get turns, bridges, ladders and helix oop
Thomas Forest
parent
8532e4ecd7
commit
2505792465
221
src/atom.py
221
src/atom.py
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@ -1,4 +1,5 @@
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import math
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from structure import *
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class Atom:
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def dist_atoms(self, atom2):
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@ -34,21 +35,225 @@ class Residue:
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def h_bond(self, res2):
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if("H" not in res2.atoms.keys()):
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return(False)
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# elementary charge in Coulomb
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#e = 1.602176634 * 10*math.exp(-19)
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# dimensionnal factor f
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# dimensionnal factor, in kcal/mole
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f = 332
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# partial charges
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q1 = 0.42
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q2 = 0.20
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# r, distance between O-N atoms, in angströms
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# distance between O-N atoms, in angströms
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r_ON = self.atoms["O"].dist_atoms(res2.atoms["N"])
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# r, distance between C-H atoms, in angströms
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# distance between C-H atoms, in angströms
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r_CH = self.atoms["C"].dist_atoms(res2.atoms["H"])
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# r, distance between O-H atoms, in angströms
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# distance between O-H atoms, in angströms
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r_OH = self.atoms["O"].dist_atoms(res2.atoms["H"])
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# r, distance between C-N atoms, in angströms
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# distance between C-N atoms, in angströms
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r_CN = self.atoms["C"].dist_atoms(res2.atoms["N"])
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# Electrostatic interaction energy, in kcal/mole
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# electrostatic interaction energy, in kcal/mole
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E = q1*q2*(1/r_ON + 1/r_CH - 1/r_OH - 1/r_CN)*f
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return(E)
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def get_turns(self, residues, turns):
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"""
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Get all the turns from a specific residue.
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"""
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i = residues.index(self)
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for j in range(3,6):
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if(i+j<len(residues)):
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if(self.h_bond(residues[i+j])<-0.5):
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print(j,"TURN", residues[i].resid, residues[i+j].resid)
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turns[i] = Turn(j,residues[i].resid)
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def get_bridges(self, residues):
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bridges = {}
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bridge = {}
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strongest_bridge = {}
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i = residues.index(self)
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if(i >= 1 and i < len(residues)-4):
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E_min = 0
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for j in range(i+2,len(residues)-1):
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# select triplet with the minimal energy
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if(residues[i-1].h_bond(residues[j])<-0.5
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and residues[j].h_bond(residues[i+1])<-0.5):
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bridge = {'res1':residues[i-1].h_bond(residues[j]),
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'res2':residues[j].h_bond(residues[i+1]),
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'ipos':residues[i].resid,
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'jpos':residues[j].resid,
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'btype':"para"}
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if(residues[j-1].h_bond(residues[i])<-0.5
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and residues[i].h_bond(residues[j+1])<-0.5):
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bridge = {'res1':residues[j-1].h_bond(residues[i]),
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'res2':residues[i].h_bond(residues[j+1]),
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'ipos':residues[i].resid,
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'jpos':residues[j].resid,
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'btype':"para"}
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if(residues[i].h_bond(residues[j])<-0.5
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and residues[j].h_bond(residues[i])<-0.5):
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bridge = {'res1':residues[i].h_bond(residues[j]),
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'res2':residues[j].h_bond(residues[i]),
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'ipos':residues[i].resid,
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'jpos':residues[j].resid,
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'btype':"anti"}
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if(residues[i-1].h_bond(residues[j+1])<-0.5
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and residues[j-1].h_bond(residues[i+1])<-0.5):
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bridge = {'res1':residues[i-1].h_bond(residues[j+1]),
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'res2':residues[j-1].h_bond(residues[i+1]),
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'ipos':residues[i].resid,
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'jpos':residues[j].resid,
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'btype':"anti"}
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if(bridge):
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if(bridge['res1']+bridge['res2']<E_min):
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E_min = bridge['res1']+bridge['res2']
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strongest_bridge = bridge
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bridge = {}
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coord_bridge = [i,j]
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# finally add the strongest bridge at i and j pos
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if(strongest_bridge):
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bridges[coord_bridge[0]] = (Bridge(strongest_bridge['btype'],
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strongest_bridge['ipos'],
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strongest_bridge['jpos']))
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bridges[coord_bridge[1]] = (Bridge(strongest_bridge['btype'],
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strongest_bridge['jpos'],
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strongest_bridge['ipos']))
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if(len(bridges)>0):
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return(bridges[coord_bridge[0]])
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else:
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return(False)
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def get_helix(self, residues, turns):
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"""
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Return if there is an helix at a given residue,
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as well as its type.
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"""
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i = residues.index(self)
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# if there are no turns or it is the first residue, skip
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if not turns or i == 0:
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return False
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if (i <= len(residues)):
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if(i in turns.keys() and i-1 in turns.keys()):
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print(turns[i].turn_type,"- HELIX at", residues[i].resid)
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return(turns[i].turn_type, residues[i].resid)
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return(False)
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def get_ladders(self, residues, ladders):
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i = residues.index(self)
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if i != 0:
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if self.get_bridges(residues):
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if (residues[i-1].get_bridges(residues)):
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local_bridge = self.get_bridges(residues)
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consec_bridge = residues[i-1].get_bridges(residues)
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if local_bridge.bridge_type == consec_bridge.bridge_type:
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print("ladder", consec_bridge.res_num, local_bridge.res_num)
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ladders[i] = {'start':i-1,
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'end':i,
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'bridges':[consec_bridge, local_bridge]}
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def get_ladders2(self, bridges, residues):
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ladders = {}
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i = residues.index(self)
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if i != 0:
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k = 1
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if i in bridges.keys():
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temp_bridges = [bridges[i]]
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while ((i+k in bridges.keys()) and
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(bridges[i].bridge_type == bridges[i+k].bridge_type)):
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temp_bridges.append(bridges[i+k])
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k+=1
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if k>1:
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print("ladder", bridges[i].res_num, bridges[i+k-1].res_num)
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ladders[i] = {'start':bridges[i].res_num,
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'end':bridges[i+k-1].res_num,
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'bridges':temp_bridges}
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i+=k-1
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else:
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i+=1
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return ladders
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def get_sheets(ladders):
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"""
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Bridges between ladders.
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Check if 1 bridge between one ladder and one or more other ladders.
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Iterate over all residues of one ladder and check if bridge with other residues
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of the other ladders.
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"""
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sheets = {}
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for ladder in ladders:
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for ladd2 in ladders:
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for bridge in ladders[ladder]['bridges']:
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if bridge.res_partner in res_list(ladders[ladd2]):
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print("ladder",ladders[ladder]['start'], ladders[ladder]['end'],"bridge",bridge.res_num, bridge.res_partner,
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"ladder 2",ladders[ladd2]['start'], ladders[ladd2]['end'])
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#print("stop ladder 2")
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print("stop ladder 1")
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def res_list(ladder):
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# TODO : method in ladder class
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l=[]
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for i in range(ladder['start'], ladder['end']):
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l.append(i)
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return(l)
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def get_bends(residues):
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bends = {}
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for i in range(2,len(residues)-2):
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angle = math.degrees(vector_angles(vectors_substr(position_vector(residues[i].atoms["CA"].coords),
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position_vector(residues[i-2].atoms["CA"].coords)),
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vectors_substr(position_vector(residues[i+2].atoms["CA"].coords),
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position_vector(residues[i].atoms["CA"].coords))))
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if(angle>70):
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print("angle", residues[i].resid, angle)
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bends[residues[i].resid] = angle
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return(bends)
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def get_chirality(residues):
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for i in range(1,len(residues)-2):
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chirality = {}
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angle = calc_dihedral(residues[i-1].atoms["CA"].coords,
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residues[i].atoms["CA"].coords,
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residues[i+1].atoms["CA"].coords,
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residues[i+2].atoms["CA"].coords)
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if(angle>0 and angle<=180):
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sign="+"
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print("chirality", residues[i].resid, "+", angle)
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if(angle<=0 and angle > -180):
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sign="-"
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print("chirality", residues[i].resid, "-", angle)
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chirality[residues[i].resid] = sign
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return chirality
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def get_phi_psi(residues):
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for i in range(len(residues)):
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if(i==0):
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phi = 360.0
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else:
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phi = calc_dihedral(residues[i-1].atoms["C"].coords,
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residues[i].atoms["N"].coords,
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residues[i].atoms["CA"].coords,
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residues[i].atoms["C"].coords)
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if(i==len(residues)-1):
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psi = 360.0
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else:
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psi = calc_dihedral(residues[i].atoms["N"].coords,
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residues[i].atoms["CA"].coords,
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residues[i].atoms["C"].coords,
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residues[i+1].atoms["N"].coords)
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print("ANGLES", i, phi, psi)
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def get_TCO(res1, res2):
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CO_res1 = vector_from_pos(res1.atoms["C"].coords,
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res1.atoms["O"].coords)
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CO_res2 = vector_from_pos(res2.atoms["C"].coords,
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res2.atoms["O"].coords)
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angle = vector_angles(CO_res1, CO_res2)
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return(math.cos(angle))
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15
src/dssp.py
15
src/dssp.py
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@ -2,6 +2,7 @@ import pdb
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import atom
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import sys
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from structure import *
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from atom import *
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def print_dssp():
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@ -21,8 +22,8 @@ else:
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#print(get_bridges(pdb_file.residues))
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turns = get_turns(pdb_file.residues)
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get_helix(pdb_file.residues, turns)
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#turns = get_turns(pdb_file.residues)
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#get_helix(pdb_file.residues, turns)
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get_bends(pdb_file.residues)
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# get_chirality(pdb_file.residues)
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# bridges = get_bridges(pdb_file.residues)
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@ -47,3 +48,13 @@ else:
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#get_phi_psi(residues)
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#print(residues[2].atoms, residues[0].resid, residues[1].resid)
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print(get_TCO(residues[2],residues[3]))
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turns = {}
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ladders = {}
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for i,res in enumerate(residues):
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# res.get_turns(residues, turns)
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# res.get_helix(residues, turns)
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res.get_bridges(residues)
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res.get_ladders(residues, ladders)
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@ -0,0 +1,66 @@
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import math
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def vector_from_pos(a, b):
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xAB = b[0]-a[0]
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yAB = b[1]-a[1]
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zAB = b[2]-a[2]
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coord_AB = [xAB,yAB,zAB]
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return coord_AB
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def vector_norm(v):
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norm = math.sqrt(v[0]**2 + v[1]**2 + v[2]**2)
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return norm
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def dot_product(v1,v2):
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dot_product = v1[0]*v2[0] + v1[1]*v2[1] + v1[2]*v2[2]
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return(dot_product)
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def position_vector(c):
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vector = vector_from_pos([0,0,0],c)
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return vector
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def vectors_substr(v1, v2):
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return ([v1[0]-v2[0],
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v1[1]-v2[1],
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v1[2]-v2[2]])
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def vector_angles(v1,v2):
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dot_prod = dot_product(v1,v2)
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norm_v1 = vector_norm(v1)
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norm_v2 = vector_norm(v2)
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term = dot_prod/(abs(norm_v1)*abs(norm_v2))
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rad_angle = math.acos(term)
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return rad_angle
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def calc_dihedral(u1, u2, u3, u4):
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""" Calculate dihedral angle method. From bioPython.PDB
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(adapted to np.array)
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Calculate the dihedral angle between 4 vectors
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representing 4 connected points. The angle is in
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[-pi, pi].
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Adapted function of dihedral_angle_from_coordinates.py
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by Eric Alcaide.
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Source : https://gist.github.com/EricAlcaide
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URL : https://gist.github.com/EricAlcaide/30d6bfdb8358d3a57d010c9a501fda56
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"""
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#convert coords to numpy arrays
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u1 = np.array(u1)
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u2 = np.array(u2)
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u3 = np.array(u3)
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u4 = np.array(u4)
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a1 = u2 - u1
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a2 = u3 - u2
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a3 = u4 - u3
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v1 = np.cross(a1, a2)
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v1 = v1 / (v1 * v1).sum(-1)**0.5
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v2 = np.cross(a2, a3)
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v2 = v2 / (v2 * v2).sum(-1)**0.5
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porm = np.sign((v1 * a3).sum(-1))
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rad = np.arccos((v1*v2).sum(-1) / ((v1**2).sum(-1) * (v2**2).sum(-1))**0.5)
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if not porm == 0:
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rad = rad * porm
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deg_angle = rad*(180/math.pi)
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return deg_angle
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@ -0,0 +1,66 @@
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def vector_from_pos(a, b):
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xAB = b[0]-a[0]
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yAB = b[1]-a[1]
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zAB = b[2]-a[2]
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coord_AB = [xAB,yAB,zAB]
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return coord_AB
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def vector_norm(v):
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norm = math.sqrt(v[0]**2 + v[1]**2 + v[2]**2)
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return norm
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def dot_product(v1,v2):
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dot_product = v1[0]*v2[0] + v1[1]*v2[1] + v1[2]*v2[2]
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return(dot_product)
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def position_vector(c):
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vector = vector_from_pos([0,0,0],c)
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return vector
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def vectors_substr(v1, v2):
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return ([v1[0]-v2[0],
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v1[1]-v2[1],
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v1[2]-v2[2]])
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def vector_angles(v1,v2):
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dot_prod = dot_product(v1,v2)
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norm_v1 = vector_norm(v1)
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norm_v2 = vector_norm(v2)
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term = dot_prod/(abs(norm_v1)*abs(norm_v2))
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rad_angle = math.acos(term)
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return rad_angle
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def calc_dihedral(u1, u2, u3, u4):
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""" Calculate dihedral angle method. From bioPython.PDB
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(adapted to np.array)
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Calculate the dihedral angle between 4 vectors
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representing 4 connected points. The angle is in
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[-pi, pi].
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Adapted function of dihedral_angle_from_coordinates.py
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by Eric Alcaide.
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Source : https://gist.github.com/EricAlcaide
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URL : https://gist.github.com/EricAlcaide/30d6bfdb8358d3a57d010c9a501fda56
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"""
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#convert coords to numpy arrays
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u1 = np.array(u1)
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u2 = np.array(u2)
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u3 = np.array(u3)
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u4 = np.array(u4)
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a1 = u2 - u1
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a2 = u3 - u2
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a3 = u4 - u3
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v1 = np.cross(a1, a2)
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v1 = v1 / (v1 * v1).sum(-1)**0.5
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v2 = np.cross(a2, a3)
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v2 = v2 / (v2 * v2).sum(-1)**0.5
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porm = np.sign((v1 * a3).sum(-1))
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rad = np.arccos((v1*v2).sum(-1) / ((v1**2).sum(-1) * (v2**2).sum(-1))**0.5)
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if not porm == 0:
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rad = rad * porm
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deg_angle = rad*(180/math.pi)
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return deg_angle
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302
src/structure.py
302
src/structure.py
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@ -1,5 +1,6 @@
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import math
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import numpy as np
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from geom import *
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class Structure:
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def __init__(self, res):
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@ -26,304 +27,3 @@ class Helix(Structure):
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self.res_num = res_num
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Structure.res = res_num
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def get_turns(residues):
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# TODO : prevent redondency of overlapping turns
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turns = {}
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for i,res in enumerate(residues):
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for j in range(3,6):
|
||||
if(i+j<len(residues)):
|
||||
if(res.h_bond(residues[i+j])<-0.5):
|
||||
print(j,"TURN", residues[i].resid, residues[i+j].resid)
|
||||
turns[i] = Turn(j,residues[i].resid)
|
||||
return(turns)
|
||||
|
||||
def get_bridges(residues):
|
||||
bridges = {}
|
||||
bridge = {}
|
||||
strongest_bridge = {}
|
||||
for i in range(1,len(residues)-4):
|
||||
E_min = 0
|
||||
for j in range(i+2,len(residues)-1):
|
||||
# select triplet with the minimal energy
|
||||
|
||||
if(residues[i-1].h_bond(residues[j])<-0.5
|
||||
and residues[j].h_bond(residues[i+1])<-0.5):
|
||||
bridge = {'res1':residues[i-1].h_bond(residues[j]),
|
||||
'res2':residues[j].h_bond(residues[i+1]),
|
||||
'ipos':residues[i].resid,
|
||||
'jpos':residues[j].resid,
|
||||
'btype':"para"}
|
||||
|
||||
if(residues[j-1].h_bond(residues[i])<-0.5
|
||||
and residues[i].h_bond(residues[j+1])<-0.5):
|
||||
bridge = {'res1':residues[j-1].h_bond(residues[i]),
|
||||
'res2':residues[i].h_bond(residues[j+1]),
|
||||
'ipos':residues[i].resid,
|
||||
'jpos':residues[j].resid,
|
||||
'btype':"para"}
|
||||
|
||||
if(residues[i].h_bond(residues[j])<-0.5
|
||||
and residues[j].h_bond(residues[i])<-0.5):
|
||||
bridge = {'res1':residues[i].h_bond(residues[j]),
|
||||
'res2':residues[j].h_bond(residues[i]),
|
||||
'ipos':residues[i].resid,
|
||||
'jpos':residues[j].resid,
|
||||
'btype':"anti"}
|
||||
|
||||
if(residues[i-1].h_bond(residues[j+1])<-0.5
|
||||
and residues[j-1].h_bond(residues[i+1])<-0.5):
|
||||
bridge = {'res1':residues[i-1].h_bond(residues[j+1]),
|
||||
'res2':residues[j-1].h_bond(residues[i+1]),
|
||||
'ipos':residues[i].resid,
|
||||
'jpos':residues[j].resid,
|
||||
'btype':"anti"}
|
||||
|
||||
if(bridge):
|
||||
if(bridge['res1']+bridge['res2']<E_min):
|
||||
E_min = bridge['res1']+bridge['res2']
|
||||
strongest_bridge = bridge
|
||||
bridge = {}
|
||||
coord_bridge = [i,j]
|
||||
# finally add the strongest bridge at i and j pos
|
||||
if(strongest_bridge):
|
||||
bridges[coord_bridge[0]] = (Bridge(strongest_bridge['btype'],
|
||||
strongest_bridge['ipos'],
|
||||
strongest_bridge['jpos']))
|
||||
bridges[coord_bridge[1]] = (Bridge(strongest_bridge['btype'],
|
||||
strongest_bridge['jpos'],
|
||||
strongest_bridge['ipos']))
|
||||
if(len(bridges)>0):
|
||||
return(bridges)
|
||||
else:
|
||||
return(False)
|
||||
|
||||
# def get_bonds(residues):
|
||||
# for i,res1 in enumerate(residues):
|
||||
# E_min = 0
|
||||
# strongest_bridge = []
|
||||
# for j in range(-5,6):
|
||||
# if(i+j < len(residues)):
|
||||
# res2 = residues[i+j]
|
||||
# if(res1.h_bond(res2)<-0.5) and (res1.h_bond(res2)<E_min):
|
||||
# E_min = res1.h_bond(res2)
|
||||
# strongest_bridge = [res1, res2]
|
||||
# if(len(strongest_bridge)>0):
|
||||
# diff = strongest_bridge[0].resid - strongest_bridge[1].resid
|
||||
# if( abs (diff) > 1 and abs(diff)<=5):
|
||||
# print(diff)
|
||||
|
||||
def get_bonds(residues):
|
||||
bonds = {}
|
||||
k = 0
|
||||
for i,res in enumerate(residues):
|
||||
E_min = 0
|
||||
for j in range(-5,-2):
|
||||
if(i+j<len(residues)):
|
||||
if(residues[i+j].h_bond(res)<-0.5):
|
||||
k+=1
|
||||
#if(res.h_bond(residues[i+j])<E_min):
|
||||
E_min = res.h_bond(residues[i+j])
|
||||
res_a = res
|
||||
res_b = residues[i+j]
|
||||
if j not in bonds:
|
||||
bonds[j] = []
|
||||
bonds[j].append([res_a.resid, res_b.resid])
|
||||
#turns[residues[i].resid] = Turn(j,residues[i].resid)
|
||||
for key in bonds.keys():
|
||||
print(key, len(bonds[key]))
|
||||
|
||||
print("LH",k)
|
||||
|
||||
def get_helix(residues, turns):
|
||||
i = 1
|
||||
helix = []
|
||||
while i <= len(residues):
|
||||
if(i in turns.keys() and i-1 in turns.keys()):
|
||||
k = 0
|
||||
temp_res = []
|
||||
while(i+k in turns):
|
||||
k+=1
|
||||
temp_res.append(residues[i])
|
||||
last_res_pos = residues[i].resid+k
|
||||
if(k>=1):
|
||||
helix_size=last_res_pos - residues[i].resid
|
||||
print(turns[i].turn_type,"- HELIX at", residues[i].resid)
|
||||
helix.append(Helix(temp_res,residues[i].resid))
|
||||
i = i+k
|
||||
else:
|
||||
i+=1
|
||||
return(helix)
|
||||
|
||||
def get_ladders(bridges, residues):
|
||||
ladders = {}
|
||||
i = 1
|
||||
while i < len(residues):
|
||||
k = 1
|
||||
if i in bridges.keys():
|
||||
temp_bridges = [bridges[i]]
|
||||
while ((i+k in bridges.keys()) and
|
||||
(bridges[i].bridge_type == bridges[i+k].bridge_type)):
|
||||
temp_bridges.append(bridges[i+k])
|
||||
k+=1
|
||||
if k>1:
|
||||
ladders[i] = k-1
|
||||
print("ladder", bridges[i].res_num, bridges[i+k-1].res_num)
|
||||
ladders[i] = {'start':bridges[i].res_num,
|
||||
'end':bridges[i+k-1].res_num,
|
||||
'bridges':temp_bridges}
|
||||
i+=k-1
|
||||
else:
|
||||
i+=1
|
||||
return ladders
|
||||
|
||||
def get_sheets(ladders):
|
||||
"""
|
||||
Bridges between ladders.
|
||||
Check if 1 bridge between one ladder and one or more other ladders.
|
||||
Iterate over all residues of one ladder and check if bridge with other residues
|
||||
of the other ladders.
|
||||
"""
|
||||
sheets = {}
|
||||
for ladder in ladders:
|
||||
for ladd2 in ladders:
|
||||
for bridge in ladders[ladder]['bridges']:
|
||||
if bridge.res_partner in res_list(ladders[ladd2]):
|
||||
print("ladder",ladders[ladder]['start'], ladders[ladder]['end'],"bridge",bridge.res_num, bridge.res_partner,
|
||||
"ladder 2",ladders[ladd2]['start'], ladders[ladd2]['end'])
|
||||
#print("stop ladder 2")
|
||||
print("stop ladder 1")
|
||||
|
||||
def res_list(ladder):
|
||||
# TODO : method in ladder class
|
||||
l=[]
|
||||
for i in range(ladder['start'], ladder['end']):
|
||||
l.append(i)
|
||||
return(l)
|
||||
|
||||
def get_bends(residues):
|
||||
bends = {}
|
||||
for i in range(2,len(residues)-2):
|
||||
angle = math.degrees(vector_angles(vectors_substr(position_vector(residues[i].atoms["CA"].coords),
|
||||
position_vector(residues[i-2].atoms["CA"].coords)),
|
||||
vectors_substr(position_vector(residues[i+2].atoms["CA"].coords),
|
||||
position_vector(residues[i].atoms["CA"].coords))))
|
||||
if(angle>70):
|
||||
print("angle", residues[i].resid, angle)
|
||||
bends[residues[i].resid] = angle
|
||||
return(bends)
|
||||
|
||||
def vector_from_pos(a, b):
|
||||
xAB = b[0]-a[0]
|
||||
yAB = b[1]-a[1]
|
||||
zAB = b[2]-a[2]
|
||||
coord_AB = [xAB,yAB,zAB]
|
||||
return coord_AB
|
||||
|
||||
def vector_norm(v):
|
||||
norm = math.sqrt(v[0]**2 + v[1]**2 + v[2]**2)
|
||||
return norm
|
||||
|
||||
def dot_product(v1,v2):
|
||||
dot_product = v1[0]*v2[0] + v1[1]*v2[1] + v1[2]*v2[2]
|
||||
return(dot_product)
|
||||
|
||||
def position_vector(c):
|
||||
vector = vector_from_pos([0,0,0],c)
|
||||
return vector
|
||||
|
||||
def vectors_substr(v1, v2):
|
||||
return ([v1[0]-v2[0],
|
||||
v1[1]-v2[1],
|
||||
v1[2]-v2[2]])
|
||||
|
||||
def vector_angles(v1,v2):
|
||||
dot_prod = dot_product(v1,v2)
|
||||
norm_v1 = vector_norm(v1)
|
||||
norm_v2 = vector_norm(v2)
|
||||
term = dot_prod/(abs(norm_v1)*abs(norm_v2))
|
||||
rad_angle = math.acos(term)
|
||||
return rad_angle
|
||||
|
||||
def calc_dihedral(u1, u2, u3, u4):
|
||||
""" Calculate dihedral angle method. From bioPython.PDB
|
||||
(adapted to np.array)
|
||||
Calculate the dihedral angle between 4 vectors
|
||||
representing 4 connected points. The angle is in
|
||||
[-pi, pi].
|
||||
|
||||
Adapted function of dihedral_angle_from_coordinates.py
|
||||
by Eric Alcaide.
|
||||
Source : https://gist.github.com/EricAlcaide
|
||||
URL : https://gist.github.com/EricAlcaide/30d6bfdb8358d3a57d010c9a501fda56
|
||||
"""
|
||||
#convert coords to numpy arrays
|
||||
u1 = np.array(u1)
|
||||
u2 = np.array(u2)
|
||||
u3 = np.array(u3)
|
||||
u4 = np.array(u4)
|
||||
|
||||
a1 = u2 - u1
|
||||
a2 = u3 - u2
|
||||
a3 = u4 - u3
|
||||
|
||||
v1 = np.cross(a1, a2)
|
||||
v1 = v1 / (v1 * v1).sum(-1)**0.5
|
||||
v2 = np.cross(a2, a3)
|
||||
v2 = v2 / (v2 * v2).sum(-1)**0.5
|
||||
porm = np.sign((v1 * a3).sum(-1))
|
||||
rad = np.arccos((v1*v2).sum(-1) / ((v1**2).sum(-1) * (v2**2).sum(-1))**0.5)
|
||||
if not porm == 0:
|
||||
rad = rad * porm
|
||||
|
||||
deg_angle = rad*(180/math.pi)
|
||||
return deg_angle
|
||||
|
||||
|
||||
def get_chirality(residues):
|
||||
|
||||
for i in range(1,len(residues)-2):
|
||||
chirality = {}
|
||||
angle = calc_dihedral(residues[i-1].atoms["CA"].coords,
|
||||
residues[i].atoms["CA"].coords,
|
||||
residues[i+1].atoms["CA"].coords,
|
||||
residues[i+2].atoms["CA"].coords)
|
||||
|
||||
if(angle>0 and angle<=180):
|
||||
sign="+"
|
||||
print("chirality", residues[i].resid, "+", angle)
|
||||
|
||||
if(angle<=0 and angle > -180):
|
||||
sign="-"
|
||||
print("chirality", residues[i].resid, "-", angle)
|
||||
|
||||
chirality[residues[i].resid] = sign
|
||||
|
||||
return chirality
|
||||
|
||||
|
||||
def get_phi_psi(residues):
|
||||
for i in range(len(residues)):
|
||||
if(i==0):
|
||||
phi = 360.0
|
||||
else:
|
||||
phi = calc_dihedral(residues[i-1].atoms["C"].coords,
|
||||
residues[i].atoms["N"].coords,
|
||||
residues[i].atoms["CA"].coords,
|
||||
residues[i].atoms["C"].coords)
|
||||
if(i==len(residues)-1):
|
||||
psi = 360.0
|
||||
else:
|
||||
psi = calc_dihedral(residues[i].atoms["N"].coords,
|
||||
residues[i].atoms["CA"].coords,
|
||||
residues[i].atoms["C"].coords,
|
||||
residues[i+1].atoms["N"].coords)
|
||||
|
||||
print("ANGLES", i, phi, psi)
|
||||
|
||||
def get_TCO(res1, res2):
|
||||
CO_res1 = vector_from_pos(res1.atoms["C"].coords,
|
||||
res1.atoms["O"].coords)
|
||||
CO_res2 = vector_from_pos(res2.atoms["C"].coords,
|
||||
res2.atoms["O"].coords)
|
||||
angle = vector_angles(CO_res1, CO_res2)
|
||||
return(math.cos(angle))
|
||||
|
|
|
|||
Loading…
Reference in New Issue