Package schrodinger :: Package application :: Package msv :: Package gui :: Module color

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Module color

Contains the color scheme constants for msv

Classes

[hide private]

ColorCell

RowColorScheme
A color scheme for a row in MSV

RulerScheme

PositionScheme
A scheme that handles coloring residues according to the length of the sequence

ConsensusSymbols

Functions

[hide private]

RowColorScheme

get_default_position_row_scheme()
Returns: A color scheme that uses position to assign colors

RowColorScheme

get_taylor_color_scheme()
Returns: A taylor color scheme

dict

get_default_row_color_schemes()
Returns: A dictionary mapping row types to default row color schemes

Variables

[hide private]

PALE_BLUE = QtGui.QColor(96, 176, 220)

RES_TYPE_COLORS = [ColorCell(* args) for args in [("A", (129, ...

TAYLOR_COLORS = [ColorCell(* args) for args in [("A", (200, 25...

HYDROPHOBICITY_KD_COLORS = [ColorCell(* args) for args in [("A...

HYDROPHOBICITY_HW_COLORS = [ColorCell(* args) for args in [("A...

SECONDARY_STRUCTURE_COLORS = [ColorCell(* args) for args in [(...

B_FACTOR_COLORS = []

helix_propensity_label = 'Helix Propensity Color Code:\nred - ...

strand_propensity_label = 'Beta Strand Color Code:\nblue - str...

turn_propensity_label = 'Turn Propensity Color Code:\ncyan - t...

helix_termination_tendency_label = 'Helix Termination Tendency...

exposure_tendency_label = 'Solvent Exposure Tendency:\nblue - ...

steric_group_label = 'Steric Group Color Code:\nred - small, n...

side_chain_chem_label = 'Side Chain Chemistry:\nred - acidic, ...

HELIX_PROPENSITY_COLORS = [ColorCell(* args) for args in [(res...

BETA_STRAND_PROPENSITY_COLORS = [ColorCell(* args) for args in...

TURN_PROPENSITY_COLORS = [ColorCell(* args) for args in [(resi...

HELIX_TERMINATION_TENDENCY_COLORS = [ColorCell(* args) for arg...

EXPOSURE_TENDENCY_COLORS = [ColorCell(* args) for args in [(re...

STERIC_GROUP_COLORS = [ColorCell(* args) for args in [(residue...

SIDE_CHAIN_CHEM_COLORS = [ColorCell(* args) for args in [(resi...

HYDROPHOBICITY_BAR_COLORS = [ColorCell('hydrophobicity', (240,...

ISOELECTRIC_BAR_COLORS = [ColorCell('isoelectric', (160, 240, ...

MEAN_HYDROPHOBICITY_BAR_COLORS = [ColorCell('mean_hydrophobici...

MEAN_ISOELECTRIC_BAR_COLORS = [ColorCell('mean_isoelectric', (...

CONSENSUS_SEQ_COLORS = [ColorCell(* args) for args in [("A", (...

CONSENSUS_FREQ_BAR_COLORS = [ColorCell('consensus_freq', (160,...

__package__ = 'schrodinger.application.msv.gui'

args = (<SIDE_CHAIN_CHEM.IMINO_ACID: 8>, (128, 128, 128), 'Sid...

Function Details

[hide private]

get_default_position_row_scheme()

Returns: RowColorScheme: A color scheme that uses position to assign colors

get_taylor_color_scheme()

Returns: RowColorScheme: A taylor color scheme

get_default_row_color_schemes()

Returns: dict: A dictionary mapping row types to default row color schemes

Variables Details

[hide private]

RES_TYPE_COLORS

Value:

[ColorCell(* args) for args in [("A", (129, 245, 137)), ("C", (240, 24
0, 32)), ("D", (240, 128, 128)), ("E", (240, 128, 128)), ("F", (240, 1
20, 32)), ("G", (129, 245, 137)), ("H", (128, 128, 240)), ("I", (129, 
245, 137)), ("K", (128, 128, 240)), ("L", (129, 245, 137)), ("M", (129
, 245, 137)), ("N", (51, 228, 240)), ("P", (126, 128, 128)), ("Q", (24
0, 145, 50)), ("R", (128, 128, 240)), ("S", (51, 228, 240)), ("T", (51
, 228, 240)), ("V", (129, 245, 137)), ("W", (240, 120, 32)), ("Y", (24
0, 120, 32))]]

TAYLOR_COLORS

Value:

[ColorCell(* args) for args in [("A", (200, 250, 0)), ("C", (250, 255,
 0)), ("D", (250, 0, 0)), ("E", (250, 0, 100)), ("F", (0, 250, 100)), 
("G", (250, 150, 0)), ("H", (0, 100, 250)), ("I", (100, 250, 0)), ("K"
, (100, 0, 250)), ("L", (50, 250, 0)), ("M", (0, 250, 0)), ("N", (200,
 0, 250)), ("P", (250, 200, 0)), ("Q", (250, 0, 200)), ("R", (0, 0, 25
0)), ("S", (250, 50, 0)), ("T", (250, 100, 0)), ("V", (150, 250, 0)), 
("W", (0, 200, 250)), ("Y", (0, 250, 200)),]]

HYDROPHOBICITY_KD_COLORS

Value:

[ColorCell(* args) for args in [("A", (255, 153, 153)), ("C", (255, 11
3, 113)), ("D", (56, 56, 255)), ("E", (56, 56, 255)), ("F", (255, 96, 
96)), ("G", (232, 232, 255)), ("H", (73, 73, 255)), ("I", (255, 0, 0))
, ("K", (34, 34, 255)), ("L", (255, 39, 39)), ("M", (255, 147, 147)), 
("N", (56, 56, 255)), ("P", (164, 164, 255)), ("Q", (56, 56, 255)), ("
R", (0, 0, 255)), ("S", (209, 209, 255)), ("T", (215, 215, 255)), ("V"
, (255, 16, 16)), ("W", (204, 204, 255)), ("Y", (181, 181, 255)),]]

HYDROPHOBICITY_HW_COLORS

Value:

[ColorCell(* args) for args in [("A", (217, 217, 255)), ("C", (179, 17
9, 255)), ("D", (255, 30, 30)), ("E", (255, 30, 30)), ("F", (67, 67, 2
55)), ("G", (255, 255, 255)), ("H", (217, 217, 255)), ("I", (120, 120,
 255)), ("K", (255, 30, 30)), ("L", (120, 120, 255)), ("M", (157, 157,
 255)), ("N", (255, 240, 240)), ("P", (255, 255, 255)), ("Q", (255, 24
0, 240)), ("R", (255, 30, 30)), ("S", (255, 232, 232)), ("T", (225, 22
5, 255)), ("V", (142, 142, 255)), ("W", (0, 0, 255)), ("Y", (82, 82, 2
55)),]]

SECONDARY_STRUCTURE_COLORS

Value:

[ColorCell(* args) for args in [(structure.SS_NONE, (255, 255, 255)), 
(structure.SS_LOOP, (255, 255, 255)), (structure.SS_HELIX, (240, 96, 6
4)), (structure.SS_STRAND, (32, 32, 32)), (structure.SS_TURN, (255, 25
5, 255))]]

helix_propensity_label

Value:

'''Helix Propensity Color Code:
red - helix-forming
magenta - weak helix-forming
grey - ambivalent
blue - helix-breaking
white - no propensity'''

strand_propensity_label

Value:

'''Beta Strand Color Code:
blue - strand-forming
grey - ambivalent
red - strand-breaking'''

turn_propensity_label

Value:

'''Turn Propensity Color Code:
cyan - turn-forming
grey - ambivalent
magenta - turn-breaking'''

helix_termination_tendency_label

Value:

'''Helix Termination Tendency:
green - helix-starting
grey - ambivalent
red - helix-ending'''

exposure_tendency_label

Value:

'''Solvent Exposure Tendency:
blue - surface
grey - ambivalent
orange - buried'''

steric_group_label

Value:

'''Steric Group Color Code:
red - small, non-interfering
magenta - ambivalent
cyan - sticky polar
blue - aromatic'''

side_chain_chem_label

Value:

'''Side Chain Chemistry:
red - acidic, hydrophilic
blue - basic, hydrophilic
green - neutral, hydrophobic, aliphatic
orange - neutral, hydrophobic, aromatic
cyan - neutral, hydrophilic
yellow - primary thiol
dark grey - imino acid'''

HELIX_PROPENSITY_COLORS

Value:

[ColorCell(* args) for args in [(residue.HELIX_PROPENSITY.NO_PROPENSIT
Y, (255, 255, 255), helix_propensity_label), (residue.HELIX_PROPENSITY
.LIKELY, (240, 64, 64), helix_propensity_label), (residue.HELIX_PROPEN
SITY.WEAK, (128, 64, 192), helix_propensity_label), (residue.HELIX_PRO
PENSITY.AMBIVALENT, (128, 128, 128), helix_propensity_label), (residue
.HELIX_PROPENSITY.HELIX_BREAKING, (64, 64, 240), helix_propensity_labe
l)]]

BETA_STRAND_PROPENSITY_COLORS

Value:

[ColorCell(* args) for args in [(residue.BETA_STRAND_PROPENSITY.NO_PRO
PENSITY, (255, 255, 255), strand_propensity_label), (residue.BETA_STRA
ND_PROPENSITY.STRAND_BREAKING, (64, 64, 240), strand_propensity_label)
, (residue.BETA_STRAND_PROPENSITY.AMBIVALENT, (128, 128, 128), strand_
propensity_label), (residue.BETA_STRAND_PROPENSITY.STRAND_FORMING, (24
0, 64, 64), strand_propensity_label)]]

TURN_PROPENSITY_COLORS

Value:

[ColorCell(* args) for args in [(residue.TURN_PROPENSITY.NO_PROPENSITY
, (255, 255, 255), turn_propensity_label), (residue.TURN_PROPENSITY.TU
RN_FORMING, (64, 240, 240), turn_propensity_label), (residue.TURN_PROP
ENSITY.AMBIVALENT, (128, 128, 128), turn_propensity_label), (residue.T
URN_PROPENSITY.TURN_BREAKING, (240, 64, 240), turn_propensity_label)]]

HELIX_TERMINATION_TENDENCY_COLORS

Value:

[ColorCell(* args) for args in [(residue.HELIX_TERMINATION_TENDENCY.NO
_TENDENCY, (255, 255, 255), helix_termination_tendency_label), (residu
e.HELIX_TERMINATION_TENDENCY.HELIX_STARTING, (64, 240, 64), helix_term
ination_tendency_label), (residue.HELIX_TERMINATION_TENDENCY.AMBIVALEN
T, (128, 128, 128), helix_termination_tendency_label), (residue.HELIX_
TERMINATION_TENDENCY.HELIX_ENDING, (240, 64, 64), helix_termination_te
ndency_label)]]

EXPOSURE_TENDENCY_COLORS

Value:

[ColorCell(* args) for args in [(residue.SOLVENT_EXPOSURE_TENDENCY.NO_
TENDENCY, (255, 255, 255), exposure_tendency_label), (residue.SOLVENT_
EXPOSURE_TENDENCY.SURFACE, (64, 64, 240), exposure_tendency_label), (r
esidue.SOLVENT_EXPOSURE_TENDENCY.AMBIVALENT, (128, 128, 128), exposure
_tendency_label), (residue.SOLVENT_EXPOSURE_TENDENCY.BURIED, (240, 128
, 32), exposure_tendency_label)]]

STERIC_GROUP_COLORS

Value:

[ColorCell(* args) for args in [(residue.STERIC_GROUP.NO_STERIC, (255,
 255, 255), steric_group_label), (residue.STERIC_GROUP.SMALL, (240, 64
, 64), steric_group_label), (residue.STERIC_GROUP.AMBIVALENT, (240, 64
, 240), steric_group_label), (residue.STERIC_GROUP.POLAR, (64, 240, 24
0), steric_group_label), (residue.STERIC_GROUP.AROMATIC, (64, 64, 240)
, steric_group_label),]]

SIDE_CHAIN_CHEM_COLORS

Value:

[ColorCell(* args) for args in [(residue.SIDE_CHAIN_CHEM.NO_SIDE_CHAIN
_CHEM, (255, 255, 255), side_chain_chem_label), (residue.SIDE_CHAIN_CH
EM.ACIDIC_HYDROPHILIC, (240, 128, 128), side_chain_chem_label), (resid
ue.SIDE_CHAIN_CHEM.BASIC_HYDROPHILIC, (128, 128, 240), side_chain_chem
_label), (residue.SIDE_CHAIN_CHEM.NEUTRAL_HYDROPHOBIC_ALIPHATIC, (128,
 240, 128), side_chain_chem_label), (residue.SIDE_CHAIN_CHEM.NEUTRAL_H
YDROPHOBIC_AROMATIC, (240, 120, 32), side_chain_chem_label), (residue.
SIDE_CHAIN_CHEM.NEUTRAL_HYDROPHILIC, (64, 240, 240), side_chain_chem_l
...

HYDROPHOBICITY_BAR_COLORS

Value:

[ColorCell('hydrophobicity', (240, 160, 240))]

ISOELECTRIC_BAR_COLORS

Value:

[ColorCell('isoelectric', (160, 240, 192))]

MEAN_HYDROPHOBICITY_BAR_COLORS

Value:

[ColorCell('mean_hydrophobicity', (240, 160, 240))]

MEAN_ISOELECTRIC_BAR_COLORS

Value:

[ColorCell('mean_isoelectric', (160, 240, 192))]

CONSENSUS_SEQ_COLORS

Value:

[ColorCell(* args) for args in [("A", (129, 245, 137)), ("C", (240, 24
0, 32)), ("D", (240, 128, 128)), ("E", (240, 128, 128)), ("F", (240, 1
20, 32)), ("G", (129, 245, 137)), ("H", (128, 128, 240)), ("I", (129, 
245, 137)), ("K", (128, 128, 240)), ("L", (129, 245, 137)), ("M", (129
, 245, 137)), ("N", (51, 228, 240)), ("P", (126, 128, 128)), ("Q", (24
0, 145, 50)), ("R", (128, 128, 240)), ("S", (51, 228, 240)), ("T", (51
, 228, 240)), ("V", (129, 245, 137)), ("W", (240, 120, 32)), ("Y", (24
0, 120, 32))]]

CONSENSUS_FREQ_BAR_COLORS

Value:

[ColorCell('consensus_freq', (160, 240, 192))]

args

Value:

(<SIDE_CHAIN_CHEM.IMINO_ACID: 8>,
 (128, 128, 128),
 '''Side Chain Chemistry:
red - acidic, hydrophilic
blue - basic, hydrophilic
green - neutral, hydrophobic, aliphatic
orange - neutral, hydrophobic, aromatic
cyan - neutral, hydrophilic
...