Tutorial:Molecular alignments - Revision history

Senes at 22:41, 10 April 2010

2010-04-10T22:41:06Z

Dwkulp: /* Program description */

2010-04-01T22:28:18Z

‎Program description

Dwkulp: /* Program description */

2010-04-01T22:27:15Z

‎Program description

Dwkulp at 22:25, 1 April 2010

2010-04-01T22:25:42Z

Dwkulp: /* Program description */

2010-04-01T22:22:50Z

‎Program description

Dwkulp at 22:21, 1 April 2010

2010-04-01T22:21:48Z

Dwkulp: /* Program description */

2010-04-01T22:21:02Z

‎Program description

Dwkulp: /* Program description */

2010-04-01T22:16:17Z

‎Program description

Dwkulp: Created page with 'This is an example on how to align whole structures or parts of structures in MSL. This tutorial explains functions in the '''Transform''' object. <…'

2010-03-31T22:43:29Z

Created page with 'This is an example on how to align whole structures or parts of structures in MSL. This tutorial explains functions in the '''Transform''' object. <…'

New page

This is an example on how to align whole structures or parts of structures in MSL. This tutorial explains functions in the '''[[MSL Objects:Transform|Transform]]''' object.

<font color="red"> This tutorial is in progress, there may be missing example files, source files or bugs in the code.</font>

[http://mslib.svn.sourceforge.net/viewvc/mslib/trunk/examples/example_molecular_alignment.cpp?view=markup Complete source of example_molecular_alignment.cpp]

In MSL the program [http://mslib.svn.sourceforge.net/viewvc/mslib/trunk/programs/alignMolecules.cpp?view=markup alignMolecules] utilizes the type of code in this tutorial to structurally align multiple PDB files, given a set of reference atoms.

=== To compile ===
<source lang="text">
% make bin/example_molecular_alignment
</source>

=== To run the program ===
Go to the main directory and run the command ('''note''', the location of the exampleFiles subdirectory needs to be provided as an argument)
<source lang="text">
% bin/example_molecular_alignment exampleFiles
</source>

=== Program description ===

<source lang="cpp">

</source>

----
'''[[Tutorial|Back to the tutorial page]]'''

[[Category:Tutorial]]

← Older revision		Revision as of 22:41, 10 April 2010
Line 1:		Line 1:
−	This is an example on how to align whole structures or parts of structures in MSL. This tutorial explains functions in the '''[[MSL Objects:~~Transform~~\|~~Transform~~]]''' object.	+	This is an example on how to align whole structures or parts of structures in MSL. This tutorial explains functions in the '''[[MSL Objects:Transforms\|Transforms]]''' object.

@@ Line 65: / Line 65: @@
 </source>
-Create a Transforms object and align the two AtomPointerVectors.
+Create a Transforms object and align the two AtomPointerVectors.   <font color="blue"> Note AtomPointerVectors must contain the same number of atoms and it will try to align the atoms in order.</font>
 <source lang="cpp">

@@ Line 57: / Line 57: @@
 </source>
-Next we check before me move any molecules what the RMSD is, by using the AtomPointerVector::rmsd(AtomPointerVector) function.
+Next we check before we move any molecules what the RMSD is, by using the AtomPointerVector::rmsd(AtomPointerVector) function.
 <source lang="cpp">

← Older revision		Revision as of 22:25, 1 April 2010
Line 1:		Line 1:
	This is an example on how to align whole structures or parts of structures in MSL. This tutorial explains functions in the '''[[MSL Objects:Transform\|Transform]]''' object.		This is an example on how to align whole structures or parts of structures in MSL. This tutorial explains functions in the '''[[MSL Objects:Transform\|Transform]]''' object.

−
−	~~<font color="red"> This tutorial is in progress, there may be missing example files, source files or bugs in the code.</font>~~

	[http://mslib.svn.sourceforge.net/viewvc/mslib/trunk/examples/example_molecular_alignment.cpp?view=markup Complete source of example_molecular_alignment.cpp]		[http://mslib.svn.sourceforge.net/viewvc/mslib/trunk/examples/example_molecular_alignment.cpp?view=markup Complete source of example_molecular_alignment.cpp]

@@ Line 23: / Line 23: @@
 === Program description ===
-First you just read two molecules into AtomContainers as seen on the [[]]
+First you just read two molecules into AtomContainers as seen on the  [[Tutorial:Reading a PDB file with the simpler molecular object: the AtomContainer | AtomContainer Tutorial]]
 <source lang="cpp">
   	string refFile = "example0005.pdb";

@@ Line 61: / Line 61: @@
 Next we check before me move any molecules what the RMSD is, by using the AtomPointerVector::rmsd(AtomPointerVector) function.
-<source lang=cpp>
+<source lang="cpp">
 	// Get RMSD before alignment
@@ Line 68: / Line 68: @@
 Create a Transforms object and align the two AtomPointerVectors.
-<source lang=cpp>
+<source lang="cpp">
 	// Create a Transforms object (includes functions to do molecular alignments)
@@ Line 81: / Line 81: @@
 Finally, get the post-alignment RMSD and print out the results... including the Transformation matrix and translation
-<source>
+<source lang="cpp">
 	// Get RMSD after alignment
 	double postRMSD = refAtoms.getAtomPointers().rmsd(moveAtoms.getAtomPointers());

← Older revision		Revision as of 22:16, 1 April 2010
Line 24:		Line 24:

	<source lang="cpp">		<source lang="cpp">
		+	string refFile = "example0005.pdb";
		+	refFile = (string)argv[1] + "/" + refFile;
		+	cout << "Create an AtomContainer and read the atoms from " << refFile << endl;
		+
		+
		+	string moveFile = "example0006.pdb";
		+	moveFile = (string)argv[1] + "/" + moveFile;
		+	cout << "Create an AtomContainer and read the atoms from " << moveFile << endl;
		+
		+

		+
		+	// read the PDB into a new AtomContainer "refAtoms"
		+	AtomContainer refAtoms;
		+	if (!refAtoms.readPdb(refFile)) {
		+	// error checking, the PDB could not be read
		+	cerr << endl;
		+	cerr << "File " << refFile << " cannot be found, please speficy the path of the \"exampleFiles\" directory as an argument" << endl;
		+	exit(1);
		+	} else {
		+	cout << "Reference PDB has "<<refAtoms.size()<<" atoms."<<endl;
		+	}
		+
		+	// read the PDB into a new AtomContainer "moveAtoms"
		+	AtomContainer moveAtoms;
		+	if (!moveAtoms.readPdb(moveFile)) {
		+	// error checking, the PDB could not be read
		+	cerr << endl;
		+	cerr << "File " << moveFile << " cannot be found, please speficy the path of the \"exampleFiles\" directory as an argument" << endl;
		+	exit(1);
		+	} else {
		+	cout << "Move PDB has "<<moveAtoms.size()<<" atoms."<<endl;
		+	}
		+
		+	// Get RMSD before alignment
		+	double preRMSD = refAtoms.getAtomPointers().rmsd(moveAtoms.getAtomPointers());
		+
		+	// Create a Transforms object (includes functions to do molecular alignments)
		+	Transforms alignAtoms;
		+
		+	// Do molecular alignment first atoms are moving, second atoms are the reference
		+	if (!alignAtoms.rmsdAlignment(moveAtoms.getAtomPointers(),refAtoms.getAtomPointers())){
		+	cerr << "ERROR alignment of molecules using all the atoms of reference: "<<refFile<<" and move: "<<moveFile<<" files."<<endl;
		+	exit(0);
		+	}
		+
		+	// Get RMSD after alignment
		+	double postRMSD = refAtoms.getAtomPointers().rmsd(moveAtoms.getAtomPointers());
		+
		+	// Query Transform object for the rotation and translations required for alignment
		+	Matrix rotMatrix = alignAtoms.getLastRotationMatrix();
		+	CartesianPoint translation = alignAtoms.getLastTranslation();
		+
		+	// Output RMSD, Rotation Matrix and Translation Vector
		+	cout << endl << endl;
		+	fprintf(stdout,"Before alignment RMSD: %8.3f\n",preRMSD);
		+	fprintf(stdout,"After alignment RMSD: %8.3f\n",postRMSD);
		+	cout << endl << endl;
		+
		+	cout << "Rotation Matix: " <<endl<<rotMatrix << endl;
		+	cout << "Translation Vector: "<<endl<<translation << endl;
		+	}
		+
		+

	</source>		</source>