Atom Properties¶

Reference for atomic properties used in molecular visualization.

Overview¶

The atomProperties module provides atomic data used for rendering molecules:

CPK Colors: Standard element coloring scheme
VDW Radii: Van der Waals radii in Angstroms
Element Symbols: Atomic number to symbol mapping

Module Reference¶

atomProperties ¶

Created on Thu Jun 27 11:51:18 2024

@author: benjaminlear

CPK Color Scheme¶

Standard CPK (Corey-Pauling-Koltun) colors for elements:

Element	Symbol	Color	RGB
Hydrogen	H	White	(255, 255, 255)
Carbon	C	Gray	(144, 144, 144)
Nitrogen	N	Blue	(48, 80, 248)
Oxygen	O	Red	(255, 13, 13)
Fluorine	F	Green	(144, 224, 80)
Phosphorus	P	Orange	(255, 128, 0)
Sulfur	S	Yellow	(255, 255, 48)
Chlorine	Cl	Green	(31, 240, 31)

Usage:

from plotlymol3d.atomProperties import CPK_COLORS

# Get color for carbon (atomic number 6)
carbon_color = CPK_COLORS[6]  # "rgb(144, 144, 144)"

Van der Waals Radii¶

Atomic radii in Angstroms:

Element	Symbol	VDW Radius (Å)
H	Hydrogen	1.20
C	Carbon	1.70
N	Nitrogen	1.55
O	Oxygen	1.52
F	Fluorine	1.47
P	Phosphorus	1.80
S	Sulfur	1.80
Cl	Chlorine	1.75

Usage:

from plotlymol3d.atomProperties import VDW_RADII

# Get VDW radius for oxygen (atomic number 8)
oxygen_radius = VDW_RADII[8]  # 1.52

Element Symbols¶

Mapping of atomic numbers to element symbols:

Usage:

from plotlymol3d.atomProperties import SYMBOLS

# Get symbol for atomic number 6
symbol = SYMBOLS[6]  # "C"

Customization¶

You can override default properties when needed:

from plotlymol3d import draw_3D_rep
from plotlymol3d.atomProperties import CPK_COLORS

# Modify colors (not recommended - creates side effects)
# Better to use Plotly's figure update methods

fig = draw_3D_rep(smiles="CCO")

# Update trace colors after creation
for trace in fig.data:
    if hasattr(trace, 'color'):
        # Customize individual trace colors
        pass

Complete Element List¶

The module includes data for elements 1-118 (Hydrogen through Oganesson).

Common Elements in Organic Chemistry:

Z	Symbol	Name	VDW (Å)	Color
1	H	Hydrogen	1.20	White
6	C	Carbon	1.70	Gray
7	N	Nitrogen	1.55	Blue
8	O	Oxygen	1.52	Red
9	F	Fluorine	1.47	Green
15	P	Phosphorus	1.80	Orange
16	S	Sulfur	1.80	Yellow
17	Cl	Chlorine	1.75	Green
35	Br	Bromine	1.85	Brown
53	I	Iodine	1.98	Purple

Transition Metals:

Z	Symbol	Name	VDW (Å)	Color
26	Fe	Iron	2.00	Orange
29	Cu	Copper	1.40	Orange
30	Zn	Zinc	1.39	Gray

Default Values¶

If an element is not found in the dictionaries, default values are used:

Color: "rgb(255, 20, 147)" (deep pink) - indicates missing data
VDW Radius: 1.70 Å (carbon-like default)
Symbol: "X" (unknown)

References¶

CPK colors: Corey, R. B.; Pauling, L. (1953)
VDW radii: Bondi, A. (1964). "van der Waals Volumes and Radii". J. Phys. Chem. 68 (3): 441–451.