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Add hydroxyproline hyp as aa #550

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Add hydroxyproline hyp as aa #550

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9505bc9
Hydroxyproline is an amino acid
smoe Jun 5, 2015
97dc1d0
Set is_proline also for HYP
smoe Jun 5, 2015
76ce286
Attempt to describe HYP structure
smoe Jun 8, 2015
b241954
Merge branch 'master' into Add_Hydroxyproline_Hyp_as_AA
smoe Jun 8, 2015
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21 changes: 21 additions & 0 deletions data/fragments/PRO.db
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Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,8 @@
<node>CB<value>C 1.34565 1.283736 -2.23033</value></node>
<node>1HB<value>H 2.062533 0.6767905 -2.785621</value></node>
<node>2HB<value>H 0.7182986 1.840951 -2.927554</value></node>
<node>1OB<value>O 0.7182986 1.840951 -2.927554</value></node>
<node>1OH<value>H 1.4182986 2.440951 -2.927554</value></node>
<node>CG<value>C 2.02933 2.275858 -1.278275</value></node>
<node>1HG<value>H 3.057449 1.966999 -1.081919</value></node>
<node>2HG<value>H 2.018846 3.280874 -1.702292</value></node>
Expand Down Expand Up @@ -42,6 +44,8 @@
<node>32<value>OXT C s</value></node>
<node>33<value>1H N s</value></node>
<node>34<value>2H N s</value></node>
<node>40<value>2OB CB s</value></node>
<node>41<value>2OH 2OB s</value></node>
</node>
<node>Connections
<node>N-term<value>N C-term s 1.33 0.5</value></node>
Expand All @@ -56,16 +60,31 @@
<node>OXT</node>
<node>1H</node>
<node>2H</node>
<node>2OB</node>
<node>2OH</node>
</node>
</node>
<node>HYP
<node>Delete
<node>2HB</node>
<node>OXT</node>
<node>1H</node>
<node>2H</node>
</node>
<node>PRO-M
<node>Delete
<node>2OB</node>
<node>2OH</node>
</node>
<node>Properties
<node>C_TERMINAL</node>
<node>N_TERMINAL</node>
</node>
</node>
<node>PRO-C
<node>Delete
<node>2OB</node>
<node>2OH</node>
<node>1H</node>
<node>2H</node>
</node>
Expand All @@ -75,6 +94,8 @@
</node>
<node>PRO-N
<node>Delete
<node>2OB</node>
<node>2OH</node>
<node>OXT</node>
</node>
<node>Properties
Expand Down
9 changes: 6 additions & 3 deletions include/BALL/STRUCTURE/peptideBuilder.h
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Expand Up @@ -159,9 +159,12 @@ namespace BALL
String chainname_;
String proteinname_;

/// The proline flag
bool is_proline_;
FragmentDB* fragment_db_;
/** The proline flag is set for side chains that
* are covalently bound to the backbone. Proline
* and hydroxyproline are among them.
*/
bool is_proline_;
FragmentDB* fragment_db_;

/** some helper functions for the construction of the residue; for internal use only
* omega is not yet implemented
Expand Down
8 changes: 8 additions & 0 deletions source/KERNEL/residue.C
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Expand Up @@ -163,6 +163,10 @@ namespace BALL
Log.error() << "No next residue!" << endl;
}
}
else
{
Log.error() << "Has no torsion Psi! (" << getFullName() << ")" << endl;
}

return result;
}
Expand Down Expand Up @@ -227,6 +231,10 @@ namespace BALL
Log.error() << "No previous residue!" << endl;
}
}
else
{
Log.error() << "Has no torsion Phi! (" << getFullName() << ")" << endl;
}

return result;
}
Expand Down
2 changes: 1 addition & 1 deletion source/STRUCTURE/peptideBuilder.C
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Expand Up @@ -226,7 +226,7 @@ namespace BALL
// special case: residue is a proline
type = i->getType();
type.toUpper();
is_proline_ = (type == "PRO") ? true : false;
is_proline_ = ("PRO" == type || "HYP" == type) ? true : false;

Residue* residue2 = createResidue_(i->getType(), id);

Expand Down
11 changes: 9 additions & 2 deletions source/STRUCTURE/peptides.C
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Expand Up @@ -19,8 +19,15 @@ namespace BALL
namespace Peptides
{

const String one_letter_codes = "ARNDCQEGHILKMFPSTWYV";
const String three_letter_codes = "ALA@ARG@ASN@ASP@CYS@GLN@GLU@GLY@HIS@ILE@LEU@LYS@MET@PHE@PRO@SER@THR@TRP@TYR@VAL@";
const String one_letter_codes = "ARNDCQEGHILKMFPSTWYVBZ";
/**
* http://www.apsstylemanual.org/oldmanual/reference/amino-acids.htm also defines Cit, Hey, Hyp, Orn, Thx
* somewhat exceptional is Xaa and the ambiguity codes like Asx and Glx"
* http://www.fao.org/docrep/004/y2775e/y2775e0e.htm has single letter for GLX and ASX
* Instead of UNK one might possibly better use "Xaa" as long as one is confident that an AA is meant.
* It may also be preferable to have another character than '?' as the representation of unknown, e.g. 'X'.
*/
const String three_letter_codes = "ALA@ARG@ASN@ASP@CYS@GLN@GLU@GLY@HIS@ILE@LEU@LYS@MET@PHE@PRO@SER@THR@TRP@TYR@VAL@ASX@GLX@CIT@HEY@HYP@ORN@THX@";

char OneLetterCode(const String& aa)
{
Expand Down