms connected to a non-polar atom

See also:

OBAtom::IsNonPolarHydrogen

Delete the supplied atom if it is a hydrogen (Helper function for DeleteHydrogens)

Add hydrogens to the entire molecule to fill out implicit valence spots

Parameters:

	polaronly	Whether to add hydrogens only to polar atoms (i.e., not to C atoms)
	correctForPH	Whether to call CorrectForPH() first

Returns:

Whether any hydrogens were added

Add hydrogens only to the supplied atom to fill out implicit valence.

Add only polar hydrogens (i.e., attached to polar atoms, not C).

Deletes all atoms except for the largest contiguous fragment.

Copies each disconnected fragment as a separate OBMol.

Converts for instance [N+]([O-])=O to N(=O)=O.

Correct for pH by applying the OBPhModel transformations.

set spin multiplicity for H-deficient atoms

Returns:

the center of the supplied conformer nconf

See also:

Center() to actually center all conformers at the origin

Set the torsion defined by these atoms, rotating bonded neighbors.

Find Smallest Set of Smallest Rings (see OBRing class for more details).

Find all ring atoms and bonds. Does not need to call FindSSSR().

Sets atom->IsChiral() to true for chiral atoms.

locates all atoms for which there exists a path to 'second' without going through 'first' children must not include 'second'

locates all atoms for which there exists a path to 'end' without going through 'bgn' children must not include 'end'

Find the largest fragment in OBMol (which may include multiple non-connected fragments)

Parameters:

frag

Return (by reference) a bit vector indicating the atoms in the largest fragment

Sort a list of contig fragments by size from largest to smallest Each vector<int> contains the atom numbers of a contig fragment

Aligns atom a on p1 and atom b along p1->p2 vector.

Adds single bonds based on atom proximity.

This method adds single bonds between all atoms closer than their combined atomic covalent radii, then "cleans up" making sure bonded atoms are not closer than 0.4A and the atom does not exceed its valence. It implements blue-obelisk:rebondFrom3DCoordinates.

Attempts to perceive multiple bonds based on geometries.

This method uses bond angles and geometries from current connectivity to guess atom types and then filling empty valences with multiple bonds. It currently has a pass to detect some frequent functional groups. It still needs a pass to detect aromatic rings to "clean up."

Fills out an OBAngleData with angles from the molecule.

Fills out an OBTorsionData with angles from the molecule.

Calculates the graph theoretical distance of each atom. Vector is indexed from zero.

Calculates a set of graph invariant indexes using the graph theoretical distance, number of connected heavy atoms, aromatic boolean, ring boolean, atomic number, and summation of bond orders connected to the atom. Vector is indexed from zero.

Calculates a set of symmetry identifiers for a molecule. Atoms with the same symmetry ID are symmetrically equivalent. Vector is indexed from zero.

Are there non-zero coordinates in two dimensions (i.e. X and Y)?

Are there non-zero coordinates in all three dimensions (i.e. X, Y, Z)?

Are there any non-zero coordinates?

Has aromatic perception been performed?

Has the smallest set of smallest rings (FindSSSR) been performed?

Have ring atoms and bonds been assigned?

Have atom types been assigned by OBAtomTyper?

Has atom chirality been assigned?

Have atomic Gasteiger partial charges been assigned by OBGastChrg?

Has atomic hybridization been assigned by OBAtomTyper?

Has implicit hydrogen valence been assigned by OBAtomTyper?

Has aromaticity and Kekule forms been assigned by Kekulize?

Have ring "closure" bonds been assigned? (e.g., OBBond::IsClosure()).

Have biomolecule chains and residues been assigned by OBChainsParser?

Have hydrogens been added to the molecule?

Have aromatic nitrogens been "corrected?" (deprecated).

Has the molecule been corrected for pH by CorrectForPH?

Has total spin multiplicity been assigned?

Is this molecule chiral?

Are there any atoms in this molecule?

Returns:

the number of conformers in this molecule

Set the entire set of conformers for this molecule to v.

Add a new set of coordinates f as a new conformer.

Set the molecule's current conformer to i Does nothing if i is less than 0 or i is larger than NumConformers()

Copy the conformer nconf into the array c

Warning:

Does no checking to see if c is large enough

Delete the conformer nconf.

Returns:

the coordinates to conformer i

Set the iterator to the beginning of the conformer list

Returns:

the array of coordinates for the first conformer

Advance the iterator to the next confomer, if possible

Returns:

The array of coordinates for the next conformer, or NULL if none exist

Returns:

the entire set of conformers for this molecule as a vector of floating point arrays

Returns:

An atom iterator pointing to the beginning of the atom list

Returns:

An atom iterator pointing to the end of the atom list

Returns:

A bond iterator pointing to the beginning of the bond list

Returns:

A bond iterator pointing to the end of the bond list

Returns:

A residue iterator pointing to the beginning of the residue list

Returns:

A residue iterator pointing to the end of the residue list

Set the iterator i to the beginning of the atom list

Returns:

the first atom (or NULL if none exist)

Advance the iterator i to the next atom in the molecule

Returns:

the next atom (if any, or NULL if none exist)

Set the iterator i to the beginning of the bond list

Returns:

the first bond (or NULL if none exist)

Advance the iterator i to the next bond in the molecule

Returns:

the next bond (if any, or NULL if none exist)

Set the iterator i to the beginning of the resdiue list

Returns:

the first residue (or NULL if none exist)

Advance the iterator i to the next residue in the molecule

Returns:

the next residue (if any, or NULL if not possible)

Set the iterator to the beginning of the internal coordinate list

Returns:

the first internal coordinate record, or NULL if none exist

See also:

SetInternalCoord

Advance the iterator to the next internal coordinate record

Returns:

the next first internal coordinate record, or NULL if none exist

See also:

SetInternalCoord

By default clears the object. Called from ReadMolecule of most format classes.

Returns:

whether the generic attribute/value pair exists

Returns:

whether the generic attribute/value pair exists

Returns:

whether the generic attribute/value pair exists, for a given OBGenericDataType

Delete any data matching the given OBGenericDataType.

Delete the given generic data from this object.

Delete all of the given generic data from this object.

Adds a data object; does nothing if d==NULL.

Returns:

the number of OBGenericData items attached to this molecule.

Returns:

the first matching data for a given type from OBGenericDataType or NULL if nothing matches

Returns:

the value given an attribute name

Returns:

the value given an attribute name

Returns:

all data, suitable for iterating

Returns:

all data with a specific origin, suitable for iterating

Returns:

An iterator pointing to the beginning of the data

Returns:

An iterator pointing to the end of the data

bitfield of flags

Assign partial charges automatically.

Assign formal charges automatically.

Molecule title.

vector of atoms

vector of bonds

Dimensionality of coordinates.

Molecular heat of formation (if applicable).

Total charge on the molecule.

Total spin on the molecule (if not specified, assumes lowest possible spin).

coordinate array

vector of conformers

Number of atoms.

Number of bonds.

Residue information (if applicable).

Internal Coordinates (if applicable).

Number of nested calls to BeginModify().

Custom data.