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C-S-S-C_BACKBONE_scan.py

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+from math import *
+import math
+import re
+import numpy as np
+class atom:
+    aid=0    
+    atype='' 
+    x=0.0  
+    y=0.0    
+    z=0.0    
+    rid=0    
+    rtype='' 
+    model=[]
+    chainid=''
+
+def getlen(atm1,atm2):
+    dist=sqrt(pow(atm1.x-atm2.x,2)+pow(atm1.y-atm2.y,2)+pow(atm1.z-atm2.z,2)) 
+    return dist
+
+def getangle(atm1,atm2,atm3):
+    dist1=sqrt(pow(atm1.x-atm2.x,2)+pow(atm1.y-atm2.y,2)+pow(atm1.z-atm2.z,2)) 
+    dist2=sqrt(pow(atm3.x-atm2.x,2)+pow(atm3.y-atm2.y,2)+pow(atm3.z-atm2.z,2)) 
+    dotp=(atm1.x-atm2.x)*(atm3.x-atm2.x)+(atm1.y-atm2.y)*(atm3.y-atm2.y)+(atm1.z-atm2.z)*(atm3.z-atm2.z) 
+    angle=acos(dotp/(dist1*dist2))*180/pi 
+    return angle
+
+def getangledihedral(atm1,atm2,atm3,atm4):
+    ab=np.zeros(3)
+    bc=np.zeros(3)
+    cd=np.zeros(3)
+    p=[]
+    q=[]
+    ab[0]=atm2.x-atm1.x
+    ab[1]=atm2.y-atm1.y
+    ab[2]=atm2.z-atm1.z
+    bc[0]=atm3.x-atm2.x
+    bc[1]=atm3.y-atm2.y
+    bc[2]=atm3.z-atm2.z
+    cd[0]=atm4.x-atm3.x
+    cd[1]=atm4.y-atm3.y
+    cd[2]=atm4.z-atm3.z
+    p.append(ab[1]*bc[2]-ab[2]*bc[1])
+    p.append(ab[2]*bc[0]-ab[0]*bc[2])
+    p.append(ab[0]*bc[1]-ab[1]*bc[0])
+    q.append(bc[1]*cd[2]-bc[2]*cd[1])
+    q.append(bc[2]*cd[0]-bc[0]*cd[2])
+    q.append(bc[0]*cd[1]-bc[1]*cd[0])
+
+
+    r1=0
+    r2=0
+    dp=0
+    dpcd=0
+    for i in range(0,3):
+        r1 += math.pow(p[i],2)
+        r2 += math.pow(q[i],2)
+        dp += p[i]*q[i]
+        dpcd += p[i]*cd[i]
+
+    dih=(dpcd/abs(dpcd))*math.acos(dp/(math.sqrt(r1)*math.sqrt(r2)))*180/math.pi
+
+
+    return dih
+
+def getdihedralstrain(a1,a2,a3,a4,a5):
+    dse=8.37*(1+math.cos(3*a1*math.pi/180))+8.37*(1+math.cos(3*a5*math.pi/180))+4.18*(1+math.cos(3*a2*math.pi/180))+4.18*(1+math.cos(3*a4*math.pi/180))+14.64*(1+math.cos(2*a3*math.pi/180))+2.51*(1+math.cos(3*a3*math.pi/180))
+    return dse
+
+s_s_l=1.6
+s_s_u=2.5
+
+filetxt=open('filelist.txt') 
+txt_lines=filetxt.read().split('\n') 
+filetxt.close()
+fileout=open('out_C-S-S-C_BACKBONE_scan.txt','w')
+f1=open('error_C-S-S-C_scan.txt','w')
+intr=[]
+lenlines=len(txt_lines)
+for ppp in range(lenlines):
+    filename=txt_lines[ppp]
+    if filename=='':
+        continue
+    print('%.2f'%((ppp+1)*100.0/(lenlines-1))+'% ('+str(ppp+1)+'/'+str(lenlines-1)+')  Executing for:'+filename)
+    file=open(filename,'r')
+    lines=file.read().split('\n')
+    file.close()
+    T=[]
+    D=[]
+    S=[] 
+    C=[]
+    SX=[]
+    TX=[]
+    A=[]
+    B=[]
+    E=[]
+    F=[]
+    modelno=[]
+
+
+    try:
+        for ln in lines:
+            if len(ln)>=6 and (ln[0:4]=='ATOM' or ln[0:6]=='HETATM'):
+                atm=atom()
+                atm.aid=int(ln[6:11]) 
+                atm.atype=ln[12:16].strip() 
+                atm.rtype=ln[17:20].strip() 
+                atm.chainid=ln[21]
+                atm.rid=int(ln[22:26]) 
+                atm.x=float(ln[30:38]) 
+                atm.y=float(ln[38:46]) 
+                atm.z=float(ln[47:54]) 
+                atm.model=modelno
+                symb=ln[13].strip()
+                if atm.atype=='CB' and (modelno==1 or modelno==A or modelno==[])  :
+                    if atm.rtype=='CYS' : 
+                        C.append(atm)
+                        D.append(atm)
+                if atm.atype=='SG'and (modelno==1 or modelno==A or modelno==[]) :
+                    if atm.rtype=='CYS': 
+                        SX.append(atm)
+                        TX.append(atm)
+                if atm.atype=='CA' and (modelno==1 or modelno==A or modelno==[]) :
+                    if atm.rtype=='CYS':
+                        B.append(atm)
+                        E.append(atm)
+                if atm.atype=='N' and (modelno==1 or modelno==A or modelno==[]) :
+                    if atm.rtype=='CYS'  :
+                        A.append(atm)
+                        F.append(atm)
+            elif len(ln)>=5 and ln[0:5]=='MODEL':
+                modelno=int(ln[12:])
+
+    except:
+        f1.write(filename+'\n')
+
+
+    for k in SX:
+        for k1 in SX:
+            if k1.chainid==k.chainid:                
+                if k1.rid==k.rid and k1.aid!=k.aid :
+                    break
+        else:
+            S.append(k)
+    for m in TX:
+        for m1 in TX:
+            if m1.chainid==m.chainid:
+                if m1.rid==m.rid and m1.aid!=m.aid :
+                    break
+        else:
+            T.append(m)
+
+    for a in range(len(A)):
+        for b in range(len(B)):
+            if A[a].rid==B[b].rid:
+                for j in range(len(C)):
+                    for k in range(len(S)):
+                        if C[j].rid==S[k].rid and C[j].rid==B[b].rid and C[j].chainid==B[b].chainid==S[k].chainid==A[a].chainid :
+                            for m in range(len(T)):
+                                if getlen(S[k],T[m])>=s_s_l and getlen(S[k],T[m])<=s_s_u and S[k].rid<T[m].rid :
+                                    for n in range(len(D)):
+                                        for e in range(len(E)):
+                                            if E[e].rid==D[n].rid:
+                                                for f in range(len(F)):
+                                                    if D[n].rid==T[m].rid and E[e].rid==F[f].rid and D[n].chainid==T[m].chainid==E[e].chainid==F[f].chainid :
+                                                        a1=getangledihedral(A[a],B[b],C[j],S[k])
+                                                        a2=getangledihedral(B[b],C[j],S[k],T[m])
+                                                        a3=getangledihedral(C[j],S[k],T[m],D[n])
+                                                        a4=getangledihedral(S[k],T[m],D[n],E[e])
+                                                        a5=getangledihedral(T[m],D[n],E[e],F[f])
+                                                        dse=getdihedralstrain(a1,a2,a3,a4,a5)
+                                                        intr.append([])
+                                                        intr[len(intr)-1].append(filename)                                                     
+                                                        intr[len(intr)-1].append(C[j].chainid)
+                                                        intr[len(intr)-1].append(C[j].rid)                
+                                                        intr[len(intr)-1].append(T[m].rid)
+                                                        intr[len(intr)-1].append(T[m].chainid)
+                                                        intr[len(intr)-1].append(getlen(C[j],S[k]))        
+                                                        intr[len(intr)-1].append(getlen(T[m],S[k]))         
+                                                        intr[len(intr)-1].append(getlen(T[m],D[n]))     
+                                                        intr[len(intr)-1].append(a1)
+                                                        intr[len(intr)-1].append(a2)
+                                                        intr[len(intr)-1].append(a3)
+                                                        intr[len(intr)-1].append(a4)
+                                                        intr[len(intr)-1].append(a5)
+                                                        intr[len(intr)-1].append(dse)
+
+
+    C=[]
+    T=[]
+    D=[]
+    S=[]
+    SX=[]
+    TX=[]
+    A=[]
+    B=[]
+    E=[]
+    F=[]
+    for line in intr:
+        for xxd in line:
+            fileout.write(str(xxd))
+            fileout.write('\t')
+        fileout.write('\n')
+    intr=[]
+    fileout.close()
+    fileout=open('out_C-S-S-C_BACKBONE_scan.txt','a')
+fileout.close()
+f1.close()