Table of Contents
SMILES, SMARTS, and SMIRKS are trademarks of Daylight Chemical Information Systems.
SYBYL is a registered trademark of Tripos, Inc..
CML is trademarks of P. Murray-Rust and H. S. Rzepa (http://www.xml-cml.org).
Python is a trademark of the Python Software Foundation.
MDL is a registered trademark in the United States of MDL Information Systems, Inc..
Other products and software packages referenced in this document are registered trademarks of their respective manufacturers.
Table of Contents
setPriority()
Sets the priority level.
emerg()
Logs a emerg message.
alert()
Logs a alert message.
crit()
Logs a critical message.
notice()
Logs a notice message.
info()
Logs a info message.
fatal()
Logs a fatal message.
error()
Logs a error message.
debug()
Logs a debug message.
warn()
Logs a waring message.
class std_vector_bool()
package base
append(bool)
Appends a element to the vector.
push_back(bool)
Appends a element as the new last element.
len
Returns the length of the vector.
int size()
Returns the size of the vector.
clear()
Clears the vector. After the call the size is zero.
boolean empty()
Returns true if the size of the vector is zero.
bool at(int)
Returns the element with an int as index
bool front(int)
Returns the first element (the element with index 0)
bool back(int)
Returns the last element (the element with index size() - 1)
erase(bool)
Erases a element.
class std_vector_double()
package base
append(double)
Appends a element to the vector.
push_back(double)
Appends a element as the new last element.
len
Returns the length of the vector.
int size()
Returns the size of the vector.
clear()
Clears the vector. After the call the size is zero.
boolean empty()
Returns true if the size of the vector is zero.
double at(int)
Returns the element with an int as index
double front(int)
Returns the first element (the element with index 0)
double back(int)
Returns the last element (the element with index size() - 1)
erase(double)
Erases a element.
class std_vector_float()
package base
append(float)
Appends a element to the vector.
push_back(float)
Appends a element as the new last element.
len
Returns the length of the vector.
int size()
Returns the size of the vector.
clear()
Clears the vector. After the call the size is zero.
boolean empty()
Returns true if the size of the vector is zero.
float at(int)
Returns the element with an int as index
float front(int)
Returns the first element (the element with index 0)
float back(int)
Returns the last element (the element with index size() - 1)
erase(float)
Erases a element.
class std_vector_int()
package base
append(int)
Appends a element to the vector.
push_back(int)
Appends a element as the new last element.
len
Returns the length of the vector.
int size()
Returns the size of the vector.
clear()
Clears the vector. After the call the size is zero.
boolean empty()
Returns true if the size of the vector is zero.
int at(int)
Returns the element with an int as index
int front(int)
Returns the first element (the element with index 0)
int back(int)
Returns the last element (the element with index size() - 1)
erase(int)
Erases a element.
class std_vector_string()
package base
append(string)
Appends a element to the vector.
push_back(string)
Appends a element as the new last element.
len
Returns the length of the vector.
int size()
Returns the size of the vector.
clear()
Clears the vector. After the call the size is zero.
boolean empty()
Returns true if the size of the vector is zero.
string at(int)
Returns the element with an int as index
string front(int)
Returns the first element (the element with index 0)
string back(int)
Returns the last element (the element with index size() - 1)
erase(string)
Erases a element.
class std_vector_Vector3()
package base
append(Vector3)
Appends a element to the vector.
push_back(Vector3)
Appends a element as the new last element.
len
Returns the length of the vector.
int size()
Returns the size of the vector.
clear()
Clears the vector. After the call the size is zero.
boolean empty()
Returns true if the size of the vector is zero.
Vector3 at(int)
Returns the element with an int as index
Vector3 front(int)
Returns the first element (the element with index 0)
Vector3 back(int)
Returns the last element (the element with index size() - 1)
erase(Vector3)
Erases a element.
class std_vector_std_map_int_int()
package base
append()
Appends a element to the vector.
push_back()
Appends a element as the new last element.
len
Returns the length of the vector.
int size()
Returns the size of the vector.
clear()
Clears the vector. After the call the size is zero.
boolean empty()
Returns true if the size of the vector is zero.
at(int)
Returns the element with an int as index
front(int)
Returns the first element (the element with index 0)
back(int)
Returns the last element (the element with index size() - 1)
erase()
Erases a element.
Matrix3x3 multiply(Matrix3x3, Matrix3x3)
Multiplies two 3d Matrices.
float distance(Vector3, Vector3)
Calculates the distance between two 3d vectors.
float det(Vector3, Vector3, Vector3)
Calculates the determinate of three 3d vectors.
float angle(Vector3, Vector3, Vector3)
Calculates the angle of three 3d vectors.
float torsion(Vector3, Vector3, Vector3, Vector3)
Calculates the torsion of four 3d vectors.
class Vector3()
class Vector3(float, float, float)
package base
float dot(vec)
Returns the dot product.
float normSquared()
Returns the squared norm.
float norm()
Returns the norm.
vec1 == vec2
Returns true if the two Vector3 objects are equal.
vec1 != vec2
Returns true if the two Vector3 objects are not equal.
vec1 + vec2
Returns the addtion of two Vector3 objects.
vec1 - vec2
Returns the difference of two Vector3 objects.
vec1 % vec2
Returns the cross product.
- vec
Returns the negative Vector3 object.
vec1 += vec2
Adds a Vector3 object.
vec1 -= vec2
Subtract a Vector3 object.
vec *= float
Multiply by a float.
vec /= float
Divide by a float.
class Matrix3x3()
class Matrix3x3(float, float, float, float, float, float, float, float, float)
class Matrix3x3(Vector3, Vector3, Vector3)
package base
mat1 != mat2
Returns true if the two Matrix33 objects are not equal.
mat1 == mat2
Returns true if the two Matrix33 objects are equal.
mat1 + mat2
Returns the addtion.
mat1 - mat2
Returns the difference.
mat1 * mat2
Returns matrix matrix product.
mat * vec
Returns matrix vector product.
- mat2
Returns the negative Matrix33 object.
mat1 += mat2
Adds a Matrix33 object.
mat1 -= mat2
Subracts a Matrix33 object.
mat *= float
Multiply by a float.
mat /= float
Divide by a float.
float __call__(int, int)
Returns the element with first int as row index and the second int as coluum index.
Table of Contents
class Object()
package framework
accept(BaseProcessor)
The accept method of an object execute a procressor with the object in hand.
int getId()
The id property of an object is a object id type used to store the id assigned to an object. The default value is none element.
setId(int)
The id property of an object is a object id type used to store the id assigned to an object. The default value is none element.
string getName()
The name property of an object is a string used to store the name assigned to an object. The default value is empty string.
setName(string)
The name property of an object is a string used to store the name assigned to an object. The default value is empty string.
string getDescription()
The description property of an object is a string used to store the description assigned to an object. The default value is empty string.
setDescription(string)
The description property of an object is a string used to store the description assigned to an object. The default value is empty string.
int getNumber()
The number property of an object is a integer used to store the number assigned to an object. The default value is null.
setNumber(int)
The number property of an object is a integer used to store the number assigned to an object. The default value is null.
setParent(Object)
insert(Object)
Inserts an object.
int isVisible()
The visible property of an object is boolean type used to store the visibility assigned to an object. The default value is true.
setVisible(int)
The visible property of an object is boolean type used to store the visibility assigned to an object. The default value is true.
int getOpen()
The open property of an object is boolean type used to store the open property assigned to an object. The default value is false.
setOpen(int)
The open property of an object is boolean type used to store the open property assigned to an object. The default value is false.
std_vector_Object getObjects()
Return a vector of all objects inserted to this object.
setObjects(std_vector_Object)
Set avector of objects.
setCurrent(Object)
The current property of an object is a object used to store the current object assigned to an object. The default value is null.
erase(Object)
The erase method of an object erases the argument object.
int getNumberOfObjects()
Returns the number of objects of an object. The result is of type integer.
int getNumberOfLeafs()
Returns the number of leafs of an object. The result is of type integer.
string getLabel()
Returns the label of an object. The result is of type string. The format depends on the type of the object.
string getClassName()
Returns the class name of an object. The result is of type string.
int isCompositeChanged()
Returns true if the composite has been changed.
__del__()
show()
The show method of an object shows the object in hand. This method sets the visible property to true.
hide()
The hide method of an object hides the object in hand. This method sets the visible property to false.
changed()
This method sets the changed property to true.
class IsVisible()
package framework
boolean __call__()(Object)
The visible property of an object is boolean type used to store the visibility assigned to an object. The default value is true.
class IsOpen()
package framework
boolean __call__()(Object)
The open property of an object is boolean type used to store the open property assigned to an object. The default value is false.
class IsCompositeChanged()
package framework
boolean __call__()(Object)
Returns true if the composite has been changed.
class HasName()
package framework
boolean __call__()(Object)
The name property of an object is a string used to store the name assigned to an object. The default value is empty string.
class HasDescription()
package framework
boolean __call__()(Object)
The description property of an object is a string used to store the description assigned to an object. The default value is empty string.
class HasNumber()
package framework
boolean __call__()(Object)
The number property of an object is a integer used to store the number assigned to an object. The default value is null.
class HasNumberOfObjects()
package framework
boolean __call__()(Object)
Returns the number of objects of an object. The result is of type integer.
class HasNumberOfLeafs()
package framework
boolean __call__()(Object)
Returns the number of leafs of an object. The result is of type integer.
class HasLabel()
package framework
boolean __call__()(Object)
Returns the label of an object. The result is of type string. The format depends on the type of the object.
class HasClassName()
package framework
boolean __call__()(Object)
Returns the class name of an object. The result is of type string.
class License()
package framework
Base class Object
string getUserName()
The user name property of an license is a string used to store the user name assigned to an license. The default value is an empty string.
string getCompanyName()
The company name property of an license is a string used to store the company name assigned to an license. The default value is an empty string.
string getKey()
The key property of an license is a string used to store the key assigned to an license. The default value is an empty string.
string getFeatureId()
The feature id property of an license is a string used to store the feature id assigned to an license. The default value is an empty string.
string getDate()
The date property of an license is a string used to store the date assigned to an license. The default value is an empty string.
class HasUserName()
package framework
boolean __call__()(License)
The user name property of an license is a string used to store the user name assigned to an license. The default value is an empty string.
class HasCompanyName()
package framework
boolean __call__()(License)
The company name property of an license is a string used to store the company name assigned to an license. The default value is an empty string.
class HasKey()
package framework
boolean __call__()(License)
The key property of an license is a string used to store the key assigned to an license. The default value is an empty string.
class HasFeatureId()
package framework
boolean __call__()(License)
The feature id property of an license is a string used to store the feature id assigned to an license. The default value is an empty string.
Table of Contents
class std_vector_AtomComposite()
package core
append(AtomComposite)
Appends a element to the vector.
push_back(AtomComposite)
Appends a element as the new last element.
len
Returns the length of the vector.
int size()
Returns the size of the vector.
clear()
Clears the vector. After the call the size is zero.
boolean empty()
Returns true if the size of the vector is zero.
AtomComposite at(int)
Returns the element with an int as index
AtomComposite front(int)
Returns the first element (the element with index 0)
AtomComposite back(int)
Returns the last element (the element with index size() - 1)
erase(AtomComposite)
Erases a element.
class std_vector_Composite()
package core
append(Composite)
Appends a element to the vector.
push_back(Composite)
Appends a element as the new last element.
len
Returns the length of the vector.
int size()
Returns the size of the vector.
clear()
Clears the vector. After the call the size is zero.
boolean empty()
Returns true if the size of the vector is zero.
Composite at(int)
Returns the element with an int as index
Composite front(int)
Returns the first element (the element with index 0)
Composite back(int)
Returns the last element (the element with index size() - 1)
erase(Composite)
Erases a element.
class std_vector_Bond()
package core
append(Bond)
Appends a element to the vector.
push_back(Bond)
Appends a element as the new last element.
len
Returns the length of the vector.
int size()
Returns the size of the vector.
clear()
Clears the vector. After the call the size is zero.
boolean empty()
Returns true if the size of the vector is zero.
Bond at(int)
Returns the element with an int as index
Bond front(int)
Returns the first element (the element with index 0)
Bond back(int)
Returns the last element (the element with index size() - 1)
erase(Bond)
Erases a element.
class std_vector_Atom()
package core
append(Atom)
Appends a element to the vector.
push_back(Atom)
Appends a element as the new last element.
len
Returns the length of the vector.
int size()
Returns the size of the vector.
clear()
Clears the vector. After the call the size is zero.
boolean empty()
Returns true if the size of the vector is zero.
Atom at(int)
Returns the element with an int as index
Atom front(int)
Returns the first element (the element with index 0)
Atom back(int)
Returns the last element (the element with index size() - 1)
erase(Atom)
Erases a element.
class std_vector_Element()
package core
append(Element)
Appends a element to the vector.
push_back(Element)
Appends a element as the new last element.
len
Returns the length of the vector.
int size()
Returns the size of the vector.
clear()
Clears the vector. After the call the size is zero.
boolean empty()
Returns true if the size of the vector is zero.
Element at(int)
Returns the element with an int as index
Element front(int)
Returns the first element (the element with index 0)
Element back(int)
Returns the last element (the element with index size() - 1)
erase(Element)
Erases a element.
float distanceAtom(Atom, Atom)
Returns the distance of the two given atoms.
float angleAtom(Atom, Atom, Atom)
Returns the angle of the three given atoms.
float torsionAtom(Atom, Atom, Atom, Atom)
Returns the torsion angle of the four given atoms.
class Amino()
package core
Base class Object
string getSymbol()
The amino property of an element is a string used to store the amino assigned to an amino.
string getAminoName()
The amino name property of an element is a string used to store the amino name assigned to an amino.
string getColor()
The color property of an element is a string used to store the color assigned to an amino.
class HasSymbol()
package core
boolean __call__()(Amino)
The amino property of an element is a string used to store the amino assigned to an amino.
class HasAminoName()
package core
boolean __call__()(Amino)
The amino name property of an element is a string used to store the amino name assigned to an amino.
class HasColor()
package core
boolean __call__()(Amino)
The color property of an element is a string used to store the color assigned to an amino.
class Array()
package geometric
Base class Composite
Vector3 getOrigin()
The origin property of an array is a coordinates type used to store the origin assigned to an array.
setOrigin(Vector3)
The origin property of an array is a coordinates type used to store the origin assigned to an array.
std_vector_int getCounts()
The counts property of an array is a vector of interger used to store the counts assigned to an array.
setCounts(std_vector_int)
The counts property of an array is a vector of interger used to store the counts assigned to an array.
std_vector_Vector3 getDeltas()
The deltas property of an array is a vector of coordinates type used to store the deltas assigned to an array.
setDeltas(std_vector_Vector3)
The deltas property of an array is a vector of coordinates type used to store the deltas assigned to an array.
int getBoundingBoxVisible()
The bounding box visible property of an array is a boolean used to store the bounding box visible assigned to an array.
setBoundingBoxVisible(int)
The bounding box visible property of an array is a boolean used to store the bounding box visible assigned to an array.
setWidth(float)
class IsBoundingBoxVisible()
package geometric
boolean __call__()(Array)
The bounding box visible property of an array is a boolean used to store the bounding box visible assigned to an array.
class Atom()
package core
Base class AtomComponent
setElementByName(string)
float getRadius()
The type property of an atom is a double used to store the radius assigned to an atom. The default value is one.
setRadius(float)
The type property of an atom is a double used to store the radius assigned to an atom. The default value is one.
int getExtId()
The extid property of an atom is an int used to store the external id assigned to an atom. The default value is zero.
setExtId(int)
The extid property of an atom is an int used to store the external id assigned to an atom. The default value is zero.
int getTypeId()
The typeid property of an atom is an int used to store the external id assigned to an atom. The default value is zero.
setTypeId(int)
The typeid property of an atom is an int used to store the external id assigned to an atom. The default value is zero.
int getIndex()
The index property of an atom is an int used to store the index assigned to an atom. The default value is zero.
setIndex(int)
The index property of an atom is an int used to store the index assigned to an atom. The default value is zero.
int getImplicitHCount()
The implicit H count property of an atom is an int used to store the implicit H count assigned to an atom. The default value is zero.
setImplicitHCount(int)
The implicit H count property of an atom is an int used to store the implicit H count assigned to an atom. The default value is zero.
int getIsotope()
The isotope property of an atom is an int used to store the isotope assigned to an atom. The default value is zero.
setIsotope(int)
The implicit H count property of an atom is an int used to store the implicit H count assigned to an atom. The default value is zero.
int getFormalCharge()
The formal charge property of an atom is an int used to store the formal charge assigned to an atom. The default value is zero.
setFormalCharge(int)
The formal charge property of an atom is an int used to store the formal charge assigned to an atom. The default value is zero.
int getInRing()
The inRing property of an atom is an int used to store the inRing assigned to an atom. The default value is zero.
setInRing(int)
The inRing property of an atom is an int used to store the inRing assigned to an atom. The default value is zero.
Vector3 getPosition()
The position property of an atom is a coordinates type used to store the position assigned to an atom. The default value is zero.
setPosition(Vector3)
The position property of an atom is a coordinates type used to store the position assigned to an atom. The default value is zero.
string getHybridization()
The hybridization property of an atom is a string used to store the hybridization assigned to an atom. The default value is an empty string.
setHybridization(string)
The hybridization property of an atom is a string used to store the hybridization assigned to an atom. The default value is an empty string.
string getChirality()
The chirality property of an atom is a string used to store the chirality assigned to an atom. The default value is an empty string.
setChirality(string)
The chirality property of an atom is a string used to store the chirality assigned to an atom. The default value is an empty string.
float getOccupancy()
The occupancy property of an atom is a string used to store the occupancy assigned to an atom. The default value is an empty string.
setOccupancy(float)
The occupancy property of an atom is a string used to store the occupancy assigned to an atom. The default value is an empty string.
translate(Vector3)
The translate method translates the atom position.
float getCharge()
The getCharge method returns charge.
setCharge(float)
int getTotalHCount()
The getTotalHCount method returns the total hydrogen count.
int getValence()
The getValence method returns the valence.
int getConnectivity()
The getConnectivity method returns the connectivity.
int getDegree()
The getDegree method returns the degree.
string getAmino()
The getAmino method returns amino of the atom.
int isHydrogen()
The isHydrogen method checks if the atom is a Hydrogen.
int isOxygen()
The isOxygen method checks if the atom is a Oxygen.
int isCarbon()
The isCarbon method checks if the atom is a Carbon.
int isCarbonAlpha()
The isCarbonAlpha method checks if the atom is a CarbonAlpha.
int isNitrogen()
The isNitrogen method checks if the atom is a Nitrogen.
int isSulfur()
The isSulfur method checks if the atom is a Sulfur.
int isPhosphorus()
The isPhosphorus method checks if the atom is a Phosphorus.
int isBoron()
The isBoron method checks if the atom is a Boron.
int isIodine()
The isIodine method checks if the atom is a Iodine.
int isBromine()
The isBromine method checks if the atom is a Bromine.
int isChlorine()
The is method checks if the atom is a Chlorine.
int isFluorine()
The isFluorine method checks if the atom is a Fluorine.
int hasAromaticBonds()
The hasAromaticBonds method checks if the atom has aromatic bonds.
int countBonds()
The method countBonds count attached bonds.
class IsInRing()
package core
boolean __call__()(Atom)
The inRing property of an atom is an int used to store the inRing assigned to an atom. The default value is zero.
class IsHydrogen()
package core
boolean __call__()(Atom)
The isHydrogen method checks if the atom is a Hydrogen.
class IsOxygen()
package core
boolean __call__()(Atom)
The isOxygen method checks if the atom is a Oxygen.
class IsCarbon()
package core
boolean __call__()(Atom)
The isCarbon method checks if the atom is a Carbon.
class IsCarbonAlpha()
package core
boolean __call__()(Atom)
The isCarbonAlpha method checks if the atom is a CarbonAlpha.
class IsNitrogen()
package core
boolean __call__()(Atom)
The isNitrogen method checks if the atom is a Nitrogen.
class IsSulfur()
package core
boolean __call__()(Atom)
The isSulfur method checks if the atom is a Sulfur.
class IsPhosphorus()
package core
boolean __call__()(Atom)
The isPhosphorus method checks if the atom is a Phosphorus.
class IsBoron()
package core
boolean __call__()(Atom)
The isBoron method checks if the atom is a Boron.
class IsIodine()
package core
boolean __call__()(Atom)
The isIodine method checks if the atom is a Iodine.
class IsBromine()
package core
boolean __call__()(Atom)
The isBromine method checks if the atom is a Bromine.
class IsChlorine()
package core
boolean __call__()(Atom)
The is method checks if the atom is a Chlorine.
class IsFluorine()
package core
boolean __call__()(Atom)
The isFluorine method checks if the atom is a Fluorine.
class IsAromatic()
package core
boolean __call__()(Atom)
The hasAromaticBonds method checks if the atom has aromatic bonds.
class HasRadius()
package core
boolean __call__()(Atom)
The type property of an atom is a double used to store the radius assigned to an atom. The default value is one.
class HasExtId()
package core
boolean __call__()(Atom)
The extid property of an atom is an int used to store the external id assigned to an atom. The default value is zero.
class HasTypeId()
package core
boolean __call__()(Atom)
The typeid property of an atom is an int used to store the external id assigned to an atom. The default value is zero.
class HasIndex()
package core
boolean __call__()(Atom)
The index property of an atom is an int used to store the index assigned to an atom. The default value is zero.
class HasImplicitHCount()
package core
boolean __call__()(Atom)
The implicit H count property of an atom is an int used to store the implicit H count assigned to an atom. The default value is zero.
class HasTotalHCount()
package core
boolean __call__()(Atom)
The getTotalHCount method returns the total hydrogen count.
class HasValence()
package core
boolean __call__()(Atom)
The getValence method returns the valence.
class HasgetConnectivity()
package core
boolean __call__()(Atom)
The getConnectivity method returns the connectivity.
class HasgetDegree()
package core
boolean __call__()(Atom)
The getDegree method returns the degree.
class HasIsotope()
package core
boolean __call__()(Atom)
The isotope property of an atom is an int used to store the isotope assigned to an atom. The default value is zero.
class HasFormalCharge()
package core
boolean __call__()(Atom)
The formal charge property of an atom is an int used to store the formal charge assigned to an atom. The default value is zero.
class HasHybridization()
package core
boolean __call__()(Atom)
The hybridization property of an atom is a string used to store the hybridization assigned to an atom. The default value is an empty string.
class HasChirality()
package core
boolean __call__()(Atom)
The chirality property of an atom is a string used to store the chirality assigned to an atom. The default value is an empty string.
class HasOccupancy()
package core
boolean __call__()(Atom)
The occupancy property of an atom is a string used to store the occupancy assigned to an atom. The default value is an empty string.
class HasAmino()
package core
boolean __call__()(Atom)
The getAmino method returns amino of the atom.
class HascountBonds()
package core
boolean __call__()(Atom)
The method countBonds count attached bonds.
class HasCharge()
package core
boolean __call__()(Atom)
The getCharge method returns charge.
class AtomComposite()
package core
Base class Composite
Properties getProperties()
The Properties property of an atom composite.
float getStickSize()
The stick size property of an atom composite is a double used to store the stick size assigned to an atom composite. The default value is 0.1.
setStickSize(float)
The stick size property of an atom composite is a double used to store the stick size assigned to an atom composite. The default value is 0.1.
float getBallSize()
The ball size property of an atom composite is a double used to store the ball size assigned to an atom composite. The default value is 0.4.
setBallSize(float)
The ball size property of an atom composite is a double used to store the ball size assigned to an atom composite. The default value is 0.4.
string getTitle()
The title property of an atom composite is a string used to store the title assigned to an atom composite. The default value is an empty string.
setTitle(string)
The title property of an atom composite is a string used to store the title assigned to an atom composite. The default value is an empty string.
float getCPKScale()
The CPK scale property of an atom composite is a double used to store the CPK scale assigned to an atom composite. The default value is 1.
setCPKScale(float)
The CPK scale property of an atom composite is a double used to store the CPK scale assigned to an atom composite. The default value is 1.
int getNameFlag()
The name flag property of an atom composite is a bool used to store the name flag assigned to an atom composite. The default value is false.
setNameFlag(int)
The name flag property of an atom composite is a bool used to store the name flag assigned to an atom composite. The default value is false.
int getTypeFlag()
The type flag property of an atom composite is a bool used to store the type flag assigned to an atom composite. The default value is false.
setTypeFlag(int)
The type flag property of an atom composite is a bool used to store the type flag assigned to an atom composite. The default value is false.
int getElementFlag()
The element flag property of an atom composite is a bool used to store the element flag assigned to an atom composite. The default value is false.
setElementFlag(int)
The element flag property of an atom composite is a bool used to store the element flag assigned to an atom composite. The default value is false.
int getIdFlag()
The id flag property of an atom composite is a bool used to store the id flag assigned to an atom composite. The default value is false.
setIdFlag(int)
The id flag property of an atom composite is a bool used to store the id flag assigned to an atom composite. The default value is false.
int getRadiusFlag()
The radius flag property of an atom composite is a bool used to store the radius flag assigned to an atom composite. The default value is false.
setRadiusFlag(int)
The radius flag property of an atom composite is a bool used to store the radius flag assigned to an atom composite. The default value is false.
int getBlink()
The blink property of an atom composite is a bool used to store the blink assigned to an atom composite. The default value is false.
setBlink(int)
The blink property of an atom composite is a bool used to store the blink assigned to an atom composite. The default value is false.
float getSelectionRadius()
The selection radius property of an atom composite is a double used to store the selection radius assigned to an atom composite. The default value is 1.
setSelectionRadius(float)
The selection radius property of an atom composite is a double used to store the selection radius assigned to an atom composite. The default value is 1.
string getSelectionName()
The selection name property of an atom composite is a string used to store the selection name assigned to an atom composite. The default value is an empty string.
setSelectionName(string)
The selection name property of an atom composite is a string used to store the selection name assigned to an atom composite. The default value is an empty string.
string getSelectionElement()
The selection element property of an atom composite is a string used to store the selection element assigned to an atom composite. The default value is an empty string.
setSelectionElement(string)
The selection element property of an atom composite is a string used to store the selection element assigned to an atom composite. The default value is an empty string.
string getSelectionType()
The selection type property of an atom composite is a string used to store the selection type assigned to an atom composite. The default value is an empty string.
setSelectionType(string)
The selection type property of an atom composite is a string used to store the selection type assigned to an atom composite. The default value is an empty string.
string getSelectionId()
The selection id property of an atom composite is a string used to store the selection id assigned to an atom composite. The default value is an empty string.
setSelectionId(string)
The selection id property of an atom composite is a string used to store the selection id assigned to an atom composite. The default value is an empty string.
float getSpeed()
The seed property of an atom composite is a float used to store the seed assigned to an atom composite. The default value is zero.
setSpeed(float)
The seed property of an atom composite is a float used to store the seed assigned to an atom composite. The default value is zero.
int getAtomDisplayStyle()
The atom display style property of an atom composite is a atom display style type used to store the atom display style assigned to an atom composite. The default value is zero.
setAtomDisplayStyle(int)
The atom display style property of an atom composite is a atom display style type used to store the atom display style assigned to an atom composite. The default value is zero.
int getNumberOfAtoms()
The getNumberOfAtoms method returns the number of atoms attached to an atom composite.
int nSelection()
Gets nSelection.
addSESurface()
Adds a SESurface.
addVDWSurface()
Adds a VDWSurface.
addHydrogens()
Adds hydrogens.
addBonds()
Adds bonds.
addEDSurface()
Adds EDSurface.
addAtom()
Adds a atom.
addMolecule()
Adds a molecule.
removeBonds()
Removes bonds.
removeAllBonds()
Removes all bonds.
removeSelections()
Removes selections.
removeAllSelections()
Removes all selections.
removeHydrogens()
Removes hydrogens.
removeAllHydrogens()
Removes all hydrogens.
removeHydrogensWithBonds()
Removes hydrogens.
removeAllHydrogensWithBonds()
Removes all hydrogens.
putColorMode()
Puts color mode.
showHydrogens()
Shows hydrogens.
hideHydrogens()
Hides hydrogens.
addDistanceMonitor()
Add distance monitor.
addAngleMonitor()
Add angle monitor.
addTorsionMonitor()
Add torsion monitor.
addChiralyMonitor()
Add chiraly monitor.
class IsNameFlag()
package core
boolean __call__()(AtomComposite)
The name flag property of an atom composite is a bool used to store the name flag assigned to an atom composite. The default value is false.
class IsTypeFlag()
package core
boolean __call__()(AtomComposite)
The type flag property of an atom composite is a bool used to store the type flag assigned to an atom composite. The default value is false.
class IsElementFlag()
package core
boolean __call__()(AtomComposite)
The element flag property of an atom composite is a bool used to store the element flag assigned to an atom composite. The default value is false.
class IsIdFlag()
package core
boolean __call__()(AtomComposite)
The id flag property of an atom composite is a bool used to store the id flag assigned to an atom composite. The default value is false.
class IsRadiusFlag()
package core
boolean __call__()(AtomComposite)
The radius flag property of an atom composite is a bool used to store the radius flag assigned to an atom composite. The default value is false.
class IsBlink()
package core
boolean __call__()(AtomComposite)
The blink property of an atom composite is a bool used to store the blink assigned to an atom composite. The default value is false.
class HasProperties()
package core
boolean __call__()(AtomComposite)
The Properties property of an atom composite.
class HasAtomCompositeStickSize()
package core
boolean __call__()(AtomComposite)
The stick size property of an atom composite is a double used to store the stick size assigned to an atom composite. The default value is 0.1.
class HasBallSize()
package core
boolean __call__()(AtomComposite)
The ball size property of an atom composite is a double used to store the ball size assigned to an atom composite. The default value is 0.4.
class HasTitle()
package core
boolean __call__()(AtomComposite)
The title property of an atom composite is a string used to store the title assigned to an atom composite. The default value is an empty string.
class HasCPKScale()
package core
boolean __call__()(AtomComposite)
The CPK scale property of an atom composite is a double used to store the CPK scale assigned to an atom composite. The default value is 1.
class HasSelectionRadius()
package core
boolean __call__()(AtomComposite)
The selection radius property of an atom composite is a double used to store the selection radius assigned to an atom composite. The default value is 1.
class HasSelectionName()
package core
boolean __call__()(AtomComposite)
The selection name property of an atom composite is a string used to store the selection name assigned to an atom composite. The default value is an empty string.
class HasSelectionElement()
package core
boolean __call__()(AtomComposite)
The selection element property of an atom composite is a string used to store the selection element assigned to an atom composite. The default value is an empty string.
class HasSelectionType()
package core
boolean __call__()(AtomComposite)
The selection type property of an atom composite is a string used to store the selection type assigned to an atom composite. The default value is an empty string.
class HasSelectionId()
package core
boolean __call__()(AtomComposite)
The selection id property of an atom composite is a string used to store the selection id assigned to an atom composite. The default value is an empty string.
class HasSpeed()
package core
boolean __call__()(AtomComposite)
The seed property of an atom composite is a float used to store the seed assigned to an atom composite. The default value is zero.
class HasAtomDisplayStyle()
package core
boolean __call__()(AtomComposite)
The atom display style property of an atom composite is a atom display style type used to store the atom display style assigned to an atom composite. The default value is zero.
class HasNumberOfAtoms()
package core
boolean __call__()(AtomComposite)
The getNumberOfAtoms method returns the number of atoms attached to an atom composite.
class HasnSelection()
package core
boolean __call__()(AtomComposite)
Gets nSelection.
class AtomComponent()
package core
Base class Selectable
float getRed()
The red property of an atom component is a float used to store the red assigned to an atom component. The default value is zero.
setRed(float)
The red property of an atom component is a float used to store the red assigned to an atom component. The default value is zero.
float getGreen()
The green property of an atom component is a float used to store the green assigned to an atom component. The default value is zero.
setGreen(float)
The green property of an atom component is a float used to store the green assigned to an atom component. The default value is zero.
float getBlue()
The blue property of an atom component is a float used to store the blue assigned to an atom component. The default value is zero.
setBlue(float)
The blue property of an atom component is a float used to store the blue assigned to an atom component. The default value is zero.
int getLabelMode()
The annotation mode property of an atom component is a annotation mode type used to store the annotation mode assigned to an atom component. The default value is zero.
setLabelMode(int)
The annotation mode property of an atom component is a annotation mode type used to store the annotation mode assigned to an atom component. The default value is zero.
int getColorMode()
The color mode property of an atom component is a color mode type used to store the color mode assigned to an atom component. The default value is zero.
setColorMode(int)
The color mode property of an atom component is a color mode type used to store the color mode assigned to an atom component. The default value is zero.
class HasRed()
package core
boolean __call__()(AtomComponent)
The red property of an atom component is a float used to store the red assigned to an atom component. The default value is zero.
class HasGreen()
package core
boolean __call__()(AtomComponent)
The green property of an atom component is a float used to store the green assigned to an atom component. The default value is zero.
class HasBlue()
package core
boolean __call__()(AtomComponent)
The blue property of an atom component is a float used to store the blue assigned to an atom component. The default value is zero.
class HasAnnotationMode()
package core
boolean __call__()(AtomComponent)
The annotation mode property of an atom component is a annotation mode type used to store the annotation mode assigned to an atom component. The default value is zero.
class HasColorMode()
package core
boolean __call__()(AtomComponent)
The color mode property of an atom component is a color mode type used to store the color mode assigned to an atom component. The default value is zero.
class Bond(Atom, Atom)
package core
Base class AtomComponent
float getStickSize()
The stick size property of an bond is a double used to store the stick size assigned to an bond. The default value is null.
setStickSize(float)
The stick size property of an bond is a double used to store the stick size assigned to an bond. The default value is null.
int getOrder()
The order property of an bond is a integer used to store the order assigned to an bond. The default value is null.
setOrder(int)
The oder property of an bond is a integer used to store the order assigned to an bond. The default value is null.
class HasStickSize()
package core
boolean __call__()(Bond)
The stick size property of an bond is a double used to store the stick size assigned to an bond. The default value is null.
class HasOrder()
package core
boolean __call__()(Bond)
The order property of an bond is a integer used to store the order assigned to an bond. The default value is null.
class Chain()
package core
Base class AtomComposite
int getProteinDisplayStyle()
The protein display style property of a chain is a integer used to store the protein display style assigned to a chain. The default value is zero.
setProteinDisplayStyle(int)
The protein display style property of a chain is a integer used to store the protein display style assigned to a chain. The default value is zero.
setProteinColorMode(int)
The protein color mode property of a chain is a integer used to store the protein color mode assigned to a chain. The default value is zero.
int getProteinColorMode()
The protein color mode property of a chain is a integer used to store the protein color mode assigned to a chain. The default value is zero.
setProteinAnnotationMode(int)
The protein annotation mode property of a chain is a integer used to store the protein annotation mode assigned to a chain. The default value is zero.
int getProteinAnnotationMode()
The protein annotation mode property of a chain is a integer used to store the protein annotation mode assigned to a chain. The default value is zero.
class HasProteinDisplayStyle()
package core
boolean __call__()(Chain)
The protein display style property of a chain is a integer used to store the protein display style assigned to a chain. The default value is zero.
class HasProteinColorMode()
package core
boolean __call__()(Chain)
The protein color mode property of a chain is a integer used to store the protein color mode assigned to a chain. The default value is zero.
class HasProteinAnnotationMode()
package core
boolean __call__()(Chain)
The protein annotation mode property of a chain is a integer used to store the protein annotation mode assigned to a chain. The default value is zero.
class Composite()
package core
Base class AtomComponent
Vector3 getInertialTensorMainAxis()
Gets the inertial tensor main axis.
setInertialTensorMainAxis(Vector3)
Sets the inertial tensor main axis.
Vector3 getCenter()
The center property of a composite is a coordinates type used to store the center assigned to a composite. The default value is zero.
setCenter(Vector3)
The center property of a composite is a coordinates type used to store the center assigned to a composite. The default value is zero.
int countAtoms()
Counts all atoms.
int countBonds()
Counts all bonds.
float helixRadius()
Gets the helix radius.
float from()
The From method returns the from value.
float to()
The To method returns the to value.
class HascountAtoms()
package core
boolean __call__()(Composite)
Counts all atoms.
class HascountBonds()
package core
boolean __call__()(Composite)
Counts all bonds.
class HasHelixRadius()
package core
boolean __call__()(Composite)
Gets the helix radius.
class HasFrom()
package core
boolean __call__()(Composite)
The From method returns the from value.
class HasTo()
package core
boolean __call__()(Composite)
The To method returns the to value.
class Element()
package core
Base class Object
string getSymbol()
The element property of an element is a string used to store the element assigned to an element.
string getElementName()
The element name property of an element is a string used to store the element name assigned to an element.
string getConfiguration()
The configuration property of an element is a string used to store the configuration assigned to an element.
string getColor()
The color property of an element is a color type used to store the color assigned to an element.
int getAtomicNumber()
The z property of an element is a integer used to store the z assigned to an element.
int getRow()
The row property of an element is a integer used to store the row assigned to an element.
int getColumn()
The column property of an element is a integer used to store the column assigned to an element.
int getMaxBond()
The max bond property of an element is a integer used to store the max bond assigned to an element.
float getCovalentRadius()
The cov radius property of an element is a double used to store the covalent radius assigned to an element.
float getVanDerWaalsRadius()
The Van Der Waals radius property of an element is a double used to store the Van Der Waals radius assigned to an element.
float getBSRadius()
The bs radius property of an element is a double used to store the bs radius assigned to an element.
float getAtomicWeight()
The mass property of an element is a float used to store the mass assigned to an element.
class HasElementSymbol()
package core
boolean __call__()(Element)
The element property of an element is a string used to store the element assigned to an element.
class HasElementName()
package core
boolean __call__()(Element)
The element name property of an element is a string used to store the element name assigned to an element.
class HasConfiguration()
package core
boolean __call__()(Element)
The configuration property of an element is a string used to store the configuration assigned to an element.
class HasElementColor()
package core
boolean __call__()(Element)
The color property of an element is a color type used to store the color assigned to an element.
class HasZ()
package core
boolean __call__()(Element)
The z property of an element is a integer used to store the z assigned to an element.
class HasRow()
package core
boolean __call__()(Element)
The row property of an element is a integer used to store the row assigned to an element.
class HasColumn()
package core
boolean __call__()(Element)
The column property of an element is a integer used to store the column assigned to an element.
class HasMaxBond()
package core
boolean __call__()(Element)
The max bond property of an element is a integer used to store the max bond assigned to an element.
class HasCovRadius()
package core
boolean __call__()(Element)
The cov radius property of an element is a double used to store the covalent radius assigned to an element.
class HasVDWRadius()
package core
boolean __call__()(Element)
The Van Der Waals radius property of an element is a double used to store the Van Der Waals radius assigned to an element.
class HasBSRadius()
package core
boolean __call__()(Element)
The bs radius property of an element is a double used to store the bs radius assigned to an element.
class HasMass()
package core
boolean __call__()(Element)
The mass property of an element is a float used to store the mass assigned to an element.
class Residue()
package core
Base class Fragment
int getSecondaryStructureType()
The secondary structure type property of a residue is a integer used to store the secondary structure type assigned to a residue. The default value is zero.
setSecondaryStructureType(int)
The secondary structure type property of a residue is a integer used to store the secondary structure type assigned to a residue. The default value is zero.
class HasSecondaryStructureType()
package core
boolean __call__()(Residue)
The secondary structure type property of a residue is a integer used to store the secondary structure type assigned to a residue. The default value is zero.
class Selectable()
package core
Base class Object
int isSelected()
The selected property of an selectable is a bool used to store selected the assigned to an selectable. The default value is false.
setSelection(int)
The selected property of an selectable is a bool used to store selected the assigned to an selectable. The default value is false.
class IsSelected()
package core
boolean __call__()(Selectable)
The selected property of an selectable is a bool used to store selected the assigned to an selectable. The default value is false.
class StaticAtom()
package core
Base class Atom
Vector3 getPosition()
The position property of an atom is a coordinates type used to store the position assigned to an atom. The default value is zero.
setPosition(Vector3)
The position property of an atom is a coordinates type used to store the position assigned to an atom. The default value is zero.
GraphPredicate createGraphPredicate(PredicateGraphEdit)
Creates a GraphPredicate object from a PredicateGraphEdit object. The comparisons between atoms and bonds is always true.
GraphPredicate createGraphPredicateWithComparators(PredicateGraphEdit)
Creates a GraphPredicate object from a PredicateGraphEdit object. Atoms and bonds are compared.
GraphPredicate createGraphPredicateWithAtomComparator(PredicateGraphEdit)
Creates a GraphPredicate object from a PredicateGraphEdit object. Atoms are compared based on the the element property. Only atoms are compared.
GraphPredicate createGraphPredicateWithBondComparator(PredicateGraphEdit)
Creates a GraphPredicate object from a PredicateGraphEdit object. Atoms are compared based on the the element property. Only bonds are compared.
Table of Contents
The AddHydrogensProcessor is used to add missing hydrogens.
class AddHydrogensProcessor()
package processor
__call__(AtomComposite)
Adds hydrogens to the AtomComposite object.
The AssignBondOrderProcessor is used to assign bond types.
class AssignBondOrderProcessor()
package processor
__call__(AtomComposite)
Assign types to the atoms in the AtomComposite object.
The AssignTypeProcessor is used to assign the index to atoms.
class AssignIndexProcessor()
package processor
__call__(AtomComposite)
Assign the index of the atoms in the AtomComposite object.
class AssignInRingProcessor()
package processor
__call__(AtomComposite)
Assign the in ring property of atoms in the AtomComposite object.
The AssignRadiusProcessor is used to assign a radius to atoms.
class AssignRadiusProcessor()
package processor
__call__(Atom)
Assigns the radius of the Atom object.
The AssignTypeProcessor is used to assign types to atoms.
class AssignTypeProcessor()
package processor
__call__(AtomComposite)
Assign types to the atoms in the AtomComposite object.
The BaseProcessor is the base Class of processors.
class BaseProcessor()
package framework
The BuildCompositesProcessor is used to build bonds.
class BuildBondsProcessor()
package processor
__call__(AtomComposite)
Build bonds of atoms in the AtomComposite object.
The BuildCompositesProcessor is used to build disconnected composites.
class BuildCompositesProcessor()
package processor
__call__(AtomComposite)
Builds disconnected composites of AtomComposite object.
The BuildRingsProcessor is used to assign the in ring property.
class BuildRingsProcessor()
package processor
__call__(AtomComposite)
Assign the ring property to the atoms in the AtomComposite object.
The RMSDeviationProcessor is used to evalute the rmsd. The reference molecule is specified by a composite.
class RMSDeviationProcessor(Composite)
package processor
__call__(AtomComposite)
Return the rms of the AtomComposite object.
Composite getComposite()
The reference Composite object of this processor.
setComposite(Composite)
The reference Composite object of this processor.
The RotationProcessor is used to rotate atoms. The rotation is specified by the rotation axis and the rotation angle.
class RotationProcessor(Vector3, float)
package processor
__call__(Atom)
Rotates the Atom object.
The TranslationProcessor is used to translate atoms. The translation is specified by a tranlation vector.
class TranslationProcessor(Vector3)
package processor
__call__(Atom)
Translates the Atom object.
Vector3 getTranslation()
The translation Vector3 object of this processor. The default value is Vector3(0, 0, 0).
setTranslation(Vector3)
The translation Vector3 object of this processor.
Table of Contents
The RMSDeviationPredicate is used to match Composite objects. The reference molecule is specified by a Composite object and the maximal RMDS by a float value.
class RMSDeviationPredicate(Composite, float)
package predicate
__call__(Composite)
Test if the RMSD of the The first property of an bond is a atom type used to store the first reference Composite object to the Composite object is smaller than the maximal RMSD.
Composite getComposite()
The reference Composite object of this predicate.
setComposite(Composite)
The reference Composite object of this predicate.
float getMaxRMSD()
The maximal RMSD that is matched.
float getRMSD()
The actual RMSD.
setMaxRMSD(float)
The maximal RMSD that is matched.
Table of Contents
AtomComposite createFromFile(string)
Creates a System object from a file specified by the full path to the file location.
Molecule fromSmiles(string)
Creates a Molecule object from a SMILES string.
string toSmiles(AtomComposite)
Creates a System object from a SMILES string.
FileIORegistry
class FileIORegistry()
package io
string getAllFileFilter()
Returns a filters for all supported file types.
std_vector_string getFileFilterVector()
Returns a vector with filters for all supported file types.
std_vector_FileType getFileTypes()
Returns all supported file types.
This class maps file type extensions to file types.
class ExtToFileType()
package io
Functions for ExtToFileType
ExtToFileType getExtToFileType()
Gets the ExtToFileType singleton object.
FileTypeToDescription getFileTypeToDescription()
Gets the FileTypeToDescription singleton object.
StructureReaderRegistry getStructureReaderRegistry()
Gets the StructureReaderRegistry singleton object.
WriterRegistry getWriterRegistry()
Gets the WriterRegistry singleton object.
Table of Contents
Graph createGraph(GraphEdit)
Creates a Graph object from a GraphEdit object. The comparisons between atoms and bonds is allways true.
Graph createGraphWithComparators(GraphEdit)
Creates a Graph object from a GraphEdit object. Atoms are compared with the element property. Bonds are compared with the bond order property.
Graph createGraphWithAtomComparator(GraphEdit)
Creates a Graph object from a GraphEdit object. Atoms are compared with the element property.
Graph createGraphWithBondComparator(GraphEdit)
Creates a Graph object from a GraphEdit object. Bonds are compared with the bond order property.
Graph
class Graph(GraphEdit)
package graph
GraphEdit getGraphEdit()
std_vector_AtomComposite matchAll(Graph)
std_vector_AtomComposite matchTotalUnique(Graph)
GraphEdit.
class GraphEdit()
package graph
insertNode(Atom)
Insert a Atom object.
insertEdge(Bond)
Inserts a Bond object.
std_map_int_map_int_Bond getEdges()
Returns a connection table of Bond objects.
int sizeOfNodes()
Returns the size of nodes.
std_vector_Atom getNodes()
Returns a vector of Atom objects.
Atom getNode(int)
Accesses Atom object with index.
Bond getEdge(int, int)
Accesses Bond object with index.
Table of Contents
Functions for Graphs
GraphPredicate createGraphPredicateFromSmartsString(string)
Creates a GraphPredicate object from a SMATRS string.
int singleMatch(Graph, Graph)
Tests if there is a match between two Graph objects.
GraphPredicate createPlainGraphPredicate(Composite)
Creates a GraphPredicate object from a Composite object.
GraphPredicate createGraphPredicate(Composite)
Creates a GraphPredicate object from a Composite object.
GraphEdit createGraphEdit(Composite)
Creates a GraphEdit object from a Composite object.
The MatchPredicate is used to match Composite objects. The reference molecule is specified by a Composite object.
class MatchPredicate(Composite)
package match
__call__(Composite)
Test if the reference molecule matches the Composite object.
PredicateGraphEdit.
class PredicateGraphEdit()
package match
insertNode(Atom)
Inserts a Atom object.
insertEdge(Bond)
Inserts a Bond object.
int sizeOfNodes()
std_vector_Atom getNodes()
std_map_int_map_int_Bond_Predicate getEdges()
Atom getNode(int)
Bond getEdge(int, int)
GraphPredicate.
class GraphPredicate(PredicateGraphEdit)
package match
PredicateGraphEdit getPredicateGraphEdit()
std_vector_AtomComposite matchAll(Graph)
std_vector_AtomComposite matchTotalUnique(Graph)
Table of Contents
The MCSProcessor is used to evalute the Maximum Common Substructure (MCS). The reference molecule is specified by a composite.
class MCSProcessor(Composite)
package matchprocessor
__call__(AtomComposite)
Evalute mcs of the AtomComposite object.
Composite getComposite()
The reference Composite object of this processor.
setComposite(Composite)
The reference Composite object of this processor.