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| OEChem - C++ Theory Manual | ||||
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Multi-conformer molecules in OEChem are represented by the abstract
base class OEMCMolBases . OEMCMolBase
derives from OEMolBase and thus contains all
of the properties of molecules discussed in
Section 4. In addition to storing the atoms
and bonds of a molecule, an OEMCMolBase is able to store
multiple conformations of a molecule. Conformations of a molecule
share the same heavy-atom graph. Here, the word ``graph''
should be thought of in the graph theory sense, such that a molecule
is modeled as vertices (atoms) and edges connecting pairs of vertices
(bonds). Therefore, all conformers share a common connection table of
the same atoms and bonds. Furthermore, because they share the
same atoms and bonds, they also share any properties stored by
the atoms and bonds (see Section 7 and
Section 8). The sharing of a common
connection table prevents tautomers from being modeled together with
an OEMCMolBase. Coordinate information is stored by the
molecule, not the shared atoms and bonds, which allows the conformers
to share the same heavy-atom graph but have different spatial
configurations. In OEChem, these conformers are represented by
OEConfBase s, which are first-class objects.
OEMol s can be used as either a molecule with a
particular one of its conformers represented as its current ``state,''
or as a container of conformers with access to many of them at once.
It should be noted that in C++ OEMCMolBase and OEConfBase are the following
typedef's of template classes.
typedef OEMCMolBaseT<float,3> OEMCMolBase; typedef OEConfBaseT<float,3> OEConfBase;
The templates allow OEChem to migrate to alternate conformer
representations. For example, if greater coordinate precision is
needed doubles could be used. However, floats are
currently used as a space optimization.
Conformers of OEMCMolBase s are accessed via
the GetConf and GetConfs methods. GetConf returns the first conformer in the molecule
for which the predicate function passed as the
argument returns true (see Section 22 for more
information on predicates). GetConfs returns an iterator over
the conformers of the molecule.
OEMCMolBase s have four functions which
control the current state of the molecule with respect to conformers.
SetActive takes an
OEConfBase as an object and makes the
OEMCMolBase act exactly like an
OEMolBase with the ``Active'' conformer as the
only conformer. The GetActive function
returns a pointer to the currently ``Active'' conformation. There are
many OEMolBase functions which access the
single-conformer coordinates of a molecule. When these functions are
called on an OEMCMolBase, the coordinates of the ``Active''
conformer are returned. Similarly, if the OEMCMolBase does not
have a title or energy of its own, the title or energy of the active
conformer will be returned. This is particularly convenient when
passing the molecule to a function which has been written to use or
manipulate the coordinates of an OEMolBase.
1 #include "openeye.h"
2 #include "oechem.h"
3 #include <iostream>
4
5 using namespace OEChem;
6 using namespace OESystem;
7 using namespace std;
8
9 float GetMaxX(const OEMolBase &mol)
10 {
11 OEIter<OEAtomBase> atom;
12 float xyz[3];
13 float maxX = 0.0f;
14 bool first = true;
15 for(atom = mol.GetAtoms();atom;++atom)
16 {
17 mol.GetCoords(atom,xyz);
18 if(first)
19 {
20 maxX = xyz[0];
21 first = false;
22 }
23 else
24 if(xyz[0] > maxX)
25 maxX = xyz[0];
26 }
27 return maxX;
28 }
29
30 int main()
31 {
32 OEIter<OEMCMolBase> mol;
33 OEIter<OEConfBase> conf;
34 oemolistream ims;
35
36 for (mol=ims.GetMCMolBases(); mol; ++mol)
37 {
38 for(conf = mol->GetConfs(); conf; ++conf)
39 {
40 mol->SetActive(conf);
41 cerr << "maxX = " << GetMaxX(*mol) << endl;
42 }
43 }
44
45 return 0;
46 }
While the SetActive and
GetActive interface is sufficient for most
uses, it is sometimes necessary to think of a more complex
representation of the state of the molecule. The
OEMCMolBase also has
PushActive and
PopActive functions which extend the control
over the active conformation. All four of these functions work
together to determine which conformation is the current active
conformation. The active conformation is the top conformation in a
stack of OEConfBase s held by the molecule.
SetActive changes the top conformation on the stack, while
GetActive returns the top conformation on the stack.
PushActive puts a new conformation in the top position of the
stack, pushing all other members of the stack down. PopActive
removes the top conformer in the stack (allowing the next lower
conformer to become the active conformer). The conformer stack is
helpful for using the state of an OEMCMolBase within a function
while restoring the molecule to its original state before returning
it.
Alternatively, a programmer may wish to use the conformers as first
class objects rather than via the state of the
OEMCMolBase . This allows one to have
multiple conformation objects at once and to treat the
OEMCMolBase as a container of single-conformer molecules. The
example below shows the use of the conformers as first class objects.
Each conformer is represented by an
OEConfBase which inherits from
OEMolBase . Thus, each conformer can be
treated as an independent molecule with respect to its coordinates as
shown in the example code below.
1 #include "openeye.h"
2 #include "oechem.h"
3 #include <iostream>
4
5 using namespace OEChem;
6 using namespace OESystem;
7 using namespace std;
8
9 float GetMaxX(const OEMolBase &mol)
10 {
11 OEIter<OEAtomBase> atom;
12 float xyz[3];
13 float maxX = 0.0f;
14 bool first = true;
15 for(atom = mol.GetAtoms();atom;++atom)
16 {
17 mol.GetCoords(atom,xyz);
18 if(first)
19 {
20 maxX = xyz[0];
21 first = false;
22 }
23 else
24 if(xyz[0] > maxX)
25 maxX = xyz[0];
26 }
27 return maxX;
28 }
29
30 int main(int, char ** argv)
31 {
32 OEIter<OEMCMolBase> mol;
33 OEIter<OEConfBase> conf;
34
35 oemolistream ims(argv[1]);
36
37 std::string maxconf;
38 float tmpx = 0.0f, maxX = 0.0f;
39
40 for (mol=ims.GetMCMolBases(); mol; ++mol)
41 {
42 for(conf = mol->GetConfs(); conf; ++conf)
43 {
44 tmpx = GetMaxX(*conf);
45 if(tmpx > maxX)
46 {
47 if(!maxconf.empty())
48 {
49 cerr << conf->GetTitle() << " has a larger value of x than " <<
50 maxconf << endl;
51 }
52 maxconf = conf->GetTitle();
53 maxX = tmpx;
54 }
55 }
56 }
57
58 return 0;
59 }
In the listing above, the function GetMaxX returns the maximum x-coordinate of a molecule. The main routine
loops over all of the conformers of each molecule and compares the
maximum x-coordinate to a running maximum of the x-coordinate of every
conformer. If there is a new maximum, the associated conformer is
stored and the user is notified.
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