edu.duke.cs.osprey
3.3
edu.
duke.
cs.
osprey
edu.
duke.
cs.
osprey
Osprey
edu.
duke.
cs.
osprey.
gui
default
Render
Settings
main()
Osprey
Gui
show()
edu.
duke.
cs.
osprey.
gui.
compiler
Atom
Pairs
causes()
check
For
Errors()
Compiled
Conf
Space
Compiler
Error
Compiler
Progress
Compiler
Warning
Conf
Space
Compiler
Conf
Space
Index
Conf
Space
Params
Fixed
Atoms
fixed
Name()
for
Each
Frag
In()
Molecule
Locker
Mol
Net
Charges
msg
Or
Name()
Net
Charges
edu.
duke.
cs.
osprey.
gui.
features.
components
Conf
Lib
Picker
Conf
Libs
Conf
Pos
Editor
Design
Position
Editor
Dihedral
Angle
Viewer
Icon
Sign
Check
Sign
Error
Sign
Info
Sign
Warning
icon()
Icons
Mol
Motion
Editor
Motion
Viewer
Translation
Rotation
Viewer
edu.
duke.
cs.
osprey.
gui.
features.
slide
Bond
Editor
Clash
Viewer
Compile
Conf
Space
Conf
Libs
Selector
Conformation
Editor
Conf
Space
Name
Editor
Duplicate
Atoms
Editor
Export
Mol2
Export
PDB
Filter
Tool
Minimizer
Tool
Missing
Atoms
Editor
Molecule
Navigator
Mutation
Editor
Net
Charge
Editor
Protonation
Editor
Save
Conf
Space
Save
OMOL
Split
Conf
Space
edu.
duke.
cs.
osprey.
gui.
features.
win
About
Osprey
Gui
Import
PDB
Local
Service
Local
Service
Runner
New
Conf
Space
Open
Conf
Space
Open
OMOL
Service
Provider
Picker
edu.
duke.
cs.
osprey.
gui.
forcefield
Atom
Index
Atom
Pairer
Forcefield
Forcefield
Calculator
Forcefield
Params
Forcefield
Set
unconnected
Distance()
edu.
duke.
cs.
osprey.
gui.
forcefield.
amber
Amber14SBParams
Amber96Params
Amber
Atom
Types
Amber
BCC
Gaff
Gaff2
SYBYL
Amber
Charge
Generation
Amber
Charge
Method
AM1BCC
CM1
CM2
ESP
Gasteiger
Mulliken
RESP
Amber
Defaults
Amber
Forcefield
Params
Amber
Mol
Params
Amber
Params
Amber
Topology
Amber
Types
Architecture
Amd64
X86
calc
Mods
Amber()
calc
Params
Amber()
calc
Types
Amber()
Crd
IO
deprotonate()
find
Protonation()
find
Type
Or
Throw()
find
Types()
Forcefield
Name
Hybridization
Sp
Sp2
Sp3
infer
Bonds
Amber()
infer
Bonds
Amber
Blocking()
infer
Missing
Atoms
Amber()
infer
Missing
Atoms
Amber
Blocking()
infer
Protonation()
infer
Protonation
Blocking()
Mapping
Exception
map
To()
minimize()
minimize
Blocking()
Minimizer
Info
Missing
Atom
Molecule
Mapper
Molecule
Type
Atomic
Ion
DNA
Protein
RNA
Small
Molecule
Solvent
Synthetic
Operating
System
Linux
Mac
Windows
Parse
Exception
partition()
partition
And
Atom
Map()
Platform
protonate()
protonate
Blocking()
Protonated
Atom
Protonation
protonations()
Top
IO
edu.
duke.
cs.
osprey.
gui.
forcefield.
eef1
atom
Type
EEF1()
atom
Type
EEF1Or
Throw()
EEF1
EEF1Forcefield
Params
edu.
duke.
cs.
osprey.
gui.
io
Chain
Generator
Bonded
Group
Chain
Generator
By
Mol
Type
Chain
Generator
Single
Residue
Chain
Id
Generator
AZ
combine
For
PDB()
Conf
Lib
exists
Fragments
TOML
from
Mol2()
from
Mol2With
Metadata()
from
OMOL()
from
OMOLWith
Atoms()
from
PDB()
from
Toml()
get
Array
Or
Throw()
get
Boolean
Or
Throw()
get
Double
Or
Throw()
get
Int()
get
Int
Or
Throw()
get
String
Or
Throw()
get
Table
Or
Throw()
Launch
Limits
Mol2Metadata
Mol2Parse
Exception
OMOLMapped
Osprey
Service
Process
Streamer
read()
read
Bytes()
stream()
temp
Folder()
to
Bytes()
Toml
Parse
Exception
to
Mol2()
to
Molecule()
to
OMOL()
to
OMOLMapped()
to
Osprey
Mol()
to
PDB()
to
Toml()
to
Toml
Key()
to
Vector3d()
User
Settings
write()
edu.
duke.
cs.
osprey.
gui.
motions
Conf
Motion
Dihedral
Angle
Mol
Motion
Translation
Rotation
edu.
duke.
cs.
osprey.
gui.
prep
Anchor
assign()
Assignments
Atom
Tree
Bond
Guesser
Conf
Space
Conf
Space
Prep
Conf
Switcher
covalent
Range()
Design
Position
Duplicate
Atoms
Forcefield
Analyzer
guess
Bonds()
Illegal
Alignment
Exception
in
Covalent
Range()
max
Covalent
Dist()
min
Covalent
Dist()
Molecule
Prep
Not
AProtein
Exception
Pos
Assignment
Proteins
to
Tree()
edu.
duke.
cs.
osprey.
gui.
tools
Array
Map
Combine
Collision
Exception
combine
Maps()
Int
Pair
next
Float
In()
pairs()
Unsupported
Class
Exception
edu.
duke.
cs.
osprey.
gui.
view
Probe
View
edu.
duke.
cs.
osprey.
molscope
main()
Molscope
Slide
Slide
Menu
edu.
duke.
cs.
osprey.
molscope.
gui
Alert
Click
Tracker
columns()
Context
Menu
disabled
If()
enabled
If()
Exception
Viewer
image()
info
Tip()
list
Box()
pop
Disabled()
push
Disabled()
Slide
Commands
Slide
Feature
View
Indexed
Window
Window
Commands
Window
Feature
Window
Menu
With
Columns
edu.
duke.
cs.
osprey.
molscope.
gui.
features
Feature
Id
Features
Has
Feature
Id
Window
State
edu.
duke.
cs.
osprey.
molscope.
gui.
features.
slide
Camera
Tool
Close
Slide
Dev
Occlusion
Field
Menu
Render
Settings
edu.
duke.
cs.
osprey.
molscope.
gui.
features.
win
Dev
Fps
Dev
Imgui
Demo
Exit
Menu
Colors
Mode
edu.
duke.
cs.
osprey.
molscope.
molecule
all
Pairs()
Atom
Atom
Map
Atom
Pair
Chain
Generator
Chain
Id
Generator
Chain
Map
combine()
Content
Atom
Pair
Element
Actinium
Aluminium
Americium
Antimony
Argon
Arsenic
Astatine
Barium
Beryllium
Bismuth
Boron
Bromine
Cadmium
Caesium
Calcium
Carbon
Cerium
Chlorine
Chromium
Cobalt
Copper
Curium
Dysprosium
Erbium
Europium
Fluorine
Francium
Gadolinium
Gallium
Germanium
Gold
Hafnium
Helium
Holmium
Hydrogen
Indium
Iodine
Iridium
Iron
Krypton
Lanthanum
Lead
Lithium
Lutetium
Magnesium
Manganese
Mercury
Molybdenum
Neodymium
Neon
Neptunium
Nickel
Niobium
Nitrogen
Osmium
Oxygen
Palladium
Phosphorus
Platinum
Plutonium
Polonium
Potassium
Praseodymium
Promethium
Protactinium
Radium
Radon
Rhenium
Rhodium
Rubidium
Ruthenium
Samarium
Scandium
Selenium
Silicon
Silver
Sodium
Strontium
Sulfur
Tantalum
Technetium
Tellurium
Terbium
Thallium
Thorium
Thulium
Tin
Titanium
Tungsten
Uranium
Vanadium
Xenon
Ytterbium
Yttrium
Zinc
Zirconium
filter()
intersection()
Molecule
Molecule
Map
Molecule
Maps
Molecule
Selectors
Polymer
Polymer
Maps
Residue
Map
to
Identity
Set()
union()
edu.
duke.
cs.
osprey.
molscope.
render
Camera
Cylinder
Renderable
Dirtyness
get
Indices()
Hover
Effects
Indices
Loaded
Image
Molecule
Render
Effects
Offscreen
Renderer
put()
Render
Effect
Render
Settings
Sphere
Renderable
to
Buffer()
to
RGBA()
Vulkan
Device
world
To
Camera()
edu.
duke.
cs.
osprey.
molscope.
shaders
Shaders
edu.
duke.
cs.
osprey.
molscope.
tools
assert()
associate
Identity()
associate
Identity
Indexed()
associate
Indexed
To()
Bijection
Identity
Change
Tracker
identity
Hash
Code()
identity
Hash
Map
Of()
identity
Hash
Set()
identity
Hash
Set
Of()
main()
map
Keys
Identity()
map
Values
Identity()
normalize
Minus
PITo
PI()
normalize
Zero
To
Two
PI()
Sphere
Grid
time()
to
Identity
Set()
to
String
Angstroms()
to
Yes
No
Two
PI
edu.
duke.
cs.
osprey.
molscope.
view
Ball
And
Stick
Color
Color
Palette
Colors
Mode
Dark
Light
Molecule
Render
Info
Molecule
Render
Stack
Molecule
Render
View
Render
View
Space
Filling
edu.
duke.
cs.
osprey.
service
delete
Folder()
Error
Info
exists
Internal
Error
main()
Osprey
Service
Point3d
Process
Streamer
read()
read
Bytes()
Request
Error
respond()
respond
Error()
Response
Info
service()
Service
Exception
Service
Response
stream()
temp
Folder()
write()
edu.
duke.
cs.
osprey.
service.
amber
Antechamber
Leap
Parmchk
Sander
SQM
edu.
duke.
cs.
osprey.
service.
clashes
Probe
edu.
duke.
cs.
osprey.
service.
services
About
Response
About
Service
Bonds
Antechamber
Error
Bonds
Leap
Error
Bonds
Request
Bonds
Response
Bonds
Service
Clashes
Error
Clashes
Request
Clashes
Response
Clashes
Service
Forcefield
Params
Error
Forcefield
Params
Request
Forcefield
Params
Response
Forcefield
Params
Service
Minimize
Error
Minimize
Request
Minimize
Response
Minimize
Service
Missing
Atoms
Error
Missing
Atoms
Request
Missing
Atoms
Response
Missing
Atoms
Service
Molecule
FFInfo
Error
Molecule
FFInfo
Request
Molecule
FFInfo
Response
Molecule
FFInfo
Service
Protonate
Error
Protonate
Request
Protonate
Response
Protonate
Service
Protonation
Antechamber
Error
Protonation
Leap
Error
Protonation
Request
Protonation
Response
Protonation
Service
Types
Antechamber
Error
Types
Leap
Error
Types
Request
Types
Response
Types
Service
edu.duke.cs.osprey
/
edu.duke.cs.osprey.gui.compiler
/
NetCharges
/
NetCharges
Net
Charges
fun
NetCharges
(
mols
:
List
<
Pair
<
MoleculeType
,
Molecule
>
>
)
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fun
NetCharges
(
)
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