kangmg/easyeda

Reaction coordinates에 대해서 SobEDA를 쉽게 실행할 수 있는 shell 스크립트 파일

• 🧪 I'm an undergraduate student majoring in chemistry.
• 💻 I'm interested in theoretical and computational chemistry.
• 📊 I'm also interested in Data analysis, as well as ML/DL.
• 🐣 I'm a novice in code development.
• 🔎 I pursue a mile wide and an inch deep philosophy.
• 📧 Please contact me via email. My email address is [email protected].

easyeda's Issues

range issue of dihedral_angle()

source/plot.py 파일 내에 아래 함수의 range가 [0,360]가 아닌 [0,180]인 문제 발견

def dihedral_angle(atom1, atom2, atom3, atom4):
    
    b2 = np.array(atom3) - np.array(atom2)
    b1 = np.array(atom2) - np.array(atom1)
    b3 = np.array(atom4) - np.array(atom3)

    v1 = np.cross(b1, b2)
    v2 = np.cross(b2, b3)

    angle = np.arctan2(np.linalg.norm(np.cross(v1, v2)), np.dot(v1, v2))
    angle_degrees = np.degrees(angle)

    if angle_degrees < 0:
        angle_degrees += 360.0
    return angle_degrees