Container class for list of atom objects.
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file | valist.h |
| Contains declarations for class Valist.
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typedef struct sValist | Valist |
| Declaration of the Valist class as the Valist structure.
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Container class for list of atom objects.
◆ Valist_ctor()
VEXTERNC Valist* Valist_ctor |
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| ) |
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Construct the atom list object.
- Author
- Nathan Baker
- Returns
- Pointer to newly allocated (empty) atom list
Definition at line 138 of file valist.c.
◆ Valist_ctor2()
VEXTERNC Vrc_Codes Valist_ctor2 |
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Valist * |
thee | ) |
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FORTRAN stub to construct the atom list object.
- Author
- Nathan Baker, Yong Huang
- Returns
- Success enumeration
- Parameters
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thee | Storage for new atom list |
Definition at line 155 of file valist.c.
◆ Valist_dtor()
VEXTERNC void Valist_dtor |
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Valist ** |
thee | ) |
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Destroys atom list object.
- Author
- Nathan Baker
- Parameters
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thee | Pointer to storage for atom list |
Definition at line 167 of file valist.c.
◆ Valist_dtor2()
VEXTERNC void Valist_dtor2 |
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Valist * |
thee | ) |
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FORTRAN stub to destroy atom list object.
- Author
- Nathan Baker
- Parameters
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thee | Pointer to atom list object |
Definition at line 176 of file valist.c.
◆ Valist_getAtom()
VEXTERNC Vatom* Valist_getAtom |
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Valist * |
thee, |
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int |
i |
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Get pointer to particular atom in list.
- Author
- Nathan Baker
- Returns
- Pointer to atom object i
- Parameters
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thee | Atom list object |
i | Index of atom in list |
Definition at line 115 of file valist.c.
◆ Valist_getAtomList()
Get actual array of atom objects from the list.
- Author
- Nathan Baker
- Returns
- Array of atom objects
- Parameters
-
Definition at line 95 of file valist.c.
◆ Valist_getCenterX()
VEXTERNC double Valist_getCenterX |
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Valist * |
thee | ) |
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Get x-coordinate of molecule center.
- Author
- Nathan Baker
- Returns
- X-coordinate of molecule center
- Parameters
-
Definition at line 66 of file valist.c.
◆ Valist_getCenterY()
VEXTERNC double Valist_getCenterY |
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Valist * |
thee | ) |
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Get y-coordinate of molecule center.
- Author
- Nathan Baker
- Returns
- Y-coordinate of molecule center
- Parameters
-
Definition at line 76 of file valist.c.
◆ Valist_getCenterZ()
VEXTERNC double Valist_getCenterZ |
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Valist * |
thee | ) |
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Get z-coordinate of molecule center.
- Author
- Nathan Baker
- Returns
- Z-coordinate of molecule center
- Parameters
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Definition at line 85 of file valist.c.
◆ Valist_getNumberAtoms()
VEXTERNC int Valist_getNumberAtoms |
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Valist * |
thee | ) |
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Get number of atoms in the list.
- Author
- Nathan Baker
- Returns
- Number of atoms in list
- Parameters
-
Definition at line 105 of file valist.c.
◆ Valist_getStatistics()
VEXTERNC Vrc_Codes Valist_getStatistics |
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Valist * |
thee | ) |
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Load up Valist with various statistics.
- Author
- Nathan Baker, Yong Huang
- Returns
- Success enumeration
Definition at line 869 of file valist.c.
◆ Valist_memChk()
VEXTERNC unsigned long int Valist_memChk |
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Valist * |
thee | ) |
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Get total memory allocated for this object and its members.
- Author
- Nathan Baker
- Returns
- Total memory in bytes
- Parameters
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Definition at line 129 of file valist.c.
◆ Valist_readPDB()
VEXTERNC Vrc_Codes Valist_readPDB |
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Valist * |
thee, |
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Vparam * |
param, |
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Vio * |
sock |
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) |
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Fill atom list with information from a PDB file.
- Author
- Nathan Baker, Todd Dolinsky, Yong Huang
- Returns
- Success enumeration
- Note
- We don't actually respect PDB format; instead recognize whitespace- or tab-delimited fields which allows us to deal with structures with coordinates > 999 or < -999.
- Parameters
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thee | Atom list object |
param | A pre-initialized parameter object |
sock | Socket read for reading PDB file |
Definition at line 515 of file valist.c.
◆ Valist_readPQR()
VEXTERNC Vrc_Codes Valist_readPQR |
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Valist * |
thee, |
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Vparam * |
param, |
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Vio * |
sock |
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) |
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Fill atom list with information from a PQR file.
- Author
- Nathan Baker, Yong Huang
- Returns
- Success enumeration
- Note
- A PQR file has PDB structure with charge and radius in the last two columns instead of weight and occupancy
- We don't actually respect PDB format; instead recognize whitespace- or tab-delimited fields which allows us to deal with structures with coordinates > 999 or < -999.
- Parameters
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thee | Atom list object |
param | A pre-initialized parameter object |
sock | Socket reading for reading PQR file |
Definition at line 606 of file valist.c.
◆ Valist_readXML()
VEXTERNC Vrc_Codes Valist_readXML |
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Valist * |
thee, |
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Vparam * |
param, |
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Vio * |
sock |
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) |
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Fill atom list with information from an XML file.
- Author
- Todd Dolinsky, Yong Huang
- Returns
- Success enumeration
- Note
- The XML file must adhere to some guidelines, notably the presence of an <atom> tag with all other useful information (x, y, z, charge, and radius) as nested elements.
- Parameters
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thee | Atom list object |
param | A pre-initialized parameter object |
sock | Socket reading for reading PQR file |
Definition at line 725 of file valist.c.