From 728729585f47c8f10909db4ede92a869411e265e Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Tue, 6 Feb 2024 09:35:48 +0100
Subject: [PATCH] update external USalign code
---
modules/bindings/src/USalign/MMalign.cpp | 54 +++++++--
modules/bindings/src/USalign/MMalign.h | 142 +++++++++++++----------
modules/bindings/src/USalign/OST_INFO | 4 +-
modules/bindings/src/USalign/USalign.cpp | 48 +++++++-
modules/bindings/src/USalign/readme.txt | 2 +
modules/bindings/src/wrap_tmalign.cc | 46 +++++++-
6 files changed, 214 insertions(+), 82 deletions(-)
diff --git a/modules/bindings/src/USalign/MMalign.cpp b/modules/bindings/src/USalign/MMalign.cpp
index 886cb7600..20f8308ab 100644
--- a/modules/bindings/src/USalign/MMalign.cpp
+++ b/modules/bindings/src/USalign/MMalign.cpp
@@ -9,7 +9,7 @@ void print_version()
cout <<
"\n"
" **********************************************************************\n"
-" * MM-align (Version 20220412): complex structure alignment *\n"
+" * MM-align (Version 20231222): complex structure alignment *\n"
" * References: S Mukherjee, Y Zhang. Nucl Acids Res 37(11):e83 (2009) *\n"
" * Please email comments and suggestions to yangzhanglab@umich.edu *\n"
" **********************************************************************"
@@ -360,6 +360,8 @@ int main(int argc, char *argv[])
len_na=(xlen_na+ylen_na)/2;
}
+ map<int,int> chainmap;
+
/* perform monomer alignment if there is only one chain */
if (xa_vec.size()==1 && ya_vec.size()==1)
{
@@ -638,11 +640,49 @@ int main(int argc, char *argv[])
// score was from monomeric chain superpositions
int max_iter=5-(int)((len_aa+len_na)/200);
if (max_iter<2) max_iter=2;
- MMalign_iter(max_total_score, max_iter, xa_vec, ya_vec, seqx_vec, seqy_vec,
- secx_vec, secy_vec, mol_vec1, mol_vec2, xlen_vec, ylen_vec,
- xa, ya, seqx, seqy, secx, secy, len_aa, len_na, chain1_num, chain2_num,
- TMave_mat, seqxA_mat, seqyA_mat, assign1_list, assign2_list, sequence,
- d0_scale, fast_opt);
+ MMalign_iter(max_total_score, max_iter, xa_vec, ya_vec,
+ seqx_vec, seqy_vec, secx_vec, secy_vec, mol_vec1, mol_vec2, xlen_vec,
+ ylen_vec, xa, ya, seqx, seqy, secx, secy, len_aa, len_na, chain1_num,
+ chain2_num, TMave_mat, seqxA_mat, seqyA_mat, assign1_list, assign2_list,
+ sequence, d0_scale, fast_opt, chainmap);
+
+ if (aln_chain_num>=4 && is_oligomer && chainmap.size()==0) // oligomer alignment
+ {
+ MMalign_final(xname.substr(dir1_opt.size()), yname.substr(dir2_opt.size()),
+ chainID_list1, chainID_list2,
+ fname_super, fname_lign, fname_matrix,
+ xa_vec, ya_vec, seqx_vec, seqy_vec,
+ secx_vec, secy_vec, mol_vec1, mol_vec2, xlen_vec, ylen_vec,
+ xa, ya, seqx, seqy, secx, secy, len_aa, len_na,
+ chain1_num, chain2_num, TMave_mat,
+ seqxA_mat, seqM_mat, seqyA_mat, assign1_list, assign2_list, sequence,
+ d0_scale, 1, 0, 5, ter_opt, split_opt,
+ 0, 0, true, true, mirror_opt, resi_vec1, resi_vec2);
+
+
+ /* extract centroid coordinates */
+ double **xcentroids;
+ double **ycentroids;
+ NewArray(&xcentroids, chain1_num, 3);
+ NewArray(&ycentroids, chain2_num, 3);
+ double d0MM=getmin(
+ calculate_centroids(xa_vec, chain1_num, xcentroids),
+ calculate_centroids(ya_vec, chain2_num, ycentroids));
+
+ /* refine enhanced greedy search with centroid superposition */
+ //double het_deg=check_heterooligomer(TMave_mat, chain1_num, chain2_num);
+ homo_refined_greedy_search(TMave_mat, assign1_list,
+ assign2_list, chain1_num, chain2_num, xcentroids,
+ ycentroids, d0MM, len_aa+len_na, ut_mat);
+
+ hetero_refined_greedy_search(TMave_mat, assign1_list,
+ assign2_list, chain1_num, chain2_num, xcentroids,
+ ycentroids, d0MM, len_aa+len_na);
+
+ /* clean up */
+ DeleteArray(&xcentroids, chain1_num);
+ DeleteArray(&ycentroids, chain2_num);
+ }
/* sometime MMalign_iter is even worse than monomer alignment */
if (max_total_score<maxTMmono)
@@ -667,7 +707,7 @@ int main(int argc, char *argv[])
secx_vec, secy_vec, mol_vec1, mol_vec2, xlen_vec, ylen_vec,
xa, ya, seqx, seqy, secx, secy, len_aa, len_na, chain1_num, chain2_num,
TMave_mat, seqxA_mat, seqyA_mat, assign1_list, assign2_list, sequence,
- d0_scale, fast_opt);
+ d0_scale, fast_opt, chainmap);
}
/* perform cross chain alignment
diff --git a/modules/bindings/src/USalign/MMalign.h b/modules/bindings/src/USalign/MMalign.h
index d9b1fb19f..71b1f784a 100644
--- a/modules/bindings/src/USalign/MMalign.h
+++ b/modules/bindings/src/USalign/MMalign.h
@@ -1495,13 +1495,12 @@ void MMalign_final(
if (!full_opt) return;
+ if (outfmt_opt<=2)
cout<<"# End of alignment for full complex. The following blocks list alignments for individual chains."<<endl;
/* re-compute chain level alignment */
for (i=0;i<chain1_num;i++)
{
- j=assign1_list[i];
- if (j<0) continue;
xlen=xlen_vec[i];
seqx = new char[xlen+1];
secx = new char[xlen+1];
@@ -1513,67 +1512,71 @@ void MMalign_final(
NewArray(&xt, xlen, 3);
do_rotation(xa, xt, xlen, t0, u0);
- ylen=ylen_vec[j];
- if (ylen<3)
+ for (j=0;j<chain2_num;j++)
{
- TMave_mat[i][j]=-1;
- continue;
+ ylen=ylen_vec[j];
+ if (ylen<3)
+ {
+ TMave_mat[i][j]=-1;
+ continue;
+ }
+ seqy = new char[ylen+1];
+ secy = new char[ylen+1];
+ NewArray(&ya, ylen, 3);
+ copy_chain_data(ya_vec[j],seqy_vec[j],secy_vec[j],
+ ylen,ya,seqy,secy);
+
+ /* declare variable specific to this pair of TMalign */
+ d0_out=5.0;
+ rmsd0 = 0.0;
+ Liden=0;
+ int *invmap = new int[ylen+1];
+ seqM="";
+ seqxA="";
+ seqyA="";
+ double Lnorm_ass=len_aa;
+ if (mol_vec1[i]+mol_vec2[j]>0) Lnorm_ass=len_na;
+ sequence[0]=seqxA_mat[i][j];
+ sequence[1]=seqyA_mat[i][j];
+
+ /* entry function for structure alignment */
+ se_main(xt, ya, seqx, seqy, TM1, TM2, TM3, TM4, TM5,
+ d0_0, TM_0, d0A, d0B, d0u, d0a, d0_out, seqM, seqxA, seqyA,
+ rmsd0, L_ali, Liden, TM_ali, rmsd_ali, n_ali, n_ali8,
+ xlen, ylen, sequence, Lnorm_ass, d0_scale,
+ 1, a_opt, 2, d_opt, mol_vec1[i]+mol_vec2[j], 1, invmap);
+
+ //TM2=TM4*Lnorm_ass/xlen;
+ //TM1=TM4*Lnorm_ass/ylen;
+ //d0A=d0u;
+ //d0B=d0u;
+ TMave_mat[i][j]=TM4*Lnorm_ass;
+
+ /* print result */
+ if (j==assign1_list[i]) output_results(xname, yname,
+ chainID_list1[i].c_str(), chainID_list2[j].c_str(),
+ xlen, ylen, t0, u0, TM1, TM2, TM3, TM4, TM5, rmsd0, d0_out,
+ seqM_mat[i][j].c_str(), seqxA_mat[i][j].c_str(),
+ seqyA_mat[i][j].c_str(), Liden, n_ali8, L_ali, TM_ali, rmsd_ali,
+ TM_0, d0_0, d0A, d0B, Lnorm_ass, d0_scale, d0a, d0u,
+ "", outfmt_opt, ter_opt, false, split_opt, 0,
+ "", false, a_opt, false, d_opt, 0, resi_vec1, resi_vec2);
+
+ /* clean up */
+ seqxA.clear();
+ seqM.clear();
+ seqyA.clear();
+ sequence[0].clear();
+ sequence[1].clear();
+ delete[]seqy;
+ delete[]secy;
+ DeleteArray(&ya,ylen);
+ delete[]invmap;
}
- seqy = new char[ylen+1];
- secy = new char[ylen+1];
- NewArray(&ya, ylen, 3);
- copy_chain_data(ya_vec[j],seqy_vec[j],secy_vec[j],
- ylen,ya,seqy,secy);
-
- /* declare variable specific to this pair of TMalign */
- d0_out=5.0;
- rmsd0 = 0.0;
- Liden=0;
- int *invmap = new int[ylen+1];
- seqM="";
- seqxA="";
- seqyA="";
- double Lnorm_ass=len_aa;
- if (mol_vec1[i]+mol_vec2[j]>0) Lnorm_ass=len_na;
- sequence[0]=seqxA_mat[i][j];
- sequence[1]=seqyA_mat[i][j];
-
- /* entry function for structure alignment */
- se_main(xt, ya, seqx, seqy, TM1, TM2, TM3, TM4, TM5,
- d0_0, TM_0, d0A, d0B, d0u, d0a, d0_out, seqM, seqxA, seqyA,
- rmsd0, L_ali, Liden, TM_ali, rmsd_ali, n_ali, n_ali8,
- xlen, ylen, sequence, Lnorm_ass, d0_scale,
- 1, a_opt, 2, d_opt, mol_vec1[i]+mol_vec2[j], 1, invmap);
-
- //TM2=TM4*Lnorm_ass/xlen;
- //TM1=TM4*Lnorm_ass/ylen;
- //d0A=d0u;
- //d0B=d0u;
-
- /* print result */
- output_results(xname, yname,
- chainID_list1[i].c_str(), chainID_list2[j].c_str(),
- xlen, ylen, t0, u0, TM1, TM2, TM3, TM4, TM5, rmsd0, d0_out,
- seqM_mat[i][j].c_str(), seqxA_mat[i][j].c_str(),
- seqyA_mat[i][j].c_str(), Liden, n_ali8, L_ali, TM_ali, rmsd_ali,
- TM_0, d0_0, d0A, d0B, Lnorm_ass, d0_scale, d0a, d0u,
- "", outfmt_opt, ter_opt, false, split_opt, 0,
- "", false, a_opt, false, d_opt, 0, resi_vec1, resi_vec2);
-
- /* clean up */
- seqxA.clear();
- seqM.clear();
- seqyA.clear();
- sequence[0].clear();
- sequence[1].clear();
- delete[]seqy;
- delete[]secy;
- DeleteArray(&ya,ylen);
delete[]seqx;
delete[]secx;
DeleteArray(&xa,xlen);
DeleteArray(&xt,xlen);
- delete[]invmap;
}
sequence.clear();
return;
@@ -1621,7 +1624,7 @@ void MMalign_iter(double & max_total_score, const int max_iter,
int len_aa, int len_na, int chain1_num, int chain2_num, double **TMave_mat,
vector<vector<string> >&seqxA_mat, vector<vector<string> >&seqyA_mat,
int *assign1_list, int *assign2_list, vector<string>&sequence,
- double d0_scale, bool fast_opt)
+ double d0_scale, bool fast_opt, map<int,int> &chainmap)
{
/* tmp assignment */
double total_score;
@@ -1637,7 +1640,7 @@ void MMalign_iter(double & max_total_score, const int max_iter,
copy_chain_assign_data(chain1_num, chain2_num, sequence_tmp,
seqxA_mat, seqyA_mat, assign1_list, assign2_list, TMave_mat,
seqxA_tmp, seqyA_tmp, assign1_tmp, assign2_tmp, TMave_tmp);
-
+
for (int iter=0;iter<max_iter;iter++)
{
total_score=MMalign_search(xa_vec, ya_vec, seqx_vec, seqy_vec,
@@ -1646,14 +1649,25 @@ void MMalign_iter(double & max_total_score, const int max_iter,
chain1_num, chain2_num,
TMave_tmp, seqxA_tmp, seqyA_tmp, assign1_tmp, assign2_tmp,
sequence, d0_scale, fast_opt);
+ if (chainmap.size())
+ {
+ int i,j;
+ for (i=0;i<chain1_num;i++) for (j=0;j<chain2_num;j++)
+ if (!chainmap.count(i) || chainmap[i]!=j) TMave_tmp[i][j]=-1;
+ }
total_score=enhanced_greedy_search(TMave_tmp, assign1_tmp,
assign2_tmp, chain1_num, chain2_num);
//if (total_score<=0) PrintErrorAndQuit("ERROR! No assignable chain");
if (total_score<=max_total_score) break;
max_total_score=total_score;
- copy_chain_assign_data(chain1_num, chain2_num, sequence,
- seqxA_tmp, seqyA_tmp, assign1_tmp, assign2_tmp, TMave_tmp,
- seqxA_mat, seqyA_mat, assign1_list, assign2_list, TMave_mat);
+ if (chainmap.size())
+ copy_chain_assign_data(chain1_num, chain2_num, sequence,
+ seqxA_tmp, seqyA_tmp, assign1_list, assign2_list, TMave_tmp,
+ seqxA_mat, seqyA_mat, assign1_tmp, assign2_tmp, TMave_mat);
+ else
+ copy_chain_assign_data(chain1_num, chain2_num, sequence,
+ seqxA_tmp, seqyA_tmp, assign1_tmp, assign2_tmp, TMave_tmp,
+ seqxA_mat, seqyA_mat, assign1_list, assign2_list, TMave_mat);
}
/* clean up everything */
@@ -2831,7 +2845,7 @@ void MMalign_cross(double & max_total_score, const int max_iter,
int len_aa, int len_na, int chain1_num, int chain2_num, double **TMave_mat,
vector<vector<string> >&seqxA_mat, vector<vector<string> >&seqyA_mat,
int *assign1_list, int *assign2_list, vector<string>&sequence,
- double d0_scale, bool fast_opt)
+ double d0_scale, bool fast_opt, map<int,int> &chainmap)
{
/* tmp assignment */
int *assign1_tmp, *assign2_tmp;
@@ -2865,7 +2879,7 @@ void MMalign_cross(double & max_total_score, const int max_iter,
secx_vec, secy_vec, mol_vec1, mol_vec2, xlen_vec, ylen_vec,
xa, ya, seqx, seqy, secx, secy, len_aa, len_na, chain1_num, chain2_num,
TMave_mat, seqxA_mat, seqyA_mat, assign1_list, assign2_list, sequence,
- d0_scale, fast_opt);
+ d0_scale, fast_opt, chainmap);
/* clean up everything */
delete [] assign1_tmp;
diff --git a/modules/bindings/src/USalign/OST_INFO b/modules/bindings/src/USalign/OST_INFO
index 7c8299cdd..888d01eb0 100644
--- a/modules/bindings/src/USalign/OST_INFO
+++ b/modules/bindings/src/USalign/OST_INFO
@@ -1,6 +1,6 @@
-Source code has been cloned Nov 14 2023 from:
+Source code has been cloned Feb 6 2024 from:
https://github.com/pylelab/USalign
last commit:
-58b42af9d58436279c21b4f4074db87f072fcc21
+444144c4edf0b43b9f573a1a4b8a0692c4c24ab3
diff --git a/modules/bindings/src/USalign/USalign.cpp b/modules/bindings/src/USalign/USalign.cpp
index 151e3ca48..5f712642d 100644
--- a/modules/bindings/src/USalign/USalign.cpp
+++ b/modules/bindings/src/USalign/USalign.cpp
@@ -11,7 +11,7 @@ void print_version()
cout <<
"\n"
" ********************************************************************\n"
-" * US-align (Version 20230609) *\n"
+" * US-align (Version 20231222) *\n"
" * Universal Structure Alignment of Proteins and Nucleic Acids *\n"
" * Reference: C Zhang, M Shine, AM Pyle, Y Zhang. (2022) Nat Methods*\n"
" * Please email comments and suggestions to zhang@zhanggroup.org *\n"
@@ -742,7 +742,7 @@ int MMalign(const string &xname, const string &yname,
TMave_mat[i][j]=-1;
continue;
}
- if (chainmap.size() && chainmap[i]!=j)
+ if (chainmap.size() && (!chainmap.count(i) || chainmap[i]!=j))
{
TMave_mat[i][j]=-1;
continue;
@@ -893,7 +893,7 @@ int MMalign(const string &xname, const string &yname,
hetero_refined_greedy_search(TMave_mat, assign1_list,
assign2_list, chain1_num, chain2_num, xcentroids,
ycentroids, d0MM, len_aa+len_na);
-
+
/* clean up */
DeleteArray(&xcentroids, chain1_num);
DeleteArray(&ycentroids, chain2_num);
@@ -922,7 +922,45 @@ int MMalign(const string &xname, const string &yname,
seqx_vec, seqy_vec, secx_vec, secy_vec, mol_vec1, mol_vec2, xlen_vec,
ylen_vec, xa, ya, seqx, seqy, secx, secy, len_aa, len_na, chain1_num,
chain2_num, TMave_mat, seqxA_mat, seqyA_mat, assign1_list, assign2_list,
- sequence, d0_scale, fast_opt);
+ sequence, d0_scale, fast_opt, chainmap);
+
+ if (byresi_opt && aln_chain_num>=4 && is_oligomer && chainmap.size()==0) // oligomer alignment
+ {
+ MMalign_final(xname.substr(dir1_opt.size()), yname.substr(dir2_opt.size()),
+ chainID_list1, chainID_list2,
+ fname_super, fname_lign, fname_matrix,
+ xa_vec, ya_vec, seqx_vec, seqy_vec,
+ secx_vec, secy_vec, mol_vec1, mol_vec2, xlen_vec, ylen_vec,
+ xa, ya, seqx, seqy, secx, secy, len_aa, len_na,
+ chain1_num, chain2_num, TMave_mat,
+ seqxA_mat, seqM_mat, seqyA_mat, assign1_list, assign2_list, sequence,
+ d0_scale, 1, 0, 5, ter_opt, split_opt,
+ 0, 0, true, true, mirror_opt, resi_vec1, resi_vec2);
+
+
+ /* extract centroid coordinates */
+ double **xcentroids;
+ double **ycentroids;
+ NewArray(&xcentroids, chain1_num, 3);
+ NewArray(&ycentroids, chain2_num, 3);
+ double d0MM=getmin(
+ calculate_centroids(xa_vec, chain1_num, xcentroids),
+ calculate_centroids(ya_vec, chain2_num, ycentroids));
+
+ /* refine enhanced greedy search with centroid superposition */
+ //double het_deg=check_heterooligomer(TMave_mat, chain1_num, chain2_num);
+ homo_refined_greedy_search(TMave_mat, assign1_list,
+ assign2_list, chain1_num, chain2_num, xcentroids,
+ ycentroids, d0MM, len_aa+len_na, ut_mat);
+
+ hetero_refined_greedy_search(TMave_mat, assign1_list,
+ assign2_list, chain1_num, chain2_num, xcentroids,
+ ycentroids, d0MM, len_aa+len_na);
+
+ /* clean up */
+ DeleteArray(&xcentroids, chain1_num);
+ DeleteArray(&ycentroids, chain2_num);
+ }
/* sometime MMalign_iter is even worse than monomer alignment */
if (byresi_opt==0 && max_total_score<maxTMmono)
@@ -947,7 +985,7 @@ int MMalign(const string &xname, const string &yname,
secx_vec, secy_vec, mol_vec1, mol_vec2, xlen_vec, ylen_vec,
xa, ya, seqx, seqy, secx, secy, len_aa, len_na, chain1_num, chain2_num,
TMave_mat, seqxA_mat, seqyA_mat, assign1_list, assign2_list, sequence,
- d0_scale, fast_opt);
+ d0_scale, fast_opt, chainmap);
}
/* perform cross chain alignment
diff --git a/modules/bindings/src/USalign/readme.txt b/modules/bindings/src/USalign/readme.txt
index 79ae2068b..fb5281061 100644
--- a/modules/bindings/src/USalign/readme.txt
+++ b/modules/bindings/src/USalign/readme.txt
@@ -74,6 +74,8 @@
2022/09/24: Support -TMscore for complex when the chain order is different
2023/06/09: Correct atom name justification in PDB file for standard amino
acids and nucleotides
+ 2023/12/13: Refine chain assignment for -TMscore >=6 for large complex
+ 2023/12/22: Forbid chain assignment refinment for -chainmap
===============================================================================
=========================
diff --git a/modules/bindings/src/wrap_tmalign.cc b/modules/bindings/src/wrap_tmalign.cc
index 91544c06c..bc45f3cc0 100644
--- a/modules/bindings/src/wrap_tmalign.cc
+++ b/modules/bindings/src/wrap_tmalign.cc
@@ -725,7 +725,7 @@ MMAlignResult WrappedMMAlign(const std::vector<geom::Vec3List>& pos_one,
TMave_mat[i][j]=-1;
continue;
}
- if (chainmap.size() && chainmap[i]!=j)
+ if (chainmap.size() && (!chainmap.count(i) || chainmap[i]!=j))
{
TMave_mat[i][j]=-1;
continue;
@@ -876,7 +876,7 @@ MMAlignResult WrappedMMAlign(const std::vector<geom::Vec3List>& pos_one,
hetero_refined_greedy_search(TMave_mat, assign1_list,
assign2_list, chain1_num, chain2_num, xcentroids,
ycentroids, d0MM, len_aa+len_na);
-
+
/* clean up */
DeleteArray(&xcentroids, chain1_num);
DeleteArray(&ycentroids, chain2_num);
@@ -905,7 +905,45 @@ MMAlignResult WrappedMMAlign(const std::vector<geom::Vec3List>& pos_one,
seqx_vec, seqy_vec, secx_vec, secy_vec, mol_vec1, mol_vec2, xlen_vec,
ylen_vec, xa, ya, seqx, seqy, secx, secy, len_aa, len_na, chain1_num,
chain2_num, TMave_mat, seqxA_mat, seqyA_mat, assign1_list, assign2_list,
- sequence, d0_scale, fast_opt);
+ sequence, d0_scale, fast_opt, chainmap);
+
+ if (byresi_opt && aln_chain_num>=4 && is_oligomer && chainmap.size()==0) // oligomer alignment
+ {
+ MMalign_final(xname.substr(dir1_opt.size()), yname.substr(dir2_opt.size()),
+ chainID_list1, chainID_list2,
+ fname_super, fname_lign, fname_matrix,
+ xa_vec, ya_vec, seqx_vec, seqy_vec,
+ secx_vec, secy_vec, mol_vec1, mol_vec2, xlen_vec, ylen_vec,
+ xa, ya, seqx, seqy, secx, secy, len_aa, len_na,
+ chain1_num, chain2_num, TMave_mat,
+ seqxA_mat, seqM_mat, seqyA_mat, assign1_list, assign2_list, sequence,
+ d0_scale, 1, 0, 5, ter_opt, split_opt,
+ 0, 0, true, true, mirror_opt, resi_vec1, resi_vec2);
+
+
+ /* extract centroid coordinates */
+ double **xcentroids;
+ double **ycentroids;
+ NewArray(&xcentroids, chain1_num, 3);
+ NewArray(&ycentroids, chain2_num, 3);
+ double d0MM=getmin(
+ calculate_centroids(xa_vec, chain1_num, xcentroids),
+ calculate_centroids(ya_vec, chain2_num, ycentroids));
+
+ /* refine enhanced greedy search with centroid superposition */
+ //double het_deg=check_heterooligomer(TMave_mat, chain1_num, chain2_num);
+ homo_refined_greedy_search(TMave_mat, assign1_list,
+ assign2_list, chain1_num, chain2_num, xcentroids,
+ ycentroids, d0MM, len_aa+len_na, ut_mat);
+
+ hetero_refined_greedy_search(TMave_mat, assign1_list,
+ assign2_list, chain1_num, chain2_num, xcentroids,
+ ycentroids, d0MM, len_aa+len_na);
+
+ /* clean up */
+ DeleteArray(&xcentroids, chain1_num);
+ DeleteArray(&ycentroids, chain2_num);
+ }
/* sometime MMalign_iter is even worse than monomer alignment */
if (byresi_opt==0 && max_total_score<maxTMmono)
@@ -930,7 +968,7 @@ MMAlignResult WrappedMMAlign(const std::vector<geom::Vec3List>& pos_one,
secx_vec, secy_vec, mol_vec1, mol_vec2, xlen_vec, ylen_vec,
xa, ya, seqx, seqy, secx, secy, len_aa, len_na, chain1_num, chain2_num,
TMave_mat, seqxA_mat, seqyA_mat, assign1_list, assign2_list, sequence,
- d0_scale, fast_opt);
+ d0_scale, fast_opt, chainmap);
}
/* perform cross chain alignment
--
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