MSL Objects:AtomContainer - Revision history

Senes: /* Get atoms (and check for their existance) */

2010-03-17T00:14:11Z

‎Get atoms (and check for their existance)

Senes: /* Get atoms (and check for their existance) */

2010-03-17T00:13:16Z

‎Get atoms (and check for their existance)

Senes: /* Description */

2010-03-16T21:31:16Z

‎Description

Senes at 20:10, 16 March 2010

2010-03-16T20:10:56Z

Senes: /* Description */

2010-03-16T20:03:41Z

‎Description

Senes: /* Description */

2010-03-16T20:02:59Z

‎Description

Senes at 19:07, 16 March 2010

2010-03-16T19:07:54Z

Senes at 02:19, 18 February 2010

2010-02-18T02:19:49Z

Senes at 23:38, 17 February 2010

2010-02-17T23:38:16Z

Senes at 23:35, 17 February 2010

2010-02-17T23:35:13Z

@@ Line 20: / Line 20: @@
 ----
 ==== Get atoms (and check for their existance) ====
-*The AtomContaners can act as an array.  It has a .size() function that returns the number of atoms and a braket operator that returns the i-th atom (or using the getAtom function).
+*The AtomContaners can act as an array.  It has a .size() function that returns the number of atoms and a bracket operator that returns the i-th atom (or using the getAtom function).
 <source lang="cpp">
 unsigned int size() const;
@@ Line 26: / Line 26: @@
 Atom & getAtom(unsigned int _n);
 </source>
-*Atoms can also be obtained by "atom id" ("chain,residue number,atom name", such as "A,37,CB") either with the () operator or a getAtom function.
+*Atoms can also be obtained by "atom id" ("chain,residue number,atom name", such as "A,37,CB") either with the [] operator or a getAtom function.
 <source lang="cpp">
 Atom & operator[](std::string _atomId); // use argument as ["A,7,CA"];

@@ Line 28: / Line 28: @@
 *Atoms can also be obtained by "atom id" ("chain,residue number,atom name", such as "A,37,CB") either with the () operator or a getAtom function.
 <source lang="cpp">
-Atom & operator()(std::string _atomId); // use argument as ("A,7,CA");
+Atom & operator[](std::string _atomId); // use argument as ["A,7,CA"];
 Atom & getAtom(std::string _atomId);
 </source>
@@ Line 43: / Line 43: @@
 ----
 ==== Add and remove atoms ====
 The AtomContainers can add atoms at the end (addAtom function) with functions such as the following (see the source for more)

@@ Line 1: / Line 1: @@
 == Description ==
-The AtomContainer is the simpler of the two molecular objects of MSL.  It is essentially the equivalent of an array of atoms, without any internal representation of chains and residues, such as is present in the '''[[MSL Objects:System|System]]'''.  The AtomContainer also lacks the support for energy calculations.  Because of its simplicity it has less of an overhead and it should be used every time that the advanced features of the System are not necessary.
+The '''AtomContainer''' is the simpler of the two molecular objects of MSL.  It is essentially the equivalent of an array of atoms, without any internal representation of chains and residues, such as is present in the '''[[MSL Objects:System|System]]'''.  The AtomContainer also lacks the support for energy calculations.  Because of its simplicity it has less of an overhead and it should be used every time that the advanced features of the System are not necessary.
 ----

@@ Line 1: / Line 1: @@
 == Description ==
 The AtomContainer is the simpler of the two molecular objects of MSL.  It is essentially the equivalent of an array of atoms, without any internal representation of chains and residues, such as is present in the '''[[MSL Objects:System|System]]'''.  The AtomContainer also lacks the support for energy calculations.  Because of its simplicity it has less of an overhead and it should be used every time that the advanced features of the System are not necessary.
 ----
 ==== Constructor ====
@@ Line 14: / Line 11: @@
 ----
 ==== Reading and writing coordinates from/to file ====
 *The AtomContainer can read and write PDB files.  The functions return true if the I/O operation was succesful.
@@ Line 23: / Line 19: @@
 ----
 ==== Get atoms (and check for their existance) ====
 *The AtomContaners can act as an array.  It has a .size() function that returns the number of atoms and a braket operator that returns the i-th atom (or using the getAtom function).
@@ Line 48: / Line 43: @@
 ----
 ==== Add and remove atoms ====
 The AtomContainers can add atoms at the end (addAtom function) with functions such as the following (see the source for more)
@@ Line 66: / Line 60: @@
 ----
 ==== Save sets of coordinates (a conformation) to a buffer and retrieve them ====
 * The current conformation of the molecule (all coordinates) can be saved to a buffer.  Saved buffers can be restored later (for example, to undo an unfavorable conformational move)
@@ Line 76: / Line 69: @@
 ==Usage examples==
 == Source from SourceForge ==

@@ Line 5: / Line 5: @@
 ===Key functions ===
 ==== Constructor ====
 * It can take a vector of atom pointers ('''[[MSL Objects:AtomPointerVector|AtomPointerVector]]''').
@@ Line 11: / Line 12: @@
 </source>
 * Note: the AtomContainer will create copies of those atoms, and it won't refer to the same memory of the original AtomPointerVector.
 ==== Reading and writing coordinates from/to file ====
@@ Line 18: / Line 21: @@
 bool writePdb(std::string _filename);
 </source>
 ==== Get atoms (and check for their existance) ====
@@ Line 41: / Line 46: @@
 </source>
 * See the example programs described below for usage.
 ==== Add and remove atoms ====
@@ Line 57: / Line 64: @@
 bool removeAtom(std::string _atomId);
 </source>
 ==== Save sets of coordinates (a conformation) to a buffer and retrieve them ====

← Older revision		Revision as of 20:02, 16 March 2010
Line 2:		Line 2:

	== Description ==		== Description ==
		+	The AtomContainer is the simpler of the two molecular objects of MSL. It is essentially the equivalent of an array of atoms, without any internal representation of chains and residues, such as is present in the '''[[MSL Objects:System\|System]]'''. The AtomContainer also lacks the support for energy calculations. Because of its simplicity it has less of an overhead and it should be used every time that the advanced features of the System are not necessary.
		+
		+	===Key functions ===
		+	==== Constructor ====
		+	* It can take a vector of atom pointers ('''[[MSL Objects:AtomPointerVector\|AtomPointerVector]]''').
		+	<source lang="cpp">
		+	AtomContainer(const AtomPointerVector & _atoms);
		+	</source>
		+	* Note: the AtomContainer will create copies of those atoms, and it won't refer to the same memory of the original AtomPointerVector.
		+
		+	==== Reading and writing coordinates from/to file ====
		+	*The AtomContainer can read and write PDB files. The functions return true if the I/O operation was succesful.
		+	<source lang="cpp">
		+	bool readPdb(std::string _filename);
		+	bool writePdb(std::string _filename);
		+	</source>
		+
		+	==== Get atoms (and check for their existance) ====
		+	*The AtomContaners can act as an array. It has a .size() function that returns the number of atoms and a braket operator that returns the i-th atom (or using the getAtom function).
		+	<source lang="cpp">
		+	unsigned int size() const;
		+	Atom & operator[](unsigned int _n);
		+	Atom & getAtom(unsigned int _n);
		+	</source>
		+	*Atoms can also be obtained by "atom id" ("chain,residue number,atom name", such as "A,37,CB") either with the () operator or a getAtom function.
		+	<source lang="cpp">
		+	Atom & operator()(std::string _atomId); // use argument as ("A,7,CA");
		+	Atom & getAtom(std::string _atomId);
		+	</source>
		+	*To avoid errors, one can check for the estance of an atom. The getLastFoundAtom function return the atom without performing a second lookup.
		+	<source lang="cpp">
		+	bool atomExists(std::string _atomId);
		+	Atom & getLastFoundAtom();
		+	</source>
		+	*All atoms can be obtained as an AtomPointerVector.
		+	<source lang="cpp">
		+	AtomPointerVector & getAtoms();
		+	</source>
		+	* See the example programs described below for usage.
		+
		+	==== Add and remove atoms ====
		+	The AtomContainers can add atoms at the end (addAtom function) with functions such as the following (see the source for more)
		+	<source lang="cpp">
		+	void addAtom(const Atom & _atom);
		+	void addAtom(std::string _atomId, const CartesianPoint & _coor=CartesianPoint(0.0, 0.0, 0.0));
		+	</source>
		+	Insert atoms in the middle (after skipping a number of positions
		+	<source lang="cpp">
		+	void insertAtom(const Atom & _atom, unsigned int _skipPositions);
		+	void insertAtom(std::string _atomId, const CartesianPoint & _coor, unsigned int _skipPositions);
		+	</source>
		+	... and remove atoms (the atom id is in the form "chain,residue number,atom name", such as "A,37,CB"
		+	<source lang="cpp">
		+	bool removeAtom(std::string _atomId);
		+	</source>
		+
		+	==== Save sets of coordinates (a conformation) to a buffer and retrieve them ====
		+	* The current conformation of the molecule (all coordinates) can be saved to a buffer. Saved buffers can be restored later (for example, to undo an unfavorable conformational move)
		+	<source lang="cpp">
		+	void saveCoor(std::string _coordName);
		+	bool applySavedCoor(std::string _coordName);
		+	void clearSavedCoor();
		+	</source>

	==Usage examples==		==Usage examples==

← Older revision		Revision as of 19:07, 16 March 2010
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	----		----
	'''[[MSL Objects\|Back to the MSL Objects page]]'''		'''[[MSL Objects\|Back to the MSL Objects page]]'''
		+
		+	[[Category:MSL Objects]]

← Older revision		Revision as of 02:19, 18 February 2010
Line 1:		Line 1:
		+	{{stub}}
		+
	== Description ==		== Description ==

← Older revision		Revision as of 23:38, 17 February 2010
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	[http://mslib.svn.sourceforge.net/viewvc/mslib/trunk/src/AtomContainer.cpp?&view=markup AtomContainer.cpp]		[http://mslib.svn.sourceforge.net/viewvc/mslib/trunk/src/AtomContainer.cpp?&view=markup AtomContainer.cpp]
		+
		+	----
		+	'''[[MSL Objects\|Back to the MSL Objects page]]'''

← Older revision		Revision as of 23:35, 17 February 2010
Line 3:		Line 3:
	==Usage examples==		==Usage examples==

−	~~{{Template~~:~~ObjectSourceLink\|object~~=AtomContainer}}	+	== Source from SourceForge ==
		+
		+	[http://mslib.svn.sourceforge.net/viewvc/mslib/trunk/src/AtomContainer.h?&view=markup AtomContainer.h]
		+
		+	[http://mslib.svn.sourceforge.net/viewvc/mslib/trunk/src/AtomContainer.cpp?&view=markup AtomContainer.cpp]