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parse insertion codes from PDB files
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PDB loading has been adapted to honor insertion codes for residues.
It also uses insertion codes for HELIX/SHEET records. There are
still a few other places that do not know about insertion codes.
Prominent examples are the coloring methods or selection by residue
number. Nonetheless, this fixes the worst of #53.
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@biasmv
biasmv committed Oct 31, 2014
1 parent 0820826 commit 9ec0a62
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Showing 3 changed files with 71 additions and 38 deletions.
34 changes: 17 additions & 17 deletions pdbs/1crn.pdb
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Original file line number Diff line number Diff line change
Expand Up @@ -332,23 +332,23 @@ ATOM 56 CA ALA A 9 5.598 5.767 11.082 1.00 3.56 C
ATOM 57 C ALA A 9 6.441 5.527 9.850 1.00 4.13 C
ATOM 58 O ALA A 9 6.052 5.933 8.744 1.00 4.36 O
ATOM 59 CB ALA A 9 6.022 6.977 11.891 1.00 4.80 C
ATOM 60 N ARG A 10 7.647 4.909 10.005 1.00 3.73 N
ATOM 61 CA ARG A 10 8.496 4.609 8.837 1.00 3.38 C
ATOM 62 C ARG A 10 7.798 3.609 7.876 1.00 3.47 C
ATOM 63 O ARG A 10 7.878 3.778 6.651 1.00 4.67 O
ATOM 64 CB ARG A 10 9.847 4.020 9.305 1.00 3.95 C
ATOM 65 CG ARG A 10 10.752 3.607 8.149 1.00 4.55 C
ATOM 66 CD ARG A 10 11.226 4.699 7.244 1.00 5.89 C
ATOM 67 NE ARG A 10 12.143 5.571 8.035 1.00 6.20 N
ATOM 68 CZ ARG A 10 12.758 6.609 7.443 1.00 7.52 C
ATOM 69 NH1 ARG A 10 12.539 6.932 6.158 1.00 10.68 N
ATOM 70 NH2 ARG A 10 13.601 7.322 8.202 1.00 9.48 N
ATOM 71 N SER A 11 7.186 2.582 8.445 1.00 5.19 N
ATOM 72 CA SER A 11 6.500 1.584 7.565 1.00 4.60 C
ATOM 73 C SER A 11 5.382 2.313 6.773 1.00 4.84 C
ATOM 74 O SER A 11 5.213 2.016 5.557 1.00 5.84 O
ATOM 75 CB SER A 11 5.908 0.462 8.400 1.00 5.91 C
ATOM 76 OG SER A 11 6.990 -0.272 9.012 1.00 8.38 O
ATOM 60 N ARG A 10A 7.647 4.909 10.005 1.00 3.73 N
ATOM 61 CA ARG A 10A 8.496 4.609 8.837 1.00 3.38 C
ATOM 62 C ARG A 10A 7.798 3.609 7.876 1.00 3.47 C
ATOM 63 O ARG A 10A 7.878 3.778 6.651 1.00 4.67 O
ATOM 64 CB ARG A 10A 9.847 4.020 9.305 1.00 3.95 C
ATOM 65 CG ARG A 10A 10.752 3.607 8.149 1.00 4.55 C
ATOM 66 CD ARG A 10A 11.226 4.699 7.244 1.00 5.89 C
ATOM 67 NE ARG A 10A 12.143 5.571 8.035 1.00 6.20 N
ATOM 68 CZ ARG A 10A 12.758 6.609 7.443 1.00 7.52 C
ATOM 69 NH1 ARG A 10A 12.539 6.932 6.158 1.00 10.68 N
ATOM 70 NH2 ARG A 10A 13.601 7.322 8.202 1.00 9.48 N
ATOM 71 N SER A 10B 7.186 2.582 8.445 1.00 5.19 N
ATOM 72 CA SER A 10B 6.500 1.584 7.565 1.00 4.60 C
ATOM 73 C SER A 10B 5.382 2.313 6.773 1.00 4.84 C
ATOM 74 O SER A 10B 5.213 2.016 5.557 1.00 5.84 O
ATOM 75 CB SER A 10B 5.908 0.462 8.400 1.00 5.91 C
ATOM 76 OG SER A 10B 6.990 -0.272 9.012 1.00 8.38 O
ATOM 77 N ASN A 12 4.648 3.182 7.446 1.00 3.54 N
ATOM 78 CA ASN A 12 3.545 3.935 6.751 1.00 4.57 C
ATOM 79 C ASN A 12 4.107 4.851 5.691 1.00 4.14 C
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31 changes: 19 additions & 12 deletions src/io.js
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Original file line number Diff line number Diff line change
Expand Up @@ -24,19 +24,27 @@ function PDBReader() {
}

function parseHelixRecord(line) {
// FIXME: handle insertion codes
var frst_num = parseInt(line.substr(21, 4), 10);
var last_num = parseInt(line.substr(33, 4), 10);
var frstNum = parseInt(line.substr(21, 4), 10);
var frstInsCode = line[25] === ' ' ? '\0' : line[25];
var lastNum = parseInt(line.substr(33, 4), 10);
var lastInsCode = line[37] === ' ' ? '\0' : line[37];
var chainName = line[19];
return { first : frst_num, last : last_num, chainName : chainName };
return { first : [frstNum, frstInsCode],
last : [lastNum, lastInsCode], chainName : chainName
};
}

function parseSheetRecord(line) {
// FIXME: handle insertion codes
var frst_num = parseInt(line.substr(22, 4), 10);
var last_num = parseInt(line.substr(33, 4), 10);
var frstNum = parseInt(line.substr(22, 4), 10);
var frstInsCode = line[26] === ' ' ? '\0' : line[26];
var lastNum = parseInt(line.substr(33, 4), 10);
var lastInsCode = line[37] === ' ' ? '\0' : line[37];
var chainName = line[21];
return { first : frst_num, last : last_num, chainName : chainName };
return {
first : [frstNum, frstInsCode],
last : [lastNum, lastInsCode],
chainName : chainName
};
}

function Remark350Reader() {
Expand Down Expand Up @@ -130,14 +138,14 @@ function pdb(text) {
var resName = line.substr(17, 3).trim();
var atomName = line.substr(12, 4).trim();
var rnumNum = parseInt(line.substr(22, 4), 10);
var insCode = line[26];
var insCode = line[26] === ' ' ? '\0' : line[26];
var updateResidue = false;
var updateChain = false;
if (!currChain || currChain.name() !== chainName) {
updateChain = true;
updateResidue = true;
}
if (!currRes || currRes.num() !== rnumNum) {
if (!currRes || currRes.num() !== rnumNum || currRes.insCode() !== insCode) {
updateResidue = true;
}
if (updateChain) {
Expand All @@ -146,8 +154,7 @@ function pdb(text) {
currChain = structure.chain(chainName) || structure.addChain(chainName);
}
if (updateResidue) {
currRes = currChain.addResidue(resName, rnumNum,
currChain.residues().length);
currRes = currChain.addResidue(resName, rnumNum, insCode);
}
var pos = vec3.create();
for (var i=0;i<3;++i) {
Expand Down
44 changes: 35 additions & 9 deletions src/mol.js
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Original file line number Diff line number Diff line change
Expand Up @@ -48,6 +48,14 @@ function covalentRadius(ele) {
return 1.5;
}

// combines the numeric part of the residue number with the insertion
// code and returns a single number. Note that this is completely safe
// and we do not have to worry about overflows, as for PDB files the
// range of permitted residue numbers is quite limited anyway.
function rnumInsCodeHash(num, insCode) {
return num << 8 | insCode.charCodeAt(0);
}

//-----------------------------------------------------------------------------
// MolBase, ChainBase, ResidueBase, AtomBase
//-----------------------------------------------------------------------------
Expand Down Expand Up @@ -671,25 +679,34 @@ Chain.prototype.name = function() { return this._name; };

Chain.prototype.full = function() { return this; };

Chain.prototype.addResidue = function(name, num) {
var residue = new Residue(this, name, num);
this._rnumsOrdered = this._residues.length === 0 ||
(this._rnumsOrdered && this._residues[this._residues.length-1].num() <= num);
Chain.prototype.addResidue = function(name, num, insCode) {
insCode = insCode || '\0';
var residue = new Residue(this, name, num, insCode);
if (this._residues.length > 0 && this._rnumsOrdered) {
var combinedRNum = rnumInsCodeHash(num, insCode);
var last = this._residues[this._residues.length-1];
var lastCombinedRNum = rnumInsCodeHash(last.num(),last.insCode());
this._rnumsOrdered = lastCombinedRNum < combinedRNum;
}
this._residues.push(residue);
return residue;
};


Chain.prototype.residuesInRnumRange = function(start, end) {
// FIXME: this currently only works with the numeric part, insertion
// codes are not honoured.
var matching = [];
var i, e;
if (this._rnumsOrdered === true) {
// binary search our way to heaven
var startIdx = indexFirstLargerEqualThan(this._residues, numify(start), rnumComp);
var startIdx = indexFirstLargerEqualThan(this._residues, numify(start),
rnumComp);
if (startIdx === -1) {
return matching;
}
var endIdx = indexLastSmallerEqualThan(this._residues, numify(end), rnumComp);
var endIdx = indexLastSmallerEqualThan(this._residues, numify(end),
rnumComp);
if (endIdx === -1) {
return matching;
}
Expand All @@ -708,16 +725,19 @@ Chain.prototype.residuesInRnumRange = function(start, end) {
};

// assigns secondary structure to residues in range from_num to to_num.
Chain.prototype.assignSS = function(from_num, to_num, ss) {
Chain.prototype.assignSS = function(fromNumAndIns, toNumAndIns, ss) {
// FIXME: when the chain numbers are completely ordered, perform binary
// search to identify range of residues to assign secondary structure to.
var from = rnumInsCodeHash(fromNumAndIns[0], fromNumAndIns[1]);
var to = rnumInsCodeHash(toNumAndIns[0], toNumAndIns[1]);
for (var i = 1; i < this._residues.length-1; ++i) {
var res = this._residues[i];
// FIXME: we currently don't set the secondary structure of the first and
// last residue of helices and sheets. that takes care of better
// transitions between coils and helices. ideally, this should be done
// in the cartoon renderer, NOT in this function.
if (res.num() <= from_num || res.num() >= to_num) {
var combined = rnumInsCodeHash(res.num(), res.insCode());
if (combined <= from || combined >= to) {
continue;
}
res.setSS(ss);
Expand Down Expand Up @@ -778,10 +798,11 @@ Chain.prototype.backboneTraces = function() {

};

function Residue(chain, name, num) {
function Residue(chain, name, num, insCode) {
ResidueBase.prototype.constructor.call(this);
this._name = name;
this._num = num;
this._insCode = insCode;
this._atoms = [];
this._ss = 'C';
this._chain = chain;
Expand All @@ -791,6 +812,7 @@ function Residue(chain, name, num) {
derive(Residue, ResidueBase);

Residue.prototype.name = function() { return this._name; };
Residue.prototype.insCode = function() { return this._insCode; };

Residue.prototype.num = function() { return this._num; };

Expand Down Expand Up @@ -996,6 +1018,10 @@ ResidueView.prototype.addAtom = function(atom) {

ResidueView.prototype.full = function() { return this._residue; };
ResidueView.prototype.num = function() { return this._residue.num(); };

ResidueView.prototype.insCode = function() {
return this._residue.insCode();
};
ResidueView.prototype.ss = function() { return this._residue.ss(); };
ResidueView.prototype.index = function() { return this._residue.index(); };
ResidueView.prototype.chain = function() { return this._chainView; };
Expand Down

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